bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predictive and robust gene selection for spatial transcriptomics
Authors: Covert Ian , Gala Rohan , Wang Tim , Svoboda Karel , Sümbül Uygar , Lee Su-In 
Published: May 2022

AbstractA prominent trend in single-cell transcriptomics is providing spatial context alongside a characterization of each cell’s molecular state. This typically requires targeting ana prioriselection of genes, often covering less than 1% of the genome, and a key question is how to optimally determine the small gene panel. Reference data from these methods covering the whole genome is unavailable, and using single-cell RNA sequencing (scRNA-seq) datasets as a surrogate can result in suboptimal gene panels due to the fundamentally different data distributions across technologies. We address these challenges by introducing a flexible deep learning framework, PERSIST, to identify informative gene targets for spatial transcriptomics studies by leveraging existing scRNA-seq data. Using datasets spanning different brain regions, species, and scRNA-seq technologies, we show that PERSIST reliably identifies gene panels that provide more accurate prediction of the genome-wide expression profile, thereby capturing more information with fewer genes. Furthermore, PERSIST can be adapted to meet specific biological goals, such as classifying cell types or discerning neuronal electrical properties. Finally, via a simulation study based on a recentin situhybridization-based dataset, we demonstrate that PERSIST’s binarization of gene expression levels enables models trained on scRNA-seq data to generalize with input data obtained using spatial transcriptomics, despite the complex domain shift between these technologies.
High- and Low-Frequency Deep Brain Stimulation in the Subthalamic Nucleus differentially modulate Response Inhibition and Action Selection in Parkinson’s Disease
Authors: Waldthaler Josefine , Sperlich Alexander , König Aylin , Stüssel Charlotte , Bremmer Frank , Timmermann Lars , Pedrosa David 
Published: May 2022

ABSTRACTBackgroundWhile deep brain stimulation (DBS) in the subthalamic nucleus (STN) improves motor functions in Parkinson’s disease (PD), it has also been associated with increased impulsivity.MethodsA combined approach of eye-tracking and high-density EEG was used to investigate how high- and low-frequency DBS impact impulsive actions in the antisaccade task in a cohort of ten persons with PD. Computational modelling of the behavioral outcomes allowed a nuanced insight into the effect of DBS on response inhibition and action selection processes. Results: Against our expectations, both 130 Hz- and 60 Hz-DBS improved response inhibition as both resulted in a reduced rate of early reflexive errors. Correspondingly, DBS with both frequencies led to increased desynchronization of beta power during the preparatory period which may be a correlate of anticipatory activation in the oculomotor network.Low-frequency DBS additionally was associated with increased midfrontal theta power, an established marker of cognitive control. While higher midfrontal theta power predicted longer antisaccade latencies in off-DBS state on a trial-by-trial basis, 130 Hz-DBS reversed this relationship. As informed by the computational model, 130 Hz-DBS further led to a shift in the speed-accuracy trade-off causing an acceleration and error-proneness of actions later in the trial.ConclusionsOur results disentangle the impact of DBS on early and late impulsive actions. Only 130 Hz-DBS may disrupt theta-mediated cognitive control mechanisms via medial frontal – STN pathways that are involved in delaying action selection. 60 Hz-DBS may provide beneficial effects on response inhibition without the detrimental effect on action selection seen with 130 Hz-DBS.FundingThis study was supported by the SUCCESS program of Philipps-University Marburg (JW), the Hessian Ministry of Sciences and the Arts, clusterproject: The Adaptive Mind – TAM (FB / AK) and the German Research Foundation (DFG). International Research Training Group 1901 (FB / AK)
The intrinsically disordered cytoplasmic tail of a dendrite branching receptor uses two distinct mechanisms to regulate the actin cytoskeleton
Authors: Kramer Daniel A. , Narvaez-Ortiz Heidy Y. , Patel Urval , Shi Rebecca , Shen Kang , Nolen Brad J. , Roche Julien , Chen Baoyu 
Published: May 2022

