bluuebunny/crossref_metadata_2025_split huggingface dataset:
Postsynaptic protein assembly in three- and two-dimensions studied by mesoscopic simulations
Authors: Yamada Risa , Takada Shoji 
Published: March 2023

ABSTRACTRecently, cellular biomolecular condensates formed via phase separation have received considerable attention. While they can be formed either in cytosol (denoted as 3D) or beneath the membrane (2D), the underlying difference between the two has not been well clarified. To compare the phase behaviors in 3D and 2D, postsynaptic density (PSD) serves as a model system. PSD is a protein condensate located under the postsynaptic membrane that influences the localization of glutamate receptors and thus contributes to synaptic plasticity. Recentin vitrostudies have revealed the formation of droplets of various soluble PSD proteins via liquid-liquid phase separation. However, it is unclear how these protein condensates are formed beneath the membrane and how they specifically affect the localization of glutamate receptors in the membrane. In this study, focusing on the mixture of a glutamate receptor complex, AMPAR-TARP, and a ubiquitous scaffolding protein, PSD-95, we constructed a mesoscopic model of protein-domain interactions in PSD and performed comparative molecular simulations. The results showed a sharp contrast in the phase behaviors of protein assemblies in 3D and those under the membrane (2D). A mixture of a soluble variant of the AMPAR-TARP complex and PSD-95 in the 3D system resulted in a phase-separated condensate, which was consistent with the experimental results. However, with identical domain interactions, AMPAR-TARP embedded in the membrane formed clusters with PSD-95, but did not form a stable separated phase. Thus, the cluster formation behaviors of PSD proteins in the 3D and 2D systems were distinct. The current study suggests that, more generally, stable phase separation can be more difficult to achieve in and beneath the membrane than in 3D systems.SIGNIFICANCESynaptic plasticity is a key factor in memory and learning. Upon learning, protein condensates that form beneath the postsynaptic membrane are known to change their nature. Recent studies have suggested that condensate formation is related to liquid-liquid phase separation based onin vitroexperiments of soluble parts. However, the phase behavior can be strongly dependent on physical dimensions. The mechanism by which condensate grows beneath the membrane is not well characterized. Taking advantage of the ease of systematic comparison using computer simulations, we investigated the phase behaviors of postsynaptic protein assemblies in 3D and 2D systems. The results revealed that even when a 3D system exhibited clear phase separation, the corresponding 2D system did not exhibit it stably.
Comparative assessment of mosquito size and receptiveness toP. falciparuminfection of two rearing procedures forAnophelesmosquitoes
Authors: Graumans Wouter , Lanke Kjerstin , van de Vegte-Bolmer Marga , Stoter Rianne , Costa Giulia , Levashina Elena A , Yang Annie S P , Gemert Geert-Jan van , Bousema Teun 
Published: March 2023

AbstractMalaria is transmitted whenAnophelinemosquitoes ingestPlasmodiumparasites during blood-feeding. Artificial feeding assays allow mosquitoes to take up blood from membrane feeders, and are widely used to study malaria transmission. These assays require large quantities of mosquitoes; insectaries optimize their rearing procedures to generate high yields of permissive, homogeneous mosquito populations. Rearing ofAnopheline stephensimosquitoes was protocolized at the Radboudumc in the 1980s, yet infection outcomes remain heterogeneous. This study explores possible improvements in mosquito rearing to improve homogeneity of the resulting mosquito populations. It compares the current mass-rearing standard with an adapted alternative approach from another institute that optimizes larval density per tray and applies a diet that has previously been reported. Differences between procedures were assessed by measuring mosquito size by proxy of wing-length and imbibed blood meal volume. To assess receptiveness toP. falciparuminfection mosquitoes were fed cultured gametocytes. We observed a slight decrease in mosquito size when applying the alternative rearing procedure, but generated equally parasite-receptiveP. falciparummosquitoes compared to the standard procedure. We conclude that both rearing protocols can be used to generate susceptible mosquitoes for conducting malaria research.
Spatiotemporal changes in secondary metabolites during graft formation in grapevine reveal tissue-specific accumulation of metabolites in necrotic and callus tissues
Authors: Loupit Grégoire , Valls Fonayet Josep , Lorensen Marcus Daniel Brandbjerg Bohn , Franc Céline , Revel Gilles De , Janfelt Christian , Cookson Sarah Jane 
Published: March 2023

