bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel preclinical secondary pharmacology resource illuminates target-adverse drug reaction associations of marketed drugs
Authors: Sutherland Jeffrey J , Yonchev Dimitar , Fekete Alexander , Urban Laszlo 
Published: February 2023

AbstractIn vitrosecondary pharmacology assays are an important tool for predicting clinical adverse drug reactions (ADRs) of investigational drugs. We created the Secondary Pharmacology Database (SPD) by testing 1958 drugs using 200 assays to validate target-ADR associations. Compared to public and subscription resources, 95% of all and 36% of active (AC50 < 1 µM) results were unique to SPD, with bias towards higher activity in public resources. Annotating drugs with free maximal plasma concentrations, we found 684 physiologically relevant novel off-target activities. Furthermore, 64% of putative ADRs linked to target activity in key literature reviews were not statistically significant in SPD. Systematic analysis of all target-ADR pairs identified several novel associations confirmed by publications. Finally, candidate mechanisms for known ADRs are proposed based on SPD off-target activities. Taken together, we present a unique freely-available resource for benchmarking ADR predictions, explaining novel phenotypic activity and investigating clinical properties of marketed drugs.
FHF2 phosphorylation and regulation of native myocardial NaV1.5 channels
Authors: Lesage Adrien , Lorenzini Maxime , Burel Sophie , Sarlandie Marine , Bibault Floriane , Maloney Dan , Silva Jonathan R. , Reid Townsend R. , Nerbonne Jeanne M. , Marionneau Céline 
Published: February 2023

AbstractPhosphorylation of the cardiac NaV1.5 channel pore-forming subunit is extensive and critical in modulating channel expression and function, yet the regulation of NaV1.5 by phosphorylation of its accessory proteins remains elusive. Using a phosphoproteomic analysis of NaVchannel complexes purified from mouse left ventricles, we identified nine phosphorylation sites on Fibroblast growth factor Homologous Factor 2 (FHF2). To determine the roles of phosphosites in regulating NaV1.5, we developed two models from neonatal and adult mouse ventricular cardiomyocytes in which FHF2 expression is knockdown and rescued by WT, phosphosilent or phosphomimetic FHF2-VY. While the increased rates of closed-state and open-state inactivation of NaVchannels induced by the FHF2 knockdown are completely restored by the FHF2-VY isoform in adult cardiomyocytes, sole a partial rescue is obtained in neonatal cardiomyocytes. The FHF2 knockdown also shifts the voltage-dependence of activation towards hyperpolarized potentials in neonatal cardiomyocytes, which is not rescued by FHF2-VY. Parallel investigations showed that the FHF2-VY isoform is predominant in adult cardiomyocytes, while expression of FHF2-VY and FHF2-A is comparable in neonatal cardiomyocytes. Similar to WT FHF2-VY, however, each FHF2-VY phosphomutant restores the NaVchannel inactivation properties in both models, preventing identification of FHF2 phosphosite roles. FHF2 knockdown also increases the late Na+current in adult cardiomyocytes, which is restored similarly by WT and phosphosilent FHF2-VY. Together, our results demonstrate that ventricular FHF2 is highly phosphorylated, implicate differential roles for FHF2 in regulating neonatal and adult mouse ventricular NaV1.5, and suggest that the regulation of NaV1.5 by FHF2 phosphorylation is highly complex.eTOC SummaryLesageet al. identify the phosphorylation sites of FHF2 from mouse left ventricular NaV1.5 channel complexes. While no roles for FHF2 phosphosites could be recognized yet, the findings demonstrate differential FHF2-dependent regulation of neonatal and adult mouse ventricular NaV1.5 channels.
CATE: A fast and scalable CUDA implementation to conduct highly parallelized evolutionary tests on large scale genomic data
Authors: Perera Deshan , Reisenhofer Elsa , Hussein Said , Higgins Eve , Huber Christian D. , Long Quan 
Published: February 2023

