bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alternative splice variants and germline polymorphisms in human immunoglobulin light chain genes
Authors: Mikocziova Ivana , Peres Ayelet , Gidoni Moriah , Greiff Victor , Yaari Gur , Sollid Ludvig M. 
Published: February 2021

ABSTRACTImmunoglobulin loci are rich in germline polymorphisms and identification of novel polymorphic variants can be facilitated by germline inference of B cell receptor repertoires. Germline gene inference is complicated by somatic hypermutations, errors arising from PCR amplification, and DNA sequencing as well as from the varying length of reference alleles. Inference of light chain genes is even more challenging than inference of heavy chain genes due to large gene duplication events on the kappa locus as well as absence of D genes in the rearranged light chain transcripts. Here, we analyzed the light chain cDNA sequences from naïve BCR repertoires of a Norwegian cohort of 100 individuals. We optimized light chain allele inference by tweaking parameters within TIgGER functions, extending the germline reference sequences, and establishing mismatch frequency patterns at polymorphic positions to filter out false positive candidates. As a result, we identified 48 previously unreported variants of light chain variable genes. Altogether, we selected 14 candidates for novel light chain polymorphisms for validation and successfully validated 11 by Sanger sequencing. Additional clustering of light chain 5’UTR, L-PART1 and L-PART2 revealed partial intron retention in alternative splice variants in 11 kappa and 9 lambda V alleles. The alternatively spliced transcripts were only observed in genes with low expression levels, suggesting a possible role in expression regulation. Our results provide novel insight into germline variation in human light chain immunoglobulin loci.
Enhanced genetic analysis of type 1 diabetes by selecting variants on both effect size and significance, and by integration with autoimmune thyroid disease
Authors: Crouch Daniel J. M. , Inshaw Jamie R.J. , Robertson Catherine C. , Zhang Jia-Yuan , Chen Wei-Min , Onengut-Gumuscu Suna , Cutler Antony J. , Sidore Carlo , Cucca Francesco , Pociot Flemming , Concannon Patrick , Rich Stephen S. , Todd John A. 
Published: February 2021

AbstractFor polygenic traits, associations with genetic variants can be detected over many chromosome regions, owing to the availability oflarge sample sizes. Most variants, however, have small effects on disease risk and, therefore, unravelling the causal variants, target genes, and biology of these variants is challenging. Here, we define the Bigger or False Discovery Rate (BFDR) as the probability that either a variant is a false-positive or a randomly drawn, true-positive association exceeds it in effect size. Using the BFDR, we identified 302 previously unreported signals with larger effect associations with type 1 diabetes and autoimmune thyroid disease. Out of 239 genome-wide significant signals in both diseases, only 66 (28%) show evidence for having a large effect using the BFDR, further demonstrating how using a combination of effect size and significance, rather than significance alone, is important in identifying SNPs and candidate genes for further investigation.
Larval nutrition impacts survival to adulthood, body size, and the allometric scaling of metabolic rate in adult honeybees
Authors: Nicholls Elizabeth , Rossi Marta , Niven Jeremy E. 
Published: February 2021

AbstractResting metabolic rate (RMR) is a fundamental physiological measure linked to numerous aspects of organismal function, including lifespan. Although dietary restriction in insects during larval growth/development affects adult RMR, the impact of larval dietqualityon adult RMR has not been studied. Usingin vitrorearing to control larval diet quality, we determined the effect of dietary protein and carbohydrate on honeybee survival-to-adulthood, time-to-eclosion, body mass/size and adult RMR. High carbohydrate larval diets increased survival-to-adulthood and time-to-eclosion compared to both low carbohydrate and high protein diets. Upon emergence, bees reared on the high protein diet were smaller and lighter than those reared on other diets, whilst those raised on the high carbohydrate diet varied more in body mass. Newly emerged adult bees’ reared on the high carbohydrate diet showed a significantly steeper increase in allometric scaling of RMR compared to those reared on other diets. This suggests that diet quality influences survival-to-adulthood, time-to-eclosion, and the allometric scaling of RMR. Given that agricultural intensification and increasing urbanisation have led to a decrease in both forage availability and dietary diversity for bees, our results are critical to improving understanding of the impacts of poor developmental nutrition on bee growth/development and physiology.Summary statementWe show, for the first time, that the nutritional quality of insect larval diets affects the scaling of metabolic rate with body mass in newly emerged adult honeybees.
Suppression of miR-199a-5p alleviates ulcerative colitis by upregulating endoplasmic reticulum stress component XBP1
Authors: Wang Shanshan , Shen Lei , Peng Shuai , Tian Minxiu , Li Xiangjie , Luo Hesheng 
Published: February 2021

