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Vásquez-Escobar J, Benjumea-Gutiérrez DM, Lopera C, Clement HC, Bolaños DI, Higuita-Castro JL, Corzo GA, Corrales-Garcia LL. Heterologous Expression of an Insecticidal Peptide Obtained from the Transcriptome of the Colombian Spider Phoneutria depilate. Toxins (Basel) 2023; 15:436. [PMID: 37505705 PMCID: PMC10467102 DOI: 10.3390/toxins15070436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 06/27/2023] [Accepted: 06/27/2023] [Indexed: 07/29/2023] Open
Abstract
Spider venoms are composed, among other substances, of peptide toxins whose selectivity for certain physiological targets has made them powerful tools for applications such as bioinsecticides, analgesics, antiarrhythmics, antibacterials, antifungals and antimalarials, among others. Bioinsecticides are an environmentally friendly alternative to conventional agrochemicals. In this paper, the primary structure of an insecticidal peptide was obtained from the venom gland transcriptome of the ctenid spider Phoneutria depilata (Transcript ID PhdNtxNav24). The peptide contains 53 amino acids, including 10 Cys residues that form 5 disulfide bonds. Using the amino acid sequence of such peptide, a synthetic gene was constructed de novo by overlapping PCRs and cloned into an expression vector. A recombinant peptide, named delta-ctenitoxin (rCtx-4), was obtained. It was expressed, folded, purified and validated using mass spectrometry (7994.61 Da). The insecticidal activity of rCtx-4 was demonstrated through intrathoracic injection in crickets (LD50 1.2 μg/g insect) and it was not toxic to mice. rCtx-4 is a potential bioinsecticide that could have a broad spectrum of applications in agriculture.
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Affiliation(s)
- Julieta Vásquez-Escobar
- Grupo de Toxinología y Alternativas Farmacéuticas y Alimentarias, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia, Medellin 1226, Colombia; (D.M.B.-G.); (C.L.)
| | - Dora María Benjumea-Gutiérrez
- Grupo de Toxinología y Alternativas Farmacéuticas y Alimentarias, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia, Medellin 1226, Colombia; (D.M.B.-G.); (C.L.)
| | - Carolina Lopera
- Grupo de Toxinología y Alternativas Farmacéuticas y Alimentarias, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia, Medellin 1226, Colombia; (D.M.B.-G.); (C.L.)
| | - Herlinda C. Clement
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, A.P. 510-3, Cuernavaca 62250, Mexico; (H.C.C.); (D.I.B.); (G.A.C.)
| | - Damaris I. Bolaños
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, A.P. 510-3, Cuernavaca 62250, Mexico; (H.C.C.); (D.I.B.); (G.A.C.)
| | - Jorge Luis Higuita-Castro
- PECET—Programa para el Estudio y Control de Enfermedades Tropicales, Facultad de Medicina, Universidad de Antioquia, Medellín 050010, Colombia;
| | - Gerardo A. Corzo
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, A.P. 510-3, Cuernavaca 62250, Mexico; (H.C.C.); (D.I.B.); (G.A.C.)
| | - Ligia Luz Corrales-Garcia
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, A.P. 510-3, Cuernavaca 62250, Mexico; (H.C.C.); (D.I.B.); (G.A.C.)
- PECET—Programa para el Estudio y Control de Enfermedades Tropicales, Facultad de Medicina, Universidad de Antioquia, Medellín 050010, Colombia;
- Departamento de Alimentos, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia, Medellín 1226, Colombia
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Josahkian JA, Brusius-Facchin AC, Netto ABO, Leistner-Segal S, Málaga DR, Burin MG, Michelin-Tirelli K, Trapp FB, Cardoso-Dos-Santos AC, Ribeiro EM, Kim CA, de Siqueira ACM, Santos ML, do Valle DA, da Silva RTB, Horovitz DDG, de Medeiros PFV, de Souza CFM, Giuliani LDR, Miguel DSCG, Santana-da-Silva LC, Galera MF, Giugliani R. Genotype-phenotype studies in a large cohort of Brazilian patients with Hunter syndrome. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2021; 187:349-356. [PMID: 33960103 DOI: 10.1002/ajmg.c.31915] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/25/2021] [Accepted: 04/18/2021] [Indexed: 11/05/2022]
Abstract
Mucopolysaccharidosis type II (MPS II) is an X-linked inherited disease caused by pathogenic variants in the IDS gene, leading to deficiency of the lysosomal enzyme iduronate-2-sulfatase and consequent widespread storage of glycosaminoglycans, leading to several clinical consequences, with progressive manifestations which most times includes cognitive decline. MPS II has wide allelic and clinical heterogeneity and a complex genotype-phenotype correlation. We evaluated data from 501 Brazilian patients diagnosed with MPS II from 1982 to 2020. We genotyped 280 of these patients (55.9%), which were assigned to 206 different families. Point mutations were present in 70% of our patients, being missense variants the most frequent. We correlated the IDS pathogenic variants identified with the phenotype (neuronophatic or non-neuronopathic). Except for two half-brothers, there was no discordance in the genotype-phenotype correlation among family members, nor among MPS II patients from different families with the same single base-pair substitution variant. Mothers were carriers in 82.0% of the cases. This comprehensive study of the molecular profile of the MPS II cases in Brazil sheds light on the genotype-phenotype correlation and helps the better understanding of the disease and the prediction of its clinical course, enabling the provision of a more refined genetic counseling to the affected families.