ABSTRACTStatistical tests for molecular evolution provide quantifiable insights into the selection pressures that govern a genome’s evolution. Increasing sample sizes used for analysis leads to higher statistical power. However, this requires more computational nodes or longer computational time. CATE (CUDA Accelerated Testing of Evolution) is a computational solution to this problem comprised of two main innovations. The first is a file organization system coupled with a novel search algorithm and the second is a large-scale parallelization of algorithms using both GPU and CPU. CATE is capable of conducting evolutionary tests such as Tajima’s D, Fu and Li’s, and Fay and Wu’s test statistics, McDonald–Kreitman Neutrality Index, Fixation Index, and Extended Haplotype Homozygosity. CATE is magnitudes faster than standard tools with benchmarks estimating it being on average over 180 times faster. For instance, CATE processes all 54,849 human genes for all 22 autosomal chromosomes across the five super populations present in the 1000 Genomes Project in less than thirty minutes while counterpart software took 3.62 days. This proven framework has the potential to be adapted for GPU-accelerated large-scale parallel analyses of many evolutionary and genomic analyses.
A Chromosome-Level Genome Assembly for the Rock Ptarmigan (Lagopus muta)
Authors: Squires Theodore E. , Rödin-Mörch Patrik , Formenti Giulio , Tracey Alan , Abueg Linelle , Brajuka Nadolina , Jarvis Erich , Halapi Eva C. , Melsted Páll , Höglund Jacob , Magnússon Kristinn Pétur 
Published: February 2023

AbstractThe Rock Ptarmigan (Lagopus muta) is a cold-adapted, largely sedentary, game bird with a Holarctic distribution. The species represents an important example of an organism likely to be affected by ongoing climatic shifts across a disparate range. We provide here a high-quality reference genome and mitogenome for the Rock Ptarmigan assembled from PacBio HiFi and Hi-C sequencing of a female bird from Iceland. The total size of the genome is 1.03 Gb with a scaffold N50 of 71.23 Mb and a contig N50 of 17.91 Mb. The final scaffolds represent all 40 predicted chromosomes, and the mitochondria with a BUSCO score of 98.6%. Gene annotation resulted in 16,078 protein-coding genes out of a total 19,831 predicted (81.08% excluding pseudogenes). The genome included 21.07% repeat sequences, and the average length of genes, exons, and introns were, 33605, 394, and 4265 bp respectively. The availability of a new reference-quality genome will contribute to understanding the Rock Ptarmigan’s unique evolutionary history, vulnerability to climate change, and demographic trajectories around the globe and serve as a reference genome for the species in the family Tetraonidae (order Galliformes).
Computational biology predicts metabolic engineering targets for increased production of 102 valuable chemicals in yeast
Authors: Domenzain Iván , Lu Yao , Shi Junling , Lu Hongzhong , Nielsen Jens 
Published: February 2023

AbstractDevelopment of efficient cell factories that can compete with traditional chemical production processes is complex and generally driven by case-specific strategies, based on the product and microbial host of interest. Despite major advancements in the field of metabolic modelling in recent years, prediction of genetic modifications for increased production remains challenging. Here we present a computational pipeline that leverages the concept of protein limitations in metabolism for prediction of optimal combinations of gene engineering targets for enhanced chemical bioproduction. We used our pipeline for prediction of engineering targets for 102 different chemicals usingSaccharomyces cerevisiaeas a host. Furthermore, we identified sets of gene targets predicted for groups of multiple chemicals, suggesting the possibility of rational model-driven design of platform strains for diversified chemical production.One sentence summaryNovel strain design algorithm ecFactory on top of enzyme-constrained models provides unprecedented chances for rational strain design and development.
Characterization and Validation of a Middle-Down Hydrophobic Interaction Chromatography Method to Monitor Methionine Oxidation in IgG1
Authors: Khalil Somar , Patel Nisha , Bevillard-Kumar Francoise , Chéry Cyrille , Burkitt William , O’Hara John , Gervais Annick 
Published: February 2023

