bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Sec1/Munc18 protein Vps45 holds the Qa-SNARE Tlg2 in an open conformation
Authors: Eisemann Travis , Allen Frederick , Lau Kelly , Shimamura Gregory R. , Jeffrey Philip D. , Hughson Frederick M. 
Published: July 2020

ABSTRACTFusion of intracellular trafficking vesicles is mediated by the assembly of solubleN-ethylmaleimide-sensitive fusion protein receptors (SNAREs) to form membrane-bridging complexes. Also required for SNARE-mediated membrane fusion are Sec1/Munc18-family (SM) proteins, SNARE chaperones that can function as templates to catalyze SNARE complex assembly. In the paradigmatic structure of an SM–SNARE complex, Munc18-1 bound to the Qa-SNARE syntaxin 1, the SNARE protein is trapped in an autoinhibited closed conformation that prevents it from entering into SNARE complexes. Here, we present the structure of a second SM–Qa-SNARE complex, Vps45–Tlg2. Strikingly, Vps45 holds Tlg2 in an open conformation, with its SNARE motif disengaged from its three-helical Habc domain and its linker region unfolded. The domain 3a helical hairpin of Vps45 is unfurled, exposing the presumptive R-SNARE binding site to allow template complex formation. Tlg2 has a pronounced tendency to self-associate via its SNARE motif, and we demonstrate that Vps45 can rescue Tlg2 oligomers into stoichiometric Vps45–Tlg2 complexes. Our findings demonstrate that SM proteins can engage Qa-SNAREs using at least two different modes, one in which the SNARE is closed and one in which it is open.
Task specialization across research careers
Authors: Robinson-Garcia Nicolas , Costas Rodrigo , Sugimoto Cassidy R. , Larivière Vincent , Nane Gabriela F. 
Published: July 2020

AbstractScientific careers are conceived as one unique pathway which scientists must follow to succeed. We report the diversity of profiles scientists exhibit based on their contributorship and look into biases in their career trajectory. We use Bayesian networks to train a prediction model based on a dataset of 70,694 publications from PLoS journals representing 347,136 distinct authors and their associated contribution statements. This model is used to predict the contributions of 222,925 authors in 6,236,239 publications, and apply a robust archetypal analysis to profile scientists by career stage. We divide scientific careers into four stages: junior, early-career, mid-career and late-career. Three scientific archetypes are found throughout the four career stages: leader, specialized, and supporting. All three archetypes are encountered for the early- and mid-career stages, whereas for junior and late-career stages only two archetypes are found. Scientists assigned to the leader and specialized archetypes tend to have longer careers than researchers who belong to the supporting archetype. There is consistent gender bias at all stages: the majority of male scientists belong to the leader archetype, while the larger proportion of women belong to the specialized archetype, especially for early and mid-career researchers.
Mitochondrial uncoupling protein 2 (UCP2), but not UCP3, is sensitive to oxygen concentration in cells
Authors: Hilse Karolina E. , Rupprecht Anne , Ford Kristopher , Andrukhova Olena , Erben Reinhold , Pohl Elena E. 
Published: July 2020

AbstractOne of the important hallmarks of cardiovascular disease is mitochondrial dysfunction, which results in abnormal energy metabolism and increased ROS production in cardiomyocytes. Members of the mitochondrial uncoupling protein family, UCP2 and UCP3, are thought to be beneficial by reducing ROS due to mild uncoupling. More recent hypotheses suggest the involvement of both proteins in cell metabolism by the transport of yet unknown substrates. The protein expression pattern under physiological and pathological conditions is an important clue for the evaluation of UCP2/UCP3 function, however, there is still no consensus about it. Previously, we demonstrated that only UCP3 is present in the adult murine heart under physiological conditions and correlated it with the predominant use of fatty acids for oxidation. In contrast, UCP2 was found only in very young (stem cell – like) cardiomyocytes, that rely mostly on glycolysis. Here, we employed three different models (ex vivo heart ischemia-reperfusion model, myocardial infarction model, and embryonic stem cell differentiation into cardiomyocytes under hypoxic conditions) to evaluate the abundance of both proteins under ischemia and hypoxia conditions. We found that (i) oxygen shortage or bursts did not influence UCP3 levels in the heart and ii) UCP2 was not present in healthy, ischemic, or re-perfused hearts. However, (iii) UCP2 was sensitive to the oxygen concentration in stem cells, in which UCP2 is normally expressed. These results further support the idea, that two highly homologous proteins – UCP2 and UCP3 – are abundant in different cells and tissues, and differently regulated under physiological and pathological conditions.
FtsZ treadmilling is essential for Z-ring condensation and septal constriction initiation inBacillus subtiliscell division
Authors: Whitley Kevin D. , Jukes Calum , Tregidgo Nicholas , Karinou Eleni , Almada Pedro , Henriques Ricardo , Dekker Cees , Holden Séamus 
Published: July 2020

