bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Virus-Packageable CRISPR System Identifies Host Dependency Factors Across Multiple HIV-1 Strains
Authors: Montoya Vanessa R. , Ready Trine M. , Felton Abby , Fine Sydney R. , OhAinle Molly , Emerman Michael 
Published: November 2022

AbstractAt each stage of the HIV life cycle, host cellular proteins are hijacked by the virus to establish and enhance infection. We adapted the virus packageable HIV-CRISPR screening technology at a genome-wide scale to comprehensively identify host factors that affect HIV replication in a human T cell line. Using a smaller, targeted HIV Dependency Factor (HIVDEP) sub-library, we then performed screens across multiple HIV strains representing different clades and with different biological properties to define which T cell host factors are strain-specific versus which ones are important across all HIV strains and different clades. Nearly 90% genes selected across multiple host pathways validated in subsequent assays as bona fide host dependency factors including numerous proteins not previously reported to play role in HIV biology such as UBE2M, MBNL1, FBXW7, PELP1, SLC39A7, and others. Our ranked list of screen hits across multiple viral strains form a resource of HIV dependency factors for future investigation of host proteins involved in HIV biology.
Methylglyoxal controls tomato fruit ripening by regulating ethylene biosynthesis
Authors: Gambhir Priya , Raghuvanshi Utkarsh , Parida Adwaita Prasad , Kujur Stuti , Sharma Shweta , Sopory Sudhir K. , Kumar Rahul , Sharma Arun Kumar 
Published: November 2022

AbstractMethylglyoxal (MG), a toxic compound produced as a byproduct in several cellular processes such as respiration and photosynthesis, is well investigated for its deleterious effects, mainly through glycation of proteins during plant stress responses. However, very little is known about its impact on fruit ripening. In the present study, we report that MG levels are maintained at high level in green tomato fruits, which declines during fruit ripening inspite of a respiratory burst during this transition. We demonstrate that this decline is mainly mediated by glutathione-dependent MG detoxification pathway and primarily catalyzed by glyoxalase enzyme encoded bySlGLY14gene.SlGLYI4is a direct target of MADS-RIN and is induced during fruit ripening. Silencing of this gene leads to drastic MG overaccumulation at ripening-stages in the transgenic fruits and interferes with the ripening process. Further investigations show that MG plausibly glycates and inhibits key enzymes such as methionine synthase (MS) and S-adenosyl methionine synthase (SAMS) of ethylene biosynthesis pathway, thereby indirectly affecting fruit pigmentation and cell was metabolism. MG overaccumulation in several non-ripening or inhibited- ripening tomato mutant fruits suggests the tightly regulated MG detoxification process is crucial for normal ripening program. Overall, we underpin aSlGLYI4-mediated novel regulatory mechanism of MG detoxification controlling fruit ripening in tomato.
Broad compatibility between yeast UAS elements and core promoters and identification of promoter elements that determine cofactor specificity
Authors: Schofield Jeremy A. , Hahn Steven 
Published: November 2022

AbstractThree general classes of yeast protein-coding genes are distinguished by their dependence on the transcription cofactors TFIID, SAGA and Mediator (MED) Tail, but little is known about whether this dependence is determined by the core promoter, Upstream activation sites (UASs), or other gene features. It is also unclear whether UASs can broadly activate transcription from the different promoter classes or whether efficient transcription requires matching UASs and promoters of similar gene class. Here we measure transcription and cofactor specificity for tens of thousands of UAS-core promoter combinations. We find that <5% of UASs display strong core promoter specificity while most UASs can broadly activate promoters regardless of regulatory class. However, we find that matching UASs and promoters from the same gene class is generally important for optimal expression. From examining the cofactor dependence of this large UAS-promoter set, we find that sensitivity to rapid depletion of MED Tail or SAGA is dependent on the identity of both UAS and promoter while dependence on TFIID localizes to only the core promoter. Our results explain why transcription factor-mediated MED recruitment to the UAS does not always result in Tail-dependent transcription and highlight the role of TATA and TATA-like promoter sequences in MED Tail function.
CrusTome: A transcriptome database resource for large-scale analyses across Crustacea
Authors: Pérez-Moreno Jorge L. , Kozma Mihika T. , DeLeo Danielle M. , Bracken-Grissom Heather D. , Durica David S. , Mykles Donald L. 
Published: November 2022

