bluuebunny/crossref_metadata_2025 huggingface dataset:
In vitroreplicative potential of an HIV-1/MO intergroup recombinant virus compared to HIV-1/M and HIV-1/O parental viruses
Authors: Moisan Alice , Oliveira Fabienne De , Mabillotte Manon , Alessandri-Gradt Elodie , Mourez Thomas , Plantier Jean-Christophe
Published: October 2022

HIV-1 is characterized by high genetic diversity and genetic recombination is one of the major evolution processes. Despite their great genetic divergence, HIV-1 group M, pandemic, and group O, endemic in Cameroon, can generate HIV-1/MO intergroup recombinants. The current description of 19 HIV-1/MO recombinant forms (URF_MO) raises the question of a possible benefit of the recombination and the modalities of their emergence.

Therefore, the objectives of this work were to studyin vitrothe replicative potential of HIV-1/MO recombinant forms.

The replicative potential was analyzed, based on a simple recombination pattern, [Ogag/pol-Menv], harboring a breakpoint in Vpr, due to a recombination hotspot in this region. For this, a chimeric infectious molecular clone (IMC) was synthesized from HIV-1/M subtype B and HIV-1/O subgroup T and recombinant viruses were obtained by transfection and co-culture. To compare the replicative potential of recombinant viruses with HIV-1/M and HIV-1/O parental viruses, two markers were monitored in culture supernatants: Reverse Transcriptase (RT) activity and P24 antigen concentration. The results showed a superiority of the group M parental virus compared to group O for both markers. In contrast, for the HIV-1/OM recombinant virus, RT activity data did not overlap with the concentration of P24 antigen, suggesting a hybrid behavior of the recombinant, in terms of enzyme activity and P24 production.

These results highlighted many hypotheses about the impact of recombination on replicative potential and demonstrated once again the significant plasticity of HIV genomes and their infinite possibility of evolution.

Importance

HIV-1/M and HIV-1/O can generate HIV-1/MO intergroup recombinants. The current description of 19 URF_MO raises the question of a possible benefit of recombination in terms of emergence. The objectives of this work were to studyin vitrothe replicative potential of HIV-1/MO recombinant viruses. For this, a chimeric infectious molecular clone (IMC) generated from HIV-1/M subtype B and HIV-1/O subgroup T and recombinant viruses were obtained by transfection and co-culture. To compare the replicative potential of recombinant viruses with HIV-1/M and HIV-1/O parental viruses, RT activity and P24 antigen concentration were monitored in culture supernatants. A superiority of the group M parental virus compared to group O was observed for both markers whereas a hybrid behavior in terms of enzyme activity and P24 production was found for the recombinant virus. These results demonstrated once again the significant plasticity of HIV genomes and their infinite possibility of evolution.
The UK BiLEVE and Mendelian randomisation: Using multivariable instrumental variables to address “damned if you, dammed if you don’t” adjustment problems
Authors: Woolf Benjamin , Gill Dipender , Sallis Hannah , Munafò Marcus R.
Published: October 2022

Objective

To explore the use of multivariable instrumental variables to resolve the “dammed if you do, dammed if you don’t” adjustment problem created for Mendelian randomisation (MR) analysis using the smoking or lung function related phenotypes in the UK Biobank (UKB).

Result

“dammed if you do, dammed if you don’t” adjustment problems occur when both adjusting and not-adjusting for a variable will induce bias in an analysis. One instance of this occurs because the genotyping chip of UKB participants differed based on lung function/smoking status. In simulations, we show that multivariable instrumental variables analyses can attenuate potential collider bias introduced by adjusting for a proposed covariate, such as the UKB genotyping chip. We then explore the effect of adjusting for genotyping chip in a multivariable MR model exploring the effect of smoking on seven medical outcomes (lung cancer, emphysema, hypertension, stroke, heart diseases, depression, and disabilities). We additionally compare our results to a traditional univariate MR analysis using genome-wide analyses summary statistics which had and had not adjusted for genotyping chip. This analysis implies that the difference in genotyping chip has introduced only a small amount of bias.
Occupational risk of SARS-CoV-2 infection: a nationwide register-based study of the Danish workforce during the Covid-19 pandemic 2020-21
Authors: Bonde Jens Peter Ellekilde , Mølenberg Begtrup Luise , Høy Jensen Johan , Flachs Esben Meulengracht , Schlünssen Vivi , Kolstad Henrik Albert , Jakobsson Kristina , Nielsen Christel , Nilsson Kerstin , Rylander Lars , Vilhelmsson Andreas , Petersen Kajsa Ugelvig , Tøttenborg Sandra Søgaard
Published: October 2022

Objectives

Most earlier studies on occupational risk of Covid-19 covering the entire workforce are based on relatively rare outcomes such as hospital admission and mortality. This study examines the incidence of SARS-CoV-2 infection by occupational group based upon real-time polymerase chain reaction tests (RT-PCR).

Methods

The cohort includes 2.4 million Danish employees, 20-69 years of age. All data were retrieved from public registries. The sex-specific incidence rate ratios (IRR) of first-occurring positive RT-PCR test from week 8 of 2020 through week 50 of 2021 were computed by Poisson regression for each 4-digit DISCO-08 job code with more than 100 employees (337 in men; 297 in women). Occupational groups with low risk of workplace infection according to a job exposure matrix constituted the reference group. Risk estimates were adjusted by demographic, social and health characteristics including household size, completed Covid-19 vaccination, pandemic wave and occupation-specific frequency of testing.