AbstractGrafting is widely used in horticulture, shortly after grafting, callus tissues appear at the graft interface and the vascular tissues of the scion and rootstock connect. The graft interface contains a complex mix of tissues, we hypothesized that each tissue have is own metabolic response to wounding/grafting and accumulate different metabolites at different rates. We made intact and wounded cuttings and grafts of grapevine, and then measured changes in bulk secondary metabolite concentration and used metabolite imaging to study tissue specific responses. We show that some metabolites rapidly accumulate in specific tissues after grafting, e.g. stilbenes accumulate in necrotic tissues surrounding mature xylem vessels and gradually oligomerize over time. We also observe that some metabolites accumulate in the newly formed callus tissue at the graft interface and identify genotype-specific responses. Here we reveal the spatiotemporal dynamics of metabolite changes occurring during graft union formation for the first time. The rapid accumulation of stilbenes in the tissues damaged during the grafting process could be a plant defence mechanism, as stilbenes have antioxidant and anti-fungal capacities. The increasing oligomerization of stilbenes often occurs in response to plant stresses (via unknown mechanisms), but it potentially increases antioxidant activity.Brief summarySecondary metabolites accumulate after wounding and grafting in plants yet we have limited knowledge of tissue specific accumulation patterns and temporal dynamics. We show that stilbenes accumulate specifically in necrotic tissues and oligomerize over the time, whereas other compounds accumulate in the newly formed callus tissues. This suggests that these compounds have different roles in wounding healing and grafting.
scDeepInsight: a supervised cell-type identification method for scRNA-seq data with deep learning
Authors: Jia Shangru , Lysenko Artem , Boroevich Keith A , Sharma Alok , Tsunoda Tatsuhiko 
Published: March 2023

AbstractAnnotation of cell-types is a critical step in the analysis of single-cell RNA sequencing (scRNA-seq) data that allows the study of heterogeneity across multiple cell populations. Currently this is most commonly done using unsupervised clustering algorithms, which project single-cell expression data into a lower dimensional space and then cluster cells based on their distances from each other. However, as these methods do not use reference datasets, they can only achieve a rough classification of cell-types, and it is difficult to improve the recognition accuracy further. To effectively solve this issue we propose a novel supervised annotation method, scDeepInsight. The scDeepInsight method is capable of performing manifold assignments. It is competent in executing data integration through batch normalization, performing supervised training on the reference dataset, doing outlier detection and annotating cell-types on query datasets. Moreover, it can help identify active genes or marker genes related to cell-types. The training of the scDeepInsight model is performed in a unique way. Tabular scRNA-seq data are first converted to corresponding images through the DeepInsight methodology. DeepInsight can create a trainable image transformer to convert non-image RNA data to images by comprehensively comparing interrelationships among multiple genes. Subsequently, the converted images are fed into convolutional neural networks (CNNs) such as EfficientNet-b3. This enables automatic feature extraction to identify the cell-types of scRNA-seq samples. We benchmarked scDeepInsight with six other mainstream cell annotation methods. The average accuracy rate of scDeepInsight reached 87.5%, which is more than 7% higher compared with the state-of-the-art methods.
ZygosityPredictor
Authors: Rheinnecker Marco , Fröhlich Martina , Rübsam Marc , Paramasivam Nagarajan , Heilig Christoph E. , Fröhling Stefan , Schlenk Richard F. , Hutter Barbara , Hübschmann Daniel 
Published: March 2023

