bluuebunny/crossref_metadata_2025_split huggingface dataset:
SNP panel for non-invasive genotyping of leopard (Panthera pardus)
Authors: Mamugy Faruk , Bertola Laura D. , De Vry Amber Mertens , Dussex Nicolas , Shiffthaler Bastian , Paijmans Joanna , Hofreiter Michael , Forbes Ryan , Kerley Graham I.H. , Everatt Kris , Becker Matthew , Creel Scott , Bourgeois Stéphanie , Drouilly Marine , Spong Göran 
Published: November 2024

AbstractGenetic resources for species monitoring are ideally relevant for the species’ full distribution range, feasible economically and logistically, and validated for the range of sample types collected from the field. This is particularly important for large carnivores that are elusive and wide-ranging, where individual and population processes often traverse administrative borders, and where obtaining high-quality samples can be challenging. Here we present a small species-specific SNP panel for leopards. We used whole genome data from across the global range and RAD sequence data from Zambian leopards to select markers for assay development. These were ascertained for 590 individual leopards from eight African countries and final selection was based on marker variation and performance on non-invasive samples. The final 96 marker panel holds 5 mitochondrial markers for species recognition, 3 Y-markers for determination of individual sex, 3 X-markers and 85 somatic markers, with an associated genetic baseline holding nearly 900 individuals. The selected autosomal markers hold variation across the global range with high power to identify individuals (PID=2,45×10−35) and in most cases their provenance with high assignment probability (>95%). Markers were also selected based on their performance on samples with low target DNA content, with distinct genotype separation in the output marker plots. The genotypes from this panel are thus straightforward to analyze and do not require computationally challenging bioinformatic resources, making this a low cost and accessible resource for leopard monitoring and research.
MaternalMed12safeguards trophoblast pluripotency and placental development
Authors: Halstead Michelle M. , Goad Jyoti , Khan Amina , Deshmukh Rutuja , Rajkovic Aleksandar 
Published: November 2024

AbstractFor a brief but critical period post-fertilization, the mammalian embryo is entirely dependent on maternal products inherited from the oocyte. Previous research showed that oocyte-specific loss ofMed12, an X-linked gene and Mediator complex subunit, leads to female sterility despite normal folliculogenesis and ovulation. Here, we show that loss of maternalMed12has minimal effect on the oocyte transcriptome and does not manifest in embryonic lethality until post-implantation. Implants derived fromMed12-null oocytes demonstrate abnormal placentation at E9.5, with an overabundance of trophoblast giant cells (TGC). This phenotype associates with downregulation of trophoblast pluripotency markers (e.g.Cdx2) and activation of drivers of TGC identity (e.g.Stra13) in the E7.5 extraembryonic ectoderm, revealing a previously undescribed role forMed12in trophoblast pluripotency maintenance. Notably, we find consistently lowMed12expression in embryos derived fromMed12-null oocytes, potentially due to programmed paternal X chromosome inactivation (XCI). To isolate the consequences of maternalMed12depletion, we introduced an autosomalMed12transgene and show that embryonic expression of the transgene rescues development ofMed12-null oocytes. We conclude that oocyte-specific deletion ofMed12produces a maternal-zygotic double knock-out in extraembryonic tissues due to paternal XCI, leading to loss of pluripotency in the trophoblast, placental malformation, and embryonic death.
Synthesis of USC-093 and comparison with its promoiety enantiomer USC-093D against adenovirus in vitro and in a Syrian hamster model
Authors: Yang Jiayi , Riemann Samantha B. , Lyu Jinglei , Feng Sudi , Bi Yang , Lentini Nicholas A. , Kang Inah , Kashemirov Boris A. , Hartline Caroll B. , James Scott H. , Tollefson Ann E. , Cline-Smith Anna , Toth Karoly , McKenna Charles E. 
Published: November 2024

