scholarly journals Large-scale comparative genomics unravels great genomic diversity across the Rickettsia and Ca. Megaira genera and identifies Torix group as an evolutionarily distinct clade.

2021 ◽  
Author(s):  
Helen Rebecca Davison ◽  
Jack Pilgrim ◽  
Nicky Wybouw ◽  
Joseph Parker ◽  
Stacy Pirro ◽  
...  
Keyword(s):  
Large Scale ◽  
Spotted Fever ◽  
Pentose Phosphate ◽  
Tsetse Fly ◽  
Genomic Diversity ◽  
Gene Marker ◽  
Metabolic Potential ◽  
Host Interactions ◽  
Glossina Morsitans Submorsitans ◽  
Transitional Group

Rickettsia are intracellular bacteria originally described as arthropod borne pathogens that are emerging as a diverse group of often biologically important, non-pathogenic symbionts of invertebrates and microeukaryotes. However, sparse genomic resources for symbiotic strains and for the sister genus (Candidatus Megaira) inhibit our understanding of Rickettsia evolution and biology. Here, we present the first closed genomes of Ca. Megaira from an alga (Mesostigma viride), and Torix Rickettsia from midge (Culicoides impunctatus) and bed bug (Cimex lectularius) hosts. Additionally, we sequenced and constructed draft genomes for Ca. Megaira from another alga (Carteria cerasiformis), Transitional group Rickettsia from tsetse fly (Glossina morsitans submorsitans), and Torix Rickettsia from a spider mite (Bryobia graminum). We further extract 22 draft genomes from arthropod genome sequencing projects, including 1 Adalia, 4 Transitional, 1 Spotted Fever, 7 Torix, 7 Belli and the first Rhyzobius and Meloidae Rickettsia group genomes. We used new and existing Rickettsia genomes to estimate the phylogeny and metabolic potential across groups and reveal transitions in genomic properties. These data reveal Torix as unique amongst currently described Rickettsia, with highly distinct and diverse accessory genomes. We confirm the presence of a third subclade of Torix, previously only known from gene marker sequences. Further, Torix share an intact pentose phosphate pathway with Ca. Megaira, not observed in other Rickettsia. Considering the distinctness and diversity of Torix, we propose that the group be named Candidatus Tisiphia. The wide host range of Ca. Tisiphia symbionts necessitates onward research to understand the biological and physiological bases of Ca. Tisiphia-host interactions.

scholarly journals 337 Metabolic Foundations of Microbiota-Host Interactions

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 69-69
Author(s):  
Dylan Dodd
Keyword(s):  
Gastrointestinal Tract ◽  
Gut Microbiota ◽  
Small Molecules ◽  
Recent Work ◽  
Mechanistic Studies ◽  
Therapeutic Approaches ◽  
Dense Population ◽  
Metabolic Potential ◽  
Host Interactions ◽  
New Therapeutic Approaches

Abstract The gastrointestinal tract of mammals is home to a dense population of microbes which influence host physiology and health. One of the most concrete ways that the gut microbiota impacts host biology is through the production of hundreds of chemically diverse small molecules. These molecules are absorbed into the bloodstream, where they reach concentrations similar to those achieved by pharmaceuticals and bind host receptors leading to changes in cellular and organ physiology. Here I will summarize recent work from our group and others that show how microbially sourced metabolites alter health and physiology of the host. I will also discuss how mechanistic studies of small molecules from the microbiota are enabling new therapeutic approaches to harness the metabolic potential of the gut microbiota.

