bluuebunny/crossref_metadata_2025 huggingface dataset:
Outcome of hospitalisation for COVID-19 in patients with Interstitial Lung Disease: An international multicentre study.
Authors: Drake Thomas M , Docherty Annemarie B , Harrison Ewen M , Quint Jennifer K , Adamali Huzaifa , Agnew Sarah , Babu Suresh , Barber Christopher M , Barratt Shaney , Bendstrup Elisabeth , Bianchi Stephen , Villegas Diego Castillo , Chaudhuri Nazia , Chua Felix , Coker Robina , Chang William , Crawshaw Anjali , Crowley Louise E. , Dosanjh Davinder , Fiddler Christine A , Forrest Ian A. , George Peter , Gibbons Michael A , Groom Katherine , Haney Sarah , Hart Simon P , Heiden Emily , Henry Michael , Ho Ling-Pei , Hoyles Rachel K , Hutchinson John , Hurley Killian , Jones Mark , Jones Steve , Kokosi Maria , Kreuter Michael , MacKay Laura , Mahendran Siva , Margaritopoulos George , Molina-Molina Maria , Molyneaux Philip L , O’Brien Aiden , O’Reilly Katherine , Packham Alice , Parfrey Helen , Poletti Venerino , Porter Joanna , Renzoni Elisabetta , Rivera-Ortega Pilar , Russell Anne-Marie , Saini Gauri , Spencer Lisa G , Stella Giulia M. , Stone Helen , Sturney Sharon , Thickett David , Thillai Muhunthan , Wallis Tim , Ward Katie , Wells Athol U , West Alex , Wickremasinghe Melissa , Woodhead Felix , Hearson Glenn , Howard Lucy , Baillie J Kenneth , Openshaw Peter J.M. , Semple Malcolm G , Stewart Iain ,   ISARIC4C Investigators, Jenkins R Gisli
Published: July 2020

Rationale

The impact of COVID-19 on patients with Interstitial Lung Disease (ILD) has not been established.

Objectives

To assess outcomes following COVID-19 in patients with ILD versus those without in a contemporaneous age, sex and comorbidity matched population.

Methods

An international multicentre audit of patients with a prior diagnosis of ILD admitted to hospital with COVID-19 between 1 March and 1 May 2020 was undertaken and compared with patients, without ILD obtained from the ISARIC 4C cohort, admitted with COVID-19 over the same period. The primary outcome was survival. Secondary analysis distinguished IPF from non-IPF ILD and used lung function to determine the greatest risks of death.

Measurements and Main Results

Data from 349 patients with ILD across Europe were included, of whom 161 were admitted to hospital with laboratory or clinical evidence of COVID-19 and eligible for propensity-score matching. Overall mortality was 49% (79/161) in patients with ILD with COVID-19. After matching ILD patients with COVID-19 had higher mortality (HR 1.60, Confidence Intervals 1.17-2.18 p=0.003) compared with age, sex and comorbidity matched controls without ILD. Patients with a Forced Vital Capacity (FVC) of <80% had an increased risk of death versus patients with FVC ≥80% (HR 1.72, 1.05-2.83). Furthermore, obese patients with ILD had an elevated risk of death (HR 1.98, 1.13−3.46).

Conclusions

Patients with ILD are at increased risk of death from COVID-19, particularly those with poor lung function and obesity. Stringent precautions should be taken to avoid COVID-19 in patients with ILD.
Noise signature in added size suggests bacteria target a commitment size to enable division
Authors: Nieto César , Arias-Castro Juan , Vargas-García César , Sánchez Carlos , Pedraza Juan Manuel
Published: July 2020

Recent experiments suggested that sizer-like division strategy, a deviation from the adder paradigm might be produced by additional degradation events of cell division machinery molecules. We revisited single cell size data from a recently microfluidics setup using the above model. We observed that such additional degradation process, although reproduces size observations in the mean sense, it is unable to capture cell size fluctuations. We further extended recently proposed power law models to include commitment size. Our proposal is in agreement of both mean and fluctuation profiles seen in experiments. Our approach suggests further uses of noise profiles on dissecting cell size regulatory mechanisms.

SIGNIFICANCE

We contrast cell division models against bacteria cell size data in minimal media. Our results seems to support the idea that division starts once bacteria meet a given commitment size.
Interleukin-10 suppression enhances T-cell antitumor immunity and responses to checkpoint blockade in chronic lymphocytic leukemia
Authors: Rivas J.R. , Liu Y. , Alhakeem S.S. , Eckenrode J.M. , Marti F. , Collard J.P. , Zhang Y. , Shaaban K.A. , Muthusamy N. , Hildebrandt G.C. , Fleischman R.A. , Chen L. , Thorson J.S. , Leggas M. , Bondada S.
Published: July 2020

