bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic structure predicts metabolite dynamics in microbial communities
Authors: Gowda Karna , Ping Derek , Mani Madhav , Kuehn Seppe 
Published: October 2020

SummaryThe metabolic function of microbial communities has played a defining role in the evolution and persistence of life on Earth, driving redox reactions that form the basis of global biogeochemical cycles. Community metabolism emerges from a hierarchy of processes including gene expression, ecological interactions, and environmental factors. In wild communities, gene content is correlated with environmental context, but predicting metabolic dynamics from genomic structure remains elusive. Here we show, for the process of denitrification, that community metabolism is predictable from the genes each member of the community possesses. Machine learning reveals a sparse and generalizable mapping from gene content to metabolite dynamics across a genomically-diverse library of bacteria. A consumer-resource model correctly predicts community metabolism from single-strain phenotypes. Our results demonstrate that the conserved impacts of metabolic genes can predict community function, enabling the prediction of metabolite dynamics from metagenomes, designing denitrifying communities, and discovering how genome evolution impacts metabolism.
Characterization and analysis of the transcriptome inArapaima gigasusing multi-tissue RNA-sequencing
Authors: Martins Danilo L. , Campos Leonardo R. S. , Ribeiro-dos-Santos André M. , Coelho Ana Carolina M. F. , Dantas Renata L. , Sobrinho Pitágoras A. A. , Sakamoto Tetsu , Vidal Amanda F. , Vinasco-Sandoval Glória T. , Assumpção Paulo P. , Santos Ândrea K. C. R. , Dalmolin Rodrigo J. S. , de Souza Sandro J. , Santos Sidney , de Souza Jorge E. S. 
Published: October 2020

AbstractArapaima gigasis a giant bony tongue air-breathing fish, and a promising species for aquaculture due to its particular features. However, there is still a lack of information on its biology and few transcriptome studies are available. Our aim was to characterize the transcriptome of arapaima in order to shed light on molecular networks contributing to its unique traits. Through RNA-sequencing, we generated a transcriptome from eight tissues (brain, pituitary, heart, muscle, kidney, lung, ovary, and testis) collected from arapaima adults specimens. Using a genome-guided strategy associated with homologous protein evidence, 57,706 transcripts were assembled, which aligned to 23,353 high confidence protein-coding genes. The analysis revealed a global view of expression patterns, as well as it allowed us to identify tissue-specific gene clusters, transcription factors within the clusters, and to compare expression patterns between male and female. These analyses has generated tissue-specific and sex-biased transcriptome profiles, which will be helpful to understand its molecular biology, evolution, and also guide future functional studies of the arapaima.
Spatially resolved transcriptome profiles of mammalian kidneys illustrate the molecular complexity of functional nephron segments, cell-to-cell interactions and genetic variants
Authors: Raghubar Arti M. , Pham Duy T. , Tan Xiao , Grice Laura F. , Crawford Joanna , Lam Pui Yeng , Andersen Stacey B. , Yoon Sohye , Ng Monica S.Y. , Teoh Siok Min , Holland Samuel E. , Stewart Anne , Francis Leo , Combes Alexander N. , Kassianos Andrew J. , Healy Helen , Nguyen Quan , Mallett Andrew J. 
Published: October 2020

AbstractUnderstanding the molecular mechanisms underlying mammalian kidney function requires transcriptome profiling of the interplay between cells comprising nephron segments. Traditional transcriptomics requires cell dissociation, resulting in loss of the spatial context of gene expression within native tissue. To address this problem, we performed spatial transcriptomics (ST) to retain the spatial context of the transcriptome in human and mouse kidneys. The generated ST data allowed spatially resolved differential gene expression analysis, spatial identification of functional nephron segments, cell-to-cell interaction analysis, and chronic kidney disease-associated genetic variant calling. Novel ST thus provides an opportunity to enhance kidney diagnostics and knowledge, by retaining the spatial context of gene expression within intact tissue.
GM-CSF differentiation of human monocytes stabilizes macrophage state via oxidative signaling
Authors: Itoh Christopher Y , Gunnarsson Cal , Babunovic Gregory H , Nibasumba Armel , Akilimali Ngomu Akeem , Wadsworth Marc H , Hughes Travis K , Solomon Sydney L , Hie Brian , Berger Bonnie , Shalek Alex K , Fortune Sarah M , Bryson Bryan D 
Published: October 2020

