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1. Complete, high-quality genomes from long-read metagenomic sequencing of two wolf lichen thalli reveals enigmatic genome architecture

Author:
McKenzie, Sean K.; Walston, Ridge F.; Allen, Jessica L.
Source:
Genomics 2020 v.112 no.5 pp. 3150-3156
ISSN:
0888-7543
Subject:
microbial genetics,   etc   ; Letharia; fungi; genome; haplotypes; lichens; metagenomics; nanopores; thallus; wolves;     Show all 10 Subjects
Abstract:
... Fungal genomes display incredible levels of complexity and diversity, and are exceptional study systems for genome evolution. Here we used the Oxford Nanopore MinION sequencing platform to generate high-quality fungal genomes from complex metagenomic samples of lichen thalli. We sequenced two wolf lichens using one flow cell per sample, generating 17.1 Gbps for Letharia lupina and 14.3 Gbps for Le ...
DOI:
10.1016/j.ygeno.2020.06.006

2. Bacterial genetics and molecular pathogenesis in the age of high throughput DNA sequencing

Author:
Davey, Lauren; Valdivia, Raphael H
Source:
Current opinion in microbiology 2020 v.54 pp. 59-66
ISSN:
1369-5274
Subject:
microbial genetics,   etc   ; genes; genetic analysis; genotype-phenotype correlation; high-throughput nucleotide sequencing; microorganisms; mutants; mutation; pathogenesis; pathogens; phylogeny; recombinant DNA; virulence; virulent strains;     Show all 14 Subjects
Abstract:
... When Stanley Falkow introduced Molecular Koch’s Postulates (Falkow, 1988) as a conceptual framework to identify microbial factors that contributed to disease, he reaffirmed the prominent role that the basic principles of genetic analysis should play in defining genotype-phenotype associations in microbial pathogens. In classical bacterial genetics the nature of mutations is inferred through cis-tr ...
DOI:
10.1016/j.mib.2020.01.007

3. Revisiting Bartonella bacilliformis MLST

Author:
Ruiz, Joaquim; Pons, Maria J.
Source:
Infection, genetics, and evolution 2018 v.63 pp. 231-235
ISSN:
1567-1348
Subject:
microbial genetics,   etc   ; Bartonella bacilliformis; genome; geographical distribution;     Show all 4 Subjects
Abstract:
... All the studies published including Bartonella bacilliformis MLST data, as well as all B. bacilliformis genomes present in GenBank were analyzed. Overall 64 isolates and their geographical distribution were analyzed, and 14 different MLST patterns were observed. The results highlight the need for expanding the MLST studies and adding a higher number of isolates from all endemic areas. ...
DOI:
10.1016/j.meegid.2018.05.032

4. Advances in targeting and heterologous expression of genes involved in the synthesis of fungal secondary metabolites

Author:
Qiao, Yun-Ming; Yu, Rui-Lin; Zhu, Ping
Source:
RSC advances 2019 v.9 no.60 pp. 35124-35134
ISSN:
2046-2069
Subject:
microbial genetics,   etc   ; biosynthesis; fungi; gene expression; gene targeting; heterologous gene expression; multigene family; penicillins; secondary metabolites; sequence analysis; translation (genetics);     Show all 11 Subjects
Abstract:
... The revolutionary discovery of penicillin only marks the start of our exploration for valuable fungal natural products. Advanced genome sequencing technologies have translated the fungal genome into a huge reservoir of “recipes” – biosynthetic gene clusters (BGCs) – for biosynthesis. Studying complex fungal genetics demands specific gene manipulation strategies. This review summarizes the current ...
DOI:
10.1039/c9ra06908a

5. Fungal biological resources to support international development: challenges and opportunities

Author:
Ryan, M. J.; McCluskey, K.; Verkleij, G.; Robert, V.; Smith, D.
Source:
World journal of microbiology & biotechnology 2019 v.35 no.9 pp. 139
ISSN:
0959-3993
Subject:
microbial genetic resources,   etc   ; United Nations; biodiversity; bioeconomics; developing countries; fungi; income; infrastructure; laws and regulations; research and development; sustainable development;     Show all 11 Subjects
Abstract:
... Exploitation of microbes, especially fungi, has the potential to help humankind meet the UN’s sustainable development goals, help feed the worlds growing population and improve bioeconomies of poorer nations. The majority of the world’s fungal genetic resources are held in collections in developed countries, primarily within the USA, Europe and Japan. Very little capacity exists in low to middle i ...
DOI:
10.1007/s11274-019-2709-7
PubMed:
31451943
PubMed Central:
PMC6710219

