bluuebunny/crossref_metadata_2025_split huggingface dataset:
BinBencher: Fast, flexible and meaningful benchmarking suite for metagenomic binning
Authors: Nissen Jakob Nybo , Lindéz Pau Piera , Rasmussen Simon 
Published: May 2024

AbstractNew methods for metagenomic binning are typically evaluated using benchmarking software, and become tuned to maximize whatever criterion is measured by the benchmark. Subtleties in benchmarking procedures can cause misleading evaluations, derailing method development. Differences between procedures used to evaluate binning tools make them hard to compare, which slows progress in the field. We introduce BinBencher, a free software suite for benchmarking, and show how BinBencher produces evaluations that are more biologically meaningful than alternative benchmarking approaches.
ELONGATED HYPOCOTYL 5 (HY5) and POPEYE (PYE) Regulate Intercellular Iron Transport in Plants
Authors: Mankotia Samriti , Dubey Abhishek , Jakhar Pooja , Satbhai Santosh B. 
Published: May 2024

ABSTRACTPlants maintain iron (Fe) homeostasis under varying environmental conditions by balancing processes such as Fe uptake, transport, and storage. In Arabidopsis, POPEYE (PYE), a basic helix-loop-helix (bHLH) transcription factor (TF), has been shown to play a crucial role in regulating this balance. In recent years, the mechanisms regulating Fe uptake have been well established but the upstream transcriptional regulators of Fe transport and storage are still poorly understood. In this study, we report that ELONGATED HYPOCOTYL5 (HY5), a basic leucine zipper (bZIP) TF which has recently been shown to play a crucial role in Fe homeostasis, interacts with PYE. Molecular, genetic and biochemical approaches revealed that PYE and HY5 have overlapping as well as some distinct roles in regulation of Fe deficiency response. We found that HY5 and PYE both act as a repressor of Fe transport genes such asYSL3, FRD3 NPF5.9, YSL2, NAS4,andOPT3. HY5 was found to directly bind on the promoter of these genes and regulate intercellular Fe transport. Further analysis revealed that HY5 and PYE directly interact at the same region onPYEandNAS4promoter. Overall, this study revealed that HY5 regulates Fe homeostasis by physically interacting with PYE as well as independently.
Communicating mass spectrometry quality information in mzQC with Python, R, and Java
Authors: Bielow Chris , Hoffmann Nils , Jimenez-Morales David , Van Den Bossche Tim , Vizcaíno Juan Antonio , Tabb David L. , Bittremieux Wout , Walzer Mathias 
Published: May 2024

AbstractMass spectrometry is a powerful technique for analyzing molecules in complex biological samples. However, inter- and intra-laboratory variability and bias can affect the data due to various factors, including sample handling and preparation, instrument calibration and performance, and data acquisition and processing. To address this issue, the Quality Control (QC) working group of the Human Proteome Organization’s Proteomics Standards Initiative has established the standard mzQC file format for reporting and exchanging information relating to data quality. mzQC is based on the JavaScript Object Notation (JSON) format and provides a lightweight yet versatile file format that can be easily implemented in software. Here, we present open-source software libraries to process mzQC data in three programming languages: Python, using pymzqc; R, using rmzqc; and Java, using jmzqc. The libraries follow a common data model and provide shared functionality to operate on mzQC files, including the (de)serialization and validation of mzQC files. We demonstrate use of the software libraries for extracting, analyzing, and visualizing QC metrics from different sources and show how these libraries can be integrated with each other, with existing software tools, and in automated workflows for the QC of mass spectrometry data. All software libraries are available as open source under the MS-Quality-Hub organization on GitHub (https://github.com/MS-Quality-Hub).
The Mycobacterium lipid transporter MmpL3 is dimeric in detergent solution, SMALPs and reconstituted nanodiscs
Authors: Cioccolo Sara , Barritt Joseph D. , Pollock Naomi , Hall Zoe , Babuta Julia , Sridhar Pooja , Just Alicia , Morgner Nina , Dafforn Tim , Gould Ian , Byrne Bernadette 
Published: May 2024

