bluuebunny/crossref_metadata_2025 huggingface dataset:
Structure and function of the Si3 insertion integrated into the trigger loop/helix of cyanobacterial RNA polymerase
Authors: Zuhaib Qayyum M. , Imashimizu Masahiko , Leanca Miron , Vishwakarma Rishi K. , Riaz-Bradley Amber , Yuzenkova Yulia , Murakami Katsuhiko S.
Published: January 2024

Cyanobacteria and evolutionarily related chloroplasts of algae and plants possess unique RNA polymerases (RNAPs) with characteristics that distinguish from canonical bacterial RNAPs. The largest subunit of cyanobacterial RNAP (cyRNAP) is divided into two polypeptides, β’1 and β’2, and contains the largest known lineage-specific insertion domain, Si3, located in the middle of the trigger loop and spans approximately half of the β’2 subunit. In this study, we present the X-ray crystal structure of Si3 and the cryo-EM structures of the cyRNAP transcription elongation complex plus the NusG factor with and without incoming nucleoside triphosphate (iNTP) bound at the active site. Si3 has a well-ordered and elongated shape that exceeds the length of the main body of cyRNAP, fits into cavities of cyRNAP and shields the binding site of secondary channel-binding proteins such as Gre and DksA. A small transition from the trigger loop to the trigger helix upon iNTP binding at the active site results in a large swing motion of Si3; however, this transition does not affect the catalytic activity of cyRNAP due to its minimal contact with cyRNAP, NusG or DNA. This study provides a structural framework for understanding the evolutionary significance of these features unique to cyRNAP and chloroplast RNAP and may provide insights into the molecular mechanism of transcription in specific environment of photosynthetic organisms.

Significance statement

Cellular RNA polymerase (RNAP) carries out RNA synthesis and proofreading reactions utilizing a mobile catalytic domain known as the trigger loop/helix. In cyanobacteria, this essential domain acquired a large Si3 insertion during the course of evolution. Despite its elongated shape and large swinging motion associated with the transition between the trigger loop and helix, Si3 is effectively accommodated within cyRNAP, with no impact on the fundamental functions of the trigger loop. Understanding the significance of Si3 in cyanobacteria and chloroplasts is expected to reveal unique transcription mechanism in photosynthetic organisms.
Raw signal segmentation for estimating RNA modification from Nanopore direct RNA sequencing data
Authors: Cheng Guangzhao , Vehtari Aki , Cheng Lu
Published: January 2024

Estimating RNA modifications from Nanopore direct RNA sequencing data is a critical task for the RNA research community. However, current computational methods often fail to deliver satisfactory results due to inaccurate segmentation of the raw signal. We have developed a new method, SegPore, which leverages a molecular jiggling translocation hypothesis to improve raw signal segmentation. SegPore is a pure white-box model with enhanced interpretability, significantly reducing structured noise in the raw signal. We demonstrate that SegPore outperforms state-of-the-art methods, such as Nanopolish and Tombo, in raw signal segmentation across three large benchmark datasets. Moreover, the improved signal segmentation achieved by SegPore enables SegPore+m6Anet to deliver state-of-the-art performance in site-level m6A identification. Additionally, SegPore surpasses baseline methods like CHEUI in single-molecule level m6A identification.
Switching to external flows: perturbations of developing vasculature within chicken chorioallantoic membrane
Authors: Padmanaban Prasanna , van Galen Danny , Salehi-Nik Nasim , Zakharova Mariia , Segerink Loes , Rouwkema Jeroen
Published: January 2024

The impact of fluid flow shear stresses, generated by the movement of blood through vasculature, on the organization and maturation of vessels is widely recognized. Nevertheless, it remains uncertain whether external fluid flows outside of the vasculature in the surrounding tissue can similarly play a role in governing these processes. In this research, we introduce an innovative technique called superfusion-induced vascular steering (SIVS). SIVS involves the controlled imposition of external fluid flow patterns onto the vascularized chick chorioallantoic membrane (CAM), allowing us to observe how this impacts the organization of vascular networks. To investigate the concept of SIVS, we conducted superfusion experiments on the intact chick CAM cultured within engineered eggshell system, using phosphate buffered saline (PBS). To capture and analyze the effects of superfusion, we employed a custom-built microscopy setup, enabling us to image both superfused and non-superfused regions within the developing CAM. This study provides valuable insights into the practical application of fluid superfusion within anin vivocontext, shedding light on its significance for understanding tissue development and manipulation in an engineering setting.
Effect of molecular weight of tyramine-modified hyaluronan on polarization state of THP-1 and peripheral blood mononuclear cells-derived macrophages
Authors: Wychowaniec Jacek K. , Bektas Ezgi Irem , Vernengo Andrea J. , Mürner Marcia , Airoldi Marielle , Tipay Paul Sean , Sapudom Jiranuwat , Teo Jeremy , Eglin David , D’Este Matteo
Published: January 2024

