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Wang S, Song F, Song M, Wei X, Zhou Y, Jiang L, Wang Z, Sun C, Yao H, Liang W, Luo H. Explore variation of salivary bacteria across time and geolocations. Int J Legal Med 2024; 138:547-554. [PMID: 37353677 DOI: 10.1007/s00414-023-03045-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/13/2023] [Indexed: 06/25/2023]
Abstract
Saliva is an informative body fluid that can be found at various crime scenes, and the salivary bacterial community has been revealed it is a potential auxiliary target for forensic identification. However, the variation of salivary bacterial community composition across time and geolocation needs to be explored. The study was designed to be carried out during the winter vacation that was across about 50 days and eight geographic locations. The high throughput sequencing was performed with the V3-V4 region of the16S rRNA gene to explore salivary bacterial community composition. An overall slight fluctuation of the salivary bacteria was observed, which primarily occurred in the relative abundance of the salivary bacterial taxa. The results of principal coordinate analysis and hierarchical clustering showed samples were clustered by the individuals. All individuals could be correctly identified with the random forest model. In summation, although the relative abundance of salivary bacteria varied across the changes of time and geolocation, the individualized characteristic of salivary bacteria remained steady, which is beneficial for the salivary bacterial application in personal identification.
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Affiliation(s)
- Shuangshuang Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Feng Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Mengyuan Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiaowen Wei
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Yuxiang Zhou
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Lanrui Jiang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Zefei Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Chaoran Sun
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Hewen Yao
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.
| | - Haibo Luo
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.
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Molecular Tools to Identify and Characterize Malignant Catarrhal Fever Viruses (MCFV) of Ruminants and Captive Artiodactyla. Viruses 2022; 14:v14122697. [PMID: 36560701 PMCID: PMC9787554 DOI: 10.3390/v14122697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022] Open
Abstract
The family Herpesviridae includes viruses identified in mammals, birds and reptiles. All herpesviruses share a similar structure, consisting of a large linear double-stranded DNA genome surrounded by a proteic icosahedral capsid further contained within a lipidic bilayer envelope. The continuous rise of genetic variability and the evolutionary selective pressure underlie the appearance and consolidation of novel viral strains. This applies also to several gamma(γ)-herpesviruses, whose role as primary pathogen has been often neglected and, among these to newly emerged viruses or virus variants responsible for the development of Malignant Catarrhal Fever (MCF) or MCF-like disease. The identification of γ-herpesviruses adapted to new zoological hosts requires specific molecular tools for detection and characterization. These viruses can cause MCF in livestock and wild animals, a disease generally sporadic but with serious welfare implications and which, in many cases, leads to death within a few days from the appearance of the clinical signs. In the absence of a vaccine, the first step to improve disease control is based on the improvement of molecular tools to identify and characterize these viruses, their phylogenetic relationships and evolutionary interaction with the host species. A Panherpes PCR-specific test, based on the conserved DNA polymerase gene, employing consensus/degenerate and deoxyinosine-substituted primers followed by sequencing, is still the preferred diagnostic test to confirm and characterize herpesviral infections. The drawback of this test is the amplification of a relatively short sequence, which makes phylogenetic analysis less stringent. Based on these diagnostic requirements, and with a specific focus on γ-herpesviruses, the present review aims to critically analyze the currently available methods to identify and characterize novel MCFV strains, to highlight advantages and drawbacks and to identify the gaps to be filled in order to address research priorities. Possible approaches for improving or further developing these molecular tools are also suggested.
