bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative imaging of species-specific lipid transport in mammalian cells
Authors: Iglesias-Artola Juan M. , Schuhmann Kai , Böhlig Kristin , Lennartz H. Mathilda , Schuhmacher Milena , Barahtjan Pavel , Jiménez López Cristina , Šachl Radek , Pombo-Garcia Karina , Lohmann Annett , Riegerová Petra , Hof Martin , Drobot Björn , Shevchenko Andrej , Honigmann Alf , Nadler André 
Published: May 2024

AbstractEukaryotic cells produce over 1000 different lipid species which tune organelle membrane properties, control signalling and store energy1,2. How lipid species are selectively sorted between organelles to maintain specific membrane identities is largely unknown due to the difficulty to image lipid transport in cells3. Here, we measured transport and metabolism of individual lipid species in mammalian cells using time-resolved fluorescence imaging of bifunctional lipid probes in combination with ultra-high resolution mass spectrometry and mathematical modelling. Quantification of lipid flux between organelles revealed that directional, non-vesicular lipid transport is responsible for fast, species-selective lipid sorting compared to slow, unspecific vesicular membrane trafficking. Using genetic perturbations, we found that coupling between active lipid flipping and passive non-vesicular transport is a mechanism for directional lipid transport. Comparison of metabolic conversion and transport rates showed that non-vesicular transport dominates the organelle distribution of lipids while species-specific phospholipid metabolism controls neutral lipid accumulation. Our results provide the first quantitative map of retrograde lipid flux in cells4. We anticipate that our pipeline for quantitative mapping of lipid flux through physical and chemical space in cells will boost our understanding of lipids in cell biology and disease.
Scalable Production and Purification of Engineered ARRDC1-Mediated Microvesicles in a HEK293 Suspension Cell System
Authors: Luther Kristin , Navaei Ali , Gens Leah , Semple Carson , Moharil Pearl , Passalacqua Ilaria , Vyas Komal , Wang Qiyu , Liu Shu-Lin , Sun Lucy , Ramaswamy Senthil , Zocco Davide , Nabhan Joseph F 
Published: May 2024

AbstractThe engineering of human ARRDC1-mediated microvesicles (ARMMs) as new non-viral vehicles for delivery of gene therapies overcomes challenges associated with current modalities. Hurdles such as generating sufficient material to meet demand and development of appropriate characterization assays, however, persist. Our study evaluated two scalable strategies to generate GFP-loaded ARMMs, transient transfection or stable cell line-based production. The upstream ARMMs production processes utilized a suspension HEK293-derived line, termed 5B8, from Lonza. Production was evaluated in shake flasks and bioreactors. Downstream ARMMs purification processes employed Tangential Flow Filtration (TFF) and Anion Exchange Chromatography (AEX). Analytical methods included single particle analysis, ELISA, and immunoblotting. Additionally, anin vivostudy was conducted in mice to investigate the half-life and biodistribution of ARMMs administered intravenously. 5B8 cells yielded robust production of ARMMs after transient transfection with the ARMMs loading construct or using a stable cell line containing a transgene that encodes the ARMMs loading cassette, in shake flasks or a stirred tank bioreactor, respectively. Approximately 50% of all vesicles produced were payload-containing ARMMs. ARMMs were purified by ultracentrifugation (small scale) or a combination of TFF and AEX (large scale). Both purification methods produced comparable ARMMs.In vivo, ARMMs showed rapid biodistribution predominantly to the spleen and liver and, to a lesser extent, kidneys, and lungs. The successful scale-up of ARMMs production illustrates the potential of engineered extracellular vesicles (EVs). Furthermore, this study highlights the potential utility of ARMMs forin vivodelivery of therapeutic molecules.
Coordination between ESCRT function and Rab conversion during endosome maturation
Authors: Ott Daniel P. , Desai Samit , Solinger Jachen A. , Kaech Andres , Spang Anne 
Published: May 2024

