bluuebunny/crossref_metadata_2025_split huggingface dataset:
Principles for Systematic Optimization of an Orthogonal Translation System with Enhanced Biological Tolerance
Authors: Mohler Kyle , Moen Jack , Rogulina Svetlana , Rinehart Jesse 
Published: May 2021

AbstractOver the past twenty years, the development of orthogonal biological systems has sparked a revolution in our ability to study cellular physiology. Orthogonal translation systems (OTSs) enable site-specific incorporation of hundreds of non-standard amino acids, offering unprecedented access to the study of cellular mechanisms modulated by post-translational modifications (e.g. protein phosphorylation). Although development of phosphoserine-OTSs (pSerOTS) has been significant, little work has focused on the biology of OTS development and utilization. To better understand the impact of OTSs on host physiology, we utilize pSerOTS as a model to systematically explore the extent to which OTS components interact with Escherichia coli. Using this information, we constructed pSerOTS variants designed to enhance OTS orthogonality by minimizing interactions with host processes and decreasing stress response activation. Our expanded understanding of OTS:host interactions enables informed OTS design practices which minimize the negative impact of OTSs while improving OTS performance across a range of experimental settings.
Combined fluorescent seed selection and multiplex CRISPR/Cas9 assembly for fast generation of multiple Arabidopsis mutants
Authors: Ursache Robertas , Fujita Satoshi , Tendon Valérie Dénervaud , Geldner Niko 
Published: May 2021

ABSTRACTMultiplex CRISPR-Cas9-based genome editing is an efficient method for targeted disruption of gene function in plants. Use of CRISPR-Cas9 has increased rapidly in recent years and is becoming a routine method for generating single and higher order Arabidopsis mutants. To facilitate rapid and efficient use of CRISPR/Cas9 for Arabidopsis research, we developed a CRISPR/Cas9-based toolbox for generating large deletions at multiple genomic loci, using two-color fluorescent seed selection. In our system, up-to eight gRNAs can be routinely introduced into a binary vector carrying either FastRed, FastGreen or FastCyan fluorescent seed selection cassette. Both, FastRed and FastGreen binary vectors, can be co-transformed as a cocktail via floral dip to introduce sixteen gRNAs at the same time. The seeds can be screened either for red or green fluorescence, or for the presence of both colors at the same time. Our approach provides fast and flexible cloning, avoids very big constructs and enables screening different order mutants in the same generation. Importantly, in the second generation after transformation, Cas9 free plants are identified simply by screening the dark, non-fluorescent seeds. Our collection of binary vectors allows to choose between two widely-used promoters to drive Cas enzymes, either the egg cell-specific (pEC1.2) or ubiquitous promoter (PcUBi4-2). Available enzymes are “classical” Cas9, a recently reported, intron-optimized version or Cpf1 (Cas12a). Finally, we have taken care to introduce convenient restriction sites flanking promoter, Cas9 and fluorescent selection cassette in the final T-DNA vectors, thus allowing straightforward swapping of all three elements for further adaptation and improvement of the system.
Taxon-specific or universal? Using target capture to study the evolutionary history of rapid radiations
Authors: Yardeni Gil , Viruel Juan , Paris Margot , Hess Jaqueline , Crego Clara Groot , de La Harpe Marylaure , Rivera Norma , Barfuss Michael H. J. , Till Walter , Guzmán-Jacob Valeria , Krömer Thorsten , Lexer Christian , Paun Ovidiu , Leroy Thibault 
Published: May 2021

AbstractTarget capture has emerged as an important tool for phylogenetics and population genetics in non-model taxa. Whereas developing taxon-specific capture probes requires sustained efforts, available universal kits may have a lower power to reconstruct relationships at shallow phylogenetic scales and within rapidly radiating clades. We present here a newly-developed target capture set for Bromeliaceae, a large and ecologically-diverse plant family with highly variable diversification rates. The set targets 1,776 coding regions, including genes putatively involved in key innovations, with the aim to empower testing of a wide range of evolutionary hypotheses. We compare the relative power of this taxon-specific set, Bromeliad1776, to the universal Angiosperms353 kit. The taxon-specific set results in higher enrichment success across the entire family, however, the overall performance of both kits to reconstruct phylogenetic trees is relatively comparable, highlighting the vast potential of universal kits for resolving evolutionary relationships. For more detailed phylogenetic or population genetic analyses, e.g. the exploration of gene tree concordance, nucleotide diversity or population structure, the taxon-specific capture set presents clear benefits. We discuss the potential lessons that this comparative study provides for future phylogenetic and population genetic investigations, in particular for the study of evolutionary radiations.
MIRO2 regulates prostate cancer cell growth via GCN1-dependent stress signaling
Authors: Furnish Madison , Boulton Dillon P. , Genther Victoria , Ellinwood Mitchell Lee , Romero Lina , Lucia M. Scott , Cramer Scott D. , Caino M. Cecilia 
Published: May 2021