6. First Report of Eutypa lata Causing Dieback of Grapevines (Vitis vinifera) in Chile

Author:
Lolas, Mauricio A.; Castro, Alvaro; Polanco, Rubén; Gainza-Cortés, Felipe; Ferrada, Enrique; Sosnowski, Mark R.; Díaz, Gonzalo A.
Source:
Plant disease 2020 v.104 no.7 pp. 2024
ISSN:
0191-2917
Subject:
microbial genetic resources,   etc   ; Basidiomycota; DNA; Diplodia seriata; Eutypa lata; Phaeoacremonium chlamydospora; Vitis vinifera; canes; conidia; conidiomata; cultivars; culture media; dieback; ethanol; fungi; internal transcribed spacers; lactic acid; leaves; longevity; mycelium; necrosis; pathogenicity; pathogens; pruning; staining; streptomycin; tetracycline; tubulin; vines; vineyards; winemaking; wood; Chile;     Show all 33 Subjects
Abstract:
... Grapevine trunk diseases (GTDs) are becoming the main limiting factor for high-quality wine production in Chile, decreasing vineyard yield and longevity. Diplodia seriata, Phaeomoniella chlamydospora, and Basidiomycetes are the main fungi associated with GTDs in Chile; Eutypa lata, which causes Eutypa dieback, has not been reported (Díaz et al. 2013). In January 2016 and December 2017, several cor ...
DOI:
10.1094/PDIS-12-19-2531-PDN

7. Temperature-sensitive cytoophidium assembly in Schizosaccharomyces pombe

Author:
Zhang, Jing; Liu, Ji-Long
Source:
Journal of genetics and genomics 2019 v.46 no.9 pp. 423-432
ISSN:
1673-8527
Subject:
microbial genetics,   etc   ; Schizosaccharomyces pombe; bacteria; cold stress; cytidine triphosphate synthetases; fruit flies; heat shock proteins; heat stress; mammals; models; temperature; yeasts;     Show all 12 Subjects
Abstract:
... The metabolic enzyme CTP synthase (CTPS) is able to compartmentalize into filaments, termed cytoophidia, in a variety of organisms including bacteria, budding yeast, fission yeast, fruit flies and mammals. A previous study in budding yeast shows that the filament-forming process of CTPS is not sensitive to temperature shift. Here we study CTPS filamentation in the fission yeast Schizosaccharomyces ...
DOI:
10.1016/j.jgg.2019.09.002
PubMed:
31611173
PubMed Central:
PMC6868507

8. Combining Viral Genetics and Statistical Modeling to Improve HIV-1 Time-of-infection Estimation towards Enhanced Vaccine Efficacy Assessment

Author:
Rossenkhan, Raabya; Rolland, Morgane; Labuschagne, Jan P.L.; Ferreira, Roux-Cil; Magaret, Craig A.; Carpp, Lindsay N.; Matsen IV, Frederick A.; Huang, Yunda; Rudnicki, Erika E.; Zhang, Yuanyuan; Ndabambi, Nonkululeko; Logan, Murray; Holzman, Ted; Abrahams, Melissa-Rose; Anthony, Colin; Tovanabutra, Sodsai; Warth, Christopher; Botha, Gordon; Matten, David; Nitayaphan, Sorachai; Kibuuka, Hannah; Sawe, Fred K.; Chopera, Denis; Eller, Leigh Anne; Travers, Simon; Robb, Merlin L.; Williamson, Carolyn; Gilbert, Peter B.; Edlefsen, Paul T.
Source:
Viruses 2019 v.11 no.7
ISSN:
1999-4915
Subject:
microbial genetics,   etc   ; HIV infections; Human immunodeficiency virus 1; calibration; cohort studies; diagnostic techniques; monoclonal antibodies; mutation; phylogeny; prediction; regression analysis; sequence alignment; statistical models; vaccines; viral load; viruses;     Show all 16 Subjects
Abstract:
... Knowledge of the time of HIV-1 infection and the multiplicity of viruses that establish HIV-1 infection is crucial for the in-depth analysis of clinical prevention efficacy trial outcomes. Better estimation methods would improve the ability to characterize immunological and genetic sequence correlates of efficacy within preventive efficacy trials of HIV-1 vaccines and monoclonal antibodies. We dev ...
DOI:
10.3390/v11070607
PubMed:
31277299
PubMed Central:
PMC6669737

