bluuebunny/crossref_metadata_2025 huggingface dataset:
CASUAL SEX AMONG MSM DURING THE PERIOD OF SHELTERING IN PLACE TO PREVENT THE SPREAD OF COVID-19: RESULTS OF NATIONAL ONLINE SURVEYS IN BRAZIL AND PORTUGAL
Authors: de Sousa Alvaro Francisco Lopes , de Oliveira Layze Braz , Queiroz Artur Acelino Francisco Luz Nunes , de Carvalho Hérica Emilia Felix , Schneider Guilherme , Camargo Emerson Lucas Silva , de Araujo Telma Evangelista , Brignol Sandra , Mendes Isabel Amélia Costa , McFarland Willi , Fronteira Inês
Published: June 2020

Background

We investigated the extent to which Brazilian and Portuguese MSM had casual sexual relations outside their homes during the period of sheltering in place for the COVID-19 pandemic.

Methods

An online survey was implemented in Brazil and Portugal in April, during the period of social isolation for COVID-19, with a sample of 2,361 MSMs. Recruitment was done through meeting apps and Facebook.

Results

Most of the sample (53.0%; considering 53.1% in Portugal and 53% in Brazil) had casual sex partners during sheltering. Factors that increased the odds of engaging in casual sex in Brazil were having group sex (aOR 2.1, 95%CI 1.3-3.4), living in a urban area (aOR 1.6, 95%CI 1.1-2.2), feeling that sheltering had high impact on daily life (aOR 3.0, 95%CI 1.1-8.3), having casual instead of steady partners (aOR 2.5, 95%CI 1.8-3.5), and not decreasing the number of partners (aOR 6.5, 95%CI 4.2-10.0). In Portugal, the odds of engaging in casual sex increased with using Facebook to find partners (aOR 4.6, 95%CI 3.0-7.2), not decreasing the number of partners (aOR 3.8, 95%CI 2.9-5.9), usually finding partners in physical venues (pre-COVID-19) (aOR 5.4, 95%CI 3.2-8.9), feeling that the isolation had high impact on daily life (aOR 3.0, 95%CI 1.3-6.7), and HIV-positive serostatus (aOR 11.7, 95%CI 4.7-29.2). Taking PrEP/Truvada to prevent COVID-19 was reported by 12.7% of MSM.

Conclusions

The pandemic has not stopped most of our MSM sample from finding sexual partners, with high risk sexual behaviors continuing. Public health messages for the prevention of COVID-19 need to be crafted to explicitly address sexual behavior to reduce contamination in the current moment.

Short Summary

The pandemic of COVID-19 did not cause changes in the sexual behavior of MSM; they continued to engage in casual sex, using drugs, having multiple partners and adopting ineffective protective measures for COVID-19.
A Survey of Potential Bacterial Hazards in Salad Vegetables Sold in Lusaka District, Zambia, in 2018
Authors: Pule Chileshe , Ndashe Kunda , Mfune Ruth , Chilumunda Abigail , Mwanza Grace , Mumba Bernadette , Silavwe Lillian Mutesu , Hang’ombe Bernard Mudenda
Published: June 2020

Salad vegetables are a source of fresh nutrition and can also serve a vehicle for foodborne pathogens. This was a cross sectional study conducted in February and March 2018 aimed at isolating some enteropathogens from some salad vegetables.

Ten samples of each salad vegetable (carrots, cabbage, cucumbers and tomatoes) were collected from two supermarkets and two open-markets. A total of 160 samples were collected and analysed microbiologically for presence of Shigella spp, Vibrio spp and Salmonella spp. The isolated bacteria were identified by conventional biochemical tests.

Vibrio spp were isolated from all the vegetables that were collected from both the two open markets (62.5% and 72.5%) and two supermarkets (67.5% and 77.5%), with the highest isolation rate recorded in cabbages. The frequency of occurrence of Shigella spp and Salmonella spp was higher in supermarkets (50% and 65%; 50% and 15%) than in the open markets (10% and 7.5%; 10% and 35%), respectively.

The present study revealed the presence of potential bacterial hazards in salad vegetables sold in both open markets and supermarkets in Lusaka district. The isolated bacterial pathogens are aetiological agents of diarrheal disease that even at low dose could be infectious for sensitive populations.
Repurposing of drugs for Covid-19: a systematic review and meta-analysis
Authors: Kotecha Pinky , Light Alexander , Checcucci Enrico , Amparore Daniele , Fiori Cristian , Porpiglia Francesco , Dasgupta Prokar , Elhage Oussama
Published: June 2020

Objective

The aim of this systematic review is to evaluate the data currently available regarding the repurposing of different drugs for Covid-19 treatment. Participants with suspected or diagnosed Covid-19 will be included. The interventions being considered are drugs being repurposed, and comparators will include standard of care treatment or placebo.

Methods

We searched Ovid-MEDLINE, EMBASE, Cochrane library, clinical trial registration site in the UK(NIHR), Europe (clinicaltrialsregister.eu), US (ClinicalTrials.gov) and internationally (isrctn.com), and reviewed the reference lists of articles for eligible articles published up to April 22, 2020. All studies in English that evaluated the efficacy of the listed drugs were included. Cochrane RoB 2.0 and ROBINS-I tool were used to assess study quality. This systematic review adheres to the PRISMA guidelines. The protocol is available at PROSPERO (CRD42020180915).