AbstractDendrite morphogenesis is essential for neural circuit formation, yet the molecular mechanisms underlying complex dendrite branching remain elusive. Previous studies on the highly branchedC. elegansPVD sensory neuron identified a membrane co-receptor complex that links extracellular signals to intracellular actin remodeling machinery, promoting high-order dendrite branching. In this complex, the claudin-like transmembrane protein HPO-30 recruits the WAVE regulatory complex (WRC) to dendrite branching sites, stimulating the Arp2/3 complex to polymerize actin. We report here our biochemical and structural analysis of this interaction, revealing that the intracellular domain (ICD) of HPO-30 is intrinsically disordered and employs two distinct mechanisms to regulate the actin cytoskeleton. First, HPO-30 ICD binding to the WRC requires dimerization and involves the entire ICD sequence, rather than a short linear peptide motif. This interaction enhances WRC activation by the GTPase Rac1. Second, HPO-30 ICD directly binds to the sides and barbed end of actin filaments. Binding to the barbed end requires ICD dimerization and inhibits both actin polymerization and depolymerization, resembling the actin capping protein CapZ. These dual functions provide an intriguing model of how membrane proteins can integrate distinct mechanisms to fine-tune local actin dynamics.
Polycomb proteins translate histone methylation to chromatin folding
Authors: Lizana Ludvig , Nahali Negar , Schwartz Yuri B. 
Published: May 2022

AbstractEpigenetic repression often involves covalent histone modifications. Yet, how the presence of a histone mark translates into changes in chromatin structure that ultimately benefit the repression is largely unclear. Polycomb group proteins comprise a family of evolutionarily conserved epigenetic repressors. They act as multi-subunit complexes one of which trimethylates histone H3 at Lysine 27 (H3K27). Here we describe a novel Monte Carlo – Molecular Dynamics simulation framework, which we employed to discover that stochastic interaction of the Polycomb Repressive Complex 1 (PRC1) with tri-methylated H3K27 is sufficient to fold the methylated chromatin. Unexpectedly, such chromatin folding leads to spatial clustering of the DNA elements bound by PRC1.
Mouse primary T cell phosphotyrosine proteomics enabled by BOOST
Authors: Chua Xien Yu , Callahan Kenneth P. , Griffith Alijah A. , Hildebrandt Tobias , Fu Guoping , Hu Mengzhou , Wen Renren , Salomon Arthur R. 
Published: May 2022

AbstractThe Broad Spectrum Optimization of Selective Triggering (BOOST) approach was recently developed to increase the quantitative depth of the tyrosine phosphoproteome by mass spectrometry-based proteomics. While BOOST has been demonstrated in the Jurkat T cell line, it has not been demonstrated in scarce mice primary T cells. Here, we show the first phosphotyrosine proteomics experiment performed in mice primary T cells using BOOST. We identify and precisely quantify more than 2,000 unique pTyr sites from more than 3,000 unique pTyr peptide PSMs using only 1 mg of protein from T cell receptor-stimulated primary T cells from mice. We further reveal the importance of the phase-constrained spectrum deconvolution method (ΦSDM) parameter on Orbitrap instruments that, when disabled, enhances quantitation depth, accuracy, and precision in low-abundance samples. Using samples with contrived ratios, we find that disabling ΦSDM allows for up to a two-fold increase in the number of statistically significant intensity ratios detected while enabling ΦSDM degrades quantitation, especially in low-abundance samples.TOC Graphic
The development of 3D bovine intestinal organoid derived models to investigate Mycobacterium avium ssp paratuberculosis pathogenesis
Authors: Blake Rosemary , Jensen Kirsty , Mabbott Neil , Hope Jayne , Stevens Jo 
Published: May 2022

