bluuebunny/crossref_metadata_2025_split huggingface dataset:
NEUROG2regulates a human-specific neurodevelopmental gene regulatory program
Authors: Chinchalongporn Vorapin , Vasan Lakshmy , Saleh Fermisk , Zinyk Dawn , Ghazale Hussein , Oproescu Ana-Maria , Patel Shruti , Rozak Matthew , Amemiya Yutaka , Han Sisu , Moffat Alexandra , Black Sandra E , McLaurin JoAnne , Near Jamie , Seth Arun , Goubran Maged , Reiner Orly , Okawa Satoshi , Schuurmans Carol 
Published: January 2024

ABSTRACTUnique hallmarks of human neocortical development include slower rates of neurogenesis and the establishment of an extracellular matrix-rich, outer-subventricular zone that supports basal neural progenitor cell expansion. How gene regulatory networks have evolved to support these human-specific neurodevelopmental features is poorly understood. Mining single cell data from cerebral organoids and human fetal cortices, we found thatNEUROG2expression is enriched in basal neural progenitor cells. To identify and purifyNEUROG2-expressing cells and trace their short-term lineage, we engineered twoNEUROG2-mCherryknock-in human embryonic stem cell lines to produce cerebral organoids. Transcriptomic profiling of mCherry-high organoid cells revealed elevated expression ofPPP1R17, associated with a fast-evolving human-accelerated regulatory region, oligodendrocyte precursor cell and extracellular matrix-associated gene transcripts. Conversely, only neurogenic gene transcripts were enriched in mCherry-high cortical cells fromNeurog2:mCherryknock-in mice. Finally, we show thatNeurog2is sufficient to inducePpp1r17, which slows human neural progenitor cell division, andCol13a1, an extracellular matrix gene, in P19 cells.NEUROG2thus regulates a human neurodevelopmental gene regulatory program implicated in supporting a pro-proliferative basal progenitor cell niche and tempering the neurogenic pace.SUMMARY STATEMENTTranscriptomic analyses ofNEUROG2-mCherryknock-in human embryonic stem cell-derived cerebral organoids reveal a link betweenNEUROG2and extracellular matrix remodeling during human cortical development.
Trans2express – de novo transcriptome assembly pipeline optimized for gene expression analysis
Authors: Kasianova Aleksandra M. , Penin Aleksey A. , Schelkunov Mikhail I. , Kasianov Artem S. , Logacheva Maria D. , Klepikova Anna V. 
Published: January 2024

AbstractBackgroundAs genomes of many eukaryotic species, especially plants, are large and complex, theirde novosequencing and assembly is still a difficult task despite progress in sequencing technologies. An alternative to genome assembly is the assembly of transcriptome, the set of RNA products of the expressed genes. While a bunch ofde novotranscriptome assemblers exists, the challenges of transcriptomes (the existence of isoforms, the uneven expression levels across genes) complicates the generation of high-quality assemblies suitable for downstream analyses.ResultsWe developed Trans2express – a web-based tool and a pipeline ofde novohybrid transcriptome assembly and postprocessing based on rnaSPAdes with a set of subsequent filtrations. The pipeline was tested onArabidopsis thalianacDNA sequencing data obtained using Illumina and Oxford Nanopore Technologies platforms. The comparison of structural characteristics of the transcriptome assembly with referenceArabidopsisgenome revealed the high quality of assembled transcriptome with 86.1% ofArabidopsisexpressed genes assembled as a single contig. We tested the applicability of the transcriptome assembly for gene expression analysis and showed high congruence of gene expression levels and sets of differentially expressed genes between analyses based on genome and based on the transcriptome assembly.ConclusionsWe present Trans2express – a protocol forde novohybrid transcriptome assembly aimed at recovering of a single transcript per gene. We expect this protocol to promote the characterization of transcriptomes and gene expression analysis in non-model plants and web-based tool to be of use to a wide range of plant biologists.
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

AbstractCyanobacteria 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 statementCellular 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

ABSTRACTEstimating 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

AbstractThe 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

AbstractThe 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

AbstractThe 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.ImportanceHeterotrophic 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

AbstractStrain-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.
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

AbstractRNA 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.ImportanceViruses 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

ABSTRACTMicrocrystal 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

ABSTRACTKnowledge 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 modelGRAPHICAL 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

AbstractBackgroundMultiple 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 MethodsWe 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 ConclusionThe results will provide evidence of the relative efficacy and safety of anti-CD20 monoclonal antibodies for the treatment of relapsing multiple sclerosis.Systematic review registrationPROSPERO registration number CRD42023437996