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Varghese TP. GENETIC BIOMARKERS OF CARDIOVASCULAR DISEASE. Curr Probl Cardiol 2024:102588. [PMID: 38657720 DOI: 10.1016/j.cpcardiol.2024.102588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 04/20/2024] [Indexed: 04/26/2024]
Abstract
Cardiovascular disorders are the leading cause mortality in developed as well as developing nations, and has now emerged as one of the leading causes of disability and mortality around the globe. According to the World Health Organization, four out of every five patients with cardiovascular disease die from a myocardial infarction each year. Numerous genes have been linked to coronary artery disease, influencing mechanisms such as blood pressure regulation, lipid metabolism, inflammation, and cardiac activity. Genetic variations or mutations in these genes can affect lipid metabolism, blood pressure management, and heart function, increasing the risk of obesity, metabolic disorders, and cardiovascular disease. Understanding the role of genes and related complications are essential for the identification, management, and prevention of cardiovascular conditions6. Performing a genetic test for variations in the gene may help identify people as well as their families who are at a greater risk of heart disease, which enables risk identification and timely intervention. 7. This article investigates the applications of genetic biomarkers in cardiac disorders such as coronary artery disease, hypertension, arrhythmias, cardiomyopathy, and heart failure, with an emphasis on individual genes and their mutation effects.
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Affiliation(s)
- Treesa P Varghese
- Department of Pharmacy Practice, Yenepoya Pharmacy College & Research centre, Yenepoya (Deemed to be University), Ayush campus, Naringana, Mangalore, Karnataka, India.
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Panti-May JA, Retana-Guiascón O, Moguel-Chin WI, Hernández-Mena DI, García-Prieto L. NEW RECORDS OF HELMINTHS OF THE JAGUAR IN MEXICO, WITH AN UPDATED LIST OF SPECIES IN THE AMERICAS. J Parasitol 2024; 110:114-126. [PMID: 38503317 DOI: 10.1645/23-56] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024] Open
Abstract
An inventory of parasites infecting the jaguar (Panthera onca) across its distribution range is relevant for the conservation of this threatened big cat. In this study, we report the occurrence of helminths in a jaguar from Mexico using morphological techniques (cleared and stained mounts and scanning electron microscopy) and partial sequences of the 28S ribosomal RNA (28S rRNA) gene and the cytochrome c oxidase 1 mitochondrial (COI) gene. We also provide an updated list of helminth species reported in jaguars in the Americas. Three helminth taxa are identified in the jaguar examined from Mexico: Toxocara cati, Physaloptera sp., and Taenia sp. The new 28S rRNA sequences of To. cati, Physaloptera sp., and Taenia sp. and the COI sequence of Taenia sp. corroborate the identity of the helminths isolated from this host. One hundred and twenty-nine records of helminths parasitizing jaguars from 49 studies up to May 2023 were identified in the Americas. In most of these studies (73.6%), helminths were identified using coproparasitological techniques. Sixteen helminths (7 nematodes, 5 cestodes, 3 acanthocephalans, and 1 trematode) were identified at the species level in free-ranging and captive jaguars. The study demonstrates the value of an integrative taxonomy approach to increase the accuracy of parasite identification in wildlife, especially when helminth specimens are scarce or poorly fixed.
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Affiliation(s)
- Jesús Alonso Panti-May
- Centro de Investigaciones Regionales "Dr. Hideyo Noguchi," Universidad Autónoma de Yucatán, Avenida Itzaés 490, Mérida, C. P. 97000, Yucatán, Mexico
| | - Oscar Retana-Guiascón
- Centro de Estudios de Desarrollo Sustentable y Aprovechamiento de la Vida Silvestre, Universidad Autónoma de Campeche, Avenida Héroe de Nacozari 480, Campeche, C. P. 24079, Campeche, Mexico
| | - Wilson Isaias Moguel-Chin
- Doctorado en Manejo de Recursos Naturales Tropicales, Universidad Autónoma de Yucatán, Carretera Mérida-Xmatkuil km 15.5, Mérida, C. P. 97315, Yucatán, Mexico
| | - David I Hernández-Mena
- Escuela Nacional de Estudios Superiores, Universidad Nacional Autónoma de México, Carretera Mérida-Tetiz km 4, Ucú, C. P. 97358, Yucatán, Mexico
- Colección Nacional de Helmintos, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad Universitaria, C. P. 04510, Ciudad de México, Mexico
| | - Luis García-Prieto
- Colección Nacional de Helmintos, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad Universitaria, C. P. 04510, Ciudad de México, Mexico
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Mujyambere V, Adomako K, Olympio OS. Effectiveness of DArTseq markers application in genetic diversity and population structure of indigenous chickens in Eastern Province of Rwanda. BMC Genomics 2024; 25:193. [PMID: 38373904 PMCID: PMC10875757 DOI: 10.1186/s12864-024-10089-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 02/04/2024] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND The application of biotechnologies which make use of genetic markers in chicken breeding is developing rapidly. Diversity Array Technology (DArT) is one of the current Genotyping-By-Sequencing techniques allowing the discovery of whole genome sequencing. In livestock, DArT has been applied in cattle, sheep, and horses. Currently, there is no study on the application of DArT markers in chickens. The aim was to study the effectiveness of DArTSeq markers in the genetic diversity and population structure of indigenous chickens (IC) and SASSO in the Eastern Province of Rwanda. METHODS In total 87 blood samples were randomly collected from 37 males and 40 females of indigenous chickens and 10 females of SASSO chickens purposively selected from 5 sites located in two districts of the Eastern Province of Rwanda. Genotyping by Sequencing (GBS) using DArTseq technology was employed. This involved the complexity reduction method through digestion of genomic DNA and ligation of barcoded adapters followed by PCR amplification of adapter-ligated fragments. RESULTS From 45,677 DArTseq SNPs and 25,444 SilicoDArTs generated, only 8,715 and 6,817 respectively remained for further analysis after quality control. The average call rates observed, 0.99 and 0.98 for DArTseq SNPs and SilicoDArTs respectively were quite similar. The polymorphic information content (PIC) from SilicoDArTs (0.33) was higher than that from DArTseq SNPs (0.22). DArTseq SNPs and SilicoDArTs had 34.4% and 34% of the loci respectively mapped on chromosome 1. DArTseq SNPs revealed distance averages of 0.17 and 0.15 within IC and SASSO chickens respectively while the respective averages observed with SilicoDArTs were 0.42 and 0.36. The average genetic distance between IC and SASSO chickens was moderate for SilicoDArTs (0.120) compared to that of DArTseq SNPs (0.048). The PCoA and population structure clustered the chicken samples into two subpopulations (1 and 2); 1 is composed of IC and 2 by SASSO chickens. An admixture was observed in subpopulation 2 with 12 chickens from subpopulation 1. CONCLUSIONS The application of DArTseq markers have been proven to be effective and efficient for genetic relationship between IC and separated IC from exotic breed used which indicate their suitability in genomic studies. However, further studies using all chicken genetic resources available and large big sample sizes are required.
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Affiliation(s)
- Valentin Mujyambere
- Department of Animal Production, School of Veterinary Medicine, University of Rwanda, Nyagatare, Rwanda.
- Department of Animal Production, University of Rwanda (UR), P.O. Box 57, Nyagatare, Rwanda.
- Department of Animal Science, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, AK-385-1973, Ghana.
| | - Kwaku Adomako
- Department of Animal Science, Faculty of Agriculture, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Oscar Simon Olympio
- Department of Animal Science, Faculty of Agriculture, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
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Domínguez-Viveros J, Molina-Villalobos JR, Camacho-Sandoval J, Cruz-Méndez A, Martínez-Rocha R, Jahuey-Martínez F. Structure and genetic variability of the Costa Rican Paso horse. J Equine Vet Sci 2024; 132:104985. [PMID: 38096926 DOI: 10.1016/j.jevs.2023.104985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/24/2023] [Accepted: 12/11/2023] [Indexed: 12/18/2023]
Abstract
The Costa Rican Paso Horse (CPC) is a breed developed in Costa Rica. The objectives were to estimate the genetic structure and evaluate the levels of genetic variability of the population. The genotypes of 14 microsatellites in 3654 records (2052 females and 1602 males) were analyzed. Expected (He) and observed (Ho) heterozygosity, polymorphic information content (CIP), fixation index (FIS), Shannon index, as well as Hardy-Weinberg disequilibrium (DHW) were evaluated. Kinship relationships (Rij) were estimated throughout the entire population. The effective population size (Ne) was calculated, alternating allele frequencies less than 0.05, 0.02 and 0.01. The Bayesian clustering study was carried out to infer how many lines are appropriate from the analysis of genotypes using multiple loci. The number of alleles per locus ranged from 7 to 17, with an average value of 9.6; nine loci presented DHW (P < 0.05); two loci presented negative FIS values, the same as Ho > He; the average of CIP, Ho and He was 0.254, 0.756 and 0.785, respectively. At the 12 loci where He > Ho, the differences ranged from 0.002 to 0.341 (0.036 on average). For Ne, the estimates were 201.9, 230.1, and 241.5. In the Rij, 54.86% of the estimates were in the interval of 0.01 to 77.7%. The number of lines that define the population corresponds to three, with an approximate composition of 33.1%, 32.4% and 34.5%, respectively. The CPC, as a subdivided population with DHW and a reduction in heterozygotes may be associated with possible Wahlund effects. Keywords: Wahlund effect, equines, genetic markers, synthetic breed, Hardy Weinberg.
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Affiliation(s)
| | | | | | - Argerie Cruz-Méndez
- Instituto Nacional de Innovación y Transferencia en Tecnología Agropecuaria, San José, Costa Rica
| | - Ricardo Martínez-Rocha
- Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Ciudad de México, México
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Murphy RO, Beckmann JF. Using Baker's Yeast to Determine Functions of Novel Wolbachia (and Other Prokaryotic) Effectors. Methods Mol Biol 2024; 2739:321-336. [PMID: 38006560 DOI: 10.1007/978-1-0716-3553-7_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2023]
Abstract
Yeasts are single-celled eukaryotic organisms classified as fungi, mostly in the phylum Ascomycota. Of about 1500 named species, Saccharomyces cerevisiae, also known as baker's yeast, domesticated by humans in the context of cooking and brewing, is a profound genetic tool for exploring functions of novel effector proteins from Wolbachia and prokaryotes in general. Wolbachia is a Gram-negative alpha-proteobacterium that infects up to ~75% of all insects as an obligate intracellular microbe (Jeyaprakash A, Hoy MA, Insect Mol Biol 9:393-405, 2000). Wolbachia's lifestyle presents unique challenges for researchers. Wolbachia cannot be axenically cultured and has never been genetically manipulated. Furthermore, many Wolbachia genes have no known function or well-annotated orthologs in other genomes. Yet given the effects of Wolbachia on host phenotypes, which have considerable practical applications for pest control, they undoubtedly involve secreted effector proteins that interact with host gene products. Studying these effectors is challenging with Wolbachia's current genetic limitations. However, some of the constraints to working with Wolbachia can be overcome by expressing candidate proteins in S. cerevisiae. This approach capitalizes on yeast's small genome (~6500 genes), typical eukaryotic cellular organization, and the sophisticated suite of genetic tools available for its manipulation in culture. Thus, yeast can serve as a powerful mock eukaryotic host background to study Wolbachia effector function. Specifically, yeast is used for recombinant protein expression, drug discovery, protein localization studies, protein interaction mapping (yeast two-hybrid system), modeling chromosomal evolution, and examining interactions between proteins responsible for complex phenotypes in less tractable prokaryotic systems. As an example, the paired genes responsible for Wolbachia-mediated cytoplasmic incompatibility (CI) encode novel proteins with limited homology to other known proteins, and no obvious function. This article details how S. cerevisiae was used as an initial staging ground to explore the molecular basis of one of Wolbachia's trademark phenotypes (CI).
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Affiliation(s)
- Richard O Murphy
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - John F Beckmann
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA.
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Tavolara TE, Su Z, Gurcan MN, Niazi MKK. One label is all you need: Interpretable AI-enhanced histopathology for oncology. Semin Cancer Biol 2023; 97:70-85. [PMID: 37832751 DOI: 10.1016/j.semcancer.2023.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 09/06/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023]
Abstract
Artificial Intelligence (AI)-enhanced histopathology presents unprecedented opportunities to benefit oncology through interpretable methods that require only one overall label per hematoxylin and eosin (H&E) slide with no tissue-level annotations. We present a structured review of these methods organized by their degree of verifiability and by commonly recurring application areas in oncological characterization. First, we discuss morphological markers (tumor presence/absence, metastases, subtypes, grades) in which AI-identified regions of interest (ROIs) within whole slide images (WSIs) verifiably overlap with pathologist-identified ROIs. Second, we discuss molecular markers (gene expression, molecular subtyping) that are not verified via H&E but rather based on overlap with positive regions on adjacent tissue. Third, we discuss genetic markers (mutations, mutational burden, microsatellite instability, chromosomal instability) that current technologies cannot verify if AI methods spatially resolve specific genetic alterations. Fourth, we discuss the direct prediction of survival to which AI-identified histopathological features quantitatively correlate but are nonetheless not mechanistically verifiable. Finally, we discuss in detail several opportunities and challenges for these one-label-per-slide methods within oncology. Opportunities include reducing the cost of research and clinical care, reducing the workload of clinicians, personalized medicine, and unlocking the full potential of histopathology through new imaging-based biomarkers. Current challenges include explainability and interpretability, validation via adjacent tissue sections, reproducibility, data availability, computational needs, data requirements, domain adaptability, external validation, dataset imbalances, and finally commercialization and clinical potential. Ultimately, the relative ease and minimum upfront cost with which relevant data can be collected in addition to the plethora of available AI methods for outcome-driven analysis will surmount these current limitations and achieve the innumerable opportunities associated with AI-driven histopathology for the benefit of oncology.
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Affiliation(s)
- Thomas E Tavolara
- Center for Artificial Intelligence Research, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Ziyu Su
- Center for Artificial Intelligence Research, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Metin N Gurcan
- Center for Artificial Intelligence Research, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - M Khalid Khan Niazi
- Center for Artificial Intelligence Research, Wake Forest University School of Medicine, Winston-Salem, NC, USA.
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Sena-Dos-Santos C, Cavalcante GC, Marques D, Silva CS, de Moraes MR, Pinto P, Santana-da-Silva MN, Ferraz RS, Costa SPT, Ventura AMR, Póvoa MM, Cunha MG, Ribeiro-Dos-Santos Â. Association of apoptosis-related variants to malaria infection and parasite density in individuals from the Brazilian Amazon. Malar J 2023; 22:295. [PMID: 37794476 PMCID: PMC10552311 DOI: 10.1186/s12936-023-04729-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 09/27/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND In malaria infection, apoptosis acts as an important immunomodulatory mechanism that leads to the elimination of parasitized cells, thus reducing the parasite density and controlling immune cell populations. Here, it was investigated the association of INDEL variants in apoptotic genes-rs10562972 (FAS), rs4197 (FADD), rs3834129 and rs59308963 (CASP8), rs61079693 (CASP9), rs4647655 (CASP3), rs11269260 (BCL-2), and rs17880560 (TP53)-and the influence of genetic ancestry with susceptibility to malaria and parasite density in an admixed population from the Brazilian Amazon. METHODS Total DNA was extracted from 126 malaria patients and 101 uninfected individuals for investigation of genetic ancestries and genotypic distribution of apoptosis-related variants by Multiplex PCR. Association analyses consisted of multivariate logistic regressions, considering the following comparisons: (i) DEL/DEL genotype vs. INS/DEL + INS/INS; and (ii) INS/INS vs. INS/DEL + DEL/DEL. RESULTS Individuals infected by Plasmodium falciparum had significantly higher African ancestry proportions in comparison to uninfected controls, Plasmodium vivax, and mixed infections. The INS/INS genotype of rs3834129 (CASP8) seemed to increase the risk for P. falciparum infection (P = 0.038; OR = 1.867; 95% CI 0.736-3.725), while the DEL/DEL genotype presented a significant protective effect against infection by P. falciparum (P = 0.049; OR = 0.446; 95% CI 0.185-0.944) and mixed infection (P = 0.026; OR = 0.545; 95% CI 0.281-0.996), and was associated with lower parasite density in P. falciparum malaria (P = 0.009; OR = 0.383; 95% CI 0.113-1.295). Additionally, the INS/INS genotype of rs10562972 (FAS) was more frequent among individuals infected with P. vivax compared to P. falciparum (P = 0.036; OR = 2.493; 95% CI 1.104-4.551), and the DEL/DEL genotype of rs17880560 (TP53) was significantly more present in patients with mono-infection by P. vivax than in individuals with mixed infection (P = 0.029; OR = 0.667; 95% CI 0.211-1.669). CONCLUSIONS In conclusion, variants in apoptosis genes are associated with malaria susceptibility and parasite density, indicating the role of apoptosis-related genetic profiles in immune responses against malaria infection.
