bluuebunny/crossref_metadata_2025_split huggingface dataset:
Delineating Structural Propensities of the 4E-BP2 Protein via Integrative Modelling and Clustering
Authors: Tsangaris Thomas E. , Smyth Spencer , Gomes Gregory-Neal W. , Liu Zi Hao , Milchberg Moses , Bah Alaji , Wasney Gregory A. , Forman-Kay Julie D. , Gradinaru Claudiu C. 
Published: June 2023

ABSTRACTThe intrinsically disordered 4E-BP2 protein regulates mRNA cap-dependent translation through the interaction with the predominantly folded eukaryotic initiation factor 4E (eIF4E). Phosphorylation of 4E-BP2 dramatically reduces eIF4E binding, in part by stabilizing a binding- incompatible folded domain (REF). Here, we used a Rosetta-based sampling algorithm optimized for IDRs to generate initial ensembles for two phospho forms of 4E-BP2, non- and five-fold phosphorylated (NP and 5P, respectively), with the 5P folded domain flanked by N- and C-terminal IDRs (N-IDR and C-IDR, respectively). We then applied an integrative Bayesian approach to obtain NP and 5P conformational ensembles that agree with experimental data from nuclear magnetic resonance, small-angle X-ray scattering and single-molecule Förster resonance energy transfer (smFRET). For the NP state, inter-residue distance scaling and 2D maps revealed the role of charge segregation and pi interactions in driving contacts between distal regions of the chain (∼70 residues apart). The 5P ensemble shows prominent contacts of the N-IDR region with the two phosphosites in the folded domain, pT37 and pT46, and, to a lesser extent, delocalized interactions with the C-IDR region. Agglomerative hierarchical clustering led to partitioning of each of the two ensembles into four clusters, with different global dimensions and contact maps. This helped delineate an NP cluster that, based on our smFRET data, is compatible with the eIF4E-bound state. 5P clusters were differentiated by interactions of C-IDR with the folded domain and of the N-IDR with the two phosphosites in the folded domain. Our study provides both a better visualization of fundamental structural poses of 4E-BP2 and a set of falsifiable insights on intrachain interactions that bias folding and binding of this protein.
Do native and introduced cover crops differ in their ability to suppress weeds and reduce seedbanks? A Case study in a Table Grape Vineyard
Authors: Fernando Margaret R. , Hale Lauren , Shrestha Anil 
Published: June 2023

AbstractCover cropping is considered a valuable tool for integrated weed management. However, weed suppression by cover crops can be inconsistent. We hypothesized that a native cover crop species may have greater capacity to suppress weeds than an introduced species owing to adaptive advantages. A study was conducted from 2020 to 2022 in a newly-established Autumn King tablegrape vineyard in Parlier, CA. Two cover crop treatments, a native plant species, phacelia (Phacelia tanacetifolia), or an introduced species, rye (Secale cerealeL. ‘Merced’), were compared to a no cover crop, herbicide-managed control for impacts on weed control. Cover crops were sown in 2019 in the center 1.8 m of the 3.6 m space between the grapevine rows. The experimental design was a randomized complete block with four replications. Percent cover, weed density, and weed biomass in different seasons were assessed in the inter-row spaces and the vine rows. Soil samples were collected in 2021 from the grape row and interrow spaces to assess the weed seedbank. After the cover crops were terminated, percent weed cover was lower in the interrow of the phacelia compared to the no cover crop plots at two sampling times. When cover crops were actively growing (winter/spring), phacelia plots had a 7-fold higher cover crop to weed biomass ratio compared to that of the rye plots, thus indicating greater weed suppression. However, weed seedling emergence from the seedbank samples of the cover crop plots were 2- to 4-fold greater (in the phacelia and rye, respectively) than from the no cover crop plots. In summary, phacelia suppressed weeds more than rye; however, they both resulted in a bigger weed seedbank size compared to the herbicide-managed no cover crop plots, so additional management practices will be needed for long term weed management with cover crops in vineyards.
A Gene Therapy for Hereditary Nonpolyposis Colorectal Cancer using CRISPR-Cas9 Nickase
Authors: Kannan Shravan , Man Joshua J 
Published: June 2023