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Hijazi G, Dakroub F, Khoueiry P, El-Kurdi A, Ezzeddine A, Alkalamouni H, Alansari K, Althani AA, Mathew S, AlKhatib HA, Yassine HM, Zaraket H. Viral metagenomics analysis of stool specimens from children with unresolved gastroenteritis in Qatar. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 105:105367. [PMID: 36115643 DOI: 10.1016/j.meegid.2022.105367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/26/2022] [Accepted: 09/12/2022] [Indexed: 06/15/2023]
Abstract
Acute gastroenteritis (AGE) is associated with significant global morbidity and mortality, especially among children under five years of age. Viruses are well established as etiologic agents of gastroenteritis since they are the most common pathogens that contribute to the disease burden in developing countries. Despite the advances in molecular diagnosis, a substantial proportion of AGE etiology remain unresolved. We implemented a viral metagenomics pipeline to determine the potential viral etiology associated with AGE among children under the age of five years in Qatar with undiagnosed etiology. Following enriching for the viral genome, ∼1.3 billion sequences were generated from 89 stool specimens using the Illumina HiSeq platform, of which 7% were mapped to viral genomes. Human viruses were detected in 34 specimens (38.2%); 14 were adenovirus, nine coxsackievirus A16, five rotavirus (G9P[8] and G4P[8]), four norovirus (GII), one influenza A virus (H3), and one respiratory syncytial virus A (RSVA). In conclusion, the viral metagenomics approach is useful for determining AGE's etiology when routine molecular diagnostic assays fail.
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Affiliation(s)
- Ghina Hijazi
- Department of Experimental Pathology, Microbiology, and Immunology, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon; Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Fatima Dakroub
- Department of Experimental Pathology, Microbiology, and Immunology, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon; Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Pierre Khoueiry
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon; Pillar Genomics Institute, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Abdullah El-Kurdi
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon; Pillar Genomics Institute, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Amani Ezzeddine
- Department of Experimental Pathology, Microbiology, and Immunology, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon; Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Habib Alkalamouni
- Department of Experimental Pathology, Microbiology, and Immunology, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon; Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | | | - Asmaa A Althani
- Biomedical Research Center, Qatar University, Doha 2713, Qatar
| | - Shilu Mathew
- Biomedical Research Center, Qatar University, Doha 2713, Qatar
| | | | - Hadi M Yassine
- Biomedical Research Center, Qatar University, Doha 2713, Qatar.
| | - Hassan Zaraket
- Department of Experimental Pathology, Microbiology, and Immunology, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon; Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon.
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Lopez D, Roberts J, Bourgeois M, Kootstra J, Minnick S, Black A, Mauss J, Flores N. Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2. PLoS One 2022; 17:e0264008. [PMID: 35171960 PMCID: PMC8849547 DOI: 10.1371/journal.pone.0264008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 01/31/2022] [Indexed: 12/31/2022] Open
Abstract
The C29197T mutation is one of 4 point mutations known to cause N-gene target failure (NGTF) in the Xpert Xpress SARS-CoV-2 and Xpert Omni SARS-CoV-2 assays from Cepheid (Sunnyvale, CA). We describe a high local prevalence in January of 8.5% (CI 4.9-14.2%) for the C29197T mutation, which was over 3-fold higher than the prevalence estimated statewide in California during the same time frame, 2.5% (CI 2.1-2.8%). Using phylogenetic analysis, we discovered that this increase in prevalence was due, at least in part, to a disproportionately large infection cluster of unknown origin. This study emphasizes the importance of sequencing at the local jurisdictional level and demonstrates the impact that regional variation can have when assessing risk due to point mutations that impact clinical test performance. It also reinforces the need for diligent reporting of abnormal test results by clinical laboratories, especially during Emergency Use Authorization (EUA) periods, as additional information is gathered about the target organism and the performance of EUA-authorized tests over time.
