bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tuneable hydrogel stiffness in a 3Din vitromodel induces epithelial to mesenchymal transition in MCF7 but not MDA-MB-231 breast cancer cells
Authors: Wise JA , Currie MJ , Woodfield TBF , Lim KS , Phillips E 
Published: July 2023

AbstractThe study ofin vitromodels of breast cancer is crucial for understanding and treating the malignancy in patients, with 3Din vitromodels providing researchers with more biomimetic systems to overcome limitations of current to 2D cultures andin vivoanimal models.Ex vivopatient tissues have shown that malignant breast tissues are stiffer than healthy or benign tissues, and that the stiffness corresponds with increasing tumour grade. Stiffening of the breast tumour environment alters tumour cell phenotype and facilitates tumour progression, invasion and metastasis. Better understanding of the relationship between extracellular matrix stiffness and breast cancer cell phenotype, and how that is important in the initiation of metastasis, should lead to designing 3D models that mimic the breast tumour microenvironment at different stages of breast cancer progression.This study investigated phenotypic response of two breast cancer cell lines that are representative of clinical breast cancer subtypes (MCF7, Luminal A; MDA-MB-231, Triple Negative Breast Cancer) in gelatin-methacryloyl (GelMA) hydrogels of varying stiffness. A visible light photoinitiation system was adopted to provide a tuneable photocrosslinking platform to systematically control hydrogel stiffness and tumour microenvironment. This allowed rapid fabrication of biocompatible hydrogels supporting high cell viability over long-term culture.The impact of a clinically relevant range of microenvironmental stiffness on breast cancer cell behaviour and phenotype was examined over a 21-day culture period using GelMA hydrogels. Results showed that MCF7 cells cultured for 21 days in high stiffness hydrogels (10 wt%; 28 kPa) responded by downregulating the epithelial marker E-cadherin and upregulating mesenchymal markers N-cadherin and Vimentin, whereas MDA-MB-231 cells showed no changes in EMT-markers when cultured in hydrogels of corresponding stiffness (10 wt%; 33 kPa). Culturing both cell lines in soft hydrogels (5 wt%; 11 kPa) maintained their phenotype over 21 days, highlighting the importance of controlling hydrogel mechanical properties when studying breast cancer cell phenotype.
Grb7 knockout mice develop normally but litters born to knockout females fail to thrive
Authors: Lofgren Kristopher A. , Kenny Paraic A. 
Published: July 2023

AbstractGrowth factor receptor-bound 7 (Grb7) is an adaptor protein involved in signal transduction downstream of multiple receptor tyrosine kinases, including ERBB, FGFR and PDGFR pathways. Experimental studies have implicated Grb7 in regulating cell proliferation, survival, migration and invasion through its large repertoire of protein-protein interactions. Here, we describe the generation and characterization of aGrb7knockout mouse. These mice are viable and fertile. AlacZknock-in reporter was used to visualizeGrb7promoter activity patterns in adult tissues, indicating widespread Grb7 expression in glandular epithelium, the central nervous system and other tissues. The sole defect observed in these animals was a failure ofGrb7knockout females to successfully raise pups to weaning age, a phenotype that was independent of both paternal and pup genotypes. These data suggest a regulatory role for Grb7 in mammary lactational physiology.
saseR: Juggling offsets unlocks RNA-seq tools for fast and Scalable differential usage, Aberrant Splicing and Expression Retrieval
Authors: Segers Alexandre , Gilis Jeroen , Van Heetvelde Mattias , Risso Davide , De Baere Elfride , Clement Lieven 
Published: July 2023