ABSTRACTHereditary non-polyposis colorectal cancer (HNPCC) is an inherited disorder characterized by an increased risk of developing colorectal cancer before age 50. HNPCC is predominantly caused by genetic mutations in MLH1 and MSH2, which are involved in DNA mismatch repair. Current standard practice is to perform prophylactic colectomy, resulting in debilitating aftereffects for life. Though the genetic cause of HNPCC is well-known, there are currently no available treatments that target these mutations. Herein we describe a novel treatment protocol using a CRISPR-Cas9n-based genetic therapy to restore DNA mismatch repair. First, gRNA and template DNA targeting the most prevalent mutation clusters in MLH1 and MSH2 as well as CRISPR-Cas9n elements will be packaged into an integrase-deficient lentiviral vector. Then, the viral vector will be used to transduce human colonic tumor-derived organoids as well as administered systemically in mouse models of HNPCC. Mice will be monitored clinically and for signs of disease progression. At termination, colonic tissue will be harvested and analyzed for restoration of the wild-type MLH1 and MSH2 sequence and biochemical markers of HNPCC. This protocol offers an alternative strategy using CRISPR-Cas9n-based gene therapy to prevent tumor formation in patients, avoid morbid surgery, and significantly improve quality of life.
Evaluation ofApolipoprotein e4allele as susceptible factor for neurodegenerative diseases among Eastern Indians
Authors: Sadhukhan Dipanwita , Mishra Smriti , Mukherjee Priyanka , Biswas Atanu , Hui Subhra Prakash , Banerjee Tapas Kumar , Biswas Arindam 
Published: June 2023

ABSTRACTIntroductionApolipoprotein E (ApoE) and age have been identified as the major risk factors for several neurodegenerative disorders. Among the three major isoforms (ApoE2, ApoE3 & ApoE4) ofAPOE, ApoE4often shows ethnicity dependent association with neurodegenerative diseases. In the present study, we aim to determine thee4allele/genotype frequency among the different neurodegenerative disorders and their correlation with several demographic and clinical parameters from eastern India.Material & MethodsA total of 826 individuals were recruited for this study which includes 128 PD-MCI, 144 PDD, 90 DLB, 114 FTD, 94 AD and 256 unrelated neurologically controls from eastern India. Subjects were analysed forAPOEgenotype (E2, E3andE4) by PCR-RFLP techniques and Sanger sequencing.ResultsTheAPOE4allele was significantly associated with each of the disease subtypes, selected for the study (P = 0.016 to 0.000), whilee3allele was predominant among controls. Further stratification of subjects identified significant overrepresentation of (a) positive family history for FTD (P = 0.0414) & AD (P = 0.029) and (b) early age at onset of for PDD (P = 0.0316) and FTD (P = 0.0034) among thee4allele carriers. Furthermore, lowering of BMSE score was also observed among thee4allele carriers of AD subjects (P = 0.0324).ConclusionThere is a significant association ofAPOE4allele with different neurodegenerative diseases influencing lowering of age at onset, BMSE score and positive family history among ethnic Bengali population of eastern India.
Tiny Earth CURE improves student persistence in science
Authors: Miller Sarah , Aldana Cristian Cervantes , Du Wenyi , Lee Hyewon , Maldonado Natalia , Sandoval Perla , Vong Janice , Young Gerald , Handelsman Jo , Broderick Nichole A. , Hernandez Paul R. , Estrada Mica 
Published: June 2023

ABSTRACTCourse-based undergraduate research experiences (CUREs) enhance student retention in STEM, particularly among students who belong to historically excluded communities. Yet the mechanisms by which CUREs contribute to student integration and persistence are poorly understood. Utilizing the Tripartite Integration Model of Social Influence (TIMSI), this longitudinal study examines how Tiny Earth, an antibiotic-discovery CURE, impacts students’ scientific self-efficacy, scientific identity, endorsement of scientific community values, and intentions to persist in science. The study also explores how gains in TIMSI factors vary as a function of student demographics and course characteristics. Results of pre-and post-course measurements show that scientific self-efficacy and identity increased among students in Tiny Earth, and some student demographics and course characteristics moderated these gains. Gains in scientific self-efficacy, identity, and values correlated with gains in persistence intentions, whereas student demographics and course characteristics did not. Results of this study show that the Tiny Earth CURE enhanced students’ integration into the scientific community, which was linked to intentions of students of both historically underrepresented and majority groups to persist in STEM. We discuss how courses that provide opportunity to learn science skills in the context of a CURE can contribute toward enlarging and diversifying the STEM workforce.
Assembly processes of bacterial and fungal community differ between desert and oasis habitats in an arid inland river basin, northwest China
Authors: Wang Wen-Juan , Ding Yi-Ming , Ren Ming-Xun , Li Jing-Wen 
Published: June 2023

