bluuebunny/crossref_metadata_2025 huggingface dataset:
Aggregative trans-eQTL analysis detects trait-specific target gene sets in whole blood
Authors: Dutta Diptavo , He Yuan , Saha Ashis , Arvanitis Marios , Battle Alexis , Chatterjee Nilanjan
Published: October 2020

Large scale genetic association studies have identified many trait-associated variants and understanding the role of these variants in downstream regulation of gene-expressions can uncover important mediating biological mechanisms. In this study, we propose Aggregative tRans assoCiation to detect pHenotype specIfic gEne-sets (ARCHIE), as a method to establish links between sets of known genetic variants associated with a trait and sets of co-regulated gene-expressions through trans associations. ARCHIE employs sparse canonical correlation analysis based on summary statistics from trans-eQTL mapping and genotype and expression correlation matrices constructed from external data sources. A resampling based procedure is then used to test for significant trait-specific trans-association patterns in the background of highly polygenic regulation of gene-expression. Simulation studies show that compared to standard trans-eQTL analysis, ARCHIE is better suited to identify "core"-like genes through which effects of many other genes may be mediated and which can explain disease specific patterns of genetic associations. By applying ARCHIE to available trans-eQTL summary statistics reported by the eQTLGen consortium, we identify 71 gene networks which have significant evidence of trans-association with groups of known genetic variants across 29 complex traits. Around half (50.7%) of the selected genes do not have any strong trans-associations and could not have been detected by standard trans-eQTL mapping. We provide further evidence for causal basis of the target genes through a series of follow-up analyses. These results show ARCHIE is a powerful tool for identifying sets of genes whose trans regulation may be related to specific complex traits. The method has potential for broader applications for identification of networks of various types of molecular traits which mediates complex traits genetic associations.
Drought duration determines the recovery dynamics of rice root microbiomes
Authors: Santos-Medellin Christian , Liechty Zachary , Edwards Joseph , Nguyen Bao , Huang Bihua , Weimer Bart C. , Sundaresan Venkatesan
Published: October 2020

As extreme droughts become more frequent, dissecting the responses of root-associated microbiomes to drying-wetting events is essential to understand their influence on plant performance. Here, we show that rhizosphere and endosphere communities associated with drought-stressed rice plants display compartment-specific recovery trends. Rhizosphere microorganisms were mostly affected during the stress period, whereas endosphere microorganisms remained altered even after irrigation was resumed. The duration of drought stress determined the stability of these changes, with more prolonged droughts leading to decreased microbiome resilience. Drought stress was also linked to a permanent delay in the temporal development of root microbiomes, mainly driven by a disruption of late colonization dynamics. Furthermore, a root-growth-promotingStreptomycesbecame the most abundant community member in the endosphere during drought and early recovery. Collectively, these results reveal that severe drought results in enduring impacts on root-associated microbiomes that could potentially reshape the recovery response of rice plants.
Eusociality through conflict dissolution
Authors: González-Forero Mauricio , Peña Jorge
Published: October 2020

Eusociality, where largely unreproductive offspring help their mothers reproduce, is a major form of social organization. An increasingly documented feature of eusociality is that mothers induce their offspring to help by means of hormones, pheromones, or behavioral displays, with evidence often indicating that offspring help voluntarily. The co-occurrence of maternal influence and offspring voluntary help may be explained by what we call the converted helping hypothesis, whereby maternally manipulated helping subsequently becomes voluntary. Such hypothesis requires that parent-offspring conflict is eventually dissolved—for instance, if the benefit of helping increases sufficiently over evolutionary time. We show that help provided by maternally manipulated offspring can enable the mother to sufficiently increase her fertility to transform parent-offspring conflict into parent-offspring agreement. This conflict-dissolution mechanism requires that helpers alleviate maternal life-history trade-offs, and results in reproductive division of labor, high queen fertility, and honest queen signaling suppressing worker reproduction—thus exceptionally recovering diverse features of eusociality. As such trade-off alleviation seemingly holds widely across eusocial taxa, this mechanism offers a potentially general explanation for the origin of eusociality, the prevalence of maternal influence, and the offspring’s willingness to help. Overall, our results explain how a major evolutionary transition can happen from ancestral conflict.
Modeling multifunctionality of genes with secondary gene co-expression networks in human brain provides novel disease insights
Authors: Sánchez Juan A. , Gil-Martinez Ana L. , Cisterna Alejandro , García-Ruíz Sonia , Gómez Alicia , Reynolds Regina , Nalls Mike , Hardy John , Ryten Mina , Botía Juan A.
Published: October 2020

Motivation

Co-expression networks are a powerful gene expression analysis method to study how genes co-express together in clusters with functional coherence that usually resemble specific cell type behaviour for the genes involved. They can be applied to bulk-tissue gene expression profiling and assign function, and usually cell type specificity, to a high percentage of the gene pool used to construct the network. One of the limitations of this method is that each gene is predicted to play a role in a specific set of coherent functions in a single cell type (i.e. at most we get a single  for each gene). We present here GMSCA (Gene Multifunctionality Secondary Co-expression Analysis), a software tool that exploits the co-expression paradigm to increase the number of functions and cell types ascribed to a gene in bulk-tissue co-expression networks.