AbstractMacrophages are central mediators of immunity that integrate diverse signals derived from differentiation cues, tissue location, and disease. Controlling macrophage state and function is an appealing therapeutic objective across many diseases including cancer, atherosclerosis, and tuberculosis. Despite the growing appreciation for thein vivocomplexity of macrophage state, existingin vitromodels of human monocyte-derived macrophages have used a limited number of individual perturbations to explore the complex phenotypic space that macrophages can occupy. Here, we leverage a tiered differentiation, activation, and stimulation strategy to generate libraries ofin vitromonocyte-derived macrophages and examine thein vitrostate space of macrophage function using high-dimensional technologies. Our tiered experimental approach further revealed a striking relationship between GM-CSF differentiation and IL-10 production. Cells that were differentiated with GM-CSF produced very low or undetectable levels of IL-10 independent of activation or stimulation condition. To nominate candidate regulators of this IL-10 response, we leverage unbiased single-cell mRNA sequencing to identify transcriptional networks associated with GM-CSF-derived cells. Using these data, we identify oxidative signaling pathways as upregulated in GM-CSF derived cells and demonstrate that scavenging of oxidative radicals can enhance IL-10 production in these cells. Collectively, these data underscore the complexity of monocyte-derived macrophage state over time and highlight a dominant role for GM-CSF in tuning macrophage inflammatory phenotype, metabolic state, and plasticity.
Chimeric single α-helical domains as rigid fusion protein connections for protein nanotechnology and structural biology
Authors: Collu Gabriella , Bierig Tobias , Krebs Anna-Sophia , Engilberge Sylvain , Varma Niveditha , Guixà-González Ramon , Deupi Xavier , Olieric Vincent , Poghosyan Emiliya , Benoit Roger M. 
Published: October 2020

SummaryChimeric fusion proteins are essential tools for protein nanotechnology. Non-optimized protein-protein connections are usually flexible, which makes them unsuitable as structural building blocks. Here we show that the ER/K motif, a single α-helical domain (SAH)1, can be seamlessly fused2to terminal helices of proteins, forming an extended and partially free-standing rigid helix. Through the intrinsic stability of the SAH, two domains can be connected with a defined distance and orientation. We designed three constructs termed YFPnano, T4Lnano, and MoStoNano, and we show that a single SAH allows the connection of two separate structural domains with sufficient rigidity to form ordered crystals. The analysis of experimentally determined structures and molecular dynamics simulations reveals a certain degree of plasticity in the connections that allows the adaptation to crystal contact opportunities. Our data show that SAHs can be stably integrated into designed structural elements, enabling new possibilities for protein nanotechnology, for example to improve the exposure of epitopes on nanoparticles (structural vaccinology), to engineer crystal contacts with minimal impact in construct flexibility (for the study of protein dynamics), and to design novel biomaterials.
iGIST - a kinetic bioassay for pertussis toxin based on its effect on inhibitory GPCR signaling
Authors: Paramonov Valeriy M. , Sahlgren Cecilia , Rivero-Müller Adolfo , Pulliainen Arto T. 
Published: October 2020

ABSTRACTDetection of pertussis toxin (PTX) activity is instrumental for the development and manufacturing of pertussis vaccines. These quality and safety measures require annually thousands of mice. Here, we describe iGIST (Interference inGαi-mediatedSignalTransduction) - an animal-free kinetic bioassay for detection of PTX by measuring its effect on inhibitory G protein-coupled receptor (GPCR) signaling. PTX ADP-ribosylates inhibitory α-subunits of the heterotrimeric G proteins, thereby perturbing the inhibitory GPCR signaling. iGIST is based on HEK293 cells co-expressing a somatostatin receptor 2 (SSTR2), which is an inhibitory GPCR controllable by a high affinity agonist octreotide, and a luminescent 3’5’-cyclic adenosine monophosphate (cAMP) probe. iGIST has a low sensitivity threshold in picogram/ml range of PTX, surpassing by 100-fold in a parallel analysis the currently usedin vitroend-point technique to detect PTX, the cluster formation assay (CFA) in Chinese hamster ovary cells. iGIST also detects PTX in complex samples, i.e. a commercial PTX- toxoid containing pertussis vaccine that was spiked with an active PTX. iGIST has an objective digital readout and is observer-independent, offering prospects for automation. iGIST emerges as a promising animal-free alternative to detect PTX activity in the development and manufacturing of pertussis vaccines. iGIST is also expected to facilitate basic PTX research, including identification and characterization of novel compounds interfering with PTX.
Positive selection inhibits plasmid coexistence in bacterial genomes
Authors: Carrilero Laura , Kottara Anastasia , Guymer David , Harrison Ellie , Hall James P. J. , Brockhurst Michael A. 
Published: October 2020