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Affiliation(s)
- Juliana Alves Josahkian
- Department of Clinical Medicine, Hospital Universitário de Santa Maria (HUSM), Santa Maria, Rio Grande do Sul, Brazil.,Postgraduate Program in Genetics and Molecular Biology, UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Alice Brinckmann Oliveira Netto
- Medical Genetics Service, HCPA, Porto Alegre, Rio Grande do Sul, Brazil.,National Institute on Population Medical Genetics, INAGEMP, Porto Alegre, Rio Grande do Sul, Brazil.,Graduate in Biological Sciences, UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Sandra Leistner-Segal
- Medical Genetics Service, HCPA, Porto Alegre, Rio Grande do Sul, Brazil.,National Institute on Population Medical Genetics, INAGEMP, Porto Alegre, Rio Grande do Sul, Brazil
| | - Diana Rojas Málaga
- Medical Genetics Service, HCPA, Porto Alegre, Rio Grande do Sul, Brazil.,Research and Development, Grupo Fleury, São Paulo, São Paulo, Brazil
| | | | | | | | - Augusto César Cardoso-Dos-Santos
- Postgraduate Program in Genetics and Molecular Biology, UFRGS, Porto Alegre, Rio Grande do Sul, Brazil.,National Institute on Population Medical Genetics, INAGEMP, Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Chong Ae Kim
- Genetic Unit, Pediatric Department, HC-FMUSP, São Paulo University, São Paulo, São Paulo, Brazil
| | | | - Mara Lucia Santos
- Neuropediatric Division, Hospital Pequeno Príncipe, Curitiba, Paraná, Brazil
| | | | | | - Dafne Dain Gandelman Horovitz
- Medical Genetics Department, National Institute of Women, Children and Adolescents Health Fernandes Figueira-Fiocruz/Reference Center for Rare Diseases, Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Liane de Rosso Giuliani
- Hospital Universitário Maria Aparecida Pedrossian (HUMAP), UFMS, Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Luiz Carlos Santana-da-Silva
- Laboratory of Innate Errors of Metabolism, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Marcial Francis Galera
- Department of Pediatrics, Faculty of Medicine, Federal University of Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Roberto Giugliani
- Medical Genetics Service, HCPA, Porto Alegre, Rio Grande do Sul, Brazil.,National Institute on Population Medical Genetics, INAGEMP, Porto Alegre, Rio Grande do Sul, Brazil.,Department of Genetics, UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
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3
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Jumaa RS, Allawi AB, Jabbar RN. Genetic Analysis of Field Isolates of Infectious Bursal Disease Virus in Iraqi Farms. THE IRAQI JOURNAL OF VETERINARY MEDICINE 2020. [DOI: 10.30539/ijvm.v44i1.931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Sixty samples of bursa of Fabricius were collected from broiler chickens suspected to be infected with infectious bursal disease virus (IBDV) in different areas of Iraq for molecular evaluation. The extracted nucleic acid was amplified using reverse transcriptase polymerase chain reaction (RT-PCR) targeting genes of segment A (Vp2, Vp3, Vp4 and Vp5 genes) and segment B (VP1 genes). The products of amplification were sent to Korea for sequencing using Sanger method. The sequencing analysis of the IBDV from the Iraqi isolates revealed that each gene had different transition and transversion (nonsense and missense of point mutation) compared to reference genes. The phylogenetic tree analysis showed that the VP2 of segment A of the Iraqi samples was similar to that of an Egyptian strain with 96%similarity, the polypeptide VP2-3-4 of segment A of the Iraqi samples was similar to those of a Chinese strain with 99% similarity and the VP5 of segment A was similar to that of Chinese strain with 99% similarity. However, the phylogenetic tree analysis showed that the VP1 of segment B had 95% similarity with that of a Chinese strain.