AbstractThe endosomal pathway is essential for regulating cell signaling and cellular homeostasis. Rab5-positive early endosomes receive proteins from the plasma membrane. Dependent on a ubiquitin mark on the protein, they will be either recycled or sorted into intraluminal vesicles (ILVs) by ESCRT. During endosome maturation Rab5 will be replaced by Rab7 on endosomes that are able to fuse with lysosomes to form endolysosomes. Whether ESCRT-driven ILV formation and Rab5-to-Rab7 conversion are coordinated remains unknown. Here we show that loss of early ESCRTs leads to enlarged Rab5-positive endosomes and prohibit Rab conversion. Reduction of ubiquitinated cargo alleviated this phenotype. Moreover, ubiquitinated proteins on the endosomal limiting membrane prevented the displacement of the Rab5GEF RABX-5 by the Rab7GEF SAND-1/CCZ-1. Overexpression of Rab7 could partially overcome this block, even in the absence of SAND-1, whereby the HOPS complex presumably acts as Rab7GEF. Our data reveal a hierarchy of events in which cargo corralling by ESCRTs is upstream of Rab conversion and thereby ESCRT-0 and ubiquitinated cargo could act as timers determining the onset of Rab conversion.
ArabidopsisABCC4encodes a cytokinin efflux transporter and is involved in root system development
Authors: Uragami Takuya , Kiba Takatoshi , Kojima Mikiko , Takebayashi Yumiko , Tozawa Yuzuru , Hayashi Yuki , Kinoshita Toshinori , Sakakibara Hitoshi 
Published: May 2024

AbstractThe directional and sequential flow of cytokinin in plants is organized by a complex network of transporters. Genes involved in several aspects of cytokinin transport have been characterized, but a large part of the elaborate system remains elusive. In this study, we have identifiedABCC4as a cytokinin efflux transporter gene. Using a transient expression system in tobacco leaves, we screened Arabidopsis transporter genes and isolatedATP-BINDING CASSETTE TRANSPORTER C4(ABCC4). Further validation through drug-induced expression in Arabidopsis and heterologous expression in budding yeast revealed that ABCC4 effluxes the active form of cytokinins. During the seedling stage,ABCC4was highly expressed in roots, and its expression was up-regulated in response to cytokinin application. Loss-of-function mutants ofABCC4displayed enhanced primary root elongation, similar to mutants impaired in cytokinin biosynthesis or signaling, which was suppressed by exogenoustrans-zeatin treatment. In contrast, overexpression of the gene led to suppression of root elongation. These results suggest that ABCC4 plays a role in the efflux of active cytokinin, thereby contributing to root growth regulation. Our findings contribute to unraveling the many complexities of cytokinin flow and enhance our understanding of the regulatory mechanisms underlying root system development in plants.
The thylakoid lumen Deg1 protease affects non-photochemical quenching via the levels of violaxanthin de-epoxidase and PsbS
Authors: Aviv-Sharon Elinor , Sultan Laure D. , Naveh Leah , Charuvi Dana , Kupervaser Meital , Reich Ziv , Adam Zach 
Published: May 2024

ABSTRACTNon-photochemical quenching (NPQ), the dissipation of excess light energy as heat, has been long recognized as a major protective mechanism that minimizes the potential for oxidative damage to photosystem II (PSII) reaction centers. Two major positive contributors to NPQ are the carotenoid zeaxanthin, generated from violaxanthin by the enzyme violaxanthin de-epoxidase (VDE or NPQ1), and the thylakoid protein PsbS (NPQ4). The involvement of the lumenal Deg proteases in the repair of PSII from photoinhibition prompted us to further explore their possible role in other responses ofArabidopsis thalianato high light. Here we show that upon exposure to high light, the singledeg1and the tripledeg158mutants display different levels and kinetics of NPQ, compared to thedeg58mutant and WT that behave alike. In response to high light, the two genotypes lacking Deg1 over-accumulate NPQ1 and NPQ4. After temporal inhibition of protein translation in vivo, the level of these two proteins indeg1is higher than in WT. Together, the results suggest that Deg1 represents a new level of regulation of the NPQ process through adjusting the quantity of NPQ1 and NPQ4 proteins, probably through their proteolysis.
The USP12/46 deubiquitinases protect integrins from ESCRT-mediated lysosomal degradation
Authors: Yu Kaikai , Guo Shiny S. , Bassermann Florian , Fässler Reinhard , Wang Guan M. 
Published: May 2024