AbstractTranscriptomes from non-traditional model organisms often harbor a wealth of unexplored data. Examining these datasets can lead to clarity and novel insights in traditional systems, as well as to discoveries across a multitude of fields. Despite significant advances in DNA sequencing technologies and in their adoption, access to genomic and transcriptomic resources for non-traditional model organisms remains limited. Crustaceans, for example, being amongst the most numerous, diverse, and widely distributed taxa on the planet, often serve as excellent systems to address ecological, evolutionary, and organismal questions. While they are ubiquitously present across environments, and of economic and food security importance, they remain severely underrepresented in publicly available sequence databases. Here, we present CrusTome, a multi-species, multi-tissue, transcriptome database of 201 assembled mRNA transcriptomes (189 crustaceans, 30 of which were previously unpublished, and 12 ecdysozoan outgroups) as an evolving, and publicly available resource. This database is suitable for evolutionary, ecological, and functional studies that employ genomic/transcriptomic techniques and datasets. CrusTome is presented in BLAST and DIAMOND formats, providing robust datasets for sequence similarity searches, orthology assignments, phylogenetic inference, etc., and thus allowing for straight-forward incorporation into existing custom pipelines for high-throughput analyses. In addition, to illustrate the use and potential of CrusTome, we conducted phylogenetic analyses elucidating the identity and evolution of the Cryptochrome Photolyase Family of proteins across crustaceans.
Positive selection drivescis-regulatory evolution across the threespine stickleback Y chromosome
Authors: Shaw Daniel E. , Naftaly Alice Shanfelter , White Michael A. 
Published: November 2022

AbstractAllele-specific gene expression evolves rapidly on heteromorphic sex chromosomes. Over time, the accumulation of mutations on the Y chromosome leads to widespread loss of gametolog expression, relative to the X chromosome. It remains unclear if expression evolution on degrading Y chromosomes is primarily driven by mutations that accumulate through processes of selective interference, or if positive selection can also favor the downregulation of coding regions on the Y chromosome that contain deleterious mutations. Identifying the relative rates ofcis-regulatory sequence evolution across Y chromosomes has been challenging due to the limited number of reference assemblies. The threespine stickleback (Gasterosteus aculeatus) Y chromosome is an excellent model to identify how regulatory mutations accumulate on Y chromosomes due to its intermediate state of divergence from the X chromosome. A large number of Y-linked gametologs still exist across three differently aged evolutionary strata to test these hypotheses. We found that putative enhancer regions on the Y chromosome exhibited elevated substitution rates and decreased polymorphism when compared to non-functional sites, like intergenic regions and synonymous sites. This suggests that manycis-regulatory regions are under positive selection on the Y chromosome. This divergence was correlated with X-biased gametolog expression, indicating the loss of expression from the Y chromosome may be favored by selection. Our findings provide evidence that Y-linkedcis-regulatory regions exhibit signs of positive selection quickly after the suppression of recombination and allow comparisons with recent theoretical models that suggest the rapid divergence of regulatory regions may be favored to mask deleterious mutations on the Y chromosome.
The structure of a Type III-A CRISPR-Cas effector complex reveals conserved and idiosyncratic contacts to target RNA and crRNA among Type III-A systems
Authors: Paraan Mohammadreza , Nasef Mohamed , Chou-Zheng Lucy , Khweis Sarah A. , Schoeffler Allyn J. , Hatoum-Aslan Asma , Stagg Scott M. , Dunkle Jack A. 
Published: November 2022