ABSTRACTThere is a continued need to identify novel therapeutic targets to prevent the mortality associated with prostate cancer. In this context, we discovered a novel mitochondrial signaling pathway that controls androgen-independent and androgen-sensitive prostate cancer cell growth. Mitochondrial Rho GTPase 2 (MIRO2) mRNA was upregulated in prostate cancer compared to localized tumors, and higher MIRO2 levels were correlated with poor patient survival. Using human cell lines that represent AR-independent or androgen-sensitive prostate cancer, we show that MIRO2 depletion impaired cell growth, colony formation and tumor growth in mice. Network analysis of MIRO2’s binding partners identified metabolism, cell cycle, and cellular responses to extracellular stimuli amongst the top over-represented pathways. The top hit on our screen was General Control Non-derepressible 1 (GCN1). GCN1 was overexpressed in prostate cancer and MIRO2-GCN1 interacted in prostate cancer cell lines and in primary prostate cancer cells. Our results showed that MIRO2 is necessary for efficient GCN1-mediated GCN2 kinase activation and signaling, triggering translation of the transcription factor ATF4. Importantly, MIRO2 controlled ATF4 levels and transcriptional activity both in amino acid replete and depleted conditions. Furthermore, MIRO2’s effect on regulating prostate cancer cell growth was partially mediated by ATF4. Finally, activation of GCN2 and ATF4 expression were correlated with MIRO2 expression in prostate cancer xenografts. Overall, we propose a new mechanism driving prostate cancer growth of both AR-independent and androgen-sensitive tumors.
ASLPrep: A Generalizable Platform for Processing of Arterial Spin Labeled MRI and Quantification of Regional Brain Perfusion
Authors: Adebimpe Azeez , Bertolero Maxwell , Dolui Sudipto , Cieslak Matthew , Murtha Kristin , Baller Erica B. , Boeve Bradley , Boxer Adam , Butler Ellyn R. , Cook Phil , Colcombe Stan , Covitz Sydney , Davatzikos Christos , Davila Diego G. , Elliott Mark A. , Flounders Matthew W. , Franco Alexandre R. , Gur Raquel E. , Gur Ruben C. , Jaber Basma , McMillian Corey ,   the ALLFTD Consortium, Milham Michael , Mutsaerts Henk J.M.M. , Oathe Desmond J. , Olm Christopher A. , Phillips Jeffrey S. , Tackett Will , Roalf David R. , Rosen Howard , Tapera Tinashe M. , Tisdall M. Dylan , Esteban Oscar , Poldrack Russell A. , Detre John A. , Satterthwaite Theodore D. 
Published: May 2021

ABSTRACTArterial spin labeled (ASL) magnetic resonance imaging (MRI) is the primary method for non-invasively measuring regional brain perfusion in humans. We introduce ASLPrep, a suite of software pipelines that ensure the reproducible and generalizable processing of ASL MRI data.
Systematic, Protein Activity-based Characterization of Single Cell State
Authors: Vlahos Lukas , Obradovic Aleksandar , Worley Jeremy , Tan Xiangtian , Howe Andrew , Laise Pasquale , Wang Alec , Drake Charles G. , Califano Andrea 
Published: May 2021