AbstractThe functions of integrins are tightly regulated via multiple mechanisms including trafficking and degradation. Integrins are repeatedly internalized, routed into the endosomal system and either degraded by the lysosome or recycled back to the plasma membrane. The ubiquitin system dictates whether internalized proteins are degraded or recycled. Here, we used a genetic screen and proximity-dependent biotin identification to identify deubiquitinase(s) that control integrin surface levels. We found that a ternary deubiquitinating complex, comprised of USP12 (or the homologous USP46), WDR48 and WDR20, stabilizes β1 integrin (Itgb1) by preventing ESCRT-mediated lysosomal degradation. Mechanistically, the USP12/46-WDR48-WDR20 complex removes ubiquitin from the cytoplasmic tail of internalized Itgb1 in early endosomes, which in turn prevents ESCRT-mediated sorting and Itgb1 degradation.
CLEAN-Contact: Contrastive Learning-enabled Enzyme Functional Annotation Prediction with Structural Inference
Authors: Yang Yuxin , Jerger Abby , Feng Song , Wang Zixu , Brasfield Christina , Cheung Margaret S. , Zucker Jeremy , Guan Qiang 
Published: May 2024

AbstractRecent years have witnessed the remarkable progress of deep learning within the realm of scientific disciplines, yielding a wealth of promising outcomes. A prominent challenge within this domain has been the task of predicting enzyme function, a complex problem that has seen the development of numerous computational methods, particularly those rooted in deep learning techniques. However, the majority of these methods have primarily focused on either amino acid sequence data or protein structure data, neglecting the potential synergy of combining of both modalities. To address this gap, we propose a novelContrastiveLearning framework forEnzyme functionalANnotation prediction combined with protein amino acid sequences andContactmaps (CLEAN-Contact). We rigorously evaluated the performance of our CLEAN-Contact framework against the state-of-the-art enzyme function prediction model using multiple benchmark datasets. Using CLEAN-Contact, we predicted novel enzyme functions within the proteome ofProchlorococcus marinusMED4. Our findings convincingly demonstrate the substantial superiority of our CLEAN-Contact framework, marking a significant step forward in enzyme function prediction accuracy.
Near real-time monitoring of wading birds using uncrewed aircraft systems and computer vision
Authors: White Ethan P. , Garner Lindsey , Weinstein Ben G. , Senyondo Henry , Ortega Andrew , Steinkraus Ashley , Yenni Glenda M. , Frederick Peter , Ernest S. K. Morgan 
Published: May 2024

AbstractWildlife population monitoring over large geographic areas is increasingly feasible due to developments in aerial survey methods coupled with the use of computer vision models for identifying and classifying individual organisms. However, aerial surveys still occur infrequently, and there are often long delays between the acquisition of airborne imagery and its conversion into population monitoring data. Near real-time monitoring is increasingly important for active management decisions and ecological forecasting. Accomplishing this over large scales requires a combination of airborne imagery, computer vision models to process imagery into information on individual organisms, and automated workflows to ensure that imagery is quickly processed into data following acquisition. Here we present our end-to-end workflow for conducting near real-time monitoring of wading birds in the Everglades, Florida, USA. Imagery is acquired as frequently as weekly using uncrewed aircraft systems (aka drones), processed into orthomosaics (using Agisoft metashape), converted into individual level species data using a Retinanet-50 object detector, post-processed, archived, and presented on a web-based visualization platform (using Shiny). The main components of the workflow are automated using Snakemake. The underlying computer vision model provides accurate object detection, species classification, and both total and species-level counts for five out of six target species (White Ibis, Great Egret, Great Blue Heron, Wood Stork, and Roseate Spoonbill). The model performed poorly for Snowy Egrets due to the small number of labels and difficulty distinguishing them from White Ibis (the most abundant species). By automating the post-survey processing, data on the populations of these species is available in near real-time (< 1 week from the date of the survey) providing information at the time-scales needed for ecological forecasting and active management.
“The best home for this paper”: A qualitative study of how authors select where to submit manuscripts
Authors: Maggio Lauren A. , Chtena Natascha , Alperin Juan Pablo , Moorhead Laura , Willinsky John M. 
Published: May 2024