AbstractPlasmids play an important role in bacterial evolution by transferring niche adaptive functional genes between lineages, thus driving genomic diversification. Bacterial genomes commonly contain multiple, coexisting plasmid replicons (i.e., plasmid coinfection), which could fuel adaptation by increasing the range of gene functions available to selection and allowing their recombination. However, plasmid coinfection is difficult to explain because the acquisition of plasmids typically incurs high fitness costs for the host cell. Here, we show that plasmid coinfection was stably maintained without positive selection for plasmid-encoded gene functions and was associated with compensatory evolution to reduce fitness costs. By contrast, with positive selection, plasmid coinfection was unstable despite compensatory evolution. Positive selection discriminated between differential fitness benefits of functionally redundant plasmid replicons, retaining only the more beneficial plasmid. These data suggest that while the efficiency of negative selection against plasmid fitness costs declines over time due to compensatory evolution, positive selection to maximise plasmid-derived fitness benefits remains efficient. Our findings help to explain the forces structuring bacterial genomes: Coexistence of multiple plasmids in a genome is likely to require either rare positive selection in nature or non-redundancy of accessory gene functions among coinfecting plasmids.
Geospatial Analysis of Individual and Community-Level Socioeconomic Factors Impacting SARS-CoV-2 Prevalence and Outcomes
Authors: Cromer Sara J. , Lakhani Chirag M. , Wexler Deborah J , Burnett-Bowie Sherri-Ann M. , Udler Miriam , Patel Chirag J. 
Published: October 2020

ABSTRACTBackgroundThe SARS-CoV-2 pandemic has disproportionately affected racial and ethnic minority communities across the United States. We sought to disentangle individual and census tract-level sociodemographic and economic factors associated with these disparities.Methods and FindingsAll adults tested for SARS-CoV-2 between February 1 and June 21, 2020 were geocoded to a census tract based on their address; hospital employees and individuals with invalid addresses were excluded. Individual (age, sex, race/ethnicity, preferred language, insurance) and census tract-level (demographics, insurance, income, education, employment, occupation, household crowding and occupancy, built home environment, and transportation) variables were analyzed using linear mixed models predicting infection, hospitalization, and death from SARS-CoV-2.Among 57,865 individuals, per capita testing rates, individual (older age, male sex, non-White race, non-English preferred language, and non-private insurance), and census tract-level (increased population density, higher household occupancy, and lower education) measures were associated with likelihood of infection. Among those infected, individual age, sex, race, language, and insurance, and census tract-level measures of lower education, more multi-family homes, and extreme household crowding were associated with increased likelihood of hospitalization, while higher per capita testing rates were associated with decreased likelihood. Only individual-level variables (older age, male sex, Medicare insurance) were associated with increased mortality among those hospitalized.ConclusionsThis study of the first wave of the SARS-CoV-2 pandemic in a major U.S. city presents the cascade of outcomes following SARS-CoV-2 infection within a large, multi-ethnic cohort. SARS-CoV-2 infection and hospitalization rates, but not death rates among those hospitalized, are related to census tract-level socioeconomic characteristics including lower educational attainment and higher household crowding and occupancy, but not neighborhood measures of race, independent of individual factors.
Estimation of novel coronavirus (covid-19) reproduction number and case fatality rate: a systematic review and meta-analysis
Authors: Ahammed Tanvir , Anjum Aniqua , Rahman Mohammad Meshbahur , Haider Najmul , Kock Richard , Uddin Md. Jamal 
Published: October 2020

