bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Framework to Determine Active Connectivity within the Mouse Brain
Authors: Sun Guanhua , Mano Tomoyuki , Shi Shoi , Li Alvin , Ode Koji , Rosi-Andersen Alex , Brown Steven A , Ueda Hiroki , Kompotis Konstantinos , Forger Daniel 
Published: December 2023

AbstractTremendous effort has focused on determining the physical connectivity within the mouse brain. However, the strength of connections within the brain constantly changes throughout the 24-hour day. Here, we combine experimental and computational methods to determine an “active connectivity” of the physical connections between the most active neurons. Brain cells of freely behaving mice are genetically marked with the activity- dependent TRAP2 system, imaged, digitized, and their connectivity is inferred from the latest brain atlases. We apply our methods to determine the most active networks in the early light and early dark hours of the day, two periods with distinct differences in sleep, wake, and feeding behavior. Increased signaling is seen through the visceral and agranular insular (AI) regions in the early day as peripheral stimuli are integrated. On the other hand, there is an increase in the activity of the retrosplenial cortex (RSP) and the anterior cingulate cortex (ACC) during the early night, when more sustained attention is required. Our framework carves a window to the three-dimensional networks of active connections in the mouse brain that underlie spontaneous behaviors or responses to environmental changes, thus providing the basis for direct computer simulations and analysis of such networks in the future.
p75NTRneurotrophin receptor function is redundant for development, growth and fertility in the rat
Authors: Meek Stephen , Singh-Dolt Karamjit , Sutherland Linda , Sharp Matthew G.F. , Del-Pozo Jorge , Walker David , Burdon Tom 
Published: December 2023

AbstractThe p75NTR neurotrophin receptor has positive and negative roles regulating cell survival in the nervous system. Unambiguous interpretation of p75NTR functionin vivohas been complicated, however, by residual expression of alternate forms of p75NTR protein in initialp75NTRknock-out mouse models. As rats are the preferred rodent for studying brain and behaviour, and to simplify interpretation of the knock-out phenotype, we report here the generation of a mutant rat devoid of the p75NTR protein. TALEN-mediated recombination in embryonic stem cells (ESCs) was used to flank exon 2 ofp75NTRwith Lox P sites and produce transgenic rats carrying either un-recombined floxedp75NTREx2-fl, or recombined, exon-2 deletedp75NTREx2-Δalleles. Crossingp75NTREx2-flrats with aCre-deleter strain efficiently removed exon 2in vivo. Excision of exon 2 causes a frameshift after p75NTR Gly23 and eliminated p75NTR protein expression. Rats lacking p75NTR were healthy, fertile, and histological analysis did not reveal significant changes in cellular density or overall structure in their brains. Thus, p75NTR function appears largely dispensable for normal development, growth and basal homeostasis in the rat. The availability of constitutive and conditionalp75NTREx2-Δrats should, however, provide new opportunities to investigate specific roles of p75NTR upon injury and during regeneration.
Structure of the hepatitis C virus E1/E2 envelope proteins in a homodimeric complex
Authors: Augestad Elias Honerød , Olesen Christina Holmboe , Grønberg Christina , Soerensen Andreas , Velázquez-Moctezuma Rodrigo , Fanalista Margherita , Bukh Jens , Wang Kaituo , Gourdon Pontus , Prentoe Jannick 
Published: December 2023

AbstractWorldwide, 58 million individuals suffer from chronic hepatitis C virus (HCV) infection, a primary driver of liver cancer. The HCV envelope proteins, E1 and E2, form a heterodimer, which is the target for neutralizing antibodies. Despite high-resolution structural models of partial heterodimer elements, the structural landscape of higher-order E1/E2 oligomers remains unexplored. We determined a ~3.5 Å cryo-electron microscopy structure of membrane-extracted HCV E1/E2 in a homodimeric arrangement. This structure includes detailed information on the homodimer interface, the E2-binding pocket for hypervariable region 1, antigenic site 412 conformation, and the organization of the E1/E2 transmembrane regions, including one internal to E1. This higher-order E1/E2 assembly could play a pivotal role in the design of novel vaccine antigens better mimicking E1/E2 complexes on the HCV particle.
Macrophages undergo functionally significant reprograming of nucleotide metabolism upon classical activation
Authors: John Steven V. , Seim Gretchen L. , Erazo-Flores Billy J. , Steill John , Freeman Jack , Votava James A. , Arp Nicholas L. , Qing Xin , Stewart Ron , Knoll Laura J. , Fan Jing 
Published: December 2023