AbstractAims: This study aimed to explore the biological activities of miR-199a-5p in dextran sulphate sodium (DSS)-induced ulcerative colitis and apoptosis and identify the direct target of miR-199a-5p in this process. Main methods: HT-29 cells and C57BL/6 mice were used to examine the function of miR-199a-5p in vitro and in vivo, respectively. Expression of miRNA and mRNA was measured using quantitative real-time PCR and western blotting was used to measure the change in protein expression. Flow cytometry was subsequently employed to determine cell apoptosis, and a luciferase assay was used to confirm the direct target of miR-199a-5p. Results: Expression of miR-199a-5p was increased by DSS treatment in mice. In parallel, miR-199a-5p is found to be involved in endoplasmic reticulum stress (ERS) and cell apoptosis in HT-29 cells, and its upregulation induced ERS, apoptosis, weight loss, and ulcerative colitis in mice in vivo, which could be prevented by the suppression of miR-199a-5p. Luciferase assay confirmed that the 3′ untranslated region (3′-UTR) of XBP1 is the target binding site of miR-199a-5p. Conclusion: miR-199a-5p promotes ulcerative colitis and cell apoptosis by targeting the 3′-UTR of XBP1. Our findings reveal a new regulatory mechanism for ERS signaling and suggest that miR-199a-5p might be a potential target for UC therapy.
G9a/GLP methyltransferases inhibit autophagy by methylation-mediated ATG12 protein degradation
Authors: Kim Chang-Hoon , Park Kyung-Tae , Ju Shin-Yeong , Lee Cheol-Ju , Lee Sang-Hun 
Published: February 2021

ABSTRACTPrevious studies have shown that G9a, a lysine methyltransferase, inhibits autophagy by repressing the transcription of autophagy genes. Here, we demonstrate a novel mechanism whereby G9a/GLP inhibit autophagy through post-translational modification of ATG12, a protein critical for the initiation of autophagosome formation. Under non-stress conditions, G9a/GLP directly methylate ATG12. The methylated ATG12 undergoes ubiquitin-mediated protein degradation, thereby inhibiting autophagy induction. By contrast, under stress conditions that elevate intracellular Ca2+levels, the activated calpain system cleaves the G9a/GLP proteins, leading to G9a/GLP protein degradation. The reduced G9a/GLP levels allow ATG12 to accumulate and form the ATG12-ATG5 conjugate, thus expediting autophagy initiation. Collectively, our findings reveal a distinct signaling pathway that links cellular stress responses involving Ca2+/calpain to G9a/GLP-mediated autophagy regulation. Moreover, our model proposes that the methylation status of ATG12 is a molecular rheostat that controls autophagy induction.
The lysosomal chloride-proton exchanger CLC7 functions in melanosomes as a negative regulator of human pigmentation
Authors: Koroma Donald C. , Scales Jessica L. , Trotman Joshaya C. , Wakamatsu Kazumasa , Ito Shosuke , Oancea Elena 
Published: February 2021

AbstractMutations in the Cl−/H+exchanger CLC7 and its subunit OSTM1 result in osteopetrosis, lysosomal disorders, and pigmentation defects in mice and humans. How CLC7/OSTM1 regulates pigmentation in skin and hair melanocytes remains unexplored. In human epidermal melanocytes, we found CLC7/OSTM1 localized to melanosomes, the organelles in which melanin is synthesized, where it negatively regulates melanin production. Using a novel ratiometric melanosomal pH indicator, we showed that CLC7 acidifies melanosomes, opposing the function of the oculocutaneous albinism II (OCA2) Cl−ion channel. Thede novoCLC7 variant (CLC7-Y715C) that causes albinism in humans and mice, decreased melanocytes pigmentation, which was restored by coexpression of OCA2. Remarkably, the enlarged hyperacidic vacuoles caused by CLC7-Y715C were also rescued by OCA2 coexpression in both melanocytes and non-melanocytic cells. Our data uncover a novel mechanism by which CLC7 regulates melanocyte pigmentation and identifies OCA2 as a tool to counteract the effects of CLC7 activating mutations.
Cotranslational folding of a periplasmic protein domain inEscherichia coli
Authors: Sandhu Hena , Hedman Rickard , Cymer Florian , Kudva Renuka , Ismail Nurzian , von Heijne Gunnar 
Published: February 2021

