bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variance-adjusted Mahalanobis (VAM): a fast and accurate method for cell-specific gene set scoring
Authors: Frost H. Robert 
Published: February 2020

AbstractSingle cell RNA sequencing (scRNA-seq) is a powerful tool for analyzing complex tissues with recent advances enabling the transcriptomic profiling of thousands to tens-of-thousands of individual cells. Although scRNA-seq provides unprecedented insights into the biology of heterogeneous cell populations, analyzing such data on a gene-by-gene basis is challenging due to the large number of tested hypotheses, high level of technical noise and inflated zero counts. One promising approach for addressing these challenges is gene set testing, or pathway analysis. By combining the expression data for all genes in a pathway, gene set testing can mitigate the impacts of sparsity and noise and improve interpretation, replication and statistical power. Unfortunately, statistical and biological differences between single cell and bulk expression measurements make it challenging to use gene set testing methods originally developed for bulk tissue on scRNA-seq data and progress on single cell-specific methods has been limited. To address this challenge, we have developed a new gene set testing method, variance-adjusted Mahalanobis (VAM), that seamlessly integrates with the Seurat framework and is designed to accommodate the technical noise, sparsity and large sample sizes characteristic of scRNA-seq data. The VAM method computes cell-specific pathway scores to transform a cell-by-gene matrix into a cell-by-pathway matrix that can be used for both exploratory data visualization and statistical gene set enrichment analysis. Because the distribution of these scores under the null of uncorrelated technical noise has an accurate gamma approximation, inference can be performed at both the population and single cell levels. As we demonstrate using both simulation studies and real data analyses, the VAM method provides superior classification accuracy at a lower computation cost relative to existing single sample gene set testing approaches.
Arabidopsis REI-LIKE proteins activate ribosome biogenesis during cold acclimation
Authors: Cheong Bo Eng , Beine-Golovchuk Olga , Gorka Michal , Ho William Wing Ho , Martinez-Seidel Federico , Firmino Alexandre Augusto Pereira , Skirycz Aleksandra , Roessner Ute , Kopka Joachim 
Published: February 2020

AbstractArabidopsis REIL proteins are cytosolic ribosomal 60S-biogenesis factors. After shift to 10°C,reilmutants deplete and slowly replenish non-translating eukaryotic ribosome complexes of root tissue, while tightly controlling the balance of non-translating 40S- and 60S-subunits.Reilmutations compensate by hyper-accumulation of non-translating subunits at steady-state temperature; after cold-shift, a KCl-sensitive 80S sub-fraction remains depleted. We infer that Arabidopsis buffers fluctuating translation by pre-existing non-translating ribosomes beforede novosynthesis meets temperature-induced demands.Reil1 reil2double mutants accumulate 43S-preinitiation and pre-60S-maturation complexes and have altered paralog composition of ribosomal proteins in non-translating complexes. With few exceptions, e.g. RPL3B and RPL24C, these changes are not under transcriptional control. Our study suggests requirement ofde novosynthesis of eukaryotic ribosomes for long-term cold acclimation, feedback control ofNUC2andeIF3C2transcription and links new proteins, AT1G03250, AT5G60530, to plant ribosome biogenesis. We propose that Arabidopsis requires biosynthesis of specialized ribosomes for cold acclimation.Highlight of this studyREIL proteins affect paralog composition of eukaryotic ribosomes and suppress accumulation of 43S-preinitiation and pre-60S-maturation complexes, suggesting functions of ribosome heterogeneity and biogenesis in plant cold acclimation.
Constitutive activation of leucine-rich repeat receptor kinase signaling pathways by BAK1-interacting receptor-like kinase 3 chimera
Authors: Hohmann Ulrich , Ramakrishna Priya , Wang Kai , Lorenzo-Orts Laura , Nicolet Joel , Henschen Agnes , Barberon Marie , Bayer Martin , Hothorn Michael 
Published: February 2020