AbstractPost-translational modifications (PTMs) of therapeutic monoclonal antibodies (mAbs) can impact the efficacy of a drug. Methionine oxidation can alter the overall hydrophobicity of an antibody, thereby inducing conformational changes and affecting its biological activity. To ensure high quality, safety, and efficacy of mAbs, routine monitoring of PTMs such as methionine (Met) oxidation is essential. Met oxidation in the fragment crystallizable (Fc) region of immunoglobulin-G1 (IgG1) is a critical quality attribute because it impacts not only the interaction with the neonatal Fc receptor and protein A but also the half-life of mAbs in serum circulation. Although bottom-up mass spectrometry provides high site specificity, it may have limited application in quality control workflows, and its complicated sample preparation could result in procedure-induced oxidation. In this study, we describe the development and characterization of a rapid and robust middle-down hydrophobic interaction chromatography method for monitoring Met oxidation in the Fc region of IgG1. Additionally, we assessed a comprehensive method validation package and demonstrated the specificity, linearity, precision, and accuracy of the new method within a range of 3.8–37.7%. The relative quantitative data provided by this method may be used in a regulated workflow to support process and formulation development as well as in the later stages of drug development and batch release and stability studies.
Hypothesis-free phenotype prediction within a genetics-first framework
Authors: Lu Chang , Zaucha Jan , Gam Rihab , Fang Hai , Smithers Ben , Oates Matt E. , Bernabe-Rubio Miguel , Williams James , Thurlby Natalie , Pandurangan Arun Prasad , Tandon Himani , Shihab Hashem , Kalaivani Raju , Sung Minkyung , Sardar Adam , Tzovoras Bastian Greshake , Danovi Davide , Gough Julian 
Published: February 2023

SummaryCohort-wide sequencing studies have revealed that the largest category of variants is those deemed ‘rare’, even for the subset located in coding regions (99% of known coding variants are seen in less than 1% of the population1–3). Our understanding of how rare genetic variants influence disease and organism-level phenotypes has achieved limited progress, partly explained by the intrinsic difficulty in statistically evaluating the biological significance of rare events. Here we show that discoveries can instead be made through a knowledge-based approach using protein domains and ontologies (function and phenotype) that considers all coding variants regardless of allele frequency. We describe anab initio, genetics-first method making molecular knowledge-based interpretations for exome-wide non-synonymous variants for phenotypes at the organism and cellular level. By using this reverse approach, we identify plausible novel genetic causes for developmental disorders that have eluded other established methods and present novel molecular hypotheses for the causal genetics of 40 phenotypes generated from a direct-to-consumer genotype cohort. This system offers a chance to extract further discovery from genetic data after standard tools have been applied.
DeepD3, an Open Framework for Automated Quantification of Dendritic Spines
Authors: Fernholz Martin H P , Guggiana Nilo Drago A , Bonhoeffer Tobias , Kist Andreas M 
Published: February 2023

ABSTRACTDendritic spines are the seat of most excitatory synapses in the brain, and a cellular structure considered central to learning, memory, and activity-dependent plasticity. The quantification of dendritic spines from light microscopy data is usually performed by humans in a painstaking and error-prone process. We found that human-to-human variability is substantial (inter-rater reliability 82.2±6.4%), raising concerns about the reproducibility of experiments and the validity of using human-annotated ‘ground truth’ as an evaluation method for computational approaches of spine identification. To address this, we present DeepD3, an open deep learning-based framework to robustly quantify dendritic spines in microscopy data in a fully automated fashion. DeepD3’s neural networks have been trained on data from different sources and experimental conditions, annotated and segmented by multiple experts and they offer precise quantification of dendrites and dendritic spines. Importantly, these networks were validated in a number of datasets on varying acquisition modalities, species, anatomical locations and fluorescent indicators. The entire DeepD3 open framework, including the fully segmented training data, a benchmark that multiple experts have annotated, and the DeepD3 model zoo is fully available, addressing the lack of openly available datasets of dendritic spines while offering a ready-to-use, flexible, transparent, and reproducible spine quantification method.
Exploring the role of task success in implicit motor adaptation
Authors: Al-Fawakhiri Naser , Ma Ambri , Taylor Jordan A. , Kim Olivia A. 
Published: February 2023

ABSTRACTWhile implicit motor adaptation is driven by sensory-prediction errors (SPEs), recent work has shown that task success modulates this process. Task success has typically been defined as hitting a target, which signifies the goal of the movement. Visuomotor adaptation tasks are uniquely situated to experimentally manipulate task success independently from SPE by changing the target size or the location of the target. These two, distinct manipulations may influence implicit motor adaptation in different ways, so, over four experiments, we sought to probe the efficacy of each manipulation. We found that changes in target size which caused the target to fully envelop the cursor only affected implicit adaptation for a narrow range of SPE sizes, while jumping the target to overlap with the cursor more reliably and robustly affected implicit adaptation. Taken together, our data indicate that, while task success exerts a small effect on implicit adaptation, these effects are susceptible to methodological variations. Future investigations of the effect of task success on implicit adaptation could benefit from employing target jump manipulations instead of target size manipulations.
The effectiveness of selection in a species affects the direction of amino acid frequency evolution
Authors: McShea Hanon , Weibel Catherine , Wehbi Sawsan , Goodman Peter , James Jennifer E. , Wheeler Andrew L. , Masel Joanna 
Published: February 2023

