bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole mouse body histology using standard IgG antibodies
Authors: Mai Hongcheng , Luo Jie , Hoeher Luciano , Al-Maskari Rami , Horvath Izabela , Paetzold Johannes C. , Todorov Mihail , Hellal Farida , Ertürk Ali 
Published: February 2023

ABSTRACTMost diseases involve multiple interconnected physiological systems, but histological evaluation of their pathology is currently limited to small tissue samples. Here, we present wildDISCO, a technology that uses cholesterol extraction to enable deep tissue penetration of standard 150 kDa IgG antibodies in chemically fixed whole mice. Combining wildDISCO with whole mouse clearing, we generate whole-body maps of the nervous, immune, and lymphatic systems and show their close interactions throughout the mouse body.Graphical AbstractHighlightsWildDISCO uses new tissue chemistry based on β-cyclodextrin to enable histology in whole mouse bodies using full-size antibodiesWildDISCO generates the first whole mouse body atlases for neurons, immune cells, blood and lymph vesselsThe whole mouse atlases are available online to study the biological systems in health and diseaseVirtual Reality (VR) exploration of these atlases disentangles complex anatomical structures between organs and biological systemsSupplementary Videos can be seen athttp://discotechnologies.org/wildDISCO/
Classification of Multiple Emotional States from Facial Expressions in Mice using a Deep Learning-Based Image Analysis
Authors: Takana Yudai , Nakata Takuto , Hibino Hiroshi , Nishiyama Masaaki , Ino Daisuke 
Published: February 2023

ABSTRACTFacial expressions are widely recognized as universal indicators of underlying internal states in most species of animals, thereby presenting as a non-invasive measure for predicting physical and mental conditions. Despite the advancement of artificial intelligence-assisted tools for automated analysis of voluminous facial expression data in human subjects, the corresponding tools for mice still remain limited so far. Considering that mice are the most prevalent model animals for studying human health and diseases, a comprehensive characterization of emotion-dependent patterns of facial expressions in mice could extend our knowledge on the basis of emotions and the related disorders. Here, we present a framework for the development of a deep learning-powered tool for classifying mouse facial expressions. We demonstrate that our machine vision was capable of accurately classifying three different emotional states from mouse facial images. Moreover, we objectively determined how our classifier characterized the differences among the facial images through the use of an interpretation technique called Gradient-weighted Class Activation Mapping. Our approach is likely to facilitate the non-invasive decoding of a variety of emotions from facial images in mice.
Yeast cell responses and survival during periodic osmotic stress are controlled by glucose availability
Authors: Duveau Fabien , Cordier Céline , Chiron Lionel , LeBec Matthias , Pouzet Sylvain , Séguin Julie , Llamosi Artémis , Sorre B. , Meglio Jean-Marc Di , Hersen Pascal 
Published: February 2023

AbstractNatural environments of living organisms are often dynamic and multifactorial, with multiple parameters fluctuating over time. To better understand how cells respond to dynamically interacting factors, we quantified the effects of dual fluctuations of osmotic stress and glucose deprivation on yeast cells using microfluidics and time-lapse microscopy. Strikingly, we observed that cell proliferation, survival and signaling depend on the phasing of the two periodic stresses. Cells divided faster, survived longer and showed decreased transcriptional response when fluctuations of hyperosmotic stress and glucose deprivation occurred in phase than when the two stresses occurred alternatively. Therefore, glucose availability regulates yeast responses to dynamic osmotic stress, showcasing the key role of metabolic fluctuations in cellular responses to dynamic stress. We also found that mutants with impaired osmotic stress response were better adapted to alternating stresses than wild-type cells, showing that genetic mechanisms of adaptation to a persistent stress factor can be detrimental under dynamically interacting conditions.
Structural Conservation of Insulin/IGF Signalling Axis at the Insulin Receptors Level inDrosophilaand humans
Authors: Viola Cristina M. , Frittmann Orsolya , Jenkins Huw T. , Shafi Talha , Meyts Pierre De , Brzozowski Andrzej M. 
Published: February 2023

