bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular control of the lymphocyte death timer
Authors: Ruhle Michelle , Thomas Evan , Dann Edward , Gottscheber Nicole , Teh Charis E. , Gray Daniel H.D. , Dowling Mark R. , Heinzel Susanne , Hodgkin Philip D. 
Published: October 2023

ABSTRACTWhen stimulated, individual lymphocytes program times for division and death that are inherited within families, revealing a common timing mechanism transmitted over generations. Here we describe a threshold-based mechanism for the time to die. By comparing protein levels in control and apoptosis disabled cells, we show that death can be predicted by a cooperating ensemble of BCL-2 family proteins falling below a critical threshold. Single cell measurements predict the time of death with a simple formula, where an additional inhibition factor explains accelerated death induced by BH3 mimetic compounds. Thus, we identify the death timer as a protein-threshold device that underlies signal integration machinery. Together these results reveal that predicting lymphocyte behavior at single cell level, in complex environments, is possible with modular multiscale models that incorporate timers and heritability features of critical proteins.
Genome rearrangements drive evolution of ANK genes inWolbachia
Authors: Vostokova Ekaterina V. , Dranenko Natalia O. , Gelfand Mikhail S. , Bochkareva Olga O. 
Published: October 2023

AbstractIntroductionGenusWolbachiacomprises endosymbionts infecting many arthropods and nematodes; it is a model for studying symbiosis as its members feature numerous, diverse mutualistic and parasitic adaptations to different hosts. In contrast to nematode-infectingWolbachia,genomes of arthropod-infecting strains contain a high fraction of repetitive elements creating possibilities for multiple recombination events and causing genome rearrangements. The mechanisms and role of these features are still not fully understood.ResultsTransposons cover up to 18% of an arthropod-infectingWolbachiagenome and drive numerous genome rearrangements including inversions and segmental amplifications. ANK (ankyrin-repeat domain family) genes are also often found at the breakpoints of rearrangements, while less than 7% of them were found within locally collinear blocks (LCBs). We observed a strong correlation between the number of ANK genes and the genome size as well as significant overrepresentation of transposons adjacent to these genes. We also revealed numerous cases of integration of transposases to the ANK genes affecting the sequences and putative products of the latter. Our results uncover the role of mobile elements in the amplification and diversification of ANK genes.ConclusionsEvolution of arthropod-infectingWolbachiawas accompanied by diverse genome rearrangements driving the evolution of ANK genes important for bacteria-host interactions. This study demonstrates the effectiveness of our LCB-based approach to theWolbachiagenomics and provides a framework for understanding the impact of genome rearrangements on their rapid host adaptation.
Women’s representation in Indian academia and conferences
Authors: Muralidhar Shruti , Ananthanarayanan Vaishnavi 
Published: October 2023

Abstract/IntroductionIndian science academia has a dearth of women researchers at all levels. Not only are they under-represented, but they are also under-highlighted, under-mentored and overlooked for awards, grants and other career-advancing steps. To effectively address this problem and devise a solution for the inequity, we need data on the proportion of women faculty across multiple STEM institutions. Such a database, currently, does not exist. To fill this gap, we formed BiasWatchIndia to (1) document the inequities, and (2) provide real-time actionable data as a basis for future remedial steps. Along with collecting data on women representation at the faculty level in Indian STEM (science, technology, engineering and mathematics) academia, BiasWatchIndia also helps highlight the lack of women representation and gender imbalance in Indian STEM talks, conferences, workshops and panels. Based on our findings, we recommend several measures that need to be implemented by universities and institutes to challenge thestatus quochanges for women in Indian academia.
Evaluation of short-term hair follicle storage conditions for maintenance of RNA integrity
Authors: Harkin Eilís E. , Browne John A. , Murphy Barbara A. 
Published: October 2023