Results

IRR’s of SARS-CoV-2 infection were elevated in 34 occupations comprising 12 % of male employees and 45 occupations comprising 41 % of female employees. All IRR estimates were below 2.0. Decreased IRRs were observed in 85 occupations in men but none in women.

Discussion

We observed a modestly increased risk of SARS-CoV-2 infection among employees in numerous occupations indicating a large potential for preventive actions, especially in the female workforce. Cautious interpretation of observed risk in specific occupations is needed because of methodological issues inherent in analyses of RT-PCR-test results and because of multiple statistical tests.

WHAT IS ALREADY KNOW ABOUT THIS TOPIC?

Epidemiological studies suggest that the workplace contribute to the Covid-19 pandemic

Results are mostly based upon studies of less frequent outcomes as Covid-19 morbidity or mortality which limits inference about risk in specific occupations

WHAT THIS STUDY ADDS

The risk of Covid-19 infection was increased in 34 of 337 occupations in men and in 45 of 297 occupations in women

Some 12% of the Danish male workforce and 41% of the female workforce are at increased risk of Covid-19 infection

HOW THIS RESEARCH MIGHT AFFECT RESEARCH, PRACTICE OR POLICY?

Preventive actions targeting the workplace may contribute substantially to alleviate disease occurrence in the ongoing Covid-19 and similar future pandemics.
Pilot Clinical Trial to test the function of a Diagnostic Sensor in predicting Impending Urinary Catheter Blockage in Long-term Catheterized Patients
Authors: Heylen Rachel A. , Mercer-Chalmers June , Morton Annette , Urie James , Jefferies Edward , Patenall Bethany L. , Laabei Maisem , Jenkins A. Toby. A.
Published: October 2022

Trial design

Pilot feasibility trial.

Methods

Participants

adults attending the Outpatient Urology Clinic, having a long-term indwelling urinary catheter and have the mental capacity to consent. Consent for the donation of the urinary catheter and drainage bag were gained at the Urology Clinic, Royal United Hospital (RUH) Bath, alongside a quality-of-life questionnaire.

Interventions

there was no direct intervention to the participants, the trial was to test the functionality of the diagnostic sensor, there was no change to the participant’s medical care.

Objectives

recruitment of 48 participants to donate catheter and drainage bags (including re-recruits); assess the functionality of the sensor to predict impending catheter blockage in human urine; assess the functionality to release at pH > 7; and assess the microbiological profile of the patients with long-term catheters.

Outcome

determination of whether the participant had a blockage event 3 weeks post catheter change, and whether this matched with the result from the sensor. Measurements of the participant’s urine to assess whether the sensor could detect human urine at a pH > 7. Determine the microbial species present in the drainage bag of the participants.

Results

Recruitment

received 35 samples from 28 individuals.

Outcome

two participants reported blockage events which were successfully detected by the sensor. However, the sensor also predicted blockage in participants that did not block within the 3-week report time period, sensitivity = 100%, specificity = 58.06%. The functionality of the sensor to detect urine above pH > 7 had a sensitivity = 78.75% and a specificity = 96.77%, which gave ap= 2.06×10−24(χ2test). Inclusion of the maintenance solution prescribed to participants, to test the predictability of the sensor, gave a sensitivity = 100%, and a specificity = 62.95%,p= 0.029 (Fisher Exact test). Microbiological analysis indicated thatProteusspp. andPseudomonasspp. were the most commonly isolated microbes.

Harm

No adverse events.

Conclusions

The sensor can predict participants more prone to catheter blockage, and it is accurate in detecting urine with a pH >7. Owing to the small sample number of this trial, the results are not statistically powered. However, the data can be used to improve the design of the sensor and inform the design of a larger, randomized clinical trial.

Trial registration

Trial was ethically approved by the Research Ethics Committee (REC) number: 20/LO/0094. Integrated Research Application System (IRAS) number: 261095.

Funding

trial was funded by the Urology Foundation and an IAA seed grant, University of Bath.
It’s not just about pads! Adolescent reproductive health in Kenya:A qualitative secondary analysis
Authors: Ayieko Sylvia , Nguku Angela , Kidula Nancy
Published: October 2022

Many adolescents face barriers to accessing reproductive health care even though quality reproductive health care is a fundamental human right. This qualitative analysis describes quality reproductive health requests among adolescent high school girls in Kenya. We conducted a secondary analysis of qualitative data from a sub-sample of adolescent girls in Kenya who participated in theWhat Women Wantglobal campaign. The campaign utilized one open-ended survey question. We also analyzed interview data from key informants involved in the survey. We used pre-existing codes and current literature to design the coding framework and thematic analysis to describe emerging themes. Atlas. ti 8 was used to organize and analyze codes. Over 4,500 high school girls, ages 12 and 19 years, were included in the analysis, with 61.6% from all-girls boarding schools and 13.8% from mixed-day schools. Data from nine key informants complemented findings from the survey. Emerging themes included: 1) The need for improved menstrual health and hygiene: Sanitary towels and cleaner toilets; 2) Prevention of adolescent pregnancy: Access to contraception; 3) Respect and dignity: Participants want privacy and confidentiality; and 4) The need to address social determinants of health: Economic stability and a safe physical environment. This study indicated that adolescent high school girls have varied requests for reproductive health care and services. While menstrual health and hygiene are key issues, reproductive needs are beyond just sanitary products. The results suggest a need for targeted reproductive health interventions using a multi-sectoral approach.
Accurate detection and identification of insects from camera trap images with deep learning
Authors: Bjerge Kim , Alison Jamie , Dyrmann Mads , Frigaard Carsten Eie , Mann Hjalte M. R. , Høye Toke Thomas
Published: October 2022

