bluuebunny/crossref_metadata_2025 huggingface dataset:
Anti-CD4 autoantibodies in immunological non-responder people living with HIV: Cause of CD4+ T-cell depletion?
Authors: Muñoz-Muela Esperanza , Trujillo-Rodríguez María , Serna-Gallego Ana , Ruiz-Mateos Ezequiel , Espinosa Nuria , Roca-Oporto Critina , Benhnia Mohamed Rafii-El-Idrissi , López-Cortés Luis F. , Gutiérrez-Valencia Alicia
Published: May 2022

Objective:

We aimed to evaluate the anti-CD4 IgG role in the poor immune recovery of immunological nonresponder people with HIV (INR).

Design:

INR display low CD4+ T-cell increase despite long-term undetectable viremia. Among other factors, autologous anti-CD4 IgG-dependent cellular cytotoxicity (ADCC) by natural killer (NK) cells has been proposed to cause CD4+ T-cell depletion.

Methods:

Plasma anti-CD4 IgG levels were quantified and purified by chromatography columns for the subsequent use in a coculture of CD4+ T and NK cells. We analyzed NK cell degranulation markers (CD107a, perforin and granzyme B) and IFN-γ release, and CD4+ T-cell death. Binding affinity of anti-CD4 IgG for CD4+ T cells was also assessed.

Results:

A total of 168 individuals were enrolled (INR, 56; immunological responders, 40; treatment-naive, 39; and healthy controls, 33). The highest anti-CD4 IgG levels were found in treatment-naive PWH, followed by participants on treatment. There were no correlations between anti-CD4 IgG levels and CD4+ T-cell counts. In a 15-participant subgroup (naive, immunological responders, and INR), anti-CD4 IgG induced a slight NK-cell expression of degranulation markers and IFN-γ; however, the percentage of CD4+ T-cell death was negligible. Consistently, no significant changes in NK cell polyfunctionality were observed. In addition, purified anti-CD4 IgG showed scarce binding affinity for CD4+ T cells. These results were similar in all analyzed participant groups.

Conclusion:

Our results suggest that autologous anti-CD4 IgG neither trigger CD4+ T-cell death by ADCC nor are responsible for CD4+ lymphocyte depletion in INR.

Video abstract:

http://links.lww.com/QAD/C518.
Joint Report on Terminology for Cosmetic Gynecology
Authors:   Developed by the Joint Writing Group of the International Urogynecological Association and the American Urogynecologic Society. Individual writing group members are noted in the Acknowledgment section.
Published: May 2022

Introduction and hypothesis

The current terminology used to describe cosmetic gynecologic procedures includes many nondescriptive, trademarked, or informal names, which contributes to substantial ambiguity about their aims and specific techniques. The development of clear, uniform descriptive terminology for cosmetic gynecology is needed for patients, researchers, and practitioners across multiple specialties.

Methods

This document was developed from a collaboration of selected members from the International Urogynecological Association (IUGA) and the American Urogynecologic Society (AUGS). Wide-ranging literature reviews were performed to identify the breadth of currently used terms and tools for measuring efficacy and safety. After extensive internal review the adoption of each definition was ratified by group consensus.

Results

A terminology report for elective cosmetic gynecology procedures, anatomical classification, outcome metrics, and reporting of complications has been developed. This document seeks to provide clear descriptive guidance for patients, researchers, and practitioners across multiple specialties. This document will be subject to internal review by IUGA and AUGS to incorporate and adopt evidence-based changes in the field.

Conclusions

A consensus-based document establishing clear terminology for cosmetic gynecology procedures has been created. Use of these terms should be encouraged to provide clarity to patients seeking these procedures and to facilitate future research to establish the safety and efficacy of these procedures.
Targeting de novo loss of function variants in constrained disease genes improves diagnostic rates in the 100,000 Genomes Project
Authors: Seaby Eleanor G. , Thomas N. Simon , Webb Amy , Brittain Helen , Taylor Tavares Ana Lisa ,   Genomics England Consortium, Baralle Diana , Rehm Heidi L. , O’Donnell-Luria Anne , Ennis Sarah
Published: May 2022

Whole genome sequencing was first offered clinically in the UK through the 100,000 Genomes Project (100KGP); however, data analysis was time and resource intensive with 3 million variants found per patient. Consequently, analysis was restricted to predefined gene panels associated with the patient’s phenotype. However, panels rely on clearly characterised phenotypes and risk missing diagnostic variants outside of the panel(s) applied. We propose a complementary method to rapidly identify diagnostic variants, including those missed by 100KGP methods.

The Loss-of-function Observed/Expected Upper-bound Fraction (LOEUF) score quantifies gene constraint, with low scores correlated with haploinsufficiency. We applied DeNovoLOEUF, a filtering strategy to sequencing data from 13,949 rare disease trios in the 100KGP, by filtering for rare, de novo, single nucleotide loss-of-function variants in OMIM disease genes with a LOEUF score <0.2. We conducted our analysis prospectively in 2019 and compared our findings with the corresponding diagnostic reports as returned in 2019 and again in 2021.