Results

We applied GMSCA to 27 co-expression networks derived from bulk-tissue gene expression profiling of a variety of brain tissues. Neurons and glial cells (microglia, astrocytes and oligodendrocytes) were considered the main cell types. Applying this approach, we increase the overall number of predicted triplets  by 46.73%. Moreover, GMSCA predicts that theSNCAgene, traditionally associated to work mainly in neurons, also plays a relevant function in oligodendrocytes.

Availability

The tool is available at GitHub,https://github.com/drlaguna/GMSCAas open source software.

Implementation

GSMCA is implemented in R.
Structural insights on the substrate-binding proteins of theMycobacterium tuberculosismammalian-cell-entry (Mce) 1 and 4 complexes
Authors: Asthana Pooja , Singh Dhirendra , Pedersen Jan Skov , Hynönen Mikko J. , Sulu Ramita , Murthy Abhinandan V. , Laitaoja Mikko , Jänis Janne , Riley Lee W. , Venkatesan Rajaram
Published: October 2020

Tuberculosis (Tb), caused byMycobacterium tuberculosis(Mtb), is responsible for more than a million deaths annually. In the latent phase of infection,Mtbuses lipids as the source of carbon and energy for its survival. The lipid molecules are transported across the cell wall via multiple transport systems. One such set of widely present and less-studied transporters is the Mammalian-cell-entry (Mce) complexes. Here, we report the properties of the substrate-binding proteins (SBPs; MceA-F) of the Mce1 and Mce4 complexes fromMtbwhich are responsible for the import of mycolic acid/fatty acids, and cholesterol respectively. MceA-F are composed of four domains namely, transmembrane, MCE, helical and tail domains. Our studies show that MceA-F are predominantly monomeric when purified individually and do not form homohexamers unlike the reported homologs (MlaD, PqiB and LetB) from other prokaryotes. The crystal structure of MCE domain ofMtbMce4A (MtMce4A39-140) determined at 2.9 Å shows the formation of an unexpected domain-swapped dimer in the crystals. Further, the purification and small-angle X-ray scattering (SAXS) analysis on MtMce1A, MtMce4A and their domains suggest that the helical domain requires hydrophobic interactions with the detergent molecules for its stability. Combining all the experimental data, we propose a heterohexameric arrangement of MtMceA-F SBPs, where the soluble MCE domain of the SBPs would remain in the periplasm with the helical domain extending to the lipid layer forming a hollow channel for the transport of lipids across the membranes. The tail domain would reach the cell surface assisting in lipid recognition and binding.
The CXCL12gamma chemokine immobilized by heparan sulfate on stromal niche cells controls adhesion and mediates drug resistance in multiple myeloma
Authors: Ren Zemin , Lantermans Hildo , Kuil Annemieke , Kraan Willem , Arenzana-Seisdedos Fernando , José Kersten Marie , Spaargaren Marcel , Pals Steven T.
Published: October 2020

The homing/retention, survival and proliferation of multiple myeloma (MM) cells critically depends on interaction with CXCL12 expressing stromal cells in the bone marrow (BM) niche. Here, we report a unique role in this interaction for the recently characterized CXCL12gamma isoform, which contains an extended C-terminal domain that binds heparan-sulfate proteoglycans (HSPGs) with an extraordinary high affinity. We observed that CXCL12γ is expressedin situby reticular stromal cells in both normal and MM BM, as well as by primary BM stromal-cell (BMSC) isolates and BMSC lines. Importantly, upon secretion, CXCL12γ, unlike the CXCL12α isoform, was retained on the surface of these BMSCs. This membrane retention of CXCL12γ is HSPG-mediated, since it was completely annulated by CRISPR-Cas9 mediated deletion of the heparan-sulfate (HS) co-polymerase EXT1. Recombinant CXCL12γ was found to induce strong adhesion of MM cells to vascular cell-adhesion molecule 1 (VCAM-1) coated plates. Furthermore, CXCL12γ expressed by BMSCs and membrane-retained by HSPGs, supported robust adhesion of MM cells to the BMSCs. Specific genetic deletion of either CXCL12γ or of EXT1 significantly attenuated the ability of BMSCs to support MM cell adhesion and, in addition, impaired their capacity to protect MM cells from bortezomib-induced cell death. Our data indicate that CXCL12γ functions as a membrane-bound ‘niche chemokine’, which plays a unique role in the interaction of MM cells with the stromal niche by controlling adhesion/retention as well as cell adhesion-mediated drug resistance (CAM-DR). These findings designate CXCL12γ and associated HSPGs as potential therapeutic targets in MM.
Integrating cyanobacterial flavodiiron proteins within the chloroplast photosynthetic electron transport chain maintains carbohydrate turnover and enhances drought stress tolerance in barley
Authors: Shahinnia Fahimeh , Tula Suresh , Hensel Goetz , Reiahisamani Narges , Nasr Nasrin , Kumlehn Jochen , Gómez Rodrigo , Lodeyro Anabella F. , Carrillo Néstor , Hajirezaei Mohammad R.
Published: October 2020

