Tag: HGT

Whole mitochondrial and chloroplast genome sequencing of Tunisian date palm cultivars: diversity and evolutionary relationships | BMC Genomics

Johnson DV, Al-Khayri JM, Jain SM. Introduction: Date Production Status and Prospects in Africa and the Americas. In: Al-Khayri J, Jain S, Johnson D, editors. Date Palm Genetic Resources and Utilization: Volume 1: Africa and the Americas. Springer Netherlands, Dordrecht; 2015. p. 1–18. doi.org/10.1007/978-94-017-9694-1_1 Gros-Balthazard M, Hazzouri KM, Flowers JM. Genomic…

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Bioinformatics Analyst – Charlottesville, Virginia, United States

  Who would you like to share this job with? 11101fb9 Categories 2c89bb9c Categories 3c530996 Academic Advising / SupportAdministrationAdministrative / ClericalAdministrative ServicesAdvancementAgriculture / Life ScienceAgriculture and Animal HealthAlumni RelationsApplied Sciences and Natural ResourcesArchitecture / Construction / PlanningArchitecture / EngineeringAudit and FinanceBusiness / Accounting / FinanceCommunications / Public Relations / MarketingData…

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Tiny Vesicles Redefine Cell Communication

A new study has uncovered the vital role of extracellular vesicles in horizontal gene transfer among ocean microorganisms. This finding challenges existing beliefs about gene exchange mechanisms and introduces ‘protected extracellular DNA’ (peDNA) as a new term to encompass the diversity of genetic carriers beyond viruses, setting a new direction…

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Study show extracellular vesicles exchange genetic information between cells in the sea

For this study, the researchers from the Max Planck Institute in Bremen also collected water samples off the North Sea Island of Helgoland. Credit: Silvia Vidal, Max Planck Institute for Marine Microbiology Researchers led by Susanne Erdmann from the Max Planck Institute for Marine Microbiology in Bremen have looked at…

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How mitochondrial DNA exchange alter metabolic pathways?

Who said this: magnetic fields “can change the mitochondria in cells and enhance plant metabolism? 3 answers What pathway does mitochondrial dysfunction trigger to induce chondrocyte apoptosis? 5 answers What is physiological process oft mitochondrial biogenesis through estrogen? 5 answers Does physical inactivity affect the mitochondrial metabolism? 5 answers What…

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Can HGT introduce foreign mtDNA into an individual’s mitochondrial genome.

Step 1: Horizontal gene transfer (HGT) can introduce foreign mtDNA into an individual’s mitochondrial genome. This process has been observed in angiosperm plants, where foreign sequences, including those derived from plastids, have been identified in mitochondrial genomes. Additionally, evidence suggests that HGT can occur between parasitic plants and their hosts,…

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Unzipped chromosome-level genomes reveal allopolyploid nematode origin pattern as unreduced gamete hybridization

Nematode materials and species identification Mi, Mj, and Mg were collected from farmlands in Wuhan city of Hubei province, Longyan city of Fujian province, and Changsha city of Hunan Provinces, respectively. Two Ma samples were collected from farmlands in Shenyang city of Liaoning province and Shiping city of Yunnan province….

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Postdoctoral Research Fellow, Molecular Microbiology and Synthetic Biology job with MACQUARIE UNIVERSITY – SYDNEY AUSTRALIA

An exciting opportunity for a researcher exists in the School of Natural Sciences at Macquarie University. We are seeking a qualified Postdoctoral Research Fellow with Molecular Microbiology and Synthetic Biology experience to join a team with an international reputation for producing high quality research outcomes in these areas. This role…

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Extracellular vesicles are the main contributor to the non-viral protected extracellular sequence space

Viromics datasets represent the sequence space of protected extracellular DNA (peDNA) The majority of samples prepared for “viromics” include GTAs and EVs, in addition to virus particles. All three entities are small protein- and/or lipid-containing particles that can enclose cellular DNA [3] or were found to bind cellular DNA on…

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Research Scientist in Bioinformatics and Computational Genomics

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A fungal sesquiterpene biosynthesis gene cluster critical for mutualist-pathogen transition in Colletotrichum tofieldiae

A Ct strain severely inhibits plant growth in a nutrient-dependent manner A Ct strain, Ct61, isolated from a wild A. thaliana population in Spain, promotes plant growth under low Pi conditions by transferring phosphorus to the host3. In addition to Ct61, five different Ct strains have been isolated from various…

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Whole genome analysis and cold adaptation strategies of Pseudomonas sivasensis W-6 isolated from the Napahai plateau wetland

Growth conditions and identification The growth of the strain W-6 was measured at different temperatures of 4, 10, 15, 20, 25, 30, and 37 °C. It can be seen that strain W-6 could grow at the range from 4 to 30 °C with the optimal growth temperature 15 °C. Then, the growth curve of…

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A genome-wide association study of blood cell morphology identifies cellular proteins implicated in disease aetiology

INTERVAL study The INTERVAL study was a randomised trial of approximately 45,000 blood donors aged eighteen years or older who were recruited at 25 NHSBT (National Health Service Blood and Transplant) static donor centres across England21. The study was approved by the Cambridge East Research Ethics Committee and we complied…

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Characterization of the pig lower respiratory tract antibiotic resistome

Composition and distribution of ARGs in the pig lower respiratory tract microbiome Using 745 metagenome data of the lower respiratory tract microbiome from 675 experimental pigs across five populations, we constructed a swine respiratory microbial gene catalog containing 10,337,194 non-redundant genes. Of these, 1228 open reading frames (ORFs) were identified…

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Microorganisms | Free Full-Text | Whole Genome Sequencing and Pan-Genomic Analysis of Multidrug-Resistant Vibrio cholerae VC01 Isolated from a Clinical Sample