Reported insect declines have dramatically increased the global demand for standardized insect monitoring data. Image-based monitoring can generate such data cost-efficiently and non-invasively. However, extracting ecological data from images is more challenging for insects than for vertebrates because of their small size and great diversity. Deep learning facilitates fast and accurate insect detection and identification, but the lack of training data for coveted deep learning models is a major obstacle for their application. We present a large annotated image dataset of functionally important insect taxa. The primary dataset consists of 29,960 annotated insects representing nine taxa including bees, hoverflies, butterflies and beetles across more than two million images recorded with ten time-lapse cameras mounted over flowers during the summer of 2019. The insect image dataset was extracted using an iterative approach: First, a preliminary detection model identified candidate insects. Second, candidate insects were manually screened by users of an online citizen science platform. Finally, all annotations were quality checked by experts. We used the dataset to train and compare the performance of selected You Only Look Once (YOLO) deep learning algorithms. We show that these models detect and classify small insects in complex scenes with unprecedented accuracy. The best performing YOLOv5 model consistently identifies nine dominant insect species that play important roles in pollination and pest control across Europe. The model reached an average precision of 92.7% and recall of 93.8 % in detection and classification across species. Importantly, when presented with uncommon or unclear insects not seen during training, our model detects 80% of individuals and usually interprets them as closely related species. This is a useful property to (1) detect rare insects for which training data are absent, and (2) generate new training data to correctly identify those insects in future. Our camera system, dataset and deep learning framework show promising results in non-destructive monitoring of insects. Furthermore, resulting data are useful to quantify phenology, abundance, and foraging behaviour of flower-visiting insects. Above all, this dataset represents a critical first benchmark for future development and evaluation of deep learning models for insect detection and identification.
bRaw: an R package for digital raw canopy imagery
Authors: Chianucci F.
Published: October 2022

Digital photography is an increasingly popular tool to estimate forest canopy attributes. However, estimates of gap fraction, upon which calculations of canopy attributes are based, are sensitive to photographic exposure in upward-facing images. Recent studies have indicated that analyzing RAW imagery, rather than other inbuilt camera format (e.g. jpeg, png, tiff) allows to obtain largely-insensitive gap fraction retrieval from digital photography. The package bRaw implemented the method proposed by Macfarlane et al. (2014). They found that shooting raw with one stop of underexposure and applying a linear contrast stretch yielded largely insensitive results, thus providing a way for standardizing and optimizing photographic exposure. The package replicate the methodology and thus it provides an effective tool to use raw imagery in canopy photography.
Lmx1a is a master regulator of the cortical hem
Authors: Iskusnykh Igor Y. , Fattakhov Nikolai , Li Yiran , Bihannic Laure , Kirchner Matthew K. , Steshina Ekaterina Y. , Northcott Paul A. , Chizhikov Victor V.
Published: October 2022

Development of the nervous system depends on signaling centers – specialized cellular populations that produce secreted molecules to regulate neurogenesis in the neighboring neuroepithelium. Some signaling centers also generate key types of neurons. The formation of a signaling center involves its induction, the maintenance of expression of its secreted molecules, and cell differentiation and migration events. How these distinct processes are coordinated during signaling center development remains unknown. Here we show that Lmx1a acts as a master regulator to orchestrate the formation and function of the cortical hem (CH), a critical signaling center that controls hippocampus development. Lmx1a co-regulates CH induction, its Wnt signaling, and the differentiation and migration of CH-derived Cajal-Retzius neurons. Combining RNAseq, genetic, and rescue experiments, we identified major downstream genes that mediate distinct Lmx1a-dependent processes. Our work revealed that signaling centers in the mammalian brain employ master regulatory genes and established a framework for analyzing signaling center development.
Benchmarking of protein interaction databases for integration with manually reconstructed signaling network models
Authors: Van de Graaf Matthew W. , Eggertsen Taylor G. , Zeigler Angela C. , Tan Philip M. , Saucerman Jeffrey J.
Published: October 2022