Spotted Fever and Transitional Group Rickettsioses

2011 ◽  
pp. 1038-1045.e1 ◽  
Author(s):  
Megan E. Reller ◽  
J. Stephen Dumler
Keyword(s):  
Spotted Fever ◽  
Transitional Group

scholarly journals System-Based Approaches to Delineate the Antiviral Innate Immune Landscape

Viruses ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 1196
Author(s):  
Karsten Krey ◽  
Aleksandra W. Babnis ◽  
Andreas Pichlmair
Keyword(s):  
Large Scale ◽  
Innate Immune ◽  
Host Interactions ◽  
Interferon Stimulated Genes ◽  
Cellular Processes ◽  
Virus Inhibition ◽  
Cellular Factors ◽  
Functional Factors ◽  
Infected Cells ◽  
Screening Approaches

Viruses pose substantial challenges for society, economy, healthcare systems, and research. Their distinctive pathologies are based on specific interactions with cellular factors. In order to develop new antiviral treatments, it is of central importance to understand how viruses interact with their host and how infected cells react to the virus on a molecular level. Invading viruses are commonly sensed by components of the innate immune system, which is composed of a highly effective yet complex network of proteins that, in most cases, mediate efficient virus inhibition. Central to this process is the activity of interferons and other cytokines that coordinate the antiviral response. So far, numerous methods have been used to identify how viruses interact with cellular processes and revealed that the innate immune response is highly complex and involves interferon-stimulated genes and their binding partners as functional factors. Novel approaches and careful experimental design, combined with large-scale, high-throughput methods and cutting-edge analysis pipelines, have to be utilized to delineate the antiviral innate immune landscape at a global level. In this review, we describe different currently used screening approaches, how they contributed to our knowledge on virus–host interactions, and essential considerations that have to be taken into account when planning such experiments.

VI. Genome Structure and Cognitive Map of Williams Syndrome

2000 ◽  
Vol 12 (supplement 1) ◽  
pp. 89-107 ◽  
Author(s):  
Julie R. Korenberg ◽  
Xiao-Ning Chen ◽  
Hamao Hirota ◽  
Zona Lai ◽  
Ursula Bellugi ◽  
...  
Keyword(s):  
Williams Syndrome ◽  
Large Scale ◽  
Hot Spot ◽  
Genome Structure ◽  
Single Copy ◽  
Human Cognition ◽  
Chromosome Band ◽  
Gene Marker ◽  
Artificial Chromosomes ◽  
Visual Spatial

Williams syndrome (WMS) is a most compelling model of human cognition, of human genome organization, and of evolution. Due to a deletion in chromosome band 7q11.23, subjects have cardiovascular, connective tissue, and neurode-velopmental deficits. Given the striking peaks and valleys in neurocognition including deficits in visual-spatial and global processing, preserved language and face processing, hypersociability, and heightened affect, the goal of this work has been to identify the genes that are responsible, the cause of the deletion, and its origin in primate evolution. To do this, we have generated an integrated physical, genetic, and transcriptional map of the WMS and flanking regions using multicolor metaphase and interphase fluorescence in situ hybridization (FISH) of bacterial artificial chromosomes (BACs) and P1 artificial chromosomes (PACs), BAC end sequencing, PCR gene marker and microsatellite, large-scale sequencing, cDNA library, and database analyses. The results indicate the genomic organization of the WMS region as two nested duplicated regions flanking a largely single-copy region. There are at least two common deletion breakpoints, one in the centromeric and at least two in the telomeric repeated regions. Clones anchoring the unique to the repeated regions are defined along with three new pseudogene families. Primate studies indicate an evolutionary hot spot for chromosomal inversion in the WMS region. A cognitive phenotypic map of WMS is presented, which combines previous data with five further WMS subjects and three atypical WMS subjects with deletions; two larger (deleted for D7S489L) and one smaller, deleted for genes telomeric to FZD9, through LIMK1, but not WSCR1 or telomeric. The results establish regions and consequent gene candidates for WMS features including mental retardation, hypersociability, and facial features. The approach provides the basis for defining pathways linking genetic underpinnings with the neuroanatomical, functional, and behavioral consequences that result in human cognition.