AbstractRNA-seq data analysis relies on many different tools, each tailored to specific applications and coming with unique assumptions and restrictions. Indeed, tools for differential transcript usage, or diagnosing patients with rare diseases through splicing and expression outliers, either lack in performance, discard information, or do not scale to massive data compendia. Here, we show that replacing the normalisation offsets unlocks bulk RNA-seq workflows for scalable differential usage, aberrant splicing and expression analyses. Our method, saseR, is much faster than state-of-the-art methods, dramatically outperforms these to detect aberrant splicing, and provides a single workflow for various short- and long-read RNA-seq applications.
Molecular quantitative trait loci in reproductive tissues impact male fertility in cattle
Authors: Mapel Xena Marie , Kadri Naveen Kumar , Leonard Alexander S. , He Qiongyu , Lloret-Villas Audald , Bhati Meenu , Hiltpold Maya , Pausch Hubert 
Published: July 2023

AbstractBreeding bulls are well suited to investigate inherited variation in male fertility because they are genotyped and their reproductive success is monitored through semen analyses and thousands of artificial inseminations. However, functional data from relevant tissues are lacking, which prevents fine-mapping fertility-associated genomic regions. Here, we characterize gene expression and splicing variation in testis, epididymis, and vas deferens transcriptomes of 118 mature bulls and conduct association tests between 417k molecular phenotypes and 21M genome-wide variants to identify 41k regulatory loci. We show broad consensus in tissue-specific and tissue-enriched gene expression between the three bovine tissues and their human and murine counterparts. Expression- and splicing-mediating variants are more than three times as frequent in testis than epididymis and vas deferens, highlighting the transcriptional complexity of testis. Finally, we identify genes (WDR19,SPATA16,KCTD19,ZDHHC1) and molecular phenotypes that are associated with quantitative variation in male fertility through transcriptome-wide association and colocalization analyses.
Endothelial Knockdown of the Tumor Suppressor, WWOX, Increases Inflammation in Ventilator-Induced Lung Injury
Authors: Zeng Zhenguo , Abdelwahid Eltyeb , Chen Weiguo , Ascoli Christian , Pham Trinh , Jacobson Jeffrey R. , Dudek Steven M. , Natarajan Viswanathan , Aldaz C. Marcelo , Machado Roberto F. , Singla Sunit 
Published: July 2023

AbstractBackgroundChronic cigarette smoke exposure downregulates lung expression of WWOX, an ARDS relevant tumor suppressor. Prior work has revealed a barrier protective function of WWOX during infectious models of ARDS. Proteomic analysis ofWWOX-silenced lung endothelial cells suggest involvement of WWOX in protection against mechanical stretch-induced inflammation.MethodsProtein lysates fromWWOX-silenced endothelial cells (ECs) were analyzed using tandem mass tag mass spectrometry (TMT-MS) to determine the differential expression status of the proteome compared to wild type ECs.WWOX-silenced ECs as well as those isolated from endothelialWwoxknockout (ECWwoxKO) mice were subjected to cyclic stretch (18% elongation, 0.5 Hz, 4 hours). Cellular lysates and media supernatant were harvested for assays of cellular signaling, protein expression, and cytokine release. Dual silencing ofWWOXand zyxin was achieved to determine the role of zyxin upregulation in IL-8 production following mechanical stretch and duringWWOXknockdown. Control and ECWwoxKO mice were subjected to high tidal volume ventilation (VILI, 40ml/kg, 65 breath/min, 4hours). Bronchoalveolar lavage fluid and mouse lung tissue were harvested for cellular signaling, cytokine secretion, and histologic assays.ResultsTMT-MS revealed upregulation of zyxin expression during WWOX knockdown which predicted a heightened inflammatory response to mechanical stretch.WWOX-silenced ECs and ECs isolated from ECWwoxmice displayed significantly increased cyclic stretch-mediated secretion of various cytokines (IL-6, KC/IL-8, IL-1β, and MCP-1) relative to controls. This was associated with increased ERK and JNK phosphorylation but decreased p38 MAPK phosphorylation. ECWwoxKO mice subjected to VILI sustained a greater degree of injury than corresponding controls. Silencing of zyxin duringWWOXknockdown abrogated stretch-induced increases in IL-8 secretion.ConclusionLoss of WWOX function in ECs is associated with a heightened inflammatory response during mechanical stretch that is associated with increased MAPK phosphorylation and appears to be dependent on upregulation of zyxin.
Prenatal alcohol exposure and white matter microstructural changes across the first 6-7 years of life: A longitudinal diffusion tensor imaging study of a South African birth cohort
Authors: Donald KA , Hendrikse CJ , Roos A , Wedderburn CJ , Subramoney S , Ringshaw JE , Bradford L , Hoffman N , Burd T , Narr KL , Woods RP , Zar HJ , Joshi SH , Stein DJ 
Published: July 2023