Protein interaction databases are critical resources for network bioinformatics and integrating molecular experimental data. Interaction databases may also enable construction of predictive computational models of biological networks, although their fidelity for this purpose is not clear. Here, we benchmark protein interaction databases X2K, Reactome, Pathway Commons, Omnipath, and Signor for their ability to recover manually curated edges from three logic-based network models of cardiac hypertrophy, mechano-signaling, and fibrosis. Pathway Commons performed best at recovering interactions from manually reconstructed hypertrophy (137 of 193 interactions, 71%), mechano-signaling (85 of 125 interactions, 68%), and fibroblast networks (98 of 142 interactions, 69%). While protein interaction databases successfully recovered central, well-conserved pathways, they performed worse at recovering tissue-specific and transcriptional regulation. This highlights a knowledge gap where manual curation is critical. Finally, we tested the ability of Signor and Pathway Commons to identify new edges that improve model predictions, revealing important roles of PKC autophosphorylation and CaMKII phosphorylation of CREB in cardiomyocyte hypertrophy. This study provides a platform for benchmarking protein interaction databases for their utility in network model construction, as well as providing new insights into cardiac hypertrophy signaling.
Quantitative profiling of pseudouridylation landscape in the human transcriptome
Authors: Zhang Meiling , Jiang Zhe , Ma Yichen , Liu Wenqing , Zhuang Yuan , Lu Bo , Li Kai , Yi Chengqi
Published: October 2022

Pseudouridine (Ψ) is an abundant post-transcriptional RNA modification in ncRNA and mRNA. However, transcriptome-wide measurement of individual Ψ sites remains unaddressed. Here, we develop “PRAISE”, via selective chemical labeling of Ψ by bisulfite to induce nucleotide deletion signature during reverse transcription, to realize quantitative assessment of the Ψ landscape in the human transcriptome. Unlike traditional RNA/DNA bisulfite treatment, our approach is based on quaternary base mapping and revealed a ~10% median modification level for 2,714 confident Ψ sites in HEK293T cells. By perturbing pseudouridine synthases, we obtained differential mRNA targets of PUS1, PUS7 and TRUB1, with TRUB1 mRNA targets showing the highest modification stoichiometry. In addition, we identified and quantified known and novel Ψ sites in mitochondrial mRNA, catalyzed by a mitochondria-localized isoform of PUS1. Collectively, we provide a sensitive and convenient method to measure transcriptome-wide Ψ; we envision this quantitative approach would facilitate emerging efforts to elucidate the function and mechanism of mRNA pseudouridylation.
Reading negative action verbs: one or two-step processing within the primary motor cortex?
Authors: Dupont W , Papaxanthis C , Lurquin L , Lebon F , Madden-Lombardi C
Published: October 2022

Controversy persists regarding the representation of negated actions, specifically concerning activation and inhibitory mechanisms in the motor system, and whether this occurs in one or two steps. We conducted two experiments probing corticospinal excitability (CSE) and short-interval intracortical inhibition (SICI) in the primary motor cortex at different latencies while reading affirmative and negative action sentences.

Twenty-six participants read action and non-action sentences in affirmative or negative forms. Using transcranial magnetic stimulation, we probed CSE in hand muscles at rest and at several latencies after verb presentation. We observed a greater CSE for action sentences compared to non-action sentences, regardless of verb form.

In experiment two, nineteen participants read affirmative and negative action sentences. We measured CSE and SICI at short and long latencies after verb presentation. CSE was greater for affirmative and negative action sentences at both latencies compared to rest. SICI did not change at the short latency but increased at longer latencies, regardless of verb form.

Our results lend partial support for a two-step model, as negated actions showed the same motor excitability as affirmed actions with no additional inhibition at early latencies. Later neural differences between affirmative and negative actions may occur outside the primary motor cortex.

Significant statement

In two TMS experiments, we probed corticospinal excitability and short-interval intracortical inhibition in the primary motor cortex at different latencies while subjects read affirmative and negative action sentences. Consistent with an embodied view of language comprehension, our results demonstrate that reading about actions indeed activates the motor system, and this for both negative and affirmative sentences. Our results lend partial support for a two-step model of negation, as negated actions showed the same increase in motor excitability as affirmed actions, with no additional inhibition at early latencies. This suggests that the motor system contributes to comprehension by simulating the negated or affirmed action. Later neural differences between affirmative and negative actions may occur outside the primary motor cortex.
‘Same same but different’ Exploring evolutionary and ecological causes of eye diversification in bumblebees
Authors: Tichit Pierre , Bodey Andrew , Rau Christoph , Baird Emily
Published: October 2022

Bees rely heavily on vision during most of their interaction with the environment, but so far, visual abilities have not been included into functional investigations of these crucial pollinators. This is probably due to the lack of comprehensive and phylogenetically-controlled quantification of visual traits across species. In the present study, we used high-throughput micro-CT tools to quantify, compare and understand the diversity of visual traits of compound eyes in bumblebees. Visual systems of bumblebees were far from identical, with variations across sizes, castes and species. While phylogenetic proximity poorly supported interspecific variations, these were better explained by two ecological factors: social parasitism and habitat. The eye parameter – a metric that measures the relative investment of a compound eye into resolution or sensitivity – was lower in queens of social parasitic species than of non-parasitic species. Workers of species associated with forested habitat had distinct visual traits, including a higher eye parameter, than those of species living in open landscapes. These diverse visual traits are likely to provide selective advantages to bumblebees given their specific ecological requirements. We thus propose that social parasitism and forest habitat are drivers of the diversification of compound eyes in bumblebees. Finally, we discuss how the present study can inspire trait-based approaches in ecology and conservation biology.
Evaluation of metabolic and functional properties of cholesterol-reducing and GABA-producerLimosilactobacillus fermentumstrain AGA52 isolated from lactic acid fermented Shalgam by usingin vitroandin silicoprobiogenomic approaches
Authors: Yetiman Ahmet , Horzum Mehmet , Akbulut Mikail
Published: October 2022

