The complex pattern of epigenomic variation between natural yeast strains at single-nucleosome resolution

International audienceBackground: Epigenomic studies on humans and model species have revealed substantial inter‑individual variation in histone modification profiles. However, the pattern of this variation has not been precisely characterized, particularly regarding which genomic features are enriched for variability and whether distinct histone marks co‑vary synergistically. Yeast allows us to investigate intra‑species variation at high resolution while avoiding other sources of variation, such as cell type or subtype. Results: We profiled histone marks H3K4me3, H3K9ac, H3K14ac, H4K12ac and H3K4me1 in three unrelated wild strains of Saccharomyces cerevisiae at single‑nucleosome resolution and analyzed inter‑strain differences statistically. All five marks varied significantly at specific loci, but to different extents. The number of nucleosomes varying for a given mark between two strains ranged from 20 to several thousands; +1 nucleosomes were significantly less subject to variation. Genes with highly evolvable or responsive expression showed higher variability; however, the variation pattern could not be explained by known transcriptional differences between the strains. Synergistic variation of distinct marks was not systematic, with surprising differences between functionally related H3K9ac and H3K14ac. Interestingly, H3K14ac differences that persisted through transient hyperacetylation were supported by H3K4me3 differences, suggesting stabilization via cross talk. Conclusions: Quantitative variation of histone marks among S. cerevisiae strains is abundant and complex. Its relation to functional characteristics is modular and seems modest, with partial association with gene expression divergences, differences between functionally related marks and partial co‑variation between marks that may confer stability. Thus, the specific context of studies, such as which precise marks, individuals and genomic loci are investigated, is primor‑ dial in population epigenomics studies. The complexity found in this pilot survey in yeast suggests that high complexity can be anticipated among higher eukaryotes, including humans

Phylogeography and domestication of Indian river buffalo

<p>Abstract</p> <p>Background</p> <p>The water buffalo- <it>Bu</it><it>balus bubalis </it>holds tremendous potential in livestock sector in many Asian countries, particularly India. The origin, domestication and genetic structure of the Indian river buffalo are poorly understood. Therefore, to understand the relationship among the maternal lineages of Indian river buffalo breeds and their domestication process, we analysed mitochondrial D-loop region of 217 animals representing eight breeds from eight different locations in India along with published sequences of Mediterranean buffalo.</p> <p>Results</p> <p>The maximum parsimony tree showed one major clade with six internal branches. Reduced median network revealed expansion from more than one set of haplotypes indicating complex domestication events for this species. In addition, we found several singleton haplotypes. Using rho statistics, we obtained a time estimate of 6300 years BP for the expansion of one set of hapltoypes of the Indian domestic buffalo. A few breed specific branches in the network indicated an ancient time depth of differentiation of some of the maternal lineages of river buffalo breeds. The multidimensional display of breed pairwise F_STvalues showed significant breed differentiation.</p> <p>Conclusion</p> <p>Present day river buffalo is the result of complex domestication processes involving more than one maternal lineage and a significant maternal gene flow from the wild populations after the initial domestication events. Our data are consistent with the available archaeological information in supporting the proposition that the river buffalo was likely to be domesticated in the Western region of the Indian subcontinent, specifically the present day breeding tracts of the Mehsana, Surati and Pandharpuri breeds.</p

A national-level analysis of life expectancy associated with the COVID-19 pandemic in India.

BACKGROUND From a demographic perspective, the impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on life expectancy is not clear. Hence, there is a need to study the number of years of life lost concerning the existing average life expectancy due to COVID-19 in India. OBJECTIVE This study aimed to estimate the impact of life expectancy due to the COVID-19 pandemic in India. METHODOLOGY We considered day-wise age-specific mortality due to COVID-19 which was extracted from the COVID-19 data repository from March 11, 2020, to June 30, 2021, in India. All-cause mortality was collected from the United Nations population estimates. An abridged life table technique was utilized for calculating life expectancies based on all-cause mortality and mortality due to COVID-19. MortPak software was used to calculate the life expectancy with and without the COVID-19 pandemic. Life expectancy at birth in different age groups was estimated with respect to with and without COVID-19. RESULTS A total of 399,459 deaths due to COVID-19 were distributed age wise, and their corresponding life expectancy was calculated. The general mortality was compared with COVID-19 mortality for the various age groups, and it was observed that mortality due to COVID-19 was significantly higher among the elderly age group [i.e., 45 to 60 years (36%) and > 60 years (51%)] when compared with < 25 years (1%) and 26-44 years (11%) (trend Chi-square 7.59; = 0.001). The life expectancy without and with COVID-19 was 69.28 years and 69.16 years, respectively. CONCLUSION Overall, it was estimated that COVID-19 has an impact on life expectancy by 0.12 years during the study period. Even though mortality due to COVID-19 was high, factors such as lockdown, vaccination, and accidents also had an influence on mortality. Thus, there is a need to assess the impact of COVID-19 on life expectancy in future