ABSTRACTDespite the central role of division in bacterial physiology, how division proteins work together as a nanoscale machine to divide the cell remains poorly understood. Cell division by cell wall synthesis proteins is guided by the cytoskeleton protein FtsZ, which assembles at mid-cell as a dense Z-ring formed of treadmilling filaments1,2. However, although FtsZ treadmilling is essential for cell division, the function of FtsZ treadmilling remains unclear2–5. Here, we systematically resolve the function of FtsZ treadmilling across each stage of division in the Gram-positive model organismBacillus subtilisusing a novel combination of nanofabrication, advanced microscopy, and microfluidics to measure the division-protein dynamics in live cells with ultrahigh sensitivity. We find that FtsZ treadmilling has two essential functions: mediating condensation of diffuse FtsZ filaments into a dense Z-ring, and initiating constriction by guiding septal cell wall synthesis. After constriction initiation, FtsZ treadmilling has a dispensable function in accelerating septal constriction rate. Our results show that FtsZ treadmilling is critical for assembling and initiating the bacterial cell division machine.
A functional overlap between actively transcribed genes and chromatin boundary elements
Authors: Harrold Caroline L , Gosden Matthew E , Hanssen Lars L P , Stolper Rosa J , Downes Damien J , Telenius Jelena M. , Biggs Daniel , Preece Chris , Alghadban Samy , Sharpe Jacqueline A , Davies Benjamin , Sloane-Stanley Jacqueline A. , Kassouf Mira T , Hughes Jim R , Higgs Douglas R 
Published: July 2020

AbstractMammalian genomes are subdivided into large (50-2000 kb) regions of chromatin referred to as Topologically Associating Domains (TADs or sub-TADs). Chromatin within an individual TAD contacts itself more frequently than with regions in surrounding TADs thereby directing enhancer-promoter interactions. In many cases, the borders of TADs are defined by convergently orientated boundary elements associated with CCCTC-binding factor (CTCF), which stabilises the cohesin complex on chromatin and prevents its translocation. This delimits chromatin loop extrusion which is thought to underlie the formation of TADs. However, not all CTCF-bound sites act as boundaries and, importantly, not all TADs are flanked by convergent CTCF sites. Here, we examined the CTCF binding sites within a ∼70 kb sub-TAD containing the duplicated mouse α-like globin genes and their five enhancers (5’-R1-R2-R3-Rm-R4-α1-α2-3’). The 5’ border of this sub-TAD is defined by a pair of CTCF sites. Surprisingly, we show that deletion of the CTCF binding sites within and downstream of the α-globin locus leaves the sub-TAD largely intact. The predominant 3’ border of the sub-TAD is defined by a steep reduction in contacts: this corresponds to the transcribed α2-globin gene rather than the CTCF sites at the 3’-end of the sub-TAD. Of interest, the almost identical α1- and α2-globin genes interact differently with the enhancers, resulting in preferential expression of the proximal α1-globin gene which behaves as a partial boundary between the enhancers and the distal α2-globin gene. Together, these observations provide direct evidence that actively transcribed genes can behave as boundary elements.Significance StatementMammalian genomes are complex, organised 3D structures, partitioned into Topologically Associating Domains (TADs): chromatin regions that preferentially self-interact. These chromatin interactions are thought to be driven by a mechanism that continuously extrudes chromatin loops, forming structures delimited by chromatin boundary elements and reflecting the activity of enhancers and promoters. Boundary elements bind architectural proteins such as CCCTC-binding factor (CTCF). Previously, an overlap between the functional roles of enhancers and promoters has been shown. However, whether there is overlap between enhancers/promoters and boundary elements is not known. Here, we show that actively transcribed genes can also behave as boundary elements, similar to CTCF boundaries. In both cases, multi-protein complexes bound to these regions may stall the process of chromatin loop extrusion.
eEF3 promotes late stages of tRNA translocation on the ribosome
Authors: Ranjan Namit , Pochopien Agnieszka A. , Wu Colin Chih-Chien , Beckert Bertrand , Blanchet Sandra , Green Rachel , Rodnina Marina V. , Wilson Daniel N. 
Published: July 2020