The objective of this study is characterization of the genomic and metabolic properties of a novelLb. fermentumstrain AGA52 which was isolated from a lactic acid fermented beverage called “Shalgam”. The genome size of AGA52 was 2,001,084 bp, which is predicted to carry 2,024 genes, including 50 tRNAs, 3 rRNAs, 3ncRNAs, 15 CRISPR repeats, 14 CRISPR spacers, and 1 CRISPR array. The genome has a GC content of 51.82% including 95 predicted pseudogenes, 56 complete or partial transposases and 2 intact prophages. The similarity of the clusters of orthologous groups (COG) was analysed by comparison with the otherLb. fermentumstrains. The detected resistome on the genome of AGA52 was found to be intrinsically originated. Based on genome analyses many CAZYmes were identified that are responsible for carbohydrate degradation and adaptation to gastrointestinal conditions. Besides, it has been determined that AGA52 has an obligate heterofermentative carbohydrate metabolism due to the absence of the 1-phosphofructokinase (pfK) enzyme. Additionally, it is determined that the strain has a higher antioxidant capacity and is adaptable to gastrointestinal simulated environments. It was also observed that the AGA52 has antimicrobial activity againstY. EnterocoliticaATCC9610,B. cereusATCC33019,S. entericasv. Typhimurium,E.coliO157:h7 ATCC43897,L.monocytogenesATCC7644,K.pneumoniaeATCC13883, andP. vulgarisATCC8427. Cholesterol assimilation (33.9±0.005%) and GABA production capacities were also confirmed by “in silico” and “in vitro”. Overall, investigation of genomic and metabolic features of the AGA52 revealed that is a potential psychobiotic and probiotic dietary supplement candidate and can bring functional benefits to the host.
Classifying directed and diffusive transport in short, noisy single-molecule trajectories with wMSD
Authors: Danné Noémie , Zhang Zhiqing , Peterman Erwin J. G.
Published: October 2022

Fluorescence imaging in combination with single-particle tracking analysis has emerged as a powerful tool to study and characterize the motion of proteins moving in biological media. One of the main challenges in this approach is to reliably distinguish between directed and diffusive transport, especially for short and often noisy trajectories showing distinct, time- and place-dependent modes of motility. In this contribution, we present a windowed Mean-Square Displacements classifier (wMSDc) that is able to reliably (i) identify periods of diffusive and directed transport, (ii) extract position-dependent diffusion coefficients and velocities, and (iii) identify the location of switches in direction or motility mode in short (< 50 time points) and noisy single-molecule trajectories. We compare the performance of this approach to a Hidden Markov Model (HMM) method and a Moment Scaling Spectrum based method (DC-MSS) previously published and show that, in most cases, its performance is superior. We present a wide range of applications: from the movement of whole organisms and cells to protein-DNA interactionsin vitroand motor-protein dynamicsin vivo.

Statement of Significance

Extracting quantitative parameters from single-particle trajectories is a challenging task, especially in biological samples, which often show a high degree of heterogeneity. Trajectories can reveal switches between different types of motion; directed, diffusive and sub-diffusive motion. Usually, the length of these trajectories and their localization precision are limited by the experimental conditions. Here, we present a novel approach to analyse single molecule trajectories, windowed Mean-Square Displacement classifier (wMSDc) to reliably distinguish between directed and diffusive transport in the short trajectories with a finite precision of localization and integration time typically obtained when imaging single fluorescent proteins in living cells or organisms. We show that, using simulated and a wide range of experimental trajectories, wMSDc is a reliable method to extract motility parameters such as diffusion coefficient and velocity.
The structure of pathogenic huntingtin exon-1 defines the bases of its aggregation propensity
Authors: Elena-Real Carlos A. , Sagar Amin , Urbanek Annika , Popovic Matija , Morató Anna , Estaña Alejandro , Fournet Aurélie , Lund Xamuel L. , Shi Zhen-Dan , Costa Luca , Thureau Aurélien , Allemand Frédéric , Swenson Rolf E. , Milhiet Pierre-Emmanuel , Barducci Alessandro , Cortés Juan , Sinnaeve Davy , Sibille Nathalie , Bernadó Pau
Published: October 2022

Huntington’s Disease is a neurodegenerative disorder caused by a CAG expansion of the first exon of theHTTgene, resulting in an extended poly-glutamine (poly-Q) tract in the N-terminus of the protein huntingtin (httex1). The structural changes occurring to the poly-Q when increasing its length remain poorly understood mainly due to its intrinsic flexibility and the strong compositional bias of the protein. The systematic application of site-specific isotopic labeling has enabled residue-specific NMR investigations of the poly-Q tract of pathogenic httex1 variants with 46 and 66 consecutive glutamines. The integrative analysis of the data reveals that the poly-Q tract adopts long α-helical conformations stabilized by glutamine side-chain to backbone hydrogen bonds.19F-NMR of site-specifically incorporated fluoro-glutamines and molecular dynamics simulations demonstrate that the mechanism propagating α-helical conformations towards the poly-Q from the upstream N17 domain is independent of the poly-Q track length. Aggregation and atomic force microscopy experiments show that the presence of long and persistent α-helices in the poly-Q tract is a stronger signature in defining the aggregation kinetics and the structure of the resulting fibrils than the number of glutamines. The ensemble of our observations provides a structural perspective of the pathogenicity of expanded httex1 and paves the way to a deeper understanding of poly-Q related diseases.
Quantitative super-resolution imaging of platelet degranulation reveals differential release of VWF and VWF propeptide from alpha-granules
Authors: Swinkels Maurice , Hordijk Sophie , Bürgisser Petra E. , Slotman Johan A. , Carter Tom , Leebeek Frank W.G. , Jansen A.J. Gerard , Voorberg Jan , Bierings Ruben
Published: October 2022