The immunomodulatory properties of hyaluronan and its derivatives are key to their use in medicine and tissue engineering. In this work we evaluated the capability of soluble tyramine-modified hyaluronan (THA) of two molecular weights (low Mw=280 kDa and high Mw=1640 kDa) for polarization of THP-1 and peripheral blood mononuclear cells (PBMCs)-derived macrophages (MΦs). We demonstrate the polarization effects of the supplemented THA by flow cytometry and multiplex ELISA for the THP-1 derived MΦs and by semi-automated image analysis from confocal microscopy, immunofluorescent staining utilising CD68 and CD206 surface markers, RT-qPCR gene expression analysis, as well as using the enzyme-linked immunosorbent assay (ELISA) for PBMCs-derived MΦs. Our data indicate that supplementation with LMW THA drives changes in THP-1 derived MΦs towards a pro-inflammatory M1-like phenotype, whereas supplementation with the HMW THA leads to a more mixed profile with some features of both M1 and M2 phenotypes, suggesting either a heterogeneous population or a transitional state. For cells directly sourced from human patients, PMBCs-derived MΦs, results exhibit a higher degree of variability, pointing out a differential regulation of factors including IL-10 and CD206 between the two cell sources. While human primary cells add to the clinical relevance, donor diversity introduces wider variability in the dataset, preventing drawing strong conclusions. Nevertheless, the MΦs profiles observed in THP-1 derived cells for treatments with LMW and HMW THA are generally consistent with what might be expected for the treatment with non-modified hyaluronans of respective molecular weights, confirming the known association holds true for the chemically tyramine-modified hyaluronan. We stipulate that these responses will provide basis for more accurate in vivo representation and translational immunomodulatory guidance for the use of THA-based biomaterials to a wider biomaterials and tissue engineering communities.

Graphical Abstract
Marine BacteriaAlteromonasspp. Require UDP-glucose-4-epimerase for Aggregation and Production of Sticky Exopolymer
Authors: Robertson Jacob M. , Garza Erin A. , Stubbusch Astrid K.M. , Dupont Christopher L. , Hwa Terence , Held Noelle A.
Published: January 2024

The physiology and ecology of particle-associated marine bacteria are of growing interest, but our knowledge of their aggregation behavior and mechanisms controlling their association with particles remains limited. We have found that a particle-associated isolate,Alteromonassp. ALT199 strain 4B03, and the related type-strainA. macleodii27126 both form large (>500 μm) aggregates while growing in rich medium. A non-clumping variant (NCV) of 4B03 spontaneously arose in the lab, and whole genome sequencing revealed a partial deletion in the gene encoding UDP-glucose-4-epimerase (galEΔ308-324). In 27126, a knock-out ofgalE(ΔgalE::kmr) resulted in a loss of aggregation, mimicking the NCV. Microscopic analysis shows that both 4B03 and 27126 rapidly form large aggregates, whereas their respectivegalEmutants remain primarily as single planktonic cells or clusters of a few cells. Strains 4B03 and 27126 also aggregate chitin particles, but theirgalEmutants do not. Alcian Blue staining shows that 4B03 and 27126 produce large transparent exopolymer particles (TEP), but theirgalEmutants are deficient in this regard. This study demonstrates the capabilities of cell-cell aggregation, aggregation of chitin particles, and production of TEP in strains ofAlteromonas, a widespread particle-associated genus of heterotrophic marine bacteria. A genetic requirement forgalEis evident for each of the above capabilities, expanding the known breadth of requirement for this gene in biofilm-related processes.

Importance

Heterotrophic marine bacteria have a central role in the global carbon cycle. Well-known for releasing CO2by decomposition and respiration, they may also contribute to particulate organic matter (POM) aggregation, which can promote CO2sequestration via the formation marine snow. We find that two members of the prevalent particle-associated genusAlteromonascan form aggregates comprising cells alone or cells and chitin particles, indicating their ability to drive POM aggregation. In line with their multivalent aggregation capability, both strains produce TEP, an excreted polysaccharide central to POM aggregation in the ocean. We demonstrate a genetic requirement forgalEin aggregation and large TEP formation, building our mechanistic understanding of these aggregative capabilities. These findings point toward a role for heterotrophic bacteria in POM aggregation in the ocean and support broader efforts to understand bacterial controls on the global carbon cycle based on microbial activities, community structure, and meta-omic profiling.
Detection of naturally acquired, strain-transcending antibodies against rosettingPlasmodium falciparumstrains in humans
Authors: McLean Florence E. , Azasi Yvonne , Sutherland Cameron , Toboh Emmanuel , Ansong Daniel , Agbenyega Tsiri , Awandare Gordon , Rowe J. Alexandra
Published: January 2024