AbstractIn Gram-negative bacteria, periplasmic domains in inner membrane proteins are cotranslationally translocated across the inner membrane through the SecYEG translocon. To what degree such domains also start to fold cotranslationally is generally difficult to determine using currently available methods. Here, we apply Force Profile Analysis (FPA) – a method where a translational arrest peptide is used to detect folding-induced forces acting on the nascent polypeptide – to follow the cotranslational translocation and folding of the large periplasmic domain of theE. coliinner membrane protease LepBin vivo. Membrane insertion of LepB’s two N-terminal transmembrane helices is initiated when their respective N-terminal ends reach 45-50 residues away from the peptidyl transferase center (PTC) in the ribosome. The main folding transition in the periplasmic domain involves all but the ~15 most C-terminal residues of the protein and happens when the C-terminal end of the folded part is ~70 residues away from the PTC; a smaller putative folding intermediate is also detected. This implies that wildtype LepB folds post-translationallyin vivo, and shows that FPA can be used to study both co- and post-translational protein folding in the periplasm.
Delayed auditory encoding and variable representation of stimulus regularity in cerebellar lesion patients
Authors: Schwartze Michael , Kotz Sonja A. 
Published: February 2021

AbstractThe dynamic and fleeting nature of sound necessitates the rapid encoding and use of information distributed over time. Here we investigated cerebellar contributions to these abilities. We measured EEG from cerebellar patients and healthy controls while they listened to “oddball” sound sequences consisting of infrequent pitch-deviant and frequent standard tones. Inter-stimulus-intervals were temporally regular (600 ms) or irregular (200-1000 ms). This allowed probing early event-related potentials (ERP; P50, N100) that reflect repetitive and changing stimulus characteristics in temporally regular or less (irregular) predictable sequences. Further, time-frequency data provided an index of temporal processing variability at the stimulation frequencies. We expected that cerebellar lesions lead to aberrant encoding and use of auditory information, reflected in the ERP morphology of peak amplitudes, latencies and typical suppression effects linked to stimulus predictability. Results confirm longer P50 peak latencies in patients and variable processing at stimulation frequencies covarying with the location of cerebellar damage. These findings further support the idea that the cerebellum might play a generalizable role in the encoding of auditory stimulation over time.
Temporo-cerebellar connectivity underlies timing constraints in audition
Authors: Stockert Anika , Schwartze Michael , Poeppel David , Anwander Alfred , Kotz Sonja A. 
Published: February 2021

AbstractThe flexible and efficient adaptation to dynamic, rapid changes in the auditory environment likely involves generating and updating of internal models. Such models arguably exploit connections between the neocortex and the cerebellum, supporting proactive adaptation. Here we test the functional mechanisms associated with temporo-cerebellar connectivity, verifying these mechanisms for speech sounds. First, we identify lesion-specific deficits for the encoding of short timescale spectro-temporal non-speech and speech properties in patients with left posterior temporal cortex stroke. Second, using lesion-guided probabilistic tractography in healthy participants, we reveal bidirectional temporo-cerebellar connectivity with cerebellar dentate nuclei and crura I/II. These findings imply that the encoding and modeling of rapidly modulated auditory spectro-temporal properties engage a temporo-cerebellar interface. The data further support the conjecture that proactive adaptation to a dynamic environment via internal models is a generalizable principle.Significance StatementAsymmetric sampling in time, the principle of duration-sensitive hemispheric specialization of the cerebral cortex in the sensory decomposition of sound, is a widely tested hypothesis in auditory neuroscience. This functional organization is mirrored in the cerebellar cortex, implicated in the internal forward-modeling of sensory feedback that arises from motor actions. The potential structural and functional integration of these systems is not well understood. Using a unique combination of causal lesion-symptom mapping in persons with temporal lobe damage and diffusion-weighted magnetic resonance neuroimaging in healthy persons, we identify one key missing link and provide evidence for cross-lateral temporo-cerebellar connectivity using probabilistic white matter fiber tractography. These cerebellar-pontine-temporal cortex connections not only support asymmetric sampling in time but also establish the basis for a generalizable role of cerebellar forward-modeling in sensation beyond the monitoring of sensory feedback in the motor domain.
Cortico-subcortical β burst dynamics underlying movement cancellation in humans
Authors: Diesburg Darcy A. , Greenlee Jeremy D. W. , Wessel Jan R. 
Published: February 2021