AbstractWhile single-cell RNA sequencing provides a remarkable window on pathophysiologic tissue biology and heterogeneity, its high gene-dropout rate and low signal-to-noise ratio challenge quantitative analyses and mechanistic understanding. To address this issue, we developed PISCES, a platform for the network-based, single-cell analysis of mammalian tissue. PISCES accurately estimates the mechanistic contribution of regulatory and signaling proteins to cell state implementation and maintenance, based on the expression of their lineage-specific transcriptional targets, thus supporting discovery and visualization of Master Regulators of cell state and cell state transitions. Experimental validation assays, including by assessing concordance with antibody and CITE-Seq-based measurements, show significant improvement in the ability to identify rare subpopulations and to elucidate key lineage markers, compared to gene expression analysis. Systematic analysis of single cell profiles in the Human Protein Atlas (HPA) produced a comprehensive resource for human tissue studies, supporting fine-grain stratification of distinct cell states, molecular determinants, and surface markers.
Genetic load may increase or decrease with selfing depending upon the recombination environment
Authors: Sianta Shelley A , Peischl Stephan , Moeller David A , Brandvain Yaniv 
Published: May 2021

ABSTRACTThe ability of natural selection to remove deleterious mutations from a population is a function of the effective population size. Increases in selfing rate, and concomitant increases in population-level homozygosity, can increase or decrease the efficacy of selection, depending on the dominance and selection coefficients of the deleterious mutations. Most theory has focused on how (partial) selfing affects the efficacy of selection for mutations of a given dominance and fitness effect in isolation. It remains unclear how selfing affects the purging of deleterious mutations in a genome-wide context where mutations with different selection and dominance coefficients co-segregate. Here, we use computer simulations to investigate how mutation, selection and recombination interact with selfing rate to shape genome-wide patterns of genetic load. We recover various mechanisms previously described for how (partial) selfing affects the efficacy of selection against mutations of a given dominance class. However, we find that the interaction of purifying selection against mutations of different dominance classes changes with selfing rate. In particular, as outcrossing populations transition from purifying selection to pseudo-overdominance they experience a dramatic increase in the genetic load caused by additive, mildly deleterious mutations. We describe the threshold selfing rate that prevents pseudo-overdominance and decreases genetic load.
Brain-inspired Weighted Normalization for CNN Image Classification
Authors: Pan Xu , Sánchez Giraldo Luis Gonzalo , Kartal Elif , Schwartz Odelia 
Published: May 2021

AbstractWe studied a local normalization paradigm, namely weighted normalization, that better reflects the current understanding of the brain. Specifically, the normalization weight is trainable, and has a more realistic surround pool selection. Weighted normalization outperformed other normalizations in image classification tasks on Cifar10, Imagenet and a customized textured MNIST dataset. The superior performance is more prominent when the CNN is shallow. The good performance of weighted normalization may be related to its statistical effect of gaussianizing the responses.
Deamidation drives molecular aging of the SARS-CoV-2 spike receptor-binding motif
Authors: Lorenzo Ramiro , Defelipe Lucas A. , Aliperti Lucio , Niebling Stephan , Custódio Tânia F. , Löw Christian , Schwarz Jennifer J. , Remans Kim , Craig Patricio O. , Otero Lisandro H. , Klinke Sebastián , García-Alai María , Sánchez Ignacio E. , Alonso Leonardo G. 
Published: May 2021

AbstractThe spike is the main protein component of the SARS-CoV-2 virion surface. The spike receptor binding motif mediates recognition of the hACE2 receptor, a critical infection step, and is the preferential target for spike-neutralizing antibodies. Post-translational modifications of the spike receptor binding motif can modulate viral infectivity and immune response. We studied the spike protein in search for asparagine deamidation, a spontaneous event that leads to the appearance of aspartic and isoaspartic residues, affecting both the protein backbone and its charge. We used computational prediction and biochemical experiments to identify five deamidation hotspots in the SARS-CoV-2 spike. Similar deamidation hotspots are frequently found at the spike receptor-binding motifs of related sarbecoviruses, at positions that are mutated in emerging variants and in escape mutants from neutralizing antibodies. Asparagine residues 481 and 501 from the receptor-binding motif deamidate with a half-time of 16.5 and 123 days at 37 °C, respectively. This process is significantly slowed down at 4 °C, pointing at a strong dependence of spike molecular aging on the environmental conditions. Deamidation of the spike receptor-binding motif decreases the equilibrium constant for binding to the hACE2 receptor more than 3.5-fold. A model for deamidation of the full SARS-CoV-2 virion illustrates that deamidation of the spike receptor-binding motif leads to the accumulation in the virion surface of a chemically diverse spike population in a timescale of days. Our findings provide a mechanism for molecular aging of the spike, with significant consequences for understanding virus infectivity and vaccine development.
Golden pompano genome resource enables discovery of valuable gene determining growth traits
Authors: Luo Honglin , Zhang Yongde , Ji Changmian , Zhao Yongzhen , Peng Jinxia , Xu Yuhui , Chen Xiuli , Huang Yin , Liu Qingyun , He Pingping , Feng Pengfei , Yang Chunling , Wei Pinyuan , Yu Haiyan , Zheng Hongkun , Lin Yong , Chen Xiaohan 
Published: May 2021

