bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional domain annotation by structural similarity
Authors: Mirzavand Borujeni Poorya , Salavati Reza 
Published: January 2023

AbstractTraditional automated insilicofunctional annotation uses tools like Pfam that rely on sequence similarities for domain annotation. However, structural conservation often exceeds sequence conservation, suggesting an untapped potential for improved annotation through structural similarity. This approach was previously overlooked before the AlphaFold2 introduction due to the need for more high-quality protein structures. Leveraging structural information especially holds significant promise to enhance accurate annotation in diverse proteins across phylogenetic distances.In our study, we evaluated the feasibility of annotating Pfam domains based on structural similarity. To this end, we created a database from segmented full-length protein structures at their domain boundaries, representing the structure of Pfam seeds. We usedTrypanosomabrucei, a phylogenetically distant protozoan parasite as our model organism. Its structome was aligned with our database using Foldseek, the ultra-fast structural alignment tool, and the top non-overlapping hits were annotated as domains. Our method identified over 400 new domains in the T.bruceiproteome, surpassing the benchmark set by sequence-based tools, Pfam and Pfam-N, with some predictions validated manually. We have also addressed limitations and suggested avenues for further enhancing structure-based domain annotation.
Regulation of Ebola GP conformation and membrane binding by the chemical environment of the late endosome
Authors: Jain Aastha , Govindan Ramesh , Berkman Alexander , Luban Jeremy , Díaz-Salinas Marco A. , Durham Natasha D. , Munro James B. 
Published: January 2023

AbstractInteraction between the Ebola virus envelope glycoprotein (GP) and the endosomal membrane is an essential step during virus entry into the cell. Acidic pH and Ca2+have been implicated in mediating the GP-membrane interaction. However, the molecular mechanism by which these environmental factors regulate the conformational changes that enable engagement of GP with the target membrane is unknown. Here, we apply fluorescence correlation spectroscopy (FCS) and single-molecule Förster resonance energy transfer (smFRET) imaging to elucidate how the acidic pH, Ca2+and anionic phospholipids in the late endosome promote GP-membrane interaction, thereby facilitating virus entry. We find that bis(monoacylglycero)phosphate (BMP), which is specific to the late endosome, is especially critical in determining the Ca2+-dependence of the GP-membrane interaction. Molecular dynamics (MD) simulations suggested residues in GP that sense pH and induce conformational changes that make the fusion loop available for insertion into the membrane. We similarly confirm residues in the fusion loop that mediate GP’s interaction with Ca2+, which likely promotes local conformational changes in the fusion loop and mediates electrostatic interactions with the anionic phospholipids. Collectively, our results provide a mechanistic understanding of how the environment of the late endosome regulates the timing and efficiency of virus entry.Author SummaryEbola virus causes disease in humans with high fatality. A better understanding of how Ebola virus enters cells is critical to inform the development of novel therapeutic and preventative measures. The viral glycoprotein present on the surface of the virus mediates attachment to cells and subsequent entry through a poorly understood mechanism involving fusion of viral and cellular membranes. Here, we employ computational and experimental biophysical techniques to understand how the Ebola glycoprotein senses chemical cues in its environment, such as pH, calcium ions, and specific lipid species to ensure that entry occurs at the right time and place. Our results specify elements of the glycoprotein that control its structure under changing physiological environments.
Trajectories of COVID-19: a longitudinal analysis of many nations and subnational regions
Authors: Burg David , Ausubel Jesse H. 
Published: January 2023