AbstractSummaryZygosityPredictor provides functionality to evaluate how many copies of a gene are affected by mutations in next generation sequencing data. In cancer samples, the tool processes both somatic and germline mutations. In particular, ZygosityPredictor computes the number of affected copies for single nucleotide variants and small insertions and deletions (Indels). In addition, the tool integrates information at gene level via phasing of several variants and subsequent logic to derive how strongly a gene is affected by mutations and provides a measure of confidence. This information is of particular interest in precision oncology, e.g. when assessing whether unmutated copies of tumor-suppressor genes remain.Availability and implementationZygosityPredictor was implemented as an R-package and is available via Bioconductor athttps://bioconductor.org/packages/ZygosityPredictor. Detailed documentation is provided in the vignette including application to an example genome.
Conservation genetics of the white-bellied pangolin in West Africa: a story of lineage admixture, declining demography and wide sourcing by urban bushmeat markets
Authors: Gossé Koffi Jules , Gonedelé-Bi Sery , Dufour Sylvain , Danquah Emmanuel , Gaubert Philippe 
Published: March 2023

AbstractDuring the last 40 years, the volumes of African pangolins feeding the illegal wildlife trade have dramatically increased. We conducted a conservation genetics survey of the most traded African species, the white bellied pangolin (WBP;Phataginus tricuspis), across three West African countries including Guinea, Côte d’Ivoire and Ghana. Our study combining mitochondrial DNA (mtDNA) sequencing and microsatellites genotyping is the first to reveal a global pattern of admixture between two of the six mitochondrial lineages as previously delimited within WBP. We found a signature of isolation-by-distance and a lack of population genetic structuring, supporting the idea that WBP may have underestimated dispersal abilities. Levels of genetic diversity were low compared to central African lineages, reinforcing the picture of genetic pauperization shared by West African WBP. We observed a 85-98% decline in the effective population size of WBP occurring c. 3200 to 400 ya, with current numbers (520–590) at the lower end of the conservative thresholds for minimum viable population size. The microsatellites markers were powerful enough to differentiate between individuals and identify replicated samples, confirming the utility of this approach in tracing the pangolin trade. Genetic diversity estimates confirmed that Yopougon, the main bushmeat market from Abidjan (Côte d’Ivoire), was fed by a large trade network as confirmed by vendors reporting 10 different sources situated 62-459 km away from the market. We conclude that WBP distributed in the Upper Guinean Block should be considered a single management unit of high conservation concern, as impacted by genetic diversity erosion, drastic decline in effective population size and wide range sourcing for feeding urban bushmeat markets. Given the genetic admixture pattern detected within WBP from West Africa, we advocate for a multi-locus strategy to trace the international trade of the species.
Facilitating Electrochemical Lateral Flow Assay using NFC-Enabled Potentiostat and Nitrocellulose-based Metal Electrodes
Authors: Gonzalez-Macia Laura , Li Yunpeng , Zhang Kaijia , Nunez-Bajo Estefania , Barandun Giandrin , Cotur Yasin , Asfour Tarek , Olenik Selin , Coatsworth Philip , Herrington Jack , Güder Firat 
Published: March 2023

AbstractRapid detection of pathogens at the point-of-need is crucial for preventing the spread of human, animal and plant diseases which can have devastating consequences both on the lives and livelihood of billions of people. Colorimetric, lateral flow assays consisting of a nitrocellulose membrane, are the preferred format today for low-cost on-site detection of pathogens. This assay format has, however, historically suffered from poor analytical performance and is not compatible with digital technologies. In this work, we report the development of a new class of digital diagnostics platform for precision point-of-need testing. This new versatile platform consists of two important innovations: i) A wireless and batteryless, microcontroller-based, low-cost Near Field Communication (NFC)-enabled potentiostat that brings high performance electroanalytical techniques (cyclic voltammetry, chronoamperometry, square wave voltammetry) to the field. The NFC-potentiostat can be operated with a mobile app by minimally trained users; ii) A new approach for producing nitrocellulose membranes with integrated electrodes that facilitate high performance electrochemical detection at the point-of-need. We produced an integrated system housed in a 3D-printed phone case and demonstrated its used for the detection of Maize Mosaic Virus (MMV), a plant pathogen, as a proof-of-concept application.
Patterns of unwanted biological and technical expression variation across 49 human tissues
Authors: Nieuwenhuis Tim O. , Giles Hunter H. , McCall Matthew N. , Halushka Marc K. 
Published: March 2023