Chloroplasts, the sites of photosynthesis in higher plants, have evolved several means to tolerate short episodes of drought stress through biosynthesis of diverse metabolites essential for plant function, but these become ineffective when the duration of the stress is prolonged. Cyanobacteria are the closest bacterial homologs of plastids with two photosystems to perform photosynthesis and to evolve oxygen as a byproduct. The presence ofFlvgenes encoding flavodiiron proteins has been shown to enhance stress tolerance in cyanobacteria. Here, the products ofSynechocystisgenesFlv1andFlv3were expressed in chloroplasts of barley in an attempt to support the growth of plants exposed to drought. The heterologous expression of bothFlv1 and Flv3accelerated days to heading, increased biomass, promoted the number of spikes and grains per plant, and improved grain yield of barley plants exposed to drought. Improved growth correlated with enhanced availability of soluble sugars, a higher turnover of amino acids and the accumulation of lower levels of proline in the leaf.Flv1andFlv3maintained the energy status of the leaves in the stressed plants by converting sucrose to glucose and fructose, immediate precursors for energy production to support plant growth under drought. The results suggest that sugars and amino acids play a fundamental role in the maintenance of the energy status and metabolic activity to ensure growth and survival under stress conditions, that is, water limitation in this particular case. Engineering chloroplasts by introducingFlvgenes, therefore, has the potential to improve plant productivity wherever drought stress represents a significant production constraint.
Population-level consequences of inheritable somatic mutations and the evolution of mutation rates in plants
Authors: Lesaffre Thomas
Published: October 2020

Inbreeding depression, that is the decrease in fitness of inbred relative to outbred individuals, was shown to increase strongly as life expectancy increases in plants. Because plants are thought to not have a separated germline, it was proposed that this pattern could be generated by somatic mutations accumulating during growth, since larger and more long-lived species have more opportunities for mutations to accumulate. A key determinant of the role of somatic mutations is the rate at which they occur, which likely differs between species because mutation rates may evolve differently in species with constrasting life-histories. In this paper, we study the evolution of the mutation rates in plants, and consider the population-level consequences of inheritable somatic mutations given this evolution. We show that despite substantially lower per year mutation rates, more long-lived species still tend to accumulate larger amounts of deleterious mutations because of higher per generation, leading to higher levels of inbreeding depression in these species. However, the magnitude of this increase depends strongly on how mutagenic meiosis is relative to growth.
Locating and dating land cover change events in the Renosterveld, a Critically Endangered shrubland ecosystem
Authors: Moncrieff Glenn R.
Published: October 2020

Land cover change is the leading cause of global biodiversity decline. New satellite platforms allow monitoring of habitats in increasingly fine detail, but most applications have been limited to forested ecosystems. I demonstrate the potential for detailed mapping and accurate dating of land cover change events in a highly biodiverse, Critically Endangered, shrubland ecosystem - the Renosterveld of South Africa. Using supervised classification of Sentinel 2 data, and subsequent manual verification with very high resolution imagery, I locate all conversion of Renosterveld to non-natural land cover between 2016 and 2020. Land cover change events are further assigned dates using high temporal frequency data from Planet labs. 478.6 hectares of Renosterveld loss was observed over this period, accounting for 0.72 % of the remaining natural vegetation in the region. 50% of change events were dated to within two weeks of their actual occurrence, and 87% to within two months. Change often preceded the planting and harvesting seasons of rainfed annual grains. These results show the potential for new satellite platforms to accurately map land cover change in non-forest ecosystems, and detect change within days of its occurrence. There is potential to use this and similar datasets to automate the process of change detection and monitor change continuously.
Cell intrinsic signaling inMEN1mutant pancreatic neuroendocrine tumors unveils novel signaling pathways associated with de-differentiation
Authors: Rheinheimer Brenna A. , Heimark Ronald L. , Grant Adam D. , Camacho Luis , Padi Megha , Jie Tun
Published: October 2020

Objectives

Preliminary genomic analysis of primary pancreatic neuroendocrine tumors revealed a complex mutational landscape with four common oncogenic events; however, critical activation pathways responsible for pancreatic neuroendocrine tumor progression and metastasis have yet to be elucidated. Here, we analyzed six primary pancreatic neuroendocrine tumors to determine which pathways are deregulated and responsible for progression.

Methods

Selected genomic profiling of six primary pancreatic neuroendocrine tumors was performed using the Ion Torrent Comprehensive Cancer Panel with matched transcriptomes analyzed by Affymetrix Clariom D arrays. Validation of gene expression changes were measured by quantitative PCR using TaqMan assays and immunohistochemistry on tumor specimens.

Results

MEN1was mutated in half (50%) of our sequenced tumors whileFGFR3was mutated in 2/6 (33%). Transcriptome analysis revealed thatITGA2andEZH2were overexpressed inMEN1mutant tumors whereasALKandVEGFAwere overexpressed inFGFR3mutant tumors. Immunohistochemistry revealed increased nuclear ITGA2 and EZH2 staining along with increased VE-Cadherin staining and loss of membranous E-cadherin localization inMEN1andFGFR3mutant tumors.