AbstractReceptor kinases with extracellular leucine-rich repeat domains (LRR-RKs) form the largest group of membrane signaling proteins in plants. LRR-RKs can sense small molecule, peptide or protein ligands, and may be activated by ligand-induced interaction with a shape complementary SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE (SERK) co-receptor kinase. We have previously shown that SERKs can also form constitutive, ligand-independent complexes with the LRR ectodomains of BAK1-interacting receptor-like kinase 3 (BIR3) receptor pseudokinases, negative regulators of LRR-RK signaling. Here we report that receptor chimaera in which the extracellular LRR domain of BIR3 is fused to the cytoplasmic kinase domains of the SERK-dependent LRR-RKs BRASSINOSTEROID INSENSITIVE1, HAESA and ERECTA form tight complexes with endogenous SERK co-receptors in the absence of ligand stimulus. Expression of these chimaera under the control of the endogenous promoter of the respective LRR-RK leads to strong gain-of-function brassinosteroid, floral abscission and stomatal patterning phenotypes, respectively. Importantly, a BIR3-GSO1/SGN3 chimera can partially complementsgn3Casparian strip formation phenotypes, suggesting that GSO1/SGN3 receptor activation is also mediated by SERK proteins. Collectively, our protein engineering approach may be used to elucidate the physiological functions of orphan LRR-RKs and to identify their receptor activation mechanism in single transgenic lines.
Single-cell chromatin profiling reveals demethylation-dependent metabolic vulnerabilities of breast cancer epigenome
Authors: Kusi Meena , Zand Maryam , Lin Chun-Lin , Wang Chiou-Miin , Lucio Nicholas D. , Kirma Nameer B. , Ruan Jianhua , Huang Tim H.-M. , Mitsuya Kohzoh 
Published: February 2020

AbstractMetabolic reprogramming in cancer cells not only sustains bioenergetic and biosynthetic needs but also influences transcriptional programs, yet how chromatin regulatory networks are rewired by altered metabolism remains elusive. Here we investigate genome-scale chromatin remodeling in response to 2-hydroxyglutarate (2HG) oncometabolite using single-cell assay for transposase accessible chromatin with sequencing (scATAC-seq). We find that 2HG enantiomers differentially disrupt exquisite control of epigenome integrity by limiting α-ketoglutarate (αKG)-dependent DNA and histone demethylation, while enhanced cell-to-cell variability in the chromatin regulatory landscape is most evident upon exposure to L2HG enantiomer. Despite the highly heterogeneous responses, 2HG largely recapitulates two prominent hallmarks of the breast cancer epigenome, i.e., global loss of 5-hydroxymethylcytosine (5hmC) and promoter hypermethylation, particularly at tumor suppressor genes involved in DNA damage repair and checkpoint control. Single-cell mass cytometry further demonstrates downregulation of BRCA1, MSH2 and MLH1 in 2HG-responsive subpopulations, along with acute reversal of chromatin remodeling upon withdrawal. Collectively, this study provides a molecular basis for metabolism-epigenome coupling and identifies metabolic vulnerabilities imposed on the breast cancer epigenome.
A Superfamily of T6SS Antibacterial Effectors Displaying L,D-carboxypeptidase Activity Towards Peptidoglycan
Authors: de Sousa Stephanie Sibinelli , Hespanhol Julia Takuno , Nicastro Gianlucca Gonçalves , Matsuyama Bruno Yasui , Mesnage Stephane , Patel Ankur , de Souza Robson Francisco , Guzzo Cristiane Rodrigues , Bayer-Santos Ethel 
Published: February 2020

SummaryType VI secretion systems (T6SSs) are contractile nanomachines used by bacteria to inject toxic effectors into competitors. The identity and mechanism of many effectors remain unknown. We characterized aSalmonellaSPI-6 T6SS antibacterial effector called Tae5STM(type VIamidaseeffector 5). Tae5STMis toxic in target-cell periplasm and is neutralized by its cognate immunity protein (Tai5STM). Microscopy analysis revealed that cells expressing the effector stop dividing and lose cell envelope integrity. Bioinformatic analysis uncovered similarities between Tae5STMand the catalytic domain of L,D-transpeptidase. Point mutations on conserved catalytic histidine and cysteine residues abrogated toxicity. Biochemical assays revealed that Tae5STMdisplays L,D-carboxypeptidase activity, cleaving peptidoglycan tetrapeptides betweenmeso-diaminopimelic acid3and D-alanine4. Phylogenetic analysis showed that Tae5STMhomologs constitutes a new superfamily of T6SS-associated amidase effectors distributed among α-, β- and γ-proteobacteria. This work expands our current knowledge about bacterial effectors used in interbacterial competition.
Chronic Chemogenetic Manipulation of Ventral Pallidum Targeted Neurons in Rats Fed an Obesogenic Diet
Authors: Doucette Wilder T. , Smedley Elizabeth B. , Ruiz-Jaquez Metztli , Khokhar Jibran Y. , Smith Kyle 
Published: February 2020