AbstractMycobacterium avium subspecies paratuberculosis (MAP) is the etiologic agent of Johne’s Disease, a chronic enteritis of ruminants prevalent across the world. It is estimated that approximately 50% of UK dairy herds are infected with MAP, but this is likely an underestimate of the true prevalence. Infection can result in reduced milk yield, infertility and premature culling of the animal, leading to significant losses to the farming economy and negatively affecting animal welfare. Understanding the initial interaction between MAP and the host is critical to develop improved diagnostic tools and novel vaccines. Here we describe the characterisation of three different multicellular in vitro models derived from bovine intestinal tissue, and their use for the study of cellular interactions with MAP. In addition to the previously described basal-out 3D bovine enteroids, we have established viable 2D monolayers and 3D apical-out organoids. The apical-out enteroids differ from previously described bovine enteroids as the apical surface is exposed on the exterior surface of the 3D structure, enabling study of host-pathogen interactions at the epithelial surface without the need for microinjection. We have characterised the cell types present in each model system using RT-qPCR to detect predicted cell type-specific gene expression and confocal microscopy for cell type-specific protein expression. Each model contained the cells present in the bovine ileum and were therefore representative of the bovine gut. Exposure of the three model systems to the reference strain MAP K10, and a recent Scottish isolate referred to as C49, led to the observation of intracellular bacteria by confocal microscopy. Enumeration of the bacteria by genome copy number quantification, indicated that K10 was less invasive than C49 at early time points in infection in all model systems. This study shows that bovine enteroid-based models are permissive to infection with MAP and that these models may be useful in investigating early stages of MAP pathogenesis in a physiologically relevant in vitro system, whilst reducing the use of animals in scientific research.
The targeted deletion of genes responsible for expression of the Mth60 fimbriae leads to loss of cell-cell connections in M. thermautotrophicus ΔH
Authors: Fink Christian , Martinez-Cano Gines , Shuster Jeremiah , Panzera Aurora , Angenent Largus T. , Molitor Bastian 
Published: May 2022

AbstractThis study was continued by the Environmental Biotechnology Group of the University of Tübingen in memoriam to Reinhard Wirth, who initiated the work on Mth60 fimbriae at the University of Regensburg.Growth in biofilms or biofilm-like structures is the prevailing lifestyle for most microbes in nature. The first step to initiate biofilms is the adherence of microbes to biotic and abiotic surfaces. Therefore, it is important to elucidate the initial step of biofilm formation, which is generally established through cell-surface structures (i.e., cell appendages), such as fimbriae or pili, that adhere to surfaces. The Mth60 fimbriae of Methanothermobacter thermautotrophicus ΔH are one of only few known archaeal cell appendages that do not assemble via the type-IV assembly mechanism. Here, we report the constitutive expression of Mth60 fimbriae-encoding genes from a shuttle-vector construct, as well as the deletion of the Mth60 fimbriae-encoding genes from the genomic DNA of M. thermautotrophicus ΔH. We expanded our system for genetic modification of M. thermautotrophicus ΔH by an allelic-exchange method. While overexpression of the respective genes resulted in an increase of the Mth60 fimbriae, deletion of the Mth60 fimbriae-encoding genes led to a loss of Mth60 fimbriae in planktonic cells of M. thermautotrophicus ΔH. This either increased or decreased number of Mth60 fimbriae correlated with a significant increase or decrease of biotic cell-cell connections in the respective M. thermautotrophicus ΔH strains compared to the wild-type strain.Originality-Significance StatementMethanothermobacter spp. have been studied for the biochemistry of hydrogenotrophic methanogenesis for many years. However, due to the lack of genetic tools, the detailed investigation of certain aspects, such as regulatory processes, was not possible. Here, we amend our genetic toolbox for M. thermautotrophicus ΔH with an allelic exchange method. We report the deletion of genes that encode for the Mth60 fimbriae. Our findings provide a first insight into the regulation of the expression of these genes and reveal a role of the Mth60 fimbriae in the formation of cell-cell connections of M. thermautotrophicus ΔH.
The Influences of Stomatal Size and Density on Rice Drought, Salinity and VPD Resilience
Authors: Caine Robert S. , Harrison Emily L. , Sloan Jennifer M. , Flis Paulina M. , Fischer Sina , Phuoc Nguyen Trong , Lang Nguyen Thi , Gray Julie E. , Croft Holly L. 
Published: May 2022