Strain-transcending antibodies against subsets ofP. falciparumblood stage surface antigens could protect children from severe malaria. However, the evidence supporting the existence of such antibodies is incomplete and inconsistent. One subset of surface antigens associated with severe malaria, rosette-mediatingPlasmodium falciparumErythrocyte Membrane Protein one (PfEMP1) variants, cause infected erythrocytes to bind to uninfected erythrocytes to form clusters of cells (rosettes) that contribute to microvascular obstruction and pathology. Here, using flow cytometry of live infected erythrocytes, we tested plasma from 80 individuals living in malaria-endemic regions for IgG recognition of the surface of fourP. falciparumrosetting strains. Broadly-reactive plasma samples were then used in antibody elution experiments in which intact IgG was eluted from the surface of infected erythrocytes and transferred to heterologous rosetting strains to look for strain-transcending antibodies. We found that seroprevalence (percentage of samples that recognised each strain) against allopatric rosetting strains was high in adults (58% - 93%), but lower in children (5%-30%). Strain-transcending antibodies were present in nine out of eleven eluted antibody experiments, with six of these recognising multiple heterologous rosetting parasite strains. One eluate had rosette disrupting activity against heterologous strains, suggesting PfEMP1 as the likely target of the strain-transcending antibodies. Naturally acquired strain-transcending antibodies to rosettingP. falciparumstrains in humans have not been directly demonstrated previously. Their existence suggests that such antibodies could play a role in clinical protection and raises the possibility that conserved epitopes recognised by strain-transcending antibodies could be targeted therapeutically.
A dual histone code specifies the binding of heterochromatin protein Rhino to a subset of piRNA source loci
Authors: Akkouche Abdou , Kneuss Emma , Bornelöv Susanne , Renaud Yoan , Eastwood Evelyn L , van Lopik Jasper , Gueguen Nathalie , Jiang Mingxuan , Creixell Pau , Maupetit-Mehouas Stephanie , Sobieszek Anna , Gui Yifan , Nicholson Benjamin Czech , Brasset Emilie , Hannon Gregory J
Published: January 2024

Animal germ cells deploy a specialized small RNA-based silencing system, called the PIWI-interacting RNA (piRNA) pathway, to prevent unwanted expression of transposable elements and maintain genome integrity. In Drosophila germ cells, the majority of piRNA populations originate from dual-strand piRNA clusters, genomic regions highly enriched in transposable element (TE) fragments, via an elaborate protein machinery centred on the heterochromatin protein 1 homolog, Rhino. Although Rhino binds to peptides carrying trimethylated H3K9 in vitro, it is not fully understood why in vivo only a fraction of H3K9me3-decorated heterochromatin is occupied by Rhino. Recent work revealed that Rhino is recruited to a subset of piRNA clusters by the zinc finger protein Kipferl. Here we identify a Kipferl-independent mode of Rhino targeting that, in addition to the previously established role of H3K9me3, also depends on the histone H3 lysine 27 methyltransferase Enhancer of Zeste. At Kipferl-independent sites, we find that Rhino, through its chromodomain, specifically binds to loci marked by both H3K9me3 and H3K27me3. Although the exact mechanism of how Rhino binding is influenced by dual histone modifications remains unclear from a structural and biochemical perspective, our work suggests that combinatorial modifications can play a crucial role in influencing the specificity of chromatin-binding protein interactions. These findings provide an enhanced understanding of the multifaceted mechanisms by which Rhino targets piRNA source loci highlighting the sophisticated epigenetic landscape governing TE silencing in Drosophila germ cells. Our work further reveals a role for dual histone modifications defining the binding specificity of a key chromatin protein.
Murine norovirus mutants adapted to replicate in human cells reveal a post-entry restriction
Authors: Budicini Melissa R. , Rodriguez-Irizarry Valerie J. , Maples Robert W. , Pfeiffer Julie K.
Published: January 2024

RNA viruses lack proofreading in their RNA polymerases and therefore exist as genetically diverse populations. By exposing these diverse viral populations to selective pressures, viruses with mutations that confer fitness advantages can be enriched. To examine factors important for viral tropism and host restriction, we passaged murine norovirus (MNV) in a human cell line, HeLa cells, to select for mutant viruses with increased fitness in non-murine cells. A major determinant of host range is expression of the MNV receptor CD300lf on mouse cells, but additional host factors may limit MNV replication in human cells. We found that viruses passaged six times in HeLa cells had enhanced replication compared with the parental virus. The passaged viruses had several mutations throughout the viral genome, which were primarily located in the viral non-structural coding regions. While viral attachment was not altered for the passaged viruses, their replication was higher than the parental virus when entry was bypassed, suggesting the mutant viruses overcame a post-entry block in human cells. Three mutations in the viral NS1 protein were sufficient for enhanced post-entry replication in human cells. We found that the human cell-adapted MNV variants had reduced fitness in mouse BV2 cells. Although the mutant viruses had increased fitness in HeLa cells, they did not have increased fitness in mice. Overall, this work suggests that MNV tropism is not only determined by the presence of the viral receptor but also post-entry factors.

Importance

Viruses infect specific species and cell types, which is dictated by expression of host factors required for viral entry as well as downstream replication steps. Murine norovirus (MNV) infects mouse cells, but not human cells. However, human cells expressing the murine CD300lf receptor support MNV replication, suggesting receptor expression is a major determinant of MNV tropism. To determine whether other factors influence MNV tropism, we selected for variants with enhanced replication in human cells. We identified mutations that enhance MNV replication in human cells and demonstrated that these mutations enhance infection at a post-entry replication step. Therefore, MNV infection of human cells is restricted at both entry and post-entry stages. These results shed new light on factors that influence viral tropism and host range.
Eliminating the Missing Cone Challenge through Innovative Approaches
Authors: Gillman Cody , Bu Guanhong , Danelius Emma , Hattne Johan , Nannenga Brent , Gonen Tamir
Published: January 2024

