Chromatin Profiles of Chromosomally Integrated Human Herpesvirus-6A

Human herpesvirus-6A (HHV-6A) and 6B (HHV-6B) are two closely related betaherpesviruses that are associated with various diseases including seizures and encephalitis. The HHV-6A/B genomes have been shown to be present in an integrated state in the telomeres of latently infected cells. In addition, integration of HHV-6A/B in germ cells has resulted in individuals harboring this inherited chromosomally integrated HHV-6A/B (iciHHV-6) in every cell of their body. Until now, the viral transcriptome and the epigenetic modifications that contribute to the silencing of the integrated virus genome remain elusive. In the current study, we used a patient-derived iciHHV-6A cell line to assess the global viral gene expression profile by RNA-seq, and the chromatin profiles by MNase-seq and ChIP-seq analyses. In addition, we investigated an in vitro generated cell line (293-HHV-6A) that expresses GFP upon the addition of agents commonly used to induce herpesvirus reactivation such as TPA. No viral gene expression including miRNAs was detected from the HHV-6A genomes, indicating that the integrated virus is transcriptionally silent. Intriguingly, upon stimulation of the 293-HHV-6A cell line with TPA, only foreign promoters in the virus genome were activated, while all HHV-6A promoters remained completely silenced. The transcriptional silencing of latent HHV-6A was further supported by MNase-seq results, which demonstrate that the latent viral genome resides in a highly condensed nucleosome-associated state. We further explored the enrichment profiles of histone modifications via ChIP-seq analysis. Our results indicated that the HHV-6 genome is modestly enriched with the repressive histone marks H3K9me3/H3K27me3 and does not possess the active histone modifications H3K27ac/H3K4me3. Overall, these results indicate that HHV-6 genomes reside in a condensed chromatin state, providing insight into the epigenetic mechanisms associated with the silencing of the integrated HHV-6A genome

Is the Hierarchy of Loss in Functional Ability Evident in Midlife? Findings from a British Birth Cohort.

Background Difficulties performing a range of physical tasks of daily living have been shown to develop in older populations in a typically observed sequence, known as the hierarchy of loss. Nearly all previous research has been undertaken using populations aged over 75. This study aimed to use cross-sectional and longitudinal data to test for evidence of the hierarchy of loss from midlife onwards. Methods The prevalence of reported difficulty undertaking 16 physical tasks in the MRC National Survey of Health and Development at age 60–64 were calculated, with Mokken scaling used to confirm the hierarchical order. Logistic regression was used to calculate the odds ratios of reporting difficulty performing tasks at the bottom of the hierarchy (i.e. feeding, washing and/or toileting) at age 60–64 by reported difficulty at the top of the hierarchy (i.e. gripping, walking and/or stair climbing) at age 43. Results At age 60–64, tasks associated with balance, strength and co-ordination, such as climbing stairs, were the first tasks participants reported difficulty with and tasks associated with upper limb mobility, such as feeding yourself, were the last. In a fully-adjusted model, participants who reported difficulty at the top of the hierarchy at age 43 were 2.85 (95% CI: 1.45–5.60) times more likely to report difficulty with tasks at the bottom of the hierarchy at age 60–64. Conclusion This study presents evidence of the hierarchy of loss in a younger population than previously observed suggesting that targeted interventions to prevent functional decline should not be delayed until old age

Real-World Results from Combined Screening for Monogenic Genomic Health Risks and Reproductive Risks in 300 Adults

New methods and demonstrations of feasibility guide future implementation of genomic population health screening programs. This is the first report of genomic population screening in a primary care, non-research setting using existing large carrier and health risk gene sequencing panels combined into one 432-gene test that is offered to adults of any health status. This report summarizes basic demographic data and analyses patterns of pathogenic and likely pathogenic genetic findings for the first 300 individuals tested in this real-world scenario. We devised a classification system for gene results to facilitate clear message development for our Genomic Medicine Action Plan messaging tool used to summarize and activate results for patients and primary care providers. Potential genetic health risks of various magnitudes for a broad range of disorders were identified in 16% to 34% of tested individuals. The frequency depends on criteria used for the type and penetrance of risk. 86% of individuals are carriers for one or more recessive diseases. Detecting, reporting, and guiding response to diverse genetic health risks and recessive carrier states in a single primary care genomic screening test appears feasible and effective. This is an important step toward exploring an exome or genome sequence as a multi-purpose clinical screening tool