SummaryA warming climate coupled with reductions in water availability and rising salinity are increasingly affecting rice yields (Oryza sativa L.). Elevated temperatures are causing vapour pressure deficit (VPD) rises, leading to stomata closure, further reducing plant productivity and cooling. It is unclear which conformation of stomatal size (SS) and stomatal density (SD) will best suit these future environmental extremes.To understand the influence of stomatal characteristics on rice abiotic stress tolerance, we screened the stomatal characteristics of 72 traditionally-bred varieties. We found significant variation in SS, SD and maximal stomatal conductance (gsmax) but did not identify any varieties with SD and gsmax as low as the genetically manipulated stomatal development mutant OsEPF1oe.Traditionally-bred varieties with high SD and small SS (resulting in high gsmax) typically had lower biomasses, and these plants were more resilient to drought than low SD and large SS plants, which were physically larger. None of the varieties tested were as resilient to drought or salinity as low SD OsEPF1oe mutants. High SD and small SS rice displayed faster stomatal closure during rising VPD, but photosynthesis and plant cooling were reduced.Compromises will be required when choosing rice SS and SD to tackle multiple future environmental stresses.
MYC Overexpression Drives Immune Evasion in Human Cancer that is Reversible Through Restoration of Pro-Inflammatory Macrophages
Authors: Dhanasekaran Renumathy , Hansen Aida S. , Park Jangho , Lai Ian , Adeniji Nia , Kuruvilla Sibu , Suresh Akanksha , Swamy Varsha , Felsher Dean W. 
Published: May 2022

ABSTRACTCancers evade immune surveillance that in some, but not in many, cases can be reversed through immune checkpoint therapy. Here we report that the MYC oncogene suppresses immune surveillance, activates immune checkpoint expression, and predicts responsiveness to immune checkpoint inhibition. First, when MYC is genomically amplified and overexpressed in 33 different human cancers, this increases immune checkpoint expression, drives immune checkpoint therapeutic resistance, and is associated with both Th2-like immune profile, and reduced CD8 T cell infiltration. Second, experimentally, MYC-driven tumors suppress pro-inflammatory antigen-presenting macrophages with increased CD40 and MHCII expression, which in turn impedes T cell response. This MYC-driven suppression of macrophages can be reversed by combined but not individual blockade of PDL1 and CTLA4. Third, the depletion of macrophages abrogated the anti-neoplastic effects of PDL1 and CTLA4 blockade. Hence, MYC is a predictor of immune checkpoint responsiveness and a key driver of immune evasion through the suppression of pro-inflammatory macrophages. The immune evasion by MYC can be overcome by combined PDL1 and CTLA4 blockade.Statement of SignificanceMYC is the most commonly activated oncogene in human cancers. In this study, we identify macrophage-mediated immune evasion as a major therapeutic vulnerability of MYC-driven cancers. Our results have implications for developing effective immunotherapies for MYC-driven human cancers and also for prioritizing patients with MYC-driven tumors for combination immunotherapy.
iPSC-derived models of PACS1 syndrome reveal transcriptional and functional deficits in neuron activity
Authors: Rylaarsdam Lauren , Rakotomamonjy Jennifer , Pope Eleanor , Guemez-Gamboa Alicia 
Published: May 2022

ABSTRACTPACS1 syndrome is a neurodevelopmental disorder characterized by intellectual disability and distinct craniofacial abnormalities resulting from ade novop.R203W variant in phosphofurin acidic cluster sorting protein 1 (PACS1). PACS1 is known to play roles in the endosomal pathway and nucleus, but how the p.R203W variant affects developing neurons is not understood, leaving patients with few therapeutic options. Here we differentiated stem cells towards various neuronal models to investigate the impact of the PACS1 syndrome-causing variant on cortical development. While few deleterious effects were detected in PACS1(+/R203W)neural precursors, mature PACS1(+/R203W)glutamatergic neurons exhibited impaired expression of genes strongly enriched for synaptic signaling processes. Subsequent characterization of neural activity using calcium imaging and multielectrode arrays revealed the p.R203W PACS1 variant leads to a strikingly prolonged neuronal network burst duration mediated by an increased inter-spike interval. This work is the first to investigate the impact of the PACS1 p.R203W variant on developing human neural tissue and uncovers putative electrophysiological underpinnings of disease along with candidate targets for pharmacological intervention.
Site pleiotropy of a stickleback tooth and fin enhancer
Authors: Rowley Alyssa J. , Square Tyler A. , Miller Craig T. 
Published: May 2022

