bluuebunny/crossref_metadata_2025_split huggingface dataset:
An anchored experimental design and meta-analysis approach to address batch effects in large-scale metabolomics
Authors: Shaver Amanda O. , Garcia Brianna M. , Gouveia Goncalo J. , Morse Alison M. , Liu Zihao , Asef Carter K. , Borges Ricardo M. , Leach Franklin E. , Andersen Erik C. , Amster I. Jonathan , Fernández Facundo M. , Edison Arthur S. , McIntyre Lauren M. 
Published: March 2022

ABSTRACTLarge-scale untargeted metabolomics studies suffer from individual variation, batch effects and instrument variability, making comparisons of common spectral features across studies difficult. One solution is to compare studies after compound identification. However, compound identification is expensive and time consuming. We successfully identify common spectral features across multiple studies, with a generalizable experimental design approach. First, we included an anchor strain, PD1074, during sample and data collection. Second, we collected data in blocks with multiple controls. These anchors enabled us to successfully integrate three studies of Caenorhabditis elegans for nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography-mass spectrometry (LC-MS) data from five different assays. We found 34% and 14% of features to be significant in LC-MS and NMR, respectively. Between 20-50% of spectral features differ in a mutant and among a set of genetically diverse natural strains, suggesting this reduced set of spectral features are excellent targets for compound identification.GRAPHICAL ABSTRACTFourteen C. elegans strains are used in three individual studies. PD1074, the anchor control strain (orange), is grown alongside test strains (green, yellow, purple). Multiple biological replicates of PD1074 captures environmental variation in growth conditions. Non-polar and polar metabolic data across the three studies (i.e., natural strains, central metabolism mutants, and UGT mutants) were collected by nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography-mass spectrometry (LC-MS). Data acquisition controls in each block included biological reference material and pooled PD1074 samples. Biological replicates of PD1074 (n = 42 for LC-MS, n = 52 for NMR) were included in all batches. Meta-analysis provided comparable inferences to mixed effects models, and the estimated relative effects of each test strain to PD1074 and straightforward comparisons of test strains across experiments.
ScanExitronLR: characterization and quantification of exitron splicing events in long-read RNA-seq data
Authors: Fry Joshua , Li Yangyang , Yang Rendong 
Published: March 2022

AbstractSummaryExitron splicing is a type of alternative splicing where coding sequences are spliced out. Recently, exitron splicing has been shown to increase proteome plasticity and play a role in cancer. Long-read RNA-seq is well suited for quantification and discovery of alternative splicing events; however, there are currently no tools available for detection and annotation of exitrons in long-read RNA-seq data. Here we present ScanExitronLR, an application for the characterization and quantification of exitron splicing events in long-reads. From a BAM alignment file, reference genome and reference gene annotation, ScanExitronLR outputs exitron events at the transcript level. Outputs of ScanExitronLR can be used in downstream analyses of differential exitron splicing. A companion tool, AnnotateExitron, reports exitron annotations such as truncation or frameshift type, nonsense-mediated decay status, and Pfam domain interruptions. We demonstrate that ScanExitronLR performs better on noisy long-reads than currently published exitron detection algorithms designed for short-read data.Availability and ImplementationScanExitronLR is freely available at https://github.com/ylab-hi/ScanExitronLR and distributed as a pip package on the Python Package Index.Contactyang4414@umn.eduSupplementary InformationSupplementary data are available at Bioinformatics online.
Coregistration of heading to visual cues in retrosplenial cortex
Authors: Sit Kevin K. , Goard Michael J. 
Published: March 2022