SummaryIn addition to the conserved translation elongation factors eEF1A and eEF2, fungi require a third essential elongation factor, eEF3. While eEF3 has been implicated in tRNA binding and release at the A and E sites, its exact mechanism of action is unclear. Here we show that eEF3 acts at the mRNA–tRNA translocation step by promoting the dissociation of the tRNA from the E site, but independent of aminoacyl-tRNA recruitment to the A site. Depletion of eEF3in vivoleads to a general slow-down in translation elongation due to accumulation of ribosomes with an occupied A site. Cryo-EM analysis ofex vivoeEF3-ribosome complexes shows that eEF3 facilitates late steps of translocation by favoring non-rotated ribosomal states as well as by opening the L1 stalk to release the E-site tRNA. Additionally, our analysis provides structural insights into novel translation elongation states, enabling presentation of a revised yeast translation elongation cycle.
Two neuronal peptides encoded from a single transcript regulate mitochondrial complex III inDrosophila
Authors: Bosch Justin A. , Ugur Berrak , Pichardo-Casas Israel , Rabasco Jorden , Escobedo Felipe , Zuo Zhongyuan , Brown Ben , Celniker Susan , Sinclair David A. , Bellen Hugo , Perrimon Norbert 
Published: July 2020

SummaryNaturally produced peptides (<100 amino acids) are important regulators of physiology, development, and metabolism. Recent studies have predicted that thousands of peptides may be translated from transcripts containing small open reading frames (smORFs). Here, we describe two peptides inDrosophilaencoded by conserved smORFs, Sloth1 and Sloth2. These peptides are translated from the same bicistronic transcript and share sequence similarities, suggesting that they encode paralogs. Yet, Sloth1 and Sloth2 are not functionally redundant, and loss of either peptide causes animal lethality, reduced neuronal function, impaired mitochondrial function, and neurodegeneration. We provide evidence that Sloth1/2 are highly expressed in neurons, imported to mitochondria, and regulate mitochondrial complex III assembly. These results suggest that phenotypic analysis of smORF genes inDrosophilacan provide a wealth of information on the biological functions of this poorly characterized class of genes.
Connexin 46 and connexin 50 gap junction channel open stability and unitary conductance are shaped by structural and dynamic features of their N-terminal domains
Authors: Yue Benny , Haddad Bassam G. , Khan Umair , Chen Honghong , Atalla Mena , Zhang Ze , Zuckerman Daniel M. , Reichow Steve L. , Bai Donglin 
Published: July 2020

AbstractThe connexins form intercellular communication channels, known as gap junctions (GJs), that facilitate diverse physiological roles in vertebrate species, ranging from electrical coupling and long-range chemical signaling, to coordinating development and nutrient exchange. GJs formed by different connexins are expressed throughout the body and harbor unique channel properties that have not been fully defined mechanistically. Recent structural studies have implicated the amino-terminal (NT) domain as contributing to isoform-specific functional differences that exist between the lens connexins, Cx50 and Cx46. To better understand the structural and functional differences in the two closely related, yet functionally distinct GJs, we constructed models corresponding to CryoEM-based structures of the wildtype Cx50 and Cx46 GJs, NT domain swapped chimeras (Cx46-50NT and Cx50-46NT), and point variants at the 9thresidue (Cx46-R9N and Cx50-N9R) for comparative MD simulation and electrophysiology studies. All of these constructs formed functional GJ channels, except Cx46-50NT, which correlated with increased dynamical behavior (instability) of the NT domain observed by MD simulation. Single channel conductance (γj) also correlated well with free-energy landscapes predicted by MD, where γjof Cx46-R9N was increased from Cx46 and the γjs of Cx50-46NT and Cx50-N9R was decreased from Cx50, but to a surprisingly greater degree. Additionally, we observed significant effects on transjunctional voltage-dependent gating (Vj-gating) and open-state dwell times induced by the designed NT domain variants. Together, these studies indicate that the NT domains of Cx46 and Cx50 play an important role in defining channel properties related to open-state stability and single channel conductance.
An evolutionary approach to systematic discovery of novel deubiquitinases, applied to Legionella
Authors: Hermanns Thomas , Woiwode Ilka , Guerreiro Ricardo F. M. , Vogt Robert , Lammers Michael , Hofmann Kay 
Published: July 2020