Genetics of the tsetse fly Glossina morsitans submorsitans Newstead (Diptera: Glossinidae): further mapping of linkage groups I, II, and III

1999 ◽  
Vol 77 (8) ◽  
pp. 1309-1313 ◽  
Author(s):  
R H Gooding ◽  
C M Challoner
Keyword(s):  
Linkage Group ◽  
X Chromosome ◽  
Aldehyde Oxidase ◽  
Female Offspring ◽  
Tsetse Fly ◽  
Glossina Morsitans ◽  
Group Iii ◽  
Glossina Morsitans Submorsitans ◽  
Group I ◽  
Group Ii

Standard mapping procedures were used to map four loci in linkage group I (the X chromosome), two loci in linkage group II, and two loci in linkage group III of Glossina morsitans submorsitans. In the presence of the allele Srd (the distorter allele favoring production of female offspring), no recombination occurred between any of the following loci: Pgm (phosphoglucomutase), wht (white eye color), Est-X (a thoracic esterase), and Sr (sex-ratio distortion). However, in the absence of Srd (i.e., in females homozygous for Srn, the allele that permits males to sire both female and male offspring in approximately equal numbers), the loci Pgm and wht were separated by 23 ± 4.0% recombination (map distance). These results indicate that ourG. m. submorsitans strains carry two forms of the X chromosome, designated XA and XB. In support of this interpretation, two lines of G. m. submorsitans were established: in both lines, males with wild-type eyes sired families that were almost exclusively female, while males with white eyes sired families having males and females in approximately equal numbers. Two loci, Ao (aldehyde oxidase) and Est-1 (a thoracic esterase) were separated by 6.1 ± 2.3% recombination in linkage group II, and two loci, Mdh (malate dehydrogenase) and Pgi (phosphoglucose isomerase), showed 51.9 ± 4.9% recombination in linkage group III.

Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity

2001 ◽  
Vol 311 (1) ◽  
pp. 17-40 ◽  
Author(s):  
Marion L Carroll ◽  
Astrid M Roy-Engel ◽  
Son V Nguyen ◽  
Abdel-Halim Salem ◽  
Erika Vogel ◽  
...  
Keyword(s):  
Large Scale ◽  
Genomic Diversity ◽  
Scale Analysis ◽  
Large Scale Analysis ◽  
Human Genomic

scholarly journals Resolving the structure of phage-bacteria interactions in the context of natural diversity

2021 ◽  
Author(s):  
Kathryn M Kauffman ◽  
William K Chang ◽  
Julia M Brown ◽  
Fatima Aysha Hussain ◽  
Joy Y Yang ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Host Range ◽  
Large Scale ◽  
Genomic Diversity ◽  
Interaction Networks ◽  
Bacterial Strains ◽  
Quantitative Estimates ◽  
Phage Evolution ◽  
Marine Vibrio ◽  
In The Wild

Microbial communities are shaped by viral predators. Yet, resolving which viruses (phages) and bacteria are interacting is a major challenge in the context of natural levels of microbial diversity. Thus, fundamental features of how phage-bacteria interactions are structured and evolve in "the wild" remain poorly resolved. Here we use large-scale isolation of environmental marine Vibrio bacteria and their phages to obtain quantitative estimates of strain-level phage predator loads, and use all-by-all host range assays to discover how phage and host genomic diversity shape interactions. We show that killing in environmental interaction networks is sparse - with phage predator loads low for most bacterial strains and phages host-strain-specific in their killing. Paradoxically, we also find that although overlap in killing is generally rare between phages, recombination is common. Together, these results indicate that the number of hosts that phages infect is often larger than the number that they kill and suggest that recombination during cryptic co-infections is an important mode of phage evolution in microbial communities. In the development of phages for bioengineering and therapeutics it will be important to consider that nucleic acids of introduced phages may spread into local phage populations through recombination, and that the likelihood of transfer is not predictable based on killing host range.

scholarly journals Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta)

2017 ◽  
Author(s):  
Matthew Parks ◽  
Teofil Nakov ◽  
Elizabeth Ruck ◽  
Norman J. Wickett ◽  
Andrew J. Alverson
Keyword(s):  
Whole Genome Duplication ◽  
Large Scale ◽  
Genome Duplication ◽  
Gene Tree ◽  
Genomic Diversity ◽  
Phylogenomic Analysis ◽  
Whole Genome ◽  
Gene Trees ◽  
Angiosperm Evolution ◽  
Polyploid Formation