Disruption of Broad Epigenetic Domains in PDAC Cells by HAT Inhibitors

The spreading of epigenetic domains has emerged as a distinguishing epigenomic phenotype for diverse cell types. In particular, clusters of H3K27ac- and H3K4me3-marked elements, referred to as super-enhancers, and broad H3K4me3 domains, respectively, have been linked to cell identity and disease states. Here, we characterized the broad domains from different pancreatic ductal adenocarcinoma (PDAC) cell lines that represent distinct histological grades. Our integrative genomic analysis found that human derived cell line models for distinct PDAC grades exhibit characteristic broad epigenetic features associated with gene expression patterns that are predictive of patient prognosis and provide insight into pancreatic cancer cell identity. In particular, we find that genes marked by overlapping Low-Grade broad domains correspond to an epithelial phenotype and hold potential as markers for patient stratification. We further utilize ChIP-seq to compare the effects of histone acetyltransferase (HAT) inhibitors to detect global changes in histone acetylation and methylation levels. We found that HAT inhibitors impact certain broad domains of pancreatic cancer cells. Overall, our results reveal potential roles for broad domains in cells from distinct PDAC grades and demonstrate the plasticity of particular broad epigenomic domains to epigenetic inhibitors

Transcriptomic Signatures of Tacaribe Virus-Infected Jamaican Fruit Bats

10.1128/mSphere.00245-17mSphere25e00245-1

Direct RT-qPCR detection of SARS-CoV-2 RNA from patient nasopharyngeal swabs without an RNA extraction step.

The ongoing COVID-19 pandemic has created an unprecedented need for rapid diagnostic testing. The World Health Organization (WHO) recommends a standard assay that includes an RNA extraction step from a nasopharyngeal (NP) swab followed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to detect the purified SARS-CoV-2 RNA. The current global shortage of RNA extraction kits has caused a severe bottleneck to COVID-19 testing. The goal of this study was to determine whether SARS-CoV-2 RNA could be detected from NP samples via a direct RT-qPCR assay that omits the RNA extraction step altogether. The direct RT-qPCR approach correctly identified 92% of a reference set of blinded NP samples (n = 155) demonstrated to be positive for SARS-CoV-2 RNA by traditional clinical diagnostic RT-qPCR that included an RNA extraction. Importantly, the direct method had sufficient sensitivity to reliably detect those patients with viral loads that correlate with the presence of infectious virus. Thus, this strategy has the potential to ease supply choke points to substantially expand COVID-19 testing and screening capacity and should be applicable throughout the world

Cretaceous paleogeography, paleoclimatology, and amniote biogeography of the low and mid-latitude South Atlantic Ocean

The Cretaceous tropical Atlantic Ocean was the setting for an initial tectonically controlled late Aptian shallow water (≤ 300 m) connection between the northern and southern portions of the Atlantic, followed by a deep-water connection by the Turonian. Ocean currents changed with deepening of the South Atlantic and progressive widening of the Equatorial Atlantic Gateway. Aptian evaporite deposition came to a halt. The Albian-Turonian interval includes a trend toward increasing sea level and was characterized by globally warm sea surface temperatures. Productive areas of coastal upwelling led to the deposition of organic-rich sediments varying in position along the African coast with time, culminating in the Benguela Upwelling that commenced in the Miocene. The drift of Africa in the Late Cretaceous indicates that throughout most of this period, the coastal area around the fossil locality of lembe, north of Luanda, Angola, lay in arid latitudes (15° S to 30° S), which are generally characterized by sparse vegetation. This presumption is consistent with the utter lack of macroscopic terrestrial plant debris washed into near shore sedimentary environments and indicates that organic rich marine shales have a minimal terrestrial carbon component. The connection of the North and South Atlantic oceans severed a direct terrestrial dispersal route between South America and Africa, but opened a north-south dispersal route for marine amniotes. This seaway was used by late Turonian mosasaurs and sea turtles as evidenced by Angolasaurus and a new turtle taxon close to Sandownia, both found at lembe and derived from northern clades. The presence of a sauropod in late Turonian sediments, also from lembe, suggests that this animal was tolerant of warm, arid conditions as the desert elephants of Namibia are today. Further, it suggests that the waning terrestrial dispersal route between South America and Africa was situated in a region where high temperature, low rainfall, and sparse vegetation would be expected to restrict the movement of more mesic and ecologically sensitive species