Microcrystal electron diffraction (MicroED) has emerged as a powerful technique for unraveling molecular structures from microcrystals too small for X-ray diffraction. However, a significant hurdle arises with plate-like crystals that consistently orient themselves flat on the electron microscopy grid. If, as is typically the case, the normal of the plate correlates with the axes of the crystal lattice, the crystal orientations accessible for measurement are restricted because the grid cannot be arbitrarily rotated. This limits the information that can be acquired, resulting in a missing cone of information. We recently introduced a novel crystallization strategy called suspended drop crystallization and proposed that this method could effectively address the challenge of preferred crystal orientation. Here we demonstrate the success of the suspended drop crystallization approach in eliminating the missing cone in two samples that crystallize as thin plates: bovine liver catalase and the COVID-19 main protease (Mpro). This innovative solution proves indispensable for crystals exhibiting preferred orientations, unlocking new possibilities for structure determination by MicroED.
PREDICTING GENE DISEASE ASSOCIATIONS WITH KNOWLEDGE GRAPH EMBEDDINGS FOR DISEASES WITH CURTAILED INFORMATION
Authors: Gualdi Francesco , Oliva Baldomero , Piñero Janet
Published: January 2024

Knowledge graph embeddings (KGE) are a powerful technique used in the biological domain to represent biological knowledge in a low dimensional space. However, a deep understanding of these methods is still missing, and in particular the limitations for diseases with reduced information on gene-disease associations. In this contribution, we built a knowledge graph (KG) by integrating heterogeneous biomedical data and generated KGEs by implementing state-of-the-art methods, and two novel algorithms: DLemb and BioKG2Vec. Extensive testing of the embeddings with unsupervised clustering and supervised methods showed that our novel approaches outperform existing algorithms in both scenarios. Our results indicate that data preprocessing and integration influence the quality of the predictions and that the embeddings efficiently encodes biological information when compared to a null model. Finally, we employed KGE to predict genes associated with Intervertebral disc degeneration (IDD) and showed that functions relevant to the disease are enriched in the genes prioritized from the model

GRAPHICAL ABSTRACT
Anti-CD20 antibodies in relapsing multiple sclerosis: Protocol for a systematic review and network meta-analysis
Authors: Navarro Cristian Eduardo , Cárdenas-Robledo Simón , Macea Jaiver , Ortíz-Cano Natalia A , Florez Ivan D
Published: January 2024

Background

Multiple sclerosis is a chronic disease of the central nervous system characterized by autoimmune demyelination. Various immunomodulatory medications are available for its treatment, among which anti-CD20 monoclonal antibodies have demonstrated superior efficacy compared to other disease-modifying therapies. However, there is a lack of direct comparison between the four available anti-CD20 monoclonal antibodies. Therefore, this study aims to systematically assess the relative efficacy and safety of anti-CD20 monoclonal antibodies for treating relapsing multiple sclerosis.

Materials and Methods

We will conduct a systematic review of phase IIb and phase III clinical trials of anti-CD20 monoclonal antibodies for the treatment of relapsing multiple sclerosis, following the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines. A comprehensive review of the Cochrane Central Register of Controlled Trials; MEDLINE; Embase; ClinicalTrials; International Clinical Trials Registry Platform; OpenGray; and MedRxiv will be performed. Two independent reviewers will select titles, abstracts, and eligible full texts to execute the data extraction. The risk of bias will be assessed with the Cochrane RoB 2 tool. Data on pre-specified outcomes will be analyzed for the selected articles using a random-effects network meta-analysis with a frequentist framework. Summary statistics, along with 95% confidence intervals will be presented, and the effectiveness and safety of each intervention will be ranked using the surface under the cumulative ranking curve. A missing data and a sensitivity analysis will be conducted. We will use the GRADE approach to assess the certainty of the direct, indirect, and network estimate for all outcomes.

Results and Conclusion

The results will provide evidence of the relative efficacy and safety of anti-CD20 monoclonal antibodies for the treatment of relapsing multiple sclerosis.

Systematic review registration

PROSPERO registration number CRD42023437996
Using a health equity lens to measure patient experiences of care in diverse healthcare settings
Authors: Browne Annette J. , Varcoe Colleen , Ford-Gilboe Marilyn , Wathen C. Nadine , Wilson Erin , Bungay Vicky , Perrin Nancy
Published: January 2024

People who are structurally disadvantaged and marginalized often report poor health care experiences due to intersecting forms of stigma and discrimination. There are many measures of patient experiences of care, however, few are designed to measure equity-oriented care. In alignment with ongoing calls to integrate actions in support of health equity, we report on the development and testing of patient experiences of care measures that explicitly use a health equity and intersectional lens. Our analysis focuses on two different equity-oriented health care scales. The first was piloted in a primary health care setting, where patients have an ongoing relationship with providers over time. The second was piloted in an emergency department, where care is provided on an episodic basis. Item Response Theory was used to develop the scales and evaluate their psychometric properties. The primary health care scale, tested with a cohort of 567 patients, showed that providing more equity-oriented health care predicted improvements in important patient self-report health outcomes over time. The episodic scale, tested in an emergency department setting with 284 patients, showed evidence of concurrent validity, based on a high correlation with quality of care. Both scales are brief, easy-to-administer self-report measures that can support organizations to monitor quality of care using an equity lens. The availability of both scales enhances the possibility of measuring equity-oriented health care in diverse contexts. Both scales can shed light on experiences of care using an intersectional lens and equity-oriented lens, providing a nuanced understanding of quality of care.
Self-perceived competence and its determinants among pre-intern (PRINT) doctors in Uganda
Authors: Ssewante Nelson , Wekha Godfrey , Nalunkuma Racheal , Sentongo Lawrence Katumba , Sanyu Bereta , Namusoke Moureen , Nkwanga Ayub , Ahabwe Rachel , Nantagya Vanessa Nalwoga , Kalembe Sharon Esther , Nampeera Catherine , Musoke Phillip , Byakika-Kibwika Pauline
Published: January 2024