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Affiliation(s)
- Denise Lopez
- College of Public Health, University of South Florida, Tampa, FL, United States of America
- Public Health Branch, County of Tulare, Tulare, CA, United States of America
| | - Jill Roberts
- College of Public Health, University of South Florida, Tampa, FL, United States of America
| | - Marie Bourgeois
- College of Public Health, University of South Florida, Tampa, FL, United States of America
| | - Joshua Kootstra
- Public Health Branch, County of Tulare, Tulare, CA, United States of America
| | - Sharon Minnick
- Public Health Branch, County of Tulare, Tulare, CA, United States of America
| | - Allison Black
- CZBiohub, San Francisco, CA, United States of America
| | - Joshua Mauss
- Public Health Branch, County of Tulare, Tulare, CA, United States of America
| | - Nick Flores
- Public Health Branch, County of Tulare, Tulare, CA, United States of America
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Benedek T, Szentgyörgyi F, Szabó I, Farkas M, Duran R, Kriszt B, Táncsics A. Aerobic and oxygen-limited naphthalene-amended enrichments induced the dominance of Pseudomonas spp. from a groundwater bacterial biofilm. Appl Microbiol Biotechnol 2020; 104:6023-6043. [PMID: 32415320 PMCID: PMC7306034 DOI: 10.1007/s00253-020-10668-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/29/2020] [Accepted: 05/04/2020] [Indexed: 12/20/2022]
Abstract
In this study, we aimed at determining the impact of naphthalene and different oxygen levels on a biofilm bacterial community originated from a petroleum hydrocarbon-contaminated groundwater. By using cultivation-dependent and cultivation-independent approaches, the enrichment, identification, and isolation of aerobic and oxygen-limited naphthalene degraders was possible. Results indicated that, regardless of the oxygenation conditions, Pseudomonas spp. became the most dominant in the naphthalene-amended selective enrichment cultures. Under low-oxygen conditions, P. veronii/P. extremaustralis lineage affiliating bacteria, and under full aerobic conditions P. laurentiana-related isolates were most probably capable of naphthalene biodegradation. A molecular biological tool has been developed for the detection of naphthalene 1,2-dioxygenase-related 2Fe-2S reductase genes of Gram-negative bacteria. The newly developed COnsensus DEgenerate Hybrid Oligonucleotide Primers (CODEHOP-PCR) technique may be used in the monitoring of the natural attenuation capacity of PAH-contaminated sites. A bacterial strain collection with prolific biofilm-producing and effective naphthalene-degrading organisms was established. The obtained strain collection may be applicable in the future for the development of biofilm-based bioremediation systems for the elimination of PAHs from groundwater (e.g., biofilm-based biobarriers).
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Affiliation(s)
- Tibor Benedek
- Regional University Centre of Excellence in Environmental Industry, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary.
| | - Flóra Szentgyörgyi
- Department of Environmental Protection and Safety, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - István Szabó
- Department of Environmental Protection and Safety, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - Milán Farkas
- Department of Environmental Protection and Safety, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - Robert Duran
- IPREM UMR CNRS 5254, Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, Pau, France
| | - Balázs Kriszt
- Department of Environmental Protection and Safety, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - András Táncsics
- Regional University Centre of Excellence in Environmental Industry, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
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Overexpression of SmANS Enhances Anthocyanin Accumulation and Alters Phenolic Acids Content in Salvia miltiorrhiza and Salvia miltiorrhiza Bge f. alba Plantlets. Int J Mol Sci 2019; 20:ijms20092225. [PMID: 31064132 PMCID: PMC6539416 DOI: 10.3390/ijms20092225] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 04/28/2019] [Accepted: 05/03/2019] [Indexed: 12/23/2022] Open
Abstract
Flavonoids play multiple roles in plant coloration and stress resistance and are closely associated with human health. Flavonoids and non-flavonoids (such as phenolic acids) are produced via the phenylpropanoid-derived pathway. Anthocyanidin synthase (ANS) catalyzes the synthesis of anthocyanins from leucoanthocyanidin in the flavonoids branched pathway. In this study, SmANS from Salvia miltiorrhiza was cloned and mainly localized in the endoplasmic reticulum (ER), plastids, Golgi, plasma membrane, and nucleus of tobacco epidermal cells, and was most highly expressed in purple petals in S. miltiorrhiza, whereas it showed almost no expression in white petals, green calyxes, and pistils in S. miltiorrhiza Bge f. alba. Overexpressed SmANS enhanced anthocyanin accumulation but reduced salvianolic acid B (SAB) and rosmarinic acid (RA) biosynthesis in S. miltiorrhiza and S. miltiorrhiza Bge f. alba plantlets, meanwhile, it restored the purple-red phenotype in S. miltiorrhiza Bge f. alba. These changes were due to reallocation of the metabolic flow, which was influenced by the SmANS gene. These findings indicate that SmANS not only plays a key role in anthocyanin accumulation in S. miltiorrhiza, but also acts as a “switch” for the coloration of S. miltiorrhiza Bge f. alba. This study provides baseline information for further research on flavonoids metabolism and improvement of anthocyanin or phenolic acid production by genetic engineering.