ABSTRACTAll tissue-based gene expression studies are impacted by biological and technical sources of variation. Numerous methods are used to normalize and batch correct these datasets. A more accurate understanding of all causes of variation could further optimize these approaches. We used 17,282 samples from 49 tissues in the Genotype Tissue Expression (GTEx) dataset (v8) to investigate patterns and causes of expression variation. Transcript expression was normalized to Z-scores and only the most variable 2% of transcripts were evaluated and clustered based on co-expression patterns. Clustered gene sets were solved to different biological or technical causes related to metadata elements and histologic images. We identified 522 variable transcript clusters (median 11 per tissue) across the samples. Of these, 64% were confidently explained, 15% were likely explained, 7% were low confidence explanations and 14% had no clear cause. Common causes included sex, sequencing contamination, immunoglobulin diversity, and compositional tissue differences. Less common biological causes included death interval (Hardy score), muscle atrophy, diabetes status, and menopause. Technical causes included brain pH and harvesting differences. Many of the causes of variation in bulk tissue expression were identifiable in the Tabula Sapiens dataset of single cell expression. This is the largest exploration of the underlying sources of tissue expression variation. It uncovered expected and unexpected causes of variable gene expression. These identified sources of variation will inform which metadata to acquire with tissue harvesting and can be used to improve normalization, batch correction, and analysis of both bulk and single cell RNA-seq data.
Arabidopsis MEB3 functions as a vacuolar transporter to regulate iron accumulation in roots
Authors: Endo Kaichiro , Basak Arpan Kumar , Wilkens Alwine , Mirzaei Mohamadreza , Kopriva Stanislav , Yamada Kenji 
Published: March 2023

ABSTRACTIron is an essential nutrient for plant photosynthesis and development, but excess iron leads to stress. After absorption from the soil, plants store iron in roots and distribute it to shoots via long-distance transport. Vacuole serves as the iron storage organ in root cells, maintaining cellular iron homeostasis, and vacuolar iron transporter (VIT) family proteins have been identified as plant vacuolar iron transporters. However, the contribution of vacuolar iron transporters to the overall iron homeostasis of plants is not fully understood. Here, we show that MEMBRANE PROTEIN OF ER BODY 3 (MEB3), a VIT family member, is a vacuolar iron transporter involved in root–shoot iron distribution inArabidopsis thaliana. Heterologous expression of ArabidopsisMEB3in yeast restored the iron resistance phenotype of the vacuolar iron transporter deficient mutantccc1, indicating that MEB3 regulates iron transport. In Arabidopsis,MEB3was expressed in almost all tissues, albeit to higher levels in roots and seedlings, and the MEB3 protein localized to the tonoplast. At low iron concentration,meb3knockout mutants accumulated less iron in shoots, suggesting that MEB3 promotes iron accumulation in shoots. Consistently,meb3mutants exhibited reduced growth compared with the wild type upon transfer to iron-deficient medium. However, at high iron concentration,meb3mutants accumulated more iron in shoots and less iron in roots than the wild type, indicating the impairment of proper iron distribution inmeb3mutants. These findings demonstrate that MEB3 is a vacuolar iron transporter involved in root-to-shoot iron distribution.
Biological Factors and Statistical Limitations Prevent Detection of Most Noncanonical Proteins by Mass Spectrometry
Authors: Wacholder Aaron , Carvunis Anne-Ruxandra 
Published: March 2023