T-cell dysfunction is a hallmark of B-cell Chronic Lymphocytic Leukemia (CLL), where CLL cells downregulate T-cell responses through regulatory molecules including programmed death ligand-1 (PD-L1) and Interleukin-10 (IL-10). Immune checkpoint blockade (ICB) aims to restore T-cell function by preventing the ligation of inhibitory receptors like PD-1. However, most CLL patients do not respond well to this therapy. Thus, we investigated whether IL-10 suppression could enhance antitumor T-cell activity and responses to ICB. Since CLL IL-10 expression depends on Sp1, we utilized a novel, better tolerated analogue of the Sp1 inhibitor mithramycin (MTMox32E) to suppress CLL IL-10. MTMox32Etreatment inhibited mouse and human CLL IL-10 production and maintained T-cell effector functionin vitro. In the Eμ-Tcl1 mouse model, treatment reduced plasma IL-10 and CLL burden and increased CD8+T-cell proliferation, effector and memory cell prevalence, and interferon-γ production. When combined with ICB, suppression of IL-10 improved responses to anti-PD-L1 as shown by a 4.5-fold decrease in CLL cell burden compared to anti-PD-L1 alone. Combination therapy also produced more interferon-γ+, cytotoxic effector KLRG1+, and memory CD8+T-cells, and fewer exhausted T-cells. Since current therapies for CLL do not target IL-10, this provides a novel strategy to improve immunotherapies.
Artificial feeding of invasive grey squirrels (Sciurus carolinensis) at urban parks: a social norms approach to understand its drivers and to guide behavioral interventions
Authors: Cerri Jacopo , Martinelli Elena , Bertolino Sandro
Published: July 2020

Artificial wildlife feeding might contribute to the successful establishment of some invasive alien species, like the Eastern grey squirrel (Sciurus carolinensis) in Europe and the UK. Reducing squirrel feeding at urban parks can be important to reduce squirrel populations while avoiding social conflicts. From April to October 2018, we conducted interviews and administered factorial surveys to two samples of visitors at the Valentino urban park in Torino (Italy). We established whether squirrel feeding can be regarded as an independent or an interdependent behavior, by eliciting visitors’ moral beliefs, and their empirical and normative expectations.

Most respondents did not regard artificial feeding as something neither intrinsically positive nor negative. Satisfaction, the need for a connection with nature and the presence of children were its main causes. On the other hand, feeding squirrels was deemed to be potentially dangerous for squirrel health, and leading to high squirrel densities and to confident squirrels.

Factorial surveys indicated that empirical expectations about the behavior of other visitors, altogether with their past behavior, lead visitors to feed squirrels, while the availability of suboptimal food types (e.g. sweets), was deemed to made people less prone to forage squirrels. Our findings indicate that supplementary feeding is an interdependent behavior, governed by descriptive norms. It might be reduced by means of informative panels containing descriptive information about the fact that most visitors indeed do not feed squirrels, as well as by panels emphasizing the potential damage that squirrels could suffer from eating suboptimal food provided by humans.
Nef enhances HIV-1 replication and infectivity independently of SERINC3 and SERINC5 in CEM T cells
Authors: Ramirez Peter W. , Vollbrecht Thomas , Acosta Francisco M. , Suarez Marissa , Angerstein Aaron A. , Wallace Jared , Connell Ryan M. O’ , Guatelli John
Published: July 2020

The lentiviralnefgene encodes several discrete activities aimed at co-opting or antagonizing cellular proteins and pathways to defeat host defenses and maintain persistent infection. Primary functions of Nef include downregulation of CD4 and MHC class-I from the cell surface, disruption or mimicry of T-cell receptor signaling, and enhancement of viral infectivity by counteraction of the host antiretroviral proteins SERINC3 and SERINC5. In the absence of Nef, SERINC5 incorporates into virions and inhibits viral fusion with target cells, decreasing infectivity. However, whether Nef’s counteraction of SERINC5 is the cause of its positive influence on viral growth-rate in CD4-positive T cells is unclear. Here, we utilized CRISPR/Cas9 to knockout SERINC3 and SERINC5 in a leukemic CD4-positive T cell line (CEM) that displays relatively robustnef-related infectivity and growth-rate phenotypes. As previously reported, viral replication was attenuated in CEM cells infected with HIV-1 lacking Nef (HIV-1ΔNef). This attenuated growth-rate phenotype was observed regardless of whether the coding regions of theserinc3orserinc5genes were intact. Moreover, knockout ofserinc3orserinc5failed to restore the infectivity of HIV1ΔNef virions produced from infected CEM cells. Taken together, our results corroborate a similar study using another T-lymphoid cell line (MOLT-3) and indicate that the antagonism of SERINC3 and SERINC5 cannot fully explain the virology of HIV-1 lacking Nef.
CRAG:De novocharacterization of cell-free DNA fragmentation hotspots in plasma whole-genome sequencing
Authors: Zhou Xionghui , Zheng Haizi , Fu Hailu , Dillehay McKillip Kelsey L. , Pinney Susan M. , Liu Yaping
Published: July 2020