SummaryOasis habitat play a critical role in arid areas, yet little is known about microbial community assembly processes and its differences in oasis and desert habitat in arid inland river basin.Herein, using 21 and 18 sample data respectively collected from oasis and desert habitats at the lower reaches of Heihe River, northwest China, we examined the assembly processes of soil bacterial and fungal communities and revealed the driving factors affecting the relative contributions of deterministic and stochastic processes.We found that deterministic processes, especially variable selection, dominated bacterial community assembly in oasis habitat, while stochastic processes were more important in desert habitat. By contrast, stochastic processes dominated fungal community assembly both in oasis and desert habitats, in which dispersal limitation played a more important role. Environmental (e.g. EC) and biotic factors (microbial species associations) significantly mediated the bacterial community assembly. However, both environmental and biotic factors had little/no effects on fungal community assembly.This study highlights the soil microbial community assembly is habitat- and taxon-dependent, and environmental (EC) and biotic factors play an important role in regulating these assembly processes in arid inland river basin.
Probing the dissociation pathway of a kinetically labile transthyretin mutant
Authors: Sun Xun , Ferguson James A. , Leach Benjamin I. , Stanfield Robyn L. , Dyson H. Jane , Wright Peter E. 
Published: June 2023

AbstractAggregation of transthyretin (TTR) is associated with devastating TTR amyloid disease. Amyloidosis begins with dissociation of the native tetramer to form a monomeric intermediate that assembles into pathogenic aggregates. This process is accelerated in vitro at low pH, but the dissociation and reassembly of TTR at neutral pH remains poorly understood, due to the low population of intermediates. We use NMR studies with a highly sensitive19F probe that allows deconvolution of relative populations of a destabilized A25T mutant at concentrations as low as 2 µM. The A25T mutation, located at the weak dimer interface, perturbs both the weak and strong dimer interfaces. A tetramer-dimer-monomer (TDM) equilibrium model is proposed to account for concentration- and temperature-dependent population changes. All thermodynamic and kinetic parameters and activation energetics for dissociation of the native A25T tetramer, as well as a destabilized alternative tetramer (T*) with a mispacked F87 side chain, were extracted by van’t Hoff and19F NMR line-shape analysis. The conversion from T to T*, the slowest first-order kinetic step, shows anti-Arrhenius behavior. The19F and methyl chemical shifts of probes close to the strong dimer interface in the dimer and T* species are degenerate, implicating interfacial perturbation as a common structural feature of these intermediate species. Molecular dynamics (MD) simulations further suggest more frequent F87 ring flipping on the nanoscale timescale in the A25T dimer than in the tetramer. Our integrated approach offers quantitative insights into the energy landscape of the dissociation pathway of TTR at neutral pH.
IRE1-mediated degradation ofpre-miR-301apromotes apoptosis through upregulation ofGADD45A
Authors: Gebert Magdalena , Bartoszewska Sylwia , Opalinski Lukasz , Collawn James F. , Bartoszewski Rafał 
Published: June 2023

AbstractThe unfolded protein response is a survival signaling pathway that is induced during various types of ER stress. Here we focus on the IRE1 pathway to determine IRE1’s role in miRNA regulation during ER stress. During induction of ER stress in human bronchial epithelial cells, we utilized next generation sequencing to demonstrate thatpre-miR-301aandpre-miR-106b, were significantly increased in the presence of an IRE1 inhibitor. Conversely, using nuclear-cytosolic fractionation on ER stressed cells, we found that these three pre-miRNAs were decreased in the nuclear fractions without the IRE1 inhibitor. We also found thatmiR-301a-3ptargets the proapoptotic UPR factor, growth arrest and DNA-damage-inducible alpha (GADD45A). InhibitingmiR-301a-3plevels or blocking its predicted miRNA binding site inGADD45A’s 3’ UTR with a target protector increasedGADD45AmRNA expression. An elevation ofXBP1sexpression had no effect onGADD45AmRNA expression. We also demonstrated that the introduction of a target protector for themiR-301a-3pbinding site inGADD45AmRNA during ER stress promoted cell death in the airway epithelial cells. These results indicated that IRE1’s endonuclease activity is a two-edged sword that splicesXBP1mRNA for survival and degradespre-miR-301ato elevate the mRNA expression of a pro-apoptotic gene, GADD45A.
Aberrant type 2 dopamine receptor availability in criminal psychopathy
Authors: Lukkarinen Lasse , Tuisku Jouni , Sun Lihua , Helin Semi , Karlsson Henry K. , Venetjoki Niina , Salomaa Marja , Rautio Päivi , Hirvonen Jussi , Lauerma Hannu , Tiihonen Jari , Nummenmaa Lauri 
Published: June 2023