AbstractUnderstanding the transmission dynamics and the severity of the novel coronavirus disease 2019 (COVID-19) informs public health interventions, surveillance, and planning. Two important parameters, the basic reproduction number (R0) and case fatality rate (CFR) of COVID-19, help in this understanding process. The objective of this study was to estimate the R0 and CFR of COVID-19 and assess whether the parameters vary in different regions of the world. We carried out a systematic review to retrieve the published estimates of the R0 and the CFR in articles from international databases between 1st January and 31st August 2020. Random-effect models and Forest plots were implemented to evaluate the mean effect size of the R0 and the CFR. Furthermore, the R0 and CFR of the studies were quantified based on geographic location, the tests/thousand population, and the median population age of the countries where studies were conducted. The I2 statistic and the Cochran’s Q test were applied to assess statistical heterogeneity among the selected studies. Forty-five studies involving R0 and thirty-four studies involving CFR were included. The pooled estimation of the R0 was 2.69 (95% CI: 2.40, 2.98), and that of the CFR was 2.67 (2.25, 3.13). The CFR in different regions of the world varied significantly, from 2.51 (2.12, 2.95) in Asia to 7.11 (6.38, 7.91) in Africa. We observed higher mean CFR values for the countries with lower tests (3.15 vs. 2.16) and greater median population age (3.13 vs. 2.27). However, the R0 did not vary significantly in different regions of the world. An R0 of 2.69 and CFR of 2.67 indicate the severity of the COVID-19. Although R0 and CFR may vary over time, space, and demographics, we recommend considering these figures in control and prevention measures.
Accessing mitochondrial protein import in living cells by protein microinjection
Authors: Bogorodskiy Andrey , Okhrimenko Ivan , Maslov Ivan , Maliar Nina , Burkatovskiy Dmitry , von Ameln Florian , Schulga Alexey , Jakobs Philipp , Altschmied Joachim , Haendeler Judith , Katranidis Alexandros , Mishin Alexey , Gordeliy Valentin , Büldt Georg , Voos Wolfgang , Gensch Thomas , Borshchevskiy Valentin 
Published: October 2020

AbstractMitochondrial protein biogenesis relies almost exclusively on the expression of nuclear-encoded polypeptides. The current model postulates that most of these proteins have to be delivered to their final mitochondrial destination after their synthesis in the cytoplasm. However, the knowledge of this process remains limited due to the absence of proper experimental real-time approaches to study mitochondria in their native cellular environment. We developed a gentle microinjection procedure for fluorescent reporter proteins allowing a direct non-invasive study of protein transport in living cells. As a proof of principle, we visualized potential-dependent protein import into mitochondria inside intact cells in real-time. We validated that our approach does not distort mitochondrial morphology and preserves the endogenous expression system as well as mitochondrial protein translocation machinery. We observed that a release of nascent polypeptides chains from actively translating cellular ribosomes by puromycin strongly increased the import rate of the microinjected preprotein. This suggests that a substantial amount of mitochondrial translocase complexes were involved in co-translational protein import of endogenously expressed preproteins. Our protein microinjection method opens new possibilities to study the role of mitochondrial protein import in cell models of various pathological conditions as well as aging processes.
DET1-mediated COP1 regulation avoids HY5 activity over second-site targets to tune plant photomorphogenesis
Authors: Cañibano Esther , Bourbousse Clara , Garcia-Leon Marta , Wolff Lea , Garcia-Baudino Camila , Barneche Fredy , Rubio Vicente , Fonseca Sandra 
Published: October 2020

AbstractDE-ETIOLATED1 (DET1) is a negative regulator of plant photomorphogenesis acting as a component of the C3D complex, which can further associate to CULLIN4 to form a CRL4C3DE3 ubiquitin ligase. CRL4C3Dis thought to act together with CRL4COP1SPAubiquitin ligase, to promote the ubiquitin-mediated degradation of the master regulatory transcription factor ELONGATED HYPOCOTYL5 (HY5), thereby controlling photomorphogenic gene regulatory networks. Yet, functional links between COP1 and DET1 have long remained elusive. Here, upon mass spectrometry identification of DET1 and COP1-associated proteins, we providein vivoevidence that DET1 associates with COP1 to promote its destabilization, a process necessary to dampen HY5 protein abundance. By regulating HY5 over-accumulation, DET1 is critical to avoid its association to second-site loci, including many PIF3 target genes. Accordingly, excessive HY5 levels result in an increased HY5 repressive activity and are sufficient to triggerfusca-like phenotypes otherwise observed typically inCOP1andCOP9signalosome mutant seedlings. This study therefore identifies that DET1-mediated regulation of COP1 stability tunes down HY5 cistrome and avoids hyper-photomorphogenic responses that might compromise plant viability.
A human monoclonal antibody targeting a conserved pocket in the SARS-CoV-2 receptor-binding domain core
Authors: Fedry Juliette , Hurdiss Daniel L. , Wang Chunyan , Li Wentao , Obal Gonzalo , Drulyte Ieva , Howes Stuart C. , van Kuppeveld Frank J.M. , Förster Friedrich , Bosch Berend-Jan 
Published: October 2020