324/336 (96%) of the variants identified through DeNovoLOEUF were classified as diagnostic or partially diagnostic. We identified 39 diagnoses that were “missed” by 100KGP standard analyses, which are now being returned to patients. We have demonstrated a highly specific and rapid method with a 96% positive predictive value that has good concordance with standard analysis, low false positive rate, and can identify additional diagnoses. Globally, as more patients are being offered genome sequencing, we anticipate that DeNovoLOEUF will rapidly identify new diagnoses and facilitate iterative analyses when new disease genes are discovered.
Immunoglobulins genes in Neoceratodus forsteri and Protopterus annectens explain the origin of the immunoglobulins of the animals that passed ashore
Authors: Mirete-Bachiller Serafin , Gambón-Deza Francisco
Published: May 2022

Sarcopterygii fish have great evolutionary interest since tetrapods and animals that came ashore arose from them. Within immunology, they can teach us about the emergence of Immunoglobulins D, A/X, and Y already present in amphibians. We have studied the genes of the immunoglobulins in the fish Sarcopterygii Neoceratodus forsteri and Protopterus annectens. In the first fish, we find that several loci for the constant chains of immunoglobulins are distributed in 4 chromosomes. We have found four genes for IgM, a gene for IgW and a gene for IgN. In the second, we find one locus with genes for IgN and IgM and another with one gene for IgW. With these sequences, together with those obtained in other publications, we have been able to study the possible evolution and emergence of immunoglobulin classes. We conclude that there are two evolutionary lines, one focused on IgM and very conservative, and the other focused on IgW, which allows high variability. The W line gave rise to the IgD of 11 domains of reptiles. IgA and IgY are unique since they arose from recombination between the two evolutionary lines. The W line gave origin to the CH1 and CH2 domains, and the M line gave the CH3 and CH4 domains.
Vitamin D constrains inflammation by modulating the expression of key genes on Chr17q12-21.1
Authors: Kılıç Ayşe , Halu Arda , Marzio Margherita De , Maiorino Enrico , Duvall Melody G. , Brueggemann Thayse , Quintero Joselyn J. Rojas , Chase Robert , Mirzakhani Hooman , Sungur Ayse Özge , Koepke Janine , Nakano Taiji , Peh Hong Yong , Krishnamoorthy Nandini , Abdulnour Raja-Elie , Georgopoulos Katia , Litonjua Augusto A. , Demay Marie B. , Renz Harald , Levy Bruce D. , Weiss Scott T.
Published: May 2022

Vitamin D possesses immunomodulatory functions and vitamin D deficiency has been associated with the rise in chronic inflammatory diseases, including asthma (1). Vitamin D supplementation studies do not provide insight into the molecular genetic mechanisms of vitamin D mediated immunoregulation. Here we provide evidence for vitamin D regulation of two human chromosomal loci, Chr17q12-21.1 and Chr17q21.2, reliably associated with autoimmune and chronic inflammatory diseases (2–4). We demonstrate increased vitamin D receptor (VDR) expression in mouse lung CD4+ Th2 cells, differential expression of Chr17q12-21.1 and Chr17q21.2 genes in Th2 cells based on vitamin D status and identify the IL-2/Stat5 pathway as a target of vitamin D signaling. Vitamin D deficiency caused severe lung inflammation after allergen challenge in mice that was prevented by long term prenatal vitamin D supplementation. Mechanistically, vitamin D induced the expression of theIkzf3encoded protein Aiolos to suppress IL-2-signaling and ameliorate cytokine production in Th2 cells. These translational findings demonstrate mechanisms for the immune protective effect of vitamin D in allergic lung inflammation with a strong molecular genetic link to the regulation of both Chr17q12-21.1 and Chr17q21.2 genes and suggest further functional studies and interventional strategies for long-term prevention of asthma and other autoimmune disorders.

One Sentence Summary

Vitamin D regulates two human chromosomal loci, Chr17q12-21.1 and Chr17q21.2, that are associated with autoimmune and chronic inflammatory diseases.
Comparing the Effect of Helical-centerline Stent Placement on Blood Flow Velocity with a Straight Stent
Authors: Kohata Yutaro , Anzai Hitomi , Ohta Makoto
Published: May 2022

Stent treatment can be used to treat blood vessel stenosis in a less invasive manner, but re-stenosis is a concern. Because a helical-stent configuration has been thought to reduce the amount of intimal hyperplasia, the helical stent is considered clinically effective. The effects of the helical stent on blood flow velocity, however, have not been studied. In this study, we estimated flow velocities before and after helical stenting using time-intensity-curve (TIC) from angiography images and compared them with straight stenting velocities. As a result, in all cases (N = 3), the velocity reduction was less with helical stenting than with straight stenting. Based on angiography images, this flow estimation method can estimate patient-specific blood flow velocity in situ even in a presence of a stent.
Assessing epidemiological parameters and dissemination characteristics of the 2000 and 2001 foot-and-mouth disease outbreaks in Rio Grande do Sul, Brazil
Authors: da Costa Joao Marcos Nacif , Cobellini Luis Gustavo , Cardenas Nicolas Cespedes , Groff Fernando Henrique Sauter , Machado Gustavo
Published: May 2022