AbstractBackgroundPsychopathy is characterized by antisocial behavior, poor behavioral control and lacking empathy, and structural alterations in the corresponding neural circuits. Molecular brain basis of psychopathy remains poorly characterized.MethodsHere we studied type 2 dopamine receptor (D2R) and mu-opioid receptor (MOR) availability in convicted violent offenders with high psychopathic traits (n=11) and healthy matched controls (n=19) using positron emission tomography (PET). D2R were measured with radioligand [11C]raclopride and MORs with radioligand [11C]carfentanil.ResultsPsychopathic subjects had lowered D2R availability in caudate and putamen, and D2R striatal availability was also associated with degree of psychopathic traits in this prisoner sample. No group differences were found in MOR availability, although in the prisoner sample, psychopathic traits were negatively correlated with MOR availability amygdala and nucleus accumbens.ConclusionsWe conclude that D2R signaling could be the putative neuromolecular pathway for psychopathy, whereas evidence for the aberrant MOR system is more limited.
Splicing factor SRSF1 is essential for homing of precursor spermatogonial stem cells in mice
Authors: Sun Longjie , Lv Zheng , Chen Xuexue , Ye Rong , Tian Shuang , Wang Chaofan , Xie Xiaomei , Yan Lu , Yao Xiaohong , Shao Yujing , Cui Sheng , Chen Juan , Liu Jiali 
Published: June 2023

AbstractSpermatogonial stem cells (SSCs) are essential for continuous spermatogenesis and male fertility. The underlying mechanisms of alternative splicing (AS) in mouse SSCs are still largely unclear. We demonstrated that SRSF1 is essential for gene expression and splicing in mouse SSCs. Crosslinking immunoprecipitation and sequencing (CLIP-seq) data revealed that spermatogonia-related genes (e.g.,Plzf,Id4,Setdb1, Stra8,Tial1/Tiar,Bcas2,Ddx5,Srsf10,Uhrf1, andBud31) were bound by SRSF1 in the mouse testes. Specific deletion ofSrsf1in mouse germ cells impairs homing of precursor SSCs leading to male infertility. Whole-mount staining data showed the absence of germ cells in the testes of adult conditional knockout (cKO) mice, which indicates Sertoli cell-only syndrome (SCOS) in cKO mice. The expression of spermatogonia-related genes (Gfra1,Pou5f1,Plzf,Dnd1,Stra8, andTaf4b) was significantly reduced in the testes of cKO mice. Moreover, multiomics analysis suggests that SRSF1 may affect survival of spermatogonia by directly binding and regulatingTial1/Tiarexpression through AS. In addition, immunoprecipitation mass spectrometry (IP-MS) and co-immunoprecipitation (Co-IP) data showed that SRSF1 interacts with RNA splicing-related proteins (SART1, RBM15, and SRSF10). Collectively, our data reveal the critical role of SRSF1 in spermatogonia survival, which may provide a framework to elucidate the molecular mechanisms of the posttranscriptional network underlying homing of precursor SSCs.
Brain Metabolic Network Covariance and Aging in a Mouse Model of Alzheimer’s Disease
Authors: Chumin EJ , Burton CP , Silvola R , Miner EW , Persohn SC , Veronese M , Territo PR 
Published: June 2023

ABSTRACTINTRODUCTIONAlzheimer’s disease (AD), the leading cause of dementia worldwide, represents a human and financial impact for which few effective drugs exist to treat the disease. Advances in molecular imaging have enabled assessment of cerebral glycolytic metabolism, and network modeling of brain region have linked to alterations in metabolic activity to AD stage.METHODSWe performed18F-FDG Positron Emission Tomography (PET) imaging in 4-, 6-, and 12-month-old 5XFAD and littermate controls (WT) of both sexes and analyzed region data via brain metabolic covariance analysis.RESULTS5XFAD model mice showed age related changes glucose uptake relative to WT mice. Analysis of community structure of covariance networks was different across age and sex, with a disruption of metabolic coupling in the 5XFAD model.DISCUSSIONThe current study replicates clinical AD findings and indicates that metabolic network covariance modeling provides a translational tool to assess disease progression in AD models.RESEARCH IN CONTEXTSYSTEMATIC REVIEWThe authors extensively reviewed literature (e.g., PubMed), meeting abstracts, and presentations on approaches to evaluate brain network analysis in animal models. Based on the available data, there were clear gaps in our understanding of how metabolic networks change with disease progression at the preclinical phase, thus limiting the utility of these measures for clinical comparison in Alzheimer’s disease (AD).INTERPRETATIONOur findings indicate that employing metabolic covariance modeling in mouse models of AD and littermate controls of both sexes with age provides a mechanism to evaluate brain changes in network function which align closely with previous clinical stages of AD. Moreover, utilizing open-source clinical tools from the Brain Connectivity Toolbox (BCT), we demonstrated that brain networks reorganize with AD progression at multiple levels, and these changes are consistent with previous reports in human AD studies.FUTURE DIRECTIONSThe open-source framework developed in the current work provides valuable tools for brain metabolic covariance modeling. Such tools can be used in both preclinical and clinical settings and they enable more direct translation of preclinical imaging studies to those in the clinic. When matched with an appropriate animal model, genetics, and/or treatments, this study will enable assessment ofin vivotarget engagement, translational pharmacodynamics, and insight into potential treatments of AD.
Spatial decomposition of ultrafast ultrasound images to identify motor unit activity – A validation study using intramuscular and surface EMG
Authors: Rohlén Robin , Lubel Emma , Sgambato Bruno Grandi , Antfolk Christian , Farina Dario 
Published: June 2023