Results

From 708 identified studies or clinical trials, 16 studies and 16 case reports met our eligibility criteria. Of these, 6 were randomized controlled trials (763 patients), 7 cohort studies (321 patients) and 3 case series (191 patients). Chloroquine (CQ) had a 100% discharge rate compared to 50% with lopinavir-ritonavir at day 14, however a trial has recommended against a high dosage due to cardiotoxic events. Hydroxychloroquine (HCQ) has shown no significant improvement in negative seroconversion rate which is also seen in our meta-analysis (p=0.68). Adverse events with HCQ have a significant difference compared to the control group (p=0.001). Lopinavir-ritonavir has shown no improvement in time to clinical improvement which is seen in our meta-analyses (p=0.1). Remdesivir has shown no significant improvement in time to clinical improvement but this trial had insufficient power.

Discussion

Due to the paucity in evidence, it is difficult to establish the efficacy of these drugs in the treatment of Covid-19 as currently there is no significant clinical effectiveness of the repurposed drugs. Further large clinical trials are required to achieve more reliable findings. A risk-benefit analysis is required on an individual basis to weigh out the potential improvement in clinical outcome and viral load reduction compared to the risks of the adverse events. (1-16)
Changes in health promoting behavior during COVID-19 physical distancing: Utilizing Wearable Technology to Examine Trends in Sleep, Activity, and Cardiovascular Indicators of Health
Authors: Capodilupo Emily R , Miller Dean J
Published: June 2020

The COVID-19 pandemic incited unprecedented restrictions on the behavior of society. The aims of this study were to quantify changes to sleep/wake behavior and exercise behavior, as well as changes in physiological markers of health during COVID-19 physical distancing. A retrospective analysis of 5,436 US-based subscribers to the WHOOP platform (mean age = 40.25 ± 11.33; 1,536 females, 3,900 males) was conducted covering the period from January 1st, 2020 through May 15th, 2020. This time period was separated into a 68-day baseline period and a 67-day physical distancing period. To provide context and allow for potential confounders (e.g., change of season), data were also extracted from the corresponding time periods in 2019. As compared to baseline, during physical distancing, all subjects fell asleep earlier (−0.25 hours), woke up later (0.48 hours), obtained more sleep (+0.35 hours) and reduced social jet lag (−0.21 hours). Contrasting sleep behavior was seen in 2019, with subjects falling asleep and waking up at a similar time (−0.01 hours; -0.05 hours), obtaining less sleep (−0.14 hours) and maintaining social jet lag (0.01 hours) in corresponding periods. Individuals exercised more intensely during physical distancing by increasing the time spent in high heart rate zones. In 2020, resting heart rate decreased (−0.9 beats per minute) and heart rate variability increased (+0.98 milliseconds) during physical distancing when compared to baseline. However, similar changes were seen in 2019, suggesting the variation may not be related to the introduction of physical distancing mandates. The findings suggest that changes in societal commitments (e.g., daily commute; working from home) during physical distancing may have resulted in changes to health-related behavior (i.e., increased exercise intensity and longer sleep duration). As the COVID-19 pandemic eases, maintenance of certain aspects of physical distancing (e.g., working from home) may allow for positive changes to sleep/wake and exercise behaviors.
Changing patterns of mortality during the COVID-19 pandemic: population-based modelling to understand palliative care implications
Authors: Bone Anna E , Finucane Anne M , Leniz Javiera , Higginson Irene J , Sleeman Katherine E
Published: June 2020

Background

COVID-19 has directly and indirectly caused high mortality worldwide.

Aim

To explore patterns of mortality during the COVID-19 pandemic and implications for palliative care provision, planning, and research.

Design

Descriptive analysis and population-based modelling of routine data.

Participants and setting

All deaths registered in England and Wales between 7th March and 15th May 2020. We described the following mortality categories by age, gender and place of death: 1) baseline deaths (deaths that would typically occur in a given period) 2) COVID-19 deaths 3) additional deaths not directly attributed to COVID-19. We estimated the proportion of COVID-19 deaths among people who would be in their last year of life in the absence of the pandemic, using simple modelling with explicit assumptions.

Results

During the first 10 weeks of the pandemic there were 101,615 baseline deaths, 41,105 COVID-19 deaths and 14,520 additional deaths. Deaths in care homes increased by 220% compared to home and hospital deaths which increased by 77% and 90%. Hospice deaths fell by 20%. Additional deaths were among older people (86% aged ≥75 years), and most occurred in care homes (56%) and at home (43%). We estimate that 44% (38% to 50%) of COVID-19 deaths occurred among people who would have been in their last year of life in the absence of the pandemic.

Conclusions

Healthcare systems must ensure availability of palliative care to support people with severe COVID-19 in community and hospital settings. Integrated models of palliative care in care homes are urgently needed.

Key statements

What is already known about the topic?

The COVID-19 pandemic has directly and indirectly resulted in high mortality in many affected nations.

Internationally the response has been focused on prevention and curative treatments, with little emphasis on palliative care needs of people dying during the COVID-19 pandemic.

We do not know how many of those dying with COVID-19 would have been in their last year of life in the absence of the pandemic, and this group may have distinct care needs.

What this paper adds

The number of people dying in care homes trebled during the first 10 weeks of the COVID-19 pandemic in England and Wales; many of these deaths were ‘additional deaths’, that is associated with the COVID-19 pandemic but not directly as a result of COVID-19.

We estimate almost half of all COVID-19 deaths occurred among people who would have been in their last year of life in the absence of the pandemic.