AbstractDevelopment and regeneration are orchestrated by gene regulatory networks that operate in part through transcriptional enhancers. Although many enhancers are pleiotropic and are active in multiple tissues, little is known about whether enhancer pleiotropy is due to 1) site pleiotropy, in which individual transcription factor binding sites (TFBS) are required for activity in multiple tissues, or 2) multiple distinct sites that regulate expression in different tissues. Here, we investigated the pleiotropy of an intronic enhancer of the stickleback Bone morphogenetic protein 6 (Bmp6) gene. This enhancer was previously shown to regulate evolved changes in tooth number and tooth regeneration, and is highly pleiotropic, with robust activity in both fins and teeth throughout embryonic, larval, and adult life. We tested the hypothesis that the pleiotropy of this enhancer is due to site pleiotropy of an evolutionarily conserved predicted Foxc1 TFBS. Transgenic analysis and site-directed mutagenesis experiments both deleting and scrambling this predicted Foxc1 TFBS revealed that the binding site is required for enhancer activity in both teeth and fins throughout embryonic, larval, and adult development. Collectively these data support a model where the pleiotropy of this Bmp6 enhancer is due to site pleiotropy and this putative binding site is required for enhancer activity in multiple anatomical sites from the embryo to the adult.
Kidney collecting duct cells make vasopressin in response to NaCl induced hypertonicity
Authors: Arroyo Juan Pablo , Terker Andrew S. , Zuchowski Yvonne , Watts Jason A. , Bock Fabian , Meyer Cameron , Luo Wentian , Kapp Meghan , Gould Edward R. , Miranda Adam X. , Carty Joshua , Jiang Ming , Vanacore Roberto , Hammock Elizabeth , Wilson Matthew H. , Zent Roy , Zhang Mingzhi , Bhave Gautam , Harris Raymond C. 
Published: May 2022

AbstractVasopressin has traditionally been thought to be produced by the neurohypophyseal system and then released into the circulation where it regulates water homeostasis. The syndrome of inappropriate secretion of anti-diuretic hormone (vasopressin) raised the question if vasopressin could be produced outside of the brain and whether the kidney could be a source of vasopressin. We found that mouse and human kidneys expressed vasopressin mRNA. Using an antibody that detects the pre-pro-vasopressin, we found that immunoreactive pre-pro-vasopressin protein is found in mouse and human kidneys. Moreover, we found that murine collecting duct cells make biologically active vasopressin which increases in response to NaCl mediated hypertonicity, and that water restriction increases the abundance of kidney-derived vasopressin mRNA and protein expression in mouse kidneys. Thus, we provide evidence of biologically active production of kidney-derived vasopressin in kidney tubular epithelial cells.
Structural basis of Yta7 ATPase-mediated nucleosome disassembly
Authors: Wang Feng , Feng Xiang , He Qing , Li Hua , Li Huilin 
Published: May 2022

ABSTRACTYta7 is a novel chromatin remodeler harboring a histone-interacting bromodomain (BRD) and two AAA+ modules. It is not well understood how Yta7 recognizes and unfolds histone H3 to promote nucleosome disassembly for DNA replication. By cryo-EM analysis, we here show that Yta7 assembles a three-tiered hexamer ring with a top spiral, a middle AAA1-tier, and a bottom AAA2-tier. Unexpectedly, the Yta7 BRD stabilizes a four-stranded β-helix termed BRD- interacting motif (BIM) of the largely disordered N-terminal region, and they together assemble the spiral structure on top of the hexamer to engage the nucleosome. We found that the Yta7 BRD lacks key residues involved in acetylated peptide recognition, and as such, it is a noncanonical BRD that does not distinguish the H3 acetylation state, consistent with its role in general DNA replication. Upon nucleosome binding, the BRD/BIM spiral transitions into a flat ring to allow threading of the histone H3 tail into the AAA+ chamber. The H3 peptide is stabilized by the AAA1 pore loops 1 and 2 that spiral around the peptide. Therefore, Yta7 unfolds the nucleosome by pulling on the H3 peptide in a rotary staircase mechanism. Our study sheds light on the nucleosome recognition and unfolding mechanism of Yta7.