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Affiliation(s)
- Camille Sena-Dos-Santos
- Laboratory of Human and Medical Genetics, Program of Genetics and Molecular Biology, Federal University of Pará (UFPA), Belém, Brazil
| | - Giovanna C Cavalcante
- Laboratory of Human and Medical Genetics, Program of Genetics and Molecular Biology, Federal University of Pará (UFPA), Belém, Brazil
| | - Diego Marques
- Laboratory of Human and Medical Genetics, Program of Genetics and Molecular Biology, Federal University of Pará (UFPA), Belém, Brazil
| | - Caio S Silva
- Laboratory of Human and Medical Genetics, Program of Genetics and Molecular Biology, Federal University of Pará (UFPA), Belém, Brazil
| | - Milene Raiol de Moraes
- Laboratory of Human and Medical Genetics, Program of Genetics and Molecular Biology, Federal University of Pará (UFPA), Belém, Brazil
| | - Pablo Pinto
- Laboratory of Human and Medical Genetics, Program of Genetics and Molecular Biology, Federal University of Pará (UFPA), Belém, Brazil
- Laboratory of Dermatoimmunology, Federal University of Pará (UFPA), Marituba, Brazil
| | - Mayara Natália Santana-da-Silva
- Laboratory of Human and Medical Genetics, Program of Genetics and Molecular Biology, Federal University of Pará (UFPA), Belém, Brazil
| | - Rafaella S Ferraz
- Laboratory of Human and Medical Genetics, Program of Genetics and Molecular Biology, Federal University of Pará (UFPA), Belém, Brazil
| | | | - Ana Maria R Ventura
- Division of Parasitology, Evandro Chagas Institute (IEC), Ananindeua, Brazil
| | - Marinete M Póvoa
- Division of Parasitology, Evandro Chagas Institute (IEC), Ananindeua, Brazil
| | - Maristela G Cunha
- Laboratory of Microbiology and Immunology, Federal University of Pará (UFPA), Belém, Brazil
| | - Ândrea Ribeiro-Dos-Santos
- Laboratory of Human and Medical Genetics, Program of Genetics and Molecular Biology, Federal University of Pará (UFPA), Belém, Brazil.
- Program of Oncology and Medical Sciences, Oncology Research Center, Belém, Brazil.
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Jindal T, Zhang L, Deshmukh P, Reyes K, Chan E, Kumar V, Zhu X, Maldonado E, Feng S, Johnson M, Angelidakis A, Kwon D, Desai A, Borno HT, Bose R, Wong A, Hong J, Carroll P, Meng M, Porten S, Aggarwal R, Small EJ, Fong L, Chou J, Friedlander T, de Kouchkovsky I, Koshkin VS. Impact of Squamous Histology on Clinical Outcomes and Molecular Profiling in Metastatic Urothelial Carcinoma Patients Treated With Immune Checkpoint Inhibitors or Enfortumab Vedotin. Clin Genitourin Cancer 2023; 21:e394-e404. [PMID: 37316414 DOI: 10.1016/j.clgc.2023.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 05/05/2023] [Accepted: 05/07/2023] [Indexed: 06/16/2023]
Abstract
INTRODUCTION Urothelial carcinoma with squamous differentiation (UCS) is associated with increased resistance to chemotherapy, but outcomes associated with newer therapies approved in this space over the last 5 to 10 years are less well defined. We investigated clinical outcomes and molecular profiling of patients with UCS treated with an immune checkpoint inhibitor (ICI) and/or Enfortumab vedotin (EV). PATIENTS AND METHODS We undertook a retrospective analysis of UC patients treated with ICI and/or EV. Objective response rate (ORR), progression free survival (PFS) and overall survival (OS) were compared between pure UC (pUC) and UCS using X2 and log-rank tests, respectively. Prevalence of the most commonly detected somatic alterations were also compared between the 2 histologic subgroups. RESULTS A total of 160 patients (40 UCS, 120 pUC) were identified for this analysis. Among 151 patients treated with ICI (38 UCS, 113 pUC), UCS patients had a shorter mPFS (1.9 vs. 4.8 months, P < 0.01) and mOS (9.2 vs. 20.7 months, P < 0.01) compared to pUC. Among 37 patients treated with EV (12 UCS, 25 pUC), UCS patients had a lower ORR (17% vs. 70%, P < 0.01) and shorter mPFS (3.4 vs. 15.8 months, P < 0.01). UCS samples were enriched for CDKN2A, CDKN2B, PIK3CA, while pUC samples were enriched for ERBB2 alterations. CONCLUSION In this single-center retrospective analysis, patients with UCS had a distinct somatic genomic profile relative to patients with pUC. Patients with UCS also had inferior outcomes to ICIs and EV compared to patients with pUC.
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Affiliation(s)
- Tanya Jindal
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Li Zhang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Prianka Deshmukh
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Kevin Reyes
- Department of Medicine, School of Medicine, University of California San Francisco, San Francisco, CA
| | - Emily Chan
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Vipul Kumar
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Xiaolin Zhu
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Edward Maldonado
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Stephanie Feng
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Michelle Johnson
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Austin Angelidakis
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Daniel Kwon
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Arpita Desai
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Hala T Borno
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Rohit Bose
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Anthony Wong
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Julian Hong
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Peter Carroll
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Maxwell Meng
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Sima Porten
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Lawrence Fong
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Jonathan Chou
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Terence Friedlander
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Ivan de Kouchkovsky
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA.
| | - Vadim S Koshkin
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA.
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Caliendo G, D'Elia G, Makker J, Passariello L, Albanese L, Molinari AM, Vietri MT. Biological, genetic and epi genetic markers in ulcerative colitis. Adv Med Sci 2023; 68:386-395. [PMID: 37813048 DOI: 10.1016/j.advms.2023.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 04/15/2023] [Accepted: 09/18/2023] [Indexed: 10/11/2023]
Abstract
In this review, we have summarized the existing knowledge of ulcerative colitis (UC) markers based on current literature, specifically, the roles of potential new biomarkers, such as circulating, fecal, genetic, and epigenetic alterations, in UC onset, disease activity, and in therapy response. UC is a complex multifactorial inflammatory disease. There are many invasive and non-invasive diagnostic methods in UC, including several laboratory markers which are employed in diagnosis and disease assessment; however, colonoscopy remains the most widely used method. Common laboratory abnormalities currently used in the clinical practice include inflammation-induced alterations, serum autoantibodies, and antibodies against bacterial antigens. Other new serum and fecal biomarkers are supportive in diagnosis and monitoring disease activity and therapy response; and potential salivary markers are currently being evaluated as well. Several UC-related genetic and epigenetic alterations are implied in its pathogenesis and therapeutic response. Moreover, the use of artificial intelligence in the integration of laboratory biomarkers and big data could potentially be useful in clinical translation and precision medicine in UC management.
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Affiliation(s)
- Gemma Caliendo
- Unity of Clinical and Molecular Pathology, AOU University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Giovanna D'Elia
- Unity of Clinical and Molecular Pathology, AOU University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Jasmine Makker
- Department of GKT School of Medical Education, King's College London, London, UK
| | - Luana Passariello
- Unity of Clinical and Molecular Pathology, AOU University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Luisa Albanese
- Unity of Clinical and Molecular Pathology, AOU University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Anna Maria Molinari
- Unity of Clinical and Molecular Pathology, AOU University of Campania "Luigi Vanvitelli", Naples, Italy; Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Maria Teresa Vietri
- Unity of Clinical and Molecular Pathology, AOU University of Campania "Luigi Vanvitelli", Naples, Italy; Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy.
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10
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Peka M, Balatsky V, Saienko A, Tsereniuk O. Bioinformatic analysis of the effect of SNPs in the pig TERT gene on the structural and functional characteristics of the enzyme to develop new genetic markers of productivity traits. BMC Genomics 2023; 24:487. [PMID: 37626279 PMCID: PMC10463782 DOI: 10.1186/s12864-023-09592-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Telomerase reverse transcriptase (TERT) plays a crucial role in synthesizing telomeric repeats that safeguard chromosomes from damage and fusion, thereby maintaining genome stability. Mutations in the TERT gene can lead to a deviation in gene expression, impaired enzyme activity, and, as a result, abnormal telomere shortening. Genetic markers of productivity traits in livestock can be developed based on the TERT gene polymorphism for use in marker-associated selection (MAS). In this study, a bioinformatic-based approach is proposed to evaluate the effect of missense single-nucleotide polymorphisms (SNPs) in the pig TERT gene on enzyme function and structure, with the prospect of developing genetic markers. RESULTS A comparative analysis of the coding and amino acid sequences of the pig TERT was performed with corresponding sequences of other species. The distribution of polymorphisms in the pig TERT gene, with respect to the enzyme's structural-functional domains, was established. A three-dimensional model of the pig TERT structure was obtained through homological modeling. The potential impact of each of the 23 missense SNPs in the pig TERT gene on telomerase function and stability was assessed using predictive bioinformatic tools utilizing data on the amino acid sequence and structure of pig TERT. CONCLUSIONS According to bioinformatic analysis of 23 missense SNPs of the pig TERT gene, a predictive effect of rs789641834 (TEN domain), rs706045634 (TEN domain), rs325294961 (TRBD domain) and rs705602819 (RTD domain) on the structural and functional parameters of the enzyme was established. These SNPs hold the potential to serve as genetic markers of productivity traits. Therefore, the possibility of their application in MAS should be further evaluated in associative analysis studies.
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Affiliation(s)
- Mykyta Peka
- Institute of Pig Breeding and Agroindustrial Production, National Academy of Agrarian Sciences of Ukraine, 1 Shvedska Mohyla St, Poltava, 36013 Ukraine
- V. N. Karazin Kharkiv National University, 4 Svobody Sq, Kharkiv, 61022 Ukraine
| | - Viktor Balatsky
- Institute of Pig Breeding and Agroindustrial Production, National Academy of Agrarian Sciences of Ukraine, 1 Shvedska Mohyla St, Poltava, 36013 Ukraine
- V. N. Karazin Kharkiv National University, 4 Svobody Sq, Kharkiv, 61022 Ukraine
| | - Artem Saienko
- Institute of Pig Breeding and Agroindustrial Production, National Academy of Agrarian Sciences of Ukraine, 1 Shvedska Mohyla St, Poltava, 36013 Ukraine
| | - Oleksandr Tsereniuk
- Institute of Pig Breeding and Agroindustrial Production, National Academy of Agrarian Sciences of Ukraine, 1 Shvedska Mohyla St, Poltava, 36013 Ukraine
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11
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Pozharskiy A, Kostyukova V, Khusnitdinova M, Adilbayeva K, Nizamdinova G, Kapytina A, Kerimbek N, Taskuzhina A, Kolchenko M, Abdrakhmanova A, Kisselyova N, Kalendar R, Gritsenko D. Genetic diversity of the breeding collection of tomato varieties in Kazakhstan assessed using SSR, SCAR and CAPS markers. PeerJ 2023; 11:e15683. [PMID: 37483968 PMCID: PMC10358335 DOI: 10.7717/peerj.15683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/14/2023] [Indexed: 07/25/2023] Open
Abstract
Tomato is one of the most prominent crops in global horticulture and an important vegetable crop in Kazakhstan. The lack of data on the genetic background of local varieties limits the development of tomato breeding in the country. This study aimed to perform an initial evaluation of the breeding collection of tomato varieties from the point of view of their genetic structure and pathogen resistance using a set of PCR based molecular markers, including 13 SSR markers for genetic structure analysis, and 14 SCAR and CAPS markers associated with resistance to five pathogens: three viruses, fungus Fusarium oxysporum, and oomycete P hytophthora infestans. Nine SSR markers were with a PIC value varying from 0.0562 (low information content) to 0.629 (high information content). A weak genetic structure was revealed in the samples of varieties including local cultivars and, predominantly, varieties from Russia and other ex-USSR countries. The local varieties were closely related to several groups of cultivars of Russian origin. Screening for a set of resistance markers revealed the common occurrence of the resistance locus I against Fusarium oxysporum and only the occasional presence of resistance alleles of other markers. No markers of resistance to the three considered viruses were revealed in local tomato varieties. Only two local cultivars had markers of resistance to P. infestans, and only the 'Meruert' cultivar had a combination of resistance markers against P. infestans and F. oxysporum. The obtained results have demonstrated the need for further studies of local tomato varieties with a wider range of molecular markers and source germplasm to lay a foundation for the development of tomato breeding in Kazakhstan.
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Affiliation(s)
- Alexandr Pozharskiy
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
- Department of Molecular Biology and Genetics, Al Farabi Kazakh National University, Almaty, Kazakhstan
| | - Valeriya Kostyukova
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
- Department of Molecular Biology and Genetics, Al Farabi Kazakh National University, Almaty, Kazakhstan
| | - Marina Khusnitdinova
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - Kamila Adilbayeva
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
- Department of Molecular Biology and Genetics, Al Farabi Kazakh National University, Almaty, Kazakhstan
| | - Gulnaz Nizamdinova
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - Anastasiya Kapytina
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - Nazym Kerimbek
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - Aisha Taskuzhina
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - Mariya Kolchenko
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - Aisha Abdrakhmanova
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | | | - Ruslan Kalendar
- Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Dilyara Gritsenko
- Laboratory of Molecular Biology, Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
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12
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Luo Z, Yao Z, Yang Y, Wang Z, Zou H, Zhang X, Chen J, Fang B, Huang L. Genetic fingerprint construction and genetic diversity analysis of sweet potato (Ipomoea batatas) germplasm resources. BMC Plant Biol 2023; 23:355. [PMID: 37434130 DOI: 10.1186/s12870-023-04329-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 06/05/2023] [Indexed: 07/13/2023]
Abstract
BACKGROUND China is the largest producer of sweet potato in the world, accounting for 57.0% of the global output. Germplasm resources are the basis for promoting innovations in the seed industry and ensuring food security. Individual and accurate identification of sweet potato germplasm is an important part of conservation and efficient utilization. RESULTS In this study, nine pairs of simple sequence repeat molecular markers and 16 morphological markers were used to construct genetic fingerprints for sweet potato individual identification. Combined with basic information, typical phenotypic photographs, genotype peak graphs, and a two-dimensional code for detection and identification were generated. Finally, a genetic fingerprint database containing 1021 sweet potato germplasm resources in the "National Germplasm Guangzhou Sweet Potato Nursery Genebank in China" was constructed. Genetic diversity analysis of the 1021 sweet potato genotypes using the nine pairs of simple sequence repeat markers revealed a narrow genetic variation range of Chinese native sweet potato germplasm resources, and Chinese germplasm was close to that from Japan and the United States, far from that from the Philippines and Thailand, and the furthest from that from Peru. Sweet potato germplasm resources from Peru had the richest genetic diversity, supporting the view that Peru is the center of origin and domestication of sweet potato varieties. CONCLUSIONS Overall, this study provides scientific guidance for the conservation, identification, and utilization of sweet potato germplasm resources and offers a reference to facilitate the discovery of important genes to boost sweet potato breeding.
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Affiliation(s)
- Zhongxia Luo
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement/Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Zhufang Yao
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement/Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Yiling Yang
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement/Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Zhangying Wang
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement/Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Hongda Zou
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement/Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Xiongjian Zhang
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement/Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Jingyi Chen
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement/Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Boping Fang
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement/Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China.
| | - Lifei Huang
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement/Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China.