Conclusions

Our results suggest that pancreatic neuroendocrine tumors containingMEN1andFGFR3mutations are more aggressive and de-differentiated than their wild-type counterparts. Additionally, we provide novel chemotherapeutic target FGFR3 for patients with this disease.
Computational identification of human biological processes and protein sequence motifs putatively targeted by SARS-CoV-2 proteins using protein-protein interaction networks
Authors: Nadeau Rachel , Fard Soroush Shahryari , Scheer Amit , Roth Emily , Nygard Dallas , Abramchuk Iryna , Chung Yun-En , Bennett Steffany A. L. , Lavallée-Adam Mathieu
Published: October 2020

While the COVID-19 pandemic is causing important loss of life, knowledge of the effects of the causative SARS-CoV-2 virus on human cells is currently limited. Investigating protein-protein interactions (PPIs) between viral and host proteins can provide a better understanding of the mechanisms exploited by the virus and enable the identification of potential drug targets. We therefore performed an in-depth computational analysis of the interactome of SARS-CoV-2 and human proteins in infected HEK293 cells published by Gordon et al. to reveal processes that are potentially affected by the virus and putative protein binding sites. Specifically, we performed a set of network-based functional and sequence motif enrichment analyses on SARS-CoV-2-interacting human proteins and on a PPI network generated by supplementing viral-host PPIs with known interactions. Using a novel implementation of our GoNet algorithm, we identified 329 Gene Ontology terms for which the SARS-CoV-2-interacting human proteins are significantly clustered in the network. Furthermore, we present a novel protein sequence motif discovery approach, LESMoN-Pro, that identified 9 amino acid motifs for which the associated proteins are clustered in the network. Together, these results provide insights into the processes and sequence motifs that are putatively implicated in SARS-CoV-2 infection and could lead to potential therapeutic targets.
BANCOVID, the first D614G variant mRNA-based vaccine candidate against SARS-CoV-2 elicits neutralizing antibody and balanced cellular immune response
Authors: Baray Juwel Chandra , Khan Md. Maksudur Rahman , Mahmud Asif , Islam Md. Jikrul , Myti Sanat , Ali Md. Rostum , Sarker Md. Enamul Haq , Kumar Samir , Chowdhury Md. Mobarak Hossain , Roy Rony , Islam Faqrul , Barman Uttam , Khan Habiba , Chakraborty Sourav , Hossain Md. Manik , Chowdhury Md. Mashfiqur Rahman , Ghosh Polash , Mohiuddin Mohammad , Sultana Naznin , Nag Kakon
Published: October 2020

Effective vaccine against SARS-CoV-2 is the utmost importance in the current world. More than 1 million deaths are accounted for relevant pandemic disease COVID-19. Recent data showed that D614G genotype of the virus is highly infectious and responsible for almost all infection for 2ndwave. Despite of multiple vaccine development initiatives, there are currently no report that has addressed this critical variant D614G as vaccine candidate. Here we report the development of an mRNA-LNP vaccine considering the D614G variant and characterization of the vaccine in preclinical trial. The surface plasmon resonance (SPR) data with spike protein as probe and competitive neutralization with RBD and S2 domain revealed that immunization generated specific antibody pools against the whole extracellular domain (RBD and S2) of the spike protein. The anti-sera and purified IgGs from immunized mice on day 7 and 14 neutralized SARS-CoV-2 pseudovirus in ACE2-expressing HEK293 cells in a dose dependent manner. Importantly, immunization protected mice lungs from pseudovirus entry and cytopathy. The immunologic responses have been implicated by a balanced and stable population of CD4+cells with a Th1 bias. The IgG2a to IgG1 and (IgG2a+IgG2b) to (IgG1+IgG3) ratios were found 1±0.2 and 1.24±0.1, respectively. These values are comparatively higher than relevant values for other published SARS-CoV-2 vaccine in development,1, 2and suggesting higher viral clearance capacity for our vaccine. The data suggested great promise for immediate translation of the technology to the clinic.
Reengineering the Specificity of the Highly SelectiveClostridium botulinumProtease via Directed Evolution
Authors: Dyer Rebekah P. , Isoda Hariny M. , Salcedo Gabriela S. , Speciale Gaetano , Fletcher Madison H. , Le Linh Q. , Liu Yi , Malik Shiazah Z. , Vazquez-Cintron Edwin J. , Chu Andrew C. , Rupp David C. , Jacky Birgitte P.S. , Nguyen Thu T.M. , Steward Lance E. , Majumdar Sudipta , Brideau-Andersen Amy D. , Weiss Gregory A.
Published: October 2020

The botulinum neurotoxin serotype A (BoNT/A) cuts a single peptide bond in SNAP25, an activity used to treat a wide range of diseases. Reengineering the substrate specificity of BoNT/A’s protease domain (LC/A) could expand its therapeutic applications; however, LC/A’s extended substrate recognition (≈60 residues) challenges conventional approaches. We report a directed evolution method for retargeting LC/A’s substrate and retaining its exquisite specificity. The resultant eight-mutation LC/A (omLC/A) has improved cleavage specificity and catalytic efficiency (1300- and 120-fold, respectively) for SNAP23 versus SNAP25 compared to a previously reported LC/A variant. Importantly, the BoNT/A holotoxin equipped with omLC/A infiltrates neurons and retains its SNAP23 activity. The identification of substrate control loops outside BoNT/A’s active site could guide the design of improved BoNT proteases and inhibitors.