ABSTRACTAdenovirus infections of immunocompromised humans are a significant source of morbidity and mortality. At present, no drug has been approved by FDA for the treatment of adenovirus infections. A current treatment of such infections is off-label use of an antiviral acyclic nucleotide phosphonate, cidofovir (CDV, (S)-HPMPC), which requires i.v. administration and has dose-limiting kidney toxicity. We recently reported that USC-093, a homoserinamide analogue of the tyrosinamide (S)- HPMPA prodrug USC-087, was orally effective at a 10 mg/kg against disseminated human adenovirus infection (HAdV-C6) in a Syrian hamster model, although their efficacy was marginal after respiratory infection. Neither prodrug manifested GI toxicity. Unlike USC-087, USC-093 showed no significant nephrotoxicity at the effective dose. Here, we describe in detail the synthesis of USC-093 and also its D-homoserinamide analogue, USC-093D, in four steps (20-40% overall yield) starting from Boc-protected L-homoserine or D-homoserine lactone, respectively. The two stereoisomeric prodrugs had EC5030-70 nM vs. Ad5 or 1-6 nM vs. Ad6 in HFF cells, with USC-093D giving the lower values. The prodrugs were 30-59x more potent vs. Ad5 and 82-332x more potent than Ad6 relative to the positive control, CDV. To ascertain whether D-chirality in the promoiety could enhance the performance of the prodrug in vivo, USC-093D and USC-093 were compared in the Syrian hamster model (treated from day 1 q.d at an experimentally determined maximum tolerated oral dose of 20 mg/kg)). In this study, the hamsters were instilled i.n. with vehicle or 4X1010PFU/kg of HAdV-C6 to promote lung infection. Oral valganciclovir (VGCV) at 200 mg/kg b.i.d. was used as the positive control. The body weights were recorded daily, and at 3 days post challenge, gross pathological observation was performed. Lung samples were collected, and the virus burden was determined by TCID50assay. The results show that altering homoserine stereochemistry did not markedly improve the efficacy of the orally administered prodrug, consistent with the premise that its mechanism of transport is likely not dependent on stereoselective pathways, such as hPEPT1-mediated uptake.
Revised diffusion law permits quantitative nanoscale characterization of membrane organization
Authors: Svobodová Barbora , Šťastný David , Blom Hans , Mikhalyov Ilya , Gretskaya Natalia , Balleková Alena , Sezgin Erdinc , Hof Martin , Šachl Radek 
Published: November 2024

AbstractFormation of functional nanoscopic domains is an inherent property of plasma membranes. Stimulated emission depletion combined with fluorescence correlation spectroscopy (STED-FCS) has been used to identify such domains, however, the information obtained by STED-FCS has been limited to presence of such domains while crucial parameters have not been accessible, such as size (Rd), the fraction of occupied membrane surface (f), in-membrane lipid diffusion inside (Din) and outside (Dout) the nanodomains as well as their self-diffusion (Dd). Here, based on a revision of the ‘diffusion law’, we present an approach to retrieve these five parameters from STED-FCS data. We verify that approach on ganglioside nanodomains in giant unilamellar vesicles (GUVs), validating the Saffman-Delbrück assumption forDd. We examined STED-FCS data in both plasma membranes of living PtK2 cells and in giant plasma membrane vesicles (GPMVs) and present a quantitative framework for molecular diffusion modes in biological membranes.
Tumor-Infiltrating Lymphocytes Display Prognostic Signatures Associated with Chemotherapy Response in TNBC Patients
Authors: Banerjee Shayantan , Tiwari Vijay K. , Raman Karthik , Inayatullah Mohammad 
Published: November 2024

AbstractTriple-negative breast cancer (TNBC) is an aggressive subtype often marked by resistance to neoadjuvant chemotherapy (NAC), making treatment particularly challenging. Tumor-infiltrating lymphocytes (TILs), crucial players in the immune landscape of tumors, have been associated with treatment outcomes, but the prognostic potential of TIL-derived gene markers in pre-NAC samples from TNBC patients remains understudied. In this research, we analyzed the single-cell transcriptional profiles of approximately 5,000 cells from four chemosensitive and four chemoresistant TNBC patients using publicly available datasets. Leveraging standard single-cell analysis, we identified differentially expressed gene signatures within the TIL subpopulation, highlighting significant immune activation pathways differentiating chemoresistant from chemosensitive tumors. By employing robust feature selection and repeated cross-validation across microarray and RNA-seq datasets, we developed a stable set of 30 TIL-based gene markers with notable prognostic relevance for NAC response in TNBC. These markers achieved an AUROC of 0.78 in the training set and validated with AUROCs of 0.8, 0.658, and 0.736 across five independent test datasets, demonstrating consistency across diverse platforms and sequencing technologies. Furthermore, increased expression of these gene signatures correlated with improved recurrence-free survival (RFS) in a cohort of 220 TNBC patients. This study enhances our understanding of the TIL transcriptional landscape in NAC response, identifying potential biomarkers and therapeutic targets for improving treatment outcomes in TNBC.
Calcium transients regulate epithelial integration of multiciliated cells during Xenopus skin development
Authors: Christodoulou Neophytos , Skourides Paris A. 
Published: November 2024