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13
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Tavares V, Assis J, Pinto R, Freitas-Silva M, Medeiros R. Venous thromboembolism-related genetic determinant F11 rs4253417 is a potential prognostic factor in ischaemic stroke. Mol Cell Probes 2023; 70:101917. [PMID: 37364690 DOI: 10.1016/j.mcp.2023.101917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 06/23/2023] [Accepted: 06/24/2023] [Indexed: 06/28/2023]
Abstract
Ischaemic stroke (IS) and venous thromboembolism (VTE) are two forms of thromboembolism that, although distinct, seem to share numerous risk factors. Concerning genetic risk factors, while many VTE genetic markers have been reported, inclusively by genome-wide association studies (GWAS), the identification and validation of genetic determinants underlying IS pathogenesis have been challenging. Considering that IS and VTE shared biological pathways and aetiological factors, the severity of IS might be also influenced by VTE-related genetic variants. Thus, the present study was designed to analyse the impact of six VTE GWAS-identified genetic variants on the clinical outcome of 363 acute IS patients. Results revealed that the single-nucleotide polymorphism (SNP) F11 rs4253417 was an independent predictor of the 5-year risk of death among patients with total anterior circulation infarct (TACI). Namely, the ones carrying the SNP C allele presented a fourfold increase in the 5-year risk of death compared to TT genotype carriers (CC/CT vs. TT; adjusted HR, 4.240; 95% CI, 1.260-14.270; P = 0.020). This SNP is known to be associated with coagulation factor XI (FXI) levels, thus with implications in haemostasis and inflammation. As such, F11 rs4253417 might be a promising prognostic biomarker among TACI patients to aid in clinical decision-making. However, additional investigation is required to confirm the study's results and dissect the underlying mechanisms.
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Affiliation(s)
- Valéria Tavares
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP), Pathology and Laboratory Medicine Dep., Clinical Pathology SV, RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center (Porto.CCC), 4200-072, Porto, Portugal; ICBAS, Abel Salazar Institute for the Biomedical Sciences, 4050-313, Porto, Portugal; FMUP, Faculty of Medicine, University of Porto, 4200-072, Porto, Portugal
| | - Joana Assis
- Clinical Research Unit, Research Center of IPO Porto (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center (Porto.CCC), 4200-072, Porto, Portugal
| | - Ricardo Pinto
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP), Pathology and Laboratory Medicine Dep., Clinical Pathology SV, RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center (Porto.CCC), 4200-072, Porto, Portugal
| | - Margarida Freitas-Silva
- FMUP, Faculty of Medicine, University of Porto, 4200-072, Porto, Portugal; Department of Medicine, Centro Hospitalar São João, Porto, Portugal
| | - Rui Medeiros
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP), Pathology and Laboratory Medicine Dep., Clinical Pathology SV, RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center (Porto.CCC), 4200-072, Porto, Portugal; ICBAS, Abel Salazar Institute for the Biomedical Sciences, 4050-313, Porto, Portugal; FMUP, Faculty of Medicine, University of Porto, 4200-072, Porto, Portugal; Research Department, Portuguese League Against Cancer (NRNorte), 4200-172, Porto, Portugal; CEBIMED, Faculty of Health Sciences, Fernando Pessoa University, 4200-150, Porto, Portugal.
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14
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Sohal A, Chaudhry H, Kowdley KV. Genetic Markers Predisposing to Nonalcoholic Steatohepatitis. Clin Liver Dis 2023; 27:333-352. [PMID: 37024211 DOI: 10.1016/j.cld.2023.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
The growing prevalence of nonalcoholic fatty liver disease (NAFLD) has sparked interest in understanding genetics and epigenetics associated with the development and progression of the disease. A better understanding of the genetic factors related to progression will be beneficial in the risk stratification of patients. These genetic markers can also serve as potential therapeutic targets in the future. In this review, we focus on the genetic markers associated with the progression and severity of NAFLD.
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Affiliation(s)
- Aalam Sohal
- Liver Institute Northwest, 3216 Northeast 45th Place Suite 212, Seattle, WA 98105, USA
| | - Hunza Chaudhry
- Department of Internal Medicine, UCSF Fresno, 155 North Fresno Street, Fresno, CA 93722, USA
| | - Kris V Kowdley
- Liver Institute Northwest, 3216 Northeast 45th Place Suite 212, Seattle, WA 98105, USA; Elson S. Floyd College of Medicine, Washington State University, WA, USA.
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15
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Zhou X, Wang L, Zhu P, Yang Z, Wang Z, Chen Y, Gu X, He R, Xu J, Jing B, Yang G, Chen S, Wu S, Xie Y. Comprehensive molecular characterization of complete mitogenome assemblies of 33 Eimeria isolates infecting domestic chickens. Parasit Vectors 2023; 16:109. [PMID: 36935516 PMCID: PMC10026407 DOI: 10.1186/s13071-023-05712-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 02/22/2023] [Indexed: 03/21/2023] Open
Abstract
BACKGROUND Coccidiosis caused by Eimeria is one of the most severe chicken diseases and poses a great economic threat to the poultry industry. Understanding the evolutionary biology of chicken Eimeria parasites underpins development of new interactions toward the improved prevention and control of this poultry disease. METHODS We presented an evolutionary blueprint of chicken coccidia by genetically characterizing complete mitogenome assemblies of 33 isolates representing all seven known Eimeria species infecting chickens in China. Further genome- and gene-level phylogenies were also achieved to better understand the evolutionary relationships of these chicken Eimeria at the species level. RESULTS 33 mitogenomes of chicken eimerian parasites ranged from 6148 bp to 6480 bp in size and encoded typical mitochondrial compositions of apicomplexan parasites including three protein-coding genes (PCGs), seven fragmented small subunit (SSU) and 12/13 fragmented large subunit (LSU) rRNAs. Comparative genomics provided an evolutionary scenario for the genetic diversity of PCGs-cytochrome c oxidase subunits 1 and 3 (cox1 and cox3) and cytochrome b (cytb); all were under purifying selection with cox1 and cox3 being the lowest and highest evolutionary rates, respectively. Genome-wide phylogenies classified the 33 Eimeria isolates into seven subgroups, and furthermore Eimeria tenella and Eimeria necatrix were determined to be more closely related to each other than to the other eight congenic species. Single/concatenated mitochondrial protein gene-based phylogenies supported cox1 as the genetic marker for evolutionary and phylogenetic studies for avain coccidia. CONCLUSIONS To our knowledge, these are the first population-level mitogenomic data on the genus Eimeria, and its comprehensive molecular characterization provides valuable resources for systematic, population genetic and evolutionary biological studies of apicomplexan parasites in poultry.
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Affiliation(s)
- Xuan Zhou
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Lidan Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Pengchen Zhu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Zijiang Yang
- Tokyo University of Marine Science and Technology, Konan Minato-Ku, Tokyo, 1088477, Japan
| | - Zhao Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Yijun Chen
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Xiaobin Gu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Ran He
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Jing Xu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Bo Jing
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Guangyou Yang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China.
| | - Shuangyang Wu
- Gregor Mendel Institute, Austrian Academy of Sciences, 1030, Vienna, Austria.
| | - Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, 611130, China.
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16
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Zhang G, Xia G, Luo J, Ye P, Wang H, Li S, Zheng D. Hedgehog signaling-related genomics signature for the accurate progress and prognosis prediction in gastric cancer. Funct Integr Genomics 2023; 23:69. [PMID: 36853390 DOI: 10.1007/s10142-023-00996-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/14/2023] [Accepted: 02/19/2023] [Indexed: 03/01/2023]
Abstract
The Hedgehog pathway is thought to be closely associated with the progression of GC; however, a specific link between the Hedgehog pathway on the prognosis and immune infiltration of gastric cancer is still lacking. This study collected Hedgehog pathway-related genes. The Hedgehog pathway-related pattern were identified by consensus cluster analysis. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA) were used to identify the biological functions which were significantly altered between predefined Cluster1 and Cluster2 in consensus clustering. The risk model of gastric cancer based on Hedgehog signaling pathway was constructed by univariate and multivariate COX regression, and the nomogram was constructed. The results showed that there were significant differences in the expression of Hedgehog pathway-related genes between the two groups. In addition, the constructed risk model was significantly correlated with the clinical prognosis and immune cell infiltration level of patients with gastric cancer. The model effectively predicted the efficacy of chemotherapy in GC patients and the sensitivity of drug treatment between groups. We systematically revealed the mechanism of Hedgehog pathway in gastric cancer and selected biomarkers with biological significance from a new perspective, providing potential direction for the treatment of gastric cancer.
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Affiliation(s)
- Guoliang Zhang
- Department of Gastrointestinal Surgery, Shaoxing Central Hospital, Shaoxing, China
| | - Guojun Xia
- Department of Gastrointestinal Surgery, Shaoxing Central Hospital, Shaoxing, China
| | - Jungang Luo
- Department of Gastrointestinal Surgery, Shaoxing Central Hospital, Shaoxing, China
| | - Ping Ye
- Department of Gastrointestinal Surgery, Shaoxing Central Hospital, Shaoxing, China
| | - Huangen Wang
- Department of Gastrointestinal Surgery, Shaoxing Central Hospital, Shaoxing, China
| | - Shaodong Li
- Department of Gastrointestinal Surgery, Shaoxing Central Hospital, Shaoxing, China
| | - Difeng Zheng
- Department of Gastrointestinal Surgery, Shaoxing Central Hospital, Shaoxing, China.
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Larroque J, Balkenhol N. A simulation-based evaluation of methods for estimating census population size of terrestrial game species from genetically-identified parent-offspring pairs. PeerJ 2023; 11:e15151. [PMID: 37070094 PMCID: PMC10105560 DOI: 10.7717/peerj.15151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 03/09/2023] [Indexed: 04/19/2023] Open
Abstract
Estimates of wildlife population size are critical for conservation and management, but accurate estimates are difficult to obtain for many species. Several methods have recently been developed that estimate abundance using kinship relationships observed in genetic samples, particularly parent-offspring pairs. While these methods are similar to traditional Capture-Mark-Recapture, they do not need physical recapture, as individuals are considered recaptured if a sample contains one or more close relatives. This makes methods based on genetically-identified parent-offspring pairs particularly interesting for species for which releasing marked animals back into the population is not desirable or not possible (e.g., harvested fish or game species). However, while these methods have successfully been applied in commercially important fish species, in the absence of life-history data, they are making several assumptions unlikely to be met for harvested terrestrial species. They assume that a sample contains only one generation of parents and one generation of juveniles of the year, while more than two generations can coexist in the hunting bags of long-lived species, or that the sampling probability is the same for each individual, an assumption that is violated when fecundity and/or survival depend on sex or other individual traits. In order to assess the usefulness of kin-based methods to estimate population sizes of terrestrial game species, we simulated population pedigrees of two different species with contrasting demographic strategies (wild boar and red deer), applied four different methods and compared the accuracy and precision of their estimates. We also performed a sensitivity analysis, simulating population pedigrees with varying fecundity characteristics and various levels of harvesting to identify optimal conditions of applicability of each method. We showed that all these methods reached the required levels of accuracy and precision to be effective in wildlife management under simulated circumstances (i.e., for species within a given range of fecundity and for a given range of sampling intensity), while being robust to fecundity variation. Despite the potential usefulness of the methods for terrestrial game species, care is needed as several biases linked to hunting practices still need to be investigated (e.g., when hunting bags are biased toward a particular group of individuals).
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Affiliation(s)
- Jeremy Larroque
- Wildlife Sciences, University of Goettingen, Goettingen, Germany
| | - Niko Balkenhol
- Wildlife Sciences, University of Goettingen, Goettingen, Germany
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18
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Wyatt PB, Satalich J, Cyrus J, O'Neill C, O'Connell R. Biochemical markers of postsurgical knee arthrofibrosis: A systematic review. J Orthop 2023; 35:1-6. [PMID: 36325249 PMCID: PMC9619298 DOI: 10.1016/j.jor.2022.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/09/2022] [Accepted: 10/19/2022] [Indexed: 12/15/2022] Open
Abstract
Introduction Postsurgical knee arthrofibrosis is a common complication associated with pain and limited range of motion. Although the mechanism is unclear, many biochemical and genetic markers have been identified within arthrofibrotic knees. The purpose of this systematic review is to synthesize the many biochemical and genetic markers that have been associated with surgery-induced knee arthrofibrosis in order to better guide future therapeutic endeavors. Methods A thorough search of literature was conducted on April 27, 2022. Seventeen studies met inclusion criteria for this systematic review. Inclusion criteria for this study were as follows: title or abstract discussed biochemical and genetic markers associated with postoperative knee arthrofibrosis, study design included human and/or animal subjects. Results A wide variety of genetic biomarkers (mRNA), proteins/enzymes, and cytokines were identified in both animal models and human subjects with postsurgical knee arthrofibrosis. These included various extracellular matrix-encoding mRNA sequences, matrix metalloproteinases, proteins and mRNA sequences involved in Transforming Growth Factor-β signaling, and interleukin-family cytokines to name just a few. Conclusion There are many biomarkers found in postsurgical arthrofibrotic knees. TGF-β, and mRNA/proteins that participate in TGF-β signaling (i.e., LOX, SERPINE1, PAI-1/Akt/mTOR, BMP-2), appear to be particularly common. Future comparative studies should aim to determine which of these are most relevant, and therefore, worthwhile therapeutic targets.
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Affiliation(s)
- Phillip B. Wyatt
- Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - James Satalich
- Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - John Cyrus
- Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Conor O'Neill
- Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Robert O'Connell
- Virginia Commonwealth University School of Medicine, Richmond, VA, USA
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Lakicevic B, Jankovic V, Pietzka A, Ruppitsch W. Wholegenome sequencing as the gold standard approach for control of Listeria monocytogenes in the food chain. J Food Prot 2023; 86:100003. [PMID: 36916580 DOI: 10.1016/j.jfp.2022.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 10/05/2022] [Accepted: 10/19/2022] [Indexed: 12/23/2022]
Abstract
Listeria monocytogenes has been implicated in numerous outbreaks and related deaths of listeriosis. In food production, L. monocytogenes occurs in raw food material and above all, through postprocessing contamination. The use of next-generation sequencing technologies such as whole-genome sequencing (WGS) facilitates foodborne outbreak investigations, pathogen source tracking and tracing geographic distributions of different clonal complexes, routine microbiological/epidemiological surveillance of listeriosis, and quantitative microbial risk assessment. WGS can also be used to predict various genetic traits related to virulence, stress, or antimicrobial resistance, which can be of great benefit for improving food safety management as well as public health.
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Affiliation(s)
- Brankica Lakicevic
- Department for Microbiological and Molecular-biological Testing, Institute of Meat Hygiene and Technology, Belgrade, Serbia.
| | - Vesna Jankovic
- Department for Microbiological and Molecular-biological Testing, Institute of Meat Hygiene and Technology, Belgrade, Serbia
| | - Ariane Pietzka
- Institute of Medical Microbiology and Hygiene/National Reference Laboratory for Listeria Division for Public Health, Austrian Agency for Health and Food Safety, Graz, Austria
| | - Werner Ruppitsch
- Institute of Medical Microbiology and Hygiene Division for Public Health, Austrian Agency for Health and Food Safety, Vienna, Austria
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20
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Cruz-López M. [Scientific evidence of the consequences of modernity]. GAC MED MEX 2022; 158:10-12. [PMID: 36921219 DOI: 10.24875/gmm.m22000686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The prevalence of type 2 diabetes (T2D) in Mexico is 14.4%. This disease is characterized by a state of hyperglycemia and chronic inflammation secondary to inadequate insulin secretion and its resistance. Among its risk factors for metabolic diseases development, the interaction between obesity, sedentary lifestyle, hypercaloric diets and genetic variants play an important role. For decades, different basic and applied research groups have worked in an interdisciplinary way to provide scientific evidence that has helped to understand the mechanisms involved in the pathophysiology of T2D in Mexicans. However, today the urgency of the advance and better proposals for prevention and management of patients with T2D makes it necessary to use translational medicine, which integrates scientific knowledge with the use of innovative technologies to provide comprehensive health care. In this sense, the present document concisely describes, with a translational approach, the implications of the interaction of environmental and genetic risk factors in the development of childhood obesity and T2D in Mexico.
