bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unraveling the kinetochore nanostructure in Schizosaccharomyces pombe using multi-color single-molecule localization microscopy
Authors: Virant David , Vojnovic Ilijana , Winkelmeier Jannik , Endesfelder Marc , Turkowyd Bartosz , Lando David , Endesfelder Ulrike 
Published: December 2021

AbstractThe key to ensuring proper chromosome segregation during mitosis is the kinetochore complex. This large and tightly regulated multi-protein complex links the centromeric chromatin to the microtubules attached to the spindle pole body and as such leads the segregation process. Understanding the architecture, function and regulation of this vital complex is therefore essential. However, due to its complexity and dynamics, only its individual subcomplexes could be studied in high-resolution structural detail so far.In this study we construct a nanometer-precise in situ map of the human-like regional kinetochore of Schizosaccharomyces pombe (S. pombe) using multi-color single-molecule localization microscopy (SMLM). We measure each kinetochore protein of interest (POI) in conjunction with two reference proteins, cnp1CENP-A at the centromere and sad1 at the spindle pole. This arrangement allows us to determine the cell cycle and in particularly the mitotic plane, and to visualize individual centromere regions separately. From these data, we determine protein distances within the complex using Bayesian inference, establish the stoichiometry of each POI for individual chromosomes and, consequently, build an in situ kinetochore model for S.pombe with so-far unprecedented precision. Being able to quantify the kinetochore proteins within the full in situ kinetochore structure, we provide valuable new insights in the S.pombe kinetochore architecture.
Rapid volumetric brain changes after acute psychosocial stress
Authors: Uhlig Marie , Reinelt Janis D. , Lauckner Mark E. , Kumral Deniz , Schaare H. Lina , Mildner Toralf , Babayan Anahit , Möller Harald E. , Engert Veronika , Villringer Arno , Gaebler Michael 
Published: December 2021

AbstractStress is an important trigger for brain plasticity: Acute stress can rapidly affect brain activity and functional connectivity, and chronic or pathological stress has been associated with structural brain changes. Measures of structural magnetic resonance imaging (MRI) can be modified by short-term motor learning or visual stimulation, suggesting that they also capture rapid brain changes. Here, we investigated volumetric brain changes (together with changes in T1 relaxation rate and cerebral blood flow) after acute stress in humans as well as their relation to psychophysiological stress measures.Sixty-seven healthy men (25.8±2.7 years) completed a standardized psychosocial laboratory stressor (Trier Social Stress Test) or a control version while blood, saliva, heart rate, and psychometrics were sampled. Structural MRI (T1 mapping / MP2RAGE sequence) at 3T was acquired 45 min before and 90 min after intervention onset. Grey matter volume (GMV) changes were analysed using voxel-based morphometry. Associations with endocrine, autonomic, and subjective stress measures were tested with linear models.We found significant group-by-time interactions in several brain clusters including anterior/mid-cingulate cortices and bilateral insula: GMV was increased in the stress group relative to the control group, in which several clusters showed a GMV decrease. We found a significant group-by-time interaction for cerebral blood flow, and a main effect of time for T1 values (longitudinal relaxation time). In addition, GMV changes were significantly associated with state anxiety and heart rate variability changes.Such rapid GMV changes assessed with VBM may be induced by local tissue adaptations to changes in energy demand following neural activity. Our findings suggest that endogenous brain changes are counteracted by acute psychosocial stress, which emphasizes the importance of considering homeodynamic processes and generally highlights the influence of stress on the brain.HighlightsWe investigated rapid brain changes using MRI in a stress and a control groupVBM-derived GMV showed a significant group-by-time interaction in several clustersMain pattern: GMV in the stress group increased relative to the control group, in which GMV decreasedGMV changes across groups were associated with state anxiety and heart rate variabilityNeither cerebral blood flow, nor T1 values fully account for the VBM results
High Efficiency Recombinant Protein Purification Using mCherry and YFP Nanobody Affinity Matrices
Authors: Cong Anh T.Q. , Witter Taylor L. , Schellenberg Matthew J. 
Published: December 2021