AbstractThe COVID-19 pandemic is the first to be rapidly and sequentially measured by nation-wide PCR community testing for the presence of the viral RNA at a global scale. We take advantage of the novel “natural experiment” where diverse nations and major subnational regions implemented various policies including social distancing and vaccination at different times with different levels of stringency and adherence. Initially, case numbers expanding exponentially with doubling times of ∼1-2 weeks. In the nations where lockdowns were not implemented or ineffectual, case numbers increased exponentially but then stabilized around 102-to-103new infections (per km2built-up area per day). Dynamics under strict lockdowns were perturbed and infections decayed to low levels. They rebounded following the lifting of the policies but converged on an equilibrium setpoint. Here we deploy a mathematical model which captures this behavior, incorporates a direct measure of lockdown efficacies, and allows derivation of a maximal estimate for the basic reproductive numberRo(mean 1.6-1.8). We were able to test this approach by comparing the approximated “herd immunity” to the vaccination coverage observed that corresponded to rapid declines in community infections during 2021. The estimates reported here agree with the observed phenomena. Moreover, the decay ratesd(0.4-0.5) and rebound ratesr0(0.2- 0.3) were similar throughout the pandemic and among all the nations and regions studied. Finally, a longitudinal analysis comparing multiple national and regional results provides insights on the underlying epidemiology of SARS-CoV-2 and lockdown and vaccine efficacy, as well as evidence for the existence of an endemic steady state of COVID-19.
Evaluation of ultrasound as diagnostic tool in patients with clinical features suggestive of carpal tunnel syndrome in comparison to nerve conduction studies: study protocol for a diagnostic testing study
Authors: de la Paz Murciano Casas María , Rodríguez-Piñero Manuel , Sarmiento Aguas-Santas Jiménez , López Mercedes Álvarez , Jurado Gema Jiménez 
Published: January 2023

AbstractBackgroundCarpal Tunnel Syndrome (CTS) is the most common compressive neuropathy, accounting for 90% of all neuropathies. Its prevalence ranges from 3.8% - 7.8% in the population. The gold standard for its diagnosis is the neurophysiological study (85% sensitivity and 95% specificity), with the disadvantage of being invasive, complex and expensive, which means an increase in cost and time for the diagnosis of the disease. The main objective of this diagnostic test evaluation study is to investigate the value of ultrasound in the diagnosis of CTS, and among the secondary objectives, to establish the ultrasound parameters that are predictors of CTS in comparison with neurophysiological studies, attempting to standardize a protocol and reference values that determine the presence or absence of CTS.MethodsProspective, cross-sectional study. The reference test with which we compared the ultrasound is the neurophysiological test (NPT). Patients will come consecutively from the Neurophysiology Department of the Virgen Macarena Hospital, with clinical suspicion of CTS and fulfilling the inclusion/exclusion criteria. To calculate the sample size (EPIDAT program) we proposed a sensitivity of 78% and specificity of 87% with a confidence level of 95%, requiring 438 patients (264 NPT positive, 174 NPT negative). We followed an ultrasound study protocol that included the ultrasound variables: cross-sectional area at the entrance and exit of the tunnel, range of nerve thinning, wrist-forearm index, flexor retinaculum bulging, power Doppler uptake and the existence of adjacent wrists or masses. We propose a timeline for the study to be performed between 2020 and 2023. Finally, we propose a cost-effectiveness analysis.DiscussionUltrasound not only allows to objectify the alterations of the median nerve but also the underlying pathological mechanisms in CTS. A multitude of ultrasound parameters have been described that should be regarded in syndrome’s study, among which we included the cross-sectional area, the range of nerve thinning, the wrist-forearm index, flexor retinaculum bulging, power Doppler uptake and assessment of anatomical alterations. The use of ultrasound as a diagnostic tool in CTS has many advantages for both doctors and the patients, as it is a non-invasive, convenient, and fast tool increasingly accessible to professionals.Administrative information
Long-read direct RNA sequencing of the mitochondrial transcriptome ofSaccharomyces cerevisiaereveals condition-dependent intron turnover
Authors: Koster Charlotte C. , Kleefeldt Askar , van den Broek Marcel , Luttik Marijke , Daran Jean-Marc , Daran-Lapujade Pascale 
Published: January 2023

AbstractMitochondria fulfil many essential roles and have their own genome, which is expressed as polycistronic transcripts that undergo co- or post-transcriptional processing and splicing. Due to inherent complexity and limited technical accessibility of the mitochondrial transcriptome, fundamental questions regarding mitochondrial gene expression and splicing remain unresolved, even in the model eukaryoteSaccharomyces cerevisiae. Long-read sequencing could address these fundamental questions. Therefore, a method for enrichment of mitochondrial RNA and sequencing using Nanopore technology was developed, enabling the resolution of splicing of polycistronic genes and the quantification the spliced RNA.This method successfully captured the full mitochondrial transcriptome and resolved RNA splicing patterns with single-base resolution, and was applied to explore the transcriptome ofS. cerevisiaegrown with glucose or ethanol as sole carbon source, revealing the impact of growth conditions on mitochondrial RNA-expression and splicing. This study uncovered a remarkable difference in turn-over of group II introns between yeast grown in mostly fermentative and fully respiratory conditions. Whether this accumulation of introns in glucose medium has an impact on mitochondrial functions remains to be explored. Combined with the high tractability of the model yeastS. cerevisiae, the developed method enables to explore mitochondrial transcriptome regulation and processing in a broad range of conditions relevant in human context, including aging, apoptosis and mitochondrial diseases.
Temporal dynamics of collateral RNA cleavage by LbuCas13a in human cells
Authors: Bot Jorik F. , Zhao Zhihan , Li Mengyuan , Kammeron Darnell , Shang Peng , Geijsen Niels 
Published: January 2023