AbstractDuring an immune response, macrophages systematically rewire their metabolism in specific ways to support their diversve functions. However, current knowledge of macrophage metabolism is largely concentrated on central carbon metabolism. Using multi-omics analysis, we identified nucleotide metabolism as one of the most significantly rewired pathways upon classical activation. Further isotopic tracing studies revealed several major changes underlying the substantial metabolomic alterations: 1)de novosynthesis of both purines and pyrimidines is shut down at several specific steps; 2) nucleotide degradation activity to nitrogenous bases is increased but complete oxidation of bases is reduced, causing a great accumulation of nucleosides and bases; and 3) cells gradually switch to primarily relying on salvaging the nucleosides and bases for maintaining most nucleotide pools. Mechanistically, the inhibition of purine nucleotidede novosynthesis is mainly caused by nitric oxide (NO)-driven inhibition of the IMP synthesis enzyme ATIC, with NO-independent transcriptional downregulation of purine synthesis genes augmenting the effect. The inhibition of pyrimidine nucleotidede novosynthesis is driven by NO-driven inhibition of CTP synthetase (CTPS) and transcriptional downregulation of thymidylate synthase (TYMS). For the rewiring of degradation, purine nucleoside phosphorylase (PNP) and uridine phosphorylase (UPP) are transcriptionally upregulated, increasing nucleoside degradation activity. However, complete degradation of purine bases by xanthine oxidoreductase (XOR) is inhibited by NO, diverting flux into nucleotide salvage. Inhibiting the activation-induced switch from nucleotidede novosynthesis to salvage by knocking out the purine salvage enzyme hypoxanthine-guanine phosporibosyl transferase (Hprt) significantly alters the expression of genes important for activated macrophage functions, suppresses macrophage migration, and increases pyroptosis. Furthermore, knocking outHprtorXorincreases proliferation of the intracellular parasiteToxoplasma gondiiin macrophages. Together, these studies comprehensively reveal the characteristics, the key regulatory mechanisms, and the functional importance of the dynamic rewiring of nucleotide metabolism in classically activated macrophages.
Small vs. Large Library Docking for Positive Allosteric Modulators of the Calcium Sensing Receptor
Authors: Liu Fangyu , Wu Cheng-Guo , Tu Chia-Ling , Glenn Isabella , Meyerowitz Justin , Kaplan Anat Levit , Lyu Jiankun , Cheng Zhiqiang , Tarkhanova Olga O. , Moroz Yurii S. , Irwin John J. , Chang Wenhan , Shoichet Brian K. , Skiniotis Georgios 
Published: December 2023

AbstractDrugs acting as positive allosteric modulators (PAMs) to enhance the activation of the calcium sensing receptor (CaSR) and to suppress parathyroid hormone (PTH) secretion can treat hyperparathyroidism but suffer from side effects including hypocalcemia and arrhythmias. Seeking new CaSR modulators, we docked libraries of 2.7 million and 1.2 billion molecules against transforming pockets in the active-state receptor dimer structure. Consistent with simulations suggesting that docking improves with library size, billion-molecule docking found new PAMs with a hit rate that was 2.7-fold higher than the million-molecule library and with hits up to 37-fold more potent. Structure-based optimization of ligands from both campaigns led to nanomolar leads, one of which was advanced to animal testing. This PAM displays 100-fold the potency of the standard of care, cinacalcet, inex vivoorgan assays, and reduces serum PTH levels in mice by up to 80% without the hypocalcemia typical of CaSR drugs. Cryo-EM structures with the new PAMs show that they induce residue rearrangements in the binding pockets and promote CaSR dimer conformations that are closer to the G-protein coupled state compared to established drugs. These findings highlight the promise of large library docking for therapeutic leads, especially when combined with experimental structure determination and mechanism.One sentence summaryStructure-based virtual screening uncovers novel CaSR allosteric modulators with enhanced efficacy and less side effects.
Expression of the transcription factor Isl1 in dopaminergic neurons of the mouse forebrain
Authors: Camarano Adriana C. , Rubinstein Marcelo , de Souza Flavio S. J. 
Published: December 2023