AbstractMammalian cell lines are important expression systems for large proteins and protein complexes, particularly when the acquisition of post-translational modifications in the protein’s native environment is desired. However, low or variable transfection efficiencies are challenges that must be overcome to use such an expression system. Expression of recombinant proteins as a fluorescent protein fusion enables real-time monitoring of protein expression, and also provides an affinity handle for one-step protein purification using a suitable affinity reagent. Here we describe a panel of anti-GFP and anti-mCherry nanobody affinity matrices and their efficacy for purification of GFP/YFP or mCherry fusion proteins. We define the molecular basis by which they bind their target protein using X-ray crystallography. From these analyses we define an optimal pair of nanobodies for purification of recombinant protein tagged with GFP/YFP or mCherry, and demonstrate these nanobody-sepharose supports are stable to many rounds of cleaning and extended incubation in denaturing conditions. Finally, we demonstrate the utility of the mCherry-tag system by using it to purify recombinant human Topoisomerase 2α expressed in HEK293F cells. The mCherry-tag and GFP/YFP-tag expression systems can be utilized for recombinant protein expression individually or in tandem for mammalian protein expression systems where real-time monitoring of protein expression levels and a high-efficiency purification step is needed.
Barcode aware adaptive sampling for GridION and PromethION Oxford Nanopore sequencers
Authors: Payne Alexander , Munro Rory , Holmes Nadine , Moore Christopher , Carlile Matt , Loose Matthew 
Published: December 2021

AbstractAdaptive sampling enables selection of individual DNA molecules from sequencing libraries, a unique property of nanopore sequencing. Here we develop our adaptive sampling tool readfish to become “barcode-aware” enabling selection of different targets within barcoded samples or filtering out individual barcodes. We show that multiple human genomes can be assessed for copy number and structural variation on a single sequencing flow cell using sample specific customised target panels on both GridION and PromethION devices.
Molecular chaperone ability to inhibit amyloid-derived neurotoxicity, but not amorphous protein aggregation, depends on a conserved pH-sensitive Asp residue
Authors: Chen Gefei , Andrade-Talavera Yuniesky , Zhong Xueying , Hassan Sameer , Biverstal Henrik , Poska Helen , Abelein Axel , Leppert Axel , Kronqvist Nina , Rising Anna , Hebert Hans , Koeck Philip J.B. , Fisahn André , Johansson Jan 
Published: December 2021

AbstractProteins can self-assemble into amyloid fibrils or amorphous aggregates and thereby cause disease. Molecular chaperones can prevent both these types of protein aggregation, but the respective mechanisms are not fully understood. The BRICHOS domain constitutes a disease-associated small heat shock protein-like chaperone family, with activities against both amyloid toxicity and amorphous protein aggregation. Here, we show that the activity of two BRICHOS domain families against Alzheimer’s disease associated amyloid-β neurotoxicity to mouse hippocampi in vitro depends on a conserved aspartate residue, while the ability to suppress amorphous protein aggregation is unchanged by Asp to Asn mutations. The conserved Asp in its ionized state promotes structural flexibility of the BRICHOS domain and has a pKa value between pH 6.0–7.0, suggesting that chaperone effects against amyloid toxicity can be affected by physiological pH variations. Finally, the Asp is evolutionarily highly conserved in >3000 analysed BRICHOS domains but is replaced by Asn in some BRICHOS families and animal species, indicating independent evolution of molecular chaperone activities against amyloid fibril formation and non-fibrillar amorphous protein aggregation.
Pupillometry and the vigilance decrement: Task-evoked but not baseline pupil measures reflect declining performance in visual vigilance tasks
Authors: Martin Joel T. , Whittaker Annalise H. , Johnston Stephen J. 
Published: December 2021

