bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fluorescence biosensor for real-time interaction dynamics of host proteins with HIV-1 capsid tubes
Authors: Lau Derrick , Walsh James , Peng Wang , Shah Vaibhav , Turville Stuart , Jacques David , Böcking Till 
Published: April 2019

AbstractThe human immunodeficiency virus 1 (HIV-1) capsid serves as a binding platform for proteins and small molecules from the host cell that regulate various steps in the virus life cycle. However, there are currently no quantitative methods that use assembled capsid lattices for measuring host-pathogen interaction dynamics. Here we developed a single molecule fluorescence biosensor using self-assembled capsid tubes as biorecognition elements and imaged capsid binders using total internal reflection fluorescence microscopy in a microfluidic setup. The method is highly sensitive in its ability to observe and quantify binding, obtain dissociation constants, extract kinetics with an extended application of using more complex analytes that can accelerate characterisation of novel capsid binders.
Genetic screening identifies a SUMO protease dynamically maintaining centromeric chromatin and the associated centromere complex
Authors: Mitra Sreyoshi , Bodor Dani L. , David Ana F. , Mata João F. , Neumann Beate , Reither Sabine , Tischer Christian , Jansen Lars E.T. 
Published: April 2019

AbstractCentromeres are defined by a unique self-propagating chromatin structure featuring nucleosomes containing the histone H3 variant CENP-A. CENP-A turns over slower than general chromatin and a key question is whether this unusual stability is intrinsic to CENP-A nucleosomes or rather imposed by external factors. We designed a specific genetic screen to identify proteins involved in CENP-A stability based on SNAP-tag pulse chase labeling. Using a double pulse-labeling approach we simultaneously assay for factors with selective roles in CENP-A chromatin assembly. We discover a series of new proteins involved in CENP-A propagation, including proteins with known roles in DNA replication, repair and chromatin modification and transcription, revealing that a broad set of chromatin regulators impacts in CENP-A transmission through the cell cycle. The key factor we find to strongly affect CENP-A stability is SENP6. This SUMO-protease controls not only the levels of chromatin bound CENP-A but is required for the maintenance of virtually the entire centromere and kinetochore, with the exception of CENP-B. Acute depletion of SENP6 protein reveals its requirement for maintaining centromeric CENP-A levels throughout the cell cycle, suggesting that a dynamic SUMO cycle underlies a continuous surveillance of the centromere complex.
Circadian regulation of microRNA-target chimeras in Drosophila
Authors: Xia Xiju , Fu Xiaonan , Wu Binbin , Zhu Jinsong , Zhao Zhangwu 
Published: April 2019

AbstractMicroRNA is critical coordinator to circadian regulation by silencing gene expression. Although many circadian related miRNAs and some of its target are known, the global functional miRNA-mRNA interaction networks remain poorly understand which is hindered by imperfect base-pairing between miRNA and target mRNA. In this study, we used CLEAR (Covalent Ligation of Endogenous Argonaute-bound RNAs) -CLIP (Cross-Linking and Immuno-Precipitation) to explore the regulatory functions of miRNAs in the circadian system by comparing the miRNA-mRNA interactions between the Drosophila wild-type strain w1118 and the Clk mutant Clkjrk. We unambiguously identified thousands of miRNA-mRNA interactions from CLEAR-CLIP data set at unprecedented depth in vivo for the first time. Among them, about 300 miRNA-mRNA interactions were involved in the regulation of circadian, in which miRNAs targeting core clock genes pdp1, tim and vri presented distinct changes in response to Clkjrk. Particularly, the mir-375-timeless interaction from CLER-CLIP shows important effects on circadian, this functional event occurred in the l-LNv neurons. Overexpression of mir-375 in tim neurons caused decreases in TIM content resulting in arrhythmicity of daily locomotion and changes of sleep. This present work provides a global view of miRNA targeting in the circadian rhythm.
Structural basis for the transport mechanism of the human glutamine transporter SLC1A5 (ASCT2)
Authors: Yu Xiaodi , Plotnikova Olga , Bonin Paul D. , Subashi Timothy A. , McLellan Thomas J. , Dumlao Darren , Che Ye , Dong Yinyao , Carpenter Elisabeth P. , West Graham M. , Qiu Xiayang , Culp Jeffrey S. , Han Seungil 
Published: April 2019