AbstractThe mycobacterial membrane protein large 3 (MmpL3) transports key precursor lipids to the outer membrane of Mycobacterium species. Multiple structures of MmpL3 from bothM. tuberculosisandM. smegmatisin various conformational states indicate that the protein is both structurally and functionally monomeric. However, most other resistance, nodulation and cell division (RND) transporters structurally characterised to date are either dimeric or trimeric. Here we present an in depth biophysical and computational analysis revealing that MmpL3 fromM. smegmatisexists as a dimer in a variety of membrane mimetic systems (SMALPs, detergent-based solution and nanodiscs). Sucrose gradient separation of MmpL3 populations fromM. smegmatis,reconstituted into nanodiscs, identified monomeric and dimeric populations of the protein using laser induced liquid bead ion desorption (LILBID), a native mass spectrometry technique. Preliminary cryo-EM analysis confirmed that MmpL3 forms physiological dimers. Untargeted lipidomics experiments on membrane protein co-purified lipids revealed PE and PG lipid classes were predominant. Molecular dynamics simulations, in the presence of physiologically-relevant lipid compositions revealed the likely dimer interface.
MicroRNA Tae-miR1130p targets wheat ferroportin1 (TaFPN1) in the absence of iron-responsive element/iron-regulatory protein1 module
Authors: Sharma Shivani , Joon Riya , Singh Ajit Pal , Tyagi Deekshikha , Kaur Gazaldeep , Pandey Ajay Kumar 
Published: May 2024

AbstractFerroportin (FPN) belongs to the Major Facilitator Superfamily of transporters and is a known iron (Fe) exporter in humans, with orthologues also present in plant species. Human FPN is subjected to multi-level regulation at transcriptional, post-transcriptional, and post-translational levels. How plant FPNs are regulated remains to be explored. In the current study, we have characterized wheat FPN1, a plasma-membrane localized protein, for its role in Fe homeostasis. A spatial-temporal expression analysis of wheat FPN1 suggested that its tissue-specific expression is differentially upregulated during Fe deficiency conditions. Unlike human FPN, plant FPN lacks the necessary sites for hepcidin binding, thereby emphasizing the need to explore the transcriptional/post-transcriptional mode of regulation. The lack of Iron Responsive Elements (IRE) inTaFPN1promoter suggests no direct regulation through the Iron Regulatory Protein (IRP) mechanism like in humans. Further, to explore the miRNA-mediated regulation, we identified Fe-regulatedtae-miR1130b-3pcapable of targetingTaFPN1underin-vivoconditions. Transcript expression oftae-miR1130b-3pnegatively correlates with theTaFPN1. This alternative regulation pathway suggests a complex network of interactions governing the expression of genes involved in iron homeostasis, highlighting the intricacies of cellular regulatory mechanisms. Altogether, the work will unravel the cellular and physiological role of wheat FPN and contribute to a comprehensive understanding of plant iron homeostasis.
The major nucleoid-associated protein WHIRLY1 promotes chloroplast development in barley
Authors: Krupinska Karin , Eirich Jürgen , Repnik Urska , Desel Christine , Nia Monireh Saeid , Schäfer Anke , Voigt Ulrike , Bennewitz Bationa , Bilger Wolfgang , Finkemeier Iris , Hensel Götz 
Published: May 2024