AbstractType III CRISPR-Cas systems employ multiprotein effector complexes bound to small CRISPR RNAs (crRNAs) to detect foreign RNA transcripts and elicit a complex immune response that leads to the destruction of invading RNA and DNA. Type III systems are among the most widespread in nature, and emerging interest in harnessing these systems for biotechnology applications highlights the need for detailed structural analyses of representatives from diverse organisms. We performed cryo-EM reconstructions of the Type III-A Cas10-Csm effector complex fromS. epidermidisbound to an intact, cognate target RNA and identified two oligomeric states, a 276 kDa complex and a 318 kDa complex. 3.1 Å density for the well-ordered 276 kDa complex allowed construction of atomic models for the Csm2, Csm3, Csm4 and Csm5 subunits within the complex along with the crRNA and target RNA. We also collected small-angle X-ray scattering data which was consistent with the 276 kDa Cas10-Csm architecture we identified. Detailed comparisons between theS. epidermidisCas10-Csm structure and the well-resolved bacterial (S. thermophilus) and archaeal (T. onnurineus) Cas10-Csm structures reveal differences in how the complexes interact with target RNA and crRNA which are likely to have functional ramifications. These structural comparisons shed light on the unique features of Type III-A systems from diverse organisms and will assist in improving biotechnologies derived from Type III-A effector complexes.
A gene-level test for directional selection on gene expression
Authors: Colbran Laura L. , Ramos-Almodovar Fabian C. , Mathieson Iain 
Published: November 2022

AbstractMost variants identified in human genome-wide association studies and scans for selection are non-coding. Interpretation of these variants’ effects and understanding of the way in which they contribute to phenotypic variation and adaptation in human populations is therefore limited by our understanding of gene regulation and by the difficulty in confidently linking non-coding variants to genes. To overcome this, we developed a gene-by-gene test for population-specific selection based on combinations of regulatory variants.We extended theQXtest for polygenic selection to test for selection on regulatory variants for 17,388 protein-coding genes across 2,504 individuals. We identified 45 genes with significant evidence (FDR <0.1) for selection, includingFADS1,KHK,SULT1A2,ITGAM, and genes in the HLA region. We further confirm that significant selection signals do correspond to plausible population-level differences in predicted expression. However, we find that very few (0.2%) genes have strong evidence for directional, population-specific selection on the component of their expression that is predicted bycis-regulatory variants. While this is consistent with mostcis-regulatory variation evolving under genetic drift or stabilizing selection, it is also possible that any effects are smaller than we can detect, or that population-specific selection is driven by tissue-specific ortranseffects.Our gene-levelQXscore is independent of other methods for detecting selection based on genomic variation, may therefore be useful when used in combination with more traditional selection tests to specifically identify selection on regulatory variation. Overall, our results demonstrate the utility of one approach to combining population-level information with functional data to understand the evolution of gene expression.
Comparative proteome analysis of differentSaccharomyces cerevisiaestrains during growth on sucrose and glucose
Authors: Rodrigues Carla Inês Soares , den Ridder Maxime , Pabst Martin , Gombert Andreas K. , Wahl Sebastian Aljoscha 
Published: November 2022

AbstractBoth the identity and the amount of a carbon source present in laboratory or industrial cultivation media have major impacts on the growth and physiology of a microbial species. In the case of the yeastSaccharomyces cerevisiae, sucrose is arguably the most important sugar used in industrial biotechnology, whereas glucose is the most common carbon and energy source used in research, with many well-known and described regulatory effects, e.g. glucose repression. Here we compared the label-free proteomes of exponentially growingS. cerevisiaecells in a defined medium containing either sucrose or glucose as the sole carbon source. For this purpose, bioreactor cultivations were employed, and three different strains were investigated, namely: CEN.PK113-7D (a common laboratory strain), UFMG-CM-Y259 (a wild isolate), and JP1 (an industrial bioethanol strain). These strains present different physiologies during growth on sucrose; some of them reach higher specific growth rates on this carbon source, when compared to growth on glucose, whereas others display the opposite behavior. It was not possible to identify proteins that commonly presented either higher or lower levels during growth on sucrose, when compared to growth on glucose, considering the three strains investigated here, except for one protein, named Mnp1 – a mitochondrial ribosomal protein of the large subunit, which had higher levels on sucrose than on glucose, for all three strains. Interestingly, following a Gene Ontology overrepresentation and KEGG pathway enrichment analyses, an inverse pattern of enriched biological functions and pathways was observed for the strains CEN.PK113-7D and UFMG-CM-Y259, which is in line with the fact that whereas the CEN.PK113-7D strain grows faster on glucose than on sucrose, the opposite is observed for the UFMG-CM-Y259 strain.
Stronger between-clan than within-clan contests and their ecological correlates in a non-territorial, fission-fusion species, the Asian elephant
Authors: Gautam Hansraj , Vidya T.N.C. 
Published: November 2022