AbstractCRISPR-Cas13 exclusively targets RNA. In prokaryotic cells, Cas13 cleaves both target and non-target RNA indiscriminately upon activation by a specific target RNA, but in eukaryotic cells collateral cleavage activity has been limited. To investigate collateral cleavage by Cas13 in eukaryotic cells, we first compared various Cas13 orthologs and found that specifically LbuCas13a exhibits strong collateral RNA cleavage activity in human cells when delivered as ribonucleoprotein, independent of cell line and targeting both exogenous and endogenous transcripts. Collateral RNA cleavage started within 50 minutes of ribonucleoprotein delivery resulting in major alterations to the total RNA profile. In response to the collateral RNA cleavage, cells upregulated genes associated with stress and innate immune response, ultimately leading to apoptotic cell death. This enabled us to use LbuCas13a as a flexible and repeatable target-RNA-specific cell elimination tool. Finally, we used Nanopore sequencing to explore the identity of collaterally cleaved RNAs, the nucleotide position at which they are cleaved, and the temporal dynamics of collateral RNA cleavage. This revealed that LbuCas13a activation leads to rapid and global cleavage of cytoplasmic RNAs at specific nucleotide positions. In conclusion, we here report that LbuCas13a has high collateral activity in human cells and describe the temporal dynamics of the collateral RNA cleavage, the cellular responses ultimately leading to apoptosis, how this can be exploited as a cell elimination tool, and the collateral cleavage preferences of LbuCas13a.
AlphaFold Prediction of Structural Ensembles of Disordered Proteins
Authors: Brotzakis Z. Faidon , Zhang Shengyu , Vendruscolo Michele 
Published: January 2023

AbstractDeep learning methods of predicting protein structures have reached an accuracy comparable to that of high-resolution experimental methods. It is thus possible to generate accurate models of the native states of hundreds of millions of proteins. An open question, however, concerns whether these advances can be translated to disordered proteins, which should be represented as structural ensembles because of their heterogeneous and dynamical nature. Here we show that the inter-residue distances predicted by AlphaFold for disordered proteins can be used to construct accurate structural ensembles. These results illustrate the application to disordered proteins of deep learning methods originally trained for predicting the structures of folded proteins.
piRNA processing by a trimeric Schlafen-domain nuclease
Authors: Podvalnaya Nadezda , Bronkhorst Alfred W. , Lichtenberger Raffael , Hellmann Svenja , Nischwitz Emily , Falk Torben , Karaulanov Emil , Butter Falk , Falk Sebastian , Ketting René F. 
Published: January 2023

AbstractTransposable elements are genomic parasites that expand within and spread between genomes1. Piwi proteins control transposon activity, notably in the germline2,3. These proteins recognize their targets through small RNA co-factors named piRNAs, making piRNA biogenesis a key specificity-determining step in this crucial genome immunity system. While the processing of piRNA precursors is an essential step in this process, many molecular details of this process remain unknown. We identify a novel endoribonuclease, PUCH, that initiates piRNA processing in the nematodeCaenorhabditis elegans. Genetic and biochemical studies show that PUCH, a trimer of Schlafen-like-domain proteins (SLFL proteins), executes 5’-end piRNA precursor cleavage. PUCH-mediated processing strictly requires an m7G-Cap and a uracil at position three. We also demonstrate how PUCH interacts with PETISCO, a complex that binds piRNA precursors4, and that this interaction enhances piRNA productionin vivo. The identification of PUCH completes the repertoire ofC. eleganspiRNA biogenesis factors and uncovers a novel type of RNA endonuclease formed by three SLFL proteins. Mammalian Schlafen (Slfn) genes have been associated with immunity responses5, exposing a thus far unknown molecular link between immune responses in mammals and deeply conserved RNA-based mechanisms that control transposable elements.
Extremely potent pan-sarbecovirus neutralizing antibodies generated by immunization of macaques with an AS03-adjuvanted monovalent subunit vaccine against SARS-CoV-2
Authors: Feng Yupeng , Yuan Meng , Powers John M. , Hu Mengyun , Munt Jennifer E. , Arunachalam Prabhu S. , Leist Sarah R. , Bellusci Lorenza , Adams Lily E. , Sundaramurthy Sumana , Shirreff Lisa M. , Mallory Michael L. , Scooby Trevor D. , Moreno Alberto , O’Hagan Derek T. , Kleanthous Harry , Villinger Francois J. , Veesler David , King Neil P. , Suthar Mehul S. , Khurana Surender , Baric Ralph S. , Wilson Ian A. , Pulendran Bali 
Published: January 2023