One Sentence Summary

Directed evolution of the BoNT/A protease targets a new cellular protein, SNAP23, expanding its therapeutic potential.
Development of a 16S metabarcoding assay for the environmental DNA (eDNA) detection of aquatic reptiles across northern Australia
Authors: West Katrina , Heydenrych Matthew , Lines Rose , Tucker Tony , Fossette Sabrina , Whiting Scott , Bunce Michael
Published: October 2020

A severe lack of distribution data for aquatic reptiles in northern Australia leaves many taxa vulnerable to extirpation and extinction. Environmental DNA (eDNA) technologies offer sensitive and non-invasive genetic alternatives to trapping and visual surveys and are increasingly employed for the detection of aquatic and semi-aquatic reptiles. However, at present, these studies have largely applied species-specific primers which do not provide a cost-effective avenue for the simultaneous detection of multiple reptilian taxa. Here, we present a 16S rRNA metabarcoding assay for the broad detection of aquatic and semi-aquatic reptile species. This assay is tested on water samples collected at multiple sampling sites at two tropical locations: 12 marine/estuarine sites in Roebuck Bay, Western Australia, and 4 estuarine sites in Cooktown, Queensland, Australia. A total of nine reptile taxa were detected from 10 of the 16 sampled sites, including marine and freshwater turtles, aquatic and semi-aquatic/terrestrial snakes, and terrestrial skinks. However, inconsistencies in the detection of previously observed aquatic reptiles at our sampled sites, such as saltwater crocodile and sea snakes, indicates that further research is required to assess the reliability, strengths and limitations of eDNA methods for aquatic reptile detection before it can be integrated as a broad-scale bioassessment tool.
Consolidation and maintenance ofDrosophilalong-term memory require LIM homeodomain protein Apterous in distinct brain neurons
Authors: Inami Show , Sato Tomohito , Suzuki Yuki , Kitamoto Toshihiro , Sakai Takaomi
Published: October 2020

The LIM-homeodomain (LIM-HD) transcription factor Apterous (Ap) and its cofactor Chip (Chi) form a complex that regulates various developmental events inDrosophila. Although Ap continues to be expressed in the adult brain, the functions of the centrally expressed Ap remain incompletely understood. Here, we show that Ap and Chi in theDrosophilamemory center, the mushroom bodies (MBs), are indispensable for long-term memory (LTM) maintenance, whereas Ap in a subset of clock neurons [large ventral-lateral neurons (l-LNvs)] plays a crucial role in memory consolidation in a Chi-independent manner.Ex vivoimaging revealed that Ap, but not Chi, in l-LNvs is essential for the appropriate Cl−responses to GABA. Furthermore, knockdown of GABAAreceptor in l-LNvs compensated for the impairment of memory consolidation inapnull mutant flies. Our results indicate thatDrosophilaAp functions differently in l-LNvs and MBs, and it contributes to the consolidation and maintenance of LTM.
Mitochondria fragment and reassemble to initiate the formation and development of the nucleus
Authors: Jiang Xuejun , Hou Bolin , Xu Yang , Li Erwei , Cao Pei , Liu Shuchun , Xi Zhijun , Yang Huaiyi , Huo Yuqing , Che Yongsheng
Published: October 2020

The function of nuclear-localized mitochondria remains unknown. We found that mitochondria assembled dense particles to fragment and disperse into the particles, which reassembled to initiate nuclear formation and development. Individually-formed nuclei in one single cell were joined together by mitochondrial fragmentation concurrently partitioning cytoplasm to form an intranuclear inclusion (INC), whose creation was not related to herniation or invagination of the cytoplasm. Along with the nuclear transition of a mitochondrion and its neighboring counterparts, the organelle included itself in the nucleus to become nuclear mitochondrion through peripherally assembling of dense particles. New medium reversed the nuclear formation of the organelles to recovery and re-establishment via the return of the particles, which consisted of dense microvesicles (MIVs).
Randomized Controlled Trials of Early Ambulatory Hydroxychloroquine in the Prevention of COVID-19 Infection, Hospitalization, and Death: Meta-Analysis
Authors: Ladapo Joseph A. , McKinnon John E. , McCullough Peter A. , Risch Harvey A.
Published: October 2020

Objective

To determine if hydroxychloroquine (HCQ) reduces the incidence of new illness, hospitalization or death among outpatients at risk for or infected with SARS-CoV-2 (COVID-19).

Design

Systematic review and meta-analysis of randomized clinical trials.

Data sources

Search of MEDLINE, EMBASE, PubMed, medRxiv, PROSPERO, and the Cochrane Central Register of Controlled Trials. Also review of reference lists from recent meta-analyses.

Study selection

Randomized clinical trials in which participants were treated with HCQ or placebo/standard-of-care for pre-exposure prophylaxis, post-exposure prophylaxis, or outpatient therapy for COVID-19.

Methods

Two investigators independently extracted data on trial design and outcomes. Medication side effects and adverse reactions were also assessed. The primary outcome was COVID-19 hospitalization or death. When unavailable, new COVID-19 infection was used. We calculated random effects meta-analysis according to the method of DerSimonian and Laird. Heterogeneity between the studies was evaluated by calculation of Cochran Q and I2parameters. An Egger funnel plot was drawn to investigate publication bias. We also calculated the fixed effects meta-analysis summary of the five studies. All calculations were done in Excel, and results were considered to be statistically significant at a two-sided threshold of P=.05.

Results

Five randomized controlled clinical trials enrolling 5,577 patients were included. HCQ was associated with a 24% reduction in COVID-19 infection, hospitalization or death, P=.025 (RR, 0.76 [95% CI, 0.59 to 0.97]). No serious adverse cardiac events were reported. The most common side effects were gastrointestinal.

