scholarly journals Gene- and genome-centric dynamics shape the diversity of oral bacterial populations

2021 ◽  
Author(s):  
Daniel R Utter ◽  
Colleen M Cavanaugh ◽  
Gary G Borisy
Keyword(s):  
Dominant Mode ◽  
Oral Microbiota ◽  
Evolutionary Mechanisms ◽  
Bacterial Populations ◽  
Genome Wide ◽  
Gene Level ◽  
Sampling Window ◽  
Total Community ◽  
High Level ◽  
Longitudinal Sampling

Two major viewpoints have been put forward for how microbes adapt to a niche, differing in whether adaptation is driven principally by gene-centric or genome-centric processes. Longitudinal sampling at microbially-relevant timescales, i.e., days to weeks, is critical for distinguishing these mechanisms. Because of its significance for both microbial ecology and human health and its accessibility and high level of curation, we used the oral microbiota to evaluate evolutionary mechanisms. Metagenomes were generated by shotgun sequencing of total community DNA from the healthy tongues of 17 volunteers at four to seven timepoints obtained over intervals of days to weeks. We obtained 390 high-quality metagenome-assembled genomes (MAGs) defining population genomes from 55 genera, the majority of which were temporally stable at the MAG level. Decomposing MAG-defined populations by single nucleotide variant frequencies revealed MAGs were composed of up to 5 haplotypes, putatively distinct strain- or subpopulation-level genotypes. Most haplotypes were stable over time, yet we found examples of individual haplotypes sweeping from low abundance to dominance in a population over a period of days, a pattern suggestive of genome-centric adaptation. At the gene level, the vast majority of genes in each MAG were tightly linked over the two-week sampling window based on their frequency in the metagenomes of different mouths. The few genes that changed in abundance independently from nearby genes did not change in a directional manner, nor did nonsynonymous codon variants within such genes. Altogether, these observations characterize the intrapopulation genomic dynamics of the oral microbiota at microbially-relevant timescales. Our results demonstrate that both gene- and genome-wide sweeps occur on daily timescales but likely with different ecological ramifications. We infer that genome-wide selection of ecotypes is the dominant mode of adaptation in the oral populations, with short-term changes in gene frequency also occurring.

scholarly journals Humans and other commonly used model organisms are resistant to cycloheximide-mediated biases in ribosome profiling experiments

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Puneet Sharma ◽  
Jie Wu ◽  
Benedikt S. Nilges ◽  
Sebastian A. Leidel
Keyword(s):  
Human Cells ◽  
Ribosome Profiling ◽  
Model Organisms ◽  
Treatment Conditions ◽  
Genome Wide ◽  
Optimized Protocol ◽  
Gene Level ◽  
Translation Inhibitor ◽  
Species Specific ◽  
Conformational Restrictions

AbstractRibosome profiling measures genome-wide translation dynamics at sub-codon resolution. Cycloheximide (CHX), a widely used translation inhibitor to arrest ribosomes in these experiments, has been shown to induce biases in yeast, questioning its use. However, whether such biases are present in datasets of other organisms including humans is unknown. Here we compare different CHX-treatment conditions in human cells and yeast in parallel experiments using an optimized protocol. We find that human ribosomes are not susceptible to conformational restrictions by CHX, nor does it distort gene-level measurements of ribosome occupancy, measured decoding speed or the translational ramp. Furthermore, CHX-induced codon-specific biases on ribosome occupancy are not detectable in human cells or other model organisms. This shows that reported biases of CHX are species-specific and that CHX does not affect the outcome of ribosome profiling experiments in most settings. Our findings provide a solid framework to conduct and analyze ribosome profiling experiments.

scholarly journals Among the shapeshifters: parasite-induced morphologies in ants (Hymenoptera, Formicidae) and their relevance within the EcoEvoDevo framework

EvoDevo ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Alice Laciny
Keyword(s):  
Social Insects ◽  
Morphological Changes ◽  
Evolutionary Developmental Biology ◽  
Caste Differentiation ◽  
Natural Experiments ◽  
Evolutionary Mechanisms ◽  
Open Questions ◽  
Caste Evolution ◽  
High Level ◽  
Host Development