Introduction

Uganda still survives way below the recommended doctor-patient ratio. This problem could be solved by increasing the number of doctors produced in the country annually. Attempts at this are ongoing, however, this is challenged by the absence of quality assurance programs amidst lack of a universal medical curriculum. With inadequate supervision and limited resources in health facilities, transitioning from students’ life to clinical practice is perhaps the most challenging time for an intern doctor. We used the domains of competencies provided by the General Medical Council to assess levels of self-perceived competence and its determinants among pre-intern doctors (PRINTs) in Uganda.

Methods

An online cross-sectional study was conducted using a quantitative questionnaire distributed to confirmed pre-interns in Uganda. Self-perceived competence was determined by 4 Likert scale questions and participants were dichotomized into competent and incompetent using a standardized Bloom’s cutoff criterion. Determinants of self-perceived competence were determined by the ANOVA test.

Results

We obtained 142 entries. Of these, 68.3% were males; median age was 26 years (range: 22-49). Majority of the participants (78.9%) had no prior medical-related training and only a third (34.5%) had previous work experience. Overall scores were poor and very few participants were confident they attained a satisfactory level of competence through their medical training. Participants reported more competence in basic procedural skills (Mean score: 19.8±3.2/21), followed by Knowledge (Mean score:12.4±3.1/15), with surgical (Mean score:11.5±3.5/18) and Emergency skills (Mean score: 12.5±4.4/21) scoring least. Participants with previous work experience were more likely to report higher competence scores than their counterparts (91.7 vs 84.9, p=0.039).

Conclusion

The study shows that majority of PRINTs feel deficient in knowledge and skills to start clinical practice, with less competence in surgical skills and emergency care.

There is need to review the training curricula to ensure adequate clinical exposure experiences for a smooth transition to clinical practice.
Global research trends in postoperative ileus from 2011 to 2023: A Scientometric study
Authors: Zhou Yan , Yin Zi-Han , Sun Ming-Sheng , Wang Yang-Yang , Yang Chen , Li Shu-Hao , Liang Fan-Rong , Liu Fang
Published: January 2024

Objective

To explore the current status, trends, and frontiers of POI research from 2011 to the present based on bibliometric analysis.

Methods

Publications published on POI research from 2011 to 2023 were retrieved on June 1, 2023, from the Web of Science Core Collection. CiteSpace 6.2.R2 and VOSviewer were used to conduct bibliometric visualization.

Results

In total, 778 POI records published from 2011 to 2023 were retrieved. Over the past few decades, the annual cumulative number of related articles has linearly increased, with China and the United States of America (USA) contributing prominently. All the publications were from 59 countries and territories. China and the University of Bonn were the top contributing country and institution, respectively.Neurogastroenterology & Motilitywas the most prolific journal. The Journal ofGastrointestinal Surgeryhad the highest number of citations. Wehner Sven was the most productive author. Burst keywords (e.g., colon, prolonged ileus, acupuncture, paralytic ileus, pathophysiology, rectal cancer, gastrointestinal function, risk) and a series of reference citation bursts provided evidence for the research frontiers in recent years.

Conclusions

This study demonstrates trends in the published literature on POI and provides new insights for researchers. It emphasizes the importance of multidisciplinary cooperation in the development of this field.
Computational investigation of BMAA and its carbamate adducts as potential GluR2 modulators
Authors: Diakogiannaki Isidora , Papadourakis Michail , Spyridaki Vasileia , Cournia Zoe , Koutselos Andreas
Published: January 2024

Beta-N-methylamino-L-alanine (BMAA) is a potential neurotoxic non-protein amino acid, which can reach the human body through the food chain. When BMAA interacts with bicarbonate in the human body, carbamate adducts are produced, which share high structural similarity with the neurotransmitter glutamate. It is believed that BMAA and its L-carbamate adducts bind in the glutamate binding site of ionotropic glutamate receptor 2 (GluR2). Chronic exposure to BMAA and its adducts could cause neurological illness such as neurodegenerative diseases. However, the mechanism of BMAA action and its carbamate adducts bound to GluR2 has not been yet elucidated. Here, we investigate the binding modes and the affinity of BMAA and its carbamate adducts to GluR2 in comparison to the natural agonist, glutamate, to understand whether these can act as GluR2 agonists. Initially, we perform Molecular Dynamics (MD) simulations of BMAA and its carbamate adducts bound to GluR2 to examine the stability of the ligands in the S1/S2 ligand-binding domain of the receptor. In addition, we perform alchemical free energy calculations to compute the difference in the free energy of binding of the beta-carbamate adduct of BMAA to GluR2 compared to glutamate. Our findings indicate that carbamate adducts of BMAA and glutamate remain stable in the binding site of the GluR2 compared to BMAA. Additionally, alchemical free energy results reveal that glutamate and the beta-carbamate adduct of BMAA have comparable binding affinity in the GluR2. These results provide a rationale that BMAA carbamate adducts may be in fact the modulators of GluR2 and not BMAA itself.
Mitochondrial metabolism sustains CD8+T cell migration for an efficient infiltration into solid tumors
Authors: Simula Luca , Fumagalli Mattia , Vimeux Lene , Rajnpreht Irena , Icard Philippe , An Dongjie , Pendino Frédéric , Damotte Diane , Lupo-Mansuet Audrey , Alifano Marco , Alves-Guerra Marie-Clotilde , Donnadieu Emmanuel
Published: January 2024