9. The Revival of the Battle between David and Goliath in the Enteric Viruses and Microbiota Struggle: Potential Implication for Celiac Disease

Author:
Lerner, Aaron; Ramesh, Ajay; Matthias, Torsten
Source:
Microorganisms 2019 v.7 no.6
ISSN:
2076-2607
Subject:
microbial genetics,   etc   ; Archaea; autoimmune diseases; bacteria; bacteriophages; celiac disease; community structure; digestive system; dysbiosis; eukaryotic cells; homeostasis; human diseases; humans; mechanism of action; microbial communities; therapeutics;     Show all 16 Subjects
Abstract:
... The human gut is inhabited by overcrowded prokaryotic communities, a major component of which is the virome, comprised of viruses, bacteriophages, archaea, eukaryotes and bacteria. The virome is required for luminal homeostasis and, by their lytic or synergic capacities, they can regulate the microbial community structure and activity. Dysbiosis is associated with numerous chronic human diseases. ...
DOI:
10.3390/microorganisms7060173
PubMed:
31207872
PubMed Central:
PMC6616392

10. Genetics is the logic of life (at least of mine)

Author:
Wickner, Reed B
Source:
FEMS yeast research 2018 v.19 no.1
ISSN:
1567-1364
Subject:
microbial genetics,   etc   ; genes; infectious diseases; medicine; nuclear magnetic resonance spectroscopy; population genetics; prions; structural biology; yeasts;     Show all 9 Subjects
Abstract:
... I retrace my path from math to medicine to biochemistry to yeast genetics, my focus on infectious diseases of yeast and finally prions. My discovery of yeast prions relied on my particular focus on the logical relations of non-chromosomal genetic elements and the chromosomal genes involved in their propagation and expression. Pursuing an understanding of yeast prions involved structural biology ba ...
DOI:
10.1093/femsyr/foy115
PubMed:
30329039
PubMed Central:
PMC6238109

11. Testing sampling effort and relative abundance descriptors of belowground ectomycorrhizal fungi in a UK planted scots pine woodland

Author:
Villarreal-Ruiz, Luis; Neri-Luna, Cecilia
Source:
Mycology 2018 v.9 no.2 pp. 106-115
ISSN:
2150-1211
Subject:
microbial genetics,   etc   ; Cortinarius; Pinus sylvestris; biodiversity; ectomycorrhizae; fungal communities; mycorrhizal fungi; root tips; soil; woodlands; Scotland;     Show all 11 Subjects
Abstract:
... The native Caledonian pinewoods of Scotland, UK contain a unique and unexplored biodiversity of below-ground ectomycorrhizal fungi which may constitute a valuable source of microbial genetics resources for woodland restoration. In this study we test the sampling effort, taxa detection (ectomycorrhiza morpho-anatotyping) and relative abundance measurements (ectomycorrhizal root tip number vs. dry w ...
DOI:
10.1080/21501203.2017.1394393
PubMed:
30123666
PubMed Central:
PMC6059046

12. Thinking Outside the Cell: Replicating Replication In Vitro

Author:
Aguilar, Rhiannon R.; Tyler, Jessica K.
Source:
Molecular cell 2017 v.65 no.1 pp. 5-7
ISSN:
1097-2765
Subject:
microbial genetics,   etc   ; DNA replication; Saccharomyces cerevisiae; chromatin; yeasts;     Show all 5 Subjects
Abstract:
... Benchmark studies by Yeeles et al. (2017), Kurat et al. (2017), and Devbhandari et al. (2017) have reconstituted rapid and regulated budding yeast DNA replication on naked and chromatinized templates in vitro, providing key insights into this fundamentally important process. ...
DOI:
10.1016/j.molcel.2016.12.019
PubMed:
28061333
PubMed Central:
PMC5859927