Implications for practice, theory or policy

Healthcare systems must ensure availability of palliative care to support people with severe COVID-19 in community and hospital settings.

The need for integrated models of palliative care in care home settings is imperative and research to underpin these models is warranted.
Structural and social determinants of health factors accounted for county-level variation in non-adherence to antihypertensive medication treatment
Authors: Donneyong Macarius M. , Chang Teng-Jen , Jackson John W. , Langston Michael A. , Juarez Paul D. , Sealy-Jefferson Shawnita , Lu Bo , Im Wansoo , Valdez R. Burciaga , Baldwin Way M. , Colen Cynthia , Fischer Michael A. , Salsberry Pamela , Bridges John F. , Hood Darryl B.
Published: June 2020

Background

Non-adherence to antihypertensive medication treatment (AHM) is a complex health behavior with determinants that extend beyond the individual patient. The structural and social determinants of health (SDH) that predispose populations to ill health and unhealthy behaviors could be potential barriers to long-term adherence to AHM. However, the role of SDH in AHM non-adherence have been understudied.

Therefore, we aimed to define and identify the SDH factors associated with non-adherence to AHM and to quantify the variation in county-level non-adherence to AHM explained by these factors.

Methods

Two cross-sectional datasets, the Centers for Disease Control and Prevention (CDC) Atlas of Heart Disease and Stroke (2014-2016 cycle) and the 2016 County Health Rankings (CHR), were linked to create an analytic dataset. Contextual SDH variables were extracted from both the CDC-CHR linked dataset. County-level prevalence of AHM non-adherence, based on Medicare fee-for-service beneficiaries’ claims data, was extracted from the CDC Atlas dataset. The CDC measured AHM non-adherence as the Proportion of Days Covered (PDC) with AHM during a 365-day period for Medicare Part D beneficiaries and aggregated these measures at the county-level. We applied Confirmatory Factor Analysis (CFA) to identify the constructs of social determinants of AHM non-adherence. AHM non-adherence variation and its social determinants were measured with structural equation models.

Results

Among 3,000 counties in the US, the weighted mean prevalence of AHM non-adherence (PDC<80%) in 2015 was 25.0%, Standard Deviation (SD), 18.8%. AHM non-adherence was directly associated with poverty/food insecurity (β=0.31, P-value<0.001) and weak social supports (β=0.27, P-value<0.001), but inversely with healthy built environment (β= −0.10, P-value=0.02). These three constructs explained a third (R2=30.0%) of the variation in county-level AHM non-adherence.

Conclusion

AHM non-adherence varies by geographical location, a third of which is explained by contextual SDH factors including poverty/food insecurity, weak social supports and healthy built environments.
Multi-model forecasts of the ongoing Ebola epidemic in the Democratic Republic of Congo, March – October 2019
Authors: Roosa Kimberlyn , Tariq Amna , Yan Ping , Hyman James M. , Chowell Gerardo
Published: June 2020

The 2018-20 Ebola outbreak in the Democratic Republic of the Congo is the first to occur in an armed conflict zone. The resulting impact on population movement, treatment centers, and surveillance has created an unprecedented challenge for real-time epidemic forecasting. Most standard mathematical models cannot capture the observed incidence trajectory when it deviates from a traditional epidemic logistic curve. We fit seven dynamic models of increasing complexity to the incidence data published in the World Health Organization Situation Reports, after adjusting for reporting delays. These models include a simple logistic model, a Richards model, an endemic Richards model, a double logistic growth model, a multi-model approach, and two sub-epidemic models. We analyze model fit to the data and compare real-time forecasts throughout the ongoing epidemic across 29 weeks from March 11 to September 23, 2019. We observe that the modest extensions presented allow for capturing a wide range of epidemic behavior. The multi-model approach yields the most reliable forecasts on average for this application, and the presented extensions improve model flexibility and forecasting accuracy, even in the context of limited epidemiological data.
Linear epitopes of SARS-CoV-2 spike protein elicit neutralizing antibodies in COVID-19 patients
Authors: Li Yang , Lai Dan-yun , Zhang Hai-nan , Jiang He-wei , Tian Xiao-long , Ma Ming-liang , Qi Huan , Meng Qing-feng , Guo Shu-juan , Wu Yan-ling , Wang Wei , Yang Xiao , Shi Da-wei , Dai Jun-biao , Ying Tian-lei , Zhou Jie , Tao Sheng-ce
Published: June 2020

SARS-CoV-2 outbreak is a world-wide pandemic. The Spike protein plays central role in cell entry of the virus, and triggers significant immuno-response. Our understanding of the immune-response against S protein is still very limited. Herein, we constructed a peptide microarray and analyzed 55 convalescent sera, three areas with rich linear epitopes were identified. Potent neutralizing antibodies enriched from sera by 3 peptides, which do not belong to RBD were revealed.
ATP2, the essential P4-ATPase of malaria parasites, catalyzes lipid-dependent ATP hydrolysis in complex with a Cdc50 β-subunit
Authors: Lamy Anaïs , Macarini-Bruzaferro Ewerton , Perálvarez-Marín Alex , le Maire Marc , Vázquez-Ibar José Luis
Published: June 2020