Conclusion

Hydroxychloroquine use in outpatients reduces the incidence of the composite outcome of COVID-19 infection, hospitalization, and death. Serious adverse events were not reported and cardiac arrhythmia was rare.

Systematic review registration

This review was not registered.
Modified Harvard Step Testing within a Clinic Setting Enables Exercise Prescription for Cancer Survivors
Authors: White Katherine R. , Lu Jana , Ibrahim Zara , Furth Priscilla A.
Published: October 2020

Purpose

To evaluate the utility of modified Harvard Step tests within the context of a comprehensive physical examination for fitness evaluation and exercise prescription for cancer survivors.

Methods

A retrospective chart review of initial cancer survivor clinic visits over a ten-year period (n=169) was conducted to evaluate correlations between demographic factors, clinical characteristics, step and strength test performance, and exercise prescriptions.

Results

Clinic population was 94% female, aged 27-79 years, predominantly breast cancer (87%), presenting within two years of cancer diagnosis with current exercise history significantly less vigorous than past exercise (p=0.00; 34% sedentary). Fifty-two percent completed a 3-minute-9-inch step test at pace (96 steps per minute). Fourteen percent required slower self-pacing, 12% both a slower pace and shortened time, and 5% a flat test. Younger age (p=0.04) and more vigorous exercise histories (p<0.04) correlated with ability to complete the at pace test but all formats led to exercise prescriptions more vigorous than current activity (p<0.0002). Stratified fitness ratings using YMCA normative data yielded associations between higher fitness levels and lower BMI (F(1,86)=4.149,p<0.05), office pulse (F(1,87)=7.677,p<0.05), and systolic blood pressure (F(1,18)=6.58,p<0.05).

Conclusions

Office-based fitness evaluation with a panel of modified step test options accommodating different baseline fitness levels enabled personalized exercise prescriptions more vigorous than current activity.

Implications for Cancer Survivors

Cancer patients frequently engage in less vigorous activity as they enter into survivorship. Modified step tests are a means for office-based evaluation of cardiovascular fitness within the context of a comprehensive physical examination.
Transgenic pyrimethamine resistantPlasmodium bergheias a model forin vivoanti-DHFR drug testing
Authors: Koonyosying Pongpisid , Jupatanakul Natapong , Vanichtanankul Jarunee , Saeyang Thanaya , Pethrak Chatpong , Pengon Jutharat , Tipsuwan Wachiraporn , Yuthavong Yongyuth , Kamchonwongpaisan Sumalee , Uthaipibull Chairat
Published: October 2020

Inhibitors forPlasmodium falciparumdihydrofolate reductase (DHFR) form an important class of antimalarial drugs widely used for malaria treatment, but have been compromised by development of resistance to the drugs. Mutations in DHFR are the main contributing factors to the resistance. Although new, rationally designed antifolates active against resistantP. falciparum, such as P218, have been developed, the activity against the quadruple mutantP. falciparum(V1/S) has only been demonstratedin vitro, andin vivoactivity has only been shown in SCID mice. A convenientin vivomodel for antifolate testing is desirable. In this study, the endogenousP. bergheidihydrofolate reductase-thymidylate synthase (Pbdhfr-ts) gene was successfully replaced by quadrupledhfr-tsmutant gene fromP. falciparum(N51I+C59R+S108N+I164L). The transgenic parasite gained resistance to pyrimethamine but not to other class of antimalarial drugs. While 30 mg/kg of pyrimethamine could not inhibit the transgenic parasite, P218 could inhibit the transgenic parasite with the ED50of 0.11±0.02 mg/kg, a level similar to theP. falciparumin SCID mice model. These results demonstrated the validity of our model and showed that P218 was very potent against quadruplePfdhfr-tsmutant parasite,in vivo.
Disturbance Triggers Non-Linear Microbe-Environment Feedbacks
Authors: Sengupta Aditi , Fansler Sarah J. , Chu Rosalie K. , Danczak Robert E. , Garayburu-Caruso Vanessa A. , Renteria Lupita , Song Hyun-Seob , Toyoda Jason , Wells Jacqueline , Stegen James C.
Published: October 2020

Conceptual frameworks linking microbial community membership, properties, and processes with the environment and emergent function have been proposed but remain untested. Here we refine and test a recent conceptual framework using hyporheic zone sediments exposed to wetting/drying transitions. Throughout the system we found threshold-like responses to the duration of desiccation. Membership of the putatively active community--but not the whole community--responded due to enhanced deterministic selection (an emergent community property). Concurrently, the thermodynamic properties of organic matter became less favorable for oxidation (an environmental component) and respiration decreased (a microbial process). While these responses were step functions of desiccation, we observed continuous monotonic relationships among community assembly, respiration, and organic matter thermodynamics. Placing the results in context of our conceptual framework points to previously unrecognized internal feedbacks that are initiated by disturbance, mediated by thermodynamics, and that cause the impacts of disturbance to be dependent on the history of disturbance.
Combining epiGBS markers with long read transcriptome sequencing to assess differentiation associated with habitat inReynoutria(akaFallopia)
Authors: Robertson Marta , Alvarez Mariano , van Gurp Thomas , Wagemaker Cornelis A. M. , Yu Fahong , Amador David Moraga , Farmerie William G. , Verhoeven Koen J. F. , Richards Christina L.
Published: October 2020