AbstractHair follicles provide an easily accessible tissue for interrogating gene expression in mammals. RNAlater® is a liquid storage solution that stabilises and preserves cellular RNA, eliminating the need to immediately process or freeze tissue specimens. The manufacturer advises storage of samples at 2-8°C overnight before transfer to –20°C. This study aimed to evaluate RNA integrity in hair follicle samples collected from horses, stabilized in RNAlater®, and stored under three short-term storage conditions. Mane hair samples complete with follicles were collected from three horses at a single time point. Approximately 15 hairs were placed in each of three 2 mL tubes containing 0.75ml RNAlater® solution. Test group A was stored at 4°C for 24-h, then decanted and stored at -20°C. Test groups B and C were stored at 4°C and 19°C (room temperature) respectively for 7 days, then decanted and stored at -20°C. RNA was isolated from all samples and RNA quantity and quality were measured. One-way ANOVA revealed no difference in RNA concentration (A:516 +/-125 ng/ml, B:273+/-93 ng/ml, C:476+/-176 ng/ml;P = 0.4293) or quality (A:9.5 +/-0.19, B:9.8+/-0.09, C:9.2+/-0.35 RIN; P = 0.3193) between the test groups. There were no group differences in mean Cycle Threshold values from qPCR validation assays confirming high-quality template cDNA. The results suggest that storage of hair follicles for one week in RNAlater® at cool or room temperature conditions will not compromise RNA integrity and will permit extended transport times from remote sampling locations without the need for freezing.
MIF Regulates M1 Macrophage Polarization via CD74/CXCR2/JNK Pathway and Mediates Aortic Dissection in Mice
Authors: Wang Lu , Wang Huishan , Yu Liming , Jiang Hui , Xia Lin 
Published: October 2023

AbstractBackgroundMacrophage polarization and vascular smooth muscle cell (VSMC) phenotypic switching are important features and critical targets in the progression of Aortic dissection (AD). High expression of macrophage migration inhibitory factor (MIF) in aortic and blood specimens has been observed in patients with aortic dissection, but its precise function and mechanism in AD are unknown. We aimed to clarify whether MIF mediates the development of aortic dissection via modulation of M1 macrophage polarization and its specific regulatory pathways.MethodsBased on the BAPN/Ang II-induced acute aortic dissection model and by intraperitoneal injection of the MIF antagonist ISO-1 to inhibit MIF activity in mice. We assayed macrophage infiltration, polarization, and VSMC phenotypic switching in the aorta of mice in each group. Further, we evaluated the polarizing effects of MIF on RAW264.7 cells directly or indirectly in vitro experiments and explored the specific cellular signaling pathways that mediate its function. At last, we evaluated the role and possible mechanisms of RAW264.7 cells with different degrees of polarization in inducing phenotypic switching of MOVAS cells based on a model of indirect co-culture of RAW264.7 cells with MOVAS cells.ResultsPharmacological inhibition of MIF decreased the incidence of BAPN/Ang II-induced aortic dissection and attenuated aortic vascular remodeling in mice by reducing M1 macrophage infiltration in mouse aorta. Through in vitro assays, we demonstrated that MIF could activate the intracellular JNK/c-Jun signaling pathway by targeting the CD74/CXCR2 receptor, promote M1 polarization and upregulate the expression of the M1 macrophage markers, iNOS, IL-18, and CD86 in RAW264.7 cells. Further experiments confirmed that upon co-culture with MIF-induced M1 macrophages, the NF-κB pathway was activated in MOVAS cells, inducing the onset of phenotypic switching and apoptosis.ConclusionsThe results indicated that MIF mediated macrophage polarization and regulated the progression of aortic dissection, which provided new scientific evidence for the pathogenesis of aortic dissection, and also suggested that MIF may be a potential preventive and therapeutic target for aortic dissection and aortic-related diseases.
HLTF Prevents G4 Accumulation and Promotes G4-induced Fork Slowing to Maintain Genome Stability
Authors: Bai Gongshi , Endres Theresa , Kühbacher Ulrike , Greer Briana H. , Peacock Emma M. , Crossley Magdalena P. , Sathirachinda Ataya , Cortez David , Eichman Brandt F. , Cimprich Karlene A. 
Published: October 2023

