bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enabling automated and reproducible spatially resolved transcriptomics at scale
Authors: Stenbeck Linnea , Taborsak-Lines Fanny , Giacomello Stefania 
Published: March 2022

AbstractTissue spatial information is an essential component to reach a holistic overview of gene expression mechanisms. The sequencing-based Spatial transcriptomics approach allows to spatially barcode the whole transcriptome of tissue sections using microarray glass slides. However, manual preparation of high-quality tissue sequencing libraries is time-consuming and subjected to technical variability. Here, we present an automated adaptation of the 10x Genomics Visium library construction on the widely used Agilent Bravo Liquid Handling Platform. Compared to the manual Visium library preparation, our automated approach reduces hands-on time by over 80% and provides higher throughput and robustness. Our automated Visium library preparation protocol provides a new strategy to standardize spatially resolved transcriptomics analysis of tissues at scale.
A conserved mechanism regulates reversible amyloids via pH-sensing regions
Authors: Cereghetti Gea , Kissling Vera Maria , Koch Lisa Maria , Arm Alexandra , Afanasyev Pavel , Linsenmeier Miriam , Eichmann Cédric , Zhou Jiangtao , Cao Yiping , Pfizenmaier Dorota Maria , Kroschwald Sonja , Wiegand Thomas , Cadalbert Riccardo , Böhringer Daniel , Mezzenga Raffaele , Arosio Paolo , Riek Roland , Peter Matthias 
Published: March 2022

AbstractAmyloids were long viewed as irreversible, pathological aggregates, often associated with neurodegenerative diseases1. However, recent insights challenge this view, providing evidence that reversible amyloids can form upon stress conditions and fulfil crucial cellular functions2. Yet, the molecular mechanisms regulating functional amyloids and the differences to their pathological counterparts remain poorly understood. Here we investigate the conserved principles of amyloid reversibility by studying the essential metabolic enzyme pyruvate kinase (PK) in yeast and human cells. We demonstrate that PK forms stress-dependent reversible amyloids through a pH-sensitive amyloid core. Stress- induced cytosolic acidification promotes aggregate formation via protonation of specific glutamate (in yeast) or histidine (in human) residues within the amyloid core. Our work thus unravels a conserved and potentially widespread mechanism underlying amyloid functionality and reversibility, fine-tuned to the respective physiological cellular pH range.
Multi-modal Imaging of Disease Progression in TH-MYCN Mouse Models of Neuroblastoma
Authors: Badachhape Andrew A. , Tao Ling , Joshi Sanshuv , Starosolski Zbigniew , Devkota Laxman , Sarkar Poonam , Bhandari Prajwal , Annapragada Ananth V. , Barbieri Eveline , Ghaghada Ketan B. 
Published: March 2022

AbstractMYCN is a major driver for neuroblastoma (NB) and the tyrosine hydroxylase (TH)-MYCN transgenic mouse model is extensively used for preclinical NB studies. However, spatio-temporal NB progression in the TH-MYCN model has not been studied, and questions remain about the value of implanted models as a surrogate for transgenic mice. In this work, we used magnetic resonance imaging (MRI) to study tumor progression and nanoparticle contrast-enhanced computed tomography (n-CECT) to assess tumor vascular architecture in TH-MYCN transgenic mice (2–7 weeks of age) and TH-MYCN+/+-derived orthotopic allograft and syngeneic mice (2–5 weeks post-tumor implantation). Tumors in TH-MYCN transgenic mice became evident in the abdominal paraspinal region at week 5. A delayed thoracic paraspinal mass became evident at week 6 and most mice succumbed by week 7. In allograft and syngeneic mice, single mass tumor growth was restricted to the peritoneal cavity. N-CECT revealed a predominantly microvascular network in TH-MYCN tumors while implanted tumors exhibited heterogeneous and tortuous vessels. N-CECT quantitative analysis demonstrated high vascularity (tumor fractional blood volume ~ 0.12) in all models. Multi-modal imaging of TH-MYCN transgenic and implanted models revealed differences in growth patterns and vascular architecture that should be considered in designing preclinical studies.
Triple Notch/Tgfβ/FoxO1 blockade converts multiple intestinal sub-lineages into β-like cells and lowers glycemia in diabetic animals
Authors: Du Wen , Wang Junqiang , Kuo Taiyi , Wang Liheng , McKimpson Wendy M. , Son Jinsook , Watanabe Hitoshi , Kitamoto Takumi , Lee YunKyoung , Ratner Lloyd E. , McCune Kasi , Chen Ya-Wen , Grubbs Brendan H. , Thornton Matthew E. , Fan Jason , Sultana Nishat , Diaz Bryan , Balasubramanian Iyshwarya , Gao Nan , Belvedere Sandro , Accili Domenico 
Published: March 2022