AbstractSARS-CoV-2 has caused a global outbreak of severe respiratory disease (COVID-19), leading to an unprecedented public health crisis. To date, there has been over thirty-three million diagnosed infections, and over one million deaths. No vaccine or targeted therapeutics are currently available. We previously identified a human monoclonal antibody, 47D11, capable of cross-neutralising SARS-CoV-2 and the related 2002/2003 SARS-CoV in vitro, and preventing SARS-CoV-2 induced pneumonia in a hamster model. Here we present the structural basis of its neutralization mechanism. We describe cryo-EM structures of trimeric SARS-CoV and SARS-CoV-2 spike ectodomains in complex with the 47D11 Fab. These data reveal that 47D11 binds specifically to the closed conformation of the receptor binding domain, distal to the ACE2 binding site. The CDRL3 stabilises the N343 glycan in an upright conformation, exposing a conserved and mutationally constrained hydrophobic pocket, into which the CDRH3 loop inserts two aromatic residues. Interestingly, 47D11 preferentially selects for the partially open conformation of the SARS-CoV-2 spike, suggesting that it could be used effectively in combination with other antibodies that target the exposed receptor-binding motif. Taken together, these results expose a cryptic site of vulnerability on the SARS-CoV-2 RBD and provide a structural roadmap for the development of 47D11 as a prophylactic or post-exposure therapy for COVID-19.
The furin cleavage site of SARS-CoV-2 spike protein is a key determinant for transmission due to enhanced replication in airway cells
Authors: Peacock Thomas P. , Goldhill Daniel H. , Zhou Jie , Baillon Laury , Frise Rebecca , Swann Olivia C. , Kugathasan Ruthiran , Penn Rebecca , Brown Jonathan C. , Sanchez-David Raul Y. , Braga Luca , Williamson Maia Kavanagh , Hassard Jack A. , Staller Ecco , Hanley Brian , Osborn Michael , Giacca Mauro , Davidson Andrew D. , Matthews David A. , Barclay Wendy S. 
Published: October 2020

SummarySARS-CoV-2 enters cells via its spike glycoprotein which must be cleaved sequentially at the S1/S2, then the S2’ cleavage sites (CS) to mediate membrane fusion. SARS-CoV-2 has a unique polybasic insertion at the S1/S2 CS, which we demonstrate can be cleaved by furin. Using lentiviral pseudotypes and a cell-culture adapted SARS-CoV-2 virus with a S1/S2 deletion, we show that the polybasic insertion is selected for in lung cells and primary human airway epithelial cultures but selected against in Vero E6, a cell line used for passaging SARS-CoV-2. We find this selective advantage depends on expression of the cell surface protease, TMPRSS2, that allows virus entry independent of endosomes thus avoiding antiviral IFITM proteins. SARS-CoV-2 virus lacking the S1/S2 furin CS was shed to lower titres from infected ferrets and was not transmitted to cohoused sentinel animals. Thus, the polybasic CS is a key determinant for efficient SARS-CoV-2 transmission.
Lipid-bound ApoE3 self-assemble into elliptical disc-shaped particles
Authors: Larsen Andreas Haahr , Johansen Nicolai Tidemand , Gajhede Michael , Arleth Lise , Midtgaard Søren Roi 
Published: October 2020

AbstractApolipoproteins are vital to lipid metabolism and cholesterol transport in the human body. Here we present a structural study of the lipid-bound particles formed by ApoE3 in a full-length and a truncated version. The particles are formed with, respectively, POPC and DMPC and investigated by small-angle X-ray scattering and negative stain electron microscopy. We find that lipid-bound ApoE3 particles are elliptical, disc-shaped particles composed of a central lipid bilayer encircled by two amphipathic ApoE3 proteins. We went on to investigate a truncated form of ApoE3 containing only residue 80 to 255 (ApoE380-255), which is the central helical repeat segment of ApoE3. The lipid-bound ApoE380-255particles are found to have the same morphology as the particles with full-length ApoE3. However, they are larger, and form more heterogeneous discoidal structures with four proteins per particle. This behavior is in contrast to ApoA1 where the highly similar helical repeat domain determines the size and stoichiometry of the formed particles both in the case of full-length and truncated ApoA1. Our data hence points towards different mechanisms for lipid bilayer structural modulation by ApoA1 and ApoE3 due to different roles of the non-repeat segments.