The ability of CD8+T cells to infiltrate solid tumors and reach cancer cells is associated with improved patient survival and responses to immunotherapy. Thus, identifying the factors controlling T cell migration in tumors is critical, so that strategies to intervene on these targets can be developed. Although interstitial motility is a highly energy-demanding process, the metabolic requirements of CD8+T cells migrating in a 3D environment remain unclear. Here, we demonstrate that the tricarboxylic acid (TCA) cycle is the main metabolic pathway sustaining human CD8+T cell motility in 3D collagen gels and tumor slices while glycolysis plays a much minor role. Using pharmacological and genetic approaches, we report that CD8+T cell migration depends on the mitochondrial oxidation of glucose and glutamine, but not fatty acids, and both ATP and ROS produced by mitochondria are required for T cells to migrate. Pharmacological interventions to increase mitochondrial activity improve CD8+T cells intra-tumoral migration and CAR T cell recruitment into tumor islets leading to better control of tumor growth in human xenograft models. Our study highlights the rationale of targeting mitochondrial metabolism to enhance the migration and antitumor efficacy of CAR T cells in treating solid tumors.
Individualized functional localization of the language and multiple demand network in chronic post-stroke aphasia
Authors: Clercq Pieter De , Gonsalves Alicia Ronnie , Gerrits Robin , Vandermosten Maaike
Published: January 2024

Recent research found a distinct dissociation between brain regions supporting domain-general cognitive processes and regions supporting core language functions. The question of whether individuals with post-stroke aphasia (IWA) exhibit a comparable dissociation remains debated, particularly as previous studies overlooked individual variability in functional network organization and aphasia heterogeneity. To address this gap, we employed an individualized functional localization approach to test the involvement of the domain-general multiple demand (MD) network during language processing in chronic aphasia.

We collected functional MRI data in 15 IWA and 13 age-matched controls. Participants performed a spatial working memory task, triggering MD network activation, as well as a listening and reading task, triggering language network activation. We compared both groups individualized activation patterns and investigated the link with aphasia severity. Involvement of the MD network during language processing was examined by investigating language task activity within subject-specific regions that are active during the MD task.

The language and MD network each generalized well across different task modalities, but exhibited robust spatial dissociation from each other in both groups. Moreover, there was no evidence of MD network activation during language processing in either group. Additionally, the language network showed weaker activation in IWA compared to controls in left-hemispheric brain regions, with higher activation values in the left correlating with improved language performance in IWA.

In conclusion, our findings suggest that the MD network does not contribute to passive, receptive language functions in chronic aphasia or healthy older adults. Instead, our results align with previous research proposing that normalized left-hemispheric language activity supports language performance in chronic aphasia.
Body-wide genetic deficiency of poly(ADP-ribose) polymerase 14 sensitizes mice to colitis
Authors: Vedantham Madhukar , Polari Lauri , Poosakkannu Anbu , Pinto Rita G. , Sakari Moona , Laine Jukka , Sipilä Petra , Määttä Jorma , Gerke Heidi , Rissanen Tiia , Rantakari Pia , Toivola Diana M. , Pulliainen Arto T.
Published: January 2024

Inflammatory bowel disease (IBD) is a debilitating and relapsing chronic disease of the gastrointestinal tract affecting millions of people. Here, we investigated the expression and functions of poly (ADP-ribose) polymerase 14 (Parp14), an important regulatory protein in immune cells, using a biobank IBD patient cohort as well as two mouse models of colitis, i.e., the IBD-mimicking oral dextran sulfate sodium (DSS) exposure model, and the oralSalmonellaexposure model. Parp14 was expressed in the human colon, by cells in the lamina propria, but, in particular, by the epithelial cells with a typical granular staining pattern in the cytosol. The same Parp14 staining pattern was evidenced in both colitis models. Body-wide genetic deficiency of Parp14 in C57BL/6N background sensitized mice to DSS colitis. The Parp14-deficient mice displayed increased rectal bleeding as well as stronger epithelial erosion, Goblet cell loss and immune cell infiltration. The absence of Parp14 did not affect the mouse colon bacterial microbiota based on PacBio long read sequencing. Also, the colon leukocyte populations of Parp14-deficient mice were normal based on flow cytometry. In contrast, we witnessed an altered transcriptional signature in Parp14-deficient mice with bulk tissue RNA-Seq. Gene Ontology (GO)-based classification of differentially expressed genes demonstrated that the colon transcriptional signature of Parp14-deficient mice was dominated by abnormalities in inflammation and infection responses both prior and after the 1-week DSS exposure. Overall, the data indicate that Parp14 has an important role in the maintenance of colon epithelial barrier integrity. The prognostic and predictive biomarker potential of Parp14 in IBD merits further investigation.
Modelling biological and resource fluxes in fluvial meta-ecosystems
Authors: Talluto Matthew , del Campo Rubén , Estévez Edurne , Fuß Thomas , Thuile Bistarelli Lukas , Martini Jan , Singer Gabriel A.
Published: January 2024