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Affiliation(s)
- Miguel Cruz-López
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades "Dr. Bernardo Sepúlveda", Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social. Ciudad de México, México
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21
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Karthik K, Anbazhagan S, Chitra MA, Sridhar R. First report of the whole genome of Moraxella bovoculi genotype 1 from India and comparative genomics of Moraxella bovoculi to identify genotype-specific markers. Arch Microbiol 2022; 204:663. [PMID: 36201053 DOI: 10.1007/s00203-022-03276-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/22/2022] [Accepted: 09/28/2022] [Indexed: 11/02/2022]
Abstract
Moraxella bovoculi has been isolated frequently from cattle with Infectious bovine keratoconjunctivitis (IBK). Two diverse genotypes of M. bovoculi, 1 and 2 were identified based on whole genome sequence analysis. It is essential to discriminate between the two genotypes to frame prevention and control measures. The whole genome of M. bovoculi TN7 was sequenced and compared to other M. bovoculi strains available in the NCBI database. M. bovoculi TN7 was found to be genotype 1, had an RTX toxin operon and pilA gene that are the known virulence factors in related Moraxella sp., but lacked antimicrobial resistance genes. M. bovoculi was found to have an open pangenome with 4051 (75.31%) accessory genes, and the addition of each new genome adds 18 genes to the pangenome. Comparison of pilin protein amino acid sequences revealed three new sequence types. Furthermore, the presence of linx, nagL, swrC and mdtA genes was found to be genotype 1 specific, whereas hyaD, garR, gbsA, yhdG, gabT, iclR, higB2, hmuU, hmuT and hemS were found only in genotype 2. Polymerase Chain Reaction (PCR) primers were designed and evaluated on strain TN7 plus seven additional strains accessible to us that had not been whole genome sequenced. This initial evaluation of the designed primers for the linX and hyaD genes produced the expected banding patterns on PCR gels for genotypes 1 and 2, respectively, among the 8 strains. The genotype-specific genes identified in this study can be used as markers for accurate diagnosis of genotype 1 isolates and this can aid in the development of autogenous or other molecular vaccines for treatment of infectious bovine keratoconjunctivitis (IBK) in resource-limited research settings.
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Affiliation(s)
- Kumaragurubaran Karthik
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, 600051, India. .,Department of Veterinary Microbiology, Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University, Udumalpet, Tamil Nadu, India.
| | - Subbaiyan Anbazhagan
- ICMR-National Animal Resource Facility for Biomedical Research, Hyderabad, Telangana, 500078, India
| | - Murugesan Ananda Chitra
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, 600051, India
| | - Ramaswamy Sridhar
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, 600051, India
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22
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Lunardi M, Al-Habbaa A, Abdelshafy M, Davey MG, Elkoumy A, Ganly S, Elzomor H, Cawley C, Sharif F, Crowley J, Kerin M, Wijns W, Lowery A, Soliman O. Genetic and RNA-related molecular markers of trastuzumab-chemotherapy-associated cardiotoxicity in HER2 positive breast cancer: a systematic review. BMC Cancer 2022; 22:396. [PMID: 35413811 PMCID: PMC9004047 DOI: 10.1186/s12885-022-09437-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 03/16/2022] [Indexed: 11/19/2022] Open
Abstract
Cancer-therapy related cardiotoxicity (CTRCT) is a significant and frequent complication of monoclonal antibody directed therapy, especially Trastuzumab, for human epidermal growth factor receptor 2 (HER2) overexpressing breast cancers. Reliable, clinically available molecular predictive markers of CTRCT have not yet been developed. Identifying specific genetic variants and their molecular markers, which make the host susceptible to this complication is key to personalised risk stratification. A systematic review was conducted until April 2021, using the Medline, Embase databases and Google Scholar, to identify studies genetic and RNA-related markers associated with CTRCT in HER2 positive breast cancer patients. So far, researchers have mainly focused on HER2 related polymorphisms, revealing codons 655 and 1170 variants as the most likely SNPs associated with cardiotoxicity, despite some contradictory results. More recently, new potential genetic markers unrelated to the HER2 gene, and linked to known cardiomyopathy genes or to genes regulating cardiomyocytes apoptosis and metabolism, have been detected. Moreover, microRNAs are gaining increasing recognition as additional potential molecular markers in the cardio-oncology field, supported by encouraging preliminary data about their relationship with cardiotoxicity in breast cancers. In this review, we sought to synthesize evidence for genetic variants and RNA-related molecular markers associated with cardiotoxicity in HER2-positive breast cancer.
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Affiliation(s)
- Mattia Lunardi
- Discipline of Cardiology, Saolta Group, Galway University Hospital, Health Service Executive and CORRIB Core Lab, National University of Ireland Galway (NUIG), Galway, H91 TK33, Ireland.,Division of Cardiology, Department of Medicine, University of Verona, Verona, Italy.,The Lambe Institute for Translational Medicine and CURAM, National University of Ireland Galway (NUIG), Galway, Ireland
| | - Ahmed Al-Habbaa
- Discipline of Cardiology, Saolta Group, Galway University Hospital, Health Service Executive and CORRIB Core Lab, National University of Ireland Galway (NUIG), Galway, H91 TK33, Ireland.,Department of Cardiology, Faculty of Medicine, Al-Azhar University, Cairo, Egypt
| | - Mahmoud Abdelshafy
- Discipline of Cardiology, Saolta Group, Galway University Hospital, Health Service Executive and CORRIB Core Lab, National University of Ireland Galway (NUIG), Galway, H91 TK33, Ireland
| | - Matthew G Davey
- Discipline of Surgery, School of Medicine, Lambe Institute for Translational Research, National University of Ireland Galway, Galway, Ireland
| | - Ahmed Elkoumy
- Discipline of Cardiology, Saolta Group, Galway University Hospital, Health Service Executive and CORRIB Core Lab, National University of Ireland Galway (NUIG), Galway, H91 TK33, Ireland
| | - Sandra Ganly
- Discipline of Cardiology, Saolta Group, Galway University Hospital, Health Service Executive and CORRIB Core Lab, National University of Ireland Galway (NUIG), Galway, H91 TK33, Ireland.,The Lambe Institute for Translational Medicine and CURAM, National University of Ireland Galway (NUIG), Galway, Ireland.,Precision Cardio-Oncology Research Enterprise (P-CORE), National University of Ireland, Galway, Ireland
| | - Hesham Elzomor
- Discipline of Cardiology, Saolta Group, Galway University Hospital, Health Service Executive and CORRIB Core Lab, National University of Ireland Galway (NUIG), Galway, H91 TK33, Ireland
| | - Christian Cawley
- Discipline of Cardiology, Saolta Group, Galway University Hospital, Health Service Executive and CORRIB Core Lab, National University of Ireland Galway (NUIG), Galway, H91 TK33, Ireland
| | - Faisal Sharif
- Discipline of Cardiology, Saolta Group, Galway University Hospital, Health Service Executive and CORRIB Core Lab, National University of Ireland Galway (NUIG), Galway, H91 TK33, Ireland
| | - James Crowley
- Discipline of Cardiology, Saolta Group, Galway University Hospital, Health Service Executive and CORRIB Core Lab, National University of Ireland Galway (NUIG), Galway, H91 TK33, Ireland
| | - Michael Kerin
- Discipline of Surgery, School of Medicine, Lambe Institute for Translational Research, National University of Ireland Galway, Galway, Ireland.,Precision Cardio-Oncology Research Enterprise (P-CORE), National University of Ireland, Galway, Ireland
| | - William Wijns
- Discipline of Cardiology, Saolta Group, Galway University Hospital, Health Service Executive and CORRIB Core Lab, National University of Ireland Galway (NUIG), Galway, H91 TK33, Ireland.,The Lambe Institute for Translational Medicine and CURAM, National University of Ireland Galway (NUIG), Galway, Ireland.,Precision Cardio-Oncology Research Enterprise (P-CORE), National University of Ireland, Galway, Ireland
| | - Aoife Lowery
- Discipline of Surgery, School of Medicine, Lambe Institute for Translational Research, National University of Ireland Galway, Galway, Ireland.,Precision Cardio-Oncology Research Enterprise (P-CORE), National University of Ireland, Galway, Ireland
| | - Osama Soliman
- Discipline of Cardiology, Saolta Group, Galway University Hospital, Health Service Executive and CORRIB Core Lab, National University of Ireland Galway (NUIG), Galway, H91 TK33, Ireland. .,Precision Cardio-Oncology Research Enterprise (P-CORE), National University of Ireland, Galway, Ireland.
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23
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Tai KY, Dhaliwal J, Balasubramaniam V. Leveraging Mann-Whitney U test on large-scale genetic variation data for analysing malaria genetic markers. Malar J 2022; 21:79. [PMID: 35264165 PMCID: PMC8905822 DOI: 10.1186/s12936-022-04104-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 02/24/2022] [Indexed: 11/10/2022] Open
Abstract
Background The malaria risk analysis of multiple populations is crucial and of great importance whilst compressing limitations. However, the exponential growth in diversity and accumulation of genetic variation data obtained from malaria-infected patients through Genome-Wide Association Studies opens up unprecedented opportunities to explore the significant differences between genetic markers (risk factors), particularly in the resistance or susceptibility of populations to malaria risk. Thus, this study proposes using statistical tests to analyse large-scale genetic variation data, comprising 20,854 samples from 11 populations within three continents: Africa, Oceania, and Asia. Methods Even though statistical tests have been utilized to conduct case–control studies since the 1950s to link risk factors to a particular disease, several challenges faced, including the choice of data (ordinal vs. non-ordinal) and test (parametric vs. non-parametric). This study overcomes these challenges by adopting the Mann–Whitney U test to analyse large-scale genetic variation data; to explore the statistical significance of markers between populations; and to further identify the highly differentiated markers. Results The findings of this study revealed a significant difference in the genetic markers between populations (p < 0.01) in all the case groups and most control groups. However, for the highly differentiated genetic markers, a significant difference (p < 0.01) was present for most genetic markers with varying p-values between the populations in the case and control groups. Moreover, several genetic markers were observed to have very significant differences (p < 0.001) across all populations, while others exist between certain specific populations. Also, several genetic markers have no significant differences between populations. Conclusions These findings further support that the genetic markers contribute differently between populations towards malaria resistance or susceptibility, thus showing differences in the likelihood of malaria infection. In addition, this study demonstrated the robustness of the Mann–Whitney U test in analysing genetic markers in large-scale genetic variation data, thereby indicating an alternative method to explore genetic markers in other complex diseases. The findings hold great promise for genetic markers analysis, and the pipeline emphasized in this study can fully be reproduced to analyse new data. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-022-04104-x.
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Affiliation(s)
- Kah Yee Tai
- School of Information Technology, Monash University Malaysia, Subang Jaya, Selangor, Malaysia
| | - Jasbir Dhaliwal
- School of Information Technology, Monash University Malaysia, Subang Jaya, Selangor, Malaysia.
| | - Vinod Balasubramaniam
- Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Subang Jaya, Selangor, Malaysia
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24
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Mekbib Y, Tesfaye K, Dong X, Saina JK, Hu GW, Wang QF. Whole-genome resequencing of Coffea arabica L. (Rubiaceae) genotypes identify SNP and unravels distinct groups showing a strong geographical pattern. BMC Plant Biol 2022; 22:69. [PMID: 35164709 PMCID: PMC8842891 DOI: 10.1186/s12870-022-03449-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/27/2022] [Indexed: 06/04/2023]
Abstract
BACKGROUND Coffea arabica L. is an economically important agricultural crop and the most popular beverage worldwide. As a perennial crop with recalcitrant seed, conservation of the genetic resources of coffee can be achieved through the complementary approach of in-situ and ex-situ field genebank. In Ethiopia, a large collection of C. arabica L. germplasm is preserved in field gene banks. Here, we report the whole-genome resequencing of 90 accessions from Choche germplasm bank representing garden and forest-based coffee production systems using Illumina sequencing technology. RESULTS The genome sequencing generated 6.41 billion paired-end reads, with a mean of 71.19 million reads per sample. More than 93% of the clean reads were mapped onto the C. arabica L. reference genome. A total of 11.08 million variants were identified, among which 9.74 million (87.9%) were SNPs (Single nucleotide polymorphisms) and 1.34 million (12.1%) were InDels. In all accessions, genomic variants were unevenly distributed across the coffee genome. The phylogenetic analysis using the SNP markers displayed distinct groups. CONCLUSIONS Resequencing of the coffee accessions has allowed identification of genetic markers, such as SNPs and InDels. The SNPs discovered in this study might contribute to the variation in important pathways of genes for important agronomic traits such as caffeine content, yield, disease, and pest in coffee. Moreover, the genome resequencing data and the genetic markers identified from 90 accessions provide insight into the genetic variation of the coffee germplasm and facilitate a broad range of genetic studies.
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Affiliation(s)
- Yeshitila Mekbib
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Ethiopian Biodiversity Institute, P.O. Box 30726, Addis Ababa, Ethiopia
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Kassahun Tesfaye
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
- Ethiopian Biotechnology Institute, Ministry of Innovation and Technology, Addis Ababa, Ethiopia
| | - Xiang Dong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Josphat K Saina
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
- Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, 666303, China
| | - Guang-Wan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
| | - Qing-Feng Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
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25
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Karachaliou GS, Alkallas R, Carroll SB, Caressi C, Zakria D, Patel NM, Trembath DG, Ezzell JA, Pegna GJ, Googe PB, Galeotti JP, Ayvali F, Collichio FA, Lee CB, Ollila DW, Gulley ML, Johnson DB, Kim KB, Watson IR, Moschos SJ. The clinical significance of adenomatous polyposis coli (APC) and catenin Beta 1 (CTNNB1) genetic aberrations in patients with melanoma. BMC Cancer 2022; 22:38. [PMID: 34986841 PMCID: PMC8734243 DOI: 10.1186/s12885-021-08908-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 10/12/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Melanoma-intrinsic activated β-catenin pathway, the product of the catenin beta 1 (CTNNB1) gene, has been associated with low/absent tumor-infiltrating lymphocytes, accelerated tumor growth, metastases development, and resistance to anti-PD-L1/anti-CTLA-4 agents in mouse melanoma models. Little is known about the association between the adenomatous polyposis coli (APC) and CTNNB1 gene mutations in stage IV melanoma with immunotherapy response and overall survival (OS). METHODS We examined the prognostic significance of somatic APC/CTNNB1 mutations in the Cancer Genome Atlas Project for Skin Cutaneous Melanoma (TCGA-SKCM) database. We assessed APC/CTNNB1 mutations as predictors of response to immunotherapies in a clinicopathologically annotated metastatic patient cohort from three US melanoma centers. RESULTS In the TCGA-SKCM patient cohort (n = 434) presence of a somatic APC/CTNNB1 mutation was associated with a worse outcome only in stage IV melanoma (n = 82, median OS of APC/CTNNB1 mutants vs. wild-type was 8.15 vs. 22.8 months; log-rank hazard ratio 4.20, p = 0.011). APC/CTNNB1 mutation did not significantly affect lymphocyte distribution and density. In the 3-melanoma institution cohort, tumor tissues underwent targeted panel sequencing using two standards of care assays. We identified 55 patients with stage IV melanoma and APC/CTNNB1 genetic aberrations (mut) and 169 patients without (wt). At a median follow-up of more than 25 months for both groups, mut compared with wt patients had slightly more frequent (44% vs. 39%) and earlier (66% vs. 45% within six months from original diagnosis of stage IV melanoma) development of brain metastases. Nevertheless, time-to-development of brain metastases was not significantly different between the two groups. Fortunately, mut patients had similar clinical benefits from PD-1 inhibitor-based treatments compared to wt patients (median OS 26.1 months vs. 29.9 months, respectively, log-rank p = 0.23). Less frequent mutations in the NF1, RAC1, and PTEN genes were seen in the mut compared with wt patients from the 3-melanoma institution cohort. Analysis of brain melanoma tumor tissues from a separate craniotomy patient cohort (n = 55) showed that melanoma-specific, activated β-catenin (i.e., nuclear localization) was infrequent (n = 3, 6%) and not prognostic in established brain metastases. CONCLUSIONS APC/CTNNB1 mutations are associated with a worse outcome in stage IV melanoma and early brain metastases independent of tumor-infiltrating lymphocyte density. However, PD1 inhibitor-based treatments provide comparable benefits to both mut and wt patients with stage IV melanoma.