Non-random cell-free DNA fragmentation is a promising signature for cancer diagnosis. However, its aberration at the fine-scale in early-stage cancers is poorly understood. Here, we developed an approach tode novocharacterize the cell-free DNA fragmentation hotspots from whole-genome sequencing. In healthy, hotspots are enriched in gene-regulatory elements, including open chromatin regions, promoters, hematopoietic-specific enhancers, and, interestingly, 3’end of transposons. Hotspots identified in early-stage hepatocellular carcinoma patients showed overall hypo-fragmentation patterns compared to healthy controls. These cancer-specific hypo-fragmented hotspots are associated with genes enriched in gene ontologies and KEGG pathways that are related to the initiations of hepatocellular carcinoma and cancer stem cells. Further, we identified the fragmentation hotspots at 297 cancer samples across 8 different cancer types (92% in stage I to III), 103 benign samples, and 247 healthy samples. The fine-scale fragmentation level at most variable hotspots showed cancer-specific fragmentation patterns across multiple cancer types and non-cancer controls. With the fine-scale fragmentation signals alone in a machine learning model, we achieved 48% to 95% sensitivity at 100% specificity in different early-stage cancer. We further validated the model at independent datasets we generated at a small number of early-stage cancers and healthy plasma samples with matched age, gender, and lifestyle. In cancer-positive cases, we further localized cancer to a small number of anatomic sites with a median of 80% accuracy. The results highlight the significance ofde novocharacterizing the cell-free DNA fragmentation hotspots for detecting early-stage cancers and dissection of gene-regulatory aberrations in cancers.
Anti-SARS-CoV-2 IgG antibodies in adolescent students and their teachers in Saxony, Germany (SchoolCoviDD19): very low seropraevalence and transmission rates
Authors: Armann Jakob P. , Unrath Manja , Kirsten Carolin , Lück Christian , Dalpke Alexander H. , Berner Reinhard
Published: July 2020

Background

School closures are part of the SARS-CoV-2 pandemic control measures in many countries, based on the assumption that children play a similar role in transmitting SARS-CoV-2 as they do in transmitting influenza. We therefore performed a SARS-CoV-2 seropraevalence-study in students and teachers to assess their role in the SARS-CoV-2 transmission.

Methods

Students grade 8–11 and their teachers in 13 secondary schools in eastern Saxony, Germany, were invited to participate in the SchoolCoviDD19 study. Blood samples were collected between May 25th and June 30th, 2020. Anti-SARS-CoV-2 IgG were assed using chemiluminescence immunoassay technology and all samples with a positive or equivocal test result were re-tested with two additional serological tests.

Findings

1538 students and 507 teachers participated in this study. The seropraevalence for SARS-CoV-2 was 0.6%. Even in schools with reported Covid-19 cases before the Lockdown of March 13th no clusters could be identified. 23/24 participants with a household history of COVID-91 were seronegative. By using a combination of three different immunoassays we could exclude 16 participants with a positive or equivocal results after initial testing.

Interpretation

Students and teachers do not play a crucial role in driving the SARS-CoV-2 pandemic in a low prevalence setting. Transmission in families occurs very infrequently, and the number of unreported cases is low in this age group, making school closures not appear appropriate as a strategy in this low prevalence settings.

Funding

This study was supported by a grant from the state of Saxony
Paracoccidioidesgenomes reflect high levels of species divergence and little interspecific gene flow
Authors: Mavengere Heidi , Mattox Katlheen , Teixeira Marcus M , Sepúlveda Victoria E. , Gomez Oscar M. , Hernandez Orville , McEwen Juan , Matute Daniel R.
Published: July 2020

The fungusParacoccidioidesspp. is a prevalent human pathogen endemic to South America. The genus is composed of five species. In this report, we use 37 whole genome sequences to study the allocation of genetic variation inParacoccidioides. We tested three genome-wide predictions of advanced speciation, namely, that all species should be reciprocally monophyletic, that species pairs should be highly differentiated along the whole genome, and that there should be low rates of interspecific gene exchange. We find support for these three hypotheses. Species pairs with older divergences show no evidence of gene exchange, while more recently diverged species pairs show evidence of modest rates of introgression. Our results indicate that as divergence progresses, species boundaries become less porous amongParacoccidioidesspecies. Our results suggest that species inParacoccidioidesare at different stages along the divergence continuum.

IMPORTANCE

Paracoccidioidesis the causal agent of the most frequent systemic mycosis in Latin America. Most of the inference of the evolutionary history ofParacoccidioideshas used only a handful of molecular markers. In this report, we evaluate the extent of genome divergence amongParacoccidioidesspecies and study the possibility of interspecific gene exchange. We find that all species are highly differentiated. We also find that the amount of gene flow between species is low and in some cases even completely absent in spite of geographic overlap. Our study constitutes a systematic effort to identify species boundaries in fungal pathogens, and determine the extent of gene exchange among fungal species.
Multiple spatial codes for navigating 2-D semantic spaces
Authors: Viganò Simone , Rubino Valerio , Di Soccio Antonio , Buiatti Marco , Piazza Manuela
Published: July 2020

When mammals navigate in the physical environment, specific neurons such as grid-cells, head-direction cells, and place-cells activate to represent the navigable surface, the faced direction of movement, and the specific location the animal is visiting. Here we test the hypothesis that these codes are also activated when humans navigate abstract language-based representational spaces. Human participants learnt the meaning of novel words as arbitrary signs referring to specific artificial audiovisual objects varying in size and sound. Next, they were presented with sequences of words and asked to process them semantically while we recorded the activity of their brain using fMRI. Processing words in sequence was conceivable as movements in the semantic space, thus enabling us to systematically search for the different types of neuronal coding schemes known to represent space during navigation. By applying a combination of representational similarity and fMRI-adaptation analyses, we found evidence of i) a grid-like code in the right postero-medial entorhinal cortex, representing the general bidimensional layout of the novel semantic space; ii) a head-direction-like code in parietal cortex and striatum, representing the faced direction of movements between concepts; and iii) a place-like code in medial prefrontal, orbitofrontal, and mid cingulate cortices, representing the Euclidean distance between concepts. We also found evidence that the brain represents 1-dimensional distances between word meanings along individual sensory dimensions: implied size was encoded in secondary visual areas, and implied sound in Heschl’s gyrus/Insula. These results reveal that mentally navigating between 2D word meanings is supported by a network of brain regions hosting a variety of spatial codes, partially overlapping with those recruited for navigation in physical space.
Altered bacteria community dominance reduces tolerance to resident fungus and seed to seedling growth performance in maize (Zea maysL. var. DBK 177)
Authors: dos Santos Lidiane Figueiredo , Souta Julie Fernandes , da Rocha Letícia Oliveira , de Paula Soares Cleiton , Santos Maria Luiza Carvalho , de Matos Clicia Grativol Gaspar , Roesch Luiz Fernando Wurdig , Olivares Fabio Lopes
Published: July 2020