Since 1998 the state of Rio Grande do Sul, Brazil, has been free of foot-and-mouth disease (FMD) with yearly mandatory vaccination, until the 2000 and 2001 reintroductions. This study gathers data from both outbreaks including official veterinary state service archives and field investigation reports to quantify epidemiological parameters such as epidemic duration, number of secondary infected farms and animals, and estimate the epidemic rate of growth. We apply a Bayesian latent variable approach to estimate the time-varying reproduction number and calculate new confirmed cases by infection date. Additionally, we utilized between-farm animal movements to reconstruct possible FMD transmission and characteristics of spread over the current at-risk population, by incorporating bovine movement data from 2018 to 2020 as standard to benchmark infected network parameters. The results were consistent with the reports generated by the official investigation of the outbreaks and the models and results presented in this study may be useful for assessing the transmission dynamics and support control measures in the future.
Exploring the utility of ssDNA aptamers directed against snake venom toxins as new therapeutics for tropical snakebite envenoming
Authors: Alomran Nessrin , Chinnappan Raja , Alsolaiss Jaffer , Casewell Nicholas R. , Zourob Mohammed
Published: May 2022

Snakebite is a neglected tropical disease that causes considerable death and disability in the tropical world. Although snakebite can cause a variety of pathologies in victims, haemotoxic effects are particularly common and are typically characterised by haemorrhage and/or venom-induced consumption coagulopathy. Antivenoms are the mainstay therapy for treating the toxic effects of snakebite, but despite saving thousands of lives annually, these therapies are associated with limited cross-snake species efficacy due to venom variation, which ultimately restricts their therapeutic utility to particular geographical regions. In this study, we sought to explore the potential of ssDNA aptamers as toxin-specific inhibitory alternatives to antibodies. As a proof of principle model, we selected snake venom serine protease toxins, which are responsible for contributing to venom-induced coagulopathy following snakebite envenoming, as our target. Using SELEX technology, we selected ssDNA aptamers against recombinantly expressed versions of the fibrinogenolytic SVSPs Ancrod from the venom of Calloselasma rhodostoma and Batroxobin from Bothrops atrox. From the resulting pool of specific ssDNA aptamers directed against each target, we identified candidates that exhibited low nanomolar binding affinities to their targets. Downstream ALISA, fibrinogenolysis, and coagulation profiling experiments demonstrated that the candidate aptamers were able to recognise native and recombinant SVSP toxins and inhibit toxin- and venom-induced prolongation of plasma clotting times and consumption of fibrinogen, with inhibitory potencies highly comparable to commercial polyvalent antivenoms. Our findings demonstrate that rationally selected toxin-specific aptamers can exhibit broad in vitro cross-reactivity against toxins found in different snake venoms and are capable of inhibiting toxins in pathologically relevant in vitro and ex vivo models of venom activity. These data highlight the potential utility of ssDNA aptamers as novel toxin-inhibiting therapeutics of value for tackling snakebite envenoming.
BOA: A Partitioned View of Genome Assembly
Authors: Ghosh Priyanka , An Xiaojing , Keppler Patrick , Kurt Sureyya Emre , Çatalyürek Ümit V. , Krishnamoorthy Sriram , Sadayappan P. , Rajam Aravind Sukumaran , Kalyanaraman Ananth
Published: May 2022

De novo genome assembly is a fundamental problem in computational molecular biology that aims to reconstruct an unknown genome sequence from a set of short DNA sequences (or reads) obtained from the genome. High throughput sequencers could generate several billions of such short reads in a single run. However, the relative ordering of the reads along the target genome is not known a priori. This lack of information is one of the main contributors to the increased complexity of the assembly process. Typically, state-of-the-art approaches produce an ordering of the reads toward the end of the assembly process, making it rather too late to benefit from the ordering information. In this paper, with the dual objective of improving assembly quality as well as exposing a high degree of parallelism for assemblers, we present a partitioning-based approach. Our framework—which we call BOA (for bucket-order-assemble)—uses a bucketing alongside graph- and hypergraph-based partitioning techniques to produce a partial ordering of the reads. This partial ordering enables us to divide the read set into disjoint blocks that can be independently assembled in parallel using any state-of-the-art serial assembler of choice. We tested the BOA framework on a variety of genomes. Experimental results show that the hypergraph variant of our approach, Hyper-BOA, consistently improves both the overall assembly quality and performance. For the inputs tested, the Hyper-BOA framework consistently improves the N50 values of the popular standalone MEGAHIT assembler by an average of 1.70× and up to 2.13×; while the largest alignment length improves 1.47× on average and up to 1.94×. The time to solution also consistently improves between 3-4× for the system sizes tested.
Social Regulation of Egg Size Plasticity in the Honey Bee is Mediated by Cytoskeleton Organizer Rho1
Authors: Han Bin , Wei Qiaohong , Amiri Esmaeil , Hu Han , Meng Lifeng , Strand Micheline K. , Tarpy David R. , Xu Shufa , Li Jianke , Rueppell Olav
Published: May 2022

