bluuebunny/crossref_metadata_2025_split huggingface dataset:
Refrigerated storage and cryopreservation of hormone induced sperm in a threatened frog
Authors: Upton Rose , Calatayud Natalie E. , Clulow Simon , Brett Darcie , Burton Alana L. , Colyvas Kim , Mahony Michael , Clulow John 
Published: July 2023

AbstractThere are strong potential benefits of incorporating assisted reproductive technologies (ARTs) into conservation programs for the management of threatened amphibians as the global amphibian decline continues. As sperm cryopreservation and other ARTs advance in common species, focus on non-lethal sperm collection methods for threatened amphibians is imperative. We aimed to realise this goal by testing various doses of exogenous hormones for non-lethal induction of spermiation in a threatened frog (Litoria aurea) and develop cold storage and cryopreservation protocols following the recovery of urinic sperm. Our major findings include: (1) that sperm release could be induced in high concentrations with 20 IU/g bodyweight of human chorionic gonadotrophin (hCG); (2) high levels (>50%) of live, motile sperm could be recovered post-cryopreservation by treating the sperm with 15% v/v DMSO and 1% w/v sucrose pre-freeze; and (3) urinic sperm stored at 5°C retained motility over a 14-day period. Our findings demonstrate that it is possible to obtain and store large quantities of quality sperm from a threatened amphibian via non-lethal means, representing an important step forward for the use of ARTs in conservation programs for rare and threatened species.Lay SummaryAmphibians are undergoing an extinction crisis unparalleled in any other taxa. The development of assisted reproductive technologies, such as sperm cryopreservation and IVF have an important role to play in the conservation management of amphibians globally. Here we report non-lethal methods of sperm collection and storage in a highly threatened amphibian. Major findings include successfully induced sperm release in high concentrations, retention of ∼50% live, motile sperm after 7 days storing it at 5°C, and successful recovery of of more than 50% live, motile sperm following cryopreservation. Our results demonstrate the viability of obtaining and storing sperm from rare and threatened species via non-lethal means, providing an important step forward for the use of ARTs in conservation programs around the globe.
In silico characterization and phylogenetic analysis of Elaeocarpus ganitrus based on ITS2 barcode sequence
Authors: Kushwaha Jyotsana , Joshi Alpana 
Published: July 2023

AbstractPlant molecular systematics relies on using DNA barcodes for studying the evolutionary relationship between species Sequences of the nuclear internal transcribed spacer (ITS) regions have been used widely in molecular phylogenetic studies because of their high variability compared to plastid sequences. Elaeocarpus is a diverse genus within the family Elaeocarpaceae and is widely distributed worldwide among tropical and subtropical climatic zones. Elaeocarpus ganitrus has important medicinal and religious values in India. However, Elaeocarpus ganitrus evolutionary relationship with other Elaeocarpus species is not much explored, especially at the molecular and phylogenetic levels. The present research successfully amplified the nuclear gene ITS2, sequenced and submitted it to NCBI Genbank after using Basic Local Alignment Search Tool (BLAST). Automatic Barcode Gap Discovery (ABGD) and Assemble Species by Automatic Partitioning (ASAP) resulted in different numbers of molecular operational taxonomic units (MOTUs). The lowest score of ASAP (4.5) segregated the sequences into 31 MOTUs with the Threshold dist. value of 0.003524. This study establishes an evolutionary relationship between Elaeocarpus ganitrus and other species belonging to the same genus through the neighbor-joining method. The 38 Elaeocarpus samples were clustered into seven major groups based on ITS2 sequence: Group I is represented by Elaeocarpus ganitrus along with Elaeocarpus sylvestris, Elaeocarpus glabripetalus, Elaeocarpus duclouxii, Elaeocarpus decipiens, and Elaeocarpus zollingeri. Group II is characterized by Elaeocarpus austroyunnanensis and Elaeocarpus glaber. Group III comprises Elaeocarpus sphaericus, Elaeocarpus angustifolius, Elaeocarpus grandis, Elaeocarpus ptilanthus, and Elaeocarpus sphaerocarpus. Three accessions of Elaeocarpus hookerianus are placed in group IV. Elaeocarpus largiflorens and Elaeocarpus thelmae represent group V. Groupr VI contains three species: Elaeocarpus sylvestris, Elaeocarpus dubius, and Elaeocarpus johnsonii. Group VII comprises five species which include Elaeocarpus glabripetalus, Elaeocarpus rugosus, Elaeocarpus tuberculatus, Elaeocarpus hainanensis, and Elaeocarpus angustifolius. The study concludes with the possibility of correctly using the ITS2 gene to identify, discriminate, and documentation of Elaeocarpus ganitrus and other species of the same genus.
Neuroendocrine Gene Expression Coupling of Interoceptive Bacterial Food Cues to Foraging Behavior ofC. elegans
Authors: Boor Sonia A. , Meisel Joshua D. , Kim Dennis H. 
Published: July 2023