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Affiliation(s)
- Georgia Sofia Karachaliou
- Department of Medicine, The University of North Carolina at Chapel Chapel Hill, Chapel Hill, NC, USA
| | - Rached Alkallas
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Sarah B Carroll
- Department of Medicine, The University of North Carolina at Chapel Chapel Hill, Chapel Hill, NC, USA
| | - Chongshan Caressi
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | - Danny Zakria
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Nirali M Patel
- Department of Pathology & Laboratory Medicine, The University of North Carolina at Chapel Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dimitri G Trembath
- Department of Pathology & Laboratory Medicine, The University of North Carolina at Chapel Chapel Hill, Chapel Hill, NC, USA
| | - Jennifer A Ezzell
- Department of Cell Biology & Physiology, Histology Research Core Facility, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Guillaume J Pegna
- Department of Medicine, The University of North Carolina at Chapel Chapel Hill, Chapel Hill, NC, USA
| | - Paul B Googe
- Department of Dermatology, The University of North Carolina at Chapel Chapel Hill, Chapel Hill, NC, USA
| | - Jonathan P Galeotti
- Department of Pathology & Laboratory Medicine, The University of North Carolina at Chapel Chapel Hill, Chapel Hill, NC, USA
| | - Fatih Ayvali
- Department of Medicine, The University of North Carolina at Chapel Chapel Hill, Chapel Hill, NC, USA
| | - Frances A Collichio
- Department of Medicine, The University of North Carolina at Chapel Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Carrie B Lee
- Department of Medicine, The University of North Carolina at Chapel Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David W Ollila
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Surgery, The University of North Carolina at Chapel Chapel Hill, Chapel Hill, NC, USA
| | - Margaret L Gulley
- Department of Pathology & Laboratory Medicine, The University of North Carolina at Chapel Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Douglas B Johnson
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Kevin B Kim
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | - Ian R Watson
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Stergios J Moschos
- Department of Medicine, The University of North Carolina at Chapel Chapel Hill, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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26
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Malik A, Malik J, Javaid M, Khan HS, Mohsin M, Shoaib M. A case of aortic dissection in familial Mediterranean fever. J Cardiol Cases 2021; 24:296-299. [PMID: 34917214 DOI: 10.1016/j.jccase.2021.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/07/2021] [Accepted: 05/13/2021] [Indexed: 01/09/2023] Open
Abstract
Familial Mediterranean fever (FMF) is an ethnicity-specific autoinflammatory disease prevalent in the Arab world. It has various presentations including amyloidosis, small-vessel vasculitis, and pericarditis. Different mutations in the Mediterranean fever (MEFV) gene can cause this disorder and it is inherited in an autosomal recessive pattern. We present a case of a 23-year-old man of Iranian descent with history of periodic fever, diagnosed as Stanford type A aortic dissection secondary to an acute attack of FMF. To the best of our knowledge, this is the first case reported of such a complication. <Learning objective:1.Diagnosis of familial Mediterranean fever is a diagnosis of exclusion as many diseases involve large arteries and present with aortic involvement.2.Familial Mediterranean fever usually involves small- and medium-sized arteries but unusual case presentations can occur in some patients involving the aorta.3.Physicians in Pakistan must be made aware of the rapidly increasing prevalence of familial Mediterranean fever due to migration of susceptible ethnic groups in order to manage patients while they are still amenable to treatment.>.
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Affiliation(s)
- Asmara Malik
- Public Health, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Jahanzeb Malik
- Cardiology, Rawalpindi Institute of Cardiology, Rawalpindi, Pakistan
| | - Muhammad Javaid
- Cardiology, Rawalpindi Institute of Cardiology, Rawalpindi, Pakistan
| | - Hamid Sharif Khan
- Cardiology, Rawalpindi Institute of Cardiology, Rawalpindi, Pakistan
| | - Muhammad Mohsin
- Cardiology, Rawalpindi Institute of Cardiology, Rawalpindi, Pakistan
| | - Muhammad Shoaib
- Cardiology, Pakistan Institute of Medical and Health Sciences, Islamabad, Pakistan
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27
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Sousa R, Vasconcelos J, Vera-Escalona I, Pinto AR, Hawkins SJ, Freitas M, Delgado J, González JA, Riera R. Pleistocene expansion, anthropogenic pressure and ocean currents: Disentangling the past and ongoing evolutionary history of Patella aspera Röding, 1798 in the archipelago of Madeira. Mar Environ Res 2021; 172:105485. [PMID: 34715642 DOI: 10.1016/j.marenvres.2021.105485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 09/12/2021] [Accepted: 09/18/2021] [Indexed: 06/13/2023]
Abstract
AIMS Rising sea-level following the Last Glacial Maximum lead to fragmentation of coastal limpet populations between islands of the Archipelago of Madeira. This fragmentation is reinforced by recent heavy exploitation reducing effective population size on Madeira Island. We use the limpet P. aspera to understand how the role of processes at different time scales (i.e. changes in the sea level and overexploitation) can influence the genetic composition of an extant species, relating these processes to reproductive phenology and seasonal shifts in ocean currents. LOCATION Madeira Island, Porto Santo and Desertas (Archipelago of Madeira, NE Atlantic Ocean). TAXON The limpet Patella aspera. METHODS Twelve microsatellite genetic markers were used. A power analysis was used to evaluate the power of the microsatellite markers to detect a signal of population differentiation. Long-term past migrations were assessed using a Bayesian Markov Montecarlo approach in the software MIGRATE-n to estimate mutation-scaled migration rates (M = m/μ; m, probability of a lineage immigrating per generation; μ, mutation rate). Two scenarios were evaluated using an Approximate Bayesian Computation (ABC) in the software DIYABC 2.1 (i) Scenario 1: considered a population scenario from a reduced Ne at time t3 to a higher Ne at time t2; and (ii) Scenario 2 considering a reduction of Ne from a time t3 to a time t2. RESULTS Colonization of the archipelago by Portuguese settlers six centuries ago probably led to an important decrease in the genetic diversity of the species (Ne). Contemporary gene flow strongly support a pattern of high asymmetric connectivity explained by the reproductive phenology of the species and spatio-temporal seasonal changes in the ocean currents. Spatio-temporal reconstructions using Bayesian methods, including coalescent and Approximate Bayesian Computation (ABC) approaches, suggest changes in the migration patterns from highly symmetric to highly asymmetric connectivity with subtle population differentiation as consequence of post-glacial maximum sea level rise during the Holocene. MAIN CONCLUSIONS Our results suggest that anthropogenic activity could have had serious effects on the genetic diversity of heavily exploited littoral species since the end of the Pleistocene, probably accelerating in recent years.
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Affiliation(s)
- Ricardo Sousa
- Observatório Oceânico da Madeira, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (OOM/ARDITI) - Edifício Madeira Tecnopolo, Funchal, Madeira, Portugal; Direção Regional do Mar (DRM)/ Direção de Serviços de Monitorização, Estudos e Investigação do Mar (DSEIMar), 9004-562, Funchal, Madeira, Portugal; MARE - Marine and Environmental Sciences Centre, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (ARDITI), Edifício Madeira Tecnopolo Piso 0, Caminho da Penteada, 9020-105, Funchal, Madeira, Portugal
| | - Joana Vasconcelos
- MARE - Marine and Environmental Sciences Centre, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (ARDITI), Edifício Madeira Tecnopolo Piso 0, Caminho da Penteada, 9020-105, Funchal, Madeira, Portugal; Faculdade de Ciências de Vida, Universidade da Madeira, Campus Universitário da Madeira, Caminho da Penteada, 9020-020, Funchal, Madeira, Portugal; Departamento de Ecología, Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Casilla 297, Concepción, Chile
| | - Iván Vera-Escalona
- CIBAS, Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Casilla 297, Concepción, Chile; IU-ECOAQUA, Group of Biodiversity and Conservation (BIOCON), Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Ana Rita Pinto
- Direção Regional do Mar (DRM)/ Direção de Serviços de Monitorização, Estudos e Investigação do Mar (DSEIMar), 9004-562, Funchal, Madeira, Portugal
| | - S J Hawkins
- Marine Biological Association of the UK, Plymouth, PL1 2PB, UK; School of Ocean and Earth Science, University of Southampton, National Oceanography Centre, Southampton, SO14 3ZH, UK
| | - Mafalda Freitas
- Observatório Oceânico da Madeira, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (OOM/ARDITI) - Edifício Madeira Tecnopolo, Funchal, Madeira, Portugal; Direção Regional do Mar (DRM)/ Direção de Serviços de Monitorização, Estudos e Investigação do Mar (DSEIMar), 9004-562, Funchal, Madeira, Portugal; MARE - Marine and Environmental Sciences Centre, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (ARDITI), Edifício Madeira Tecnopolo Piso 0, Caminho da Penteada, 9020-105, Funchal, Madeira, Portugal
| | - João Delgado
- Direção Regional do Mar (DRM)/ Direção de Serviços de Monitorização, Estudos e Investigação do Mar (DSEIMar), 9004-562, Funchal, Madeira, Portugal; Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Porto, Portugal
| | - José A González
- Ecología Marina Aplicada y Pesquerías (i-UNAT), Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Rodrigo Riera
- Departamento de Ecología, Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Casilla 297, Concepción, Chile; IU-ECOAQUA, Group of Biodiversity and Conservation (BIOCON), Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain.
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Al-Amri O, Al-Quraishy S, Al-Shaebi EM, Aljawdah HMA, Abdel-Gaber R. Molecular identification of the rodent-borne pathogen Rodentolepis nana using the genetic markers of ITS-1, 18 S, and 28 S rDNA. Mol Biol Rep 2021. [PMID: 34802115 DOI: 10.1007/s11033-021-06966-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 11/16/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Rodentolepis nana (syn. Hymenolepis nana), the most common cyclophyllid tapeworm infecting rodents, is a well-studied gastrointestinal parasite in mice and belongs to the family Hymenolepididae. METHODS The present study focuses on the molecular analysis for the nuclear genes (ITS-1, 18 S, and 28 S rDNA) used for the accurate recognition of the recovered Rodentolepis species. RESULTS The annotated partial ITS-1, 18 S, and 28 S rDNA gene regions were deposited in GenBank (gbǀ MW310394.1, gbǀ MW327585.1, and gbǀ MW324479.1, respectively) and further used in the maximum likelihood method (ML) to clarify their genetic relationships at the species level. The interrogation sequence of R. nana was aligned and belonged to the family Hymenolepididae, in the same group as all Hymenolepis species, which were distinct from Cyclophyllidea cestodes, especially species belonging to Anoplocephalidae and Taeniidae. Sequence data support the paraphyly of Hymenolepis species. CONCLUSIONS The phylogeny supports the availability of the ITS-1, 18 S, and 28 S rDNA genes as reliable genetic markers for evolutionary relationships.
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Gomes Rios T, Larios G, Marangoni B, Oliveira SL, Cena C, Alberto do Nascimento Ramos C. FTIR spectroscopy with machine learning: A new approach to animal DNA polymorphism screening. Spectrochim Acta A Mol Biomol Spectrosc 2021; 261:120036. [PMID: 34116415 DOI: 10.1016/j.saa.2021.120036] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 06/12/2023]
Abstract
Technological advances in recent decades, especially in molecular genetics, have enabled the detection of genetic DNA markers associated with productive characteristics in animals. However, the prospection of polymorphisms based on DNA sequencing is still expensive for the reality of many food-producing regions around the world, such as Brazil, demanding more accessible prospecting methods. In the present study, the Fourier transform infrared spectroscopy (FTIR) and machine learning algorithms were used to identify single nucleotide polymorphism (SNP) in animal DNA. The fragments of bovine DNA with well-known polymorphisms were used as a model. The DNA fragments were produced and genotyped by PCR-RFLP and classified according to the genotype (homozygous or heterozygous). FTIR spectra of DNA fragments were analyzed by principal component analysis (PCA) and machine learning algorithms. The best results exhibited 75-95% accuracy in the classification of bovine genotypes. Therefore, FTIR spectroscopy and multivariate analysis can be used as an alternative tool for prospecting polymorphisms in animal DNA. The method can contribute with studies to identify genetic markers associated with animal production and indirectly with food production itself, and reduce pressure on available natural resources.
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Affiliation(s)
- Thaynádia Gomes Rios
- Faculdade de Medicina Veterinária e Zootecnia, Universidade Federal de Mato Grosso do Sul, 79070-900 Campo Grande, MS, Brazil
| | - Gustavo Larios
- Grupo de Óptica e Fotônica, Instituto de Física, Universidade Federal de Mato Grosso do Sul, 79070-900 Campo Grande, MS, Brazil
| | - Bruno Marangoni
- Grupo de Óptica e Fotônica, Instituto de Física, Universidade Federal de Mato Grosso do Sul, 79070-900 Campo Grande, MS, Brazil
| | - Samuel L Oliveira
- Grupo de Óptica e Fotônica, Instituto de Física, Universidade Federal de Mato Grosso do Sul, 79070-900 Campo Grande, MS, Brazil
| | - Cícero Cena
- Grupo de Óptica e Fotônica, Instituto de Física, Universidade Federal de Mato Grosso do Sul, 79070-900 Campo Grande, MS, Brazil
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Agaimy A, Hartmann A. [SMARCB1(INI1)-deficient renal cell carcinoma: medullary and beyond : Evolving concepts]. Pathologe 2021; 42:571-577. [PMID: 34609565 DOI: 10.1007/s00292-021-00985-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/11/2021] [Indexed: 10/20/2022]
Abstract
During the last decades, the SWI/SNF chromatin-remodeling complex has received enormous recognition as a major player in the molecular pathogenesis of diverse neoplasms. Accordingly, SWI/SNF defects affecting different subunits of the complex became defining genetic features in the nosology of different neoplastic entities. In the kidney, loss of SMARCB1(INI1) as a major component of the SWI/SNF complex has emerged as the defining genetic marker for renal medullary carcinoma and pediatric malignant rhabdoid tumor. Diagnosis of these two rare entities is based on a set of defined demographic, clinicopathological, immunophenotypic, and genetic (SMARCB1 loss) criteria. Moreover, the sickle cell trait is considered a prerequisite for renal medullary carcinoma. Current knowledge illustrates that SMARCB1 loss is encountered in three major tumor categories in the kidney: (1) histologically defined neoplasms that are primarily driven by de novo SMARCB1 loss (renal medullary carcinoma and malignant rhabdoid tumor); (2) SMRACB1-deficient renal cell carcinoma (RCC) with variable non-specific histology ranging from collecting duct-like, papillary high-grade (papillary type 2), or medullary-like (lacking sickle cell trait), to fully undifferentiated; and (3) biphasic (dedifferentiated) RCC showing a variable SMARCB1-deficient undifferentiated component. The latter variant most frequently originates from pre-existing clear cell RCC but may rarely superimpose on papillary or chromophobe RCC. This review summarizes the major defining features of the emerging SMARCB1-deficient renal neoplasms. All SMARCB1-deficient carcinomas have a poor prognosis in common. Therefore, exact diagnosis of these tumors is a prerequisite for studies investigating new therapies.