Meta-ecosystem theory predicts that cross-ecosystem flows of energy, nutrients, and organisms have important implications for local community assembly and ecosystem functioning. Developments in the theory also have the potential to enhance our under-standing of biodiversity-ecosystem functioning relationships. Meta-ecosystem theory is particularly well-suited to the study of rivers, because water flow forces strong spatial interrelationships among connected ecosystems. However, models that address flows of both resources and organisms and explicitly link both are lacking. We present a model and associated R-package for cross-ecosystem flows of both resources and organisms that can be used to predict their distribution in river networks, as well as meta-ecosystem functioning. The model incorporates feedbacks between these two crucial components. To illustrate the capabilities of the model, we present an in silico experiment and analysis, as well as providing sample code.
Pervasive sublethal effects of agrochemicals as contributing factors to insect decline
Authors: Gandara Lautaro , Jacoby Richard , Laurent François , Spatuzzi Matteo , Vlachopoulos Nikolaos , Borst Noa O , Ekmen Gülina , Potel Clement M , Garrido-Rodriguez Martin , Böhmert Antonia L , Misunou Natalia , Bartmanski Bartosz J , Li Xueying C , Kutra Dominik , Hériché Jean-Karim , Tischer Christian , Zimmermann-Kogadeeva Maria , Ingham Victoria , Savitski Mikhail M , Masson Jean-Baptiste , Zimmermann Michael , Crocker Justin
Published: January 2024

Insect biomass is declining across the globe at an alarming rate. Climate change and the widespread use of pesticides have been hypothesized as two underlying drivers. However, the lack of systematic experimental studies across chemicals and species limits our causal understanding of this problem. Here, we employed a chemical library encompassing 1024 different molecules—including insecticides, herbicides, fungicides, and plant growth inhibitors —to investigate how insect populations are affected by varying concentrations of pesticides, focusing on sublethal doses. Using a controlled laboratory pipeline forDrosophila melanogaster, we found that 57% of these chemicals affect the behavior of larvae at sublethal concentrations, and an even higher proportion compromises long-term survivability after acute exposure. Consistent with these results, we observed that exposure to chemicals at doses orders of magnitude below lethality induced widespread phosphorylation changes across the larval proteome. The effects of agrochemicals were amplified when the ambient temperature was increased by four degrees. We also tested the synergistic effects of multiple chemicals at doses found widely in nature and observed fitness-reducing changes in larval developmental time, behavior, and reproduction. Finally, we expanded our investigation to additional fly species, mosquitos, and butterflies and detected similar behavioral alterations triggered by pesticides at sublethal concentrations. Our results provide experimental evidence that strongly suggests sublethal doses of agrochemicals coupled with changes in environmental temperatures are contributing to the global decline in insect populations. We anticipate that our assays can contribute to improving chemical safety assessment, better protect the environment, secure food supplies, and safeguard animal and human health, as well as understand our rapidly changing world.
Joint-specific rheumatoid arthritis fibroblast-like synoviocyte regulation identified by integration of chromatin access and transcriptional activity
Authors: Choi Eunice , Machado Camilla R. L. , Okano Takaichi , Boyle David , Wang Wei , Firestein Gary S.
Published: January 2024

The mechanisms responsible for the distribution and severity of joint involvement in rheumatoid arthritis (RA) are not known. To explore whether site-specific FLS biology might be associated with location-specific synovitis and explain the predilection for hand (wrist/metacarpal phalangeal joints) involvement in RA, we generated transcriptomic and chromatin accessibility data from FLS to identify the transcription factors (TFs) and pathways. Networks were constructed by integration of chromatin accessibility and gene expression data. Analysis revealed joint-specific patterns of FLS phenotype, with proliferative, migratory, proinflammatory, and matrix-degrading characteristics observed in resting FLS derived from the hand joints compared with hip or knee. TNF-stimulation amplified these differences, with greater enrichment of proinflammatory and proliferative genes in hand FLS compared with hip and knee FLS. Hand FLS also had the greatest expression of markers associated with an ‘activated’ state relative to the ‘resting’ state, with the greatest cytokine and MMP expression in TNF-stimulated hand FLS. Predicted differences in proliferation and migration were biologically validated with hand FLS exhibiting greater migration and cell growth than hip or knee FLS. Distinctive joint-specific FLS biology associated with a more aggressive inflammatory response might contribute to the distribution and severity of joint involvement in RA.
SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data
Authors: Yu Hongyu , Wu Daiqing , Shen Guning , Hu Ming , Li Yun
Published: January 2024

Chromatin spatial organization plays a crucial role in gene regulation. Recently developed and prospering multiplexed DNA FISH technologies enable direct visualization of chromatin conformation in nucleus. However, incomplete data caused by limited detection efficiency can substantially complicate and impair downstream analysis. Here, we present SnapFISH-IMPUTE that imputes missing values in multiplexed DNA FISH data. Analysis on multiple published datasets shows that the proposed method preserves the distribution of pairwise distances between imaging loci, and the imputed chromatin conformations are indistinguishable from the observed conformations. Additionally, imputation greatly improves downstream analyses such as identifying enhancer-promoter loops and clustering cells into distinct cell types. SnapFISH-IMPUTE is freely available athttps://github.com/hyuyu104/SnapFISH-IMPUTE.
Identification, characterization and transcriptional analysis of the long non-coding RNA landscape in the familyCucurbitaceae
Authors: Villalba-Bermell Pascual , Marquez-Molins Joan , Gomez Gustavo
Published: January 2024