ABSTRACTThe insulin-related hormones regulate key life processes in Metazoa, from metabolism to growth, lifespan and aging, through an evolutionarily conserved insulin signalling axis (IIS). In humans the IIS axis is controlled by insulin, two insulin-like growth factors, two isoforms of the insulin receptor (hIR-A and -B), and its homologous IGF-1R. InDrosophila, this signalling engages seven insulin-like hormones (DILP1-7) and a single receptor (dmIR). This report describes the cryoEM structure of the dmIR ectodomain:DILP5 complex, revealing high structural homology between dmIR and hIR. The excess of DILP5 yields dmIR complex in an asymmetric ‘T’ conformation, similar to that observed in some complexes of human IRs. However, dmIR binds three DILP5 molecules in a hitherto-unseen arrangement, showing also dmIR-specific features. This work adds structural support to evolutionary conservation of the IIS axis at the IR level, underpinning also a better understanding of an important model organism.
Assessing preferences for adult vs juvenile features in young animals: newly-hatched chicks spontaneously approach red and large stimuli
Authors: Freeland Laura , Vasas Vera , Gomes Josephine , Versace Elisabetta 
Published: February 2023

AbstractYoung precocial birds benefit from staying close to both their mother and siblings, while prioritising adults, which provide better care. Which features of the stimuli are used by young birds to prioritise attachment to adults over siblings is unknown. We started to address this question in newly hatched domestic chicks (Gallus gallus), focusing on their spontaneous preferences for visual stimuli that systematically vary between adult and juvenile chickens: size (larger in adults than in juveniles) and colour (darker and redder in adults than in juveniles). Overall, chicks at their first visual experience, that had never seen a conspecific beforehand, were most attracted to the red and large stimuli (two adult features) and interacted with red stimuli more than with yellow stimuli. When tested with red large vs. small objects (Exp. 1), chicks preferred the large shape. When tested with yellow large and small objects (Exp. 2), chicks did not show a preference. These results suggest that the combination of size and colour form the predisposition that helps chicks to spontaneously discriminate between adult and juvenile features from the first stages of life, in the absence of previous experience.
Hsp70/Hsp90 organizing protein (HOP) maintains CRAF kinase activity and regulates MAPK signaling by enhancing Hsp90-CRAF association
Authors: Gayen Nilanjan , Mitra Sahana , Roy Somesh , Mandal Atin K. 
Published: February 2023

AbstractThe stability and activity of CRAF kinase are stringently regulated by heat shock protein 90 (Hsp90). Hsp90-mediated client folding and maturation is governed by its co-chaperones, but their functionality in chaperoning CRAF/Raf1 kinase to accomplish signaling under physiological conditions remains poorly understood. Here, we show that Hsp70/Hsp90 organizing protein (HOP) associates with CRAF kinase for maintaining its kinase activity and facilitates the activation of the MAPK pathway. Such activation is mediated by TPR2A-2B-DP2 domain of HOP and requires efficient binding to Hsp90. Being a recruiter of Hsp90, Cdc37 is unable to supplement the function of HOP/Sti1. Downregulation of HOP/Sti1 in yeast andin vitrocell culture significantly reduces the CRAF signaling. Our data suggest that Hsp90 is recruited to CRAF in two steps, separately initiated by co-chaperones HOP and Cdc37 respectively during CRAF folding/maturation, and again upon CRAF activation mediated by HOP during MAPK signaling. Therefore, HOP is a regulator of CRAF kinase during activation of MAPK pathway and serves as a sensor of growth signaling beyond its client folding and maturation function.
Sequence assignment validation in protein crystal structure models with checkMySequence
Authors: Chojnowski Grzegorz 
Published: February 2023

AbstractSequence register shifts remain one of the most elusive errors in experimental macromolecular models. They may affect model interpretation and propagate to newly built models from older structures. In a recent publication I have shown that register shifts in cryo-EM models of proteins can be detected using a systematic re-assignment of short model fragments to the target sequence. Here, I show that the same approach can be used to detect register shifts in crystal structure models using standard, model-bias corrected electron-density maps. I describe in detail five register shift errors detected using the method in models deposited in the PDB.SynopsisI show thatcheckMySequence, an automated method for validating sequence assignment in cryo-EM structures of proteins, can be used for validating crystal structure models.
Diversity in the internal functional feeding elements of sympatric morphs of Arctic charr (Salvelinus alpinus)
Authors: Jónsdóttir Guðbjörg Ósk , von Elm Laura-Marie , Ingimarsson Finnur , Tersigni Samuel , Snorrason Sigurður Sveinn , Pálsson Arnar , Steele Sarah Elizabeth 
Published: February 2023