AbstractInsulin is the essential treatment of Type 1 (T1D) and is often used in Type 2 Diabetes. For nearly five decades, efforts have been focused on replenishing β-cells in T1D patients as a more durable treatment. Gut endocrine cells can be converted into insulin-producing cells, but their numbers are limited. In this study we report that insulin-immunoreactive cells with Paneth/goblet cell features are present in human fetal intestine, in addition to enteroendocrine cells. Accordingly, lineage tracing experiments show that, besides enterochromaffin cells, the Paneth/goblet lineage can undergo conversion to the insulin lineage upon genetic or pharmacologic Foxo1 ablation in mice. We leveraged these data to design a screening platform in organoids to accurately quantitate β-like cell reprogramming and fine-tune a combination treatment to increase the efficiency of the conversion process by expanding the intestinal secretory lineage. We identified a triple blockade of FoxO1, Notch, and Tgfβ that, when tested in insulin-deficient diabetic animals resulted in a near-normalization of glucose levels, associated with the appearance of gut insulin-producing cells. The findings illustrate a therapeutic approach to replace insulin treatment in diabetes.
The CD58:CD2 axis is co-regulated with PD-L1 via CMTM6 and governs anti-tumor immunity
Authors: Ho Patricia , Melms Johannes C. , Rogava Meri , Frangieh Chris J. , Shah Shivem B. , Walsh Zachary , Kyrysyuk Oleksandr , Amin Amit Dipak , Caprio Lindsay , Fullerton Benjamin T. , Soni Rajesh , Ager Casey R. , Biermann Jana , Wang Yiping , Mu Michael , Fatima Hijab , Moore Emily K. , Vasan Neil , Bakhoum Samuel F. , Reiner Steven L. , Bernatchez Chantale , Mace Emily M. , Wucherpfennig Kai W. , Schadendorf Dirk , Schwartz Gary K. , Izar Benjamin 
Published: March 2022

ABSTRACTThe cell autonomous balance of immune-inhibitory and -stimulatory signals is a critical yet poorly understood process in cancer immune evasion. Using patient-derived co-culture models and humanized mouse models, we show that an intact CD58:CD2 interaction is necessary for anti-tumor immunity. Defects in this axis lead to multi-faceted immune evasion through impaired CD2-dependent T cell polyfunctionality, T cell exclusion, impaired intra-tumoral proliferation, and concurrent protein stabilization of PD-L1. We performed genome-scale CRISPR-Cas9 and CD58 coimmunoprecipitation mass spectrometry screens identifying CMTM6 as a key stabilizer of CD58, and show that CMTM6 is required for concurrent upregulation of PD-L1 in CD58 loss. Single-cell RNA-seq analysis of patient melanoma samples demonstrates that most TILs lack expression of primary costimulatory signals required for response to PD-1 blockade (e.g. CD28), but maintain strong CD2 expression, thus providing an opportunity to mobilize a so far therapeutically untapped pool of TILs for anti-tumor immunity. We identify two potential therapeutic avenues, including rescued activation of human CD2-expressing TILs using recombinant CD58 protein, and targeted disruption of PD-L1/CMTM6 interactions. Our work identifies an underappreciated yet critical axis at the nexus of cancer immunity and evasion, uncovers a fundamental mechanism of co-inhibitory and -stimulatory signal balancing, and provides new approaches to improving cancer immunotherapies.
Quantitative prediction of ensemble dynamics, shapes and contact propensities of intrinsically disordered proteins
Authors: Yu Lei , Brüschweiler Rafael 
Published: March 2022