Egg size plasticity represents an adaptive reproductive strategy in numerous organisms, including the honey bee, Apis mellifera. However, the proximate causation of this plasticity and egg size in general is unknown. We show that honey bee queens predictably and reversibly adjust egg size in response to their colony size and that this plasticity is an active response to the queens’ perception of colony size instead of a consequence of egg laying rate. The egg size increase involves changes of 290 ovarian proteins, mostly related to increased energy metabolism, protein transport, and cytoskeleton functions. Spatio-temporal expression analysis of the small GTPase Rho1 indicates its central role in egg size regulation, which we confirm by RNAi-mediated gene knock-down and expression analyses. The molecular adjustments that promote maternal investment of honey bee queens in response to their social environment thus reveal a novel mechanism of egg size regulation.
Selectivity for food in human ventral visual cortex
Authors: Jain Nidhi , Wang Aria , Henderson Margaret M. , Lin Ruogu , Prince Jacob S. , Tarr Michael J. , Wehbe Leila
Published: May 2022

Visual cortex contains regions of selectivity for domains of ecological importance. Food is an evolutionarily critical category whose visual heterogeneity may make the identification of selectivity more challenging. We investigate neural responsiveness to food using natural images combined with large-scale human fMRI. Leveraging the improved sensitivity of modern designs and statistical analyses, we identify two food-selective regions in the ventral visual cortex. Our results are robust across 8 subjects from the Natural Scenes Dataset (NSD), multiple independent image sets and multiple analysis methods. We then test our findings of food selectivity in an fMRI “localizer” using grayscale food images. These independent results confirm the existence of food selectivity in ventral visual cortex and help illuminate why earlier studies may have failed to do so. Our identification of food-selective regions stands alongside prior findings of functional selectivity and adds to our understanding of the organization of knowledge within the human visual system.
A crescendo of competent coding (c3) contains the Standard Genetic Code
Authors: Yarus Michael
Published: May 2022

The Standard Genetic Code (SGC) can arise by fusion of partial codes evolved in different individuals, perhaps for differing prior tasks. Such code fragments can be unified into an SGC after later evolution of accurate third-position Crick wobble. Late wobble advent fills in the coding table, leaving only later development of final translational initiation and termination in separate domains of life. This code fusion mechanism is computationally implemented here. C3 fusion before late Crick wobble (c3-lCw) is tested for its ability to evolve the SGC. Compared with the previously-studied evolution of isolated coding tables, or with increasing numbers of similar, but non-fusing codes, code fusions reach the SGC sooner, work in a smaller population, and present more accurate and more complete codes more frequently. Notably, a crescendo of SGC-like codes is exposed to selection for an extended period. c3-lCw also effectively suppresses varied disordered assignments, unifying the coding table. Such codes approach the SGC, making its selection seem likely. Given unexceptional conditions, ≈ 1 of 22 c3-lCw environments evolves codes with ≥ 20 assignments and ≤ 3 differences from the SGC, including some with assignments identical to the SGC.
Machine learning enables accurate prediction of breast cancer five-year survival using somatic genomic variants
Authors: Jiang Xiaosen , Zhang Laizhi , Cao Guangshuo , Li Jia , Bai Yong
Published: May 2022

Breast cancer is one of the most common cancers, accounting for about 30% of female cancers and a mortality rate of 15%. The 5-year survival rate is most commonly used to assess cancer progression and guide clinical practice. We used the CatBoost model to systematically construct a five-year mortality risk prediction model based on two independent data sets (BRCA_METABRIC, BRCA_TCGA). The model input data are the somatic genomic variants (copy number variation, SNP locus, cumulative mutation number of genes) and phenotype data of cancer samples. The optimal model combined all the above characteristics, and the AUC reached 0.70 in an independent external data set. At the same time, we also conducted a biological analysis of the characteristics of the model and found some potential biomarkers (TP53, DNAH11, MAP3K1, PHF20L1, etc.). The results of model risk stratification can be used as a guide for the prognosis of breast cancer.
Neural mechanisms underlying distractor suppression guided by spatial cues
Authors: Zhao Chenguang , Kong Yuanjun , Li Dongwei , Huang Jing , Li Xiaoli , Jensen Ole , Song Yan
Published: May 2022

A growing body of research demonstrates that distracting inputs can be proactively suppressed via spatial cues, nonspatial cues, or experience, which are governed by more than one top-down mechanism of attention. However, how the neural mechanisms underlying spatial distractor cues guide proactive suppression of distracting inputs remains unresolved. Here, we recorded electroencephalography signals from 110 subjects in three experiments to identify the role of alpha activity in proactive distractor suppression induced by spatial cues and its influence on subsequent distractor inhibition. Behaviorally, we found novel spatial changes in spatial distractor cues: cueing distractors far away from the target improves search performance for the target while cueing distractors close to the target hampers performance. Crucially, we found dynamic characteristics of spatial representation for distractor suppression during anticipation. This result was further verified by alpha power increased relatively contralateral to the cued distractor. At both the between- and within-subjects levels, we found that these activities further predicted the decrement of subsequent PDcomponent, which was indicative of reduced distractor interference. Moreover, anticipatory alpha activity and its link with subsequent PDcomponent were specific to the high predictive validity of distractor cue. Together, these results provide evidence for the existence of proactive suppression mechanisms of spatial distractors, support the role of alpha activity as gating by proactive suppression and reveal the underlying neural mechanisms by which cueing the spatial distractor may contribute to reduced distractor interference. (235).