SummaryG-quadruplexes (G4s) form throughout the genome and influence important cellular processes, but their deregulation can challenge DNA replication fork progression and threaten genome stability. Here, we demonstrate an unexpected, dual role for the dsDNA translocase HLTF in G4 metabolism. First, we find that HLTF is enriched at G4s in the human genome and suppresses G4 accumulation throughout the cell cycle using its ATPase activity. This function of HLTF affects telomere maintenance by restricting alternative lengthening of telomeres, a process stimulated by G4s. We also show that HLTF and MSH2, a mismatch repair factor that binds G4s, act in independent pathways to suppress G4s and to promote resistance to G4 stabilization. In a second, distinct role, HLTF restrains DNA synthesis upon G4 stabilization by suppressing PrimPol-dependent repriming. Together, the dual functions of HLTF in the G4 response prevent DNA damage and potentially mutagenic replication to safeguard genome stability.
Spatial N-glycan rearrangement on α5β1integrin nucleates galectin-3 oligomers to determine endocytic fate
Authors: Shafaq-Zadah Massiullah , Dransart Estelle , Wunder Christian , Chambon Valérie , Valades-Cruz Cesar A. , Leconte Ludovic , Sarangi Nirod Kumar , Robinson Jack , Bai Siau-Kun , Regmi Raju , Cicco Aurélie Di , Hovasse Agnès , Bartels Richard , Nilsson Ulf J. , Cianférani-Sanglier Sarah , Leffler Hakon , Keyes Tia E. , Lévy Daniel , Raunser Stefan , Roderer Daniel , Johannes Ludger 
Published: October 2023

SummaryMembrane glycoproteins frequently adopt different conformations when altering between active and inactive states. Here, we discover a molecular switch that exploits dynamic spatial rearrangements of N-glycans during such conformational transitions to control protein function. For the conformationally switchable cell adhesion glycoprotein α5β1integrin, we find that only the bent-closed state arranges N-glycans to nucleate the formation of up to tetrameric oligomers of the glycan-binding protein galectin-3. We propose a structural model of how these galectin-3 oligomers are assembled and how they clamp the bent-closed state to prime it for endocytic uptake and subsequent retrograde trafficking to the Golgi for polarized distribution in cells. Our findings highlight an unexpectedly dynamic regulation of the glycan landscape at the cell surface to achieve oligomerization of galectin-3. Galectin-3 oligomers are thereby identified as decoders of defined spatial patterns of N-glycans and as functional extracellular interactors of specifically the bent- closed conformational state of α5β1integrin and possibly other family members.
Spatial protein and RNA analysis on the same tissue section using MICS technology
Authors: Neil Emily , Park Dongju , Hennessey Rebecca C. , DiBiasio Eric C. , DiBuono Michael , Lafayette Hanna , Lloyd Erica , Lo Hsinyi , Femel Julia , Makrigiorgos Alex , Soliman Sameh , Mangiardi Dominic , Praveen Paurush , Rüberg Silvia , Staubach Fabian , Hindman Ryan , Rothmann Thomas , Meyer Hansueli , Wantenaar Tanya , Wang Jinling , Müller Werner , Pinard Robert , Bosio Andreas 
Published: October 2023

AbstractSpatial Biology has evolved from the molecular characterization of microdissected cells to high throughput spatial RNA and protein expression analysis at scale. The main limitation of spatial technologies so far is the inability to resolve protein and RNA information in the same histological section. Here, we report for the first time the integration of highly multiplexed RNA and protein detection on the same tissue section. We developed a new, automated, spatial RNA detection method (RNAsky™), which is based on targeted rolling circle amplification and iterative staining. We combine RNAsky with MACSima™ Imaging Cyclic Staining (MICS) based protein analysis and show compatibility with subsequent standard hematoxylin and eosin (H&E) staining. Using both, open-source tools and our recently developed software suite MACS® iQ View, we demonstrate our multiomics MICS workflow by characterizing key immune-oncology markers at subcellular resolution across normal and diseased tissues.
Tri-n-butyl phosphate inhibits neurogenesis and motor functions during embryonic development in zebrafish
Authors: Chakraborty Gourav , Ahire Kedar , Joshi Bhgyashri , Patra Chinmoy 
Published: October 2023