Efficient mechanisms of lipid transport are indispensable for thePlasmodiummalaria parasite along the different stages of its intracellular life-cycle. Gene targeting approaches have recently revealed the irreplaceable role of thePlasmodium-encodedtype 4 P-type ATPases (P4-ATPases or lipid flippases), ATP2, together with its potential involvement as antimalarial drug target. In eukaryotic membranes, P4-ATPases assure their asymmetric phospholipid distribution by translocating phospholipids from the outer to the inner leaflet. As ATP2 is a yet putative transporter, in this work we have used a recombinantly-producedP. chabaudiATP2, PcATP2, to gain insights into the function and structural organization of this essential transporter. Our work demonstrates that PcATP2 heterodimerizes with two of the threePlasmodium-encodedCdc50 proteins: PcCdc50B and PcCdc50A, indispensable partners for most P4-ATPases. Moreover, the purified PcATP2/PcCdc50B complex catalyses ATP hydrolysis in the presence of phospholipids containing either phosphatidylserine, phosphatidylethanolamine or phosphatidylcholine head groups, and that this activity is upregulated by phosphatidylinositol 4-phosphate. Overall, our work provides the first study of the function and quaternary organization of ATP2, a promising antimalarial drug target candidate.
Mismatch repair deficiency predicts response to HER2 blockade in HER2-negative breast cancer
Authors: Punturi Nindo B , Seker Sinem , Devarakonda Vaishnavi , Kalra Rashi , Chen Ching-Hui , Mazumder Aloran , Li Shunqiang , Primeau Tina , Ellis Matthew J , Kavuri Shyam M , Haricharan Svasti
Published: June 2020

Estrogen receptor positive (ER+) breast cancer is a leading cause of cancer-related death globally. Resistance to standard of care endocrine treatment occurs in at least 30% of ER+breast cancer patients resulting in ~40,000 deaths every year in the US alone. Preclinical studies strongly implicate activation of growth factor receptor, HER2 in endocrine treatment resistance of ER+breast cancer that is HER2-at diagnosis1,2. However, clinical trials of pan-HER inhibitors in ER+/HER2-patients have disappointed, likely due to a lack of predictive biomarkers3-6. Here we demonstrate that loss ofMLH1, a principal mismatch repair gene, causally activates HER2 in ER+/HER2-breast cancer upon endocrine treatment. Additionally, we show that HER2 activation is indispensable for endocrine treatment resistant growth of MLH1-cellsin vitroandin vivo.Consequently, inhibiting HER2 restores sensitivity to endocrine treatment in multiple experimental models including patient-derived xenograft tumors. Patient data from multiple clinical datasets (TCGA, METABRIC, Alliance (Z1031) and E-GEOD-28826) supports an association betweenMLH1loss, HER2 upregulation, and sensitivity to trastuzumab in endocrine treatment-resistant ER+/HER2-patients. These results provide strong rationale that MLH1 could serve as a first-in-class predictive marker of sensitivity to combinatorial treatment with endocrine drugs and HER inhibitors in endocrine treatment-resistant ER+/HER2-breast cancer patients. Implications of this study extend beyond breast cancer to Lynch Syndrome cancers.

One Sentence Summary

Defective mismatch repair activates HER2 in HER2-negative breast cancer cells and renders them susceptible to HER2 inhibitors.
SF3B1-targeted Splicing Inhibition Triggers Global Alterations in Transcriptional Dynamics and R-Loop Metabolism
Authors: Castillo-Guzman Daisy , Hartono Stella R. , Sanz Lionel A. , Chédin Frédéric
Published: June 2020

Efficient co-transcriptional splicing is thought to suppress the formation of genome-destabilizing R-loops upon interaction between nascent RNA and the DNA template. Inhibition of the SF3B splicing complex using Pladienolide B (PladB) in human K562 cells caused widespread intron retention and nearly 2,000 instances of R-loops gains. However, only minimal overlap existed between these events, arguing that unspliced introns do not cause excessive R-loops. R-loop gains were instead driven by readthrough transcription resulting from loss of transcription termination over a subset of stress-response genes, defining a new class of aberrant “downstream of genes” (DoG) R-loops. Such DoG R-loops were temporally and spatially uncoupled from loci experiencing DNA damage. Unexpectedly, the predominant response to splicing inhibition was a global R-loop loss resulting from accumulation of promoter-proximal paused RNA polymerases and defective elongation. Thus, SF3B1-targeted splicing inhibition triggered profound alterations in transcriptional dynamics, leading to unexpected disruptions in the global R-loop landscape.

HIGHLIGHTS

Intron retention caused by SF3B1 inhibition does not lead to excessive R-loops

A subset of genes shows readthrough transcription and accompanying R-loop gains

SF3B1 inhibition causes broad reduction in nascent transcription and R-loop loss

R-loop gains and DNA damage are temporally and spatially uncoupled
Dorsal horn CGRP-expressing interneurons contribute to nerve injury-induced mechanical hypersensitivity
Authors: Löken LS , Etlin A , Bernstein M , Steyert M , Kuhn J , Hamel K , Llewellyn-Smith I , Braz JM , Basbaum AI
Published: June 2020