Significance

In space, the attention-capturing distractors are obstacles to successfully identifying targets. How to sidestep task-irrelevant distractors that stand between the target and our focus in advance is essential but still unclear. This research investigated how dynamic spatial cues can help us proactively eliminate attention-capturing distractors. Using three cue-distractor tasks that manipulate the predictive validity of distractor occurrence, we provide a series of evidence for the presence of alpha power activity related to distractor anticipation. Critically, this was the first study linking cue-elicited alpha power and distractor-elicited PD, indicating that spatial modulation of alpha power may reduce distractor interference. These findings delineate the neural mechanisms of proactive suppression for spatial distractors. (109)
RAREFAN: A webservice to identify REPINs and RAYTs in bacterial genomes
Authors: Fortmann-Grote Carsten , von Irmer Julia , Bertels Frederic
Published: May 2022

Compared to eukaryotes, repetitive sequences are rare in bacterial genomes and usually do not persist for long. Yet, there is at least one class of persistent prokaryotic mobile genetic elements: REPINs. REPINs are non-autonomous transposable elements replicated by single-copy transposases called RAYTs. REPIN-RAYT systems are mostly vertically inherited and have persisted in individual bacterial lineages for millions of years. Discovering and analyzing REPIN populations and their corresponding RAYT transposases in bacterial species can be rather laborious, hampering progress in understanding REPIN-RAYT biology and evolution. Here we present RAREFAN, a webservice that identifies REPIN populations and their corresponding RAYT transposase in a given set of bacterial genomes. We demonstrate RAREFAN’s capabilities by analyzing a set of 49Stenotrophomonas maltophiliagenomes, containing nine different REPIN-RAYT systems. We guide the reader through the process of identifying and analyzing REPIN-RAYT systems acrossS. maltophilia, highlighting erroneous associations between REPIN and RAYTs, and providing solutions on how to find correct associations. RAREFAN enables rapid, large-scale detection of REPINs and RAYTs, and provides insight into the fascinating world of intragenomic sequence populations in bacterial genomes. RAREFAN is available athttp://rarefan.evolbio.mpg.de.
Breastfeeding duration is associated with larger cortical gray matter volumes in children from the ABCD study
Authors: Núñez Christian , García-Alix Alfredo , Arca Gemma , Agut Thais , Carreras Nuria , Portella Maria J. , Stephan-Otto Christian
Published: May 2022

Despite the numerous studies in favor of breastfeeding for its benefits in cognition and mental health, the long-term effects of breastfeeding on brain structure are still largely unknown. Here we analyzed 7,860 MRI images of children 9 to 11 years of age from the Adolescent Brain Cognitive Development (ABCD) dataset in order to study the relationship between breastfeeding duration and cerebral gray matter volumes. We also explored the potential mediatory role of brain volumes on behavior. Whole-brain voxel-based morphometry analyses revealed an association mainly between breastfeeding duration and larger bilateral volumes of the pars orbitalis and the lateral orbitofrontal cortex. In particular, the association with the left pars orbitalis and the lateral orbitofrontal cortex proved to be very robust, and it appeared to mediate the relationship between breastfeeding duration and the negative urgency dimension of the UPPS-P Impulsive Behavior Scale. Global gray matter volumes were also significant mediators for behavioral problems as measured with the Child Behavior Checklist. Overall, our findings suggest that breastfeeding is an important factor in the proper development of the brain, particularly for the pars orbitalis and lateral orbitofrontal regions. This, in turn, may impact impulsive personality and mental health in early puberty.
Nab3 nuclear granule accumulation is driven by respiratory capacity
Authors: Hutchinson Katherine M. , Hunn Jeremy C. , Reines Daniel
Published: May 2022

Numerous biological processes involve proteins capable of transiently assembling into subcellular compartments necessary for cellular functions. One process is the RNA polymerase II transcription cycle which involves initiation, elongation, co-transcriptional modification of nascent RNA, and termination. The essential yeast transcription termination factor Nab3 is required for termination of small non-coding RNAs and accumulates into a compact nuclear granule upon glucose removal. Nab3 nuclear granule accumulation varies in penetrance across yeast strains and a higher Nab3 granule accumulation phenotype is associated with petite strains, suggesting a possible ATP-dependent mechanism for granule disassembly. Here, we demonstrate the uncoupling of mitochondrial oxidative phosphorylation by drug treatment or deletions of nuclear-encoded ATP synthase subunit genes, were sufficient to increase Nab3 granule accumulation and led to an inability to proliferate during prolonged glucose deprivation, which requires respiration. Additionally, by enriching for respiration competent cells from a petite-prone strain, we generated a low granule-accumulating strain from a relatively high one, providing another link between respiratory competency and Nab3 granules. Consistent with the resulting idea that ATP is involved in granule accumulation, the addition of extracellular ATP to semi-permeabilized cells was sufficient to reduce Nab3 granule accumulation. Deleting the SKY1 gene, which encodes a kinase that phosphorylates nuclear SR repeat-containing proteins and is involved in efficient stress granule disassembly, also resulted in increased granule accumulation. This observation implicates Sky1 in Nab3 granule biogenesis. Taken together, these findings suggest there is normally an equilibrium between termination factor granule assembly and disassembly mediated by ATP-requiring nuclear machinery.
Predictions of immunogenicity reveal potent SARS-CoV-2 CD8+ T-cell epitopes
Authors: Gfeller David , Schmidt Julien , Croce Giancarlo , Guillaume Philippe , Bobisse Sara , Genolet Raphael , Queiroz Lise , Cesbron Julien , Racle Julien , Harari Alexandre
Published: May 2022