SummaryDominant neuroanatomical models hold that humans regulate their movements via loop-like cortico-subcortical networks, including the subthalamic nucleus (STN), thalamus, and sensorimotor cortices (SMC). Inhibitory commands across these networks are purportedly sent via transient, burst-like signals in the β frequency (15-29Hz). However, since human depth-recording studies are typically limited to one recording site, direct evidence for this proposition is hitherto lacking. Here, we present simultaneous multi-site depth-recordings from SMC and either STN or thalamus in humans performing the stop-signal task. In line with their purported function as inhibitory signals, subcortical β-bursts were increased on successful stop-trials and were followed within 50ms by increased β-bursting over SMC. Moreover, between-site comparisons (including in a patient with simultaneous recordings from all three sites) confirmed that β-bursts in STN precede thalamic β-bursts. This provides first empirical evidence for the role of β-bursts in conveying inhibitory commands along long-proposed cortico-subcortical networks underlying movement regulation in humans.
Molecular and structural mechanisms of ZZ domain-mediated cargo recognition by autophagy receptor Nbr1
Authors: Wang Ying-Ying , Zhang Jianxiu , Liu Xiao-Man , Dong Meng-Qiu , Ye Keqiong , Du Li-Lin 
Published: February 2021

AbstractIn selective autophagy, cargo selectivity is determined by autophagy receptors. However, it remains scarcely understood how autophagy receptors recognize specific protein cargos. In the fission yeastSchizosaccharomyces pombe, a selective autophagy pathway termed Nbr1-mediated vacuolar targeting (NVT) employs Nbr1, an autophagy receptor conserved across eukaryotes including humans, to target cytosolic hydrolases into the vacuole. Here, we identify two new NVT cargos, the mannosidase Ams1 and the aminopeptidase Ape4, that bind competitively to the first ZZ domain of Nbr1 (Nbr1-ZZ1). High-resolution cryo-EM analyses reveal how a single ZZ domain recognizes two distinct protein cargos. Nbr1-ZZ1 not only recognizes the N-termini of cargos via a conserved acidic pocket, similar to other characterized ZZ domains, but also engages additional parts of cargos in a cargo-specific manner. Our findings unveil a single-domain bispecific mechanism of autophagy cargo recognition, elucidate its underlying structural basis, and expand the understanding of ZZ domain-mediated protein-protein interactions.
Expansion of cortical layers 2 and 3 in human left temporal cortex associates with verbal intelligence
Authors: Heyer DB , Wilbers R , Galakhova AA , Hartsema E , Braak S , Hunt S , Verhoog MB , Muijtjens ML , Mertens EJ , Idema S , Baayen JC , de Witt Hamer P , Klein M , McGraw M , Lein ES , de Kock CPJ , Mansvelder HD , Goriounova NA 
Published: February 2021

AbstractThe expansion of supragranular cortical layers is thought to have enabled evolutionary development of human cognition and language. However, whether increased volume of supragranular cortical layers can actually support greater cognitive and language abilities in humans has not been demonstrated. Here, we find that subjects with higher general and verbal intelligence test (VIQ) scores have selectively expanded layers 2 and 3 only in the left temporal cortex, an area associated with language and IQ-test performance. This expansion is accompanied by lower neuron densities and larger cell-body size. Furthermore, individuals with higher VIQ scores had neurons with larger dendritic trees in left temporal cortex, potentially impacting their function. Indeed, neurons of subjects with higher VIQ scores had faster action potential upstroke kinetics, which improves information processing. These data show that expansion of supragranular layer volume, cortical and cellular micro-architecture and function are associated with improved verbal mental ability in human subjects.
TNF signalling fine-tunes Langerhans cell transcriptional programmes mediating adaptive immunity
Authors: Davies James , Vallejo Andres F. , Sirvent Sofia , Porter Gemma , Clayton Kalum , Qumbelo Yamkela , Stumpf Patrick , West Jonathan , Gray Clive M. , Chigorimbo-Murefu Nyaradzo T.L , MacArthur Ben , Polak Marta E 
Published: February 2021