Primary sensory neurons are generally considered the only source of dorsal horn calcitonin gene-related peptide (CGRP), a neuropeptide critical to the transmission of pain messages. Using a tamoxifen-inducible CGRPCreERtransgenic mouse, here we identified a distinct population of CGRP-expressing excitatory interneurons in lamina III of the spinal cord dorsal horn and trigeminal nucleus caudalis. These interneurons have spine-laden, dorsally-directed, dendrites and ventrally-directed axons. Neither innocuous nor noxious stimulation provoked significant Fos expression in these neurons. However, synchronous, electrical non-nociceptive Aβ primary afferent stimulation of dorsal roots depolarized the CGRP interneurons, consistent with their receipt of a VGLUT1 innervation. In contrast, chemogenetic activation produced a significant mechanical hypersensitivity. Importantly, the CGRP interneurons could be activated after peripheral nerve injury, but only with concurrent innocuous, brush stimulation. These findings suggest that hyperexcitability of dorsal horn CGRP interneurons is an important contributor to the circuits that render touch painful after peripheral nerve damage.
DIFFERENTIAL BIOENERGETICS IN ADULT RAT CARDIOMYOCYTES ISOLATED FROM THE RIGHT VERSUS LEFT VENTRICLE
Authors: Nguyen Quyen L. , Rao Krithika , Mullett Steven J. , Wendell Stacy G. , Croix Claudette St. , Goetzman Eric , Shiva Sruti
Published: June 2020

The right and left ventricle of the heart have distinctly different developmental origins and are affected differently by similar pathological stimuli. Though it is well established that the heart relies almost entirely on mitochondrial function to sustain energy production, it remains unclear whether bioenergetics differ in the two ventricles. Herein, we define a novel methodology to optimize the isolation of intact cardiomyocytes from the right versus the left ventricle. We demonstrate that this segmental Langendorff-free methodology yields viable cardiomyocytes with intact mitochondrial function. Further, we compare bioenergetics in right versus left ventricle cardiomyocytes and show that cardiomyocytes from the right ventricle have a greater maximal capacity for respiration and enhanced glycolytic rate. This increase in respiration was concomitant with increased fatty acid oxidation and levels of fatty acid oxidation proteins, but no change in mitochondrial electron transport complex expression. These data validate a potentially powerful tool to evaluate differences in right and left ventricular function and advance the understanding of cardiac bioenergetic differences. These data will be discussed in the context of differential responses by the right versus ventricle in pathology.
Spatially discrete signalling niches regulate fibroblast heterogeneity in human lung cancer
Authors: Hanley CJ , Waise S , Parker R , Lopez MA , Taylor J , Kimbley LM , West J , Ottensmeier CH , Rose-Zerilli MJJ , Thomas GJ
Published: June 2020

Fibroblasts are functionally heterogeneous cells, capable of promoting and suppressing tumour progression. Across cancer types, the extent and cause of this phenotypic diversity remains unknown. We used single-cell RNA sequencing and multiplexed immunohistochemistry to examine fibroblast heterogeneity in human lung and non-small cell lung cancer (NSCLC) samples. This identified seven fibroblast subpopulations: including inflammatory fibroblasts and myofibroblasts (representing terminal differentiation states), quiescent fibroblasts, proto-myofibroblasts (x2) and proto-inflammatory fibroblasts (x2). Fibroblast subpopulations were variably distributed throughout tissues but accumulated at discrete niches associated with differentiation status. Bioinformatics analyses suggested TGF-β1 and IL-1 as key regulators of myofibroblastic and inflammatory differentiation respectively. However,in vitroanalyses showed that whilst TGF-β1 stimulation in combination with increased tissue tension could induce myofibroblast marker expression, it failed to fully re-capitulateex-vivophenotypes. Similarly, IL-1β treatment only induced upregulation of a subset of inflammatory fibroblast marker genes.In silicomodelling of ligand-receptor signalling identified additional pathways and cell interactions likely to be involved in fibroblast activation, which can be examined using publicly available R shiny applications (at the following links:myofibroblast activationandinflammatory fibroblast activation). This highlighted a potential role for IL-11 and IL-6 (among other ligands) in myofibroblast and inflammatory fibroblast activation respectively. This analysis provides valuable insight into fibroblast subtypes and differentiation mechanisms in NSCLC.
Activation-induced re-organization of chromatin in human T cells
Authors: Bediaga Naiara G. , Coughlan Hannah D. , Johanson Timothy M. , Garnham Alexandra L. , Naselli Gaetano , Schröder Jan , Fearnley Liam G. , Bandala-Sanchez Esther , Allan Rhys S. , Smyth Gordon K. , Harrison. Leonard C.
Published: June 2020

Remodelling of chromatin architecture is known to regulate gene expression and has been well characterized in cell lineage development but less so in response to cell perturbation. Activation of T cells, which triggers extensive changes in transcriptional programs, serves as an instructive model to elucidate how changes in genome organization orchestrate gene expression in response to cell perturbation. To characterize coordinate changes at different levels of chromatin architecture, we analysed chromatin accessibility, chromosome conformation and gene expression after activation of human T cells. T cell activation led to widespread changes in chromatin interactions and accessibility that were mostly shared between CD4+and CD8+T cells. Differential chromatin interactions were associated with upregulation or downregulation of linked target genes. Moreover, activation was associated with the formation of shorter chromatin interactions, partitioning of topologically associating domains (TADs) and acquisition of new TAD boundaries characterized by higher nucleosome occupancy, and lower chromatin accessibility and gene expression. These findings render an integrated and multiscale characterization of activation-induced re-organization of chromatin architecture underlying gene transcription in human T cells.
Single-cell RNA transcriptomics identifies Hivep3 as essential in regulating the development of innate-like T lymphocytes
Authors: Krovi Sai Harsha , Zhang Jingjing , Michaels-Foster Mary Jessamine , Brunetti Tonya , Loh Liyen , Scott-Browne James , Gapin Laurent
Published: June 2020