The recognition of pathogen or cancer-specific epitopes by CD8+ T cells is crucial for the clearance of infections and the response to cancer immunotherapy. This process requires epitopes to be presented on class I Human Leukocyte Antigen (HLA-I) molecules and recognized by the T-Cell Receptor (TCR). Machine learning models capturing these two aspects of immune recognition are key to improve epitope predictions. Here we assembled a high-quality dataset of naturally presented HLA-I ligands and experimentally verified neo-epitopes. We then integrated these data with new algorithmic developments to improve predictions of both antigen presentation and TCR recognition. Applying our tool to SARS-CoV-2 proteins enabled us to uncover several epitopes. TCR sequencing identified a monoclonal response in effector/memory CD8+ T cells against one of these epitopes and cross-reactivity with the homologous SARS-CoV-1 peptide.
Cellular segregation in co-cultures driven by differential adhesion and contractility on distinct time scales
Authors: Skamrahl Mark , Schünemann Justus , Mukenhirn Markus , Pang Hongtao , Gottwald Jannis , Jipp Marcel , Ferle Maximilian , Rübeling Angela , Oswald Tabea A. , Honigmann Alf , Janshoff Andreas
Published: May 2022

Cellular sorting and pattern formation are crucial for many biological processes such as development, tissue regeneration, and cancer progression. Prominent physical driving forces for cellular sorting are differential adhesion and contractility. Here, we studied the segregation of epithelial co-cultures containing highly contractile, ZO1/2-depleted MDCKII cells (dKD) and their wildtype (WT) counterparts using multiple quantitative, high-throughput methods to monitor their dynamical and mechanical properties. We observe a time-dependent segregation process, governed mainly by differential contractility on short (< 5 h) and differential adhesion on long (> 5 h) time scales, respectively. The overly contractile dKD cells exert strong lateral forces on their WT neighbors, thereby apically depleting their surface area. This is reflected in a six-fold difference in excess surface area between both cell types. The lateral forces lead to a four-to sixfold increase in tension at all junctions that are in contact with the contractile cells including the interface between heterotypic cell-cell contacts. Concomitantly, the tight junction-depleted, contractile cells exhibit weaker cell-cell adhesion and lower traction force. Drug-induced contractility reduction and partial calcium depletion delay the initial segregation but cease to change the final demixed state, rendering differential adhesion the dominant segregation force at longer time scales.

This well-controlled model system shows how cell sorting is accomplished through a complex interplay between differential adhesion and contractility and can be explained largely by generic physical driving forces.

Significance Statement

Fundamental biological processes, such as tissue morphogenesis during development, rely on the correct sorting of cells. Cellular sorting is governed by basic physical properties such as the adhesion between cells and their individual contractility. Here, we study the impact of these parameters in co-cultures consisting of epithelial wildtype cells and overly contractile, less adhesive tight junction-depleted ones. We find time-dependent segregation into clusters: differential contractility drives fast segregation on short-time scales, while differential adhesion dominates the final segregated state over longer times.
Native size exclusion chromatography-based mass spectrometry (SEC-MS) identifies novel components of the Heat Shock Protein 90-dependent proteome
Authors: Samant Rahul S. , Batista Silvia , Larance Mark , Ozer Bugra , Milton Christopher I. , Bludau Isabell , Biggins Laura , Andrews Simon , Hervieu Alexia , Johnston Harvey E. , Al-Lazikhani Bissan , Lamond Angus I. , Clarke Paul A. , Workman Paul
Published: May 2022

The molecular chaperone heat shock protein 90 (HSP90) works in concert with co-chaperones to stabilize its client proteins, which include multiple drivers of oncogenesis and malignant progression. Pharmacologic inhibitors of HSP90 have been observed to exert a wide range of effects on the proteome, including depletion of client proteins, induction of heat shock proteins, dissociation of co-chaperones from HSP90, disruption of client protein signaling networks, and recruitment of the protein ubiquitylation and degradation machinery—suggesting widespread remodeling of cellular protein complexes. However, proteomics studies to date have focused on inhibitor-induced changes in total protein levels, often overlooking protein complex alterations. Here, we use size-exclusion chromatography in combination with mass spectrometry (SEC-MS) to characterize the changes in native protein complexes following treatment with the HSP90 inhibitor tanespimycin (17-AAG) in the HT29 colon adenocarcinoma cell line. After confirming the signature cellular response to HSP90 inhibition (e.g., induction of heat shock proteins, decreased total levels of client proteins), we were surprised to find only modest perturbations to the global distribution of protein elution profiles in inhibitor-treated cells. Similarly, co-chaperones that co-eluted with HSP90 displayed no clear difference between control and treated conditions. However, two distinct analysis strategies identified multiple inhibitor-induced changes, including several known components of the HSP90 proteome, as well as numerous proteins and protein complexes with no previous links to HSP90. We present this dataset as a resource for the HSP90, proteostasis, and cancer communities (https://www.bioinformatics.babraham.ac.uk/shiny/HSP90/SEC-MS/), laying the groundwork for future mechanistic and therapeutic studies related to HSP90 pharmacology. Data are available via ProteomeXchange with identifier PXD033459.
Computational epitope mapping of class I fusion proteins using Bayes classification
Authors: Fischer Marion F.S. , Crowe James E. , Meiler Jens
Published: May 2022