ABSTRACTIntrinsically disordered proteins (IDPs) are highly dynamic systems that play an important role in cell signaling processes and their misfunction often causes human disease. Proper understanding of IDP function not only requires the realistic characterization of their three-dimensional conformational ensembles at atomic-level resolution but also of the time scales of interconversion between their conformational substates. Large sets of experimental data are often used in combination with molecular modeling to restrain or bias models to improve agreement with experiment. It is shown here for the N-terminal transactivation domain of p53 (p53TAD) and Pup how the latest advancements in molecular dynamics (MD) simulations methodology produces native conformational ensembles by combining replica exchange with series of microsecond MD simulations. They closely reproduce experimental data at the global conformational ensemble level, in terms of the distribution properties of the radius of gyration tensor, and at the local level, in terms of NMR properties including 15N spin relaxation, without the need for reweighting. The IDP ensembles were analyzed by graph theory to identify dominant inter-residue contact clusters and characteristic amino-acid contact propensities. These findings indicate that modern MD force fields with residue-specific backbone potentials can produce highly realistic IDP ensembles sampling a hierarchy of nano- and picosecond time scales providing new insights into their biological function.AUTHOR SUMMARYAccurate prediction of the conformational ensemble dynamics sans bias is shown for intrinsically disordered proteins including the transactivation domain of p53.
CROSS-GENERATIONAL IMPACT OF EPIGENETIC MALE INFLUENCE ON PHYSICAL ACTIVITY IN RAT
Authors: Sudakov Sergey K. , Bogdanova Natalia G. , Nazarova Galina A. 
Published: March 2022

AbstractThe aim of this work was to study whether epigenetic events at conception influence the formation of behavioral features found in adult rats. First generational inheritance of activity level, anxiety, and learning ability was studied. To separate genetic and non-genetic inheritance, mating of males and females with average motor activity was carried out in the presence males with high or low activity. Our results show that offspring of parents who mated in the presence of males with a high motor activity were significantly more active than offspring of parents that were paired in the presence of males with low activity. Anxiety level and learning ability were not inherited in this way. It is possible that the phenomenon we discovered is important for maintaining a certain level of activity of specific populations of animals. It counteracts natural selection, which should lead to a constant increase in the activity of animals.
Irc3 of the thermotolerant yeast Ogataea polymorpha is a branched-DNA-specific mitochondrial helicase
Authors: Piljukov Vlad-Julian , Sillamaa Sirelin , Sedman Tiina , Garber Natalja , Rätsep Margus , Freiberg Arvi , Sedman Juhan 
Published: March 2022

SummaryThe Saccharomyces cerevisiae Irc3 protein is a mitochondrial Superfamily II DNA helicase that, according to genomic data, is conserved in different yeast species. Here we characterize Irc3 helicase from the thermotolerant yeast Ogataea polymorpha (Irc3op) that throughout its helicase motor domain has approximately 82% similarity with the S. cerevisiae protein. Irc3op retains enzymatic activity at considerably higher temperatures than Irc3sc, displaying the fastest rate of ATP hydrolysis at 41 °C and a Tm of 45.3 °C for its secondary structure melting. We demonstrate that Irc3op is a structure-specific DNA helicase translocating on both single- and double-stranded DNA molecules. Like the homolog of S. cerevisiae, Irc3op can unwind only DNA molecules that contain branched structures. Different DNA molecules containing three- and four-way branches are utilized by Irc3op as unwinding substrates. Importantly, the preferred unwinding substrate of Irc3op is a DNA fork containing the nascent lagging strand, suggesting a possible role in replication restart following a block in leading strand polymerization. A lower unwinding efficiency of four-way branched DNA molecules could explain why Irc3op only partially complements the irc3Δ phenotype in S. cerevisiae.
Deep topographic proteomics of a human brain tumour
Authors: Davis Simon , Scott Connor , Oetjen Janina , Charles Philip D , Kessler Benedikt M , Ansorge Olaf , Fischer Roman 
Published: March 2022

AbstractThe spatial organisation of cellular protein expression profiles within tissue determines cellular function and is key to understanding disease pathology. To define molecular phenotypes in the spatial context of tissue, there is a need for unbiased, quantitative technology capable of mapping proteomes within tissue structures. Here, we present a workflow for spatially-resolved, quantitative proteomics of tissue that generates maps of protein abundance across tissue slices derived from a human atypical teratoid-rhabdoid tumour (AT/RT). We employ spatially-aware algorithms that do not require prior knowledge of the fine tissue structure to detect proteins and pathways with spatial abundance patterns. We identified PYGL, ASPH and CD45 as spatial markers for tumour boundary and reveal immune response-driven, spatially-organised protein networks of the extracellular tumour matrix. Overall, this work informs on methods for spatially resolved deep proteo-phenotyping of tissue heterogeneity, to push the boundaries of understanding tissue biology and pathology at the molecular level.
Disruption of the MICOS complex leads to an aberrant cristae structure and an unexpected, pronounced lifespan extension in Podospora anserina
Authors: Warnsmann Verena , Marschall Lisa-Marie , Meeßen Anja C. , Wolters Maike , Schürmanns Lea , Basoglu Marion , Eimer Stefan , Osiewacz Heinz D. 
Published: March 2022