AbstractThe rapid emergence of SARS-CoV-2 variants that evade immunity to vaccination has placed a global health imperative on the development of therapeutic countermeasures that provide broad protection against SARS-CoV-2 and related sarbecoviruses. Here, we identified extremely potent pan-sarbecovirus antibodies from non-human primates vaccinated with an AS03 adjuvanted subunit vaccine against SARS-CoV-2 that recognize conserved epitopes in the receptor binding domain (RBD) with femtomolar affinities. Longitudinal analysis revealed progressive accumulation of somatic mutation in the immunoglobulin genes of antigen-specific memory B cells for at least one year following primary vaccination. 514 monoclonal antibodies (mAbs) were generated from antigen-specific memory B cells. Antibodies isolated at 5 to 12 months following vaccination displayed greater potency and breadth, relative to those identified at 1.4 months. Notably, 15 out of 338 (∼4.4%) antibodies isolated at 1.4∼6 months after the primary vaccination showed extraordinary neutralization potency against SARS-CoV-2 omicron BA.1, despite the absence of BA.1 neutralization in serum. Two of them, 25F9 and 20A7, neutralized authentic clade Ia sarbecoviruses (SARS-CoV, WIV-1, SHC014) and clade Ib sarbecoviruses (SARS-CoV-2 D614G, SARS-CoV-2 BA.1, Pangolin-GD) with half-maximal inhibition concentrations of (0.85 ng/ml, 3 ng/ml, 6 ng/ml, 6 ng/ml, 42 ng/ml, 6 ng/ml) and (13 ng/ml, 2 ng/ml, 18 ng/ml, 9 ng/ml, 6 ng/ml, 345 ng/ml), respectively. Furthermore, 20A7 and 27A12 showed potent neutralization against all SARS-CoV-2 variants of concern and multiple Omicron sublineages, including BA.1, BA.2, BA.3, BA.4/5, BQ.1, BQ.1.1 and XBB variants. X-ray crystallography studies revealed the molecular basis of broad and potent neutralization through targeting conserved RBD sites. In vivo prophylactic protection of 25F9, 20A7 and 27A12 was confirmed in aged Balb/c mice. Notably, administration of 25F9 provided complete protection against SARS-CoV-2, SARS-CoV-2 BA.1, SARS-CoV, and SHC014 challenge, underscoring that these mAbs are promising pan-sarbecovirus therapeutic antibodies.One Sentence SummaryExtremely potent pan-sarbecovirus neutralizing antibodies
Downregulation and delayed induction of photosynthesis by coordinated transcriptomic changes induced by sink-source imbalance
Authors: Ozawa Yui , Tanaka Aiko , Suzuki Takamasa , Sugiura Daisuke 
Published: January 2023