Seeds are reservoirs of beneficial and harmful microorganism that modulates plant growth and health. Here, we access seed to seedling bacteriome assembly modified by seed-disinfection and the underlined effect over maize germination performance and root-seedlings microbial colonization. Seed-disinfection was performed with sodium hypochlorite (1.25%, 30 min), resulting in a reduction of the cultivable-dependent fraction of seed-borne bacteria population, but not significantly detected by real-time PCR, microscopy, and biochemical analysis of the roots on germinated seeds. 16S rRNA sequencing revealed that the seed and root bacteriome exhibited similar diversity and did not differ in the structure concerning seed-disinfection. On the other hand, the abundance reduction of the genera f_Enterobacteriaceae_922761 (unassigned genus),Azospirillum,andAcinetobacterin disinfected-seed prior germination seems to display changes in prominence of several new taxa in the roots of germinated seeds. Interestingly, this reduction in the bacteriome negatively affected the germination speed and growth of maize plantlets. Additionally, bacteriome re-shape increased the maize var DKB 177 susceptible to the seed-borne plant pathogenPenicilliumsp. Such changes in the natural seed-borne composition removed the natural barrier, increasing susceptibility to pathogens, impairing disinfected seeds to germinate, and develop. We conclude that bacteria borne in seeds modulate the relative abundance of taxa in the root, promote germination, seedling growth, and protect the maize against fungal pathogens.
Genome-scale functional profiling of cell cycle controls in African trypanosomes
Authors: Marques Catarina A. , Tinti Michele , Cassidy Andrew , Horn David
Published: July 2020

Trypanosomatids, which include major pathogens of humans and livestock, are divergent eukaryotes for which cell cycle controls and the underlying mechanisms are not completely understood. Here, we describe a genome-wide RNA-interference library screen for cell cycle regulators in bloodstream formTrypanosoma brucei. We induced massive parallel knockdown and sorted the perturbed population into cell cycle stages using flow cytometry. RNAi-targets were deep-sequenced from each stage and cell cycle profiles were digitally reconstructed at a genomic scale. We identify hundreds of proteins that impact cell cycle progression; glycolytic enzymes required for G1S progression, DNA replication factors, mitosis regulators, proteasome and kinetochore complex components required for G2M progression, flagellar and cytoskeletal components required for cytokinesis, mRNA-binding factors, protein kinases and many previously uncharacterised proteins. The outputs facilitate functional annotation and drug-target prioritisation and provide comprehensive functional genomic evidence for the machineries, pathways and regulators that coordinate progression through the trypanosome cell cycle.

The data can be searched and browsed using an interactive, open access, online data visualization tool (https://tryp-cycle.onrender.com).
Trade-off between reducing mutational accumulation and increasing commitment to differentiation determines tissue organization
Authors: Demeter Márton , Derényi Imre , Szöllősi Gergely J.
Published: July 2020

Species-specific differences control cancer risk across orders of magnitude variation in body size and lifespan, e.g., by varying the copy numbers of tumor suppressor genes. It is unclear, however, how different tissues within an organism can control somatic evolution despite being subject to markedly different constraints, but sharing the same genome. Hierarchical differentiation, characteristic of self-renewing tissues, can restrain somatic evolution both by limiting divisional load, thereby reducing mutation accumulation, and by increasing cells’ commitment to differentiation, which can “wash out” mutants. Here, we explore the organization of hierarchical tissues that have evolved to limit their lifetime incidence of cancer. Estimating the likelihood of cancer in the presence of mutations that enhance self-proliferation, we demonstrate that a trade-off exists between mutation accumulation and the strength of washing out. Our results explain differences in the organization of widely different hierarchical tissues, such as colon and blood.
Translation regulation of Japanese encephalitis virus revealed by ribosome profiling
Authors: Rizvi Vaseef A. , Sarkar Maharnob , Roy Rahul
Published: July 2020