AbstractThe diversity of functional feeding anatomy is particularly impressive in fishes and correlates with various interspecific ecological specializations. Intraspecific polymorphism can manifest in divergent feeding morphology and ecology, often along a benthic–pelagic axis. Arctic charr (Salvelinus alpinus) is a freshwater salmonid known for morphological variation and sympatric polymorphism and in Lake Þingvallavatn, Iceland, four morphs of charr coexist that differ in preferred prey, behaviour, habitat use, and external feeding morphology. We studied variation in six upper and lower jaw bones in adults of these four morphs using geometric morphometrics and univariate statistics. We tested for allometric differences in bone size and shape among morphs, morph effects on bone size and shape, and divergence along the benthic-pelagic axis. We also examined the degree of integration between bone pairs. We found differences in bone size between pelagic and benthic morphs for two bones (dentary and premaxilla). There was clear bone shape divergence along a benthic–pelagic axis in four bones (dentary, articular-angular, premaxilla and maxilla), as well as allometric shape differences between morphs in the dentary. Notably for the dentary, morph explained more shape variation than bone size. Comparatively, benthic morphs possess a compact and taller dentary, with shorter dentary palate, consistent with visible (but less prominent) differences in external morphology. As these morphs emerged in the last 10,000 years, these results indicate rapid functional evolution of specific feeding structures in arctic charr. This sets the stage for studies of the genetics and development of rapid and parallel craniofacial evolution.
doubleHelix: nucleic acid sequence identification, assignment and validation tool for cryo-EM and crystal structure models
Authors: Chojnowski Grzegorz 
Published: February 2023

ABSTRACTSequence assignment is a key step of the model building process in both cryogenic electron microscopy (cryo-EM) and macromolecular crystallography (MX). If the assignment fails, it can result in difficult to identify errors affecting the interpretation of a model. There are many model validation strategies that help experimentalists in this step of protein model building, but they are virtually non-existent for nucleic acids. Here I present doubleHelix – a comprehensive method for assignment, identification, and validation of nucleic acid sequences in structures determined using cryo-EM and MX. The method combines a neural network classifier of nucleobase identities and a sequence-independent secondary structure assignment approach. I show that the presented method can successfully assist model building at lower resolutions, where visual map interpretation is very difficult. Moreover, I present examples of sequence assignment errors detected using doubleHelix in cryo-EM and MX structures of ribosomes deposited in the Protein Data Bank, which escaped the scrutiny of available model-validation approaches.The doubleHelix program source code is available under BSD-3 license athttps://gitlab.com/gchojnowski/doublehelix.
Hepatitis delta virus RNA decline post inoculation in human NTCP transgenic mice is biphasic
Authors: Maya Stephanie , Hershkovich Leeor , Cardozo-Ojeda E Fabian , Shirvani-Dastgerdi Elham , Srinivas Jay , Shekhtman Louis , Uprichard Susan L , Berneshawi Andrew R , Cafiero Thomas R , Dahari Harel , Ploss Alexander 
Published: February 2023