ABSTRACTPrenatal alcohol exposure (PAE) can affect brain development in early life, but few studies have investigated the effects of PAE ontrajectoriesof white matter tract maturation in young children. Here we used diffusion weighted imaging (DWI) repeated over three time points in a South African birth cohort, to measure the effects of PAE on patterns of white matter microstructural development during the pre-school years. A total of 342 scans acquired from 237 children as neonates (N=82 scans: 30 PAE; 52 controls) and at ages 2-3 (N=121 scans: 27 PAE; 94 controls) and 6-7 years (N=139 scans: 45 PAE; 94 controls) were included. Maternal alcohol use during pregnancy and other antenatal covariates were collected from 28-32 weeks’ gestation. Linear mixed effects models were implemented to investigate the effects of PAE on fractional anisotropy (FA) and mean diffusivity (MD) in specific white matter tracts over time, while adjusting for child sex and maternal education. We found significant PAE-by-time effects on trajectories of FA development in the left superior cerebellar peduncle (SCP-L: p=0.001; survived FDR correction) and right superior longitudinal fasciculus (SLF-R: p=0.046), suggesting altered white matter development among children with PAE. Compared with controls, children with PAE demonstrated a more rapid change in FA in these tracts from the neonatal period to 2-3 years of age, followed by a more tapered trajectory for the period from 2-3 to 6-7 years of age, with these trajectories differing from unexposed control children. Given their supporting roles in various aspects of neurocognitive functioning (i.e., motor regulation, learning, memory, language), altered patterns of maturation in the SCP and SLF may contribute to a spectrum of physical, social, emotional, and cognitive difficulties often experienced by children with PAE. This study highlights the value of repeated early imaging in longitudinal studies of PAE, and focus for early childhood as a critical window of potential susceptibility as well as an opportunity for early intervention.
Human brain single nucleus cell type enrichments in neurodegenerative diseases
Authors: Alvarado Chelsea X. , Weller Cory A. , Johnson Nicholas , Leonard Hampton L. , Singleton Andrew B. , Reed Xylena , Blauewendraat Cornelis , Nalls Mike 
Published: July 2023

AbstractSingle cell RNA sequencing has opened a window into clarifying the complex underpinnings of disease, particularly in quantifying the relevance of tissue- and cell-type-specific gene expression. To identify the cell types and genes important to therapeutic target development across the neurodegenerative disease spectrum, we leveraged genome-wide association studies, recent single cell sequencing data, and bulk expression studies in a diverse series of brain region tissues. We were able to identify significant immune-related cell types in the brain across three major neurodegenerative diseases: Alzheimer’s Disease, Amyotrophic Lateral Sclerosis, and Parkinson’s Diseases. Subsequently, we identified the major role of 30 fine-mapped loci implicating seven genes in multiple neurodegenerative diseases and their pathogenesis.
Application of an EEG-based deep learning model to discriminate children with epileptic spasms from normal controls
Authors: Lu Mingjian , Zhang Yipeng , Diada Atsuro , Oana Shingo , Rajaraman Rajsekar R. , Nariai Hiroki , Roychowdhury Vwani , Hussain Shaun A. 
Published: July 2023