13. Co-circulation dynamics and persistence of newly introduced clades of 2012 outbreak associated West Nile Virus in Texas, 2012–2015

Author:
Aroh, Chukwuemika; Liang, Chaoying; Raj, Prithvi; Wakeland, Benjamin; Yan, Nan; Wakeland, Edward
Source:
Infection, genetics, and evolution 2018 v.66 pp. 13-17
ISSN:
1567-1348
Subject:
microbial genetics,   etc   ; Culicidae; West Nile fever; West Nile virus; genome; genotype; mutation; niches; overwintering; summer; New York; Texas;     Show all 12 Subjects
Abstract:
... The second largest outbreak of West Nile encephalitis and West Nile fever ever recorded occurred in the United States (U.S) in the summer of 2012. The outbreak was related to the widespread circulation of closely related clades, or groups, of West Nile virus (WNV) into multiple states where they were not previously found. Whether the invading 2012 strains were able to circulate and overwinter in s ...
DOI:
10.1016/j.meegid.2018.08.025

14. Multiple introductions of dengue virus strains contribute to dengue outbreaks in East Kalimantan, Indonesia, in 2015–2016

Author:
Sasmono, R. Tedjo; Kalalo, Lily Pertiwi; Trismiasih, Suryani; Denis, Dionisius; Yohan, Benediktus; Hayati, Rahma F.; Haryanto, Sotianingsih
Source:
Virology journal 2019 v.16 no.1 pp. 93
ISSN:
1743-422X
Subject:
microbial genetics,   etc   ; Dengue virus; antibody detection; antigens; cities; dengue hemorrhagic fever; genotype; herd immunity; immunoglobulin G; immunoglobulin M; nucleic acids; nucleotide sequences; patients; phylogeny; reverse transcriptase polymerase chain reaction; serology; serotypes; subtropics; virology; viruses; Borneo; Indonesia;     Show all 22 Subjects
Abstract:
... BACKGROUND: Dengue fever is a febrile disease caused by dengue virus (DENV), which affects people throughout the tropical and subtropical regions of the world, including Indonesia. East Kalimantan (Borneo) province suffered a dramatic increase in dengue cases in 2015 and 2016, making it the province with the second highest incidence of dengue in Indonesia. Despite this, dengue in East Kalimantan i ...
DOI:
10.1186/s12985-019-1202-0
PubMed:
31345242
PubMed Central:
PMC6659258

15. A Comparative Metagenomics Study on Gastrointestinal Microbiota in Amphibious Mudskippers and Other Vertebrate Animals

Author:
Yi, Yunhai; Liang, Lifeng; Wang, Zhilin; Ai, Peng; You, Xinxin; Bian, Chao; Shi, Qiong; Dong, Bo
Source:
Animals 2019 v.9 no.9
ISSN:
2076-2615
Subject:
microbial genetic resources,   etc   ; Bacteroidetes; Ctenopharyngodon idella; Cyanobacteria; Firmicutes; Fusobacteria; Photobacterium; amphibians; aquaculture; bacteria; carnivores; freshwater; gastrointestinal system; genes; habitats; herbivorous fish; high-throughput nucleotide sequencing; hosts; intestinal microorganisms; metagenomics; microbial communities; microbiome; omnivores; pathogens; surveys;     Show all 25 Subjects
Abstract:
... Gut microbiomes in various fish species were widely investigated with the rapid development of next-generation sequencing technologies. However, little is known about gastrointestinal (GI) microbial communities in mudskippers, a representative group of marine amphibious fishes, and their comparisons with other vertebrate animals from different habitats. Here, we performed a comprehensive analysis ...
DOI:
10.3390/ani9090660
PubMed:
31489883
PubMed Central:
PMC6769816