AbstractNearly neutral theory predicts that species with higher effective population size (Ne) are better able to purge slightly deleterious mutations. We compare evolution in high-Nevs. low-Nevertebrates to reveal which amino acid frequencies are subject to subtle selective preferences. We take three complementary approaches, two measuring flux and one measuring outcomes. First, we fit non-stationary substitution models of amino acid flux using maximum likelihood, comparing the high-Neclade of rodents and lagomorphs to its low-Nesister clade of primates and colugos. Second, we compare evolutionary outcomes across a wider range of vertebrates, via correlations between amino acid frequencies andNe. Third, we dissect the details of flux in human, chimpanzee, mouse, and rat, as scored by parsimony – this also enables comparison to a historical paper. All three methods agree on which amino acids are preferred under more effective selection. Preferred amino acids tend to be smaller, less costly to synthesize, and to promote intrinsic structural disorder. Parsimony-induced bias in the historical study produces an apparent reduction in structural disorder, perhaps driven by slightly deleterious substitutions. Within highly exchangeable pairs of amino acids, arginine is strongly preferred over lysine, and valine over isoleucine, consistent with more effective selection preferring a marginally larger free energy of folding. These two preferences match differences between thermophiles and mesophilic relatives. These results reveal the biophysical consequences of mutation-selection-drift balance, and demonstrate the utility of nearly neutral theory for understanding protein evolution.Significance statementAccording to the nearly neutral theory of molecular evolution, selection is less able to distinguish between similar alleles in species with lower population size. We identify which amino acids are subject to such weak preferences – these tend to be smaller, to be less costly to make, to promote structural disorder of proteins, and to be enriched in thermophiles relative to mesophiles. The latter agrees with theories of marginal protein stability under mutation-selection-drift balance.
CAM evolution is associated with gene family expansion in an explosive bromeliad radiation
Authors: Crego Clara Groot , Hess Jaqueline , Yardeni Gil , de La Harpe Marylaure , Priemer Clara , Beclin Francesca , Saadain Sarah , Cauz-Santos Luiz A. , Temsch Eva M. , Weiss-Schneeweiss Hanna , Barfuss Michael H.J. , Till Walter , Weckwerth Wolfram , Heyduk Karolina , Lexer Christian , Paun Ovidiu , Leroy Thibault 
Published: February 2023

1.AbstractThe subgenusTillandsia(Bromeliaceae) belongs to one of the fastest radiating clades in the plant kingdom and is characterised by the repeated evolution of Crassulacean Acid Metabolism (CAM). Despite its complex genetic basis, this water-conserving trait has evolved independently across many plant families and is regarded as a key innovation trait and driver of ecological diversification in Bromeliaceae. By producing high-quality genome assemblies of aTillandsiaspecies pair displaying divergent photosynthetic phenotypes, and combining genome-wide investigations of synteny, TE dynamics, sequence evolution, gene family evolution and temporal differential expression, we were able to pinpoint the genomic drivers of CAM evolution inTillandsia. Several large-scale rearrangements associated with karyotype changes between the two genomes and a highly dynamic TE landscape shaped the genomes ofTillandsia. However, our analyses show that rewiring of photosynthetic metabolism is mainly obtained through regulatory evolution rather than coding sequence evolution, as CAM-related genes are differentially expressed across a 24-hour cycle between the two species, but are no candidates of positive selection. Gene orthology analyses reveal that CAM-related gene families manifesting differential expression underwent accelerated gene family expansion in the constitutive CAM species, further supporting the view of gene family evolution as a driver of CAM evolution.
Effective Rapid Blood Perfusion inXenopus
Authors: Jonas-Closs Rachael A , Peshkin Leonid 
Published: February 2023