AbstractRibosome profiling experiments indicate pervasive translation of short open reading frames (ORFs) outside of annotated protein-coding genes. However, shotgun mass spectrometry experiments typically detect only a small fraction of the predicted protein products of this noncanonical translation. The rarity of detection could indicate that most predicted noncanonical proteins are rapidly degraded and not present in the cell; alternatively, it could reflect technical limitations. Here we leveraged recent advances in ribosome profiling and mass spectrometry to investigate the factors limiting detection of noncanonical proteins in yeast. We show that the low detection rate of noncanonical ORF products can largely be explained by small size and low translation levels and does not indicate that they are unstable or biologically insignificant. In particular, proteins encoded by evolutionarily young genes, including those with well-characterized biological roles, are too short and too lowly-expressed to be detected by shotgun mass spectrometry at current detection sensitivities. Additionally, we find that decoy biases can give misleading estimates of noncanonical protein false discovery rates, potentially leading to false detections. After accounting for these issues, we found strong evidence for four noncanonical proteins in mass spectrometry data, which were also supported by evolution and translation data. These results illustrate the power of mass spectrometry to validate unannotated genes predicted by ribosome profiling, but also its substantial limitations in finding many biologically relevant lowly-expressed proteins.
T-CLEARE: A Pilot Community-Driven Tissue-Clearing Protocol Repository
Authors: Weiss Kurt , Huisken Jan , Bakalov Vesselina , Engle Michelle , Gridley Lauren , Krzyzanowski Michelle C. , Madden Tom , Maiese Deborah , Waterfield Justin , Williams David , Wu Xin , Hamilton Carol M. , Huggins Wayne 
Published: March 2023

ABSTRACTSelecting and implementing a tissue-clearing protocol is challenging. Established more than 100 years ago, tissue clearing is still a rapidly evolving field of research. There are currently many published protocols to choose from, and each performs better or worse across a range of key evaluation factors (e.g., speed, cost, tissue stability, fluorescence quenching). Additionally, tissue-clearing protocols are often optimized for specific experimental contexts, and applying an existing protocol to a new problem can require a lengthy period of adaptation by trial and error. Although the primary literature and review articles provide a useful starting point for optimization, there is growing recognition that many articles do not provide sufficient detail to replicate or reproduce experimental results. To help address this issue, we have developed a novel, freely available repository of tissue-clearing protocols named T-CLEARE (Tissue CLEAring protocol REpository;https://doryworkspace.org/doryviz). T-CLEARE incorporates community responses to an open survey designed to capture details not commonly found in the scientific literature, including modifications to published protocols required for specific use cases and instances when tissue-clearing protocols did not perform well (negative results). The goal of T-CLEARE is to provide a forum for the community to share evaluations and modifications of tissue-clearing protocols for various tissue types and potentially identify best-in-class methods for a given application.
Spatial and temporal representation of marine fish occurrences available online
Authors: Pizarro Vanessa , Castillo Andrea , Piñones Andrea , Samaniego Horacio 
Published: March 2023

AbstractDespite the 243,000 species of marine species described by 2022, our knowledge about the biodiversity in the oceans is still incomplete. This may have dreaded and detrimental effect for the conservation of marine ecosystems under the current anthropization of our biota and the fast pacing climate and global change scenario.However, a large number of online repositories cataloging, storing and distributing biodiversity information hosting taxonomic information and species occurrence data have emerged recently. FishBase, the Global Biodiversity Information Facility (GBIF) and the Ocean Biodiversity Information System (OBIS) are part of these publicly available repositories representing a variety of sources that have exploded in number. However, despite the incredible accumulation of biodiversity records, not all the information is really useful, nor does it represent any new knowledge regarding global species richness patterns.In this study we evaluated the spatial and temporal representativeness of the records of marine fishes (order Actinopterygii) available in the GBIF and OBIS global repositories. We provide a methodological framework based on a set of non-parametric estimators to calculate species richness from incidence data, using hexagonal grids as sampling units overlapped on the marine bioregions worldwide.Using standard ecological and spatial analysis tools, we identify regions that are adequately represented in terms of available records and therefore have more reliable data, as well as regions with few records that do not represent current species richness. We overlap these results with the location of marine protected areas and fishing exploitation zones to understand the anthropogenic effect on marine ichthyofauna. We additionally evaluate hypotheses regarding the taxonomic, geographic, and temporal distribution of information biases to deepen our current understanding of public records of species occurrences worldwide.Considering that more than 40 years of information was analyzed, the results showed that on a global scale, the primary data on marine fish available on GBIF and OBIS platforms are still far from being representative and complete. Only 1.14% of the records were useful for our analyses. In addition, we found that the information seems to be biased towards coastal areas, regions close to developed countries and areas where there is a large fishing activity. Finally, the best represented species and families are those with a small body size, which use shallow habitats and have commercial cultural value.