Background

Platelet alpha-granules contain Von Willebrand factor (VWF), which is stored in eccentric alpha-granule nanodomains, and VWF propeptide (VWFpp). Differential release of VWF and VWFpp has been reported from endothelial cells. It is unclear if this also occurs during platelet alpha-granule exocytosis. We have recently developed a 3D super-resolution imaging workflow for quantification of platelet alpha-granule content based on Structured Illumination Microscopy (SIM). With this we can study alpha-granule cargo release following platelet activation in hundreds of platelets simultaneously.

Aims

To study release of VWF and VWFpp from alpha-granules using quantitative super-resolution microscopy.

Methods

Platelets were activated with PAR-1 activating peptide (PAR-1 ap) or collagen-related peptide (CRP-XL). Alpha-tubulin, VWF, VWFpp, SPARC and fibrinogen were imaged using 3D-SIM, followed by semi-automated analysis in FIJI. Uptake of anti-VWF nanobody during degranulation was used to identify alpha-granules that partially released content.

Results

VWF+ and VWFpp+ structures overlapped nearly completely (∼90%) in resting platelets, implying they are stored in similar eccentric alpha-granule nanodomains. A subset of VWF+/VWFpp+-structures was released completely at 0.6 µM PAR-1 ap, but at higher concentration (20 µM) significantly more VWFpp (85.3±1.6%) was released than VWF (37.6±1.4%). Release of other cargo was intermediate at 20 µM (SPARC: 62.2±1.4%; fibrinogen: 51.9±2.9%), providing further evidence for differential cargo release. Similar results were obtained using CRP-XL. Anti-VWF nanobody was taken up by VWF+/VWFpp-structures and increased with stimulus strength, demonstrating these were post-exocytotic structures.

Conclusions

VWF and VWFpp are differentially released from alpha-granules. This may affect how platelet-derived VWF and VWFpp contribute to formation and stabilization of hemostatic clots.

Key points

VWFpp and VWF are localized in the same, eccentric alpha-granule subdomain in resting platelets and do not overlap with other alpha-granule cargo proteins such as fibrinogen

VWFpp and VWF are differentially secreted from individual alpha-granules upon activation with platelet agonists PAR-1 activating peptide and collagen-related peptide
Assembly of the 81.6 Mb centromere of pea chromosome 6 elucidates the structure and evolution of metapolycentric chromosomes
Authors: Macas Jiří , Robledillo Laura Ávila , Kreplak Jonathan , Novák Petr , Koblížková Andrea , Vrbová Iva , Burstin Judith , Neumann Pavel
Published: October 2022

Centromeres in the legume generaPisumandLathyrusexhibit unique morphological characteristics, including extended primary constrictions and multiple separate domains of centromeric chromatin. These so-called metapolycentromeres resemble an intermediate form between monocentric and holocentric types, and therefore provide a great opportunity for studying the transitions between different types of centromere organizations. However, because of the exceedingly large and highly repetitive nature of metapolycentromeres, highly contiguous assemblies needed for these studies are lacking. Here, we report on the assembly and analysis of a 177.6 Mb region of pea (Pisum sativum) chromosome 6, including the 81.6 Mb centromere region (CEN6) and adjacent chromosome arms. Genes, DNA methylation profiles, and most of the repeats were uniformly distributed within the centromere, and their densities in CEN6 and chromosome arms were similar. The exception was an accumulation of satellite DNA in CEN6, where it formed multiple arrays up to 2 Mb in length. Centromeric chromatin, characterized by the presence of the CENH3 protein, was predominantly associated with arrays of three different satellite repeats; however, five other satellites present in CEN6 lacked CENH3. The presence of CENH3 chromatin was found to determine the spatial distribution of the respective satellites during the cell cycle. Finally, oligo-FISH painting experiments, performed using probes specifically designed to label the genomic regions corresponding to CEN6 inPisum,Lathyrus, andViciaspecies, revealed that metapolycentromeres evolved via the expansion of centromeric chromatin into neighboring chromosomal regions and the accumulation of novel satellite repeats. However, in some of these species, centromere evolution also involved chromosomal translocations and centromere repositioning.