ABSTRACTPremise of the studyDiatoms are one of the most species-rich lineages of microbial eukaryotes. Similarities in clade age, species richness, and contributions to primary production motivate comparisons to flowering plants, whose genomes have been inordinately shaped by whole genome duplication (WGD). These events that have been linked to speciation and increased rates of lineage diversification, identifying WGDs as a principal driver of angiosperm evolution. We synthesized a relatively large but scattered body of evidence that, taken together, suggests that polyploidy may be common in diatoms.MethodsWe used data from gene counts, gene trees, and patterns of synonymous divergence to carry out the first large-scale phylogenomic analysis of genome-scale duplication histories for a phylogenetically diverse set of 37 diatom taxa.Key resultsSeveral methods identified WGD events of varying age across diatoms, though determining the exact number and placement of events and, more broadly, inferences of WGD at all, were greatly impacted by gene-tree uncertainty. Gene-tree reconciliations supported allopolyploidy as the predominant mode of polyploid formation, with particularly strong evidence for ancient allopolyploid events in the thalassiosiroid and pennate diatom clades.ConclusionsWhole genome duplication appears to have been an important driver of genome evolution in diatoms. Denser taxon sampling will better pinpoint the timing of WGDs and likely reveal many more of them. We outline potential challenges in reconstructing paleopolyploid events in diatoms that, together with these results, offer a framework for understanding the evolutionary roles of genome duplication in a group that likely harbors substantial genomic diversity.

scholarly journals Apparent density, trypanosome infection rates and host preference of tsetse flies in the sleeping sickness endemic focus of Northwestern Uganda

2020 ◽  
Author(s):  
Robert Opiro ◽  
Robert Opoke ◽  
Harriet Angwech ◽  
Esther Nakafu ◽  
Francis A. Oloya ◽  
...  
Keyword(s):  
Infection Rate ◽  
Apparent Density ◽  
Blood Meal ◽  
Nested Pcr ◽  
Large Scale ◽  
Tsetse Fly ◽  
Tsetse Flies ◽  
Trypanosome Species ◽  
Infection Rates ◽  
Monitor Lizard

Abstract Background: African trypanosomiasis, caused by protozoa of the genus Trypanosoma and transmitted by the tsetse fly, is a serious parasitic disease of humans and animals. Reliable data on the vector distribution, feeding preference and the trypanosome species they carry is pertinent to planning sustainable control strategies.Methodology: We deployed 109 biconical traps in 10 villages in two districts of northwestern Uganda to obtain information on the apparent density, infection rates and blood meal sources of tsetse flies. A subset (272) of the collected samples was analyzed for detection of trypanosomes species and sub-species using a nested PCR protocol based on primers amplifying the Internal Transcribed Spacer (ITS) region of ribosomal DNA. 34 blood-engorged adult tsetse midguts were analyzed for blood meal sources by sequencing of the mitochondrial cytochrome c oxidase 1 (COI) and cytochrome b (cytb) genes. Results: Out of the 109 traps deployed, we captured 622 Glossina fuscipes fuscipes tsetse flies (269 males and 353 females). Apparent density (AD) ranged from 0.6 to 3.7 flies/trap/day in the two districts. 29 (10.7%) of the flies were infected with one or more trypanosome species. Infection rate was not significantly associated with neither age group (χ2 = 5.001, df=2, 0.082), sex of the fly (χ2 = 0.099, df = 1, p = 0.753), district of origin (χ2= 0.629, df = 1, p = 0.428) nor village (χ2= 9.252, df = 9, p = 0.414). Nested PCR revealed several species of trypanosomes: T. vivax (6.62%), T. congolense (2.57%), and T. brucei and T. simiae each at 0.73%. Blood meal analyses revealed five principal vertebrate hosts, namely, cattle (Bos taurus), humans (Homo sapiens), Nile monitor lizard (Varanus niloticus), African mud turtle (Pelusio schapini) and the African Savanna elephant (Loxodonta africana).Conclusion: We found a moderately high infection rate of 10.78%, with all infections attributed to trypanosome species that are causative agents for the animal disease only. However, more validation using large-scale passive and active screening of human and tsetse samples should be done. Cattle and humans appear to be the most important tsetse hosts in the region and should be considered in the design of interventions.

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