AbstractAs social insects, ants represent extremely interaction-rich biological systems shaped by tightly integrated social structures and constant mutual exchange with a multitude of internal and external environmental factors. Due to this high level of ecological interconnection, ant colonies can harbour a diverse array of parasites and pathogens, many of which are known to interfere with the delicate processes of ontogeny and caste differentiation and induce phenotypic changes in their hosts. Despite their often striking nature, parasite-induced changes to host development and morphology have hitherto been largely overlooked in the context of ecological evolutionary developmental biology (EcoEvoDevo). Parasitogenic morphologies in ants can, however, serve as “natural experiments” that may shed light on mechanisms and pathways relevant to host development, plasticity or robustness under environmental perturbations, colony-level effects and caste evolution. By assessing case studies of parasites causing morphological changes in their ant hosts, from the eighteenth century to current research, this review article presents a first overview of relevant host and parasite taxa. Hypotheses about the underlying developmental and evolutionary mechanisms, and open questions for further research are discussed. This will contribute towards highlighting the importance of parasites of social insects for both biological theory and empirical research and facilitate future interdisciplinary work at the interface of myrmecology, parasitology, and the EcoEvoDevo framework.

scholarly journals Coex-Rank: An approach incorporating co-expression information for combined analysis of microarray data

2012 ◽  
Vol 9 (1) ◽  
pp. 32-43 ◽  
Author(s):  
Jinlu Cai ◽  
Henry L. Keen ◽  
Curt D. Sigmund ◽  
Thomas L. Casavant
Keyword(s):  
Microarray Data ◽  
Statistical Power ◽  
Meta Analysis ◽  
Rank Aggregation ◽  
Microarray Data Analysis ◽  
Combined Approach ◽  
Linear Modeling ◽  
Modeling Process ◽  
Genome Wide ◽  
Gene Level

Summary Microarrays have been widely used to study differential gene expression at the genomic level. They can also provide genome-wide co-expression information. Biologically related datasets from independent studies are publicly available, which requires robust combined approaches for integration and validation. Previously, meta-analysis has been adopted to solve this problem.As an alternative to meta-analysis, for microarray data with high similarity in biological experimental design, a more direct combined approach is possible. Gene-level normalization across datasets is motivated by the different scale and distribution of data due to separate origins. However, there has been limited discussion about this point in the past. Here we describe a combined approach for microarray analysis, including gene-level normalization and Coex-Rank approach. After normalization, a linear modeling process is used to identify lists of differentially expressed genes. The Coex-Rank approach incorporates co-expression information into a rank-aggregation procedure. We applied this computational approach to our data, which illustrated an improvement in statistical power and a complementary advantage of the Coex-Rank approach from a biological perspective.Our combined approach for microarray data analysis (Coex-rank) is based on normalization, which is naturally driven. The Coex-rank process not only takes advantage of merging the power of multiple methods regarding normalization but also assists in the discovery of functional clusters of genes.

scholarly journals H3 K79 dimethylation marks developmental activation of the β-globin gene but is reduced upon LCR-mediated high-level transcription

Blood ◽  
2008 ◽  
Vol 112 (2) ◽  
pp. 406-414 ◽  
Author(s):  
Tomoyuki Sawado ◽  
Jessica Halow ◽  
Hogune Im ◽  
Tobias Ragoczy ◽  
Emery H. Bresnick ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcriptional Activation ◽  
Globin Gene ◽  
Erythroid Differentiation ◽  
Genome Wide ◽  
Activation Of Transcription ◽  
High Level ◽  
The Relationship ◽  
Mutant Genes ◽  
Gene Expression Levels

Abstract Genome-wide analyses of the relationship between H3 K79 dimethylation and transcription have revealed contradictory results. To clarify this relationship at a single locus, we analyzed expression and H3 K79 modification levels of wild-type (WT) and transcriptionally impaired β-globin mutant genes during erythroid differentiation. Analysis of fractionated erythroid cells derived from WT/Δ locus control region (LCR) heterozygous mice reveals no significant H3 K79 dimethylation of the β-globin gene on either allele prior to activation of transcription. Upon transcriptional activation, H3 K79 di-methylation is observed along both WT and ΔLCR alleles, and both alleles are located in proximity to H3 K79 dimethylation nuclear foci. However, H3 K79 di-methylation is significantly increased along the ΔLCR allele compared with the WT allele. In addition, analysis of a partial LCR deletion mutant reveals that H3 K79 dimethylation is inversely correlated with β-globin gene expression levels. Thus, while our results support a link between H3 K79 dimethylation and gene expression, high levels of this mark are not essential for high level β-globin gene transcription. We propose that H3 K79 dimethylation is destabilized on a highly transcribed template.

scholarly journals Genome-wide characterization and expression profiling of B3 superfamily during flower induction stage in pineapple (Ananas comosus L.)