Significance

Despite their conserved function, plant centromeres exhibit considerable variation in their morphology and sequence composition. For example, centromere activity is restricted to a single region in monocentric chromosomes, but is distributed along the entire chromosome length in holocentric chromosomes. The principles of centromere evolution that led to this variation are largely unknown, partly due to the lack of high-quality centromere assemblies. Here, we present an assembly of the pea metapolycentromere, a unique type of centromere that represents an intermediate stage between monocentric and holocentric organizations. This study not only provides a detailed insight into sequence organization, but also reveals possible mechanisms for the formation of the metapolycentromere through the spread of centromeric chromatin and the accumulation of satellite DNA.
Aggregation and Defence
Authors: Durieux David M. , Gemmell Brad J.
Published: October 2022

Cassiopeasp., the Upside-Down Jellyfish, are considered to be sedentary epibenthic organisms which exhibit little to no movement on the seafloor. In this study, we use time-lapse videography of a Cassiopea population in the Florida Keys to demonstrate that Cassiopea sp. exhibit a greater degree of benthic locomotion than previously understood, with animals covering distances up to 178 cm per day. In addition, Cassiopea seem to aggregate on the bottom, with average number of neighbours consistently higher than would be expected for random distributions. Given the ability of Cassiopea to release nematocysts directly into the water column, we present this aggregation as a potential defensive behaviour in this species.
Bayesian Pharmacometrics Analysis of Baclofen for Alcohol Use Disorder
Authors: Baldy Nina , Hashemi Meysam , Simon Nicolas , Jirsa Viktor K.
Published: October 2022

Alcohol use disorder (AUD) also called alcohol dependence is a major public health problem, which affects almost 10% of the world’s population. Baclofen as a selective GABABreceptor agonist has emerged as a promising drug for the treatment of AUD, however, its optimal dosage varies according to individuals, and its exposure-response relationship has not been well established yet. In this study, we use a principled Bayesian workflow to estimate the parameters of a pharmacokinetic (PK) population model from Baclofen administration to patients with AUD. By monitoring various convergence diagnostics, the probabilistic methodology is first validated on synthetic longitudinal datasets and then, applied to infer the PK model parameters based on the clinical data that were retrospectively collected from outpatients treated with oral Baclofen. We show that state-of-the-art advances in automatic Bayesian inference using self-tuning Hamiltonian Monte Carlo (HMC) algorithms with a leveraged level of information in priors provide accurate predictions on Baclofen plasma concentration in individuals. This approach may pave the way to render non-parametric HMC sampling methods sufficiently easy and reliable to use in clinical schedules for personalized treatment of AUD.
Discovery of intratumoral oncolytic bacteria toward targeted anticancer theranostics
Authors: Goto Yamato , Iwata Seigo , Miyako Eijiro
Published: October 2022

Unveiling the different biomedical functions of tumor-resident microbiota has remained challenging for the development of advanced anticancer medicines. Here we show that isolated intratumoral bacteria with its association with natural purple photosynthetic bacteria have a high innate biocompatibility and drastic immunogenic anticancer efficacies. They preferentially grow and proliferate within targeted tumor milieu, which effectively causes immune cells to infiltrate the tumor and provoke strong anticancer responses in various syngeneic mouse models including those of colorectal cancer, sarcoma, metastatic lung cancer, and extensive drug-resistant breast cancer. Furthermore, these functional bacteria-treated mice, that exhibit excellent anticancerous responses of tumors, have significantly prolonged survival rates with effective immunological memory. Notably, light-harvesting nanocomplexes of microbial consortium of intratumoral bacteria and purple photosynthetic bacteria is capable of tumor diagnosis using bio-optical-window near-infrared light, making them useful theranostic agents for highly targeted immunological elimination of the tumor and for precisely marking tumor location.
Importance of Glutamine in Synaptic Vesicles Revealed by Functional Studies of SLC6A17 and Its Mutations Pathogenic for Intellectual Disability
Authors: Jia Xiaobo , Zhu Jiemin , Bian Xiling , Liu Sulin , Yu Sihan , Liang Wenjun , Jiang Lifen , Mao Renbo , Rao Yi
Published: October 2022

Human mutations in the gene encoding the solute carrier (SLC) 6A17 caused intellectual disability (ID). The physiological role of SLC6A17 and pathogenesis of Slc6a17-based-ID were both unclear. Here we report learning deficits in SLC6A17 knockout and point mutants. Biochemistry, proteomics and electron microscopy (EM) support SLC6A17 protein localization in synaptic vesicles (SVs). Chemical analysis of SVs by liquid chromatography coupled to mass spectrometry (LC-MS) revealed glutamine (Gln) in SVs containing SLC6A17. Virally mediated overexpression of SLC6A17 increased Gln in SVs. Either genetic or virally mediated targeting of SLC6A17 reduced Gln in SVs. One ID mutation caused SLC6A17 mislocalization while the other caused defective Gln transport. Multidisciplinary approaches with 7 types of genetically modified mice have shown Gln as an endogenous substrate of SLC 6A17, uncovered Gln as a new molecule in SVs, established the necessary and sufficient roles of SLC6A17 in Gln transport into SVs, and suggested SV Gln decrease as the key pathogenetic mechanism in human ID.
The temporal regulation inter-leaves from domesticated-tomato contrasts with timelessness of its wild ancestors
Authors: Siqueira João Antonio , Martins Auxiliadora O. , Wakin Thiago , Silva Marcelle Ferreira , Batista-Silva Willian , Brito Fred A.L. , Fernie Alisdair R. , Nunes-Nesi Adriano , Araújo Wagner L.
Published: October 2022