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Base-By-Base Version 3: New Comparative Tools for Large Virus Genomes. Viruses 2018; 10:v10110637. [PMID: 30445717 PMCID: PMC6265842 DOI: 10.3390/v10110637] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/10/2018] [Accepted: 11/13/2018] [Indexed: 11/24/2022] Open
Abstract
Base-By-Base is a comprehensive tool for the creation and editing of multiple sequence alignments that is coded in Java and runs on multiple platforms. It can be used with gene and protein sequences as well as with large viral genomes, which themselves can contain gene annotations. This report describes new features added to Base-By-Base over the last 7 years. The two most significant additions are: (1) The recoding and inclusion of “consensus-degenerate hybrid oligonucleotide primers” (CODEHOP), a popular tool for the design of degenerate primers from a multiple sequence alignment of proteins; and (2) the ability to perform fuzzy searches within the columns of sequence data in multiple sequence alignments to determine the distribution of sequence variants among the sequences. The intuitive interface focuses on the presentation of results in easily understood visualizations and providing the ability to annotate the sequences in a multiple alignment with analytic and user data.
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Pathogen Discovery. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Feng H, Wei L, Chen H, Zhou Y. Calreticulin is required for responding to stress, foraging, and fertility in the white-tip nematode, Aphelenchoides besseyi. Exp Parasitol 2015; 155:58-67. [PMID: 25999293 DOI: 10.1016/j.exppara.2015.05.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 04/10/2015] [Accepted: 05/11/2015] [Indexed: 11/26/2022]
Abstract
Calreticulin (CRT) regulates a wide array of cellular responses in physiological and pathological processes. A full-length cDNA-encoding CRT protein, namely AbCRT-1, was isolated from Aphelenchoides besseyi, an ectoparasitic plant nematode and the agent of white tip disease of rice. The deduced amino acid sequence of AbCRT-1 was highly homologous with other nematode CRTs, and showed the closest evolutionary relationship with BxCRT-1. In-situ hybridization showed that AbCRT-1 is specifically located in the oesophageal gland and gonads of A. besseyi, suggesting its potential role in parasitism and reproduction. Quantity real-time PCR analysis showed that AbCRT-1 is highly expressed in female nematodes but poorly expressed in eggs, juveniles, and male nematodes. Exposing the nematode to relatively low osmotic stress promotes the transcription of AbCRT-1 whereas extreme desiccation suppresses the transcription significantly. Nematodes in which AbCRT-1 mRNA level had been knocked down by soaking them in AbCRT-1 dsRNA solution distributed randomly and did not aggregate temporally, with a decreased capacity of food discernment. Thus the affected nematodes were markedly less fecund. These results demonstrate that AbCRT-1 is required in A. besseyi for responding to stress, foraging, and fertility.
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Affiliation(s)
- Hui Feng
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Lihui Wei
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
| | - Huaigu Chen
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Yijun Zhou
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
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Wen F, Caputo G, Hooey S, Bowman S, Pinkney K, Krell PJ, Arif B, Doucet D. Establishment of a cell line from the ash and privet borer beetle Tylonotus bimaculatus Haldeman and assessment of its sensitivity to diacylhydrazine insecticides. In Vitro Cell Dev Biol Anim 2015; 51:905-14. [PMID: 25952767 DOI: 10.1007/s11626-015-9917-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 04/14/2015] [Indexed: 12/18/2022]
Abstract
A novel cell line, NRCAN-Tb521, was developed from larvae of the longhorn beetle Tylonotus bimaculatus (Coleoptera: Cerambycidae), a pest of North American ash trees. The cell line has been successfully passaged more than 50 times and displayed very strong attachment to the substrate and a modal chromosomal count distribution of 19. Sequencing of a 649 bp fragment of the mitochondrial cytochrome oxidase I gene confirmed the identity of NRCAN-Tb521 as T. bimaculatus. The response of the cell line to 20-hydroxyecdysone and diacylhydrazine ecdysone agonist insecticides was also studied. At 10(-6) M, 20-hydroxyecdysone, tebufenozide, methoxyfenozide and halofenozide triggered the production of numerous filamentous cytoplasmic extensions, and the cells tended to form aggregates, indicative of a cell differentiation response. This response was followed by a strong decrease in viability after 4 d. Reverse transcription polymerase chain reaction (PCR) experiments and sequencing of PCR fragments showed that the 20E receptor gene EcR is expressed in the cells and that 20E, tebufenozide, methoxyfenozide and halofenozide also induce the expression of the nuclear hormone receptor gene HR3. This report establishes that NRCAN-Tb521 is a valuable in vitro model to study effects of ecdysone agonists in wood-boring cerambycids.