AbstractThe development of the bewildering assortment of neuronal types found in the vertebrate central nervous system (CNS) depends on the distribution of transcription factors and signalling molecules along the embryonic neural tube. TheIslet-1(Isl1) gene, which encodes a transcription factor of the LIM-homeodomain family, is known to be expressed in the nervous system, playing crucial funtions in the differentiation of neuronal populations located in the spinal cord, striatum, hypothalamus and retina. Here, we use immunofluorencence to trace the distribution of Isl1 protein during the development of the mouse forebrain, with an emphasis on the hypothalamic area and its neighbouring regions. Isl1 is abundantly expressed in the subpallium, most of the hypothalamus and in the prethalamus. Interestingly, we found that Isl1 is expressed in most dopaminergic neurons of the forebrain in early development (e10.5, e11.5), as revealed by colabelling with the enzyme tyrosine hydroxylase (TH). At later stages (e18.5) and adulthood, the degree of colocalisation of Isl1 with TH decreases, but the factor is still found in most dopaminergic neurones of the forebrain, in particular of the prethalamic region (A13 group), tuberal hypothalamus (A12), preoptic area (A15) and part of the periventricular area (part of the A14 group). Altogether, our observations indicate that Isl1 is a molecular marker of forebrain dopaminergic groups and might play a role in the development of these neuronal populations.
Contribution of CENP-F to FOXM1-mediated discordant centromere and kinetochore transcriptional regulation
Authors: Khurana Sakshi , Foltz Daniel R. 
Published: December 2023

AbstractProper chromosome segregation is required to ensure genomic and chromosomal stability. The centromere is a unique chromatin domain present throughout the cell cycle on each chromosome defined by the CENP-A nucleosome. Centromeres (CEN) are responsible for recruiting the kinetochore (KT) during mitosis, ultimately regulating spindle attachment and mitotic checkpoint function. Upregulation of many genes that encode the CEN/KT proteins is commonly observed in cancer. Here, we show although that FOXM1 occupies the promoters of many CEN/KT genes with MYBL2, occupancy is insufficient alone to drive the FOXM1 correlated transcriptional program. We show that CENP-F, a component of the outer kinetochore, functions with FOXM1 to coregulate G2/M transcription and proper chromosome segregation. Loss of CENP-F results in alteration of chromatin accessibility at G2/M genes, including CENP-A, and leads to reduced FOXM1-MBB complex formation. The FOXM1-CENP-F transcriptional coordination is a cancer-specific function. We observed that a few CEN/KT genes escape FOXM1 regulation such as CENP-C which when upregulated with CENP-A, leads to increased chromosome misegregation and cell death. Together, we show that the FOXM1 and CENP-F coordinately regulate G2/M gene expression, and this coordination is specific to a subset of genes to allow for proliferation and maintenance of chromosome stability for cancer cell survival.
A catalogue of small proteins from the global microbiome
Authors: Duan Yiqian , Santos-Junior Celio Dias , Schmidt Thomas Sebastian , Fullam Anthony , de Almeida Breno L. S. , Zhu Chengkai , Michael Kuhn , Zhao Xing-Ming , Bork Peer , Coelho Luis Pedro 
Published: December 2023

AbstractSmall open reading frames (smORFs) shorter than 100 codons are widespread and perform essential roles in microorganisms, where they encode proteins active in several cell functions, including signal pathways, stress response, and antibacterial activities. However, the ecology, distribution and role of small proteins in the global microbiome remain unknown. Here, we constructed a global microbial smORFs catalogue (GMSC) derived from 63,410 publicly available metagenomes across 75 distinct habitats and 87,920 high-quality isolate genomes. GMSC contains 965 million non-redundant smORFs with comprehensive annotations. We found that archaea harbor more small proteins proportionally than bacteria. We moreover provide a tool called GMSC-mapper to identify and annotate small proteins from microbial (meta)genomes. Overall, this publicly-available resource demonstrates the immense and underexplored diversity of small proteins.
Applicability of Castration Model in Sex Difference Studies: Insights from Metabolome and Transcriptome Analyses
Authors: Jiang Jianjun , Ge Na , Wang Yuzhi , Qi Juntao , Wen Guibiao , Gu Xiufen , Yu Xuewen , Shao Muming , Luo Yueming , Gu Kangshuyun , Lin Feng , Yang Shudong , Wei Wei 
Published: December 2023