Japanese encephalitis virus (JEV), a neurotropic flavivirus, is the leading cause of viral encephalitis in endemic regions of Asia. Although the mechanisms modulating JEV virulence and neuroinvasiveness are poorly understood, several acquired mutations in the live attenuated vaccine strain (SA14-14-2) point towards translation regulation as a key strategy. Using ribosome profiling, we identify multiple mechanisms including frameshifting, tRNA dysregulation and alternate translation initiation sites that regulate viral protein synthesis. A significant fraction (~ 40%) of ribosomes undergo frameshifting on NS1 coding sequence leading to early termination, translation of NS1′ protein and modulation of viral protein stoichiometry. Separately, a tRNA subset (glutamate, serine, leucine and histidine) was found to be associated in high levels with the ribosomes upon JEV infection. We also report a previously uncharacterised translational initiation event from an upstream UUG initiation codon in JEV 5′ UTR. A silent mutation at this start site in the vaccine strain has been shown to abrogate neuroinvasiveness suggesting the potential role of translation from this region. Together, our study sheds light on distinct mechanisms that modulate JEV translation with likely consequences for viral pathogenesis.
Demography, education, and research trends in the interdisciplinary field of disease ecology
Authors: Brandell Ellen E. , Becker Daniel J. , Sampson Laura , Forbes Kristian M.
Published: July 2020

Micro- and macroparasites are a leading cause of mortality for humans, animals, and plants, and there is great need to understand their origins, transmission dynamics, and impacts. Disease ecology formed as an interdisciplinary field in the 1970s to fill this need and has recently rapidly grown in size and influence. Because interdisciplinary fields integrate diverse scientific expertise and training experiences, understanding their composition and research priorities is often difficult. Here, for the first time, we quantify the composition and educational experiences of a subset of disease ecology practitioners and identify topical trends in published research. We combined a large survey of self-declared disease ecologists with a literature synthesis involving machine-learning topic detection of over 18,500 disease ecology research articles. The number of graduate degrees earned by disease ecology practitioners has grown dramatically since the early 2000s. Similar to other science fields, we show that practitioners in disease ecology have diversified in the last decade in terms of gender identity and institution, with weaker diversification in race and ethnicity. Topic detection analysis revealed how the frequency of publications on certain topics have declined (e.g., HIV, serology), increased (e.g., the dilution effect, infectious disease in bats), remained relatively common (e.g., malaria ecology, influenza, vaccine research and development), or have consistently remained relatively infrequent (e.g., theoretical models, field experiments). Other topics, such as climate change, superspreading, emerging infectious diseases, and network analyses, have recently come to prominence. This study helps identify the major themes of disease ecology and demonstrates how publication frequency corresponds to emergent health and environmental threats. More broadly, our approach provides a framework to examine the composition and publication trends of other major research fields that cross traditional disciplinary boundaries.
Empagliflozin inhibits proximal tubule NHE3 activity, preserves GFR and restores euvolemia in nondiabetic rats with induced heart failure
Authors: Borges-Júnior Flávio A. , dos Santos Danúbia Silva , Benetti Acaris , Crajoinas Renato O. , Antonio Ednei L. , Jensen Leonardo , Caramelli Bruno , Malnic Gerhard , Tucci Paulo J. , Girardi Adriana C.
Published: July 2020

Background

Sodium-glucose cotransporter type 2 (SGLT2) inhibitors reduce the risk of heart failure (HF) mortality and morbidity, regardless of the presence or absence of diabetes, but the mechanisms underlying this benefit remain unclear. We tested the hypothesis that the SGLT2 inhibitor empagliflozin inhibits proximal tubule (PT) Na+/H+ exchanger isoform 3 (NHE3) activity and improves renal salt and water handling in nondiabetic rats with HF.

Methods and Results

Male Wistar rats were subjected to myocardial infarction or sham operation. After four weeks, rats that developed HF and sham rats were treated with empagliflozin (EMPA) or untreated for an additional four weeks. EMPA-treated HF rats displayed lower levels of serum brain natriuretic peptide (BNP) and lower right ventricle and lung weight to tibia length than untreated HF rats. Upon saline challenge, the diuretic and natriuretic responses of EMPA-treated HF rats were similar to those of sham rats and were higher than those of untreated HF rats. Additionally, EMPA treatment normalized the glomerular filtration rate and proteinuria in HF rats. PT NHE3 activity was higher in HF rats than in sham rats, whereas treatment with EMPA markedly reduced NHE3 activity. Unexpectedly, SGLT2 function and protein and mRNA abundance were upregulated in the PT of HF rats.

Conclusion

Collectively, our data show that the prevention of HF progression by empagliflozin is associated with inhibition of PT NHE3 activity and restoration of euvolemia. Moreover, we propose that the dysregulation of PT SGLT2 may be involved in the pathophysiology of nondiabetic HF.

SIGNIFICANCE STATEMENT

SGLT2 inhibitors represent a class of drugs that were originally developed for improving glycemic control. Cardiovascular outcome trials that were designed to evaluate cardiovascular safety yielded unexpected and unprecedented evidence of the cardiorenal benefits of SGLT2 inhibitor. Many hypotheses have been proposed to explain the mechanisms underlying these effects. Our study demonstrates that SGLT2 inhibition restores extracellular volume homeostasis in nondiabetic heart failure (HF) rats by preserving GFR and inhibiting proximal tubule NHE3-mediated sodium reabsorption. The attenuation of kidney dysfunction may constitute an essential mechanism by which SGLT2 inhibitors attenuate HF development and progression either in the presence or absence of diabetes.
A series of Orai1 gating checkpoints in transmembrane and cytosolic regions requires clearance for CRAC channel opening: Clearance and synergy of Orai1 gating checkpoints controls pore opening
Authors: Tiffner Adéla , Schober Romana , Höglinger Carmen , Bonhenry Daniel , Pandey Saurabh , Lunz Victoria , Sallinger Matthias , Frischauf Irene , Fahrner Marc , Lindinger Sonja , Maltan Lena , Berlansky Sascha , Stadlbauer Michael , Schindl Rainer , Ettrich Rudiger , Romanin Christoph , Derler Isabella
Published: July 2020