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Affiliation(s)
- Fayuan Wen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada, N1G 2W1.,Canadian Forest Service, Natural Resources Canada, 1219 Queen St. East, Sault Ste Marie, ON, Canada, P6A 2E5
| | - Guido Caputo
- Canadian Forest Service, Natural Resources Canada, 1219 Queen St. East, Sault Ste Marie, ON, Canada, P6A 2E5
| | - Sharon Hooey
- Canadian Forest Service, Natural Resources Canada, 1219 Queen St. East, Sault Ste Marie, ON, Canada, P6A 2E5
| | - Susan Bowman
- Canadian Forest Service, Natural Resources Canada, 1219 Queen St. East, Sault Ste Marie, ON, Canada, P6A 2E5
| | - Kristine Pinkney
- Canadian Forest Service, Natural Resources Canada, 1219 Queen St. East, Sault Ste Marie, ON, Canada, P6A 2E5
| | - Peter J Krell
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada, N1G 2W1
| | - Basil Arif
- Canadian Forest Service, Natural Resources Canada, 1219 Queen St. East, Sault Ste Marie, ON, Canada, P6A 2E5
| | - Daniel Doucet
- Canadian Forest Service, Natural Resources Canada, 1219 Queen St. East, Sault Ste Marie, ON, Canada, P6A 2E5.
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Reilly BD, Cramp RL, Franklin CE. Activity, abundance and expression of Ca2+-activated proteases in skeletal muscle of the aestivating frog, Cyclorana alboguttata. J Comp Physiol B 2014; 185:243-55. [DOI: 10.1007/s00360-014-0880-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Revised: 11/18/2014] [Accepted: 11/27/2014] [Indexed: 10/24/2022]
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12
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Chen J, Pei Z, Dai L, Wang B, Liu L, An X, Peng D. Transcriptome profiling using pyrosequencing shows genes associated with bast fiber development in ramie (Boehmeria nivea L.). BMC Genomics 2014; 15:919. [PMID: 25339420 PMCID: PMC4326285 DOI: 10.1186/1471-2164-15-919] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 10/13/2014] [Indexed: 12/13/2022] Open
Abstract
Background Ramie (Boehmeria nivea L.), popularly known as “China grass”, is one of the oldest crops in China and the second most important fiber crop in terms of area sown. Ramie fiber, extracted from the plant bast, is important in the textile industry. However, the molecular mechanism of ramie fiber development remains unknown. Results A whole sequencing run was performed on the 454 GS FLX + platform using four separately pooled parts of ramie bast. This generated 1,030,057 reads with an average length of 457 bp. Among the 58,369 unigenes (13,386 contigs and 44,983 isotigs) that were generated through de novo assembly, 780 were differentially expressed. As a result, 13 genes that belong to the cellulose synthase gene family (four), the expansin gene family (three) and the xyloglucan endotransglucosylase/hydrolase (XTH) gene family (six) were up-regulated in the top part of the bast, which was in contrast to the other three parts. The identification of these 13 concurrently up-regulated unigenes indicated that the early stage (represented by the top part of the bast) might be important for the molecular regulation of ramie fiber development. Further analysis indicated that four of the 13 unigenes from the expansin (two) and XTH (two) families shared a coincident expression pattern during the whole growth season, which implied they were more relevant to ramie fiber development (fiber quality, etc.) during the different seasons than the other genes. Conclusions To the best of our knowledge, this study is the first to characterize ramie fiber development at different developmental stages. The identified transcripts will improve our understanding of the molecular mechanisms involved in ramie fiber development. Moreover, the identified differentially expressed genes will accelerate molecular research on ramie fiber growth and the breeding of ramie with better fiber yields and quality. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-919) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Bo Wang
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, No, 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei Province, China.