Most T lymphocytes leave the thymus as naïve cells with limited functionality. However, unique populations of T cells, commonly known as innate-like T cells, differentiate into functionally distinct effector subsets during thymic development under the influence of the transcription factor PLZF. Here, we profiled >10,000 differentiating thymic iNKT cells using single-cell RNA sequencing to provide a comprehensive transcriptional landscape of their maturation, function, and fate decision in steady state. We identifiedHivep3, a zinc finger transcription factor and adaptor protein, as a key factor that is expressed in early precursors and regulates the post-selection proliferative burst, differentiation and functions of iNKT cells. Importantly, we extended these results to other PLZF+innate-like T cell populations, highlighting the unique and common requirement ofHivep3to the development of all innate-like T cells.
Enrichment and physiological characterization of a novel comammoxNitrospiraindicates ammonium inhibition of complete nitrification
Authors: Sakoula Dimitra , Koch Hanna , Frank Jeroen , Jetten Mike SM , van Kessel Maartje AHJ , Lücker Sebastian
Published: June 2020

The recent discovery of bacteria within the genusNitrospiracapable of complete ammonia oxidation (comammox) demonstrated that the sequential oxidation of ammonia to nitrate via nitrite can also be performed within a single bacterial cell. Although comammoxNitrospiraexhibit a wide distribution in natural and engineered ecosystems, information on their physiological properties is scarce due to the limited number of cultured representatives. Furthermore, most available genomic information is derived from metagenomic sequencing and high-quality genomes ofNitrospirain general are limited. In this study, we obtained a high (90%) enrichment of a novel comammox species, tentatively named “CandidatusNitrospira kreftii”, and performed a detailed genomic and physiological characterization. The complete genome of “Ca.N. kreftii” allowed reconstruction of its basic metabolic traits. Similar toNitrospira inopinata, the enrichment culture exhibited a very high ammonia affinity (Km(app)_NH3≈ 0.036 µM), but a higher nitrite affinity (Km(app)_NO2- ≈ 13.8 µM), indicating an adaptation to highly oligotrophic environments. Counterintuitively for a nitrifying microorganism, we also observed an inhibition of ammonia oxidation at ammonium concentrations as low as 25 µM. This substrate inhibition of “Ca.N. kreftii” indicate that differences in ammonium tolerance rather than affinity can be a niche determining factor for different comammoxNitrospira.
Effects of Renin-Angiotensin Inhibition on ACE2 and TMPRSS2 Expression: Insights into COVID-19
Authors: Wu Congqing , Ye Dien , Mullick Adam E. , Li Zhenyu , Danser A.H. Jan , Daugherty Alan , Lu Hong S.
Published: June 2020

Angiotensin-converting enzyme 2 (ACE2), a component of the renin-angiotensin system, is a receptor for SARS-CoV-2, the virus that causes COVID-19. To determine whether the renin-angiotensin inhibition regulates ACE2 expression, either enalapril (an angiotensin-converting enzyme inhibitor) or losartan (an AT1 receptor blocker) was infused subcutaneously to male C57BL/6J mice for two weeks. Neither enalapril nor losartan changed abundance of ACE2 mRNA in lung, ileum, kidney, and heart. Viral entry also depends on transmembrane protease serine 2 (TMPRSS2) to prime the S protein. TMPRSS2 mRNA was abundant in lungs and ileum, modest in kidney, but barely detectable in heart. TMPRSS2 mRNA abundance was not altered by either enalapril or losartan in any of the 4 tissues. Next, we determined whether depletion of angiotensinogen (AGT), the unique substrate of the renin-angiotensin system, changes ACE2 and TMPRSS2 mRNA abundance. AGT antisense oligonucleotides (ASO) were injected subcutaneously to male C57BL/6J mice for 3 weeks. Abundance of ACE2 mRNA was unchanged in any of the 4 tissues, but TMPRSS2 mRNA was significantly decreased in lungs. Our data support that the renin-angiotensin inhibition does not regulate ACE2 and hence are not likely to increase risk for COVID-19.
Comparative Modeling of CDK9 Inhibitors to Explore Selectivity and Structure-Activity Relationships
Authors: Kirubakaran Palani , Morton George , Zhang Pingfeng , Zhang Hanghang , Gordon John , Abou-Gharbia Magid , Issa Jean-Pierre J. , Wu Jinhua , Childers Wayne , Karanicolas John
Published: June 2020

Cyclin-dependent kinase 9 (CDK9) plays a key role in transcription elongation, and more recently it was also identified as the molecular target of a series of diaminothiazole compounds that reverse epigenetic silencing in a phenotypic assay. To better understand the structural basis underlying these compounds’ activity and selectivity, we developed a comparative modeling approach that we describe herein. Briefly, this approach draws upon the strong structural conservation across the active conformation of all protein kinases, and their shared pattern of interactions with Type I inhibitors. Because of this, we hypothesized that the large collection of inhibitor/kinase structures available in the Protein Data Bank (PDB) would enable accurate modeling of this diaminothiazole series in complex with each CDK family member. We apply this new comparative modeling pipeline to build each of these structural models, and then demonstrate that these models provide retrospective rationale for the structure-activity relationships that ultimately guided optimization to the lead diaminothiazole compound MC180295 (14e). We then solved the crystal structure of the14e/CDK9 complex, and found the resulting structure to be in excellent agreement with our corresponding comparative model. Finally, inspired by these models, we demonstrate how structural changes to14ecan be used to rationally tune this compound’s selectivity profile. With the emergence of CDK9 as a promising target for therapeutic intervention in cancer, we anticipate that comparative modeling can provide a valuable tool to guide optimization of potency and selectivity of new inhibitors targeting this kinase.
Multi-ancestry Genome- and Phenome-wide Association Studies of Diverticular Disease in Electronic Health Records with Natural Language Processing enriched phenotype algorithm
Authors: Joo Yoonjung Yoonie , Pacheco Jennifer A , Thompson William K , Rasmussen-Torvik Laura J , Rasmussen Luke V , Lin Frederick TJ , de Andrade Mariza , Borthwick Kenneth M , Bottinger Erwin , Cagan Andrew , Carrell David S , Denny Joshua C , Ellis Stephen B , Gottesman Omri , Linneman James G , Pathak Jyotishman , Peissig Peggy L , Shang Ning , Tromp Gerard , Veerappan Annapoorani , Smith Maureen E , Chisholm Rex L , Gawron Andrew , Kho Abel N , Hayes M Geoffrey
Published: June 2020