The initial activation step in gating of ubiquitously expressed Orai1 Calcium (Ca2+) ion channels represents the store-dependent coupling to the Ca2+sensor protein STIM1. An array of constitutively active Orai1 mutants gave rise to the hypothesis that STIM1 mediated Orai1 pore opening is accompanied by a global conformational change of all Orai TM helices within the channel complex. Here, we prove that a local conformational change spreads omnidirectionally within the Orai1 complex. Our results demonstrate that a global, opening-permissive allosteric communication of TM helices is indispensable for pore opening and requires clearance of a series of Orai1 gating checkpoints. We discovered these gating checkpoints in middle and cytosolic extended TM domain regions. Our findings are based on a library of double point mutants that contain each one loss-of-function (LoF) with one gain-of-function (GoF) point mutation in a series of possible combinations. We demonstrated that an array of LoF mutations act dominant over most GoF mutations within the same as well as of an adjacent Orai subunit. We further established inter- and intramolecular salt-bridge interactions of Orai subunits as a core element of an opening-permissive Orai channel architecture. Collectively, clearance and synergistic action of all these gating checkpoints is required to allow STIM1 coupling and Orai1 pore opening.

Graphical Abstract
Patient-derived glioblastoma cells (GBM) exhibit distinct biomechanical profiles associated with altered activity in the cytoskeleton regulatory pathway
Authors: Foss Amelia , Zanoni Michele , So Woong Young , Jenkins Lisa , Tosatto Luigino , Bartolini Daniela , Gottesman Michael M , Tesei Anna , Tanner Kandice
Published: July 2020

Glioblastoma multiforme (GBM) is the most commonly diagnosed brain cancer in adults, characterized by rapid proliferation and aggressive invasion into the stroma. Advances in our understanding of the molecular subtypes of GBM have provided attractive druggable targets. However, the high degree of heterogeneity both among patients and within individual tumors has proven a significant challenge for the development of effective therapies. We hypothesized that this heterogeneity is also represented in the mechanical phenotypes of GBM, as the physical properties of tumor tissue strongly influence elements of tumor progression including cell cycle regulation, migration, and therapeutic resistance. To assess these phenotypes, we employed optical trap-based active microrheology to determine the viscoelastic properties of patient-derived GBM cells in 3D hydrogels mimicking the brain ECM. We found that each GBM cell line had a distinct rheological profile as a function of treatment status, and cell lines could be further characterized by strong power law dependence describing intracellular viscoelastic behavior. Single-cell phenotyping according to power law dependence was able to identify subpopulations of cells within the treatment-resistant line. Finally, proteomic analysis indicated that altered mechanical profiles were associated with differential cytoskeletal regulation, particularly in actin - and myosin-binding pathways. This work suggests that evaluating mechanical properties may serve as a valuable strategy for the further stratification of these tumors, and encourages the investigation of cytoskeleton regulation as a potential therapeutic target for GBM.
Success Criteria for Preclinical Testing of Cell-Instructive Hydrogels for Tendon Regeneration
Authors: Locke Ryan C. , Ford Eden M. , Silbernagel Karin G. , Kloxin April M. , Killian Megan L.
Published: July 2020

Tendon injuries are difficult to heal in part because intrinsic tendon healing, which is dominated by scar tissue formation, does not effectively regenerate the native structure and function of healthy tendon. Further, many current treatment strategies also fall short of producing regenerated tendon with the native properties of healthy tendon. There is increasing interest in the use of cell-instructive strategies to limit the intrinsic fibrotic response following injury and improve the regenerative capacity of tendonin vivo. We have established multi-functional, cell-instructive hydrogels for treating injured tendon that afford tunable control over the biomechanical, biochemical, and structural properties of the cell microenvironments. Specifically, we incorporated integrin-binding domains (RGDS) and assembled multi-functional collagen mimetic peptides (mfCMPs) that enable cell adhesion and elongation of stem cells within synthetic hydrogels of designed biomechanical properties and evaluated these materials using targeted success criteria developed for testing in mechanically-demanding environments like tendon healing. Thein vitroandin situsuccess criteria were determined based on systematic reviews of the most commonly reported outcome measures of hydrogels for tendon repair and established standards for testing of biomaterials. We then showed, using validation experiments, that multi-functional and synthetic hydrogels meet these criteria. Specifically, these hydrogels have mechanical properties comparable to developing tendon; are non-cytotoxic both in 2D bolus exposure (hydrogel components) and 3D encapsulation (full hydrogel); are formed, retained, and visualized within tendon defects over time (two-weeks); and provide mechanical support to tendon defects at the time of injection andin situformation. Ultimately, thein vitroandin situsuccess criteria evaluated in this study were designed for preclinical research to rigorously test the potential to achieve successful tendon repair prior toin vivotesting and indicate the promise of multi-functional and synthetic hydrogels for continued translation.