Antibody epitope mapping of viral proteins plays a vital role in understanding immune system mechanisms of protection. In the case of class I viral fusion proteins, recent advances in cryo-electron microscopy and protein stabilization techniques have highlighted the importance of cryptic or ‘alternative’ conformations that expose epitopes targeted by potent neutralizing antibodies. Thorough epitope mapping of such metastable conformations is difficult, but is critical for understanding sites of vulnerability in class I fusion proteins that occur as transient conformational states during viral attachment and fusion. We introduce a novel method Accelerated class I fusion protein Epitope Mapping (AxIEM) that accounts for fusion protein flexibility to significantly improve out-of-sample prediction of discontinuous antibody epitopes. Harnessing data from previous experimental epitope mapping efforts of several class I fusion proteins, we demonstrate that accuracy of epitope prediction depends on residue environment and allows for the precise prediction of conformation-dependent antibody target residues. We also show that AxIEM can to identify common epitopes and provide structural insights for the development and rational design of vaccines.

Author Summary

Efficient determination of neutralizing epitopes of viral fusion proteins is paramount in the development of antibody-based therapeutics against rapidly evolving or undercharacterized viral pathogens. Advances in the determination of viral fusion proteins in multiple conformations with ‘cryptic epitopes’ during attachment and fusion has highlighted the importance of epitope accessibility due to viral fusion protein flexibility, a physical trait not accounted for in previous B-cell epitope prediction methods. Given the relatively limited number of viral fusion proteins that have been determined in multiple conformations that also have been extensively subjected to epitope mapping techniques,, which are predominantly class I fusion proteins, we chose a limited feature set in combination with a low-complexity Bayesian classifier model to avoid overfitting. We show that this model demonstrates higher accuracy in out-of-sample performance than publicly available epitope prediction methods. Additionally, due to limited structural annotation of neutralizing epitope residues, we provide examples of how our model better discerns conformation-specific epitopes, which is critical for subunit vaccine design, and how this may provide a novel approach to assess the structural changes of antigenicity of viral fusion protein homologues.
Regulation by cyclic-di-GMP attenuates dynamics and enhances robustness of bimodal curli gene activation in Escherichia coli
Authors: Lamprecht Olga , Ratnikava Maryia , Jacek Paulina , Kaganovitch Eugen , Buettner Nina , Fritz Kirstin , Biazruchka Ina , Köhler Robin , Pietsch Julian , Sourjik Victor
Published: May 2022

Curli amyloid fibers are a major constituent of the extracellular biofilm matrix formed by bacteria of the Enterobacteriaceae family. Within Escherichia coli biofilms, curli gene expression is limited to a subpopulation of bacteria, leading to heterogeneity of extracellular matrix synthesis. Here we show that bimodal activation of curli expression occurs not only in submerged and macrocolony biofilms, but also in well-mixed planktonic cultures of E. coli, resulting in all-or-none stochastic differentiation into distinct subpopulations of curli-positive and curli-negative cells at the entry into the stationary phase of growth. Stochastic curli activation in individual E. coli cells could further be observed during continuous growth in a conditioned medium in a microfluidic device, which further revealed that the curli-positive state is only metastable. In agreement with previous reports, regulation of curli gene expression by c-di-GMP via two pairs of diguanylate cyclase and phosphodiesterase enzymes, DgcE/PdeH and DgcM/PdeR, modulates the fraction of curli-positive cells under all tested growth conditions. Unexpectedly, removal of this regulatory network does not abolish the bimodality of curli gene expression, although it affects dynamics of activation and increases heterogeneity of expression levels among individual cells. Moreover, the fraction of curli-positive cells within an E. coli population shows stronger dependence on growth conditions in the absence of c-di-GMP regulation. We thus conclude that, while not required for the emergence of bimodal curli gene expression in E. coli, this c-di-GMP regulatory network attenuates the frequency and dynamics of gene activation and increases its robustness to cellular heterogeneity and environmental variation.
Intrinsic excitability in layer IV-VI anterior insula to basolateral amygdala projection neurons encodes the confidence of taste valence
Authors: Chandran Sailendrakumar Kolatt , Yiannakas Adonis , Kayyal Haneen , Salalha Randa , Cruciani Federica , Mizrahi Liron , Khamaisy Mohammad , Stern Shani , Rosenblum Kobi
Published: May 2022

Avoiding potentially harmful, and consuming safe food is crucial for the survival of living organisms. However, sensory information can change its valence following conflicting experiences. Novelty and aversiveness are the two crucial parameters defining the currently perceived valence of taste. Importantly, the ability of a given taste to serve as CS in conditioned taste aversion (CTA) is dependent on its valence. Activity in anterior insula (aIC) layer IV-VI pyramidal neurons projecting to the basolateral amygdala (BLA) is correlative and necessary for CTA learning and retrieval, as well as the expression of neophobia towards novel tastants, but not learning taste familiarity. Yet, the cellular mechanisms underlying the updating of taste valence representation in this specific pathway are poorly understood. Here, using retrograde viral tracing and whole cell patch-clamp electrophysiology in trained mice, we demonstrate that the intrinsic properties of deep-lying layer IV-VI, but not superficial layer I-III aIC-BLA neurons, are differentially modulated by both novelty and valence, reflecting the subjective predictability of taste valence arising from prior experience. These correlative changes in the profile of intrinsic properties of LIV-VI aIC-BLA neurons were detectable following both simple taste experiences, as well as following memory retrieval, extinction learning and reinstatement.
Video-based automated analysis of MDS-UPDRS III parameters in Parkinson disease
Authors: Vignoud Gaëtan , Desjardins Clément , Salardaine Quentin , Mongin Marie , Garcin Béatrice , Venance Laurent , Degos Bertrand
Published: May 2022