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Bertalovitz AC, Badhey MLO, McDonald TV. Synonymous nucleotide modification of the KCNH2 gene affects both mRNA characteristics and translation of the encoded hERG ion channel. J Biol Chem 2018; 293:12120-12136. [PMID: 29907571 PMCID: PMC6078446 DOI: 10.1074/jbc.ra118.001805] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 06/06/2018] [Indexed: 11/06/2022] Open
Abstract
Synonymous nucleotide variation is increasingly recognized as a factor than can affect protein expression, but the underlying mechanisms are incompletely understood. Here, we investigated whether synonymous changes could affect expression of the potassium voltage-gated channel subfamily H member 2 (KCNH2) gene, encoding the human ether-a-go-go-related gene (hERG) ion channel, which is linked to hereditary cardiac arrhythmia. We examined a previously described synthetic version (hERG-codon modified (CM)) with synonymous substitutions designed to reduce GC content, rare codons, and mRNA secondary structure relative to the native construct (hERG-NT). hERG-CM exhibited lower protein expression than hERG-NT in HEK293T cells. We found that the steady-state abundance of hERG-NT mRNA was greater than hERG-CM because of an enhanced transcription rate and increased mRNA stability for hERG-NT. Translation of hERG-CM was independently reduced, contributing to the overall greater synthesis of hERG-NT channel protein. This was partially offset, however, by a higher aggregation of a newly synthesized hERG-NT channel, resulting in nonfunctional protein. Regional mRNA analyses of chimeras of hERG-NT and hERG-CM revealed that synonymous changes in the 5' segments of the coding region had the greatest influence on hERG synthesis at both the mRNA and protein levels. Taken together, these results indicate that synonymous nucleotide variations within the coding region, particularly in the 5' region of the hERG mRNA, can affect both transcription and translation. These findings support the notion that greater attention should be given to the effects of synonymous genetic variation when analyzing hERG DNA sequences in the study of hereditary cardiac disease.
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Affiliation(s)
- Alexander C Bertalovitz
- Department of Molecular Pharmacology, Department of Medicine, Division of Cardiology, Albert Einstein College of Medicine, Bronx, New York 10461; Department of Cardiovascular Sciences, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612
| | - Marika L Osterbur Badhey
- Department of Molecular Pharmacology, Department of Medicine, Division of Cardiology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Thomas V McDonald
- Department of Molecular Pharmacology, Department of Medicine, Division of Cardiology, Albert Einstein College of Medicine, Bronx, New York 10461; Department of Cardiovascular Sciences, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612.
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Hashemi S, Nowzari Dalini A, Jalali A, Banaei-Moghaddam AM, Razaghi-Moghadam Z. Cancerouspdomains: comprehensive analysis of cancer type-specific recurrent somatic mutations in proteins and domains. BMC Bioinformatics 2017; 18:370. [PMID: 28814324 PMCID: PMC5559820 DOI: 10.1186/s12859-017-1779-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/02/2017] [Indexed: 01/19/2023] Open
Abstract
Background Discriminating driver mutations from the ones that play no role in cancer is a severe bottleneck in elucidating molecular mechanisms underlying cancer development. Since protein domains are representatives of functional regions within proteins, mutations on them may disturb the protein functionality. Therefore, studying mutations at domain level may point researchers to more accurate assessment of the functional impact of the mutations. Results This article presents a comprehensive study to map mutations from 29 cancer types to both sequence- and structure-based domains. Statistical analysis was performed to identify candidate domains in which mutations occur with high statistical significance. For each cancer type, the corresponding type-specific domains were distinguished among all candidate domains. Subsequently, cancer type-specific domains facilitated the identification of specific proteins for each cancer type. Besides, performing interactome analysis on specific proteins of each cancer type showed high levels of interconnectivity among them, which implies their functional relationship. To evaluate the role of mitochondrial genes, stem cell-specific genes and DNA repair genes in cancer development, their mutation frequency was determined via further analysis. Conclusions This study has provided researchers with a publicly available data repository for studying both CATH and Pfam domain regions on protein-coding genes. Moreover, the associations between different groups of genes/domains and various cancer types have been clarified. The work is available at http://www.cancerouspdomains.ir. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1779-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Adrin Jalali
- Max Planck Institute for Informatics, Saarland Informatics, Campus, 66123, Saarbrücken, Germany
| | | | - Zahra Razaghi-Moghadam
- Faculty of New Sciences and Technologies, University of Tehran, North Kargar St, Tehran, Tehran, 1439957131, Iran.