SummaryAnimal internal state is modulated by nutrient intake, resulting in behavioral responses to changing food conditions. The neural mechanisms by which internal states are generated and maintained are not well understood. Here, we show that in the nematodeCaenorhabditis elegans,distinct cues from bacterial food – interoceptive signals from the ingestion of bacteria and gustatory molecules sensed from nearby bacteria – act antagonistically on the expression of the neuroendocrine TGF-beta ligand DAF-7 from the ASJ pair of sensory neurons to modulate foraging behavior. A positive-feedback loop dependent on the expression ofdaf-7from the ASJ neurons acts to promote transitions between roaming and dwelling foraging states and influence the persistence of roaming states. SCD-2, theC. elegansortholog of mammalian Anaplastic Lymphoma Kinase (ALK), which has been implicated in the central control of metabolism of mammals, functions in the AIA interneurons to regulate foraging behavior and cell-non-autonomously control the expression of DAF-7 from the ASJ neurons. Our data establish how a dynamic neuroendocrinedaf-7expression feedback loop regulated by SCD-2 functions to couple sensing and ingestion of bacterial food to foraging behavior. We further suggest that this neuroendocrine feedback loop underlies previously characterized exploratory behaviors inC. elegans. Our data suggest that the expression ofdaf-7from the ASJ neurons contributes to and is correlated with an internal state of “unmet need” that regulates exploratory foraging behavior in response to bacterial cues in diverse physiological contexts.
Extrusion fountains are hallmarks of chromosome organization emerging upon zygotic genome activation
Authors: Galitsyna Aleksandra , Ulianov Sergey V. , Bykov Nikolai S. , Veil Marina , Gao Meijiang , Perevoschikova Kristina , Gelfand Mikhail , Razin Sergey V. , Mirny Leonid , Onichtchouk Daria 
Published: July 2023

AbstractThe first activation of gene expression during development (zygotic genome activation, ZGA) is accompanied by massive changes in chromosome organization. The connection between these two processes remains unknown. Using Hi-C for zebrafish embryos, we found that chromosome folding starts by establishing “fountains”, novel elements of chromosome organization, emerging selectively at enhancers upon ZGA. Using polymer simulations, we demonstrate that fountains can emerge as sites of targeted cohesin loading and require two-sided, yet desynchronized, loop extrusion. Specific loss of fountains upon loss of pioneer transcription factors that drive ZGA reveals a causal connection between enhancer activity and fountain formation. Finally, we show that fountains emerge in early Medaka andXenopusembryos; moreover, we found cohesin-dependent fountain pattern on enhancers of mouse embryonic stem cells. Taken together, fountains are the first enhancer-specific elements of chromosome organization; they constitute starting points of chromosome folding during early development, likely serving as sites of targeted cohesin loading.
Introducingπ-HelixNovo for practical large-scale de novo peptide sequencing
Authors: Yang Tingpeng , Ling Tianze , Sun Boyan , Liang Zhendong , Xu Fan , Huang Xiansong , Xie Linhai , He Yonghong , Li Leyuan , He Fuchu , Wang Yu , Chang Cheng 
Published: July 2023

AbstractDe novo peptide sequencing is a promising approach for novel peptide discovery. We use a novel concept of complementary spectra to enhance ion information and propose a de novo sequencing modelπ-HelixNovo based on Transformer architecture.π-HelixNovo outperforms other state-of-the-art models and enhances the taxonomic resolution of gut metaproteome, taking a significant step forward in de novo sequencing.
GIS-FA: An approach to integrate thematic maps, factor-analytic and envirotyping for cultivar targeting
Authors: Araújo Maurício S. , Chaves Saulo F. S. , Dias Luiz A. S. , Ferreira Filipe M. , Pereira Guilherme R. , Bezerra André R. G. , Alves Rodrigo S. , Heinemann Alexandre B. , Breseghello Flávio , Carneiro Pedro C. S. , Krause Matheus D. , Costa-Neto Germano , Dias Kaio O. G. 
Published: July 2023