ABSTRACTBackground and AimsChronic infection with hepatitis B and hepatitis delta viruses (HDV) is considered the most serious form of viral hepatitis due to more severe manifestations of and accelerated progression to liver fibrosis, cirrhosis, and hepatocellular carcinoma. There is no FDA-approved treatment for HDV and current interferon-alpha treatment is suboptimal. We characterized early HDV kinetics post inoculation and incorporated mathematical modeling to provide insights into host-HDV dynamics.MethodsWe analyzed HDV RNA serum viremia in 192 immunocompetent (C57BL/6) and immunodeficient (NRG) mice that did or did not transgenically express the HDV receptor - human sodium taurocholate co-transporting peptide (hNTCP).ResultsKinetic analysis indicates an unanticipated biphasic decline consisting of a sharp first-phase and slower second-phase decline regardless of immunocompetence. HDV decline after re-inoculation again followed a biphasic decline; however, a steeper second-phase HDV decline was observed in NRG-hNTCP mice compared to NRG mice. HDV-entry inhibitor bulevirtide administration and HDV re-inoculation indicated that viral entry and receptor saturation are not major contributors to clearance, respectively. The biphasic kinetics can be mathematically modeled by assuming the existence of a non-specific binding compartment with a constant on/off-rate and the steeper second-phase decline by a loss of bound virus that cannot be returned as free virus to circulation. The model predicts that free HDV is cleared with a half-life of 18 minutes (standard error, SE: 2.4), binds to non-specific cells with a rate of 0.06 hour-1(SE: 0.03), and returns as free virus with a rate of 0.23 hour-1(SE: 0.03).ConclusionsUnderstanding early HDV-host kinetics will inform pre-clinical therapeutic kinetic studies on how the efficacy of anti-HDV therapeutics can be affected by early kinetics of viral decline.LAY SUMMARYThe persistence phase of HDV infection has been studied in some animal models, however, the early kinetics of HDV in vivo is incompletely understood. In this study, we characterize an unexpectedly HDV biphasic decline post inoculation in immunocompetent and immunodeficient mouse models and use mathematical modeling to provide insights into HDV-host dynamics. Understanding the kinetics of viral clearance in the blood can aid pre-clinical development and testing models for anti-HDV therapeutics.
Vimentin supports cell polarization by enhancing centrosome function and microtubule acetylation
Authors: Saldanha Renita , Ho Thanh Minh Tri , Krishnan Nikhila , Hehnly Heidi , Patteson Alison 
Published: February 2023

AbstractCell polarity is important for controlling cell shape, motility, and cell division processes. Vimentin intermediate filaments are necessary for proper polarization of migrating fibroblasts and assembly of vimentin and microtubule networks is dynamically coordinated, but the precise details of how vimentin mediates cell polarity remain unclear. Here, we characterize the effects of vimentin on the structure and function of the centrosome and the stability of microtubule filaments in wild-type and vimentin-null mouse embryonic fibroblasts (mEFs). We find that vimentin mediates the structure of the pericentrosomal material, promotes centrosome-mediated microtubule regrowth, and increases the level of stable acetylated microtubules in the cell. Loss of vimentin also impairs centrosome repositioning during cell polarization and migration processes that occur during wound closure. Our results suggest that vimentin modulates centrosome structure and function as well as microtubule network stability, which has important implications for how cells establish proper cell polarization and persistent migration.
HECTD1 is both a positive regulator and substrate of caspase-3 activity during apoptotic cell death
Authors: Scholz Nico , Siebzehnrubl Florian , Licchesi Julien D. F 
Published: February 2023

AbstractProgrammed cell death is a complex and tightly regulated sequence of events that determines cell fate during tissue homeostasis, development, and pathogenesis. The small protein modifier ubiquitin mediates important regulatory functions during cell death by regulating the stability and activity of checkpoint proteins and the assembly of cell death signalling complexes. The caspase family of cysteine aspartases are essential effectors of apoptotic cell death. Components of the ubiquitin system including RING ubiquitin ligases XIAP, MDM2, RBX1; RBR E3 ubiquitin ligases Parkin and LUBAC; and HECT E3 ubiquitin ligases NEDD4 and Itch are also substrates of caspase-mediated cleavage. In the case of NEDD4 and Itch, the single cleavage event occurs outside of the catalytic HECT domain and it remains unclear whether such cleavage events impact on ubiquitin ligase activity and/or function. Here, we identified the E3 ubiquitin ligase HECTD1 as the third HECT E3 cleaved by caspase-mediated cleavage during apoptotic cell death, in a manner which does not affect the integrity of the catalytic C-ter HECT domain. We mapped the single cleavage event to DFLD1664↓S and showed that the cleaved C-ter product, which contains the HECT ligase domain, is as stable as the endogenous full length protein. We also found that HECTD1 transient depletion led to reduced caspase-3 activity, but not caspase 8 nor 9. Furthermore, we also identified caspase-3 as the protease responsible for HECTD1 cleavage at Asp1664 suggesting that HECTD1 and caspase-3 might be part of a novel feedback loop mechanism during apoptotic cell death. This study highlight novel crosstalk between cell death mechanisms and the ubiquitin system and raises important questions on whether proteolytic cleavage of E3 ubiquitin ligases might represent an underappreciated mode of regulation during cell death mechanisms.
Age-related changes in network controllability are mitigated by redundancy in large-scale brain networks
Authors: Stanford William , Mucha Peter J. , Dayan Eran 
Published: February 2023