AbstractDeubiquitinating enzymes (DUBs) are important regulators of the posttranslational protein ubiquitination system. Mammalian genomes encode about hundred different DUBs, which can be grouped into seven different classes. Members of other DUB classes are found in pathogenic bacteria, which use them to target the host defense. By combining bioinformatical and experimental approaches, we address the question if the known DUB families have a common evolutionary ancestry and share conserved features that set them apart from other proteases. By systematically comparing family-specific Hidden-Markov-Models, we uncovered distant relationships between established DUBs and other cysteine protease families. Most DUB families share a conserved aromatic residue linked to the active site, which restricts the cleavage of substrates with sidechains at the S2 position, corresponding to Gly-75 in ubiquitin. By applying these criteria toLegionella pneumophilaORFs, we identified lpg1621 and lpg1148 as deubiquitinases, characterized their cleavage specificities, and confirmed the importance of the aromatic gatekeeper motif for substrate selection.
SARS-CoV-2 reactive T cells in uninfected individuals are likely expanded by beta-coronaviruses
Authors: Stervbo Ulrik , Rahmann Sven , Roch Toralf , Westhof Timm H. , Babel Nina 
Published: July 2020

AbstractThe current pandemic is caused by the SARS-CoV-2 virus and large progress in understanding the pathology of the virus has been made since its emergence in late 2019. Several reports indicate short lasting immunity against endemic coronaviruses, which contrasts repeated reports that biobanked venous blood contains SARS-CoV-2 reactive T cells even before the outbreak in Wuhan. This suggests there exists a preformed T cell memory in individuals not exposed to the pandemic virus. Given the similarity of SARS-CoV-2 to other members of the Coronaviridae family, the endemic coronaviruses appear likely candidates to generate this T cell memory. However, given the apparent poor immunological memory created by the endemic coronaviruses, other immunity against other common pathogens might offer an alternative explanation. Here, we utilize a combination of epitope prediction and similarity to common human pathogens to identify potential sources of the SARS-CoV-2 T cell memory. We find that no common human virus, other than beta-coronaviruses, can explain the pre-existing SARS-CoV-2 reactive T cells in uninfected individuals. Our study suggests OC43 and HKU1 are the most likely pathogens giving rise to SARS-CoV-2 preformed immunity.
Detection of complex genetic architecture using two-locus population differentiation: modeling epistasis
Authors: Huang Minjun , Graham Britney , Zhang Ge , Bartlett Jacquelaine , Moore Jason H. , Muglia Louis , Williams Scott M. 
Published: July 2020

AbstractRecent advances in genetics have increased our understanding of epistasis as important in the genetics of complex phenotypes. However, current analytical methods often cannot detect epistasis, given the multiple testing burden. To address this, we extended our previous method, Evolutionary Triangulation (ET), that uses differences among populations in both disease prevalence and allele frequencies to filter SNPs from association studies to generate novel interaction models. We show that two-locus ET identified several co-evolving gene pairs, where both genes associate with the same disease, and that the number of such pairs is significantly greater than expected by chance. Traits found by two-locus ET included those related to pigmentation and schizophrenia. We then applied two-locus ET to the analysis of preterm birth (PTB) genetics. Using ET to filter SNPs at loci identified by genome-wide association studies (GWAS), we showed that ET derived PTB two-locus models are novel and were not seen when only the index SNPs were used to generate epistatic models. One gene pair,ADCY5andKCNAB1 5’, was identified as significantly interacting in a model of gestational age (pas low as 3 × 10−3). Notably, the same ET SNPs in these genes showed significant interactions in three of four cohorts analyzed. The robustness of this gene pair and others, demonstrated that the ET method can be used without prior biological hypotheses based on SNP function to select variants for epistasis testing that could not be identified otherwise. Two-locus ET clearly increased the ability to identify epistasis in complex traits.
Aedes aegyptivision-guided target recognition requires two redundant rhodopsins
Authors: Zhan Yinpeng , San Alberto Diego Alonso , Rusch Claire , Riffell Jeffrey A. , Montell Craig 
Published: July 2020