Long non-coding RNAs (lncRNAs) constitute a fascinating class of regulatory RNAs, widely distributed in eukaryotes. In plants, they exhibit features such as tissue-specific expression, spatiotemporal regulation, and responsiveness to stress, suggesting their involvement in specific biological processes. Although an increasing number of studies support the regulatory role of lncRNAs in model plants, our knowledge about these transcripts in relevant crops is limited. In this study we employ a custom pipeline on a dataset of over 1,000 RNA-seq studies across nine representative species of the familyCucurbitaceaeto predict 91,209 non-redundant lncRNAs. LncRNAs were predicted according to three confidence levels and classified into intergenic, natural antisense, intronic, and sense overlapping. Predicted lncRNAs have lower expression levels compared to protein-coding genes but a more specific behavior when considering plant tissues, developmental stages, and response to stress, emphasizing their potential roles in regulating various aspects of plant-biology. The evolutionary analysis indicates higher positional conservation than sequence conservation, which may be linked to the presence of conserved modular motifs within syntenic lncRNAs. In short, this research provides a comprehensive map of lncRNAs in the agriculturally relevantCucurbitaceaefamily, offering a valuable resource for future investigations in crop improvement.
Fine-Grained Forecasting of COVID-19 Trends at the County Level in the United States
Authors: Song Tzu-Hsi , Clemente Leonardo , Pan Xiang , Jang Junbong , Santillana Mauricio , Lee Kwonmoo
Published: January 2024

The novel coronavirus (COVID-19) pandemic, first identified in Wuhan China in December 2019, has profoundly impacted various aspects of daily life, society, healthcare systems, and global health policies. There have been more than half a billion human infections and more than 6 million deaths globally attributable to COVID-19. Although treatments and vaccines to protect against COVID-19 are now available, people continue being hospitalized and dying due to COVID-19 infections. Real-time surveillance of population-level infections, hospitalizations, and deaths has helped public health officials better allocate healthcare resources and deploy mitigation strategies. However, producing reliable, real-time, short-term disease activity forecasts (one or two weeks into the future) remains a practical challenge. The recent emergence of robust time-series forecasting methodologies based on deep learning approaches has led to clear improvements in multiple research fields. We propose a recurrent neural network model named Fine-Grained Infection Forecast Network (FIGI-Net), which utilizes a stacked bidirectional LSTM structure designed to leverage fine-grained county-level data, to produce daily forecasts of COVID-19 infection trends up to two weeks in advance. We show that FIGI-Net improves existing COVID-19 forecasting approaches and delivers accurate county-level COVID-19 disease estimates. Specifically, FIGI-Net is capable of anticipating upcoming sudden changes in disease trends such as the onset of a new outbreak or the peak of an ongoing outbreak, a skill that multiple existing state-of-the-art models fail to achieve. This improved performance is observed across locations and periods. Our enhanced forecasting methodologies may help protect human populations against future disease outbreaks.
A putative hepatitis B virus sequence motif associated with hepatocellular carcinoma in South African adults
Authors: Maponga Tongai G , McNaughton Anna L , Campbell Cori , de Cesare Mariateresa , Mokaya Jolynne , Lumley Sheila F , Bonsall David , Ip Camilla LC , Chai Haiting , Van Rensburg Christo , Glashoff Richard H , Waddilove Elizabeth , Preiser Wolfgang , Blackard Jason T , Ansari M Azim , Kramvis Anna , Andersson Monique I , Matthews Philippa C
Published: January 2024

Aim

Chronic hepatitis B virus (HBV) infection is a major risk factor for hepatocellular carcinoma (HCC) particularly in African populations, in whom malignancy frequently presents at an advanced stage with poor outcomes. We derived HBV whole genome sequences (WGS) from individuals with HCC and compared them to sequences from individuals without HCC.Methods:We identified adults with HBV infection, with and without complicating HCC, in Cape Town, South Africa and utilized pan-genotypic probe-based enrichment followed by Illumina sequencing to derive HBV WGS.

Results

Compared to the non-HCC group, HCC patients were more likely to be male (p < 0.0001), older (p = 0.01), HIV-negative (p = 0.006), and to have higher HBV viral loads (p < 0.0001). Among 19 HCC and 12 non-HCC patients, genotype A dominated (74%), of which 96% were subtype A1. PreS2 deletions (Δ38–55) were enriched in HBV sequences from HCC patients (n = 7). The sequence motif most strongly associated with HCC comprised either deletion or polymorphism at site T53 in PreS2 – collectively coined ‘non-T53’ – together with a basal core promoter (BCP) mutation G1764A (AUROC 0.79).

Conclusions

In this setting, HBV sequence polymorphisms and deletions are associated with HCC, and ‘non-T53 + G1764A’ represents a putative signature motif for HCC. Additional investigations are needed to disaggregate the impact of age, sex and HIV status, to ascertain the extent to which viral polymorphisms contribute to oncogenesis, and to determine whether HBV sequence is a useful biomarker for risk stratification.