SummarySpatial cognition depends on an accurate representation of orientation within an environment. Head direction cells in distributed brain regions receive a range of sensory inputs, but visual input is particularly important for aligning their responses to environmental landmarks. To investigate how population-level heading responses are aligned to visual input, we recorded from retrosplenial cortex (RSC) of head-fixed mice in a moving environment using two-photon calcium imaging. We show that RSC neurons are tuned to the animal’s relative orientation in the environment, even in the absence of head movement. Next, we found that RSC receives functionally distinct projections from visual and thalamic areas, and contains several functional classes of neurons. While some functional classes mirror RSC inputs, a newly discovered class coregisters visual and thalamic signals. Finally, decoding analyses reveal unique contributions to heading from each class. Our results suggest an RSC circuit for anchoring heading representations to environmental visual landmarks.
HIV-1 CD4-binding site germline antibody–Env structures inform vaccine design
Authors: Dam Kim-Marie A. , Barnes Christopher O. , Gristick Harry B. , Schoofs Till , Nussenzweig Michel C. , Bjorkman Pamela J. 
Published: March 2022

AbstractBG24, a VRC01-class broadly neutralizing antibody (bNAb) against HIV-1 Env with relatively few somatic hypermutations (SHMs), represents a promising target for vaccine strategies to elicit CD4-binding site (CD4bs) bNAbs. To understand how SHMs correlate with BG24 neutralization of HIV-1, we solved 4.1 Å and 3.4 Å single-particle cryo-EM structures of two inferred germline (iGL) BG24 precursors complexed with engineered Env-based immunogens lacking CD4bs N-glycans. Structures revealed critical Env contacts by BG24iGL and identified antibody light chain structural features that impede Env recognition. In addition, biochemical data and cryo-EM structures of BG24iGL variants bound to Envs with CD4bs glycans present provided insights into N-glycan accommodation, including structural modes of light chain adaptations in the presence of the N276gp120 glycan. Together, these findings revealed Env regions critical for germline antibody recognition and potential sites to alter in immunogen design.
RNA-targeting CRISPR-Cas13 Provides Broad-spectrum Phage Immunity
Authors: Adler Benjamin A. , Hessler Tomas , Cress Brady F , Mutalik Vivek K. , Barrangou Rodolphe , Banfield Jillian , Doudna Jennifer A 
Published: March 2022

AbstractCRISPR-Cas13 proteins are RNA-guided RNA nucleases that defend against invasive phages through general, non-specific RNA degradation upon complementary target transcript binding. Despite being RNA nucleases, Cas13 effectors are capable of inhibiting the infection of dsDNA phages but have only been investigated across a relatively small sampling of phage diversity. Here, we employ a systematic, phage-centric approach to determine the anti-phage capacity of Cas13 and find LbuCas13a to be a remarkably potent phage inhibitor. LbuCas13a confers robust, consistent antiviral activity regardless of gene essentiality, gene expression timing or target sequence location. Furthermore, after challenging LbuCas13a with eight diverse E. coli phages distributed across E. coli phage phylogenetic groups, we find no apparent phage-encoded limits to its potent antiviral activity. In contrast to other Class 2 CRISPR-Cas proteins, these results suggest that DNA phages are generally vulnerable to Cas13a targeting. Leveraging this effective anti-phage activity, LbuCas13a can be used seamlessly as a counter-selection agent for broad-spectrum phage editing. Using a two-step phage editing and enrichment approach, we show that LbuCas13a enables markerless genome edits in phages with exceptionally high efficiency and precision, including edits as small as a single codon. By taking advantage of the broad vulnerability of RNA during viral infection, Cas13a enables a generalizable strategy for editing the most abundant and diverse biological entities on Earth.
High-resolution Ribosome Profiling Reveals Translational Selectivity for Transcripts in Bovine Preimplantation Embryo Development
Authors: Zhu Linkai , Zhou Tong , Iyyappan Rajan , Ming Hao , Wang Yinjuan , Dvoran Michal , Chen Qi , Roberts R. Michael , Susor Andrej , Jiang Zongliang 
Published: March 2022