ABSTRACTWHIRLY1 is a DNA-binding protein of high abundance in chloroplast nucleoids, which have a complex proteome consisting of proteins involved in gene expression and unexpected proteins indicating links to energy production and biosynthetic activities of chloroplasts. In addition, WHIRLY1 has a second localization in the nucleus making it an excellent candidate for chloroplast-to-nucleus communication. To unravel the role of WHIRLY1 for structure and protein composition of nucleoids and its potential involvement in retrograde signaling during chloroplast development, knockout mutants ofHvWHIRLY1were prepared by site-directed mutagenesis using Cas9 endonuclease. In contrast to mutants of rice and maize, which die after the seedling stage, the barleywhy1mutants survive and produce grains. Leaves of the mutants are initially pale and get green with time (xantha-to-greenphenotype). However, the chlorophyll content of primary leaves stayed distinctly lower than that of the wild-type leaves, coinciding with a rather heterogeneous plastid population, whereby only 50% developed a rather normal thylakoid membrane system. For comparison, mature foliage leaves had almost normal levels of chlorophyll but a severely reduced photosynthetic capacity.A proteome analysis of chloroplasts isolated from mature foliage leaves revealed that in the absence of WHIRLY1, the abundances of a considerable fraction of proteins were downregulated. The fraction included multiple nucleoid-associated proteins including components of the transcriptional apparatus. Furthermore, ribosomal proteins, subunits of pyruvate dehydrogenase, CLP protease, ATP synthase, Rubisco and chaperons/chaperonins were found to be downregulated.In conclusion, the characterization of the barleywhy1mutant plants revealed that WHIRLY1 is not essential for chloroplast development. Rather, it ensures a fast and failure-free progression of chloroplast development by remodeling nucleoids, which serve as assembly platforms for a concerted workflow of the numerous processes required for chloroplast development. Gene expression analyses revealed that the disturbance of chloroplast development is signaled to the nucleus, indicating that WHIRLY1 is not part of the biogenic retrograde signaling of plastids.
Transcriptional repression and enhancer decommissioning silence cell cycle genes in postmitotic tissues
Authors: Fogarty Elizabeth A. , Buchert Elli M. , Ma Yiqin , Nicely Ava B. , Buttitta Laura A. 
Published: May 2024

AbstractThe mechanisms that maintain a non-cycling status in postmitotic tissues are not well understood. Many cell cycle genes have promoters and enhancers that remain accessible even when cells are terminally differentiated and in a non-cycling state, suggesting their repression must be maintained long term. In contrast, enhancer decommissioning has been observed for rate-limiting cell cycle genes in theDrosophilawing, a tissue where the cells die soon after eclosion, but it has been unclear if this also occurs in other contexts of terminal differentiation. In this study, we show that enhancer decommissioning also occurs at specific, rate-limiting cell cycle genes in the long-lived tissues of theDrosophilaeye and brain, and we propose this loss of chromatin accessibility may help maintain a robust postmitotic state. We examined the decommissioned enhancers at specific rate-limiting cell cycle genes and show that they encode dynamic temporal and spatial expression patterns that include shared, as well as tissue-specific elements, resulting in broad gene expression with developmentally controlled temporal regulation. We extend our analysis to cell cycle gene expression and chromatin accessibility in the mammalian retina using a published dataset, and find that the principles of cell cycle gene regulation identified in terminally differentiatingDrosophilatissues are conserved in the differentiating mammalian retina. We propose a robust, non-cycling status is maintained in long-lived postmitotic tissues through a combination of stable repression at most cell cycle gens, alongside enhancer decommissioning at specific rate-limiting cell cycle genes.HighlightsIn long-lived postmitoticDrosophilatissues, most cell cycle genes retain accessible chromatin despite persistent transcriptional downregulation.Cell cycle genes with accessible enhancers remain activatable during terminal differentiation, suggesting their repression must be continuously maintained in the postmitotic state.Long-lived postmitotic tissues decommission enhancers at specific, rate-limiting cell cycle genes in a developmentally regulated manner.Genome-wide enhancer identification performed in cell culture misses many developmentally dynamic enhancersin vivo.Decommissioned enhancers at cell cycle genes include shared and tissue-specific elements that in combination, result in broad gene expression with temporal regulation.The principles of cell cycle gene regulation identified inDrosophilaare conserved in the mammalian retina.
Proteomic Profiling of Mesenchymal Stem Cell-Derived Extracellular Vesicles: Impact of Isolation Methods on Protein Cargo
Authors: Abyadeh Morteza , Mirshahvaladi Shahab , Assar Kashani Sara , A. Paulo Joao , Amirkhani Ardeshir , Mehryab Fatemeh , Seidi Homeira , Moradpour Niloufar , Jodeiryjabarzade Sheyda , Mirzaei Mehdi , Gupta Vivek , Shekari Faezeh , Hosseini Salekdeh Ghasem 
Published: May 2024