AbstractIntegration basally located progenitors into an existing epithelium is crucial for tissue morphogenesis during embryogenesis and tissue homeostasis of epithelial organs. In this study, using Xenopus as a model system, we explore the role of intracellular calcium in multiciliated cell (MCC) progenitors’ epithelial integration during mucociliary skin epithelium development. Our findings reveal that calcium transients precede MCC apical emergence and are essential for their successful insertion into the overlying skin epithelium. Furthermore, we demonstrate that phospholipase C (PLC) activity is required for the generation of calcium transients, which in turn regulate MCC epithelial integration via the calcium-binding protein calmodulin. Last, we demonstrate that the PLC/Ca²⁺/calmodulin axis is necessary for proper formation of the apical actin network, by influencing its stability. This study advances our understanding of the molecular mechanisms governing epithelial integration of basal progenitors and highlights the importance of calcium signalling in coordinating cytoskeletal dynamics during epithelial morphogenesis.
Secretome analysis of human and rat pancreatic islets co-cultured with adipose-derived stromal cells reveals a signature with enhanced regenerative capacities
Authors: Pinheiro-Machado Erika , de Haan Bart J. , Engelse Marten A. , Smink Alexandra M. 
Published: November 2024

AbstractPancreatic islet transplantation (PIT), a promising treatment for Type 1 Diabetes (T1D), encounters challenges in the pre- and post-transplantation phases. Co-culturing or co-transplantation of islets with mesenchymal stromal cells (MSC), known for their regenerative properties, emerged as a potential solution and was shown to increase islet function and improve PIT outcomes. This study explored the changes in the islets’ secretion signature (secretome) when co-cultured with adipose-derived stromal cells (ASC), an MSC subtype. The secretome profile of islets and co-cultures under various stressors, i.e., cytokines, high glucose, hypoxia, and a combination of hypoxia and high glucose, was investigated. The results shed light on the potential mechanisms through which ASC support islets’ functional survival. Co-culturing pancreatic islets with ASC induced substantial proteomic changes, impacting pathways crucial for energy metabolism, angiogenesis, extracellular matrix organization, and immune responses. The analysis of key signaling molecules (VEGF, PDGF, bFGF, Collagen I alpha 1, IL-1α, and IL-10) revealed alterations influenced by the culturing conditions and the presence of the ASC.In vitrofunctional assays using the secretomes also demonstrated their potential to differentially influence angiogenic processes, enhance collagen deposition, and modulate the immune system based on the conditions in which they were generated. These findings offer valuable insights into the potential of ASC co-culturing to address challenges in PIT, paving the way for enhanced therapeutic interventions in T1D and regenerative medicine.HighlightsBothin-silicoandin-vitrodata support that co-culturing pancreatic islets with ASC enhances islet function.Co-culturing islets with ASC induces changes in the secretome, impacting pathways related to energy metabolism, angiogenesis, extracellular matrix organization, and immune response.Key signaling molecules, including VEGF, PDGF, bFGF, Collagen I alpha 1, IL-1α, and IL-10, are differentially affected by various co-culturing conditions.
Structural Model of Bacteriophage P22 Scaffolding Protein in a Procapsid by Magic-Angle Spinning NMR
Authors: Guo Changmiao , Whitehead Richard D. , Struppe Jochem , Porat-Dahlerbruch Gal , Hassan Alia , Gronenborn Angela M. , Alexandrescu Andrei T. , Teschke Carolyn M. , Polenova Tatyana 
Published: November 2024