1. Introduction The pathogen Vibrio cholerae is widespread and has long coevolved with humans. It is the agent that causes cholera, a severe intestinal illness that can result in up to 140,000 fatalities and affects between 1 and 5 million people annually [1]. V. cholerae carries the cholera toxin and…

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Understanding the mechanisms behind rising antifungal drug resistance

In a recent study published in npj Antimicrobials and Resistance, researchers addressed the issue of the rise of antifungal drugs-resistant infections and the advent of multidrug-resistant fungal pathogens. In addition, they described the strategies used by fungal pathogens to evolve resistance and the mechanism(s) governing the same.  To this end,…

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hypervariable region of 16s rrna

The mock community was created from pure cultures, whose 16S rRNA genes were determined through Sanger sequencing to be >3% different (Table S1). Bartram, Andrea. WebWhile 16S hypervariable region analysis is a powerful tool for bacterial taxonomic studies, it struggles to differentiate between closely related species. Limited by sequencing Rarefaction…

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Incongruence in the phylogenomics era

Simpson, G. G. The Principles of Classification and a Classification of Mammals Vol. 85 (American Museum of Natural History, 1945). Jarvis, E. D. et al. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346, 1320–1331 (2014). Article  CAS  PubMed  PubMed Central  Google Scholar  Parks,…

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Plasmid Permissiveness of Wastewater Microbiomes can be Predicted from 16S rRNA Sequences by Machine Learning

Motivation: Wastewater Treatment Plants (WWTPs) harbor a dense and diverse microbial community. They constantly receive antimicrobial residues and resistant strains, and therefore provide conditions for Horizontal Gene Transfer (HGT) of antimicrobial resistance determinants. This facilitates the transmission of clinically important genes between, e.g., enteric and environmental bacteria, and vice versa….

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Complexity is a barrier to horizontal gene transfer, shows new study

Tests of the balance and connectivity hypotheses. Plots show the mean transferability (A–C) and effect of divergence on transferability (D–F), after first controlling for the effects of native expression level and COG functional category. Each point shows the deviation (i.e., residual) of each gene’s value from the expected value given…

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Barrier to Horizontal Gene Transfer: Complexity

The recognition of the phenomenon known as horizontal (or lateral) gene transfer (HGT/LGT) revolutionized our understanding of evolutionary mechanisms. Unlike the conventional vertical transmission of genes from parent to offspring, HGT involves the exchange of genetic material laterally, across species boundaries. This process is a major contributor to microbial evolution,…

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3c. You isolate all of the bacterial species present

Transcribed image text: 3c. You isolate all of the bacterial species present in your favorite local environment. After you sequence all of the 16S rRNA sequences present in this environment, how would creation of your phylogenetic tree be affected by this particular environment being highly mutagenic? How would this phylogenetic…

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Metagenome-based metabolic modelling predicts unique microbial interactions in deep-sea hydrothermal plume microbiomes

Design of this study In this study, we use 98 MAGs described previously from Guaymas Basin hydrothermal plumes (see Metagenomic datasets and model building in Methods) to understand metabolic interactions and evolution in hydrothermal systems (Refer Supplementary File S1 for the short name references used in this article). Both bacteria and archaea…

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Rickettsial DNA and a trans-splicing rRNA group I intron in the unorthodox mitogenome of the fern Haplopteris ensiformis

Our choice of the shoestring fern H. ensiformis as a leptosporangiate fern for complete assembly of both organelle genomes was based on pronounced variability in mitochondrial RNA editing and intron (co-)evolution in the monilophyte family Pteridaceae and the sub-family Vittarioideae in particular22. We used next-generation sequencing (NGS) data to assemble…

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Subspecies-level genome comparison of Lactobacillus delbrueckii

Genomic characteristics of L. delbrueckii Analysis of 31 L. delbrueckii genomes determined that this group has a genome size of 1.93 ± 0.16 Mb and a G + C content of 49.8 ± 0.4% (Table 1). The average genome size and G + C content across the Lactobacillus genus listed on GenBank were 1.96 Mb and 37.2%, respectively. This indicates…

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High-throughput microbial culturomics using automation and machine learning

Data-driven culturomics using phenotypes and automation Colony picking is a classic microbiology method for clonally isolating bacterial strains. Colony growth on plates depends on many factors, including the composition of the media (for example, available nutrients), atmospheric conditions (for example, level of oxygenation), presence of inhibitory molecules (for example, antibiotics),…

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ST7 becomes one of the most common S. aureus clones

Introduction Staphylococcus aureus (S. aureus), a major human opportunistic pathogen, can cause a variety of infectious diseases including skin and soft-tissue infections, bacteremia, ventilator-associated pneumonia and toxic shock syndrome.1,2 A rapid and proper administration of antibiotics is the most important means to inhibit S. aureus’ growth and prevent disease progression….

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Hypersaline Lake Urmia: a potential hotspot for microbial genomic variation

Physico-chemical features of Lake Urmia Sampling was performed during the period of lowest rainfall and input volume in the year when the lake water reached the highest salt concentration (locations shown in Fig. 1, Supplementary Table S1). The measured ionic composition of the collected brine showed the typical composition of halite-dominated…

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Genome-wide estimation of recombination, mutation and positive selection enlightens diversification drivers of Mycobacterium bovis

Global phylogenetic analysis A Maximum Likelihood (ML) phylogenetic tree based on the 69 M. bovis isolates and reference genome was obtained (Fig. 2A). This strategy allows the generation of a more robust tree, when comparing with single gene based trees or multi-locus based trees, that do not capture the variability across the…

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