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Affiliation(s)
- Abbas Agaimy
- Institut für Pathologie, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Krankenhausstraße 8-10, 91054, Erlangen, Deutschland.
| | - Arndt Hartmann
- Institut für Pathologie, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Krankenhausstraße 8-10, 91054, Erlangen, Deutschland
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Bahji A, Forth E, Hargreaves T, Harkness K. Genetic markers of the stress generation model: A systematic review. Psychiatry Res 2021; 304:114139. [PMID: 34371296 DOI: 10.1016/j.psychres.2021.114139] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/16/2021] [Accepted: 07/24/2021] [Indexed: 01/15/2023]
Abstract
AIM Robust evidence suggests that depression, and risk for depression, are associated with the generation of stressful life events. This tendency to generate stress may be genetically determined. This systematic review aimed to identify specific molecular genetic markers associated with the generation of interpersonal stressful life events, at least in part dependent on individuals' behavior. METHOD We followed the PRISMA guidelines in searching six electronic databases (PubMed, MEDLINE, PsycINFO, CINAHL, Cochrane, and EMBASE) from inception to January 2021, and we reviewed the reference lists of eligible articles for additional records. We restricted eligibility to empirical studies involving at least one genetic marker and including proximal life events. We evaluated the risk of bias using the Newcastle Ottawa Scale for observational studies. The outcome permitted a distinction between life events dependent on the individual's agency versus independent events. RESULTS Seven studies, including 3585 participants, met eligibility criteria. Three were longitudinal, and four were cross-sectional; six included adolescents and young adults, and one focused on middle adulthood. Four examined the serotonin-transporter-linked promoter region (5-HTTLPR), two examined the rs53576 single nucleotide polymorphism of the oxytocin receptor gene (OXTR), and one examined a multilocus genetic profile score including four hypothalamic-pituitary-adrenal (HPA) axis genes. There were no significant direct correlations between genotype and life events in any study. Instead, their relation was significantly moderated by symptoms, exposure to early adversity, or attachment. Consistent with the stress generation hypothesis, this moderation relation was significant in predicting exposure to dependent life events but was not significant in predicting independent life event exposure. CONCLUSIONS There is evidence that genetic variation in the serotonin, HPA axis, and oxytocin systems moderates the effects of psychosocial vulnerability markers on the generation of proximal, dependent life events. Future research should examine additional genetic markers in systems known to confer risk for stress generation. PROSPERO CRD42019136886.
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Affiliation(s)
- Anees Bahji
- Department of Psychiatry, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada.
| | - Evan Forth
- Centre for Neuroscience Studies, Queen's University, Kingston, ON, Canada
| | - Tegan Hargreaves
- Department of Psychiatry, Queen's University, Kingston, ON, Canada
| | - Kate Harkness
- Department of Psychiatry, Queen's University, Kingston, ON, Canada; Department of Psychology, Queen's University, Kingston, ON, Canada
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Adeel M, Shakoor N, Hussain T, Azeem I, Zhou P, Zhang P, Hao Y, Rinklebe J, Rui Y. Bio-interaction of nano and bulk lanthanum and ytterbium oxides in soil system: Biochemical, genetic, and histopathological effects on Eisenia fetida. J Hazard Mater 2021; 415:125574. [PMID: 33756203 DOI: 10.1016/j.jhazmat.2021.125574] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/22/2021] [Accepted: 03/01/2021] [Indexed: 06/12/2023]
Abstract
The massive application of rare earth elements (REEs) in electronic industries cause their inevitable release into the environment; however, its effects on soil biota remain largely unaddressed. We investigated the E. fetida detoxification potential of nano and bulk La2O3 and Yb2O3 and their potential impact on biochemical and genetic markers at 50, 100, 200, 500 and 1000 mg kg-1 concentration. We found that earthworms bioremediate 3-15% La2O3 and Yb2O3 contaminated soil at low and medium levels, while this potential was limited at higher levels. Nano and bulk La2O3 and Yb2O3 treatment induced neurotoxicity in earthworm by inhibiting acetylcholinesterase by 49-65% and 22-36% at 500 and 1000 mg kg-1, respectively. Nano La2O3 proved to be highly detrimental, mainly through oxidative stress and subsequent failure of antioxidant system. Nano La2O3 and Yb2O3 at 100 mg kg-1 significantly down-regulated the expression of annetocin mRNA in the parental and progeny earthworms by 50% and 20%, which is crucial for earthworm reproduction. Similarly, expression level of heat shock protein 70 (HSP70) and metallothionein was significantly upregulated in both generations at medium exposure level. Histological observations showed that nano REEs at 200 mg kg-1 induced drastic changes in the intestinal epithelium and typhlosole of E. fetida. To date, our results enhance the understanding of interaction between REEs and earthworms.
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Affiliation(s)
- Muhammad Adeel
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Noman Shakoor
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Tariq Hussain
- College of Veterinary Sciences, The University Agriculture Peshawar, 25000, Pakistan
| | - Imran Azeem
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Pingfan Zhou
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Peng Zhang
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Yi Hao
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Jörg Rinklebe
- University of Wuppertal, School of Architecture and Civil Engineering, Institute of Foundation Engineering, Water and Waste Management, Laboratory of Soil, and Groundwater Management, Pauluskirchstraße7, 42285 Wuppertal, Germany; Department of Environment, Energy and Geoinformatics, Sejong University, Seoul 05006, Republic of Korea
| | - Yukui Rui
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.
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Poulain M, Herm A, Errigo A, Chrysohoou C, Legrand R, Passarino G, Stazi MA, Voutekatis KG, Gonos ES, Franceschi C, Pes GM. Specific features of the oldest old from the Longevity Blue Zones in Ikaria and Sardinia. Mech Ageing Dev 2021; 198:111543. [PMID: 34265327 DOI: 10.1016/j.mad.2021.111543] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 06/17/2021] [Accepted: 07/09/2021] [Indexed: 11/23/2022]
Abstract
Human longevity may be found in single individuals as well as in the population as a whole ("population longevity"). Longevity Blue Zones (LBZs), which are areas with an unusually high number of oldest old, have been identified in Sardinia and the Greek island of Ikaria. We compared the lifestyle, health status and some genetic markers of the LBZ populations with those of reference populations from Italy and Greece; the data were extracted from the GEHA database. In the LBZs, the proportion of individuals who never married or were married and still living with their spouse was significantly greater. Nonagenarians males and females with a high self‒perception of optimism and/or a high score for self-rated health were also found in larger proportions in LBZs. Among the variables with lower frequency were the proportion of the widowed, the percentage of subjects who had suffered a stroke and the frequency of Apoε4 and Apoε2 and the TT genotype of FOXO3A gene. Compared to behavioral and health indicators, the impact of genetic factors might be relatively less important in the LBZs. Nevertheless, further research is needed to identify potential epigenetic traits that might play a predominant role due to the interaction between genetics and the human and physical environments.
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Abstract
Heart failure is a global health burden responsible for high morbidity and mortality with a prevalence of greater than 60 million individuals worldwide. One of the major causes of heart failure is dilated cardiomyopathy (DCM), characterized by associated systolic dysfunction. During the last few decades, there have been remarkable advances in our understanding about the genetics of dilated cardiomyopathy. The genetic causes were initially thought to be associated with mutations in genes encoding proteins that are localized to cytoskeleton and sarcomere only; however, with the advancement in mechanistic understanding, the roles of ion channels, Z-disc, mitochondria, nuclear proteins, cardiac transcription factors (e.g., NKX-2.5, TBX20, GATA4), and the factors involved in calcium homeostasis have also been identified and found to be implicated in both familial and sporadic DCM cases. During past few years, next-generation sequencing (NGS) has been established as a diagnostic tool for genetic analysis and it has added significantly to the existing candidate gene list for DCM. The animal models have also provided novel insights to develop a better treatment strategy based on phenotype-genotype correlation, epigenetic and phenomic profiling. Most of the DCM biomarkers that are used in routine genetic and clinical testing are structural proteins, but during the last few years, the role of mi-RNA has also emerged as a biomarker due to their accessibility through noninvasive methods. Our increasing genetic knowledge can improve the clinical management of DCM by bringing clinicians and geneticists on one platform, thereby influencing the individualized clinical decision making and leading to precision medicine.
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Affiliation(s)
- Prerna Giri
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Uttar Pradesh, Varanasi-5, India
| | - Amrita Mukhopadhyay
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Uttar Pradesh, Varanasi-5, India
| | - Mohini Gupta
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Uttar Pradesh, Varanasi-5, India
| | - Bhagyalaxmi Mohapatra
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Uttar Pradesh, Varanasi-5, India.
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Chernova AI, Gubaev RF, Singh A, Sherbina K, Goryunova SV, Martynova EU, Goryunov DV, Boldyrev SV, Vanyushkina AA, Anikanov NA, Stekolshchikova EA, Yushina EA, Demurin YN, Mukhina ZM, Gavrilova VA, Anisimova IN, Karabitsina YI, Alpatieva NV, Chang PL, Khaitovich P, Mazin PV, Nuzhdin SV. Genotyping and lipid profiling of 601 cultivated sunflower lines reveals novel genetic determinants of oil fatty acid content. BMC Genomics 2021; 22:505. [PMID: 34225652 PMCID: PMC8256595 DOI: 10.1186/s12864-021-07768-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 06/03/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sunflower is an important oilseed crop domesticated in North America approximately 4000 years ago. During the last century, oil content in sunflower was under strong selection. Further improvement of oil properties achieved by modulating its fatty acid composition is one of the main directions in modern oilseed crop breeding. RESULTS We searched for the genetic basis of fatty acid content variation by genotyping 601 inbred sunflower lines and assessing their lipid and fatty acid composition. Our genome-wide association analysis based on the genotypes for 15,483 SNPs and the concentrations of 23 fatty acids, including minor fatty acids, revealed significant genetic associations for eleven of them. Identified genomic regions included the loci involved in rare fatty acids variation on chromosomes 3 and 14, explaining up to 34.5% of the total variation of docosanoic acid (22:0) in sunflower oil. CONCLUSIONS This is the first large scale implementation of high-throughput lipidomic profiling to sunflower germplasm characterization. This study contributes to the genetic characterization of Russian sunflower collections, which made a substantial contribution to the development of sunflower as the oilseed crop worldwide, and provides new insights into the genetic control of oil composition that can be implemented in future studies.
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Affiliation(s)
- Alina I Chernova
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia. .,LLC "OIL GENE", Skolkovo Innovation Center, Moscow, Russia.
| | - Rim F Gubaev
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia.,LLC "OIL GENE", Skolkovo Innovation Center, Moscow, Russia
| | - Anupam Singh
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Katrina Sherbina
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Svetlana V Goryunova
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia.,Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkin st. 3, Moscow, 119991, Russia.,FSBSI Lorch Potato Research Institute, Lorkha Str. 23, Kraskovo, 140051, Russia
| | - Elena U Martynova
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia
| | - Denis V Goryunov
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia.,MSU A.N. Belozersky Institute of Physico-Chemical Biology, Leninsky Gori 1, Building 40, Moscow, 119992, Russia
| | - Stepan V Boldyrev
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia.,LLC "OIL GENE", Skolkovo Innovation Center, Moscow, Russia
| | - Anna A Vanyushkina
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia
| | - Nikolay A Anikanov
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia
| | - Elena A Stekolshchikova
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia
| | - Ekaterina A Yushina
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia.,FSBSI N P Bochkov Research Center of Medical Genetics, Moskvorechye St.1, Moscow, 115522, Russia
| | - Yakov N Demurin
- Pustovoit All-Russia Research Institute of Oilseed Crops, Filatova St. 17, Krasnodar, 350038, Russia
| | | | - Vera A Gavrilova
- N. I. Vavilov Research Institute of Plant Genetic Resources (VIR), 42 B. Morskaja, St. Petersburg, 190000, Russia
| | - Irina N Anisimova
- N. I. Vavilov Research Institute of Plant Genetic Resources (VIR), 42 B. Morskaja, St. Petersburg, 190000, Russia
| | - Yulia I Karabitsina
- N. I. Vavilov Research Institute of Plant Genetic Resources (VIR), 42 B. Morskaja, St. Petersburg, 190000, Russia
| | - Natalia V Alpatieva
- N. I. Vavilov Research Institute of Plant Genetic Resources (VIR), 42 B. Morskaja, St. Petersburg, 190000, Russia
| | - Peter L Chang
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Philipp Khaitovich
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia
| | - Pavel V Mazin
- Skolkovo Institute of Science and Technology (Skoltech), Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia
| | - Sergey V Nuzhdin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
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Kang HJ, Kim KT, Park Y, Yoo KH, Kim JW, Lee JY, Kim SW, Shin IS, Kim JH, Kim JM. Genetic markers for depressive disorders with earlier age at onset. Prog Neuropsychopharmacol Biol Psychiatry 2021; 108:110176. [PMID: 33189858 DOI: 10.1016/j.pnpbp.2020.110176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 10/25/2020] [Accepted: 11/09/2020] [Indexed: 12/30/2022]
Abstract
Age at onset has been considered a potential indicator of underlying genetic risk in depression research. However, the variants associated with earlier age at onset of depressive disorder have not been elucidated. To evaluate the genetic architecture of depression onset, whole-exome sequencing of samples from 1000 patients with depressive disorder was performed. Cox proportional hazard models with false discovery rate-adjusted P-values were used to estimate the hazard ratios; carriers and non-carriers of individual coding variants were compared in terms of age at onset of depression with adjustment for sociodemographic and clinical characteristics. The clinical relevance of the candidate variants was also examined. Whole-exome sequencing revealed four variants in the CCL14, FYB, GPRASP1, and CTNND2 genes associated with an increased risk of depressive disorder with earlier age at onset. Although no individual variant was associated with any clinical characteristic except AAO, together they were associated with younger AAO, younger age at visit for treatment, and recurrent and atypical depression. Our data suggest novel candidate genes for depressive disorder with earlier age at onset. These genes could serve as markers allowing early identification of patients at risk of depression, and thus earlier intervention.
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Affiliation(s)
- Hee-Ju Kang
- Departments of Psychiatry, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Ki-Tae Kim
- Department of Laboratory Medicine, Korea University Anam Hospital, Seoul, Republic of Korea
| | - Yoomi Park
- Seoul National University Biomedical Informatics (SNUBI), Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyung-Hun Yoo
- Seoul National University Biomedical Informatics (SNUBI), Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ju-Wan Kim
- Departments of Psychiatry, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Ju-Yeon Lee
- Departments of Psychiatry, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Sung-Wan Kim
- Departments of Psychiatry, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Il-Seon Shin
- Departments of Psychiatry, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Ju Han Kim
- Seoul National University Biomedical Informatics (SNUBI), Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul, Republic of Korea.
| | - Jae-Min Kim
- Departments of Psychiatry, Chonnam National University Medical School, Gwangju, Republic of Korea.
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Smart U, Cihlar JC, Budowle B. International Wildlife Trafficking: A perspective on the challenges and potential forensic genetics solutions. Forensic Sci Int Genet 2021; 54:102551. [PMID: 34134047 DOI: 10.1016/j.fsigen.2021.102551] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 12/29/2022]
Abstract
International wildlife trafficking (IWT) is a thriving and pervasive illegal enterprise that adversely affects modern societies. Yet, despite being globally recognized as a threat to biodiversity, national security, economy, and biosecurity, IWT remains largely unabated and is proliferating at an alarming rate. The increase in IWT is generally attributed to a lack of prioritization to curb wildlife crime through legal and scientific infrastructure. This review: (1) lays out the damaging scope and influence of IWT; (2) discusses the potential of DNA marker systems, barcodes, and emerging molecular technologies, such as long-read portable sequencing, to facilitate rapid, in situ identification of species and individuals; and (3) encourages initiatives that promote quality and innovation. Interdisciplinary collaboration promises to be one of the most effective ways forward to surmounting the complex scientific and legal challenges posed by IWT.
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Affiliation(s)
- Utpal Smart
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA.
| | - Jennifer Churchill Cihlar
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
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Williams DM, Almanza SM, Sifuentes-Romero I, Detwiler KM. The history, taxonomy, and geographic origins of an introduced African monkey in the southeastern United States. Primates 2021; 62:617-627. [PMID: 33963936 DOI: 10.1007/s10329-021-00890-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 01/23/2021] [Indexed: 11/24/2022]
Abstract
The origins and taxonomy of the introduced vervet monkey population in Dania Beach, Florida has been unconfirmed due to a lack of documentation and genetic research. Our goal was to determine the introduction history, species identification, and geographic origins of the monkeys. Through interviews, historical archives, and popular media, we traced the monkeys to an escape from the Dania Chimpanzee Farm in 1948. The facility imported primates from Africa for medical research purposes. Historical archives suggest the monkeys were caught in Sierra Leone. We tested the hypothesis of West African origins using three genetic markers: one mitochondrial DNA gene (cytochrome b) and two fragments from the Y-chromosome, the sex-determining gene and the zinc-finger gene. We ran Bayesian and maximum-likelihood analyses to reconstruct phylogenetic trees. Results from all loci confirmed the species identification is Chlorocebus sabaeus. We found no variation among the sampled individuals and found the cytochrome b haplotype to be a complete match to a C. sabaeus sample from Senegal. Phylogenetic analyses showed strong support for the Dania Beach mitochondrial and Y-chromosome lineages to group within a monophyletic C. sabaeus clade endemic to West Africa. Our study provides critical baseline information to the scientific community about a little-known population of Chlorocebus monkeys that have adapted to a novel environment in the southeastern United States.