16. Regulations governing the multicellular lifestyle of Myxococcus xanthus

Author:
Mercier, Romain; Mignot, Tâm
Source:
Current opinion in microbiology 2016 v.34 pp. 104-110
ISSN:
1369-5274
Subject:
microbial genetics,   etc   ; Myxococcus xanthus; bacteria; bacterial motility; fruiting bodies; spores;     Show all 6 Subjects
Abstract:
... In living organisms, cooperative cell movements underlie the formation of differentiated tissues. In bacteria, Myxococcus xanthus uses cooperative group movements, to predate on prey and to form multicellular fruiting bodies, where the cells differentiate into dormant spores. Motility is controlled by a central signaling Che-like pathway, Frz. Single cell studies indicate Frz regulates the frequen ...
DOI:
10.1016/j.mib.2016.08.009

17. The quest for the minimal bacterial genome

Author:
Martínez-García, Esteban; de Lorenzo, Víctor
Source:
Current opinion in biotechnology 2016 v.42 pp. 216-224
ISSN:
0958-1669
Subject:
microbial genetics,   etc   ; DNA; bacteria; chromosomes; genes; nucleotide sequences;     Show all 6 Subjects
Abstract:
... The onset of techniques for both editing extant bacterial chromosomes and synthesizing long DNA sequences has enabled addressing the question on the smallest set of genes and biological functions that are required for running an operative cell. But this is not only a fundamental scientific endeavour: simpler genomes could be easier to understand and eventually reprogram for the sake of diverse app ...
DOI:
10.1016/j.copbio.2016.09.001

18. Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution

Author:
Corel, Eduardo; Lopez, Philippe; Méheust, Raphaël; Bapteste, Eric
Source:
Trends in microbiology 2016 v.24 no.3 pp. 224-237
ISSN:
0966-842X
Subject:
microbial genetics,   etc   ; data collection; evolution; gene transfer; genes; microorganisms; models;     Show all 7 Subjects
Abstract:
... The tree model and tree-based methods have played a major, fruitful role in evolutionary studies. However, with the increasing realization of the quantitative and qualitative importance of reticulate evolutionary processes, affecting all levels of biological organization, complementary network-based models and methods are now flourishing, inviting evolutionary biology to experience a network-think ...
DOI:
10.1016/j.tim.2015.12.003
PubMed:
26774999
PubMed Central:
PMC4766943

19. A journey through the microscopic ages of DNA replication

Author:
Reinhart, Marius; Cardoso, M. Cristina
Source:
Protoplasma 2017 v.254 no.3 pp. 1151-1162
ISSN:
0033-183X
Subject:
microbial genetics,   etc   ; DNA; DNA replication; digital images; fluorescence microscopy; image analysis;     Show all 6 Subjects
Abstract:
... Scientific discoveries and technological advancements are inseparable but not always take place in a coherent chronological manner. In the next, we will provide a seemingly unconnected and serendipitous series of scientific facts that, in the whole, converged to unveil DNA and its duplication. We will not cover here the many and fundamental contributions from microbial genetics and in vitro bioche ...
DOI:
10.1007/s00709-016-1058-8
PubMed:
27943022
PubMed Central:
PMC5376393

20. A genetic screen for plant mutants with altered nodulation phenotypes in response to rhizobial glycan mutants

Author:
Liu, Huijun; Sandal, Niels; Andersen, Kasper R.; James, Euan K.; Stougaard, Jens; Kelly, Simon; Kawaharada, Yasuyuki
Source:
Thenew phytologist 2018 v.220 no.2 pp. 526-538
ISSN:
0028-646X
Subject:
microbial genetics,   etc   ; Lotus; Mesorhizobium loti; alanine; alleles; chromosome mapping; cytokinins; ethylene production; gain-of-function mutation; mutants; nitrogen fixation; nodulation; organogenesis; phenotype; plant response; polysaccharides; valine;     Show all 17 Subjects
Abstract:
... Nodule primordia induced by rhizobial glycan mutants often remain uninfected. To identify processes involved in infection and organogenesis we used forward genetics to identify plant genes involved in perception and responses to bacterial glycans. To dissect the mechanisms underlying the negative plant responses to the Mesorhizobium loti R7AexoU and ML001cep mutants, a screen for genetic suppresso ...
DOI:
10.1111/nph.15293