Cells, tissues, and organs are characterized by harbouring complex systems allowing communication between one another. Plant domestication was demonstrated to have structured the circadian rhythms, while also synchronising flowering and metabolism. Here, we demonstrate that the domesticated tomato (Solanum lycopersicum) manifests more synchronized rhythmicity across the whole plant. Consequently, the leaf development program is more coordinated in this species than in its wild relatives, whereinS. lycopersicumyoung leaves develop slowly in comparison to mature leaves. Young leaves from wild tomatoes display higher photosynthesis than mature leaves, while large metabolite accumulations occur across plant segments. Consequently, the diel metabolite levels are rather similar between young and mature leaves in the wild tomatoS. pennellii, whereas the expression patterns for circadian clock genes are widely contrasting between both leaves. We further demonstrated that additions of genes related to domestication into the wild tomatoS. pimpinellifoliumappear to synchronize the development of young and mature leaves to be rather similar to that observed forS. lycopersicum. Collectively, the strengthening of inter-organs relationships on domesticated tomato indicates a synchronized biology, which is most likely fundamental to explaining its elevated yield.
Comprehensive interrogation of aDrosophilaembryonic patterning network reveals the impact of chromatin state on tissue-specific burst kinetics and RNA Polymerase II promoter-proximal pause release
Authors: Hunt George , Vaid Roshan , Pirogov Sergei , Pfab Alexander , Ziegenhain Christoph , Sandberg Rickard , Reimegård Johan , Mannervik Mattias
Published: October 2022

Formation of tissue-specific transcriptional programs underlies multicellular development, but how the chromatin landscape influences transcription is not fully understood. Here we comprehensively resolve differential transcriptional and chromatin states duringDrosophiladorsoventral (DV) patterning. We find that RNA Polymerase II pausing is established at DV promoters prior to zygotic genome activation (ZGA), that pausing persists irrespective of cell fate, but that release into productive elongation is tightly regulated and accompanied by tissue-specific P-TEFb recruitment. DV enhancers acquire distinct tissue-specific chromatin states through CBP-mediated histone acetylation that predict the transcriptional output of target genes, whereas promoter states are more tissue invariant. Transcriptome-wide inference of burst kinetics in different cell types revealed that while DV genes are generally characterized by a high burst size, either burst size or frequency can differ between tissues. The data suggest that pausing is established by pioneer transcription factors prior to ZGA and that release from pausing is imparted by enhancer chromatin state to regulate bursting in a tissue-specific manner in the early embryo. Our results uncover how developmental patterning is orchestrated by tissue-specific bursts of transcription from Pol II primed promoters in response to enhancer regulatory cues.
Calcitic prisms of the giant seashellPinna nobilisform light guide arrays
Authors: Amini Shahrouz , Zhu Tingting , Biswas Abin , Charsooghi Mohammad A. , Kim Kyoohyun , Reber Simone , Dauphin Yannicke , Fratzl Peter
Published: October 2022

The shells of thePinnidaefamily are based on a double layer of single-crystal-like calcitic prisms and inner aragonitic nacre, a structure known for its outstanding mechanical performance. However, on the posterior side, shells are missing the nacreous layer, which raises the question of whether there could be any functional role in giving up this mechanical performance. Here, we demonstrate that the prismatic part of thePinna nobilisshell exhibits unusual optical properties, whereby each prism acts as an individual optical fiber guiding the ambient light to the inner shell cavity by total internal reflection. This pixelated light channeling enhances both spatial resolution and contrast while reducing angular blurring, an apt combination for acute tracking of a moving object. Our findings may offer insights into the evolutionary aspects of light-sensing and imaging by biological materials and introduce a conceptual framework for the development of bio-inspired multifunctional ceramics and architectured light-tracking materials.
Staphylococcus aureusFtsZ and PBP4 bind to the conformationally dynamic N-terminal domain of GpsB
Authors: Sacco Michael D. , Hammond Lauren R. , Noor Radwan E. , Bhattacharya Dipanwita , Madsen Jesper J. , Zhang Xiujun , Butler Shane G. , Kemp M. Trent , Jaskolka-Brown Aiden C. , Khan Sebastian J. , Gelis Ioannis , Eswara Prahathees J. , Chen Yu
Published: October 2022

Bacterial cell division is a tightly regulated process that requires the formation of a dynamic multi-protein complex. In the Firmicutes phylum, GpsB is a membrane associated protein that coordinates peptidoglycan synthesis for cell growth and division. Although GpsB has been studied in several organisms, the structure, function, and interactome ofStaphylococcus aureusGpsB is largely uncharacterized, despite being reported as uniquely essential for growth in this clinically relevant bacterium. To address this knowledge gap, we solved the crystal structure of the N-terminal domain ofS. aureusGpsB. This structure reveals an atypical asymmetric dimer, and major conformational flexibility that can be mapped to a hinge region formed by a three-residue insertion exclusive toStaphylococci. When this three-residue insertion is excised, its thermal stability increases, and the mutant no longer produces a previously reported lethal phenotype when overexpressed inBacillus subtilis. Furthermore, we provide the first biochemical, biophysical, and crystallographic evidence that the N-terminal domain of GpsB binds not only PBP4, but also FtsZ, through a conserved recognition motif located on their C-terminus, thus linking peptidoglycan synthesis with cell division. Taken together, the unique structure ofS. aureusGpsB and its direct interaction with FtsZ/PBP4 provide deeper insight into the central role of GpsB inS. aureuscell division.