AbstractExtracellular vesicles (EVs) are nanosized vesicles with a lipid bilayer that are secreted by cells and play a critical role in cell-to-cell communication. Despite the promising reports regarding their diagnostic and therapeutic potential, the utilization of EVs in the clinical setting is limited due to insufficient information about their cargo and a lack of standardization in isolation and analysis methods. Considering protein cargos in EVs as key contributors to their therapeutic potency, we conducted a tandem mass tag (TMT) quantitative proteomics analysis of three subpopulations of mesenchymal stem cell (MSC)-derived EVs obtained through three different isolation techniques: ultracentrifugation (UC), high-speed centrifugation (HS), and ultracentrifugation on sucrose cushion (SU). Subsequently, we checked EV marker expression, size distribution, and morphological characterization, followed by bioinformatic analysis. The bioinformatic analysis of the proteome results revealed that these subpopulations exhibit distinct molecular and functional characteristics. The choice of isolation method impacts the proteome of isolated EVs by isolating different subpopulations of EVs. Specifically, EVs isolated through the high-speed centrifugation (HS) method exhibited a higher abundance of ribosomal and mitochondrial proteins. Functional apoptosis assays comparing isolated mitochondria with different EV isolation methods revealed that HS-EVs, but not other EVs, induced early apoptosis in cancer cells. On the other hand, EVs isolated using the sucrose cushion (SU) and ultracentrifugation (UC) methods demonstrated a higher abundance of proteins primarily involved in the immune response, cellLJcell interactions, and extracellular matrix interactions. Our analyses unveil notable disparities in proteins and associated biological functions among EV subpopulations, underscoring the importance of meticulously selecting isolation methods and resultant EV subpopulations based on the intended application.
Helping behavior is associated with increased affiliative behavior, activation of the prosocial brain network and elevated oxytocin receptor expression in the nucleus accumbens
Authors: Hazani R. , Breton J.M. , Trachtenberg E. , Kantor B. , Maman A. , Bigelman E. , Cole S. , Weller A. , Ben-Ami Bartal I. 
Published: May 2024

AbstractA prosocial response to others in distress is increasingly recognized as a natural behavior for many social species, from humans to rodents. While prosocial behavior is more frequently observed towards familiar conspecifics, even within the same social context some individuals are more prone to help than others. For instance, in a rat helping behavior test, rats can release a distressed conspecific trapped inside a restrainer by opening the restrainer door. Typically, rats are motivated to release a trapped cagemate, and consistently release the trapped rat (‘openers’), yet around 30% do not open the restrainer (‘non-openers’). To characterize the difference between these populations, behavioral and neural activity were compared between opener and non-opener rats tested with a trapped cagemate in the helping test. Behaviorally, openers showed significantly more social affiliative behavior both before and after door-opening compared to non-openers. Analysis of brain-wide neural activity based on the immediate early gene c-Fos revealed increased activity in openers in the previously identified prosocial neural network compared to non-openers. The network includes regions associated with empathy in humans (somatosensory cortex, insula, cingulate cortex and frontal cortex), and motivation and reward regions such as the nucleus accumbens. Oxytocin receptor mRNA expression levels were higher in the accumbens but not the anterior insula. Several transcription control pathways were also significantly upregulated in openers’ accumbens. These findings indicate that prosocial behavior may be predicted by affiliative behavior and activity in the prosocial neural network and provide targets for the investigation of causal mechanisms underlying prosocial behavior.Significance StatementProsocial behavior is observed in many social species, including rodents, yet the determinants underlying why some animals help and others do not is poorly understood. Here, we show behavioral and neural differences between prosocial and non-prosocial pairs in a rat helping behavior test, with increased social interaction and nucleus accumbens oxytocin receptor gene expression in animals that helped.
A Comparative Study of Explainability Methods for Whole Slide Classification of Lymph Node Metastases using Vision Transformers
Authors: Rahnfeld Jens , Naouar Mehdi , Kalweit Gabriel , Boedecker Joschka , Dubruc Estelle , Kalweit Maria 
Published: May 2024