The authors have withdrawn this manuscript owing to duplicate posting. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.The correct manuscript can be found athttps://doi.org/10.1101/754515.
Mapping of the podocin proximity-dependent proteome reveals novel components of the kidney podocyte foot process
Authors: Gerlach Gary F. , Imseis Zachary H. , Cooper Shamus L. , Santos Anabella N. , O’Brien Lori L. 
Published: November 2022

AbstractThe unique architecture of glomerular podocytes is integral to kidney filtration. Interdigitating foot processes extend from the podocyte cell body, wrap around fenestrated capillaries, and form specialized junctional complexes termed slit diaphragms to create a molecular sieve. However, the full complement of proteins which maintain foot process integrity, and how this localized proteome changes with disease, remains to be elucidated. Proximity-dependentbiotinidentification (BioID) enables the identification of spatially localized proteomes. To this end, we developed a novelin vivoBioID knock-in mouse model. We utilized the slit diaphragm protein podocin (Nphs2) to create a podocin-BioID fusion. Podocin-BioID localizes to the slit diaphragm and biotin injection leads to podocyte-specific protein biotinylation. We isolated the biotinylated proteins and performed mass spectrometry to identify proximal interactors. Gene ontology analysis of 54 proteins specifically enriched in our podocin-BioID sample revealed ‘cell junctions’, ‘actin binding’, and ‘cytoskeleton organization’ as top terms. Known foot process components were identified and we further uncovered two novel proteins: the tricellular junctional protein Ildr2 and the CDC42 and N-WASP interactor Fnbp1l. We confirmed Ildr2 and Fnbp1l are expressed by podocytes and partially colocalize with podocin. Finally, we investigated how this proteome changes with age and uncovered a significant increase in Ildr2. This was confirmed by immunofluorescence on human kidney samples and suggests altered junctional composition may preserve podocyte integrity. Together, these assays have led to new insights into podocyte biology and supports the efficacy of utilizing BioIDin vivoto interrogate spatially localized proteomes in health, aging, and disease.
Magnetic Levitation and Sorting of Neoplastic Circulating Cell Hybrids
Authors: Liang Kaitlyn , Yaman Sena , Patel Ranish K. , Parappilly Michael S. , Walker Brett S. , Wong Melissa H. , Durmus Naside Gozde 
Published: November 2022

AbstractCirculating hybrid cells (CHCs) are a novel, rare cell population that harbor tumor and immune cell phenotypes and genotypes and are detectible in peripheral blood. Several recent reports implicated CHCs in the metastatic cascade and found their enumeration to provide better prognostic value than conventionally-defined circulating tumor cells (CTCs). However, methods for isolation and enrichment of CHCs are not well-studied or established. Here, we developed an ultrasensitive, antigen-independent platform leveraging the principles of magnetic levitation for the detection and isolation of disseminated neoplastic CHCs. For the first time, we demonstrate that CHCs can be magnetically focused to different levitation heights, under various paramagnetic conditions using a static levitation system, and we quantified the biophysical properties of CHCs (i.e., levitation heights). In addition, we investigated whether magnetic levitation approach can be combined with the affinity-based strategies to enrich CHCs under the magnetic field. Using clinical samples from breast and colorectal cancer patients, we demonstrated that neoplastic cells can be sorted with a magnetic levitation-based sorting device, without relying on any surface markers. Overall, we demonstrated the feasibility of the magnetic levitation method for unbiased enrichment of rare neoplastic-immune hybrid cells from peripheral blood specimens from cancer patients. This approach can be expanded to more clinical samples and cancer types to unprecedentedly explore the biology of rare neoplastic cells and develop metastasis-tailored therapies broadly impacting personalized and precision clinical treatments.
A retrograde GCN2/eIF2α, but ATF4 independent, mechanism maintains synaptic strength under acute amino acid scarcity at the NMJ
Authors: Kauwe Grant , Mori Megumi , Liao Edward H. , Scott Gary , Haghighi A. Pejmun 
Published: November 2022