AbstractBlood-feeding insects, such as the mosquito,Aedes(Ae.)aegypti, use multiple senses to seek out and bite humans [1, 2]. Upon exposure to CO2, the attention of female mosquitoes to potential human targets is greatly increased. Female mosquitoes use vision to assist them in honing in on hosts that may be up to 10 meters away [3–9]. Only after coming into close range do convective heat from skin and odors from volatile organic compounds come into play, allowing female mosquitoes to evaluate whether the object of interest might be a host [10, 11]. Here, using CRISPR/Cas9 we mutated the gene encoding Op1, which is the most abundant of the five rhodopsins expressed in the compound eyes ofAe. aegypti. Using a cage assay and a wind tunnel assay, we surprisingly found that elimination ofop1did not impair CO2-induced target seeking. We then mutatedop2, which encodes the rhodopsin most similar to Op1, and also found that there was no impact on this behavior. Rather, mutation of bothop1andop2was required to abolish vision-guided target recognition. In contrast to this defect, the double mutants still exhibited normal light attraction. By measuring the optomotor response, we found that the double mutants still recognized moving cues in their environment. In further support of the conclusion that the double mutant is not blind, we found that the animals retained an electrophysiological response to light, although it was diminished. This represents the first perturbation of vision in mosquitoes and indicates that hostseeking byAe. aegyptidepends on redundant rhodopsins.
A translational multiplex serology approach to profile the prevalence of anti-SARS-CoV-2 antibodies in home-sampled blood
Authors: Roxhed Niclas , Bendes Annika , Dale Matilda , Mattsson Cecilia , Hanke Leo , Dodig-Crnkovic Tea , Christian Murray , Meineke Birthe , Elsässer Simon , Andréll Juni , Havervall Sebastian , Thålin Charlotte , Eklund Carina , Dillner Joakim , Beck Olof , Thomas Cecilia E , McInerney Gerald , Hong Mun-Gwan , Murrell Ben , Fredolini Claudia , Schwenk Jochen M 
Published: July 2020

AbstractThe COVID-19 pandemic has posed a tremendous challenge for the global community. We established a translational approach combining home blood sampling by finger-pricking with multiplexed serology to assess the exposure to the SARS-CoV-2 virus in a general population. The developed procedure determines the immune response in multiplexed assays against several spike (S, here denoted SPK), receptor binding domain (RBD) and nucleocapsid (NCP) proteins in eluates from dried capillary blood. The seroprevalence was then determined in two study sets by mailing 1000 blood sampling kits to random households in urban Stockholm during early and late April 2020, respectively. After receiving 55% (1097/2000) of the cards back within three weeks, 80% (878/1097) were suitable for the analyses of IgG and IgM titers. The data revealed diverse pattern of immune response, thus seroprevalence was dependent on the antigen, immunoglobulin class, stringency to include different antigens, as well as the required analytical performance. Applying unsupervised dimensionality reduction to the combined IgG and IgM data, 4.4% (19/435; 95% CI: 2.4%-6.3%) and 6.3% (28/443; 95% CI: 4.1%-8.6%) of the samples clustered with convalescent controls. Using overlapping scores from at least two SPK antigens, prevalence rates reached 10.1% (44/435; 95% CI: 7.3%-12.9%) in study set 1 and 10.8% (48/443; 95% CI: 7.9%-13.7%). Measuring the immune response against several SARS-CoV-2 proteins in a multiplexed workflow can provide valuable insights about the serological diversity and improve the certainty of the classification. Combining such assays with home-sampling of blood presents a viable strategy for individual-level diagnostics and towards an unbiased assessment of the seroprevalence in a population and may serve to improve our understanding about the diversity of COVID-19 etiology.One Sentence SummaryA multiplexed serology assay was developed to determine antibodies against SARS-CoV-2 proteins in home-sampled dried blood spots collected by finger pricking.