ABSTRACTRecent advancements in deep learning (DL), such as transformer networks, have shown promise in enhancing the performance of medical image analysis. In pathology, automated whole slide imaging (WSI) has transformed clinical workflows by streamlining routine tasks and diagnostic and prognostic support. However, the lack of transparency of DL models, often described as “black boxes”, poses a significant barrier to their clinical adoption. This necessitates the use of explainable AI methods (xAI) to clarify the decision-making processes of the models. Heatmaps can provide clinicians visual representations that highlight areas of interest or concern for the prediction of the specific model. Generating them from deep neural networks, especially from vision transformers, is non-trivial, as typically their self-attention mechanisms can lead to overconfident artifacts. The aim of this work is to evaluate current xAI methods for transformer models in order to assess which yields the best heatmaps in the histopathological context. Our study undertakes a comparative analysis for classifying a publicly available dataset comprising of N=400 WSIs of lymph node metastases of breast cancer patients. Our findings indicate that heatmaps calculated from Attention Rollout and Integrated Gradients are limited by artifacts and in quantitative performance. In contrast, removal-based methods like RISE and ViT-Shapley exhibit better qualitative attribution maps, showing better results in the well-known interpretability metrics for insertion and deletion. In addition, ViT-Shapley shows faster runtime and the most promising, reliable and practical heatmaps. Incorporating the heatmaps generated from approximate Shapley values in pathology reports could help to integrate xAI in the clinical workflow and increase trust in a scalable manner.
A low pre-existing anti-NS1 humoral immunity to DENV is associated with microcephaly development after gestational ZIKV exposure
Authors: Castro-Trujillo Sebastián , Mejía William R. , Segura Katherine , Vega Rocío , Salgado Doris , Fonseca Carlos E. , Ortiz Ángela M. , Perdomo-Celis Federico , Bosch Irene , Narváez Carlos F. 
Published: May 2024

ABSTRACTBackgroundGestational Zika virus (ZIKV) infection is associated with the development of congenital Zika syndrome (CZS), which includes microcephaly and fetal demise. The magnitude and quality of orthoflavivirus-specific humoral immunity have been previously linked to the development of CZS. However, the role of ZIKV NS1-specific humoral immunity in mothers and children with prenatal ZIKV exposure and CZS remains undefined. In addition, considering that most of the at-risk population lives in dengue virus (DENV)-endemic areas, it is not clear what is the association between pre-existing DENV NS1-specific humoral immunity and CZS.MethodsHere, we studied 328 mothers and children with a clinical diagnosis and seropositivity for ZIKV infection during pregnancy, included during the 2015-2016 ZIKV epidemic in Colombia. We also performed clinical evaluation and pediatric neurological follow-up. The relative levels of circulating NS1-specific IgM and IgG against ZIKV and DENV were evaluated in mothers and children, and the association with the development of microcephaly was analyzed.ResultsDENV and ZIKV IgG-NS1 antibodies in pregnant women were placentally transferred, and this passage and its duration in children depended on the maternal levels of the antibodies. We reported that higher concentrations of pre-existing DENV, but not ZIKV IgG-NS1 antibodies, were associated with a reduced risk of CZS-related microcephaly. Also, we observed that the IgM-NS1 response presents as long-term and has a minor association with poor outcomes.ConclusionsThe development of microcephaly in children prenatally exposed to ZIKV is associated with low plasma levels of placentally transferred, pre-existing DENV IgG-NS1 antibodies. These data are compatible with a protective role of anti-NS1 IgG antibodies against ZIKV infection during pregnancy and highlight the promising role of NS1 as an orthoflavivirus vaccine target in high-risk populations.
Evolution of the sex-determination geneDoublesexwithin the termite lineage
Authors: Fujiwara Kokuto , Miyazaki Satoshi , Maekawa Kiyoto 
Published: May 2024

ABSTRACTThe molecular mechanism of sex determination has long been considered conserved in insects. However, recent studies of hemimetabolous insects have challenged this notion. One notable example is termites. InReticulitermes speratus, a homolog of sex determination gene,Doublesex(RsDsx), exhibits characteristics that are distinct from those of other insects, including sister-group cockroaches. It comprises a single exon, contains only doublesex/mab-3 DNA-binding domain (DM) but lacks a conserved oligomerization domain (OD), and exhibits transcriptional activity only in males. To investigate whether these characteristics are widespread within the termite lineage, we identifiedDsxhomologs in three different families. The loss of the conserved OD sequences was observed in all termite species examined, whereas the number of exons and expression patterns between sexes varied among families. Particularly, distinctive differences inDsxwere found in species from the Archotermopsidae and Kalotermitidae, both of which have a linear caste developmental pathway. Our findings indicate that diversification ofDsxstructure and expression patterns may have contributed to ecological diversification, such as caste developmental pathways, within the termite lineage.