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Affiliation(s)
- Deborah M Williams
- Biological Sciences Department, Florida Atlantic University, Boca Raton, USA.
| | - Sandra M Almanza
- Anthropology Department, Florida Atlantic University, Boca Raton, USA
| | | | - Kate M Detwiler
- Biological Sciences Department, Florida Atlantic University, Boca Raton, USA
- Anthropology Department, Florida Atlantic University, Boca Raton, USA
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Wilson N, Robb E, Gajwani R, Minnis H. Nature and nurture? A review of the literature on childhood maltreatment and genetic factors in the pathogenesis of borderline personality disorder. J Psychiatr Res 2021; 137:131-46. [PMID: 33677217 DOI: 10.1016/j.jpsychires.2020.12.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 11/22/2020] [Accepted: 12/09/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND Borderline Personality Disorder (BPD) is a psychiatric disorder associated with significant morbidity and mortality. However, the neurobiological alterations underlying the condition remain poorly understood. As a result, existing treatments remain inadequate. One of the main risk factors for the development of BPD is a history of childhood maltreatment. However, it is considered neither causative nor specific to the condition. Current theory is therefore increasingly moving toward a 'Gene x Environment' (GxE) model of the condition. The purpose of the current work was to conduct a systematic literature review, which comprehensively identifies all published molecular level GxE studies that have explored the role of specific genetic loci, in influencing the risk of BPD following exposure to childhood abuse or neglect. METHODS Four electronic databases were used to systematically search for molecular level GxE studies of any design, which focused on the development of BPD following exposure to childhood abuse or neglect, without language or date restrictions. Articles were screened independently by two reviewers and results were synthesized narratively. RESULTS A total of 473 articles were screened of which sixteen were selected for inclusion in our review. Implicated genes were categorised according to their influence on; Neurotransmitter Systems, Neurodevelopment and Neuroendocrine Systems. CONCLUSIONS The identified studies have produced several relevant and statistically significant results. Of particular note, is the repeated finding that genes involved in HPA axis regulation, may be altered by exposure to childhood maltreatment, influencing subsequent susceptibility to BPD. This is both biologically plausible and of potential clinical significance.
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Zhang Y, Wu R, Li W, Chen Z, Li K. Occurrence and distributions of human-associated markers in an impacted urban watershed. Environ Pollut 2021; 275:116654. [PMID: 33582625 DOI: 10.1016/j.envpol.2021.116654] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 01/26/2021] [Accepted: 01/31/2021] [Indexed: 06/12/2023]
Abstract
Numerous genetic markers for microbial source tracking (MST) have been evaluated by testing a panel of target and nontarget faecal samples. However, the performance of MST markers may vary between faecal and water samples, thereby resulting in inaccurate water quality assessment. In this study, a 30-day sampling study was conducted in an urban river impacted by human- and sewage-associated pollution to evaluate the performance of different human-associated markers in environmental water. Additionally, marker decay was assessed via a microcosms approach. Overall, Bacteroidales 16sRNA and crAssphage markers exhibited higher prevalence in the study area, and their detection frequencies exceeded 90%. In contrast, Bacteroidales protein markers exhibited poor detection frequencies compared to other markers, with the prevalence of Hum2 and Hum163 reaching only 63% and 84%, respectively. Regarding marker abundance, there was no significant difference in the detection concentrations between Bacteroidales 16sRNA and crAssphage markers (p > 0.05); however, the concentrations of Bacteroidales protein markers were nearly 1 order of magnitude lower than those of other MST markers. The microcosm experiments indicated that the decay rate of crAssphage markers was significantly lower than that of other bacterial target markers, which may improve their detectability when the pollution source is located far from the sampling site. Due to the observed differences in performance and decay patterns among Bacteroidales 16sRNA, crAssphage, and Bacteroidales protein markers, we recommend the simultaneous use of multiple markers from different target microorganisms to obtain a more comprehensive understanding of the pollution sources. This approach would also provide an accurate assessment of pollution levels and health risks.
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Affiliation(s)
- Yang Zhang
- The Key Laboratory of Water and Air Pollution Control of Guangdong Province, South China Institute of Environmental Sciences, Ministry of Ecology and Environment of the People's Republic of China, Guangzhou, 510000, PR China; State Environmental Protection Key Laboratory of Water Environmental Simulation and Pollution Control, South China Institute of Environmental Sciences, Ministry of Ecology and Environment of the People's Republic of China, Guangzhou, 510530, PR China
| | - Renren Wu
- The Key Laboratory of Water and Air Pollution Control of Guangdong Province, South China Institute of Environmental Sciences, Ministry of Ecology and Environment of the People's Republic of China, Guangzhou, 510000, PR China; State Environmental Protection Key Laboratory of Water Environmental Simulation and Pollution Control, South China Institute of Environmental Sciences, Ministry of Ecology and Environment of the People's Republic of China, Guangzhou, 510530, PR China.
| | - Wenjing Li
- State Environmental Protection Key Laboratory of Water Environmental Simulation and Pollution Control, South China Institute of Environmental Sciences, Ministry of Ecology and Environment of the People's Republic of China, Guangzhou, 510530, PR China
| | - Zhongying Chen
- State Environmental Protection Key Laboratory of Water Environmental Simulation and Pollution Control, South China Institute of Environmental Sciences, Ministry of Ecology and Environment of the People's Republic of China, Guangzhou, 510530, PR China
| | - Kaiming Li
- The Key Laboratory of Water and Air Pollution Control of Guangdong Province, South China Institute of Environmental Sciences, Ministry of Ecology and Environment of the People's Republic of China, Guangzhou, 510000, PR China
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Jian A, Jang K, Manuguerra M, Liu S, Magnussen J, Di Ieva A. Machine Learning for the Prediction of Molecular Markers in Glioma on Magnetic Resonance Imaging: A Systematic Review and Meta-Analysis. Neurosurgery 2021; 89:31-44. [PMID: 33826716 DOI: 10.1093/neuros/nyab103] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/24/2021] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Molecular characterization of glioma has implications for prognosis, treatment planning, and prediction of treatment response. Current histopathology is limited by intratumoral heterogeneity and variability in detection methods. Advances in computational techniques have led to interest in mining quantitative imaging features to noninvasively detect genetic mutations. OBJECTIVE To evaluate the diagnostic accuracy of machine learning (ML) models in molecular subtyping gliomas on preoperative magnetic resonance imaging (MRI). METHODS A systematic search was performed following PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analysis) guidelines to identify studies up to April 1, 2020. Methodological quality of studies was assessed using the Quality Assessment for Diagnostic Accuracy Studies (QUADAS)-2. Diagnostic performance estimates were obtained using a bivariate model and heterogeneity was explored using metaregression. RESULTS Forty-four original articles were included. The pooled sensitivity and specificity for predicting isocitrate dehydrogenase (IDH) mutation in training datasets were 0.88 (95% CI 0.83-0.91) and 0.86 (95% CI 0.79-0.91), respectively, and 0.83 to 0.85 in validation sets. Use of data augmentation and MRI sequence type were weakly associated with heterogeneity. Both O6-methylguanine-DNA methyltransferase (MGMT) gene promoter methylation and 1p/19q codeletion could be predicted with a pooled sensitivity and specificity between 0.76 and 0.83 in training datasets. CONCLUSION ML application to preoperative MRI demonstrated promising results for predicting IDH mutation, MGMT methylation, and 1p/19q codeletion in glioma. Optimized ML models could lead to a noninvasive, objective tool that captures molecular information important for clinical decision making. Future studies should use multicenter data, external validation and investigate clinical feasibility of ML models.
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Affiliation(s)
- Anne Jian
- Computational NeuroSurgery (CNS) Lab, Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia.,Melbourne Medical School, University of Melbourne, Melbourne, Australia
| | - Kevin Jang
- Computational NeuroSurgery (CNS) Lab, Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia.,Discipline of Surgery, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Maurizio Manuguerra
- Department of Mathematics and Statistics, Faculty of Science and Engineering, Macquarie University, Sydney, Australia
| | - Sidong Liu
- Computational NeuroSurgery (CNS) Lab, Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia.,Centre for Health Informatics, Macquarie University, Sydney, Australia
| | - John Magnussen
- Computational NeuroSurgery (CNS) Lab, Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia.,Macquarie Medical Imaging, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Antonio Di Ieva
- Computational NeuroSurgery (CNS) Lab, Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia.,Macquarie Neurosurgery, Macquarie University, Sydney, Australia
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Xie G, Fair JM. Hidden Markov Model: a shortest unique representative approach to detect the protein toxins, virulence factors and antibiotic resistance genes. BMC Res Notes 2021; 14:122. [PMID: 33785071 PMCID: PMC8011099 DOI: 10.1186/s13104-021-05531-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/15/2021] [Indexed: 12/04/2022] Open
Abstract
Objective Currently, next generation sequencing (NGS) is widely used to decode potential novel or variant pathogens both in emergent outbreaks and in routine clinical practice. However, the efficient identification of novel or diverged pathogenomic compositions remains a big challenge. It is especially true for short DNA sequence fragments from NGS, since sequence similarity searching is vulnerable to false negatives or false positives, as is mismatching or matching with unrelated proteins. Therefore, this study aimed to establish a bioinformatics approach that can generate unique motif sequences for profiling searching, resulting in high specificity and sensitivity. Results In this study, we introduced a Shortest Unique Representative Hidden Markov Model (HMM) approach to identify bacterial toxin, virulence factor (VF), and antimicrobial resistance (AR) in short sequence reads. We first construct unique representative domain sequences of toxin genes, VFs, and ARs to avoid potential false positives, and then to use HMM models to accurately identify potential toxin, VF, and AR fragments. The benchmark shows this approach can achieve relatively high specificity and sensitivity if the appropriate cutoff value is applied. Our approach can be used to recognize the protein sequences of known toxins and pathogens, identifies their common characteristics and then searches for similar sequences in other organisms.
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Affiliation(s)
- Gary Xie
- Biosecurity & Public Health, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM, 87545, USA.
| | - Jeanne M Fair
- Biosecurity & Public Health, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM, 87545, USA
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Miller CN, Busch W. Using natural variation to understand plant responses to iron availability. J Exp Bot 2021; 72:2154-2164. [PMID: 33458759 PMCID: PMC7966951 DOI: 10.1093/jxb/erab012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 05/08/2023]
Abstract
Iron bioavailability varies dramatically between soil types across the globe. This has given rise to high levels of natural variation in plant iron responses, allowing members of even a single species to thrive across a wide range of soil types. In recent years we have seen the use of genome-wide association analysis to identify natural variants underlying plant responses to changes in iron availability in both Arabidopsis and important crop species. These studies have provided insights into which genes have been important in shaping local adaptation to iron availability in different plant species and have allowed the discovery of novel regulators and mechanisms, not previously identified using mutagenesis approaches. Furthermore, these studies have allowed the identification of markers that can be used to accelerate breeding of future elite varieties with increased resilience to iron stress and improved nutritional quality. The studies highlighted here show that, in addition to studying plant responses to iron alone, it is important to consider these responses within the context of plant nutrition more broadly and to also consider iron regulation in relation to additional traits of agronomic importance such as yield and disease resistance.
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Affiliation(s)
- Charlotte N Miller
- Salk Institute For Biological Studies, Plant Molecular and Cellular Biology Laboratory, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Wolfgang Busch
- Salk Institute For Biological Studies, Plant Molecular and Cellular Biology Laboratory, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
- Correspondence:
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Fonseca AS, Ramão A, Bürger MC, de Souza JES, Zanette DL, de Molfetta GA, de Araújo LF, de Barros E Lima Bueno R, Aguiar GM, Plaça JR, Alves CDP, Dos Santos ARD, Vidal DO, Silva GEB, Panepucci RA, Peria FM, Feres O, da Rocha JJR, Zago MA, Silva WA. ETV4 plays a role on the primary events during the adenoma-adenocarcinoma progression in colorectal cancer. BMC Cancer 2021; 21:207. [PMID: 33648461 PMCID: PMC7919324 DOI: 10.1186/s12885-021-07857-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/31/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most common cancers worldwide; it is the fourth leading cause of death in the world and the third in Brazil. Mutations in the APC, DCC, KRAS and TP53 genes have been associated with the progression of sporadic CRC, occurring at defined pathological stages of the tumor progression and consequently modulating several genes in the corresponding signaling pathways. Therefore, the identification of gene signatures that occur at each stage during the CRC progression is critical and can present an impact on the diagnosis and prognosis of the patient. In this study, our main goal was to determine these signatures, by evaluating the gene expression of paired colorectal adenoma and adenocarcinoma samples to identify novel genetic markers in association to the adenoma-adenocarcinoma stage transition. METHODS Ten paired adenoma and adenocarcinoma colorectal samples were subjected to microarray gene expression analysis. In addition, mutations in APC, KRAS and TP53 genes were investigated by DNA sequencing in paired samples of adenoma, adenocarcinoma, normal tissue, and peripheral blood from ten patients. RESULTS Gene expression analysis revealed a signature of 689 differentially expressed genes (DEG) (fold-change> 2, p< 0.05), between the adenoma and adenocarcinoma paired samples analyzed. Gene pathway analysis using the 689 DEG identified important cancer pathways such as remodeling of the extracellular matrix and epithelial-mesenchymal transition. Among these DEG, the ETV4 stood out as one of the most expressed in the adenocarcinoma samples, further confirmed in the adenocarcinoma set of samples from the TCGA database. Subsequent in vitro siRNA assays against ETV4 resulted in the decrease of cell proliferation, colony formation and cell migration in the HT29 and SW480 colorectal cell lines. DNA sequencing analysis revealed KRAS and TP53 gene pathogenic mutations, exclusively in the adenocarcinomas samples. CONCLUSION Our study identified a set of genes with high potential to be used as biomarkers in CRC, with a special emphasis on the ETV4 gene, which demonstrated involvement in proliferation and migration.
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Affiliation(s)
- Aline Simoneti Fonseca
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av Bandeirantes, 3900, CEP: 14049-900, Monte Alegre, Ribeirão Preto, SP, Brazil.
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil.
- Center for Integrative Systems Biology - CISBi, NAP/USP, Ribeirão Preto, SP, Brazil.
- Research Institute Pelé Pequeno Príncipe, Av Silva Jardim, 1632, CEP: 80250-060, Água Verde, Curitiba, PR, Brazil.
| | - Anelisa Ramão
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av Bandeirantes, 3900, CEP: 14049-900, Monte Alegre, Ribeirão Preto, SP, Brazil
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Matheus Carvalho Bürger
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Jorge Estefano Santana de Souza
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Dalila Lucíola Zanette
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av Bandeirantes, 3900, CEP: 14049-900, Monte Alegre, Ribeirão Preto, SP, Brazil
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
- Center for Integrative Systems Biology - CISBi, NAP/USP, Ribeirão Preto, SP, Brazil
- Laboratory of Applied Science and Technology in Health (LASTH), Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba, PR, Brazil
| | - Greice Andreotti de Molfetta
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av Bandeirantes, 3900, CEP: 14049-900, Monte Alegre, Ribeirão Preto, SP, Brazil
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
- Center for Integrative Systems Biology - CISBi, NAP/USP, Ribeirão Preto, SP, Brazil
| | - Luiza Ferreira de Araújo
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av Bandeirantes, 3900, CEP: 14049-900, Monte Alegre, Ribeirão Preto, SP, Brazil
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
- Center for Integrative Systems Biology - CISBi, NAP/USP, Ribeirão Preto, SP, Brazil
| | - Rafaela de Barros E Lima Bueno
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av Bandeirantes, 3900, CEP: 14049-900, Monte Alegre, Ribeirão Preto, SP, Brazil
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Graziela Moura Aguiar
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Jessica Rodrigues Plaça
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Cleidson de Pádua Alves
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Anemari Ramos Dinarte Dos Santos
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Daniel Onofre Vidal
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Gyl Eanes Barros Silva
- Laboratory of Immunofluorescence and Electron Microscopy (LIME), Presidente Dutra University Hospital (HUUFMA), São Luís, MA, Brazil
| | - Rodrigo Alexandre Panepucci
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Fernanda Maris Peria
- Departament of Medical Clinic, Medical School of Ribeirão Preto, University of São Paulo, USP, Ribeirão Preto, SP, Brazil
| | - Omar Feres
- Department of Surgery and Anatomy, School of Medicine of Ribeirão Preto, University of São Paulo, Sao Paulo, Brazil
| | | | - Marco Antonio Zago
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil
| | - Wilson Araújo Silva
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Av Bandeirantes, 3900, CEP: 14049-900, Monte Alegre, Ribeirão Preto, SP, Brazil.