IntroductionFor academics selecting a target journal to submit a manuscript is a critical decision with career implications. In medical education, research conducted in 2016 found that authors were influenced by multiple factors such as a journal’s prestige and its mission. However, since this research was conducted the publishing landscape has shifted to include a broader variety of journals, an increased threat of predatory journals, and new publishing models. This study updates and expands upon how medical education authors decide which journal to submit to with the aim of describing the motivational factors and journal characteristics that guide authors’ decision making.MethodsThe authors conducted five qualitative focus groups in which twenty-two medical education authors and editors participated. During the focus groups participants were engaged in a discussion about how they select a journal to submit their manuscripts. Audio from all focus groups was transcribed. Transcripts were analyzed using codebook thematic analysis.ResultsParticipants considered multiple factors when selecting a target journal. Factors included a journal’s impact, the scope of a journal, journal quality, and technical factors (e.g., word limits). Participants also described how social factors influenced their process and that open access plays a role that could both encourage or deter submission.DiscussionThe findings describe the motivational factors and influential signals that guide authors in their journal selection decision making. These findings confirm, extend, and update journal selection factors reported in medical education and other disciplines. Notably, these findings emphasize the role of social factors, relationships and personal experiences, which were absent from previous work. Additionally, we observed increased consideration of OA and a shift away from an emphasis on journal prestige.
CD4 T cells and CD8α+ lymphocytes are necessary for intravenous BCG-induced protection against tuberculosis in macaques
Authors: Simonson Andrew W. , Zeppa Joseph J. , Bucsan Allison N. , Chao Michael C. , Pokkali Supriya , Hopkins Forrest , Chase Michael R. , Vickers Andrew J. , Sutton Matthew S. , Winchell Caylin G. , Myers Amy J. , Ameel Cassaundra L. , Kelly Ryan , Krouse Ben , Hood Luke E. , Li Jiaxiang , Lehman Chelsea C. , Kamath Megha , Tomko Jaime , Rodgers Mark A. , Donlan Rachel , Chishti Harris , Borish H. Jacob , Klein Edwin , Scanga Charles A. , Fortune Sarah , Lin Philana Ling , Maiello Pauline , Roederer Mario , Darrah Patricia A. , Seder Robert A. , Flynn JoAnne L. 
Published: May 2024

AbstractTuberculosis (TB) is a major cause of morbidity and mortality worldwide despite widespread intradermal (ID) BCG vaccination in newborns. We previously demonstrated that changing the route and dose of BCG vaccination from 5ξ105CFU ID to 5ξ107CFU intravenous (IV) resulted in prevention of infection and disease in a rigorous, highly susceptible non-human primate model of TB. Identifying the immune mechanisms of protection for IV BCG will facilitate development of more effective vaccines against TB. Here, we depleted select lymphocyte subsets in IV BCG vaccinated macaques prior to Mtb challenge to determine the cell types necessary for that protection. Depletion of CD4 T cells or all CD8α expressing lymphoycytes (both innate and adaptive) resulted in loss of protection in most macaques, concomitant with increased bacterial burdens (∼4-5 log10 thoracic CFU) and dissemination of infection. In contrast, depletion of only adaptive CD8αβ+ T cells did not significantly reduce protection against disease. Our results demonstrate that CD4 T cells and innate CD8α+ lymphocytes are critical for IV BCG-induced protection, supporting investigation of how eliciting these cells and their functions can improve future TB vaccines.One Sentence SummaryAntibody depletion of lymphocytes in rhesus macques demonstrates key roles for CD4 T cells and innate-like CD8α+ lymphocytes in conferring sterilizing immunity against tuberculosis following intravenous BCG vaccination.
ADAPT: Analysis of Microbiome Differential Abundance by Pooling Tobit Models
Authors: Wang Mukai , Fontaine Simon , Jiang Hui , Li Gen 
Published: May 2024