ABSTRACTLangerhans cells (LCs) reside in the epidermis as a dense network of immune system sentinels, coordinating both immunogenic and tolerogenic immune responses. To determine molecular switches directing induction of LC immune activation, we performed mathematical modelling of gene regulatory networks identified by single cell RNA sequencing of LCs exposed to TNF, a key pro-inflammatory signal produced by the skin. Our approach delineated three programmes of LC phenotypic activation (immunogenic, tolerogenic or ambivalent), and confirmed that TNF enhanced LC immunogenic programming. Through regulon analysis followed by mutual information modelling, we identifiedIRF1as the key transcription factor for the regulation of immunogenicity in LCs. Application of a mathematical toggle switch model, couplingIRF1with tolerance-inducing transcription factors, determined the key set of transcription factors regulating the switch between tolerance and immunogenicity, and correctly predicted LC behaviour in LCs derived from different body sites. Our findings provide a mechanistic explanation of how combinatorial interactions between different transcription factors can coordinate specific transcriptional programmes in human LCs, interpreting the microenvironmental context of the local tissue microenvironments.
NEDD4 Regulates Ubiquitination and Stability of the Cell adhesion Molecule IGPR-1 via Lysosomal Pathway
Authors: Sun Linzi , Amraei Razie , Rahimi Nader 
Published: February 2021

ABSTRACTThe cell adhesion molecule immunoglobulin and proline-rich receptor-1 (IGPR-1) regulates various critical cellular processes including, cell-cell adhesion, mechanosensing and autophagy. However, the molecular mechanisms governing IGPR-1 cell surface expression levels remains unknown. In the present study, we used anin vitroubiquitination assay and identified ubiquitin E3 ligase NEDD4 and the ubiquitin conjugating enzyme UbcH6 involved in the ubiquitination of IGPR-1.In vitroGST-pulldown andin vivoco-immunoprecipitation assays demonstrated that NEDD4 binds to IGPR-1. Over-expression of wild-type NEDD4 downregulated IGPR-1 and deletion of WW domains (1-4) of NEDD4 revoked its effects on IGPR-1. Similarly, knockdown of NEDD4 increased IGPR-1 levels in A375 melanoma cells. Furthermore, deletion of 57 amino acids encompassing polyproline rich (PPR) motif on the C-terminus of IGPR-1 nullified the binding of NEDD4 with IGPR-1. Moreover, we demonstrate that NEDD4 promotes K48- and K63-dependent polyubiquitination of IGPR-1. The NEDD4-mediated polyubiquitination of IGPR-1 stimulated lysosomal degradation of IGPR-1 as the treatment of cells with the lysosomal inhibitors, bafilomycine and ammonium chloride increased IGPR-1 levels in the HEK-293 cells ectopically expressing IGPR-1 and in multiple human skin melanoma cell lines. Hence, these findings suggest that ubiquitin E3 ligase NEDD4 is a key regulator of IGPR-1 with a significant implication in the therapeutic targeting of IGPR-1.
Elucidating the Mechanical Energy for Cyclization of a DNA Origami Tile
Authors: Li Ruixin , Chen Haorong , Lee Hyeongwoon , Choi Jong Hyun 
Published: February 2021

ABSTRACTDNA origami has emerged as a versatile method to synthesize nanostructures with high precision. This bottom-up self-assembly approach can produce not only complex static architectures, but also dynamic reconfigurable structures with tunable properties. While DNA origami has been explored increasingly for diverse applications such as biomedical and biophysical tools, related mechanics are also under active investigation. Here we studied the structural properties of DNA origami and investigated the energy needed to deform the DNA structures. We used a single-layer rectangular DNA origami tile as a model system and studied its cyclization process. This origami tile was designed with an inherent twist by placing crossovers every 16 base-pairs (bp), corresponding to a helical pitch of 10.67 bp/turn which is slightly different from that of native B-form DNA (10.5 bp/turn). We used molecular dynamics (MD) simulations based on a coarse-grained model on an open-source computational platform, oxDNA. We calculated the energies needed to overcome the initial curvature and induce mechanical deformation by applying linear spring forces. We found that the initial curvature may be overcome gradually during cyclization and a total of ~33.1 kcal/mol is required to complete the deformation. These results provide insights into the DNA origami mechanics and should be useful for diverse applications such as adaptive reconfiguration and energy absorption.