AbstractAlanine-serine-cysteine transporter 2 (ASCT2, SLC1A5) is the primary transporter of glutamine in cancer cells and regulates the mTORC1 signaling pathway. The SLC1A5 function involves finely tuned orchestration of two domain movements that include the substrate-binding transport domain and the scaffold domain. Here, we present cryo-EM structures of human SLC1A5 and its complex with the substrate, L-glutamine in an outward-facing conformation. These structures reveal insights into the conformation of the critical ECL2a loop which connects the two domains, thus allowing rigid body movement of the transport domain throughout the transport cycle. Furthermore, the structures provide new insights into substrate recognition, which involves conformational changes in the HP2 loop. A putative cholesterol binding site was observed near the domain interface in the outward-facing state. Comparison with the previously determined inward-facing structure of SCL1A5 provides a basis for a more integrated understanding of substrate recognition and transport mechanism in the SLC1 family. Our structures are likely to aid the development of potent and selective SLC1A5 inhibitors for the treatment of cancer and autoimmune disorders.
Acetyl-CoA production by select metabolic pathways promotes cardiac repair after myocardial infarction via mediating histone acetylation
Authors: Lei Ienglam , Tian Shuo , Gao Wenbin , Liu Liu , Guo Yijing , Wang Zhong 
Published: April 2019

AbstractMyocardial infarction (MI) is accompanied by severe energy deprivation and extensive epigenetic changes. However, how energy metabolism and chromatin modifications are interlinked during MI and heart repair has been poorly explored. Here, we examined the effect of different carbon sources that involved in the major metabolic pathways of acetyl-CoA synthesis on myocardial infarction and found that elevation of acetyl-CoA significantly improved heart function in I/R rats by administration of sodium octanoate (8C). Mechanistically, 8C prevented I/R injury by promoting histone acetylation which in turn activated the expression of antioxidant genes HO1, NQO1 and SOD2 and inhibited cardiomyocyte apoptosis. Furthermore, we identified that 8C-promoted histone acetylation and heart repair were carried out by metabolic enzyme medium-chain acyl-CoA dehydrogenase (MCAD) and histone acetyltransferase Kat2a. Therefore, our results demonstrate that 8C dramatically improves cardiac function through metabolic acetyl-CoA-mediated histone acetylation. This study uncovers an interlinked metabolic/epigenetic network comprising 8C, acetyl-CoA, MCAD, and Kat2a in stimulating histone acetylation and anti-oxidative stress gene expression to combat heart injury.
Bone Fracture Detection by Electrical Bioimpedance: First Non-Invasive Measurements in Ex-Vivo Mammalian Femur
Authors: Dell’Osa A. H. , Concu A. , Dobarro F. R. , Felice J. C. 
Published: April 2019

AbstractThe fracture of long bones is one of the pathologies of greater demand of systems of medical emergencies, the method used for the diagnosis, the radiology of X-rays, produces damages to the patients and to the hospitals environment. For these reasons, our group is studying the implementation of a new diagnostic technique for the detection of bone fractures by bioimpedance measurements. To simulate a limb, two phantom of bovine femurs (the one with an entire bone and the other with a sawn bone) were constructed and non-invasive Electrical Impedance Spectroscopy measurements were taken on them in order to identify differences in their respective Cole Cole diagrams. Impedance spectroscopy was performed by a frequency sweep between 1 Hz and 65 kHz at a fixed current of 1 mA. The results obtained show wide differences in the Cole Cole diagrams of both phantoms (entire and fractured bone), especially concerning the real component of the, which latter, around the bones section corresponding to that of the lesion in both femurs, was always lower in the fractured femur than the entire one. These first superficial (non-invasive) measurements correspond to the electrical impedance spectroscopy bases and these could -in turn- correspond to what occurs in mammals immediately after the fracture happens, i. e. a dramatic increase in electrical conductivity due to diffusion into the fracture site of more conductive materials such as the blood and the extravascular fluids.
An elastic-net logistic regression approach to generate classifiers and gene signatures for types of immune cells and T helper cell subsets
Authors: Torang Arezo , Gupta Paraag , Klinke David J. 
Published: April 2019

AbstractBackgroundHost immune response is coordinated by a variety of different specialized cell types that vary in time and location. While host immune response can be studied using conventional low-dimensional approaches, advances in transcriptomics analysis may provide a less biased view. Yet, leveraging transcriptomics data to identify immune cell subtypes presents challenges for extracting informative gene signatures hidden within a high dimensional transcriptomics space characterized by low sample numbers with noisy and missing values. To address these challenges, we explore using machine learning methods to select gene subsets and estimate gene coefficients simultaneously.ResultsElastic-net logistic regression, a type of machine learning, was used to construct separate classifiers for ten different types of immune cell and for five T helper cell subsets. The resulting classifiers were then used to develop gene signatures that best discriminate among immune cell types and T helper cell subsets using RNA-seq datasets. We validated the approach using single-cell RNA-seq (scRNA-seq) datasets, which gave consistent results. In addition, we classified cell types that were previously unannotated. Finally, we benchmarked the proposed gene signatures against other existing gene signatures.ConclusionsDeveloped classifiers can be used as priors in predicting the extent and functional orientation of the host immune response in diseases, such as cancer, where transcriptomic profiling of bulk tissue samples and single cells are routinely employed. Information that can provide insight into the mechanistic basis of disease and therapeutic response. The source code and documentation are available through GitHub: https://github.com/KlinkeLab/ImmClass2019.
Autoregulation of pre-mRNA processing for buffering noisy gene expression
Authors: Smith Madeline , Ghusinga Khem Raj , Singh Abhyudai 
Published: April 2019