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13
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Glutathione reductase-mediated synthesis of tellurium-containing nanostructures exhibiting antibacterial properties. Appl Environ Microbiol 2014; 80:7061-70. [PMID: 25193000 DOI: 10.1128/aem.02207-14] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tellurium, a metalloid belonging to group 16 of the periodic table, displays very interesting physical and chemical properties and lately has attracted significant attention for its use in nanotechnology. In this context, the use of microorganisms for synthesizing nanostructures emerges as an eco-friendly and exciting approach compared to their chemical synthesis. To generate Te-containing nanostructures, bacteria enzymatically reduce tellurite to elemental tellurium. In this work, using a classic biochemical approach, we looked for a novel tellurite reductase from the Antarctic bacterium Pseudomonas sp. strain BNF22 and used it to generate tellurium-containing nanostructures. A new tellurite reductase was identified as glutathione reductase, which was subsequently overproduced in Escherichia coli. The characterization of this enzyme showed that it is an NADPH-dependent tellurite reductase, with optimum reducing activity at 30°C and pH 9.0. Finally, the enzyme was able to generate Te-containing nanostructures, about 68 nm in size, which exhibit interesting antibacterial properties against E. coli, with no apparent cytotoxicity against eukaryotic cells.
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Gahoi S, Arya L, Anil R, Marla S. DPPrimer - A Degenerate PCR Primer Design Tool. Bioinformation 2013; 9:937-40. [PMID: 24307773 PMCID: PMC3842581 DOI: 10.6026/97320630009937] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Revised: 10/02/2013] [Accepted: 10/19/2013] [Indexed: 11/23/2022] Open
Abstract
Designed degenerate primers unlike conventional primers are superior in matching and amplification of large number of genes,
from related gene families. DPPrimer tool was designed to predict primers for PCR amplification of homologous gene from related
or diverse plant species. The key features of this tool include platform independence and user friendliness in primer design.
Embedded features such as search for functional domains, similarity score selection and phylogebetic tree further enhance the user
friendliness of DPPrimer tool. Performance of DPPrimer tool was evaluated by successful PCR amplification of ADP-glucose
phosphorylase genes from wheat, barley and rice.
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Affiliation(s)
- Shachi Gahoi
- National Bureau of Plant Genetic Resources, Pusa campus, New Delhi-12
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15
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de Melo NR, Abdrahman A, Greig C, Mukherjee K, Thornton C, Ratcliffe NA, Vilcinskas A, Butt TM. Myriocin significantly increases the mortality of a non-mammalian model host during Candida pathogenesis. PLoS One 2013; 8:e78905. [PMID: 24260135 PMCID: PMC3829820 DOI: 10.1371/journal.pone.0078905] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 09/17/2013] [Indexed: 12/14/2022] Open
Abstract
Candida albicans is a major human pathogen whose treatment is challenging due to antifungal drug toxicity, drug resistance and paucity of antifungal agents available. Myrocin (MYR) inhibits sphingosine synthesis, a precursor of sphingolipids, an important cell membrane and signaling molecule component. MYR also has dual immune suppressive and antifungal properties, potentially modulating mammalian immunity and simultaneously reducing fungal infection risk. Wax moth (Galleria mellonella) larvae, alternatives to mice, were used to establish if MYR suppressed insect immunity and increased survival of C. albicans-infected insects. MYR effects were studied in vivo and in vitro, and compared alone and combined with those of approved antifungal drugs, fluconazole (FLC) and amphotericin B (AMPH). Insect immune defenses failed to inhibit C. albicans with high mortalities. In insects pretreated with the drug followed by C. albicans inoculation, MYR+C. albicans significantly increased mortality to 93% from 67% with C. albicans alone 48 h post-infection whilst AMPH+C. albicans and FLC+C. albicans only showed 26% and 0% mortalities, respectively. MYR combinations with other antifungal drugs in vivo also enhanced larval mortalities, contrasting the synergistic antifungal effect of the MYR+AMPH combination in vitro. MYR treatment influenced immunity and stress management gene expression during C. albicans pathogenesis, modulating transcripts putatively associated with signal transduction/regulation of cytokines, I-kappaB kinase/NF-kappaB cascade, G-protein coupled receptor and inflammation. In contrast, all stress management gene expression was down-regulated in FLC and AMPH pretreated C. albicans -infected insects. Results are discussed with their implications for clinical use of MYR to treat sphingolipid-associated disorders.