Background and aims

Diverticular disease is among the most prevalent conditions encountered by gastroenterologists, affecting ∼50% of Americans before the age of 60. Our aim was to identify genetic risk variants and clinical phenotypes associated with diverticular disease, utilizing the electronic health record (EHR) with Natural Language Processing (NLP).

Methods

We developed a NLP-enriched phenotype algorithm that incorporated colonoscopy or abdominal imaging reports to accurately identify patients with diverticulosis and diverticulitis from multicenter EHRs. We performed genome-wide association studies (GWAS) of diverticular disease in European, African and multi-ancestry participants, followed by phenome-wide association studies (PheWAS) of the risk variants to identify their potential comorbid/pleiotropic effects in the clinical phenome. For more in-depth investigation of associated clinical phenotypes, we also performed PheWAS with the previously reported 52 GWAS susceptibility variants for diverticular disease.

Results

Ancestry-stratified GWAS analyses confirmed the well-established associations betweenARHGAP15loci with diverticular disease in European cohorts, and found similar positive effect sizes in African cohorts but with non-significant p-values. With overall intensified GWAS signals in diverticulitis patients compared to diverticulosis patients, we found substantial genetic correlations between diverticulosis and diverticulitis, up to 0.997 in European ancestry. PheWAS analyses identified associations between the diverticular disease GWAS variants and circulatory system, genitourinary, and neoplastic EHR phenotypes.

Conclusion

Our multiancestry GWAS-PheWAS study demonstrated an effective use of multidimensional EHR information in disease case/control classification with NLP for more comprehensive and scalable phenotyping, and implementation of an integrative analytical pipeline to facilitate etiological investigation of a disease from a clinical perspective.
Deciphering complex mechanisms of resistance and loss of potency through coupled molecular dynamics and machine learning.
Authors: Leidner Florian , Kurt-Yilmaz Nese , Schiffer Celia A
Published: June 2020

Drug resistance threatens many critical therapeutics through mutations in the drug target. The molecular mechanisms by which combinations of mutations, especially involving those distal from the active site, alter drug binding to confer resistance are poorly understood and thus difficult to counteract. A machine learning strategy was developed that couples parallel molecular dynamics simulations and experimental potency to identify specific conserved mechanisms underlying resistance. A series of 28 HIV-1 protease variants with 0-24 substitutions each were used as a rigorous model of this strategy. Many of the mutations were distal from the active site and the potency of variants to a drug (darunavir) varied from low picomolar to near micromolar. With features extracted from the simulations, elastic network machine learning was applied to correlate physical interactions with loss of potency and succeeded to within 1 kcal/mol of experimental affinity for both the training and test sets, outperforming MM/GBSA calculations. Feature reduction resulted in a model with 4 specific features that describe interactions critical for potency for all 28 variants. These predictive features, that specifically vary with potency, occur throughout the enzyme and would not have been identified without dynamics and machine learning. This strategy thus captures the conserved dynamic mechanisms by which complex combinations of mutations confer resistance and identifies critical features that serve as bellwethers of loss of inhibitor potency. Machine learning models leveraging molecular dynamics can thus elucidate mechanisms of drug resistance that confer loss of affinity and will serve as predictive tools in future drug design.
Rab5 regulates macropinosome closure through recruitment of the inositol 5-phosphatases OCRL/Inpp5b and the hydrolysis of PtdIns(4,5)P2
Authors: Maxson Michelle E. , Sarantis Helen , Volchuk Allen , Brumell John H. , Grinstein Sergio
Published: June 2020

Abstract

Rab5 is required for macropinosome formation, but its site and mode of action remain unknown. We report that Rab5 acts at the plasma membrane, downstream of ruffling, to promote macropinosome sealing and scission. Dominant-negative Rab5, which obliterates macropinocytosis, had no effect on the development of membrane ruffles. However, Rab5-containing vesicles were recruited to circular membrane ruffles, and SNARE-dependent endomembrane fusion was necessary for completion of macropinocytosis. This fusion event coincided with the disappearance of PtdIns(4,5)P2that accompanies macropinosome closure. Counteracting the depletion of PtdIns(4,5)P2by expression of phosphatidylinositol-4-phosphate 5-kinase impaired macropinosome formation. Importantly, we found that removal of PtdIns(4,5)P2is dependent on Rab5, through the Rab5-mediated recruitment of the inositol 5-phosphatases OCRL and Inpp5b, via APPL1. Knockdown of OCRL and Inpp5b, or APPL1 prevented macropinosome closure, without affecting ruffling. We therefore propose that Rab5 is essential for the clearance of PtdIns(4,5)P2needed to complete macropinosome scission from the plasmalemma.
VirusDIP: Virus Data Integration Platform
Authors: Wang Lina , Chen Fengzhen , Guo Xueqin , You Lijin , Yang Xiaoxia , Yang Fan , Yang Tao , Gao Fei , Hua Cong , Ding Yuantong , Cai Jia , Yang Linlin , Huang Wei , Xu Zhicheng , Wan Bo , Tong Jiawei , Peng Chunhua , Yang Yawen , Zhang Lei , Liu Ke , Zhou Feiyu , Zhang Minwen , Tan Cong , Zeng Wenjun , Wang Bo , Wei Xiaofeng
Published: June 2020