AbstractMitochondria are dynamic eukaryotic organelles involved in a variety of essential cellular processes including the generation of adenosine triphosphate (ATP) and reactive oxygen species (ROS) as well as in the control of apoptosis and autophagy. Impairments of mitochondrial functions lead to aging and disease. Previous works with the ascomycete Podospora anserina demonstrated that mitochondrial morphotype as well as mitochondrial ultrastructure change during aging. The latter goes along with an age-dependent reorganization of the inner mitochondrial membrane leading to a change from lamellar cristae to vesicular structures. Especially from studies with yeast it is known that beside the F1Fo-ATP-synthase and the phospholipid cardiolipin also the ‘mitochondrial contact site and cristae organizing system’ (MICOS) complex, existing of the Mic60- and Mic10-subcomplex, is essential for proper cristae formation. In the present study, we aimed to understand the mechanistic basis of age-related changes of the mitochondrial ultrastructure. We observed that MICOS subunits are co-regulated at the posttranscriptional level. This regulation partially depends on the mitochondrial iAAA-protease PaIAP. Most surprisingly, we made the counterintuitive observation that, despite the loss of lamellar cristae and of mitochondrial impairments, the ablation of MICOS subunits (except of PaMIC12) leads to a pronounced lifespan extension. Moreover, simultaneous ablation of subunits of both MICOS subcomplexes synergistically increases lifespan, providing formal genetic evidence that both subcomplexes affect lifespan by different and at least partially independent pathways. At the molecular level we found that ablation of Mic10-subcomplex components leads to a mitohormesis-induced lifespan extension, while lifespan extension of Mic60-subcomplex mutants seems to be controlled by another pathway. Overall, our data demonstrate that both MICOS subcomplexes have different functions and play distinct roles in the aging process of P. anserina.
Transcriptomic response to ISAV infection in the gills, head kidney and spleen of resistant and susceptible Atlantic salmon
Authors: Gervais O. , Papadopoulou A. , Gratacap R. , Hillestad B. , Tinch A.E. , Martin S.A.M. , Houston R.D. , Robledo D. 
Published: March 2022

ABSTRACTBackgroundInfectious Salmonid Anaemia virus (ISAV) is an orthomyxovirus responsible of large losses in Atlantic salmon (Salmo salar) aquaculture. Current available treatments and vaccines are not fully effective, and therefore selective breeding to produce ISAV-resistant strains of Atlantic salmon (Salmo salar) is a high priority for the industry. Genomic selection and potentially genome editing can be applied to enhance the disease resistance of aquaculture stocks, and both approaches can benefit from increased knowledge on the genomic mechanisms of resistance to ISAV. To improve our understanding of the mechanisms underlying resistance to ISAV in Atlantic salmon we performed a transcriptomic study in ISAV-infected salmon with contrasting levels of resistance to this virus.ResultsThree different tissues (gills, head kidney and spleen) were collected on 12 resistant and 12 susceptible fish at three timepoints (pre-challenge, 7 and 14 days post infection) and RNA sequenced. The transcriptomes of Infected and non-infected fish and of resistant and susceptible fish were compared at each timepoint. The results show that the responses to ISAV are organ-specific; an important response to the infection was observed in the head kidney, with up-regulation of immune processes such as interferon and NLR pathways, while in gills and spleen the response was more moderate. In addition to immune related genes our results suggest that other processes such as ubiquitination or ribosomal processing are important during early infection to ISAV. Moreover, the comparison between resistant and susceptible have also highlighted some interesting genes related to ubiquitination, intracellular transport or the inflammasome.ConclusionsAtlantic salmon infection by ISAV revealed an organ-specific response, implying differential function during the infection. An early immune response was observed in the head kidney, while gills and spleen showed modest responses in comparison. Comparison between resistance and susceptible samples have highlighted genes of interest for further studies, for instance those related to ubiquitination or the inflammasome.
Synergistic regulation of Notch signaling by different O-glycans promotes hematopoiesis
Authors: Tanwar Ankit , Stanley Pamela 
Published: March 2022