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Affiliation(s)
| | - Ahmed Abdrahman
- Department of Biosciences, College of Science, Swansea University, Singleton Park, Swansea, United Kingdom
| | - Carolyn Greig
- Department of Biosciences, College of Science, Swansea University, Singleton Park, Swansea, United Kingdom
| | - Krishnendu Mukherjee
- Institut für Phytopathologie und Angewandte Zoologie, Abteilung Angewandte Entomologie, Gieβen, Germany
| | - Catherine Thornton
- College of Medicine, Swansea University, Singleton Park, Swansea, United Kingdom
| | - Norman A. Ratcliffe
- Department of Biosciences, College of Science, Swansea University, Singleton Park, Swansea, United Kingdom
- Department of Biological Sciences, Universidade Federal Fluminense, Rio de Janeiro, Brazil
| | - Andreas Vilcinskas
- Institut für Phytopathologie und Angewandte Zoologie, Abteilung Angewandte Entomologie, Gieβen, Germany
| | - Tariq M. Butt
- Department of Biosciences, College of Science, Swansea University, Singleton Park, Swansea, United Kingdom
- * E-mail:
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16
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A newly designed degenerate PCR primer based on pmoA gene for detection of nitrite-dependent anaerobic methane-oxidizing bacteria from different ecological niches. Appl Microbiol Biotechnol 2013; 97:10155-62. [PMID: 24201910 DOI: 10.1007/s00253-013-5260-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 09/10/2013] [Accepted: 09/11/2013] [Indexed: 10/26/2022]
Abstract
A new pmoA gene-based PCR primer set was designed for detection of nitrite-dependent anaerobic oxidation of methane (n-damo) bacteria from four different ecosystems, namely rice paddy soil, freshwater reservoir, reed bed, and sludge from wastewater treatment plant. This primer set showed high specificity and efficiency in recovering n-damo bacteria from these diverse samples. The obtained sequences showed 88-94 and 90-96% similarity to nucleotide and amino acid sequences, respectively, with the known NC10 phylum bacterium. According to the UniFrac principal coordinates analysis (PCoA), DNA sequences retrieved by the new PCR primer set in this study formed a separate group from the reported sequences, indicating higher diversity of n-damo in the environment. This newly designed PCR primer is capable of amplifying not only the currently known n-damo bacteria but also those that have not been reported, providing new information on the ecological diversity and distribution of this group of microorganisms in the ecosystem.
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17
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Li XF, Jia LY, Xu J, Deng XJ, Wang Y, Zhang W, Zhang XP, Fang Q, Zhang DM, Sun Y, Xu L. FT-like NFT1 gene may play a role in flower transition induced by heat accumulation in Narcissus tazetta var. chinensis. PLANT & CELL PHYSIOLOGY 2013; 54:270-81. [PMID: 23303875 DOI: 10.1093/pcp/pcs181] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The low-temperature flowering-response pathway, used as an inductive stimulus to induce flowering in plant species from temperate regions in response to cold temperature, has been extensively studied. However, limited information is available on the flower transition of several bulbous species, which require high temperature for flower differentiation. Narcissus tazetta var. chinensis (Chinese narcissus) exhibits a 2 year juvenile phase, and flower initiation within its bulbs occurs during summer dormancy. The genetic factors that control flower initiation are mostly unknown in Chinese narcissus. In the present study, we found that a high storage temperature is necessary for flower initiation. Flower initiation was advanced in bulbs previously exposed to extended high temperature. The heat accumulation required for flower transition was also determined. High temperature treatment rescued the low flower percentage resulting from short storage duration under natural conditions. In addition, extended high storage temperature was found to increase the flowering percentage of 2-year-old plants, which can be applied in breeding. Narcissus FLOWERING LOCUS T1 (NFT1), a homolog of the Arabidopsis thaliana gene FLOWERING LOCUS T, was isolated in this study. NFT1 transcripts were abundant during flower initiation in mature bulbs and were up-regulated by high temperature. The genetic experiments, coupled with an expression profiling assay, suggest that NFT1 possibly takes part in flower transition control in response to high temperature.