AbstractCurrent treatments for obesity are unable to reliably reduce weight over time and alternative treatments need to address this challenge. New interventions that target the nervous system could manipulate brain networks underlying reward, metabolic rate and behavior. Here, the ventral pallidum was evaluated as a target of manipulation due to its established role in the networks underlying motivation, pleasure and behavioral output. Chronic inhibitory or excitatory chemogenetic activation was used to modulate the activity of ventral pallidum (VP) targeted neurons in rats on an obesogenic diet. We hypothesized that inhibition of VP activity would decrease the salience of the rats’ high-sugar, high-fat diet and lead to reduced food consumption and weight gain over time. Paradoxically, measurements of weight, water and food consumption revealed significantly increased weight gain in both groups receiving VP targeted manipulation that was not readily explained by food or water consumption. We theorize that the complex reciprocal feedback between ventral striatal structures (e.g., VP) and metabolic centers of the hypothalamus and brainstem, demonstrated by prior research, likely underpin our findings. This study suggests that the treatment of appetitive disorders (e.g., obesity) with chronic neuromodulation-based interventions could be burdened by the delayed onset of outcomes that are difficult to predict from related prior studies that used acute interventions.
Molecular mechanism for direct actin force-sensing by α-catenin
Authors: Mei Lin , de los Reyes Santiago Espinosa , Reynolds Matthew J. , Liu Shixin , Alushin Gregory M. 
Published: February 2020

SUMMARYThe actin cytoskeleton mediates mechanical coupling between cells and their tissue microenvironments. The architecture and composition of actin networks are modulated by force, but it is unclear how interactions between actin filaments (F-actin) and associated proteins are mechanically regulated. Here, we employ both optical trapping and biochemical reconstitution with myosin motor proteins to show force greater than one piconewton applied solely to F-actin enhances binding by the essential cell-cell adhesion protein αE-catenin, but not its homolog vinculin. Near atomic-resolution cryo-electron microscopy structures of both proteins bound to F-actin reveal unique rearrangements that facilitate their flexible C-termini refolding to engage distinct interfaces. Truncating α-catenin’s C-terminus eliminates force-activated F-actin binding, and addition of this motif to vinculin confers force-activated binding, demonstrating that α-catenin’s C-terminus is a modular detector of F-actin tension. Our studies establish that piconewton force on F-actin can enhance partner binding, which we propose mechanically regulates cellular adhesion throughα-catenin.
The endometrial transcription landscape of MRKH syndrome
Authors: Hentrich T , Koch A , Weber N , Kilzheimer A , Burkhardt S , Rall K , Casadei N , Kohlbacher O , Riess O , Schulze-Hentrich JM , Brucker SY 
Published: February 2020

AbstractThe Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome (OMIM 277000) is characterized by agenesis of the uterus and upper part of the vagina in females with normal ovarian function. While genetic causes have been identified for a small subset of patients and epigenetic mechanisms presumably contribute to the pathogenic unfolding, too, the etiology of the syndrome has remained largely enigmatic. A comprehensive understanding of gene activity in the context of the disease is crucial to identify etiological components and their potential interplay. So far, this understanding is lacking, primarily due to the scarcity of samples and suitable tissue.In order to close this gap, we profiled endometrial tissue of uterus rudiments in a large cohort of MRKH patients using RNA-seq and thereby provide a genome-wide view on the altered transcription landscape of the MRKH syndrome. Differential and co-expression analyses of the data identified cellular processes and candidate genes that converge on a core network of interconnected regulators that emerge as pivotal for the perturbed expression space. With these results and browsable access to the rich data through an online tool we seek to accelerate research to unravel the underlying biology of this syndrome.
Cerebral Atrophy in Amyotrophic Lateral Sclerosis Parallels the Pathological Distribution of TDP43
Authors: Dadar Mahsa , Manera Ana Laura , Zinman Lorne , Korngut Lawrence , Genge Angela , Graham Simon J. , Frayne Richard , Collins D. Louis , Kalra Sanjay 
Published: February 2020

AbstractAmyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by a preferential involvement of both upper and lower motor neurons. Evidence from neuroimaging and post-mortem studies confirms additional involvement of brain regions extending beyond the motor cortex. The aim of this study was to assess the extent of cerebral disease in ALS cross-sectionally and longitudinally, and to compare the findings with a recently proposed disease-staging model of ALS pathology. Deformation-based morphometry (DBM) was used to identify the patterns of brain atrophy associated with ALS and to assess their relationship with clinical symptoms. Longitudinal T1-weighted MRI data and clinical measures were acquired at baseline, 4 months, and 8 months, from 66 ALS patients and 43 age-matched controls who participated in the Canadian ALS Neuroimaging Consortium (CALSNIC) study. Whole brain voxel-wise mixed-effects modelling analysis showed extensive atrophy patterns differentiating ALS patients from the normal controls. Cerebral atrophy was present in the motor cortex and corticospinal tract, involving both GM and WM, and to a lesser extent in non-motor regions. More specifically, the results showed significant bilateral atrophy in the motor cortex, the corticospinal tract including the internal capsule and brainstem, with an overall pattern of ventricular enlargement; along with significant progressive longitudinal atrophy in the precentral gyrus, frontal and parietal white matter, accompanied by ventricular and sulcal enlargement. Atrophy in the precentral gyrus was significantly associated with greater disability as quantified with the ALS Functional Rating Scale-Revised (ALSFRS-R) (p<0.0001). The pattern of atrophy observed using DBM was consistent with the Brettschneider’s four stage pathological model of the disease. Deformation based morphometry provides a sensitive indicator of atrophy in ALS, and has potential as a biomarker of disease burden, in both gray and white matter.
Allosteric regulation of Thioesterase Superfamily Member 1 by free fatty acids and lysophosphatidylcholine
Authors: Tillman Matthew C. , Imai Norihiro , Li Yue , Khadka Manoj , Okafor C. Denise , Juneja Puneet , Adhiyaman Akshitha , Hagen Susan J. , Cohen David E. , Ortlund Eric A. 
Published: February 2020

AbstractNon-shivering thermogenesis occurs in brown adipose tissue to generate heat in response to cold temperatures. Thioesterase superfamily member 1 (Them1) is transcriptionally upregulated in brown adipose tissue upon cold exposure and suppresses thermogenesis to conserve energy reserves. Them1 hydrolyzes long-chain fatty acyl-CoAs, preventing their use as fuel for thermogenesis. Them1 contains a C-terminal StAR-related lipid transfer domain (StarD) with unknown ligand or function. By complementary biophysical approaches, we show that StarD binds to long-chain fatty acids, products of Them1’s enzymatic reaction, as well lysophosphatidylcholine (LPC), which activate thermogenesis in brown adipocytes. Certain fatty acids stabilize the StarD and allosterically enhance Them1 catalysis of acyl-CoA, whereas 18:1 LPC destabilizes and inhibits activity, which we verify in cell culture. Additionally, we demonstrate that the StarD functions to localize Them1 near lipid droplets. These findings define the role of the StarD as a lipid sensor that allosterically regulates Them1 activity and localization.
Development of a honey bee RNA virus vector based on the genome of Deformed wing virus
Authors: Ryabov Eugene V. , Christmon Krisztina , Heerman Matthew C. , Posada-Florez Francisco , Harrison Robert L. , Chen Yanping , Evans Jay D. 
Published: February 2020

AbstractWe developed a honey bee RNA-virus vector based on the genome of a picorna-like Deformed wing virus (DWV), the main viral pathogen of the honey bee (Apis mellifera). To test the potential of DWV to be utilized as a vector, the 717 nt sequence coding for the enhanced green fluorescent protein (eGFP), flanked by the peptides targeted by viral protease, was inserted into an infectious cDNA clone of DWV in-frame between the leader protein and the virus structural protein VP2 genes. Thein vitroRNA transcripts fromegfp-tagged DWV cDNA clones were infectious when injected into honey bee pupae. Stable DWV particles containing genomic RNA of the recovered DWV withegfpinserts were produced, as evidenced by cesium chloride density gradient centrifugation. These particles were infectious to honey bee pupae when injected intra-abdominally. Fluorescent microscopy showed GFP expression in the infected cells and Western blot analysis demonstrated accumulation of free eGFP rather than its fusions with DWV LP and/or VP2 proteins. Analysis of the progenyegfp-tagged DWV showed gradual accumulation of genome deletions foregfp, providing estimates for the rate of loss of a non-essential gene an insect RNA virus genome during natural infection.
Acoustogenetic Control of CAR T Cells via Focused Ultrasound
Authors: Wu Yiqian , Liu Yahan , Huang Ziliang , Wang Xin , Jin Zhen , Li Jiayi , Limsakul Praopim , Zhu Linshan , Allen Molly , Pan Yijia , Bussell Robert , Jacobson Aaron , Liu Thomas , Chien Shu , Wang Yingxiao 
Published: February 2020