AbstractHigh resolution ribosome fractionation and low-input ribosome profiling of bovine oocytes and preimplantation embryos has enabled us to define the translational landscapes of early embryo development at an unprecedented level. We analyzed the transcriptome, polysome- and non-polysome-bound RNA profiles of bovine oocytes (GV and MII stage) and early embryos at 2-, 8-cell, morula, and blastocyst stage, and revealed four modes of translational selectivity: i. selective translation of non-abundant mRNAs, ii. active, but modest translation of a selection of highly expressed mRNAs, iii. translationally suppressed abundant to moderately abundant mRNAs, and iv. mRNAs associated specifically with monosomes. A strong translational selection of low abundance mRNAs encoding protein components involved in metabolic pathways and lysosome was found throughout bovine oocyte and preimplantation development. In particular, genes encoding components involved in mitochondrial function were prioritized for translation. Notably, transcripts encoding proteins regulating chromatin modifications selectively translated in oocytes. We found that the translational dynamics largely reflects transcriptional profiles in oocytes and 2-cell embryos, but observed marked shift in translational control in 8-cell embryos associated with the main phase of embryonic genome activation. Subsequently, transcription and translation become better synchronized in morulae and blastocysts. Together, these data reveal a unique spatiotemporal translational regulation that accompanies bovine preimplantation development.Significance StatementTranslational control during preimplantation embryo development is poorly understood, mostly due to the scarcity of samples and the corresponding inability to analyze low quantities of these materials. By developing a low-input method, we have been able to explore the transcriptome, polysome- and non-polysome-bound RNA profiles of bovine oocytes (GV and MII stage) and preimplantation embryos at 2-, 8-cell, morula, and blastocyst stages. We reveal four different modes of translational selectivity, plus novel temporal regulatory mechanisms during early embryo development. The spatiotemporal translation dynamics of bovine oocytes and preimplantation embryos offer an entirely new insight into mammalian embryo development research and new possibilities for improving efficiency of assisted reproduction technologies (ARTs).
Limitations of principal components in quantitative genetic association models for human studies
Authors: Yao Yiqi , Ochoa Alejandro 
Published: March 2022

AbstractPrincipal Component Analysis (PCA) and the Linear Mixed-effects Model (LMM), sometimes in combination, are the most common genetic association models. Previous PCA-LMM comparisons give mixed results, unclear guidance, and have several limitations, including not varying the number of principal components (PCs), simulating simple population structures, and inconsistent use of real data and power evaluations. We evaluate PCA and LMM both varying number of PCs in realistic genotype and complex trait simulations including admixed families, subpopulation trees, and real multiethnic human datasets with simulated traits. We find that LMM without PCs usually performs best, with the largest effects in family simulations and real human datasets and traits without environment effects. Poor PCA performance on human datasets is driven by large numbers of distant relatives more than the smaller number of closer relatives. While PCA was known to fail on family data, we report strong effects of family relatedness in genetically diverse human datasets, not avoided by pruning close relatives. Environment effects driven by geography and ethnicity are better modeled with LMM including those labels instead of PCs. This work better characterizes the severe limitations of PCA compared to LMM in modeling the complex relatedness structures of multiethnic human data for association studies.
Multiplealrgenes exhibit allorecognition-associated variation in the colonial cnidarianHydractinia
Authors: Rodriguez-Valbuena Henry , Gonzalez-Muñoz Andrea , Cadavid Luis F. 
Published: March 2022

ABSTRACTThe genetics of allorecognition has been determined from inbred lines ofHydractinia symbiolongicarpus, in which genetic control is attributed mainly to the highly polymorphic lociallorecognition 1 (alr1)andallorecognition 2 (alr2)located within the Allorecognition Complex (ARC). While allelic variation atalr1andalr2can predict the phenotypes in inbred lines, these two loci do not entirely predict the allorecognition phenotypes in wild-type colonies and their progeny, suggesting the presence of additional uncharacterized genes that improve the prediction of these phenotypes. Comparative genomics analyses were used to identify coding sequence differences in assembled chromosomal intervals of the ARC and genomic scaffold sequences between two incompatibleH. symbiolongicarpussiblings from a backcross population. New IgSF-like genes are reported for the ARC, five of these genes are closely related to thealr1andalr2genes, suggesting the presence of multiplealr-typegenes within this complex. Cloning evidence revealed that the allelic polymorphism of eight Ig-SF-like genes is associated with allorecognition phenotypes in a backcross population ofH. symbiolongicarpus. Remarkably, alternative splicing was found as a mechanism that contributes to the functional variability of these genes by changing putative activating receptors to inhibitory receptors, or generating secreted isoforms of allorecognition proteins. Our findings demonstrate that allorecognition inH. symbiolongicarpusis a multigenic phenomenon controlled by genetic variation in at least eight genes in the ARC complex, as well as putative uncharacterized variation outside of this region.
Infection dynamics of co-transmitted reproductive symbionts are mediated by sex, tissue, and development
Authors: Jones Megan W , Fricke Laura C , Thorpe Cody J , Vander Esch Lauren O , Lindsey Amelia RI 
Published: March 2022