AbstractBaseline and task-evoked pupil measures are known to reflect the activity of the nervous system’s central arousal mechanisms. With the increasing availability, affordability and flexibility of video-based eye tracking hardware, these measures may one day find practical application in real-time biobehavioral monitoring systems to assess performance or fitness for duty in tasks requiring vigilant attention. But real-world vigilance tasks are predominantly visual in their nature and most research in this area has taken place in the auditory domain. Here we explore the relationship between pupil size—both baseline and task-evoked—and behavioral performance measures in two novel vigilance tasks requiring visual target detection: 1) a traditional vigilance task involving prolonged, continuous, and uninterrupted performance (n = 28), and 2) a psychomotor vigilance task (n = 25). In both tasks, behavioral performance and task- evoked pupil responses declined as time spent on task increased, corroborating previous reports in the literature of a vigilance decrement with a corresponding reduction in task-evoked pupil measures. Also in line with previous findings, baseline pupil size did not show a consistent relationship with performance measures. We discuss our findings considering the adaptive gain theory of locus coeruleus function and question the validity of the assumption that baseline (prestimulus) pupil size and task-evoked (poststimulus) pupil measures correspond to the tonic and phasic firing modes of the LC.
A Nascent Peptide Code for Translational Control of mRNA Stability in Human Cells
Authors: Burke Phillip C. , Park Heungwon , Subramaniam Arvind Rasi 
Published: December 2021

AbstractStability of eukaryotic mRNAs is associated with their codon, amino acid, and GC content. Yet, coding sequence motifs that predictably alter mRNA stability in human cells remain poorly defined. Here, we develop a massively parallel assay to measure mRNA effects of thousands of synthetic and endogenous coding sequence motifs in human cells. We identify several families of simple dipeptide repeats whose translation triggers acute mRNA instability. Rather than individual amino acids, specific combinations of bulky and positively charged amino acids are critical for the destabilizing effects of dipeptide repeats. Remarkably, dipeptide sequences that form extended β strands in silico and in vitro drive ribosome stalling and mRNA instability in vivo. The resulting nascent peptide code underlies ribosome stalling and mRNA-destabilizing effects of hundreds of endogenous peptide sequences in the human proteome. Our work reveals an intrinsic role for the ribosome as a selectivity filter against the synthesis of bulky and aggregation-prone peptides.
Genomic architecture drives population structuring in Amazonian birds
Authors: Thom Gregory , Moreira Lucas Rocha , Batista Romina , Gehara Marcelo , Aleixo Alexandre , Smith Brian Tilston 
Published: December 2021

AbstractLarge rivers are ubiquitously invoked to explain the distributional limits and speciation of the Amazon Basin’s mega-diversity. However, inferences on the spatial and temporal origins of Amazonian species have narrowly focused on evolutionary neutral models, ignoring the potential role of natural selection and intrinsic genomic processes known to produce heterogeneity in differentiation across the genome. To test how genomic architecture impacts our ability to reconstruct patterns of spatial diversification across multiple taxa, we sequenced whole genomes for populations of bird species that co-occur in southeastern Amazonian. We found that phylogenetic relationships within species and demographic parameters varied across the genome in predictable ways. Genetic diversity was positively associated with recombination rate and negatively associated with the species tree topology weight. Gene flow was less pervasive in regions of low recombination, making these windows more likely to retain patterns of population structuring that matched the species tree. We further found that approximately a third of the genome showed evidence of selective sweeps and linked selection skewing genome-wide estimates of effective population sizes and gene flow between populations towards lower values. In sum, we showed that the effects of intrinsic genomic characteristics and selection can be disentangled from the neutral processes to elucidate how speciation hypotheses and biogeographic patterns are sensitive to genomic architecture.
Chromosome-level reference genomes for two strains of Caenorhabditis briggsae: an improved platform for comparative genomics
Authors: Stevens Lewis , Moya Nicolas D. , Tanny Robyn E. , Gibson Sophia B. , Tracey Alan , Na Huimin , Zhan Ye , Chitrakar Rojin , Dekker Job , Walhout Albertha J.M. , Baugh L. Ryan , Andersen Erik C. 
Published: December 2021