ABSTRACTBackgroundSex, as a critical biological variable, has historically been underappreciated, despite the pervasive influence of sexual dimorphism across physiological and pathological processes. A significant obstacle to advancing sex-biased biological research is the absence of an effective animal model. In recent years, castration has emerged as a potential model for elucidating sex-based differences in the context of healthy aging, where it has been shown to equalize lifespan and growth trajectories in genetically diverse mice. However, the molecular shifts induced by castration in common laboratory models, such as C57BL/6 mice, and the broader applicability of this model to other sex-related biological contexts remain largely unexplored.MethodsWe employed multi-omics and observational analyses to investigate the molecular changes associated with sex and sex hormones following castration. We analyzed serum, kidney, and liver samples from 12-week-old and 18-month-old castrated male C57BL/6 mice, alongside intact male and female counterparts. The castration model was further applied to assess differences in cisplatin-induced toxicity and age-related cognitive decline in comparison to unaltered controls.ResultsLC-MS/MS metabolomics revealed that castrated males exhibited substantial alterations in steroid hormone levels and increased concentrations of antioxidant compounds, such as taurine, despite identical diets. Integrated metabolome-transcriptome analysis confirmed distinct patterns of lipid peroxidation and oxidative stress across sham-operated female, male, and castrated male mice. Histopathological evaluations following cisplatin treatment and aging-related behavioral tests demonstrated the model’s utility in investigating sex-dependent drug toxicity and cognitive decline. These findings underscored the critical role of sex hormones in modulating both toxicity defense mechanisms and cognitive performance.ConclusionThis study provides a systematic multi-omics spectrum on the castration model and demonstrates its capacity to feminize metabolic and transcriptomic profiles, establishing it as a valuable tool for exploring sex hormone-driven biological differences. Our findings lay the groundwork for further mechanistic studies and broaden the potential applications of the castration model in diverse biomedical research domains.
Complex allometric relationships and ecological factors shape the development and evolution of eye size in the modular visual system of spiders
Authors: Chong Kaylin , Grahn Angelique , Perl Craig D. , Sumner-Rooney Lauren 
Published: December 2023

ABSTRACTEye size affects many aspects of visual function, most notably including contrast sensitivity and achievable spatial resolution, but eyes are costly to grow and maintain. The allometry of eyes can provide insight to this trade-off in the context of visual ecology, but to date, this has mainly been explored in species that have a single pair of eyes of equal size. By contrast, animals possessing larger visual systems can exhibit variable eye sizes within individuals. Spiders have up to four pairs of eyes whose size often varies, but their ontogenetic, static, and evolutionary allometry has not yet been studied in a comparative context. We report variable evolutionary and developmental dynamics in eye size across 1098 individuals in 39 species and 8 families, indicating selective pressures and constraints driving the evolution of different eye pairs and lineages. We observed variation in the relationship between eye and body size not only between taxa and visual ecologies, but between eye pairs within species, indicating that growth dynamics are variable and can be divergently adapted in particular eye pairs. Supplementing our sampling with a phylogenetically comprehensive dataset recently published by Wolff et al. (2022), we confirmed these findings across more than 400 species, found that ecological factors such as visual hunting, web building, and diurnality can also impact eye diameter, and identified significant allometric shifts across spider phylogeny using an unbiased approach, many of which coincide with ecological changes such as visual pursuit hunting strategies. This study represents the first detailed comparative exploration of visual allometry in spiders, revealing striking differences in eye growth not only between families but also within species. Our findings shed light on the relationship between spider visual systems and their diverse ecologies, and how spiders exploit the modular nature of their visual systems to balance selective pressures and optical and energetic constraints.
Unveiling Elevated Spontaneous Mutation Rates inPhyllostachys edulis(Moso Bamboo) through Whole Genome Sequencing (WGS) and Investigating the Impact of Atmospheric and Room Temperature Plasma (ARTP) Induced Mutagenesis
Authors: Bai Yiwei , Ma Yanjun , Chang Yanting , Zhang Wenbo , Deng Yayun , Fan Keke , Zhang Na , Zhang Xue , Ye Yaqin , Chu Tiankui , Jiang Zehui , Hu Tao 
Published: December 2023