Motivation

The Coronavirus Disease 2019 (COVID-19) pandemic poses a huge threat to human public health. Viral sequence data plays an important role in the scientific prevention and control of epidemics. A comprehensive virus database will be vital useful for virus data retrieval and deep analysis. To promote sharing of virus data, several virus databases and related analyzing tools have been created.

Results

To facilitate virus research and promote the global sharing of virus data, we present here VirusDIP, a one-stop service platform for archive, integration, access, analysis of virus data. It accepts the submission of viral sequence data from all over the world and currently integrates data resources from the National GeneBank Database (CNGBdb), Global initiative on sharing all influenza data (GISAID), and National Center for Biotechnology Information (NCBI). Moreover, based on the comprehensive data resources, BLAST sequence alignment tool and multi-party security computing tools are deployed for multi-sequence alignment, phylogenetic tree building and global trusted sharing. VirusDIP is gradually establishing cooperation with more databases, and paving the way for the analysis of virus origin and evolution. All public data in VirusDIP are freely available for all researchers worldwide.

Availability

https://db.cngb.org/virus/

Contact

weixiaofeng@cngb.org
Incorporating climate velocity into the design of climate-smart networks of protected areas
Authors: Arafeh-Dalmau Nur , Brito-Morales Isaac , Schoeman David S. , Possingham Hugh P. , Klein Carissa J. , Richardson Anthony J.
Published: June 2020

Climate change is redistributing terrestrial and marine biodiversity and altering fundamental ecological interactions. To adequately conserve biodiversity and promote its long-term persistence, protected areas should account for the ecological implications of species redistribution. Data paucity across many systems means that achieving this goal requires generic metrics that represent likely responses of multiple taxa to climate change. Climate velocity is one such metric, reflecting potential species range shifts at a generic level. Here, we explore four approaches to incorporating climate velocity metrics into the design of protected areas using the Mediterranean Sea as an illustrative example. Our methods are designed to meet two climate-smart planning objectives: 1) protect climate refugia by selecting slow-moving climate velocity areas, and 2) maintain the capacity of ecological systems to adapt by representing a suite of climate-velocity trajectory classes. We found that incorporating climate velocity as a cost measure in Marxan is the best approach for selecting slower-moving areas, which are good indicators of climate refugia. However, this approach fails to accommodate socio-economic cost data, and is probably impractical. Incorporating climate velocity as a boundary or as a feature provides both selection of slower-moving areas and solutions with lower socio-economic cost. Finally, we were able to design cost-effective networks of protected areas representing a suite of climate-velocity trajectories classes, which have the potential to help species adapt to a changing climate. This work presents simple and practical ways of including climate velocity in conservation plans on land and in the ocean to achieve the key climate-smart objectives of protecting climate refugia and enhancing ecological resilience.
eDNA metabarcoding reveals a core and secondary diets of the greater horseshoe bat with strong spatio-temporal plasticity
Authors: Tournayre Orianne , Leuchtmann Maxime , Galan Maxime , Trillat Marine , Piry Sylvain , Pinaud David , Filippi-Codaccioni Ondine , Pontier Dominique , Charbonnel Nathalie
Published: June 2020

Dietary plasticity is an important issue for conservation biology as it may be essential for species to cope with environmental changes. However, this process still remains scarcely addressed in the literature, potentially because diet studies have long been constrained by methodological limits. The advent of molecular approaches now makes it possible to get a precise picture of diet and its plasticity, even for endangered and elusive species. Here we focused on the greater horseshoe bat (Rhinolophus ferrumequinum) in Western France, where this insectivorous species has been classified as ‘Vulnerable’ on the Regional Red List in 2016. We applied an eDNA metabarcoding approach on 1986 fecal samples collected in six maternity colonies at three sampling dates. We described its diet and investigated whether the landscape surrounding colonies and the different phases of the maternity cycle influenced the diversity and the composition of this diet. We showed thatR. ferrumequinumfeed on a highly more diverse spectrum of prey than expected from previous studies, therefore highlighting how eDNA metabarcoding can help improving diet knowledge of a flying elusive endangered species. Our approach also revealed thatR. ferrumequinumdiet is composed of two distinct features: the core diet consisting in a few preferred taxa shared by all the colonies (25% of the occurrences) and the secondary diet consisting in numerous rare prey that were highly different between colonies and sampling dates (75% of the occurrences). Energetic needs and constraints associated with the greater horseshoe bat life-cycle, as well as insect phenology and landscape features, strongly influenced the diversity and composition of both the core and whole diets. Further research should now explore the relationships betweenR. ferrumequinumdietary plasticity and fitness, to better assess the impact of core prey decline onR. ferrumequinumpopulations viability.