AbstractThe aging brain undergoes major changes in its topology. The mechanisms by which the brain mitigates age-associated changes in topology to maintain robust control of brain networks are unknown. Here we used diffusion MRI data from cognitively intact participants (n=480, ages 40-90) to study age-associated changes in the controllability of structural brain networks, features that could mitigate these changes, and the overall effect on cognitive function. We found age-associated declines in controllability in control hubs and large-scale networks, particularly within the and frontoparietal control and default mode networks. Redundancy, quantified via the assessment of multi-step paths within networks, mitigated the effects of changes in topology on network controllability. Lastly, network controllability, redundancy, and grey matter volume each played important complementary roles in cognitive function. In sum, our results highlight the importance of redundancy for robust control of brain networks and in cognitive function in healthy-aging.
Astrocytic TIMP-1 regulates production of Anastellin, a novel inhibitor of oligodendrocyte differentiation and FTY720 responses
Authors: Sutter Pearl A. , Willis Cory M. , Menoret Antoine , Nicaise Alexandra M. , Sacino Anthony , Sikkema Arend. H. , Jellison Evan , Win Kyaw K. , Han David K. , Church William , Baron Wia , Vella Anthony T. , Crocker Stephen J. 
Published: February 2023

AbstractAstrocyte activation is associated with neuropathology and the production of tissue inhibitor of metalloproteinase-1 (TIMP1). TIMP1 is a pleiotropic extracellular protein that functions both as a protease inhibitor and as a growth factor. We have previously demonstrated that murine astrocytes that lack expression ofTimp1do not support rat oligodendrocyte progenitor cell (rOPC) differentiation, and adult globalTimp1knockout (Timp1KO) mice do not efficiently remyelinate following a demyelinating injury. To better understand the basis of this, we performed unbiased proteomic analyses and identified a fibronectin-derived peptide called anastellin that is unique to the murineTimp1KOastrocyte secretome. Anastellin was found to block rOPC differentiationin vitroand enhanced the inhibitory influence of fibronectin on rOPC differentiation. Anastellin is known to act upon the sphingosine-1-phosphate receptor 1 (S1PR1), and we determined that anastellin also blocked the pro-myelinating effect of FTY720 (or fingolimod) on rOPC differentiationin vitro. Further, administration of FTY720 to wild-type C57BL/6 mice during MOG35-55-EAE ameliorated clinical disability while FTY720 administered to mice lacking expression ofTimp1in astrocytes (Timp1cKO) had no effect. Analysis of humanTIMP1and fibronectin (FN1) transcripts from healthy and multiple sclerosis (MS) patient brain samples revealed an inverse relationship where lowerTIMP1expression was coincident with elevatedFN1in MS astrocytes. Lastly, we analyzed proteomic databases of MS samples and identified anastellin peptides to be more abundant in the cerebrospinal fluid (CSF) of human MS patients with high versus low disease activity. The prospective role for anastellin generation in association with myelin lesions as a consequence of a lack of astrocytic TIMP-1 production could influence both the efficacy of fingolimod responses and the innate remyelination potential of the the MS brain.Significance StatementAstrocytic production of TIMP-1 prevents the protein catabolism of fibronectin. In the absence of TIMP-1, fibronectin is further digested leading to a higher abundance of anastellin peptides that can bind to sphingosine-1-phosphate receptor 1. The binding of anastellin with the sphingosine-1-phosphate receptor 1 impairs the differentiation of oligodendrocytes progenitor cells into myelinating oligodendrocytesin vitro, and negates the astrocyte-mediated therapeutic effects of FTY720 in the EAE model of chronic CNS inflammation. These data indicate that TIMP-1 production by astrocytes is important in coordinating astrocytic functions during inflammation. In the absence of astrocyte produced TIMP-1, elevated expression of anastellin may represent a prospective biomarker for FTY720 therapeutic responsiveness.