Despite the limitations of genetic bottlenecks, several invasive species appear to thrive in non-native ranges with extremely low levels of sequence-based genetic variation. We previously demonstrated differentiation of DNA methylation to habitat types of the highly clonal, genetically depauperate Japanese knotweeds using anonymous markers, but the functional relevance of this DNA methylation variation is unknown. Here, we sequenced the full transcriptome combined with a reduced representation bisulfite sequencing approach, epigenotyping by sequencing (epiGBS), to characterize the association among DNA methylation, functional transcripts and the diverse habitat types occupied by the invasiveReynoutriaspecies. We identified 50,435 putative transcripts overall, of which 48,866 were annotated with the NCBI NR database. Of these 17,872 (35%) and 16,122 (32%) transcripts shared sequence identity withArabidopsis thalianaandBeta vulgaris, respectively. We found genetic differentiation by habitat type suggesting the action of selection and a marginal pattern of differentiation of DNA methylation among habitats, which appears to be associated with sequence differences. However, we found no individual methylation loci associated with habitat, limiting our ability to make functional interpretations. Regardless of the source of variation in DNA methylation, these changes may represent an important component of the response to environmental conditions, particularly in highly clonal plants, but more fine scale genomics analysis is required to test if DNA methylation variation in this system is responsible for functional divergence.
The Role of DOT1L Methyltransferase Activity in Fetal Hematopoiesis
Authors: Malcom Carrie A. , Piaseka-Srader Joanna , Chakravarthi V. Praveen , Borosha Shaon , Ratri Anamika , Alvarez Nehemiah , Vivian Jay L. , Fields Timothy A. , Rumi M.A. Karim , Fields Patrick E.
Published: October 2020

Early mammalian erythropoiesis requires the DOT1L methyltransferase. We demonstrated that loss of DOT1L in mutant mice resulted in lethal anemia during midgestation. The molecular mechanisms by which DOT1L regulates embryonic erythropoiesis have not yet been elucidated. In this study, a methyltransferase mutant mouse line (Dot1L-MM) was generated to determine whether the methyltransferase activity of DOT1L is essential for erythropoiesis.Dot1L-MM mice displayed embryonic lethality between embryonic days 10.5 and 13.5, similar toDot1lLknockout (Dot1L-KO) mice. However, when examined at E10.5, unlike theDot1L-KO,Dot1L-MM embryos did not exhibit evidence of anemia. Inex vivohematopoietic differentiation cultures,Dot1L-KO andDot1L-MM yolk sac (YS) cells both formed reduced numbers of myeloid, and mixed hematopoietic colonies. Erythroid colonies were able to be formed in numbers equal to wildtype embryos. Extensively self-renewing erythroblast (ESRE) cultures were established using YS cells from E10.5 embryos.Dot1L-KO andDot1L-MM cells expanded significantly less than wild-type cells and exhibited increased cell death. Strikingly,Dot1L-KO andDot1L-MM cells of YS origin exhibited profound genomic instability, implicating DOT1L methyltransferase activity in maintenance of the genome as well as viability of hematopoietic progenitors. Our results indicate that the methyltransferase activity of DOT1L plays an important role early murine hematopoiesis.
Estimating the extrinsic incubation period of malaria using a mechanistic model of sporogony
Authors: Stopard Isaac J. , Churcher Thomas S. , Lambert Ben
Published: October 2020

During sporogony, malaria-causing parasites infect a mosquito, reproduce and migrate to the mosquito salivary glands where they can be transmitted the next time blood-feeding occurs. The time required for sporogony, or extrinsic incubation period (EIP), is a crucial determinant of malaria transmission intensity. The EIP is typically estimated as the time for a given percentile of infected mosquitoes to have salivary gland sporozoites (the infectious parasite life stage). Many mechanisms, however, affect the observed sporozoite prevalence including the human-to-mosquito transmission probability and possibly differences in mosquito mortality according to infection status. To account for these various mechanisms, we present a mechanistic mathematical model (“mSOS”), which explicitly models key processes at the parasite, mosquito and observational scales. Fitting this model to experimental data, we find greater variation in EIP than previously thought: we estimated the range between two percentiles of the distribution, EIP10–EIP90(at 27°C), as 4.5 days, compared to 0.9 days using existing methods. This pattern holds over the range of study temperatures included in the dataset. Increasing temperature from 21°C to 34°C decreased the EIP50from 16.1 to 8.8 days and the human-to-mosquito transmission probability from 84% to 42%. Our work highlights the importance of mechanistic modelling of sporogony to (1) improve estimates of malaria transmission under different environmental conditions or disease control programs and (2) evaluate novel interventions that target the mosquito life stages of the parasite.