2020 ◽  
Author(s):  
Cheng Cheng Ruan ◽  
Zhe Chen ◽  
Fu Chu Hu ◽  
Xiang He Wang ◽  
Li Jun Guo ◽  
...  
Keyword(s):  
Development Process ◽  
Purifying Selection ◽  
Ananas Comosus ◽  
Flower Bud ◽  
Genome Wide ◽  
Localization Analysis ◽  
Ethephon Treatment ◽  
High Level ◽  
Differentiation Period ◽  
Induction Stage

AbstractThe B3 superfamily is a plant-specific family, which involves in growth and development process. By now, the identification of B3 superfamily in pineapple (Ananas comosus) has not reported. In this study, 57 B3 genes were identified and further phylogenetically classified into five subfamilies, all genes contained B3 domain. Chromosomal localization analysis revealed that 54 of 57 AcB3 genes were located on 21 chromosomes.Collinearity analysis indicated that the segmental duplication was the main event in the evolution of B3 gene superfamily and most of them were under purifying selection. Moreover, there were 7 and 39 pairs of orthologous B3s were identified between pineapple and Arabidopsis or rice, respectively, which indicated the closer genetic relationship between pineapple and rice. Most genes had cis-element of abscisic acid, ethylene, MeJA, light, and abiotic stress. qRT-PCR showed that the expression level of most AcB3 genes were up-regulated within 1 d after ethephon treatment and expressed high level in flower bud differentiation period in stem apex. This study provide a comprehensive understanding of AcB3s and a basis for future molecular studies of ethephon induced pineapple flowering.

scholarly journals Death and population dynamics affect mutation rate estimates and evolvability under stress in bacteria

2017 ◽  
Author(s):  
Antoine Frénoy ◽  
Sebastian Bonhoeffer
Keyword(s):  
Population Dynamics ◽  
Mutation Rate ◽  
Death Rate ◽  
Mutation Rates ◽  
Resistance Mutations ◽  
Bacterial Populations ◽  
Plasmid Segregation ◽  
Genome Wide ◽  
Response To Stress ◽  
Induced Mutagenesis

AbstractThe stress-induced mutagenesis paradigm postulates that in response to stress, bacteria increase their genome-wide mutation rate, in turn increasing the chances that a descendant is able to withstand the stress. This has implications for antibiotic treatment: exposure to sub-inhibitory doses of antibiotics has been reported to increase bacterial mutation rates, and thus probably the rate at which resistance mutations appear and lead to treatment failure.Measuring mutation rates under stress, however, is problematic, because existing methods assume there is no death. Yet sub-inhibitory stress levels may induce a substantial death rate. Death events need to be compensated by extra replication to reach a given population size, thus giving more opportunities to acquire mutations. We show that ignoring death leads to a systematic overestimation of mutation rates under stress.We developed a system using plasmid segregation to measure death and growth rates simultaneously in bacterial populations. We use it to replicate classical experiments reporting antibiotic-induced mutagenesis. We found that a substantial death rate occurs at the tested sub-inhibitory concentrations, and taking this death into account lowers and sometimes removes the signal for stress-induced mutagenesis. Moreover even when antibiotics increase mutation rate, sub-inhibitory treatments do not increase genetic diversity and evolvability, again because of effects of the antibiotics on population dynamics.Beside showing that population dynamic is a crucial but neglected parameter affecting evolvability, we provide better experimental and computational tools to study evolvability under stress, leading to a re-assessment of the magnitude and significance of the stress-induced mutagenesis paradigm.

scholarly journals Capture-based enrichment of Theileria parva DNA enables full genome assembly of first buffalo-derived strain and reveals exceptional intra-specific genetic diversity