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MESH Headings
- Amino Acid Sequence
- Arabidopsis/genetics
- Arabidopsis/metabolism
- Cloning, Molecular
- DNA, Complementary/genetics
- DNA, Complementary/metabolism
- Flowers/genetics
- Flowers/growth & development
- Flowers/ultrastructure
- Gene Expression Regulation, Plant
- Genes, Plant
- Hot Temperature
- Meristem/genetics
- Meristem/metabolism
- Microscopy, Electron, Scanning
- Molecular Sequence Data
- Narcissus/anatomy & histology
- Narcissus/genetics
- Narcissus/growth & development
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/growth & development
- Plants, Genetically Modified/metabolism
- Sequence Alignment
- Species Specificity
- Time Factors
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Affiliation(s)
- Xiao-Fang Li
- School of Life Science, East China Normal University, 500 Dongchuan Rd., Shanghai, PR China
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18
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Gulvik CA, Effler TC, Wilhelm SW, Buchan A. De-MetaST-BLAST: a tool for the validation of degenerate primer sets and data mining of publicly available metagenomes. PLoS One 2012. [PMID: 23189198 PMCID: PMC3506598 DOI: 10.1371/journal.pone.0050362] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Development and use of primer sets to amplify nucleic acid sequences of interest is fundamental to studies spanning many life science disciplines. As such, the validation of primer sets is essential. Several computer programs have been created to aid in the initial selection of primer sequences that may or may not require multiple nucleotide combinations (i.e., degeneracies). Conversely, validation of primer specificity has remained largely unchanged for several decades, and there are currently few available programs that allows for an evaluation of primers containing degenerate nucleotide bases. To alleviate this gap, we developed the program De-MetaST that performs an in silico amplification using user defined nucleotide sequence dataset(s) and primer sequences that may contain degenerate bases. The program returns an output file that contains the in silico amplicons. When De-MetaST is paired with NCBI’s BLAST (De-MetaST-BLAST), the program also returns the top 10 nr NCBI database hits for each recovered in silico amplicon. While the original motivation for development of this search tool was degenerate primer validation using the wealth of nucleotide sequences available in environmental metagenome and metatranscriptome databases, this search tool has potential utility in many data mining applications.
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Affiliation(s)
- Christopher A. Gulvik
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - T. Chad Effler
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Steven W. Wilhelm
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Alison Buchan
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail:
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19
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Fancello L, Raoult D, Desnues C. Computational tools for viral metagenomics and their application in clinical research. Virology 2012; 434:162-74. [PMID: 23062738 PMCID: PMC7111993 DOI: 10.1016/j.virol.2012.09.025] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 09/15/2012] [Accepted: 09/23/2012] [Indexed: 02/06/2023]
Abstract
There are 100 times more virions than eukaryotic cells in a healthy human body. The characterization of human-associated viral communities in a non-pathological state and the detection of viral pathogens in cases of infection are essential for medical care and epidemic surveillance. Viral metagenomics, the sequenced-based analysis of the complete collection of viral genomes directly isolated from an organism or an ecosystem, bypasses the “single-organism-level” point of view of clinical diagnostics and thus the need to isolate and culture the targeted organism. The first part of this review is dedicated to a presentation of past research in viral metagenomics with an emphasis on human-associated viral communities (eukaryotic viruses and bacteriophages). In the second part, we review more precisely the computational challenges posed by the analysis of viral metagenomes, and we illustrate the problem of sequences that do not have homologs in public databases and the possible approaches to characterize them.
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Affiliation(s)
- L Fancello
- Aix Marseille University, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
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