AbstractTri-n-butyl phosphate (TBP), an organophosphate ester (OPE), is heavily used as a solvent in synthetic resins, inks, and adhesives and as an antifoaming agent in detergents and emulsion products. Further, it is used as a flame retardant and plasticizer in the fabric and electronics industry. Further, TBP is used to extract uranium, plutonium, and thorium. Thus, widespread uses of TBP in industrialized countries led to the release of TBP and its metabolites, dibutyl phosphate (DBP) and monobutyl phosphate (MBP), in the environment, including air, soil, and water, and get detected in human samples. Accumulating these OPEs over time in humans and other animals may develop toxicological effects. The reports also say OPEs contaminants pass through the mother-fetal transmission route and may affect embryonic development. However, the impact of TBP and its metabolites on vertebrate development has been poorly studied.Ex-Uterodevelopment, short generation time, high fecundity, optical transparency, and genetic and physiological similarity to humans make the zebrafish a preferred model for studying vertebrate development, organogenesis, small molecule screening, toxicological evaluation, etc. Thus, we aim to explore the toxic effects of TBP, DBP, and MBP on vertebrate organogenesis and overall embryonic development using zebrafish as a model organism. Our study found that TBP inhibits neural growth resulting in decreased spontaneous movements frequency at 22 and 28 hpf without altering the somite and overall embryonic growth in lower doses. In contrast, in lower concentrations, DBP-treated embryos showed normal neuronal and embryonic development and increased spontaneous movement frequency at 22 and 28 hpf. Further, we found that in higher concentrations, TBP is teratogenic, DBP is lethal to the embryos, and MBP did not show detectable toxic effects in the developing embryos. Altogether, we found that TBP inhibits neurogenesis, and its metabolite DBP is neuroexcitatory during embryonic development.
Transcriptomic Landscape of Hyperthyroidism in Mice Overexpressing Thyroid Stimulating Hormone
Authors: Yamauchi Ichiro , Sugawa Taku , Hakata Takuro , Yoshizawa Akira , Kita Tomoko , Kishimoto Yo , Kimura Sadahito , Kosugi Daisuke , Fujita Haruka , Okamoto Kentaro , Ueda Yohei , Fujii Toshihito , Taura Daisuke , Sakane Yoriko , Yasoda Akihiro , Inagaki Nobuya 
Published: October 2023

AbstractHyperthyroidism is a condition with excessive thyroid hormone secretion. Activation of thyroid stimulating hormone receptor (TSHR) fundamentally leads to hyperthyroidism. The details of TSHR signaling remain to be elucidated. We conducted transcriptome analyses for hyperthyroid mice that we generated by overexpressing TSH. TSH overexpression via hydrodynamic gene delivery with pLIVE-TSHBand pLIVE-CGAvectors consistently caused hyperthyroidism and goiters for at least 4 weeks in C57BL/6J mice. RNA sequencing analysis of their thyroid glands revealed that thiamazole slightly changed the thyroid transcriptome, which reinforces a conventional theory that thiamazole decreases thyroid hormone secretion via inhibition of thyroid peroxidase activity. Meanwhile, TSH overexpression drastically changed the thyroid transcriptome. In particular, enrichment analyses identified the cell cycle, phosphatidylinositol-3 kinase/Akt pathway, and Ras-related protein 1 pathway as possibly associated with goiter development. Regarding the role of TSHR signaling in hyperthyroidism, it is noteworthy thatSlc26a4was exclusively upregulated among genes crucial to thyroid hormone secretion at both 1 and 4 weeks after hydrodynamic gene delivery. To verify the relationship between this upregulation and hyperthyroidism, we overexpressed TSH inSlc26a4knockout mice. TSH overexpression caused hyperthyroidism inSlc26a4knockout mice, equivalent to that in control mice. To summarize, we analyzed hyperthyroid mice generated by TSH overexpression. We did not observe significant changes in known genes and pathways involved in thyroid hormone secretion. Thus, our datasets might include candidate genes that have not yet been identified as regulators of thyroid function. Our transcriptome datasets regarding hyperthyroidism can contribute to future research on TSHR signaling.
A high-content RNA-based imaging assay reveals integrin beta 1 as a cofactor for cell entry of non-enveloped hepatitis E virus
Authors: Fu Rebecca , Engels Zoé , Weihs Jasmin Alara , Mürle Josias , Klöhn Mara , Todt Daniel , Hu Jungen , Steinmann Eike , Böttler Tobias , Lozach Pierre-Yves , Lemon Stanley M. , Thi Viet Loan Dao 
Published: October 2023