AbstractKey message: We propose an enviromics prediction model for cultivar recommendation based on thematic maps for decision-makers.Parsimonious methods that capture genotype-by-environment interaction (GEI) in multi-environment trials (MET) are important in breeding programs. Understanding the causes and factors of GEI allows the utilization of genotype adaptations in the target population of environments through environmental features and Factor-Analytic (FA) models. Here, we present a novel predictive breeding approach called GIS-FA that integrates geographic information systems (GIS) techniques, FA models, Partial Least Squares (PLS) regression, and Enviromics to predict phenotypic performance in untested environments. The GIS-FA approach allows: (i) predict the phenotypic performance of tested genotypes in untested environments; (ii) select the best-ranking genotypes based on their over-all performance and stability using the FA selection tools; (iii) draw thematic maps showing overall or pairwise performance and stability for decision-making. We exemplify the usage of GIS-FA approach using two datasets of rice [Oryza sativa(L.)] and soybean [Glycine max(L.) Merr.] in MET spread over tropical areas. In summary, our novel predictive method allows the identification of new breeding scenarios by pinpointing groups of environments where genotypes have superior predicted performance and facilitates/optimizes the cultivar recommendation by utilizing thematic maps.
Disrupting actin filaments enhances glucose-stimulated insulin secretion independent of the cortical actin cytoskeleton
Authors: Polino Alexander J. , Ng Xue Wen , Rooks Rebecca , Piston David W. 
Published: July 2023

AbstractJust under the plasma membrane of most animal cells lies a dense meshwork of actin filaments called the cortical cytoskeleton. In insulin-secreting pancreatic β cells, a longstanding model posits that the cortical actin layer primarily acts to restrict access of insulin granules to the plasma membrane. Here we test this model and find that stimulating β cells with pro-secretory stimuli (glucose and/or KCl) has little impact on the cortical actin layer. Chemical perturbations of actin polymerization, by either disrupting or enhancing filamentation, dramatically enhances glucose-stimulated insulin secretion. We find that this enhancement does not correlate with the state of the cortical actin layer, suggesting filament disruptors act on insulin secretion independently of the cortical cytoskeleton.
A bespoke analytical workflow for the confident identification of sulfopeptides and their discrimination from phosphopeptides
Authors: Daly Leonard A. , Byrne Dominic P. , Perkins Simon , Brownridge Philip J , McDonnell Euan , Jones Andrew R. , Eyers Patrick A. , Eyers Claire E. 
Published: July 2023

ABSTRACTProtein tyrosine sulfation (sY) is a post-translational modification (PTM) catalysed by Golgi-resident Tyrosyl Protein SulfoTransferases (TPSTs). Information on protein tyrosine sulfation is currently limited to ∼50 human proteins with only a handful having verified sites of sulfation. The contribution of this chemical moiety for the regulation of biological processes, both inside and outside the cell, remains poorly defined, in large part due to analytical limitations. Mass spectrometry-based proteomics is the method of choice for PTM analysis, but has yet to be applied for the systematic investigation and large-scale analysis of biomolecular sulfation (constituting the ‘sulfome’), primarily due to issues associated with discrimination of sY-from phosphotyrosine (pY)-containing peptides. In this study, we developed a mass spectrometry (MS)-based workflow centred on the characterization of sY-peptides, incorporating optimised Zr4+-IMAC and TiO2enrichment strategies. Extensive characterization of a panel of sY- and pY-peptides using an array of MS fragmentation regimes (CID, HCD, EThcC, ETciD, UVPD) highlights differences in the ability to generate site-determining product ions, which can be exploited to differentiate sulfated peptides from nominally isobaric phosphopeptides based on precursor ion neutral loss at low collision energy. Application of our analytical workflow to a HEK-293 cell extracellular secretome facilitated identification of 21 new sulfotyrosine-containing proteins, several of which we validate enzymatically usingin vitrosulfation assays. This study demonstrates the applicability of our strategy for confident, high-throughput, ‘sulfomics’ studies, and reveals new sY interplay between enzymes relevant to both protein and glycan sulfation.
Loss of Progranulin Results in Increased Pan-Cathepsin Activity and Reduced LAMP1 Lysosomal Protein
Authors: Anderson Abigail , Tansey Malú G. 
Published: July 2023