AbstractMoso bamboo, recognized for its wide distribution and economic importance, encounters challenges in varietal enhancement due to its protracted sexual reproduction cycle. This study employed whole-genome resequencing to uncover spontaneous mutations in Moso bamboo and investigated mutagenesis using atmospheric and room temperature plasma (ARTP). Through the sequencing results, we identified the population of flowering bamboo as an asexual breeding line. Notably, the flowering Moso bamboo population, exclusively derived from asexual reproduction, exhibited a high spontaneous mutation rate (4.54 × 10-4 to 1.15 × 10-3/bp) during sexual reproduction, considering parental and cross-pollination effects. Genetic disparities between offspring and parents exhibited a bimodal distribution, indicating a substantial cross-pollination rate. ARTP mutagenesis increased structural variations in offspring, while changes in SNPs and INDELs were less pronounced. Sanger sequencing validated a gene subset, providing a foundation for spontaneous mutation rate investigation via whole-genome sequencing. These insights, particularly from mutagenized offspring sequencing, contribute to Moso bamboo breeding strategies.HighlightMoso bamboo breeding revolutionized—high spontaneous mutations in asexually derived flowering population. ARTP mutagenesis boosts structural variations, shaping innovative breeding approaches.
Simultaneous detection of membrane contact dynamics and associated Ca2+signals by reversible chemogenetic reporters
Authors: Casas Paloma García , Rossini Michela , Påvénius Linnea , Saeed Mezida , Arnst Nikita , Sonda Sonia , Bruzzone Matteo , Berno Valeria , Raimondi Andrea , Sassano Maria Livia , Naia Luana , Agostinis Patrizia , Sturlese Mattia , Niemeyer Barbara A. , Brismar Hjalmar , Ankarcrona Maria , Gautier Arnaud , Pizzo Paola , Filadi Riccardo 
Published: December 2023

AbstractMembrane contact sites (MCSs) are hubs allowing various cell organelles to coordinate their activities. The dynamic nature of these sites and their small size hinder analysis by current imaging techniques. To overcome these limitations, we here designed a series of reversible chemogenetic reporters incorporating improved, low-affinity variants of splitFAST, and studied the dynamics of different MCSs at high spatiotemporal resolution, bothin vitroandin vivo. We demonstrated that these versatile reporters suit different experimental setups well, allowing one to address challenging biological questions. Using these novel probes, we identified a hitherto unknown pathway, in which calcium (Ca2+) signalling dynamically regulates endoplasmic reticulum-mitochondria juxtaposition, characterizing the underlying mechanism. Finally, by integrating Ca2+-sensing capabilities into the splitFAST technology, we introduced PRINCESS (PRobe forINterorganelleCa2+-ExchangeSites based onSplitFAST), an unprecedented class of reporters to simultaneously detect MCSs and measure the associated Ca2+dynamics using a single biosensor.
Interplay between Two Paralogous Human Silencing Hub (HuSH) Complexes in Regulating LINE-1 Element Silencing
Authors: Jensvold Zena D. , Christenson Anna E. , Flood Julia R. , Lewis Peter W. 
Published: December 2023

AbstractThe Human Silencing Hub (HuSH) complex is composed of TASOR, MPP8, and PPHLN1 subunits and serves as a conserved protein complex responsible for silencing transposable elements in vertebrate animals. Despite its importance, the regulatory mechanisms and recruitment dynamics governing this complex remain poorly understood. In this study, we have identified a second HuSH complex, termed HuSH2, centered around TASOR2, a paralog of the core TASOR protein in HuSH. Our findings indicate that every subunit in both HuSH and HuSH2 has an important role in achieving precise genomic localization to distinct, non-overlapping genomic loci. We utilized in silico protein structure prediction to simulate the interactions between MPP8 and both TASOR paralogs. Drawing on the insights gained from these predictions, we implemented amino acid substitutions that interfered with the binding of MPP8 to each HuSH complex. Leveraging these MPP8 transgenes and other constructs, we identified an important role played by the relative quantities of HuSH complexes in controlling the activity of LINE-1 elements. Furthermore, our results suggest that dynamic changes in TASOR and TASOR2 expression enable cells to finely tune the extent of HuSH-mediated silencing. Our study provides insights into the intricate interplay between HuSH complexes, illuminating their important role in the regulation of retrotransposon silencing.Key PointsThe identification of a previously unknown HuSH2 complex, with TASOR2 as its central component.HuSH and HuSH2 complexes exhibit unique genomic localization patterns within the human genome.Disruption of the delicate balance between the two HuSH complexes results in the desilencing of LINE-1.TASOR and TASOR2 engage in a competitive interaction for the HuSH subunit MPP8.The localization of MPP8 to either HuSH or HuSH2 sites is intricately regulated by its interaction with TASOR and TASOR2.