2020 ◽  
Author(s):  
Nicholas C Palmateer ◽  
Kyle Tretina ◽  
Joshua Orvis ◽  
Olukemi O Ifeonu ◽  
Jonathan Crabtree ◽  
...  
Keyword(s):  
Vaccine Development ◽  
De Novo ◽  
High Specificity ◽  
Theileria Parva ◽  
Nucleotide Polymorphisms ◽  
Specificity And Sensitivity ◽  
Genome Wide ◽  
Dna Capture ◽  
High Level ◽  
Genome Assemblies

AbstractTheileria parva is an economically important, intracellular, tick-transmitted parasite of cattle. A live vaccine against the parasite is effective against challenge from cattle-transmissible T. parva but not against genotypes originating from the African Cape buffalo, a major wildlife reservoir, prompting the need to characterize genome-wide variation within and between cattle- and buffalo-associated T. parva populations. Here, we describe a capture-based target enrichment approach that enables, for the first time, de novo assembly of nearly complete T. parva genomes derived from infected host cell lines. This approach has exceptionally high specificity and sensitivity and is successful for both cattle- and buffalo-derived T. parva parasites. De novo genome assemblies generated for cattle genotypes differ from the reference by ∼54K single nucleotide polymorphisms (SNPs) throughout the 8.31 Mb genome, an average of 6.5 SNPs/kb. We report the first buffalo-derived T. parva genome, which is larger than the genome from the reference, cattle-derived, Muguga strain. The average non-synonymous nucleotide diversity (πN) per gene, between buffalo-derived T. parva and the Muguga strain, was 1.3%. This remarkably high level of genetic divergence is supported by an average FST, genome-wide, of 0.44, reflecting a degree of genetic differentiation between cattle- and buffalo-derived T. parva parasites more commonly seen between, rather than within, species, with clear implications for vaccine development. The DNA capture approach used provides clear advantages over alternative T. parva DNA enrichment methods used previously and enables in-depth comparative genomics in this apicomplexan parasite.

scholarly journals Expression of the apoptosis-releated genes in patients with newly diagnosed chronic lymphocytic leukemia in clinical data context

2018 ◽  
Vol 17 (2) ◽  
pp. 41-46 ◽  
Author(s):  
S. G. Zakharov ◽  
A. K. Golenkov ◽  
A. V. Misyurin ◽  
E. V. Kataeva ◽  
A. A. Rudakova ◽  
...  
Keyword(s):  
Gene Expression ◽  
Clinical Manifestations ◽  
Multivariate Regression Analysis ◽  
Lymphocytic Leukemia ◽  
Newly Diagnosed ◽  
Expression Of Genes ◽  
Gene Level ◽  
Genes Encoding ◽  
Group Ii ◽  
High Level

Introduction.The given data of fundamental studies of apoptosis processes in B-cell lymphocytic leukemia (B-CLL) testifies about the complexity and variety of mechanisms affecting the kinetics of normal cells and tumor lymphocytes in this disease. It is important to study the severity of clinical manifestations of the disease depending on the expression of the genes that modulate apoptosis.The purposeof the study is to compare the activity of genes encoding apoptosis modulators, the cell cycle and cancer-testicular PRAME protein with clinical manifestations of the disease in primary patients with B-CLL.Materials and methods.The level of expression of the proapoptotic genes FAS, TRAIL, TNFR2, DR4/5 and DR3, as well as the HSP27, XIAP genes, blocking apoptosis was determined in 23 patients with newly diagnosed chronic B-CLL. In addition, expression of genes TP53 and P21 and cancer-testis gene PRAME are tested.Results.According to the multivariate regression analysis, the FAS gene expression in the onset of the disease had the greatest impact on the clinical characteristics of the disease. In this connection, the patients were divided into groups with normal (group) and low gene level (group II). A low level of FAS expression (Me 387 %) was associated with stage II disease (p = 0.03), a large number of lympho cytes (p = 0.001), fewer erythrocytes (p = 0.08), and a lower level of TNFR2 gene expression (p = 0.08), high level of expression of XIAP, HSP27, P21. Overall, the anti-apoptotic potential in Group II patients was higher, which was accompanied by more pronounced clinical manifestations of the disease.Conclusions.The increased anti-apoptotic potential of tumor lymphocytes in newly diagnosed B-CLL is accompanied by a larger tumor mass and greater clinical and hematological manifestation of the disease.

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