AbstractThe smallest voluntarily controlled structure of the human body is the motor unit (MU), comprised of a motoneuron and its innervated fibres. MUs have been investigated in neurophysiology research and clinical applications, primarily using electromyographic (EMG) techniques. Nonetheless, EMG (both surface and intramuscular) has a limited detection volume. A recent alternative approach to detect MUs is ultrafast ultrasound (UUS) imaging. The possibility of identifying MU activity from UUS has been shown by blind source separation (BSS) of UUS images. However, this approach has yet to be fully validated for a large population of MUs. Here we validate the BSS method on UUS images using a large population of MUs from eleven participants based on concurrent recordings of either surface or intramuscular EMG from forces up to 30% of the maximum voluntary contraction (MVC) force. We assessed the BSS method’s ability to identify MU spike trains from direct comparison with the EMG-derived spike trains as well as twitch areas and temporal profiles from comparison with the spike-triggered-averaged UUS images when using the EMG-derived spikes as triggers. We found a moderate rate of correctly identified spikes (53.0 ± 16.0%) with respect to the EMG-identified firings. However, the MU twitch areas and temporal profiles could still be identified accurately, including at 30% MVC force. These results suggest that the current BSS methods for UUS can accurately identify the location and average twitch of a large pool of MUs in UUS images, providing potential avenues for studying neuromechanics from a large cross-section of the muscle. On the other hand, more advanced methods are needed to address the non-linear summation of velocities for recovering the full spike trains.
Structural Elucidation of Intact Rough-Type Lipopolysaccharides using Field Asymmetric Ion Mobility Spectrometry and Kendrick Mass Defect Plots
Authors: Mikhael Abanoub , Hardie Darryl , Smith Derek , Pětrošová Helena , Ernst Robert K. , Goodlett David R. 
Published: June 2023

AbstractLipopolysaccharide (LPS) is a hallmark virulence factor of Gram-negative bacteria. It is a complex, structurally heterogeneous mixture due to variations in number, type, and position of its simplest units: fatty acids and monosaccharides. Thus, LPS structural characterization by traditional mass spectrometry (MS) methods is challenging. Here, we describe the benefits of field asymmetric ion mobility spectrometry (FAIMS) for analysis of intact R-type lipopolysaccharide complex mixture (lipooligosaccharide; LOS). Structural characterization was performed usingEscherichia coliJ5 (Rc mutant) LOS, a TLR4 agonist widely used in glycoconjugate vaccine research. FAIMS gas phase fractionation improved the (S/N) ratio and number of detected LOS species. Additionally, FAIMS allowed the separation of overlapping isobars facilitating their tandem MS characterization and unequivocal structural assignments. In addition to FAIMS gas phase fractionation benefits, extra sorting of the structurally related LOS molecules was further accomplished using Kendrick mass defect (KMD) plots. Notably, a custom KMD base unit of [Na-H] created a highly organized KMD plot that allowed identification of interesting and novel structural differences across the different LOS ion families; i.e., ions with different acylation degrees, oligosaccharides composition, and chemical modifications. Defining the composition of a single LOS ion by tandem MS along with the organized KMD plot structural network was sufficient to deduce the composition of 179 LOS species out of 321 species present in the mixture. The combination of FAIMS and KMD plots allowed in-depth characterization of the complex LOS mixture and uncovered a wealth of novel information about its structural variations.