AbstractHepatitis E virus (HEV) is a major cause of acute hepatitis and mainly transmitted faecal-orally. HEV particles in faeces are non-enveloped, while those in the blood possess a cell-derived lipid envelope. Despite being a global health concern, there is limited understanding of the steps in the HEV life cycle, particularly cell entry. A previous study proposed integrin alpha 3 (ITGA3) as a potential host factor for nHEV entry, but the β-integrin partner that co-mediates HEV entry has not been described. To address this knowledge gap and resolve the existing controversies surrounding HEV cell entry, we developed an RNA-FISH-based high-content imaging assay alllowing investigation of the entry pathways of both naked and enveloped HEV particles. Our observations indicate that naked HEV particles interact with the surface receptor integrin beta 1 (ITGB1), which likely facilitates their trafficking through the recycling endosome. In contrast, enveloped HEV particles do not interact with ITGB1 and instead use the classical endocytic pathway via the early endosome. Importantly, both forms of HEV require endosomal acidification and proteolytic cleavage by lysosomal cathepsins, which ultimately results in delivery of the HEV genome to the cytoplasm.
Placode and neural crest origins of congenital deafness in mouse models of Waardenburg-Shah syndrome
Authors: Tan Jamie , Duron Alicia , Sucov Henry M. , Makita Takako 
Published: October 2023

SummaryMutations in the human genes encoding the endothelin ligand-receptor pairEDN3andEDNRBcause Waardenburg-Shah syndrome (WS4), which includes congenital hearing impairment. The current explanation for auditory dysfunction is a deficiency in migration of neural crest-derived melanocytes to the inner ear. We explored the role of endothelin signaling in auditory development in mice using neural crest-specific and placode-specificEdnrbmutation plus related genetic resources. On an outbred strain background, we find a normal representation of melanocytes in hearing-impaired mutant mice. Instead, our results in neural crest-specificEdnrbmutant mice implicate a previously unrecognized role for glial support of synapse assembly between auditory neurons and cochlear hair cells. Placode-specificEdnrbmutation also caused impaired hearing, resulting from deficient synaptic transmission. Our observations demonstrate the significant influence of genetic modifiers in auditory development, and invoke independent and separable new roles for endothelin signaling in the neural crest and placode lineages to create a functional auditory circuitry.
Islet amyloid polypeptide tagged with green fluorescent protein localises to mitochondria and forms filamentous aggregates inCaenorhabditis elegans
Authors: Akdag Mehmet , Schijndel Vera van , Sinnige Tessa 
Published: October 2023

AbstractType 2 diabetes (T2D) is the most common form of diabetes and represents a growing health concern. A characteristic feature of T2D is the aggregation of islet amyloid polypeptide (IAPP), which is thought to be associated with the death of pancreatic β-cells. Inhibiting IAPP aggregation is a promising therapeutic avenue to treat T2D, but the mechanisms of aggregation and toxicity are not yet fully understood.Caenorhabditis elegansis a well-characterised multicellular model organism that has been extensively used to study protein aggregation diseases. In this study, we aimed to develop a simplein vivomodel to investigate IAPP aggregation and toxicity based on expression in theC. elegansbody wall muscle cells. We show that IAPP tagged with green fluorescent protein (GFP) localises to mitochondria in this tissue, in line with previous observations in mouse and human pancreatic β-cells. The IAPP-GFP fusion protein forms solid aggregates, which have a filamentous appearance as seen by electron microscopy. However, the animals do not display a strong motility phenotype, suggesting that the IAPP-GFP aggregates are not considerably toxic. Nevertheless, the mitochondrial localisation and aggregate formation may be useful read-outs to screen for IAPP-solubilizing compounds as a therapeutic strategy for T2D.Graphical abstract