IMPACT STATEMENT

Tendon healing results in a weak scar that forms due to poor cell-mediated repair of the injured tissue. Treatments that tailor the instructions experienced by cells during healing afford opportunities to regenerate the healthy tendon. Engineered cell-instructive cues, including the biomechanical, biochemical, and structural properties of the cell microenvironment, within multi-functional synthetic hydrogels are promising therapeutic strategies for tissue regeneration. In this paper, the preclinical efficacy of multi-functional synthetic hydrogels for tendon repair is tested against rigorousin vitroandin situsuccess criteria. This study indicates the promise for continued preclinical translation of synthetic hydrogels for tissue regeneration.
Redefining theClostridioides difficileσBregulon: σBactivates genes involved in detoxifying radicals that can result from the exposure to antimicrobials and hydrogen peroxide
Authors: Boekhoud Ilse M. , Michel Annika-Marisa , Corver Jeroen , Jahn Dieter , Smits Wiep Klaas
Published: July 2020

In many gram-positive bacteria the general stress response is regulated at the transcriptional level by the alternative sigma factor sigma B (σB). InC. difficileσBhas been implicated in protection against stressors such as reactive oxygen species and antimicrobial compounds. Here, we used an anti-σBantibody to demonstrate time-limited overproduction of σBinC. difficiledespite its toxicity at higher cellular concentrations. This toxicity eventually led to the loss of the plasmid used for anhydrotetracycline-induced σBgene expression. Inducible σBoverproduction uncouples σBexpression from its native regulatory network and allowed for the refinement of the previously proposed σBregulon. At least 32% the regulon was found to consist of genes involved in the response to reactive radicals. Direct gene activation byC. difficileσBwas demonstrated throughin vitrorun-off transcription of specific target genes (cd0350, cd3614, cd3605, cd2963). Finally, we demonstrated that different antimicrobials and hydrogen peroxide induce these genes in a manner dependent on this sigma factor, using a plate-based luciferase reporter assay. Together, our work suggests that lethal exposure to antimicrobials may result in the formation of toxic radicals that lead to σB-dependent gene activation.

Importance

Sigma B is the alternative sigma factor governing stress response in many gram-positive bacteria. InC. difficile, asigBmutant shows pleiotropic transcriptional effects. Here, we determine genes that are likely direct targets of σBby evaluating the transcriptional effects of σBoverproduction, provide biochemical evidence of direct transcriptional activation by σB, and show that σB-dependent genes can be activated by antimicrobials. Together our data suggest that σBis a key player in dealing with toxic radicals.
Incorporating genome-based phylogeny and functional similarity into diversity assessments helps to resolve a global collection of human gut metagenomes
Authors: Youngblut Nicholas D. , de la Cuesta-Zuluaga Jacobo , Ley Ruth E.
Published: July 2020

Tree-based diversity measures incorporate phylogenetic or functional relatedness into comparisons of microbial communities. This can improve the identification of explanatory factors compared to tree-agnostic diversity measures. However, applying tree-based diversity measures to metagenome data is more challenging than for single-locus sequencing (e.g., 16S rRNA gene). The Genome Taxonomy Database (GTDB) provides a genome-based reference database that can be used for species-level metagenome profiling, and a multi-locus phylogeny of all genomes that can be employed for diversity calculations. This approach also allows for functional diversity measures based on genomic content or traits inferred from it. Still, it is unclear how metagenome-based assessments of microbiome diversity benefit from incorporating phylogeny or function into measures of diversity. We assessed this by measuring phylogeny-based, function-based, and tree-agnostic diversity measures from a large, global collection of human gut metagenomes composed of 33 studies and 3348 samples. We found tree-based measures to explain phenotypic variation (e.g., westernization, disease status, and gender) better or on par with tree-agnostic measures. Ecophylogenetic and functional diversity measures provided unique insight into how microbiome diversity was partitioned by phenotype. Tree-based measures greatly improved machine learning model performance for predicting westernization, disease status, and gender, relative to models trained solely on tree-agnostic measures. Notably, ecophylogenetic and functional diversity measures were generally the most important features for predictive performance. Our findings illustrate the usefulness of tree- and function-based measures for metagenomic assessments of microbial diversity – a fundamental component of microbiome science.

Importance

Estimations of microbiome diversity are fundamental to understanding spatiotemporal changes of microbial communities and identifying which factors mediate such changes. Tree-based measures of diversity, which consider species relatedness, are widespread for amplicon-based microbiome studies due to their utility relative to tree-agnostic measures. However, tree-based measures are seldomly applied to shotgun metagenomics data. We evaluated the utility of phylogeny, functional relatedness, and tree-agnostic diversity measures on a large scale human gut metagenome dataset to help guide researchers with the complex task of evaluating microbiome diversity via metagenomics.
VNTR prediction on sequence characteristics using long-read annotation and validation by short-read pileup
Authors: van Batenburg Diederik Cames , Linthorst Jasper , Holstege Henne , Reinders Marcel
Published: July 2020

Tandem repeats (TRs) are contiguously repetitive sequences with a high mutation rate. Several human diseases have been associated with an expansion of TR, a mutation which constitutes a change in their number of repetitions. Nevertheless, these Variable Number Tandem Repeats (VNTRs) have not been included in many genome-wide studies. The reason is that VNTR genotyping is inaccurate using short-read sequencing while new technology like long-read sequencing is expensive and lacks throughput.