AbstractOptogenetics can control specific molecular events in living systems, but the penetration depth of light is typically limited at hundreds of micrometers. Focused ultrasound (FUS), on the other hand, can deliver energy safely and noninvasively into tissues at depths of centimeters. Here we have developed an acoustogenetic approach using short-pulsed FUS to remotely and directly control the genetics and cellular functions of engineered mammalian cells for therapeutic purposes. We applied this acoustogenetic approach to control chimeric antigen receptor (CAR) T cells with high spatiotemporal precision, aiming to mitigate the potentially lethal “on-target off-tumor” effects of CAR T cell therapy. We first verified the controllability of our acoustogenetic CAR T cells in recognizing and killing tumor cellsin vitro, and then applied this approachin vivoto suppress tumor growth of both lymphoma and prostate cancers. The results indicate that FUS-based acoustogenetics can allow the noninvasive and remote activation, without any exogenous cofactor, of different types of CAR T cells for cancer therapeutics.
Analysis of Circulating Exosomes Reveals a Peripheral Signature of Astrocytic Pathology in Schizophrenia
Authors: Ranganathan Mohini , Rahman Mohamed , Ganesh Suhas , D’Souza Deepak C , Skosnik Patrick D , Radhakrishnan Rajiv , Pathania Surbhi , Mohanakumar Thalachallour 
Published: February 2020

AbstractBackgroundThere is considerable interest in identifying peripheral biomarkers that reflect neuropathological changes in schizophrenia. Extracellular vesicles, including exosomes can cross the blood brain barrier with their contents intact and their cargo, including lipids, proteins and genetic materials can be assayed peripherally. Circulating exosomes have been studied in other neurodegenerative disorders, but there is scarce data in schizophrenia.MethodsWe examined neuropathology relevant protein biomarkers in circulating exosomes from patients with schizophrenia and age and gender matched healthy controls using methods consistent with the recommended “Minimal information for studies of extracellular vesicles 2018” (MISEV2018) guidelines. Nanoparticle tracking analysis was used to determine the size and concentration of exosomes. Exosomal membrane marker (CD9) and specific target cargo proteins (glial fibrillary acid protein[GFAP], synaptophysin and α-II-spectrin) immunopositivity was examined using Western blot analyses and band intensity quantified.ResultsNo group differences were observed between schizophrenia and control samples in plasma exosomal concentration and size or in CD9 or calnexin positivity. Exosomal GFAP concentration was significantly higher and α-II-spectrin expression significantly lower in schizophrenia samples and there were no group differences observed for exosomal synaptophysin concentration.ConclusionsOur results demonstrate for the first time, a differential pattern of exosomal protein expression in schizophrenia compared to matched healthy controls, consistent with the hypothesized astro-glial pathology in this disorder. These results warrant further examination of circulating exosomes as vehicles of novel peripheral biomarkers of disease in schizophrenia and other neuropsychiatric disorders.
Human-specific staphylococcal virulence factors enhance pathogenicity in a humanised zebrafish C5a receptor model
Authors: Buchan Kyle D. , van Gent Michiel , Prajsnar Tomasz K. , Ogryzko Nikolay V. , de Jong Nienke W.M. , Kolata Julia , Foster Simon J. , van Strijp Jos A.G. , Renshaw Stephen A. 
Published: February 2020

AbstractStaphylococcus aureusinfects approximately 30% of the human population and causes a spectrum of pathologies ranging from mild skin infections to life-threatening invasive diseases. The strict host specificity of its virulence factors has severely limited the accuracy ofin vivomodels for the development of vaccines and therapeutics. To resolve this, we generated a humanised zebrafish model and determined that neutrophil-specific expression of the human C5a receptor conferred susceptibility to theS. aureustoxins PVL and HlgCB, leading to reduced neutrophil numbers at the site of infection and increased infection-associated mortality as a direct result of the interaction betweenS. aureusand the receptor. These results show that humanised zebrafish provide a valuable platform to study the contribution of human-specificS. aureusvirulence factors to infectionin vivothat could facilitate the development of novel therapeutic approaches and essential vaccines.