AbstractThe publication of the Caenorhabditis briggsae reference genome in 2003 enabled the first comparative genomics studies between C. elegans and C. briggsae, shedding light on the evolution of genome content and structure in the Caenorhabditis genus. However, despite being widely used, the currently available C. briggsae reference genome is substantially less complete and structurally accurate than the C. elegans reference genome. Here, we used high-coverage Oxford Nanopore long-read and chromosome conformation capture data to generate chromosomally resolved reference genomes for two C. briggsae strains: QX1410, a new reference strain closely related to the laboratory AF16 strain, and VX34, a highly divergent strain isolated in China. We also sequenced 99 recombinant inbred lines (RILs) generated from reciprocal crosses between QX1410 and VX34 to create a recombination map and identify chromosomal domains. Additionally, we used both short- and long-read RNA sequencing (RNA-seq) data to generate high-quality gene annotations. By comparing these new reference genomes to the current reference, we reveal that hyper-divergent haplotypes cover large portions of the C. briggsae genome, similar to recent reports in C. elegans and C. tropicalis. We also show that the genomes of selfing Caenorhabditis species have undergone more rearrangement than their outcrossing relatives, which has biased previous estimates of rearrangement rate in Caenorhabditis. These new genomes provide a substantially improved platform for comparative genomics in Caenorhabditis and narrow the gap between the quality of genomic resources available for C. elegans and C. briggsae.
Intron dynamics reveal principles of gene regulation during the maternal-to-zygotic transition
Authors: Riemondy Kent , Henriksen Jesslyn C. , Rissland Olivia S. 
Published: December 2021

ABSTRACTThe maternal-to-zygotic transition (MZT) is a conserved embryonic process in animals where developmental control shifts from the maternal to zygotic genome. A key step in this transition is zygotic transcription, and deciphering the MZT requires classifying newly transcribed genes. However, due to current technological limitations, this starting point remains a challenge for studying many species. Here we present an alternative approach that characterizes transcriptome changes based solely on RNA-seq data. By combining intron-mapping reads and transcript-level quantification, we characterized transcriptome dynamics during the Drosophila melanogaster MZT. Our approach provides an accessible platform to investigate transcriptome dynamics that can be applied to the MZT in non-model organisms. In addition to classifying zygotically transcribed genes, our analysis revealed that over 300 genes express different maternal and zygotic transcript isoforms due to alternative splicing, polyadenylation, and promoter usage. The vast majority of these zygotic isoforms have the potential to be subject to different regulatory control, and over two-thirds encode different proteins. Thus, our analysis reveals an additional layer of regulation during the MZT, where new zygotic transcripts can generate additional proteome diversity.
Tajima D test accurately forecasts Omicron / COVID-19 outbreak
Authors: Yeh Ting-Yu , Contreras Gregory P. 
Published: December 2021