AbstractObjectiveGiven that epileptic spasms are often subtle, and that identification of hypsarrhythmia is limited by inadequate inter-rater reliability, there is a significant need for novel tools to aid the clinical identification of Infantile Epileptic Spasms Syndrome (IESS). Deep learning is an emerging technology which may enable efficient classification of disease states and may facilitate discovery of novel biomarkers. In this study, we set out to evaluate whether children with epileptic spasms can be distinguished from normal controls with use of an EEG-based deep learning model.MethodsA deep learning model was trained and validated (5-fold cross validation) using 400 EEG samples (2 awake and 2 sleep samples from 50 children with epileptic spasms and 50 normal controls). Salient frequency bands and specific morphologic EEG features were identified with occlusion sensitivity analysis and targeted input perturbation, respectively.ResultsThe model accurately distinguishes children with epileptic spasms from normal controls, solely on the basis of relatively short EEG samples. Using sleep data, accuracy = 0.95, recall = 0.96, precision (sensitivity) = 0.94, specificity = 0.94, and F1 score = 0.95. With awake data, accuracy = 0.91, recall = 0.84, precision = 0.98, specificity = 0.98, and F1 score = 0.90. The salient frequency bands for classification are 9.7 – 22.0 Hz and 1.0 – 6.8 Hz in sleep and awake EEG, respectively. With visual analysis of extracted salient features, we suspect that the model is identifying cases on the basis of paroxysmal fast activity in sleep and spike-wave activity in wakefulness.ConclusionThis deep learning model represents a first step in the development of efficient algorithms that may aid in identification of epileptic spasms and IESS. More importantly, this approach may facilitate novel EEG-based biomarkers of epileptic spasms.
Multifactorial analysis of terminator performance on heterologous gene expression in Physcomitrella
Authors: Niederau Paul Alexander , Eglé Pauline , Willig Sandro , Parsons Juliana , Hoernstein Sebastian N.W. , Decker Eva L. , Reski Ralf 
Published: July 2023

AbstractThe production of recombinant proteins for health applications accounts for a large share of the biopharmaceutical market. While many drugs are produced in microbial and mammalian systems, plants gain more attention as expression hosts to produce eukaryotic proteins. In particular the GMP-compliant moss Physcomitrella (Physcomitrium patens) has outstanding features such as excellent genetic amenability, reproducible bioreactor cultivation, and humanized protein glycosylation patterns. In this study, we selected and characterized novel terminators for their effects on heterologous gene expression. The Physcomitrella genome contains 53,346 unique 3’UTRs (untranslated regions) of which 7,964 transcripts contain at least one intron. Over 91% of 3’UTRs exhibit more than one polyadenylation site, indicating the prevalence of alternative polyadenylation in Physcomitrella. Out of all 3’UTRs, 14 terminator candidates were selected and characterized via transient Dual Luciferase assays, yielding a collection of endogenous terminators performing equally high as established heterologous terminators CaMV35S, AtHSP90, and NOS. High performing candidates were selected for testing as double terminators which impact reporter levels, dependent on terminator identity and positioning. Testing of 3’UTRs among the different promoters NOS, CaMV35S, and PpActin5 showed an increase of more than 1,000-fold between promoters PpActin5 and NOS, whereas terminators increased reporter levels by less than 10-fold, demonstrating the stronger effect promoters play as compared to terminators. The number of polyadenylation sites as well as polyadenylation signals were found to be major determinants of terminator performance. Our results improve the biotechnology platform Physcomitrella and further our understanding of how terminators influence gene expression in plants in general.Key messageCharacterization of Physcomitrella 3’UTRs across different promoters yields endogenous single and double terminators for usage in molecular pharming and indicates promoters and terminators to synergistically control gene expression.
Carbon source and surface type influence the early-stage biofilm formation by rhizosphere bacteriumPseudomonas donghuensisP482
Authors: Rajewska Magdalena , Maciąg Tomasz , Jafra Sylwia 
Published: July 2023