ABSTRACTOne of the most prevalent intracellular infections on earth is with Wolbachia: a bacterium in the Rickettsiales that infects a range of insects, crustaceans, chelicerates, and nematodes. Wolbachia is maternally transmitted to offspring and has profound effects on the reproduction and physiology of its hosts, which can result in reproductive isolation, altered vectorial capacity, mitochondrial sweeps, and even host speciation. Some populations stably harbor multiple Wolbachia strains, which can further contribute to reproductive isolation and altered host physiology. However, almost nothing is known about the requirements for multiple intracellular microbes to be stably maintained across generations while they likely compete for space and resources. Here we use a coinfection of two Wolbachia strains (“wHa” and “wNo”) in Drosophila simulans to define the infection and transmission dynamics of an evolutionarily stable double infection. We find that a combination of sex, tissue, and host development contribute to the infection dynamics of the two microbes and that these infections exhibit a degree of niche partitioning across host tissues. wHa is present at a significantly higher titer than wNo in most tissues and developmental stages, but wNo is uniquely dominant in ovaries. Unexpectedly, the ratio of wHa to wNo in embryos does not reflect those observed in the ovaries, indicative of strain-specific transmission dynamics. Understanding how Wolbachia strains interact to establish and maintain stable infections has important implications for the development and effective implementation of Wolbachia-based vector biocontrol strategies, as well as more broadly defining how cooperation and conflict shape intracellular communities.IMPORTANCEWolbachia are maternally transmitted intracellular bacteria that manipulate the reproduction and physiology of arthropods, resulting in drastic effects on the fitness, evolution, and even speciation of their hosts. Some hosts naturally harbor multiple strains of Wolbachia that are stably transmitted across generations, but almost nothing is known about the factors that limit or promote these co-infections which can have profound effects on the host’s biology and evolution, and are under consideration as an insect-management tool. Here we define the infection dynamics of a known stably transmitted double infection in Drosophila simulans with an eye towards understanding the patterns of infection that might facilitate compatibility between the two microbes. We find that a combination of sex, tissue, and development all contribute how the coinfection establishes.
Conserved GYXLI motif of FlhA is involved in dynamic domain motions of FlhA required for flagellar protein export
Authors: Minamino Tohru , Kinoshita Miki , Inoue Yumi , Kitao Akio , Namba Keiichi 
Published: March 2022