AbstractOn 26 November 2021, the World Health Organization designated the SARS-CoV-2 variant B.1.1.529, Omicron, a variant of concern. However, the phylogenetic and evolutionary dynamics of this variant remain unclear. An analysis of the 131 Omicron variant sequences from November 9 to November 28, 2021 reveals that variants have diverged into at least 6 major subgroups. 86.3% of the cases have an insertion at amino acid 214 (INS214EPE) of the spike protein. Neutrality analysis of DH (−2.814, p<0.001) and Zeng’s E (0.0583, p=1.0) tests suggested that directional selection was the major driving force of Omicron variant evolution. The synonymous (Dsyn) and nonsynonymous (Dnonsyn) polymorphisms of the Omicron variant spike gene were estimated with Tajima’s D statistic to eliminate homogenous effects. Both D ratio (Dnonsyn/Dsyn, 1.57) and ΔD (Dsyn-Dnonsyn, 0.63) indicate that purifying selection operates at present. The low nucleotide diversity (0.00008) and Tajima D value (−2.709, p<0.001) also confirms that Omicron variants had already spread in human population for more than the 6 weeks than has been reported. These results, along with our previous analysis of Delta and Lambda variants, also supports the validity of the Tajima’s D test score, with a threshold value as −2.50, as an accurate predictor of new COVID-19 outbreaks.
Extreme Sampling for Genetic Rare Variant Association Analysis of Dichotomous Traits with Focus on Infectious Disease Susceptibility
Authors: Emond MJ. , West T. Eoin 
Published: December 2021

AbstractAs genomic sequencing becomes more accurate and less costly, large cohorts and consortiums of cohorts are providing high power for rare variant association studies for many conditions. When large sample sizes are not attainable and the phenotype under study is continuous, an extreme phenotypes design can provide high statistical power with a small to moderate sample size. We extend the extreme phenotypes design to the dichotomous infectious disease outcome by sampling on extremes of the pathogenic exposure instead of sampling on extremes of phenotype. We use a likelihood ratio test (LRT) to test the significance of association between infection status and presence of susceptibility rare variants. More than 10 billion simulations are studied to assess the method. The method results in high sample enrichment for rare variants affecting susceptibility. Greater than 90% power to detect rare variant associations is attained in reasonable scenarios. The ordinary case-control design requires orders of magnitude more samples to achieve the same power. The Type I error rate of the LRT is accurate even for p-values < 10-7. We find that erroroneous exposure assessment can lead to power loss more severe than excluding the observations with errors. Nevertheless, careful sampling on exposure extremes can make a study feasible by providing adequate statistical power. Limitations of this method are not unique to this design, and the power is never less than that of the ordinary case-control design. The method applies without modification to other dichotomous outcomes that have strong association with a continuous covariate.
FIRST REPORT OF HALOBACTERIA DOMINANCE IN A TROPICAL CAVE MICROBIOME
Authors: Paula Caio César Pires de , Sirová Dagmara , Sarmento Hugo , Fernandes Camila Cesario , Kishi Luciano Takeshi , Bichuette Maria Elina , Seleghim Mirna Helena Regali 
Published: December 2021

AbstractScarce studies on microbial diversity in tropical caves have been published, a subterranean system still neglected from a microbiological point of view. Although most published studies are about temperate caves, usually archaeas and fungi have less attention than bacterial communities. Here, the microbiome structure and composition in a tropical cave system, as well the main environmental drivers, were studied during the wet and dry season. Soil and sediments from three different habitats at the cave (surface, entrance cave and dark zone) were sampled. Samples were characterized (temperature, air and substrate humidity, salinity, pH, nitrogen and organic carbon content, and chemical composition) and the microbiome was assessed by high-throughput sequencing, using amplicon sequencing (16S and ITS). Prokaryotic communities were dominated byHalobacteria, ActinobacteriaandBacilli, while fungal communities showed high abundance ofSordariomycetes. Microbiomes from the cave entrance, where a significantly elevated salinity levels were found, supported up to 63% ofHaloarchaeacompared to the other habitats studied. Differences in community structure were significant between habitats, but no influence of the season was observed. Main environmental drivers of community assembly included nitrogen and organic carbon content, temperature, and salinity. This is the first report ofHalobacteriadominance in cave habitats, where they likely play important roles in nitrogen and phosphorus cycles. The cave entrance had lower diversity, but higher degree of microbial endemism, which characterize it as an important cave ecotone. The prevalence of heterotrophic microbial groups implies trophic structure based on detritivores, particularly in the dark zones. Our study brings new insights on microbiome composition in the underexplored tropical cave habitats.