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Pan Y, Yan C, Hu Y, Fan Y, Pan Q, Wan Q, Torcivia-Rodriguez J, Mazumder R. Distribution bias analysis of germline and somatic single-nucleotide variations that impact protein functional site and neighboring amino acids. Sci Rep 2017; 7:42169. [PMID: 28176830 PMCID: PMC5296879 DOI: 10.1038/srep42169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 01/05/2017] [Indexed: 01/13/2023] Open
Abstract
Single nucleotide variations (SNVs) can result in loss or gain of protein functional sites. We analyzed the effects of SNVs on enzyme active sites, ligand binding sites, and various types of post translational modification (PTM) sites. We found that, for most types of protein functional sites, the SNV pattern differs between germline and somatic mutations as well as between synonymous and non-synonymous mutations. From a total of 51,138 protein functional site affecting SNVs (pfsSNVs), a pan-cancer analysis revealed 142 somatic pfsSNVs in five or more cancer types. By leveraging patient information for somatic pfsSNVs, we identified 17 loss of functional site SNVs and 60 gain of functional site SNVs which are significantly enriched in patients with specific cancer types. Of the key pfsSNVs identified in our analysis above, we highlight 132 key pfsSNVs within 17 genes that are found in well-established cancer associated gene lists. For illustrating how key pfsSNVs can be prioritized further, we provide a use case where we performed survival analysis showing that a loss of phosphorylation site pfsSNV at position 105 in MEF2A is significantly associated with decreased pancreatic cancer patient survival rate. These 132 pfsSNVs can be used in developing genetic testing pipelines.
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Affiliation(s)
- Yang Pan
- The Department of Biochemistry &Molecular Medicine, The George Washington University Medical Center, Washington, DC 20037, United States of America
| | - Cheng Yan
- The Department of Biochemistry &Molecular Medicine, The George Washington University Medical Center, Washington, DC 20037, United States of America
| | - Yu Hu
- The Department of Biochemistry &Molecular Medicine, The George Washington University Medical Center, Washington, DC 20037, United States of America
| | - Yu Fan
- The Department of Biochemistry &Molecular Medicine, The George Washington University Medical Center, Washington, DC 20037, United States of America
| | - Qing Pan
- The Department of Statistics, The George Washington University, Washington, DC 20037, United States of America
| | - Quan Wan
- The Department of Biochemistry &Molecular Medicine, The George Washington University Medical Center, Washington, DC 20037, United States of America
| | - John Torcivia-Rodriguez
- The Department of Biochemistry &Molecular Medicine, The George Washington University Medical Center, Washington, DC 20037, United States of America
| | - Raja Mazumder
- The Department of Biochemistry &Molecular Medicine, The George Washington University Medical Center, Washington, DC 20037, United States of America.,McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC 20037, United States of America
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7
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Ge Z, Li M, Zhao G, Xiao L, Gu Y, Zhou X, Yu MD, Li J, Dovat S, Song C. Novel dynamin 2 mutations in adult T-cell acute lymphoblastic leukemia. Oncol Lett 2016; 12:2746-2751. [PMID: 27698851 DOI: 10.3892/ol.2016.4993] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 07/20/2016] [Indexed: 12/31/2022] Open
Abstract
Genetic mutations on signaling pathways are found in patients with T-cell acute lymphoblastic leukemia (T-ALL) and act as markers of high-risk leukemia. Mutations in dynamin 2 (DNM2) have been reported in T-ALL, particularly in early T-cell precursor-ALL. In the present study, DNM2 mutations were screened by sequencing DNM2 exons obtained by polymerase chain reaction amplification and gel purification in adult T-ALL patients. A total of 4 novel DNM2 mutations were identified in adult T-ALL patients, with a mutation rate of 9.5%, and the DNM2 mutations were found to co-exist with NOTCH1 and PHD finger protein 6, and were also associated with high-risk leukemia. A high rate of silent mutation was also found in the patients, but no significant association was found between the silent mutations and patients' clinical features. The present findings suggested the DNM2 mutations may be involved in the oncogenesis of T-ALL.