AbstractMicrobiome differential abundance analysis remains a challenging problem despite multiple methods proposed in the literature. The excessive zeros and compositionality of metagenomics data are two main challenges for differential abundance analysis. We propose a novel method called “analysis of differential abundance by pooling Tobit models” (ADAPT) to overcome these two challenges. ADAPT uniquely treats zero counts as left-censored observations to facilitate computation and enhance interpretation. ADAPT also encompasses a theoretically justified way of selecting non-differentially abundant microbiome taxa as a reference for hypothesis testing. We generate synthetic data using independent simulation frameworks to show that ADAPT has more consistent false discovery rate control and higher statistical power than competitors. We use ADAPT to analyze 16S rRNA sequencing of saliva samples and shotgun metagenomics sequencing of plaque samples collected from infants in the COHRA2 study. The results provide novel insights into the association between the oral microbiome and early childhood dental caries.
Melanoma antigens in pediatric medulloblastoma contribute to tumor heterogeneity and species-specificity of group 3 tumors
Authors: Collins Rebecca R.J. , Gee Rebecca R. Florke , Sanchez Maria Camila Hoyos , Tozandehjani Sima , Bayat Tara , Breznik Barbara , Lee Anna K. , Peters Samuel T. , Connelly Jon P. , Pruett-Miller Shondra M. , Roussel Martine F. , Rakheja Dinesh , Tillman Heather S. , Potts Patrick Ryan , Fon Tacer Klementina 
Published: May 2024

AbstractBackgroundMedulloblastoma (MB) is the most malignant childhood brain cancer. Group 3 MB subtype accounts for about 25% of MB diagnoses and is associated with the most unfavorable outcomes. Herein, we report that more than half of group 3 MB tumors express melanoma antigens (MAGEs), which are potential prognostic and therapeutic markers. MAGEs are tumor antigens, expressed in several types of adult cancers and associated with poorer prognosis and therapy resistance; however, their expression in pediatric cancers is mostly unknown. The aim of this study was to determine whetherMAGEsare activated in pediatric MB.MethodsTo determineMAGEfrequency in pediatric MB, we obtained formalin-fixed paraffin-embedded tissue (FFPE) samples of 34 patients, collected between 2008 – 2015, from the Children’s Medical Center Dallas pathology archives and applied our validated reverse transcription quantitative PCR (RT-qPCR) assay to measure the relative expression of 23MAGEcancer-testis antigen genes. To validate our data, we analyzed several published datasets from pediatric MB patients and patient-derived orthotopic xenografts, totaling 860 patients. We then examined howMAGEexpression affects the growth and oncogenic potential of medulloblastoma cells by CRISPR-Cas9- and siRNA-mediated gene depletion.ResultsOur RT-qPCR analysis suggested thatMAGEswere expressed in group 3/4 medulloblastoma. Further mining of bulk and single-cell RNA-sequencing datasets confirmed that 50-75% of group 3 tumors activate a subset ofMAGEgenes. Depletion of MAGEAs, B2, and Cs alter MB cell survival, viability, and clonogenic growth due to decreased proliferation and increased apoptosis.ConclusionsThese results indicate that targeting MAGEs in medulloblastoma may be a potential therapeutic option for group 3 medulloblastomas.Key PointsSeveral Type IMAGECTAs are expressed in >60% of group 3 MBs.Type I MAGEs affect MB cell proliferation and apoptosis.MAGEsare potential biomarkers and therapeutic targets for group 3 MBs.Importance of the StudyThis study is the first comprehensive analysis of all Type IMAGECTAs (MAGEA,-B, and-Csubfamily members) in pediatric MBs. Our results show that more than 60% of group 3 MBs expressMAGEgenes, which are required for the viability and growth of cells in which they are expressed. Collectively, these data provide novel insights into the antigen landscape of pediatric MBs. The activation ofMAGEgenes in group 3 MBs presents potential stratifying and therapeutic options.Abstract Figure
ProteinCLIP: enhancing protein language models with natural language
Authors: Wu Kevin E. , Chang Howard , Zou James 
Published: May 2024

AbstractLanguage models have enabled a new era of biological sequence modeling. However, extracting meaningful sequence-level embeddings from these models remains challenging. In this work, we introduce ProteinCLIP, which applies contrastive learning between a protein’s amino acid sequence and curated text describing its function. ProteinCLIP thus learns to take a pre-trained protein language model’s sequence embedding and refines it produce a function-centric embedding. We show that this embedding space yields sequence representations that enable state-of-the-art performance across a variety of important yet challenging tasks in the study of proteins – from predicting protein protein interactions to accurately detecting homologous proteins despite low sequence similarity. More broadly, ProteinCLIP demonstrates the effectiveness of multi-modal learning in biological contexts, and how such strategies can help isolate key signals from large models and further improve their utility.