AbstractGlycosylation of Notch receptors by O-fucose glycans regulates Notch ligand binding and Notch signaling during hematopoiesis. However, roles in hematopoiesis for other O-glycans that modify Notch receptors have not been determined. Here we show that the EGF domain-specific GlcNAc transferase EOGT is required in mice for the optimal production of lymphoid and myeloid cells. The phenotype of Eogt null mice was largely cell-autonomous, and Notch target gene expression was reduced in T cell progenitors. Moreover, EOGT supported residual Notch signaling following conditional deletion of Pofut1 in hematopoietic stem cells (HSC). Eogt:Pofut1 double mutant HSC had more severe defects in bone marrow, and in T and B cell development in thymus and spleen, compared to deletion of Pofut1 alone. The combined results show that EOGT and O-GlcNAc glycans are required for optimal hematopoiesis and T and B cell development, and that they act synergistically with POFUT1 and O-fucose glycans to promote Notch signaling in lymphoid and myeloid differentiation.Key pointsO-GlcNAc glycans and EOGT promote lymphopoiesis and myelopoiesisEOGT supports Notch signaling in the absence of POFUT1 and O-fucose glycans
Proteasomal subunit depletions differentially affect germline integrity in C. elegans
Authors: Fernando Lourds Michelle , Quesada-Candela Cristina , Murray Makaelah , Ugoaru Caroline , Yanowitz Judith L. , Allen Anna K. 
Published: March 2022

AbstractThe 26S proteasome is a multi-subunit protein complex that is canonically known for its ability to degrade proteins in cells and maintain protein homeostasis. Non-canonical or non-proteolytic roles of proteasomal subunits exist, but remain less well studied. We provide characterization of germline-specific functions of different 19S RP proteasome subunits in C. elegans using RNAi specifically from the L4 stage and through generation of endogenously tagged 19S RP lid subunit strains. We show functions for the 19S RP in regulation of proliferation and maintenance of integrity of mitotic zone nuclei, in polymerization of the synaptonemal complex (SC) onto meiotic chromosomes and in the timing of SC subunit redistribution to the short arm of the bivalent, and in turnover of XND-1 proteins at late pachytene. Furthermore, we report that certain 19S RP subunits are required for proper germ line localization of WEE-1.3, a major meiotic kinase. Additionally, endogenous fluorescent labeling revealed that the two isoforms of the essential 19S RP proteasome subunit RPN-6.1 are expressed in a tissue-specific manner in the hermaphrodite. Also, we demonstrate that the 19S RP subunits RPN-6.1 and RPN-7 are crucial for the nuclear localization of the lid subunits RPN-8 and RPN-9 in oocytes, potentially introducing C. elegans germ line as model to study proteasome assembly real-time. Collectively, our data support the premise that certain 19S RP proteasome subunits are playing tissue-specific roles, especially in the germ line. We propose C. elegans as a versatile multicellular model to study the diverse proteolytic and non-proteolytic roles that proteasome subunits play in vivo.
Prot2Prot: A Deep Learning Model for Rapid, Photorealistic Macromolecular Visualization
Authors: Durrant Jacob D. 
Published: March 2022

AbstractMotivationMolecular visualization is a cornerstone of structural biology, providing insights into the form and function of biomolecules that are difficult to achieve any other way. Scientific analysis, publication, education, and outreach often benefit from photorealistic molecular depictions rendered using advanced computer-graphics programs such as Maya, 3ds Max, and Blender. However, setting up molecular scenes in these programs can be laborious even for expert users, and rendering often requires substantial time and computer resources.ResultsWe have created a deep-learning model called Prot2Prot that quickly imitates photorealistic visualization styles, given a much simpler, easy-to-generate molecular representation. The resulting images are often indistinguishable from images rendered using industry-standard 3D graphics programs, but they can be created in a fraction of the time, even when running in a web browser. To the best of our knowledge, Prot2Prot is the first example of image-to-image translation applied to macromolecular visualization.AvailabilityProt2Prot is available free of charge, released under the terms of the Apache License, Version 2.0. Users can access a Prot2Prot-powered web app without registration at http://durrantlab.com/prot2prot.