A study on tuberculosis disease disclosure patterns and its associated factors: Findings from a prospective observational study in Chennai

BACKGROUND: Disclosure of tuberculosis (TB) status by patients is a critical step in their treatment cascade of care. There is a lack of systematic assessment of TB disclosure patterns and its positive outcomes which happens dynamically over the disease period of individual patients with their family and wider social network relations. METHODS: This prospective observational study was conducted in Chennai Corporation treatment units during 2019–2021. TB patients were recruited and followed-up from treatment initiation to completion. Information on disease disclosures made to different social members at different time points, and outcomes were collected and compared. Bivariate and multi variate analysis were used to identify the patients and contact characteristics predictive of TB disclosure status. RESULTS: A total of 466 TB patients were followed-up, who listed a total of 4039 family, extra familial and social network contacts of them. Maximum disclosures were made with family members (93%) and half of the relatives, occupational contacts and friendship contacts (44–58%) were disclosed within 15 days of treatment initiation. Incremental disclosures made during the 150–180 days of treatment were highest among neighbourhood contacts (12%), and was significantly different between treatment initiation and completion period. Middle aged TB patients (31 years and 46–55 years) were found less likely to disclose (AOR 0.56 and 0.46 respectively; p71%). CONCLUSION: Findings explain that family level disclosures were predominant and disclosures made to extra familial network contacts significantly increased during the latter part of treatment. Emotional support was predominantly received by TB patients from all their contacts post disclosure. Findings could inform in developing interventions to facilitate disclosure of disease status in a beneficial way for TB patients

An economic evaluation of implementing a decentralized dengue screening intervention under the National Vector Borne Disease Control Programme in Tamil Nadu, South India.

BACKGROUND Lack of effective early screening is a major obstacle for reducing the fatality rate and disease burden of dengue. In light of this, the government of Tamil Nadu has adopted a decentralized dengue screening strategy at the primary healthcare (PHC) facilities using blood platelet count. Our objective was to determine the cost-effectiveness of a decentralized screening strategy for dengue at PHC facilities compared with the current strategy at the tertiary health facility (THC) level. METHODS Decision tree analysis followed a hypothetical cohort of 1000 suspected dengue cases entering the model. The cost-effectiveness analysis was performed at a 3% discount rate for the proposed and current strategy. The outcomes are expressed in incremental cost-effectiveness ratios (ICERs) per quality-adjusted life years gained. One-way sensitivity analysis and probabilistic sensitivity analysis were done to check the uncertainty in the outcome. RESULTS The proposed strategy was found to be cost-saving and ICER was estimated to be -41 197. PSA showed that the proposed strategy had a 0.84 probability of being an economically dominant strategy. CONCLUSIONS The proposed strategy is cost-saving, however, it is recommended to consider optimal population coverage, costs to economic human resources and collateral benefits of equipment

An influence of dew point temperature on the occurrence of Mycobacterium tuberculosis disease in Chennai, India.

Climate factors such as dew point temperature, relative humidity and atmospheric temperature may be crucial for the spread of tuberculosis. This study was conducted for the first time to investigate the relationship of climatic factors with TB occurrence in an Indian setting. Daily tuberculosis notification data during 2008-2015 were generated from the National Treatment Elimination Program, and analogous daily climatic data were obtained from the Regional Meteorological Centre at Chennai city, Tamil Nadu, India. The decomposition method was adopted to split the series into deterministic and non-deterministic components, such as seasonal, non-seasonal, trend and cyclical, and non-deterministic climate factors. A generalized linear model was used to assess the relation independently. TB disease progression from latent stage infection to active was supported by higher dew point temperature and moderate temperature. It had a significant association with TB progression in the summer and monsoon seasons. The relative humidity may be favored in the winter and post-monsoon. The water tiny dew droplets may support the TB bacterium to recuperate in the environment