ABSTRACTIcosahedral dsDNA viruses such as the tailed bacteriophages and herpesviruses have a conserved pathway to virion assembly that is initiated from a scaffolding protein driven procapsid formation. The dsDNA is actively packaged into procapsids, which undergo complex maturation reactions to form infectious virions. In bacteriophage P22, scaffolding protein (SP) directs the assembly of coat proteins into procapsids that have a T=7 icosahedral arrangement, en route to the formation of the mature P22 capsid. Other than the C-terminal helix-turn-helix involved in interaction with coat protein, the structure of the P22 303 amino acid scaffolding protein within the procapsid is not understood. Here, we present a structural model of P22 scaffolding protein encapsulated within the 23 MDa procapsid determined by magic angle spinning NMR spectroscopy. We took advantage of the 10-fold sensitivity gains afforded by the novel CPMAS CryoProbe to establish the secondary structure of P22 scaffolding protein and employed19F MAS NMR experiments to probe its oligomeric state in the procapsid. Our results indicate that the scaffolding protein has both α-helical and disordered segments and forms a trimer of dimers when bound to the procapsid lattice. This work provides the first structural information for P22 SP beyond the C-terminal helix-turn-helix and demonstrates the power of MAS NMR to understand higher-order viral protein assemblies involving structural components that are inaccessible to other structural biology techniques.
Habenula-ventral tegmental area functional coupling and risk-aversion in humans
Authors: Lin Wanjun , Xu Jiahua , Zhang Xiaoying , Dolan Raymond J 
Published: November 2024

AbstractMaladaptive responses to uncertainty, including excessive risk avoidance, are linked to a range of mental disorders. One expression of these is a pro-variance bias (PVB), wherein risk-seeking manifests in a preference for choosing options with higher variances/uncertainty. Here, using a magnitude learning task, we provide a behavioural and neural account of PVB in humans. We show that individual differences in PVB are captured by a computational model that includes asymmetric learning rates, allowing differential learning from positive prediction errors (PPEs) and negative prediction errors (NPEs). Using high-resolution 7T functional magnetic resonance imaging (fMRI), we identify distinct neural responses to PPEs and NPEs in value-sensitive regions including habenula (Hb), ventral tegmental area (VTA), nucleus accumbens (NAcc), and ventral medial prefrontal cortex (vmPFC). Prediction error signals in NAcc and vmPFC were boosted for high variance options. NPEs responses in NAcc were associated with a negative bias in learning rates linked to a stronger negative Hb-VTA functional coupling during NPE encoding. A mediation analysis revealed this coupling influenced NAcc responses to NPEs via an impact on learning rates. These findings implicate Hb-VTA coupling in the emergence of risk preferences during learning, with implications for psychopathology.
Bystander activation across a TAD boundary supports a cohesin-dependent hub-model for enhancer function
Authors: Williamson Iain , Graham Katy A. , Becher Hannes , Hill Robert E. , Bickmore Wendy A. , Lettice Laura A. 
Published: November 2024

AbstractEnhancers in the mammalian genome are able to control their target genes over very large genomic distances, often across intervening genes. Yet the spatial and temporal specificity of developmental gene regulation would seem to demand that enhancers are constrained so that they only activate the correct target gene. The sculpting of three-dimensional chromosome organization, especially that brought about through cohesin-dependent loop extrusion, is thought to be important for facilitating and constraining the action of enhancers. In particular, the boundaries of topologically associating domains (TADs) are thought to delimit regulatory landscapes and prevent enhancers acting on genes close in the linear genome, but located in adjacent TADs. However, there are some examples where enhancers appear to act across TAD boundaries. In these cases it was not determined whether an enhancer can simultaneously activate transcription at genes in its own TAD and in an adjacent TAD. Here, using a combination of mouse developmental genetics, and synthetic activators in stem cells, we show that some Shh enhancers can activate transcription simultaneously, not only ofShhbut also at a geneMnx1located in an adjacent TAD. This occurs in the context of a chromatin configuration that maintains both genes and the enhancers close together and is influenced by cohesin. To the best of our knowledge this is the first report of two endogenous mammalian genes transcribed simultanously under the control of the same enhancer, and across a TAD boundary. Our data have implications for understanding the design rules of gene regulatory landscapes, and are most consistent with a transcription hub model of enhancer-promoter communication.
Inhibition of H3K27M-enhanced ATM signaling increases radiation efficacy in diffuse midline glioma
Authors: Peterson Erik , Parsels Leslie A. , Parsels Joshua D. , Zhao Xinyi , Castro Maria G. , Lawrence Theodore S. , Koschmann Carl , Zhang Qiang , Wahl Daniel R. , Morgan Meredith A. 
Published: November 2024