ABSTRACTNeuronal response to nutrient availability plays an important role in the maintenance of cellular homeostasis and behavioral response to the environment in higher eukaryotes. However, we know little about how neuronal function is influenced by acute changes in nutrients at high resolution. Taking advantage of powerful fly genetics and the amenability of theDrosophilalarval neuromuscular junction (NMJ), we have investigated the synaptic response to acute amino acid restriction. Our findings indicate that the presence of general control nonderepressible 2 (GCN2) and phosphorylation of its target eukaryotic initiation factor 2 alpha (eIF2α) are essential for the ability of the NMJ to maintain normal neurotransmitter output when the larvae are deprived of amino acids. Surprisingly, activating transcription factor 4 (ATF4), which normally acts downstream of GCN2/eIF2α, appears dispensable in this regulation. Furthermore, we show that GCN2/eIF2α dependent cascade acts retrogradely from muscle back to motoneuron to adjust synaptic release. These results provide a mechanistic insight into the intricate regulation of synaptic strength through the action of GCN2 when organisms are faced with amino acid scarcity.
Pupil size reflects activation of subcortical ascending arousal system nuclei during rest
Authors: Lloyd Beth , de Voogd Lycia D. , Mäki-Marttunen Verónica , Nieuwenhuis Sander 
Published: November 2022

AbstractNeuromodulatory nuclei that are part of the ascending arousal system (AAS) play a crucial role in regulating cortical state and optimizing task performance. Pupil diameter, under constant luminance conditions, is increasingly used as an index of activity of these AAS nuclei. Indeed, task-based functional imaging studies in humans have begun to provide evidence of stimulus-driven pupil-AAS coupling. However, whether there is such a tight pupil-AAS coupling during rest is not clear. To address this question, we examined simultaneously acquired resting-state fMRI and pupil-size data from 74 participants, focusing on six AAS nuclei: the locus coeruleus, ventral tegmental area, substantia nigra, dorsal and median raphe nuclei, and cholinergic basal forebrain. Activation in all six AAS nuclei was optimally correlated with pupil size at 0-to 2-second lags, suggesting that spontaneous pupil changes were almost immediately followed by corresponding BOLD-signal changes in the AAS. These results suggest that spontaneous changes in pupil size that occur during states of rest can be used as a noninvasive general index of activity in AAS nuclei. Importantly, the nature of pupil-AAS coupling during rest appears to be vastly different from the relatively slow canonical hemodynamic response function that has been used to characterize task-related pupil-AAS coupling.
Development of a high-throughput starch digestibility assay reveals wide variation among the A. E. Watkins wheat landrace collection
Authors: Zafeiriou Petros , Savva George M. , Ahn-Jarvis Jennifer H. , Warren Frederick J. , Pasquariello Marianna , Griffiths Simon , Seung David , Hazard Brittany A. 
Published: November 2022

AbstractBreeding for less digestible starch in wheat can improve the health impact of bread and other wheat foods. Based on an establishedin vitrostarch digestibility assay by Edwards et al. (2019) we developed a high-throughput assay to measure starch digestibility in hydrothermally processed samples for use in forward genetic approaches. Digestibility of purified starch from maize and wheat was measured using both methods and produced comparable results. Using the high-throughput assay, we estimated starch digestibility of 118 wheat landraces from the core Watkins collection and found wide variation across lines and elite UK varieties, (20% to 40% and 31% to 44% starch digested after 90 minutes respectively). Sieved flour fractions and purified starch for selected lines showed altered starch digestibility profiles compared with wholemeal flour, suggesting that matrix properties of flour rather than intrinsic properties of starch granules conferred the low starch digestibility observed.