Background

Among motor symptoms of Parkinson’s disease (PD), including rigidity and resting tremor, bradykinesia is a mandatory feature to define the parkinsonian syndrome. MDS-UPDRS III is the worldwide reference scale to evaluate the parkinsonian motor impairment, especially bradykinesia. However, MDS-UPDRS III constitutes an agent-based score making reproducible measurements and follow-up challenging.

Objectives

Using a deep learning approach, we developed a tool to compute an objective score of bradykinesia based on the gold-standard MDS-UPDRS III.

Methods

In the Movement Disorder unit of Avicenne University Hospital, we acquired a large database of videos of parkinsonian patients performing MDS-UPDRS III protocols. We applied two deep learning algorithms to detect a two-dimensional (2D) skeleton of the hand composed of 21 predefined points, and transposed it into a three-dimensional (3D) skeleton.

Results

We developed a 2D and 3D automated analysis tool to study the evolution of several key parameters during the protocol repetitions of the MDS-UPDRS III. Scores from 2D automated analysis showed a significant correlation with gold-standard ratings of MDS-UPDRS III, measured with coefficients of determination for the tapping (0.609) and hand movements (0.701) protocols using decision tree algorithms. The individual correlations of the different parameters measured with MDS-UPDRS III scores carry meaningful information and are consistent with MDS-UPDRS III guidelines.

Conclusion

We developed a deep learning-based tool to reliably score and analyze bradykinesia for parkinsonian patients.
Molecular and developmental signatures of genital size macro-evolution in bugs
Authors: Genevcius Bruno C. , Callandrielo Denis C. , Torres Tatiana T.
Published: May 2022

With the advance of the evo-devo research program, our understanding of the genes and pathways that determine the architecture of novel traits has experienced drastic growth. Nevertheless, single-species approaches are insufficient to understand the processes by which evolution shapes morphological changes after their emergence. As such, we still have an elusive knowledge of how these genetic-developmental architectures evolve themselves for most of the structures, as well as how their evolution is mirrored in the phenotypic change across large time scales. Here, we tackle this gap by reconstructing the evolution of male genital size, one of the most complex traits in insects, together with its underlying genetic architecture. Using the order Hemiptera as a model, which spans over 350 million years of evolution, we estimate the correlation between genital size and three features: development rate, body size, and rates of DNA substitution in 68 genes previously associated with genital development. We demonstrate that genital size macro-evolution has been largely dependent on body size and weakly influenced by development rate and the phylogenetic history. Our results further revealed positive correlations between mutation rates and genital size for 18 genes. Interestingly, there is great diversity in the function of these genes, in the signaling pathways that they participate in, and in the specific genital parts that they control. These results suggest that fast genital size evolution has been enabled by molecular changes associated with diverse morphogenetic processes, such as cuticle composition, patterning of sensory apparatus, and organ growth itself. Our data further demonstrate that the majority of DNA evolution correlated with the genitalia has been shaped by negative selection or neutral evolution. This indicates that genital changes are predominantly facilitated by relaxation of constraints rather than positive selection, possibly due to the high pleiotropic nature of the morphogenetic genes.
Limitations of qPCR to estimate DNA quantity: An RFU method to facilitate inter-laboratory comparisons for activity level, and general applicability
Authors: Gill Peter , Bleka Øyvind , Fonneløp Ane Elida
Published: May 2022

The application of qPCR to estimate the quantity of DNA present is usually based upon a short amplicon (typically c.80bp) and a longer amplicon (typically c.200-300bp) where the latter is used to determine the amount of degradation present in a sample. The data are used to make decisions about a) whether there is sufficient template to amplify? b) how much of the elution volume to forward to PCR? A typical multiplex amplifies template in the region of 100-500bp. Consequently, the results from an 80bp amplicon will tend to overestimate the actual amplifiable quantity that is present in a degraded sample. To compensate, a method is presented that relates the quantity of amplifiable DNA to the average RFU of the amplified fragments. This provides greatly improved accuracy of the estimated quantity of DNA present, which may differ by more than an order of magnitude compared to qPCR. The relative DNA quantities can be apportioned per contributor once mixture proportions are ascertained with probabilistic genotyping software (EuroForMix). The motivation for this work was to provide an improved method to generate data to prepare distributions that are used to inform activity level propositions. However, other applications will benefit, particularly those where extraction and quantification are bypassed: For example direct PCR and Rapid DNA technology. The overall aim of this work was to provide a method of quantification that is standardised and can be used to compare results between different laboratories that use different multiplexes. A software solution ”ShinyRFU” is provided to aid calculations.