ABSTRACTH3K27-altered diffuse midline glioma (DMG) is an aggressive and treatment-resistant form of pediatric high-grade glioma (pHGG). The disease is defined by point mutations in histone H3 that convert lysine 27 to methionine (termed H3K27M), resulting in genome-wide epigenetic changes that drive tumorigenesis. While radiation therapy is the standard of care, subsequent recurrence, often within the high dose radiation field, is universal. We found that the apical DNA damage response (DDR) kinase Ataxia Telangiectasia-Mutated (ATM) was uniquely upregulated in H3K27M-expressing patient tumor samples compared to pHGG expressing only wild-type histone H3. Using a panel of H3K27 isogenic DMG cell lines, we further found that H3K27M was associated with reduced H3K27me3within theATMpromoter, increased ATM mRNA levels, and elevated DDR signaling, even in the absence of exogenous DNA damage. Consistent with these results, AZD1390, a clinical-grade, CNS-penetrant ATM inhibitor, sensitized H3K27M neurospheres to the long-term effects of radiation on survival, in part due to attenuated repair of radiation-induced DNA damage. Finally, AZD1390 sensitized orthotopic H3K27M mutant tumors to radiotherapy and significantly extended median survival relative to vehicle, AZD1390 or radiation alone (50 days vs 31, 36 or 39 days, respectively) with minimal adverse effects. Taken together, these data provide a direct mechanistic link between the H3K27M mutation and ATM expression and support the clinical investigation of AZD1390 with radiotherapy in H3K27M-altered DMG.
The ecological memory of landscape complexity shapes diversity of freshwater communities
Authors: Tabi Andrea , Santos Edineusa Pereira , Brejão Gabriel , Siqueira Tadeu 
Published: November 2024

AbstractLand use change affects the biodiversity of terrestrial landscapes as well as of the freshwater systems they surround, and thereby numerous ecosystem services that are essential for human well-being. Previous research suggests that freshwater systems show delayed responses to abrupt disturbances such as deforestation, however less is known about whether there is a legacy effect of landscape history on freshwater communities under a long history of land use change. We addressed this research gap here by first quantifying the historical complexity of landscapes, including natural and agricultural formations, in terms of their composition and configuration in 26 tropical catchment areas surrounding 101 streams over a 30-year period. We identified clear evidence for a memory effect of past events, whereby historical landscape complexity, measured as the information entropy of landscape composition, positively affected freshwater biodiversity. Finally, using a causal discovery approach, we showed that species richness was causally related to landscape complexity only when historical values were incorporated. Our results corroborate previous work on the positive effect of landscape complexity on biodiversity, and also confirm the role of historical contingencies in predicting future ecological outcomes.
Novel structure and composition of the unusually large germline determinant of the wasp Nasonia vitripennis
Authors: Kemph Allie , Kharel Kabita , Tindell Samuel J. , Arkov Alexey L. , Lynch Jeremy A. 
Published: November 2024

AbstractSpecialized, maternally derived ribonucleoprotein (RNP) granules play an important role in specifying the primordial germ cells in many animal species. Typically, these germ granules are small (∼100 nm to a few microns in diameter) and numerous; in contrast, a single, extremely large granule called the oosome plays the role of germline determinant in the waspNasonia vitripennis.The organizational basis underlying the form and function of this unusually large membraneless RNP granule remains an open question. Here we use a combination of super-resolution and transmission electron microscopy to investigate the composition and morphology of the oosome. We show that the oosome has properties of a viscous liquid or elastic solid. The most prominent feature of the oosome is a branching mesh-like network of high abundance mRNAs that pervades the entire structure. Homologs of the core polar granule proteins Vasa and Oskar do not appear to nucleate this network, but rather are distributed adjacently as separate puncta. Low abundance RNAs appear to cluster in puncta that similarly do not overlap with the protein puncta. Several membrane-bound organelles, including lipid droplets and rough ER-like vesicles, are incorporated within the oosome, whereas mitochondria are nearly entirely excluded. Our findings show that the remarkably large size of the oosome is reflected in a complex sub-granular organization and suggest that the oosome is a powerful model for probing interactions between membraneless and membrane-bound organelles, structural features that contribute to granule size, and the evolution of germ plasm in insects.