AbstractUnderstanding comprehensive mechanisms of the downregulation of photosynthesis induced by accumulation of non-structural carbohydrates (NSCs) is essential for the future food security.x Despite numerous studies, whether NSCs accumulation directly affects steady-state maximum photosynthesis and photosynthetic induction, as well as underlying gene expression profiles, remains unknown so far.We evaluated the relationship between photosynthetic capacity and NSCs accumulation induced by cold-girdling, sucrose feeding, and low nitrogen treatment inGlycine maxandPhaseolus vulgaris. InG. max, changes in transcriptome profiles were further investigated focusing on physiological processes of photosynthesis and NSCs accumulation.NSCs accumulation decreased maximum photosynthetic capacity and delayed photosynthetic induction in both species. InG. max, such photosynthetic downregulation was explained by coordinated downregulation of photosynthetic genes involved in Calvin cycle, Rubisco activase, photochemical reactions, and stomatal opening. Furthermore, sink-source imbalance may have triggered a change in the balance of sugar-phosphate translocators in chloroplast membranes, which may have promoted starch accumulation in chloroplasts.Our findings provided an overall picture of the photosynthetic downregulation and NSCs accumulation inG. max, demonstrating that the photosynthetic downregulation is triggered by NSCs accumulation and cannot be explained simply by N deficiency.One Sentence SummaryAccumulation of nonstructural carbohydrates directly induced both downregulation and delayed induction of photosynthesis by coordinated transcriptomic changes in photosynthetic genes inGlycine max.
Task-specific patterns of odorant receptor expression in worker antennae indicates a sensory filter regulating division of labor in ants
Authors: Caminer Marcel A. , Libbrecht Romain , Majoe Megha , Ho David V. , Baumann Peter , Foitzik Susanne 
Published: January 2023

AbstractDivision of labor (DOL) is a characteristic trait of insect societies, where tasks are generally performed by groups of specialized individuals. In social insects, young workers perform duties within the safety of the nest (e.g., brood care), while older ones undertake riskier tasks (e.g., foraging for food). This DOL remains dynamic, and workers may switch back and forth when colony needs require. Theoretical models propose that workers differ in their thresholds to take on certain tasks when confronted to task-related stimuli, resulting in variation in their response to such stimuli, task-specialization, and thus DOL. Such models assume that workers differ in how they respond to task-related information rather than in how they perceive such information. Here, we test the hypothesis that DOL rather stems from workers differing in their efficiency to detect task-related stimuli. We used transcriptomics to compare gene expression in the antennae and in the brain between nurses and foragers in the antTemnothorax longispinosus. We found that seven times as many genes were differentially expressed between the behavioral phenotypes in the antennae compared to the brain. Moreover, nearly half of all odorant receptors genes were differentially expressed, with an overrepresentation of the 9-exon gene subfamily upregulated in the antennae of nurses. These findings suggest that nurses and foragers differ in how they perceive their olfactory environment, and task-related signals. The results of this study support the hypothesis that a sensory filter in the antennaepredisposes workers to specialize in specific tasks, and may improve our understanding of DOL in insect societies.
Organic line extensions: do they make sense for brands?
Authors: Hernandez-Olalla Maria-Luisa , Valor Carmen , Abril Carmen 
Published: January 2023

PurposePast work on the role of brands in the acceptance of organic products is partial and inconclusive. Research has failed to examine the consumer sense-making process underpinning fit assessment, despite the centrality of this assessment in the acceptance of line extensions. This study reconceptualizes the fit construct, showing the relationship of the fit dimensions (noncompensatory) and contributes to the literature with a deeper understanding of the role of a brand's association in the assessment process, which has been poorly examined in the past.Design/methodology/approachGrounded theory was used to unearth the process followed by consumers to assess the fit of organic line extensions. The study was based on 14 in-depth interviews.FindingsThe findings show that the dimensions of fit that consumers consider in assessing organic line extensions depend on the schema used in the assessment process. Moreover, it demonstrates that these dimensions have disparate structural relationships with one another, depending on consumers' previous commitment to organic products. Finally, the paper identifies three possible behavioral reactions by consumers toward organic line extensions.Research limitations/implicationsThe main limitation of this research concerns the settings in which it was developed. Therefore, and as stated by Strauss and Corbin (1990) the model applies to the situation analyzed and not to others. Future research could study if there are cultural differences in the assessment process of an organic line extension. Moreover, the contribution presented in this paper needs further empirical testing; specifically, the configuration of dimensions needed to accept an organic line extension and the relationship among dimensions.Originality/valueThis paper contributes to the literature by studying the impact of brand association on assessing an organic line extension and reconceptualizing the fit construct by showing the dimensions and the relationship between them that are not additive to the overall fit, as shown in past literature. Additionally, it provides a guide to brands wishing to launch an organic product using a line extension strategy and the potential implications for the parent brand that should be considered.