- Center for Cell Based Therapy and National Institute of Science and Technology in Stem Cell and Cell Therapy, Ribeirão Preto, SP, Brazil.
- Center for Integrative Systems Biology - CISBi, NAP/USP, Ribeirão Preto, SP, Brazil.
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Sharma K, Yannawar VN, Kotalwar GR, Madanshetty P, Grover I, Lagali PS. Single Nucleotide Polymorphisms of BMP2 Gene Association with Skeletal Class I Crowding: A PCR Study. J Contemp Dent Pract 2021; 22:248-252. [PMID: 34210923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
AIM AND OBJECTIVE This study is conducted to find the association of BMP2 (bone morphogenic protein 2) gene variant rs1005464 and rs15705 with skeletal class I crowding cases. MATERIALS AND METHODS Blood samples from 60 subjects who visited the Department of Orthodontics and Dentofacial Orthopaedics, D.A.P.M.R.V. Dental College, Bengaluru, were taken after written informed consent. These were divided into two groups: group A with 30 subjects having skeletal class I bases with crowding and group B with 30 subjects having skeletal class I bases without visible crowding or spacing (±2 mm). Around 2 mL of venous blood sample was procured from cases and controls after careful examination. All the samples were then subjected to polymerase chain reaction followed by DNA sequencing and capillary electrophoresis. BMP2 rs1005464 and rs15705 gene variants were assessed and Z-Test was used for statistical analysis. RESULT GG (p = 0.001) and CC (p = 0.0024) genotype of BMP2 gene variant rs1005464 and rs15705, respectively, are significantly associated with skeletal class I crowding cases. CONCLUSION This study concludes that BMP2 variants rs1005464 and rs15705 can be used as genetic markers for skeletal class I bases having crowding. CLINICAL SIGNIFICANCE Predisposing genetic markers BMP2 can be identified prior and this would help in predicting the probability of potential crowding in the future and this would help in early prevention and intervention of crowding.
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Affiliation(s)
- Kalpesh Sharma
- Department of Orthodontics, Albaha Dental Centre, Al Bahah, Kingdom of Saudi Arabia
| | - Vijay N Yannawar
- Department of Orthodontics and Dentofacial Orthopedics, Dr HSRSM Dental College, Hingoli, Maharashtra, India, e-mail:
| | - Ganesh R Kotalwar
- Department of Orthodontics and Dentofacial Orthopedics, Nanded Rural Dental College and Research Center, Nanded, Maharashtra, India
| | - Pallavi Madanshetty
- Department of Prosthodontics, Rural Dental College, Loni, Maharashtra, India
| | - Ishita Grover
- Department of Prosthodontics, MA Rangoonwala College of Dental Science and Research Centre, Pune, Maharashtra, India
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Estrada-Reyes ZM, Rae DO, Mateescu RG. Genome-wide scan reveals important additive and non-additive genetic effects associated with resistance to Haemonchus contortus in Florida Native sheep. Int J Parasitol 2021; 51:535-543. [PMID: 33549580 DOI: 10.1016/j.ijpara.2020.11.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 11/05/2020] [Accepted: 11/08/2020] [Indexed: 01/07/2023]
Abstract
Florida Native sheep is among the sheep breeds best adapted to humid and hot climatic conditions such as those of Florida, USA, and have shown a superior ability to regulate nematode burdens. This is one of the oldest sheep breeds in North America and is an endangered species. To ensure genetic diversity and long-term survival of the breed, protection of the current genetic stock is critical and conservation efforts are required to promote its breeding and production. The objective of the present study was to investigate the importance of additive and non-additive genetic effects on resistance to natural Haemonchus contortus infections in Florida Native sheep using a whole genome scan. A total of 200 sheep were evaluated in the present study. Phenotypic records included faecal egg count (FEC, eggs/gram), FAMACHA® score, packed cell volume (PCV, %), body condition score and average daily gain (ADG, kg). Sheep were genotyped using the GGP Ovine 50K SNP chip and 45.2 k single nucleotide polymorphism (SNP) markers spanning the entire genome were available for quality control procedures. Mixed models were used to analyse the response variables and included the identity by state matrix to control for population structure. Bonferroni correction was used to control for multiple testing and a second arbitrary threshold (0.1 × 10-3) was used. Fifteen SNPs with additive and non-additive genetic effects and located in Ovis aries chromosome OAR1, 2, 3, 6, 8, 10, 11, 12, 13 and 21 were associated with FEC, FAMACHA® score, PCV and ADG. These SNPs could be potential genetic markers for resistance to natural H. contortus exposure in Florida Native sheep.
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Affiliation(s)
- Zaira M Estrada-Reyes
- College of Agriculture, Family Sciences, and Technology, Fort Valley State University, Fort Valley, GA 31030, USA; Department of Animal Sciences, University of Florida, Gainesville, FL, USA.
| | - D Owen Rae
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Raluca G Mateescu
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
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Aasdahl L, Nilsen TIL, Meisingset I, Nordstoga AL, Evensen KAI, Paulsen J, Mork PJ, Skarpsno ES. Genetic variants related to physical activity or sedentary behaviour: a systematic review. Int J Behav Nutr Phys Act 2021; 18:15. [PMID: 33482856 PMCID: PMC7821484 DOI: 10.1186/s12966-020-01077-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/16/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Research shows that part of the variation in physical activity and sedentary behaviour may be explained by genetic factors. Identifying genetic variants associated with physical activity and sedentary behaviour can improve causal inference in physical activity research. The aim of this systematic review was to provide an updated overview of the evidence of genetic variants associated with physical activity or sedentary behaviour. METHODS We performed systematic literature searches in PubMed and Embase for studies published from 1990 to April 2020 using keywords relating to "physical activity", "exercise", "sedentariness" and "genetics". Physical activity phenotypes were either based on self-report (e.g., questionnaires, diaries) or objective measures (e.g., accelerometry, pedometer). We considered original studies aiming to i) identify new genetic variants associated with physical activity or sedentary behaviour (i.e., genome wide association studies [GWAS]), or ii) assess the association between known genetic variants and physical activity or sedentary behaviour (i.e., candidate gene studies). Study selection, data extraction, and critical appraisal were carried out by independent researchers, and risk of bias and methodological quality was assessed for all included studies. RESULTS Fifty-four out of 5420 identified records met the inclusion criteria. Six of the included studies were GWAS, whereas 48 used a candidate gene approach. Only one GWAS and three candidate gene studies were considered high-quality. The six GWAS discovered up to 10 single nucleotide polymorphisms (SNPs) associated with physical activity or sedentariness that reached genome-wide significance. In total, the candidate gene studies reported 30 different genes that were associated (p < 0.05) with physical activity or sedentary behaviour. SNPs in or close to nine candidate genes were associated with physical activity or sedentary behaviour in more than one study. CONCLUSION GWAS have reported up to 10 loci associated with physical activity or sedentary behaviour. Candidate gene studies have pointed to some interesting genetic variants, but few have been replicated. Our review highlights the need for high-quality GWAS in large population-based samples, and with objectively assessed phenotypes, in order to establish robust genetic instruments for physical activity and sedentary behaviour. Furthermore, consistent replications in GWAS are needed to improve credibility of genetic variants. TRIAL REGISTRATION Prospero CRD42019119456 .
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Affiliation(s)
- Lene Aasdahl
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Postboks 8905, MTFS, 7491, Trondheim, Norway. .,Unicare Helsefort Rehabilitation Centre, Rissa, Norway.
| | - Tom Ivar Lund Nilsen
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Postboks 8905, MTFS, 7491, Trondheim, Norway.,Clinic of Anaesthesia and Intensive Care, St. Olavs Hospital, Trondheim, Norway
| | - Ingebrigt Meisingset
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Postboks 8905, MTFS, 7491, Trondheim, Norway
| | - Anne Lovise Nordstoga
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Postboks 8905, MTFS, 7491, Trondheim, Norway
| | - Kari Anne I Evensen
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Postboks 8905, MTFS, 7491, Trondheim, Norway.,Department of Clinical and Molecular Medicine, NTNU, Trondheim, Norway.,Department of Physiotherapy, Oslo Metropolitan University, Oslo, Norway.,Unit for Physiotherapy Services, Trondheim, Norway
| | - Julie Paulsen
- Department of Medical Genetics, St. Olavs Hospital, Trondheim, Norway
| | - Paul Jarle Mork
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Postboks 8905, MTFS, 7491, Trondheim, Norway
| | - Eivind Schjelderup Skarpsno
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Postboks 8905, MTFS, 7491, Trondheim, Norway.,Department of Neurology and Clinical Neurophysiology, St. Olavs Hospital, Trondheim, Norway
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Kliman HJ, Firestein MR, Hofmann KM, Milano KM, Holzer PH, Brink LT, Odendaal HJ, Fifer WP. Trophoblast inclusions in the human placenta: Identification, characterization, quantification, and interrelations of subtypes. Placenta 2021; 103:172-176. [PMID: 33152642 PMCID: PMC8448462 DOI: 10.1016/j.placenta.2020.10.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/23/2020] [Accepted: 10/12/2020] [Indexed: 11/26/2022]
Abstract
We sought to examine placentas enriched for trophoblast inclusions (TIs) in order to characterize, quantify, and examine the interrelations between subtypes of TIs to better understand their underlying biology. We examined a cohort of 600 placentas from deliveries between 200 and 430 weeks of gestation. Forty-five percent of the placentas had at least one TI in the two slides examined. Four percent of the placentas had 10 or more TIs and two placentas had more than 70 TIs. Four distinct TI subtypes were observed: inclusionoids (early forming inclusions), inclusions, calcified inclusions, and calcified bodies. We suggest this reflects a developmental trajectory of TI maturation, the timing of which might be useful when comparing TI expression to clinical outcomes.
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Affiliation(s)
- Harvey J Kliman
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT, USA.
| | - Morgan R Firestein
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Kristin M Milano
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT, USA
| | - Parker H Holzer
- Department of Statistics & Data Science, Yale University, New Haven, CT, USA
| | - Lucy T Brink
- Department of Obstetrics and Gynaecology, Faculty of Medicine and Health Science, Stellenbosch University, Cape Town, Western Cape, South Africa
| | - Hein J Odendaal
- Department of Obstetrics and Gynaecology, Faculty of Medicine and Health Science, Stellenbosch University, Cape Town, Western Cape, South Africa
| | - William P Fifer
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA; Department of Obstetrics and Gynaecology, Faculty of Medicine and Health Science, Stellenbosch University, Cape Town, Western Cape, South Africa; Division of Developmental Neuroscience, New York State Psychiatric Institute, New York, NY, USA; Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
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Valette M, Rey M, Doré J, Gerin F, Wisniewski-Dyé F. Identification of a small set of genes commonly regulated in rice roots in response to beneficial rhizobacteria. Physiol Mol Biol Plants 2020; 26:2537-2551. [PMID: 33424163 PMCID: PMC7772126 DOI: 10.1007/s12298-020-00911-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 11/06/2020] [Accepted: 11/11/2020] [Indexed: 06/12/2023]
Abstract
Rhizosphere bacteria, whether phytopathogenic or phytobeneficial, are thought to be perceived by the plant as a threat. Plant Growth-Promoting Rhizobacteria (PGPR), such as many strains of the Azospirillum genus known as the main phytostimulator of cereals, cooperate with host plants and favorably affect their growth and health. An earlier study of rice root transcriptome, undertaken with two rice cultivars and two Azospirillum strains, revealed a strain-dependent response during the rice-Azospirillum association and showed that only a few genes, including some implicated in plant defense, were commonly regulated in all tested conditions. Here, a set of genes was selected from previous studies and their expression was monitored by qRT-PCR in rice roots inoculated with ten PGPR strains isolated from various plants and belonging to various genera (Azospirillum, Herbaspirillum, Paraburkholderia). A common expression pattern was highlighted for four genes that are proposed to be markers of the rice-PGPR interaction: two genes involved in diterpenoid phytoalexin biosynthesis (OsDXS3 and OsDTC2) and one coding for an uncharacterized protein (Os02g0582900) were significantly induced by PGPR whereas one defense-related gene encoding a pathogenesis-related protein (PR1b, Os01g0382000) was significantly repressed. Interestingly, exposure to a rice bacterial pathogen also triggered the expression of OsDXS3 while the expression of Os02g0582900 and PR1b was down-regulated, suggesting that these genes might play a key role in rice-bacteria interactions. Integration of these results with previous data led us to propose that the jasmonic acid signaling pathway might be triggered in rice roots upon inoculation with PGPR.
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Affiliation(s)
- Marine Valette
- Ecologie Microbienne, CNRS UMR-5557, INRAe UMR-1418, VetAgroSup, Université de Lyon, Université Lyon1, 16 rue Dubois, 69622 Villeurbanne, France
| | - Marjolaine Rey
- Ecologie Microbienne, CNRS UMR-5557, INRAe UMR-1418, VetAgroSup, Université de Lyon, Université Lyon1, 16 rue Dubois, 69622 Villeurbanne, France
| | - Jeanne Doré
- Ecologie Microbienne, CNRS UMR-5557, INRAe UMR-1418, VetAgroSup, Université de Lyon, Université Lyon1, 16 rue Dubois, 69622 Villeurbanne, France
| | - Florence Gerin
- Ecologie Microbienne, CNRS UMR-5557, INRAe UMR-1418, VetAgroSup, Université de Lyon, Université Lyon1, 16 rue Dubois, 69622 Villeurbanne, France
| | - Florence Wisniewski-Dyé
- Ecologie Microbienne, CNRS UMR-5557, INRAe UMR-1418, VetAgroSup, Université de Lyon, Université Lyon1, 16 rue Dubois, 69622 Villeurbanne, France
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50
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Cubides-Cubillos SD, Patané JSL, Pereira da Silva KM, Almeida-Santos SM, Polydoro DS, Galassi GG, Travaglia Cardoso SR, Silva MJDJ. Evidence of facultative parthenogenesis in three Neotropical pitviper species of the Bothrops atrox group. PeerJ 2020; 8:e10097. [PMID: 33240594 PMCID: PMC7680053 DOI: 10.7717/peerj.10097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 09/14/2020] [Indexed: 11/20/2022] Open
Abstract
We examined four suspected cases of facultative parthenogenesis in three species of a neotropical lineage of pitvipers of the Bothrops atrox group. Reproduction without mating was observed in captive females of B. atrox, B. moojeni and B. leucurus housed alone for seven years (the two former species) and nine years (the latter one). In addition to the observation of captivity data, we investigated molecularly this phenomenon using heterologous microsatellites. DNA was extracted from the mothers’ scales or liver, from embryo and newborn fragments, and yolked ova. Four of the microsatellites showed good amplification using Polymerase Chain Reaction and informative band segregation patterns among each mother and respective offspring. Captivity information, litter characteristics (comparison of the number of newborns, embryos and yolked ova) and molecular data altogether agreed with facultative parthenogenesis predictions in at least three out of the four mothers studied: B. atrox (ID#933) was heterozygous for three out of the four markers, and the sons S1 and S2 were homozygous; B. moojeni (BUT86) was heterozygous for two out of four markers, offspring S1, S3, E2, and E4, and O1 to O6 were homozygous; and B. leucurus (MJJS503) was heterozygous for three out of four markers, and son E1 and O1 were homozygous. B. moojeni (BUT44) was homozygous for all loci analyzed in the mother and offspring, which although not informative is also consistent with parthenogenesis. This study represents the first molecular confirmation of different pitviper species undergoing facultative parthenogenesis among Neotropical endemic snakes.
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Affiliation(s)
| | - José S L Patané
- Laboratório de Ecologia e Evolução, Instituto Butantan, São Paulo, Brazil.,Laboratório Especial de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
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