AbstractOne important goal of fish genetic breeding is to identify valuable loci and genes that can facilitate growth and thereby productivity. Few such loci or genes have been identified in golden pompano (Trachinotus ovatus), a species of significant economic value. In this study, we produced a high-quality chromosome-level genome assembly of the golden pompano byde novosequencing and assemblies for 2 parents and 200 F1offspring by genome re-sequencing. We exploited these assemblies to identify loci and genes by QTL mapping, Kompetitive Allele Specific PCR (KASP) genotyping, and haplotype-based regional association analysis based on growth records of a 64 biparental and 147 individuals from a naturally occurring population. At a locus 291kb from BSNP21031, we identified a somatostatin receptor type 1-like (designated as gpsstr1) gene in which the BSNP1369 of the promoter region was highly associated with growth. Loss of sstr1a, the homolog of gpsstr1 in zebrafish, caused growth retardation. Sstr1a mediated growth via sstr2 and Wnt-gsk-3β signaling pathways. Our findings provide new insights into the underlying mechanisms controlling growth. Our strategy can serve as an effective way to uncover novel genomic information and facilitate improvement of fish growth.
A systematic review and meta-analysis of genetic parameters for complex quantitative traits in aquatic animal species
Authors: Nguyen Nguyen Hong 
Published: May 2021

AbstractA systematic review and meta-analysis of genetic parameters underlying inheritance and complex biological relationships for quantitative traits are not available for aquatic animal species. I synthesised and conducted a comprehensive meta-analysis of the published information from 1985 to 2017 on heritability, common full-sib effects and genetic correlations for quantitative characters of biological importance (growth, carcass and flesh quality, disease resistance, deformity and reproduction) for aquaculture species. A majority of the studies (73.5%) focussed on growth related traits (body weight), followed by those on disease resistance (15.9%), whereas only a limited number of studies (10.6%) reported heritability estimates for carcass and flesh quality, deformity or reproduction characteristics. The weighted means of heritability for growth (weight, food utilisation efficiency, maturity) and carcass (fillet weight and yield) traits were moderate. Resistance against various bacteria, virus and parasites were moderately to highly heritable. Across aquatic animal species, the weighted heritability for a range of deformity measures and reproductive traits (fecundity, early survival) was low and not significantly different from zero. The common full-sibs (c2) accounted for a large proportion of total variance for body traits but it was of smaller magnitude in later phase of the growth development. The c2 effects however were not significant or in many cases they were not reported for carcass and flesh quality attributes as well as survival and deformity. The maternal genetic effects were not available for all traits studied especially for reproductive and early growth characters. Genetic correlations between body and carcass traits were high and positive, suggesting that selection for rapid growth can improve fillet weight, a carcass trait of paramount importance. Body weight, the most commonly used selection criterion in aquatic animals, showed non-significant genetic correlation with disease resistance, likely because both positive and negative genetic associations between the two types of traits. Interestingly the genetic associations between growth and reproductive performance (fecundity) and fry traits (fry weight, fry survival) were favourable. To date, there are still no published data on genetic relationships of carcass and flesh quality with disease resistance or reproductive performance in any aquaculture species. Additionally, the present study discussed new traits, including functional, immunological, behavioural and social interaction as well as uniformity that are emerging as potential selection criteria and which can be exploited in future genetic improvement programs for aquatic animals.
Endurance Exercise to Improve Physical Function in Adult and Older Mice: High Intensity Interval Training (HIIT) versus Voluntary Wheel Running (VWR)
Authors: Pajski Megan L. , Byrd Chris , Nandigama Nainika , Seguin Emily , Seguin Anna , Fennell Alyssa , Graber Ted G. 
Published: May 2021