Author summary

Anophelesmosquitoes become infected with malaria-causing parasites when blood feeding on an infectious human host. The parasites then process through a number of life stages, which begin in the mosquito gut and end in the salivary glands, where the newly formed infectious parasites can be transmitted to another host the next time a mosquito blood-feeds. The large variability in parasite numbers and development times that exists between mosquitoes, environments and parasites, mean that understanding parasite population dynamics from individual mosquito dissections is difficult. Here, we introduce a mathematical model of the mosquito life stages of parasites that mimics key characteristics of the biology. We show that the model’s parameters can be chosen so that its predictions correspond with experimental observations. In doing so, we estimate key system characteristics that are crucial determinants of malaria transmission intensity. Our work is a step towards a realistic model of within-mosquito parasite dynamics, which is increasingly important given that many recently proposed disease interventions specifically target mosquito life stages of the parasite.
A novel regulatory element upstream ofTNFAIP3promoter may be influenced by SLE risk variants
Authors: Nair Ajay , Rao Archana S
Published: October 2020

Almost all of Genome Wide Association Studies (GWAS) hits come from non-coding DNA elements. Data from chromatin interaction analyses suggest a long-range interaction with a putative enhancer upstream ofTNFAIP3. Disrupting the enhancer may impairTNFAIP3expression and enhance SLE risk. Two variants, rs10499197 and rs58905141 carried on the SLE risk haplotype are situated near this enhancer and could affect its function. Cloning the regulatory region surrounding rs10499197 into an expression plasmid containing a CRISPR-Cas9 backbone, and then performing a genome editing assay, we found that the variant is located near an enhancer. And any changes to the SNP region might impair enhancer and its ability to regulateTNFAIP3expression.
Implicit counterfactual effect in partial feedback reinforcement learning: behavioral and modeling approach
Authors: Barakchian Zahra , Vahabie Abdol-hossein , Ahmadabadi Majid Nili
Published: October 2020

Context by distorting values of options with respect to the distribution of available alternatives, remarkably affects learning behavior. Providing an explicit counterfactual component, outcome of unchosen option alongside with the chosen one (Complete feedback), would increase the contextual effect by inducing comparison-based strategy during learning. But It is not clear in the conditions where the context consists only of the juxtaposition of a series of options, and there is no such explicit counterfactual component (Partial feedback), whether and how the relativity will be emerged. Here for investigating whether and how implicit and explicit counterfactual components can affect reinforcement learning, we used two Partial and Complete feedback paradigms, in which options were associated with some reward distributions. Our modeling analysis illustrates that the model which uses the outcome of chosen option for updating values of both chosen and unchosen options, which is in line with diffusive function of dopamine on the striatum, can better account for the behavioral data. We also observed that size of this bias depends on the involved systems in the brain, such that this effect is larger in the transfer phase where subcortical systems are more involved, and is smaller in the deliberative value estimation phase where cortical system is more needed. Furthermore, our data shows that contextual effect is not only limited to probabilistic reward but also it extends to reward with amplitude. These results show that by extending counterfactual concept, we can better account for why there is contextual effect in a condition where there is no extra information of unchosen outcome.
Multiple pathways to homothallism in closely related yeast lineages in the Basidiomycota
Authors: Cabrita Alexandra , David-Palma Márcia , Brito Patrícia H. , Heitman Joseph , Coelho Marco A. , Gonçalves Paula
Published: October 2020

Sexual reproduction in fungi relies on proteins with well-known functions encoded by the mating-type (MAT) loci. In the Basidiomycota,MATloci are often bipartite, with theP/Rlocus encoding pheromone precursors and pheromone receptors and theHDlocus encoding heterodimerizing homeodomain transcription factors (Hd1/Hd2). The interplay between different alleles of these genes within a single species usually generates at least two compatible mating types. However, a minority of species are homothallic, reproducing sexually without an obligate need for a compatible partner. Here we examine the organization and function of theMATloci ofCystofilobasidium capitatum, a species in the order Cystofilobasidiales, which is unusually rich in homothallic species. We determinedMATgene content and organization inC. capitatumand found that it resembles a mating type of the closely related heterothallic speciesCystofilobasidium ferigula. To explain the homothallic sexual reproduction observed inC. capitatumwe examined HD-protein interactions in the twoCystofilobasidiumspecies and determinedC. capitatum MATgene expression both in a natural setting and upon heterologous expression inPhaffia rhodozyma, a homothallic species belonging to a clade sister toCystofilobasidium. We conclude that the molecular basis for homothallism inC. capitatumappears to be distinct from that previously established forP. rhodozyma. Unlike the latter species, homothallism inC. capitatummay involve constitutive activation or dispensability of the pheromone receptor and the functional replacement of the usual Hd1/Hd2 heterodimer by an Hd2 homodimer. Overall, our results suggest that homothallism evolved multiple times within the Cystofilobasidiales.

Importance

Sexual reproduction is important for the biology of eukaryotes because it strongly impacts the dynamics of genetic variation. In fungi, although sexual reproduction is usually associated with the fusion between cells belonging to different individuals (heterothallism), sometimes a single individual is capable of completing the sexual cycle alone (homothallism). Homothallic species are unusually common in a fungal lineage named Cystofilobasidiales. Here we studied the genetic bases of homothallism in one species in this lineage,Cystofilobasidium capitatum, and found it to be different in several aspects when compared to another homothallic species,Phaffia rhodozyma, belonging to the genus most closely related toCystofilobasidium. Our results strongly suggest that homothallism evolved independently inPhaffiaandCystofilobasidium, lending support to the idea that transitions between heterothallism and homothallism are not as infrequent as previously thought. Our work also helps to establish the Cystofilobasidiales as a model lineage in which to study these transitions.