ABSTRACTXenopushas been a powerful model organism for understanding vertebrate development and disease for over a hundred years. Here we define a rapid blood perfusion protocol inXenopusaimed at a consistent and drastic reduction of blood across tissues. Perfusion is done by inserting a needle directly into the ventricle and pumping heparin in PBS through the vascular system. The whole procedure should take about 10 minutes per frog. Blood is dominated by a few highly abundant proteins and cell types which create numerous issues by masking most other molecules and cell types of interest. Reproducible characterization of adultXenopustissues with quantitative proteomics and single cell transcriptomics will gain from applying this protocol prior to organ dissections defined in companion papers. The procedure is aimed at standardization of practice across the animals of different gender, age andXenopusspecies, specificallyX.laevisandX.tropicalis.SUMMARYAn effective rapid blood perfusion protocol to prepare tissue samples for transcriptomics and proteomics studies.
Deficient mitochondrial respiration impairs sirtuin activity in dorsal root ganglia in Friedreich Ataxia mouse and cell models
Authors: Sanz-Alcázar Arabela , Britti Elena , Delaspre Fabien , Medina-Carbonero Marta , Pazos-Gil Maria , Tamarit Jordi , Ros Joaquim , Cabiscol Elisa 
Published: February 2023

ABSTRACTFriedreich ataxia (FA) is a rare, recessive neuro-cardiodegenerative disease caused by deficiency of the mitochondrial protein frataxin. Mitochondrial dysfunction, a reduction in the activity of iron-sulfur enzymes, iron accumulation, and increased oxidative stress have been described. However, the mechanisms causing such cellular disturbances in mammals are not completely understood. Dorsal root ganglion (DRG) sensory neurons are among the cellular types most affected in the early stages of this disease. We have previously demonstrated that frataxin depletion in primary cultures of DRG neurons results in calcium dysregulation, neurite degeneration and apoptotic cell death. However, its effect on mitochondrial function remains to be elucidated. In the present study, we found that in primary cultures of DRG neurons as well as in DRGs from the FXNI151Fmouse model, frataxin deficiency resulted in lower activity and levels of the electron transport complexes, mainly complexes I and II. As a consequence, the NAD+/NADH ratio was reduced and SirT3, a mitochondrial NAD+-dependent deacetylase, was impaired. We identified alpha tubulin as the major acetylated protein from DRG homogenates whose levels were increased in FXNI151Fmice compared to WT mice. Mitochondrial superoxide dismutase (SOD2), a SirT3 substrate, displayed increased acetylation in frataxin-deficient DRG neurons. Since SOD2 acetylation inactivates the enzyme, and higher levels of mitochondrial superoxide anion were detected, oxidative stress markers were analyzed. Elevated levels of hydroxynonenal bound to proteins and mitochondrial Fe2+accumulation were detected when frataxin decreased. Honokiol, a SirT3 activator, restores mitochondrial respiration. Altogether, these results provide the molecular bases to understand mitochondria dysfunction in sensory neurons which have greater susceptibility to frataxin deficiency compared to other tissues.
Imaging Architecture of Granulomas Induced byMycobacterium tuberculosisInfections with Single-Molecule FISH
Authors: Kumar Ranjeet , Kolloli Afsal , Subbian Selvakumar , Kaushal Deepak , Shi Lanbo , Tyagi Sanjay 
Published: February 2023

AbstractGranulomas are an important hallmark ofMycobacterium tuberculosis(Mtb) infection. They are organized and dynamic structures created by an assembly of immune cells around the sites of infection in the lungs to locally restrict the bacterial growth and the host’s inflammatory responses. The cellular architecture of granulomas is traditionally studied by immunofluorescence labeling of phenotypic surface markers. However, very few antibodies are available for model animals used in tuberculosis research, such as non-human primates and rabbits; secreted immunological markers such as cytokines cannot be imagedin situusing antibodies; and traditional phenotypic surface markers do not provide sufficient resolution for the detection of many subtypes and differentiation states of immune cells. Using single-molecule fluorescentin situhybridization (smFISH) and its derivatives, amplified smFISH (ampFISH) and iterative smFISH, we developed a platform for imaging mRNAs encoding immune markers in rabbit and macaque tuberculosis granulomas. Multiplexed imaging for several mRNA and protein markers was followed by quantitative measurement of expression of these markers in single cellsin situ. A quantitative analysis of combinatorial expressions of these markers allowed us to classify the cells into several subtypes and chart their distributions within granulomas. For one mRNA target, HIF-1α, we were able to image its mRNA and protein in the same cells, demonstrating the specificity of probes. This method paves the way for defining granular differentiation states and cell subtypes from transcriptomic data, identifying key mRNA markers for these cell subtypes, and then locating the cells in the spatial context of granulomas.