Here, we propose a sequence based random forest classifier that is able to predict variable expansion of TR regions, given by incomplete VNTR annotation from long-read sequencing of 5 haplotypes. The classifier mainly predicted VNTRs using the features TR length. The second most used feature is a novel finding: the Mfold predicted likelihood of self-folding for which more stable foldings are correlated with VNTRs. We validated VNTR candidates predicted by this classifier by clustering short-read pileup patterns compared across 17 genomes. TRs labeled VNTR by the classifier showed similar local variance in their pileup profiles.

Contact

diederik.cvb@gmail.com

Supplementary information

Supplementary data are available at bioRxiv
Impact of climatic, demographic and disease control factors on the transmission dynamics of COVID-19 in large cities worldwide
Authors: Metelmann Soeren , Pattni Karan , Brierley Liam , Cavalerie Lisa , Caminade Cyril , Blagrove Marcus S C , Turner Joanne , Sharkey Kieran J , Baylis Matthew
Published: July 2020

We are now over seven months into a pandemic of COVID-19 caused by the SARS-CoV-2 virus and global incidence continues to rise. In some regions such as the temperate northern hemisphere there are fears of “second waves” of infections over the coming months, while in other, vulnerable regions such as Africa and South America, concerns remain that cases may still rise, further impacting local economies and livelihoods. Despite substantial research efforts to date, it remains unresolved as to whether COVID-19 transmission has the same sensitivity to climate and seasonality observed for other common respiratory viruses such as seasonal influenza. Here we investigate any empirical evidence of seasonality using a robust estimation framework. For 304 large cities across the world, we estimated the basic reproduction number (R0) using logistic growth curves fitted to cumulative case data. We then assessed evidence for association with climatic variables through mixed-effects and ordinary least squares (OLS) regression while adjusting for city-level variation in demographic and disease control factors. We find evidence of association between temperature and R0 during the early phase of the epidemic in China only. During subsequent pandemic spread outside China, we instead find evidence of seasonal change in R0, with greater R0 within cities experiencing shorter daylight hours (direct effect coefficient = −0.247, p = 0.006), after separating out effects of calendar day. The effect of daylight hours may be driven by levels of UV radiation, which is known to have detrimental effects on coronaviruses, including SARS-CoV-2. In the global analysis excluding China, climatic variables had weaker explanatory power compared to demographic or disease control factors. Overall, we find a weak but detectable signal of climate variables on the transmission of COVID-19. As seasonal changes occur later in 2020, it is feasible that the transmission dynamics of COVID-19 may shift in a detectable manner. However, rates of transmission and health burden of the pandemic in the coming months will be ultimately determined by population factors and disease control policies.
Leave no stone unturned: The hidden potential of carbon and nitrogen cycling by novel, highly adapted Thaumarchaeota in the Atacama Desert hyperarid core
Authors: Hwang Yunha , Schulze-Makuch Dirk , Arens Felix L. , Saenz Johan S. , Adam Panagiotis S. , Bornemann Till L. V. , Airo Alessandro , Schloter Michael , Probst Alexander J.
Published: July 2020

The hyperarid core of the Atacama Desert is an extremely harsh environment previously thought to be colonized by only a few heterotrophic bacterial species. In addition, carbon and nitrogen cycling in these highly oligotrophic ecosystems are poorly understood. Here we genomically resolved a novel genus of Thaumarchaeota, Ca. Nitrosodesertus, found below boulders of the Atacama hyperarid core, and used comparative genomics to analyze their pangenome and site-specific adaptations. Their genomes contain genes for ammonia oxidation and the 3-hydroxypropionate/4-hydroxybutyrate carbon fixation pathway, indicating a chemolithoautotrophic lifestyle. Ca. Nitrosodesertus possesses the capacity for tolerating extensive environmental stress highlighted by the presence of genes against oxidative stress, DNA damage and genes for the formation of biofilms. These features are likely responsible for their dominance in samples with extremely low water content across three different boulder fields and eight different boulders. Genome-specific adaptations of the genomes included the presence of additional genes for UV resistance, heavy metal transporters, multiple types of ATP synthases, and divergent genes for aquaporins. Our results suggest that Thaumarchaeota mediate important carbon and nitrogen cycling in the hyperarid core of the Atacama and are part of its continuous and indigenous microbiome.
Crystal structures of SARS-CoV-2 ADP-ribose phosphatase: from the apo form to ligand complexes
Authors: Michalska Karolina , Kim Youngchang , Jedrzejczak Robert , Maltseva Natalia I. , Stols Lucy , Endres Michael , Joachimiak Andrzej
Published: July 2020

Among 15 nonstructural proteins (Nsps), the newly emerging Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) encodes a large, multidomain Nsp3. One of its units is the ADP-ribose phosphatase domain (ADRP; also known as the macrodomain, MacroD), which is believed to interfere with the host immune response. Such a function appears to be linked to the ability of the protein to remove ADP-ribose from ADP-ribosylated proteins and RNA, yet the precise role and molecular targets of the enzyme remain unknown. Here, five high-resolution (1.07–2.01 Å) crystal structures corresponding to the apo form of the protein and its complexes with 2-(N-morpholino)ethanesulfonic acid (MES), AMP and ADP-ribose have been determined. The protein is shown to undergo conformational changes to adapt to the ligand in the manner previously observed in close homologues from other viruses. A conserved water molecule is also identified that may participate in hydrolysis. This work builds foundations for future structure-based research on ADRP, including the search for potential antiviral therapeutics.