AbstractThe competence of bacteria to colonize different environmental niches is often determined by their ability to form biofilms. This depends on both cellular and extracellular factors, such as individual characteristics of a strain, type of colonized surface (abiotic or biotic) or availability and source of nutrients.Pseudomonas donghuensisP482 efficiently colonizes rhizosphere of various plant hosts, but a connection between plant tissue colonization and biofilm formation has not been verified for P482 up to date. Here we demonstrate that the ability of P482 to form biofilm on abiotic surfaces and the structural characteristics of the biofilm are connected to the type of carbon source available to the bacteria, with glycerol promoting formation of developed biofilm at early stages. Also, the type of substratum, polystyrene or glass, significantly influences the ability of P482 to attach to the surface, possibly due to hydrophobic effects. Moreover, mutants in genes associated with motility or chemotaxis, synthesis of polysaccharides, and encoding proteases or regulatory factors, affected in biofilm formation on glass were fully capable of colonizing root tissue of both tomato and maize hosts. This indicates that the ability to form biofilm on distinct abiotic surfaces does not simply correlate with the efficient colonization of rhizosphere and formation of biofilm on plant tissue by P482.
S-nitrosylation-mediated unfolded protein response maintains hematopoietic progenitors
Authors: Cho Bumsik , Shin Mingyu , Chang Eunji , Son Seogho , Shim Jiwon 
Published: July 2023

SummaryTheDrosophilalymph gland houses blood progenitors that give rise to myeloid-like blood cells. Initially, blood progenitors proliferate, but later become quiescent to maintain multipotency before differentiation. Despite the identification of various factors involved in multipotency maintenance, the cellular mechanism regulating blood progenitor quiescence remains elusive. Here, we reveal the expression of nitric oxide synthase in blood progenitors, generating nitric oxide for post-translational S-nitrosylation of protein cysteine residues. S-nitrosylation activates the Ire1-Xbp1-mediated unfolded protein response, leading to G2 cell cycle arrest. Specifically, we identify the epidermal growth factor receptor as a target of S-nitrosylation, resulting in its retention within the endoplasmic reticulum and blockade of its receptor function. Collectively, our findings highlight developmentally programmed S-nitrosylation as a critical mechanism that induces protein quality control in blood progenitors, maintaining their undifferentiated state by inhibiting cell cycle progression and rendering them unresponsive to paracrine factors.
Environmental enrichment promotes adaptive responding during tests of behavioral regulation in male heterogeneous stock rats
Authors: Ishiwari Keita , King Christopher P. , Martin Connor D. , Tripi Jordan A. , George Anthony M. , Lamparelli Alexander C. , Chitre Apurva , Polesskaya Oksana , Richards Jerry B. , Solberg Woods Leah C. , Gancarz Amy , Palmer Abraham A. , Dietz David M. , Mitchell Suzanne H. , Meyer Paul J. 
Published: July 2023

AbstractOrganisms must regulate their behavior flexibly in the face of environmental challenges. Failure can lead to a host of maladaptive behavioral traits associated with a range of neuropsychiatric disorders, including attention deficit hyperactivity disorder, autism, and substance use disorders. This maladaptive dysregulation of behavior is influenced by genetic and environmental factors. For example, environmental enrichment produces beneficial neurobehavioral effects in animal models of such disorders. The present study determined the effects of environmental enrichment on a range of measures related to behavioral regulation using a large cohort of male, outbred heterogeneous stock (HS) rats as subjects to mimic the genetic variability found in the human population. Subjects were reared from late adolescence onwards either in pairs in standard housing with minimal enrichment (n=200) or in groups of 16 in a highly enriched environment consisting of a large multi-level cage filled with toys, running wheels, and shelters (n=64). Rats were subjected to a battery of tests, including: (i) locomotor response to novelty, (iI) light reinforcement, (iii) social reinforcement, (iv) reaction time, (v) a patch-depletion foraging test, (vi) Pavlovian conditioned approach, (vii) conditioned reinforcement, and (viii) cocaine conditioned cue preference. Results indicated that rats housed in the enriched environment were able to filter out irrelevant stimuli more effectively and thereby regulate their behavior more efficiently than standard-housing rats. The dramatic impact of environmental enrichment suggests that behavioral studies using standard housing conditions may not generalize to more complex environments that may be more ethologically relevant.