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Affiliation(s)
- Zheng Ge
- Department of Hematology, Key Department of Jiangsu Medicine, Zhongda Hospital, Southeast University Medical School, Nanjing, Jiangsu 210009, P.R. China; Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, Jiangsu 210029, P.R. China; Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Min Li
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, Jiangsu 210029, P.R. China
| | - Gang Zhao
- Department of Hematology, Key Department of Jiangsu Medicine, Zhongda Hospital, Southeast University Medical School, Nanjing, Jiangsu 210009, P.R. China
| | - Lichan Xiao
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, Jiangsu 210029, P.R. China
| | - Yan Gu
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, Jiangsu 210029, P.R. China
| | - Xilian Zhou
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, Jiangsu 210029, P.R. China
| | - Michael D Yu
- Department of Internal Medicine, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Jianyong Li
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, Jiangsu 210029, P.R. China; Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing, Jiangsu 210029, P.R. China
| | - Sinisa Dovat
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Chunhua Song
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
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Common variable immunodeficiency associated with microdeletion of chromosome 1q42.1-q42.3 and inositol 1,4,5-trisphosphate kinase B (ITPKB) deficiency. Clin Transl Immunology 2016; 5:e59. [PMID: 26900472 PMCID: PMC4735063 DOI: 10.1038/cti.2015.41] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Revised: 11/11/2015] [Accepted: 11/25/2015] [Indexed: 12/11/2022] Open
Abstract
Common variable immunodeficiency (CVID) is a heterogenous disorder characterized by hypogammaglobulinemia and impaired specific antibody response and increased susceptibility to infections, autoimmunity and malignancies. A number of gene mutations, including ICOS, TACI and BAFF-R, and CD19, CD20, CD21, CD81, MSH5 and LRBA have been described; however, they account for approximately 20–25% of total cases of CVID. In this study, we report a patient with CVID with an intrinsic microdeletion of chromosome 1q42.1-42.3, where gene for inositol 1,3,4, trisphosphate kinase β (ITPKB) is localized. ITPKB has an important role in the development, survival and function of B cells. In this subject, the expression of ITPKB mRNA as well as ITKPB protein was significantly reduced. The sequencing of ITPKB gene revealed three variants, two of them were missense variants and third was a synonymous variant; the significance of each of them in relation to CVID is discussed. This case suggests that a deficiency of ITPKB may have a role in CVID.
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Mukherjee D, Mukherjee A, Ghosh TC. Evolutionary Rate Heterogeneity of Primary and Secondary Metabolic Pathway Genes in Arabidopsis thaliana. Genome Biol Evol 2015; 8:17-28. [PMID: 26556590 PMCID: PMC4758233 DOI: 10.1093/gbe/evv217] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Primary metabolism is essential to plants for growth and development, and secondary metabolism helps plants to interact with the environment. Many plant metabolites are industrially important. These metabolites are produced by plants through complex metabolic pathways. Lack of knowledge about these pathways is hindering the successful breeding practices for these metabolites. For a better knowledge of the metabolism in plants as a whole, evolutionary rate variation of primary and secondary metabolic pathway genes is a prerequisite. In this study, evolutionary rate variation of primary and secondary metabolic pathway genes has been analyzed in the model plant Arabidopsis thaliana. Primary metabolic pathway genes were found to be more conserved than secondary metabolic pathway genes. Several factors such as gene structure, expression level, tissue specificity, multifunctionality, and domain number are the key factors behind this evolutionary rate variation. This study will help to better understand the evolutionary dynamics of plant metabolism.
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Affiliation(s)
- Dola Mukherjee
- Bioinformatics Centre, Bose Institute, Kolkata, West Bengal, India
| | - Ashutosh Mukherjee
- Department of Botany, Vivekananda College, Thakurpukur, Kolkata, West Bengal, India
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10
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Mutational Consequences of Aberrant Ion Channels in Neurological Disorders. J Membr Biol 2014; 247:1083-127. [DOI: 10.1007/s00232-014-9716-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Accepted: 07/25/2014] [Indexed: 12/25/2022]
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