ABSTRACTFlagellar structural subunits are transported via the flagellar type III secretion system (fT3SS) and assemble at the distal end of the growing flagellar structure. The C-terminal cytoplasmic domain of FlhA (FlhAC) serves as a docking platform for export substrates and flagellar chaperones and plays an important role in hierarchical protein targeting and export. FlhAC consists of domains D1, D2, D3, and D4 and adopts open and closed conformations. Gly-368 of Salmonella FlhA is located within the highly conserved GYXLI motif and is critical for the dynamic domain motions of FlhAC. However, it remains unclear how it works. Here, we report that periodic conformational changes of the GYXLI motif induce a remodeling of hydrophobic side-chain interaction networks in FlhAC and promotes the cyclic open-close domain motions of FlhAC. The temperature- sensitive flhA(G368C) mutation stabilized a completely closed conformation at 42°C through strong hydrophobic interactions between Gln-498 of domain D1 and Pro-667 of domain D4 and between Phe-459 of domain D2 and Pro-646 of domain D4, thereby inhibiting flagellar protein export by the fT3SS. Its intragenic suppressor mutations reorganized the hydrophobic interaction networks in the closed FlhAC structure, restoring the protein export activity of the fT3SS to a significant degree. Furthermore, the conformational flexibility of the GYXLI motif was critical for flagellar protein export. We propose that the conserved GYXLI motif acts as a structural switch to induce the dynamic domain motions of FlhAC required for efficient and rapid protein export by the fT3SS.IMPORTANCEMany motile bacteria employ the flagellar type III secretion system (fT3SS) to construct flagella beyond the cytoplasmic membrane. The C-terminal cytoplasmic domain of FlhA (FlhAC), a transmembrane subunit of the fT3SS, provides binding-sites for export substrates and flagellar export chaperones to coordinate flagellar protein export with assembly. FlhAC undergoes cyclic open- close domain motions. The highly conserved Gly-368 residue of FlhA is postulated to be critical for dynamic domain motions of FlhAC. However, it remains unknown how it works. Here, we carried out mutational analysis of FlhAC combined with molecular dynamics simulation and provide evidence that the conformational flexibility of FlhAC by Gly-368 is important for remodeling hydrophobic side-chain interaction networks in FlhAC to facilitate its cyclic open-close domain motions, allowing the fT3SS to transport flagellar structural subunits for efficient and rapid flagellar assembly.
Genomic diversity across Candida auris clinical isolates shapes rapid development of antifungal resistance in vitro and in vivo
Authors: Burrack Laura S. , Todd Robert T. , Soisangwan Natthapon , Wiederhold Nathan P. , Selmecki Anna 
Published: March 2022

AbstractAntifungal drug resistance and tolerance poses a serious threat to global public health. In the human fungal pathogen, Candida auris, resistance to triazole, polyene, and echinocandin antifungals is rising, resulting in multidrug resistant isolates. Here, we use genome analysis and in vitro evolution of seventeen new clinical isolates of C. auris from clades I and IV to determine how quickly resistance mutations arise, the stability of resistance in the absence of drug, and the impact of genetic background on evolutionary trajectories. We evolved each isolate in the absence of drug as well as in low and high concentrations of fluconazole. In just three passages, we observed genomic and phenotypic changes including karyotype alterations, aneuploidy, acquisition of point mutations, and increases in MIC values within the populations. Fluconazole resistance was stable in the absence of drug, indicating little to no fitness cost associated with resistance. Importantly, two isolates substantially increased fluconazole resistance to ≥256µg/ml fluconazole. Multiple evolutionary pathways and mechanisms to increase fluconazole resistance occurred simultaneously within the same population. Strikingly, the sub-telomeric regions of C. auris were highly dynamic as deletion of multiple genes near the sub-telomeres occurred during the three passages in several populations. Finally, we discovered a mutator phenotype in a clinical isolate of C. auris. This isolate had elevated mutation rates compared to other isolates and acquired substantial resistance during evolution in vitro and in vivo supporting that the genetic background of clinical isolates can have a significant effect on evolutionary potential.ImportanceDrug resistant Candida auris infections are recognized by the CDC as an urgent threat. Here, we obtained and characterized a set of clinical isolates of C. auris including multiple isolates from the same patient. To understand how drug resistance arises, we evolved these isolates and found that resistance to fluconazole, the most commonly prescribed antifungal, can occur rapidly and that there are multiple pathways to resistance. During our experiment, resistance was gained, but it was not lost, even in the absence of drug. We also found that some C. auris isolates have higher mutation rates than others and are primed to acquire antifungal resistance mutations. Furthermore, we found that multidrug resistance can evolve within a single patient. Overall, our results highlight the high stability and high rates of acquisition of antifungal resistance of C. auris that allow evolution of pan-resistant, transmissible isolates in the clinic.