AbstractMutations in the progranulin (PGRN) encoding gene,GRN, cause familial frontotemporal dementia (FTD) and neuronal ceroid lipofuscinosis (NCL) and PGRN is also implicated in Parkinson’s disease (PD). These mutations result in decreased PGRN expression. PGRN is highly expressed in peripheral immune cells and microglia and regulates cell growth, survival, repair, and inflammation. When PGRN is lost, the lysosome becomes dysfunctional, but the exact mechanism by which PGRN plays a role in lysosome function and how this contributes to inflammation and degeneration is not entirely understood. To better understand the role of PGRN in regulating lysosome function, this study examined how loss ofGRNimpacts total LAMP1 protein expression and cathepsin activities. Using mouse embryonic fibroblasts (MEFs), immunocytochemistry and immunoblotting assays were performed to analyze fluorescent signal from LAMP1 (lysosomal marker) and BMV109 (marker for pan-cathepsin activity).GRN-/-MEFs exhibit increased expression of pan-cathepsin activity relative toGRN+/+MEFs, and significantly impacts expression of LAMP1. The significant increase in pan-cathepsin activity in theGRN-/-MEFs confirms that PGRN loss does alter cathepsin expression, which may be a result of compensatory mechanisms happening within the cell. Using NTAP PGRN added toGRN-/-MEFs, specific cathepsin activity is rescued. Further investigations should include assessing LAMP1 and BMV109 expression in microglia fromGRN-/-mice, in the hopes of understanding the role of PGRN in lysosomal function in immune cells of the central nervous system and the diseases in which it is implicated.
A multiplexed time-resolved fluorescence resonance energy transfer ultrahigh-throughput screening assay for targeting SMAD4-SMAD3-DNA complex
Authors: Ouyang Wukun , Niu Qiankun , Qui Min , Fu Haian , Du Yuhong , Mo Xiulei 
Published: July 2023

AbstractThe signaling pathway of transforming growth factor-beta (TGFβ) plays crucial roles in the establishment of an immunosuppressive tumor microenvironment, making anti-TGFβ agents a significant area of interest in cancer immunotherapy. However, the clinical translation of current anti-TGFβ agents that target upstream cytokines and receptors remains challenging. Therefore, the development of small molecule inhibitors specifically targeting SMAD4, the downstream master regulator of TGFβ pathway, would offer an alternative approach with significant therapeutic potential for anti-TGF-β signaling. In this study, we present the development of a cell lysate-based multiplexed time-resolved fluorescence resonance energy transfer (TR-FRET) assay in an ultrahigh-throughput screening (uHTS) 1536-well plate format. This assay enables simultaneous monitoring of the protein-protein interaction (PPI) between SMAD4 and SMAD3, as well as the protein-DNA interaction (PDI) between SMADs and their consensus DNA binding motif. The multiplexed TR-FRET assay exhibits high sensitivity, allowing the dynamic analysis of the SMAD4-SMAD3-DNA complex at single amino acid resolution. Moreover, the multiplexed uHTS assay demonstrates robustness for screening small molecule inhibitors. Through a pilot screening of an FDA-approved and bioactive compound library, we identified gambogic acid and gambogenic acid as potential hit compounds. These proof-of-concept findings underscore the utility of our optimized multiplexed TR-FRET platform for large-scale screening to discover small molecule inhibitors that target the SMAD4-SMAD3-DNA complex as novel anti-TGFβ signaling agents.
Ubiquitination-mediated Golgi-to-endosome sorting determines the toxin-antidote duality ofwtfmeiotic drivers
Authors: Zheng Jin-Xin , Du Tong-Yang , Shao Guang-Can , Ma Zhu-Hui , Jiang Zhao-Di , Hu Wen , Suo Fang , He Wanzhong , Dong Meng-Qiu , Du Li-Lin 
Published: July 2023

AbstractKiller meiotic drivers (KMDs) skew allele transmission in their favor by killing meiotic progeny not inheriting the driver allele. Despite their widespread presence in eukaryotes, the molecular mechanisms behind their selfish behavior are poorly understood. Here we investigate how the toxin and antidote products of a fission yeastwtf-family KMD gene can act antagonistically. Both the toxin and the antidote are multi-transmembrane proteins, differing only in their N-terminal cytosolic tails. We find that the antidote employs N-terminal PY motifs (Leu/Pro-Pro-X-Tyr) to bind Rsp5/NEDD4 family ubiquitin ligases, which ubiquitinate the antidote. Mutating PY motifs or attaching a deubiquitinating enzyme transforms the antidote into a toxic protein. Ubiquitination promotes the transport of the antidote from the trans-Golgi network to the endosome, thereby preventing it from causing toxicity. A physical interaction between the antidote and the toxin enables the ubiquitinated antidote to translocate the toxin to the endosome and neutralize its toxicity. We propose that post-translational modification-mediated protein localization and/or activity changes may be a common mechanism governing the antagonistic duality of single-gene KMDs.
Cardiomyocyte-specific adenylyl cyclase type-8 overexpression induces activation of RelA together with myocardial and systemic inflammation
Authors: Kumar Vikas , Bermea Kevin Christian , Kumar Dhaneshwar , Singh Amit , Verma Anjali , Kaileh Mary , Sen Ranjan , Lakatta Edward G. , Adamo Luigi 
Published: July 2023