AbstractWith age comes a gradual decline in physical function and exercise capacity, concurrent with a progressive propensity for development of sarcopenia /(age-related loss of muscle mass and strength) and frailty (inability of body to thrive and maintain homeostasis). Prior research has demonstrated that exercise, while not a cure, can help mitigate sarcopenia/frailty and restore functional capacity. Reliable, validated, pre-clinical models are necessary to elucidate the underlying molecular mechanisms at the intersection of age, exercise, and functional decline. In this study, we hypothesized that endurance exercise programs mimicking typical human exercise protocols would improve physical function in both adult and older adult mice. Furthermore, our secondary hypothesis was that older mice would receive less benefit from a similar volume of exercise than adult mice. To test these hypotheses, we randomly assigned (with some selection criteria) male C57BL/6 mice either at adult ages during the study (n=24, designated 10m, aged 6 months to 10 months) or at older adult ages (n=18, designated 26m, aged 22 months to 26 months) to a 13-week program of voluntary wheel running (VWR, group termed RUN) or high intensity interval training (HIIT), with an additional 10m sedentary control (CON). The functional aptitude of each mouse was determined pre- and post-training using our composite CFAB (comprehensive functional assessment battery) scoring system consisting of voluntary wheel running (volitional exercise and activity rate), treadmill (endurance), rotarod (overall motor function), grip meter (forelimb strength), and inverted cling (whole body strength/endurance). To measure sarcopenia, we tracked body mass and body composition changes with EchoMRI, and measured muscle wet mass post-training.
Generation of potent cellular and humoral immunity against SARS-CoV-2 antigens via conjugation to a polymeric glyco-adjuvant
Authors: Gray Laura T. , Raczy Michal M. , Briquez Priscilla S. , Marchell Tiffany M. , Alpar Aaron T. , Wallace Rachel P. , Volpatti Lisa R. , Sasso Maria Stella , Cao Shijie , Nguyen Mindy , Mansurov Aslan , Budina Erica , Watkins Elyse A. , Solanki Ani , Mitrousis Nikolaos , Reda Joseph W. , Yu Shann S. , Tremain Andrew C. , Wang Ruyi , Nicolaescu Vlad , Furlong Kevin , Dvorkin Steve , Manicassamy Balaji , Randall Glenn , Wilson D. Scott , Kwissa Marcin , Swartz Melody A. , Hubbell Jeffrey A. 
Published: May 2021

ABSTRACTThe SARS-CoV-2 virus has caused an unprecedented global crisis, and curtailing its spread requires an effective vaccine which elicits a diverse and robust immune response. We have previously shown that vaccines made of a polymeric glyco-adjuvant conjugated to an antigen were effective in triggering such a response in other disease models and hypothesized that the technology could be adapted to create an effective vaccine against SARS-CoV-2. The core of the vaccine platform is the copolymer p(Man-TLR7), composed of monomers with pendant mannose or a toll-like receptor 7 (TLR7) agonist. Thus, p(Man-TLR7) is designed to target relevant antigen-presenting cells (APCs) via mannose-binding receptors and then activate TLR7 upon endocytosis. The p(Man-TLR7) construct is amenable to conjugation to protein antigens such as the Spike protein of SARS-CoV-2, yielding Spike-p(Man-TLR7). Here, we demonstrate Spike-p(Man-TLR7) vaccination elicits robust antigen-specific cellular and humoral responses in mice. In adult and elderly wild-type mice, vaccination with Spike-p(Man-TLR7) generates high and long-lasting titers of anti-Spike IgGs, with neutralizing titers exceeding levels in convalescent human serum. Interestingly, adsorbing Spike-p(Man-TLR7) to the depot-forming adjuvant alum, amplified the broadly neutralizing humoral responses to levels matching those in mice vaccinated with formulations based off of clinically-approved adjuvants. Additionally, we observed an increase in germinal center B cells, antigen-specific antibody secreting cells, activated T follicular helper cells, and polyfunctional Th1-cytokine producing CD4+and CD8+T cells. We conclude that Spike-p(Man-TLR7) is an attractive, next-generation subunit vaccine candidate, capable of inducing durable and robust antibody and T cell responses.