AbstractBackgroundMice with cardiac-specific overexpression of adenylyl cyclase (AC) type 8 (TGAC8) are under a constant state of severe myocardial stress. They have a remarkable ability to adapt to this stress, but they eventually develop accelerated cardiac aging and experience reduced longevity.ResultsHere we demonstrate that activation of ACVIII in cardiomyocytes results in cell-autonomous RelA-mediated NF-κB signaling. This is associated with non-cell-autonomous activation of proinflammatory and age-associated signaling in myocardial endothelial cells and myocardial smooth muscle cells, expansion of myocardial immune cells, increase in serum levels of inflammatory cytokines, and changes in the size or composition of lymphoid organs. These changes precede the appearance of cardiac fibrosis. We provide evidence indicating that ACVIII-driven RelA activation in cardiomyocytes is mediated by calcium-Protein Kinase A (PKA) signaling.ConclusionsUsing a model of chronic cardiomyocyte stress and accelerated aging we highlight a novel, PKA/RelA-dependent connection between cardiomyocyte stress, myocardial para-inflammation and systemic inflammation. These findings point to RelA-mediated signaling in cardiomyocytes and inter-organ communication between the heart and lymphoid organs as novel potential therapeutic targets to reduce age-associated myocardial deterioration.
Rapid Identification of Bacterial isolates Using Microfluidic Adaptive Channels and Multiplexed Fluorescence Microscopy
Authors: Chatzimichail Stelios , Turner Piers , Feehily Conor , Farrar Alison , Crook Derrick , Andersson Monique , Oakley Sarah , Barrett Lucinda , Sayyed Hafez El , Kyropoulos Jingwen , Nellåker Christoffer , Stoesser Nicole , Kapanidis Achillefs N. 
Published: July 2023

AbstractWe demonstrate the rapid capture, enrichment, and identification of bacterial pathogens using Adaptive Channel Bacterial Capture (ACBC) devices. Using controlled tuning of device backpressure in polydimethylsiloxane (PDMS) devices, we enable the controlled formation of capture regions capable of trapping bacteria from low cell density samples with near 100% capture efficiency. The technical demands to prepare such devices are much lower compared to conventional methods for bacterial trapping and can be achieved with simple benchtop fabrication methods. We demonstrate the capture and identification of seven species of bacteria with bacterial concentrations lower than 1000 cells/mL, including common Gram-negative and Gram-positive pathogens such asEscherichia coliandStaphylococcus aureus. We further demonstrate that species identification of the trapped bacteria can be undertaken in the order of one-hour using multiplexed 16S rRNA-FISH with identification accuracies of 73-99% with unsupervised classification methods.
An AluYb8 retrotransposon characterises a risk haplotype of TMEM106B associated in neurodegeneration
Authors: Salazar Alex , Tesi Niccolò , Knoop Lydian , Pijnenburg Yolande , van der Lee Sven , Wijesekera Sanduni , Krizova Jana , Hiltunen Mikko , Damme Markus , Petrucelli Leonard , Reinders Marcel , Hulsman Marc , Holstege Henne 
Published: July 2023

AbstractGenome-wide association studies identified a role forTMEM106Bin various neurodegenerative diseases. Based on long-read whole-genome sequencing data of 256 individuals, we identified an AluYb8 retrotransposon in the 3’ UTR of the risk haplotype ofTMEM106B. When transcriptionally active, Alu-elements can propogate throughout the genome, and mediate (post-)transcriptional dysregulation of nearby genes. We found thatTMEM106Bhaplotypes carrying the AluYb8 element are more methylated than those without, likely reflecting an evolutionary selection to suppress propagation. AluYb8 activation can be further suppressed by TDP-43, in its role in post-transcriptional RNA-processing. However, age-related loss of TDP-43, by reduced methylation in the 3’ UTR ofTARDBP,may release AluYb8 suppression. Together, our findings suggest that in the aging brain, the AluYb8 insertion may mediate dysregulation ofTMEM106B, impacting the endolysosomal system via a negative-feedback loop, ultimately leading to neurodegenerative disease. Notably,TMEM106Bhaplotype sequences are different between African and European genomes, which likely explains the different effects on disease-risk between both populations. Overall, our research advances the understanding of the roles of TDP-43 and TMEM106B in neurodegenerative diseases, and provides a novel connection between genetic variation and age-related changes in genomic and cellular regulation.