AbstractStochastic variation in the level of a protein among cells of the same population is ubiquitous across cell types and organisms. These random variations are a consequence of low-copy numbers, amplified by the characteristically probabilistic nature of biochemical reactions associated with gene-expression. We systematically compare and contrast negative feedback architectures in their ability to regulate random fluctuations in protein levels. Our stochastic model consists of gene synthesizing pre-mRNAs in transcriptional bursts. Each pre-mRNA transcript is exported to the cytoplasm and is subsequently translated into protein molecules. In this setup, three feedbacks architectures are implemented: protein inhibiting transcription of its own gene (I), protein enhancing the nuclear pre-mRNA decay rate (II), and protein inhibiting the export of pre-mRNAs (III). Explicit analytic expressions are developed to quantify the protein noise levels for each feedback strategy. Mathematically controlled comparisons provide insights into the noise-suppression properties of these feedbacks. For example, when the protein half-life is long, or the pre-mRNA decay is fast, then feedback architecture I provides the best noise attenuation. In contrast, when the timescales of export, mRNA, and protein turnover are similar, then III is superior to both II and I. We finally discuss biological relevance of these findings in context of noise suppression in an HIV cell-fate decision circuit.
The ebb and flow of heteroplasmy during intra-species hybridization inCaenorhabditis briggsae
Authors: Adineh Shadi , Ross Joseph A. 
Published: April 2019

ABSTRACTMitochondria are typically maternally inherited. In many species, this transmission pattern is produced by sperm-borne mitochondria being eliminated either from sperm before fertilization or from the embryo after fertilization. In the nematodeCaenorhabditis briggsae, repeatedly backcrossing hybrids to genetically diverse males can elicit paternal mitochondrial transmission. Studies of other taxa also suggest that hybridization increases paternal mitochondrial transmission. Thus, hybrid genotypes might disrupt the systems that normally prevent paternal mitochondrial transmission. Given the reliance of a number of genetic analyses on the assumption of purely maternal mitochondrial inheritance, it would be broadly valuable to learn more about the processes embryos employ to prevent sperm-borne mitochondria from persisting in offspring, as well as the circumstances under which paternal transmission might be expected to occur. To quantify the tempo of paternal mitochondrial transmission in hybrids, we assessed the presence of paternal mitotypes in replicate lines at three timepoints spanning fifteen generations. All lines exhibited paternal mitochondrial transmission. However, this heteroplasmy always then resolved to homoplasmy for the maternal mitotype. Additionally, one nuclear locus exhibited allele transmission ratio distortion that might reflect mito-nuclear co-evolution. This study frames the genetic architecture of a hybrid genetic incompatibility that leads to paternal mitochondrial transmission and to a reduction in hybrid fitness.
Free circular introns with an unusual branchpoint in neuronal projections
Authors: Saini Harleen , Bicknell Alicia A. , Eddy Sean R. , Moore Melissa J. 
Published: April 2019

AbstractThe polarized structure of axons and dendrites in neuronal cells depends in part on RNA localization. Previous studies have looked at which polyadenylated RNAs are enriched in neuronal projections or at synapses, but less is known about the distribution of non-adenylated RNAs. By physically dissecting projections from cell bodies of primary rat hippocampal neurons and sequencing total RNA, we found an unexpected set of free circular introns with a non-canonical branchpoint enriched in neuronal projections. These introns appear to be tailless lariats that escape debranching. They lack ribosome occupancy, sequence conservation, and known localization signals, and their function, if any, is not known. Nonetheless, their enrichment in projections has important implications for our understanding of the mechanisms by which RNAs reach distal compartments of asymmetric cells.
Stabilization of α-synuclein oligomers using formaldehyde
Authors: Ruesink Harm , Reimer Lasse , Gregersen Emil , Moeller Arne , Betzer Cristine , Jensen Poul Henning 
Published: April 2019

AbstractThe group of neurodegenerative diseases, Parkinson’s disease (PD), dementia with Lewy bodies (DLB), and multiple system atrophy (MSA) all exhibit inclusions containing amyloid-type α-synuclein (α-syn) aggregates within degenerating brain cells. α-syn also exists as soluble oligomeric species that are hypothesized to represent intermediates between its native and aggregated states. These oligomers are present in brain extracts from patients suffering from synucleinopathies and hold great potential as biomarkers. Although easily prepared in vitro, oligomers are metastable and dissociate over time, thereby complicating α-syn oligomer research. Using the small amine-reactive cross-linker, formaldehyde (FA), we successfully stabilized α-syn oligomers without affecting their size, overall structure or antigenicity towards aggregate-conformation specific α-syn antibodies FILA and MJFR-14-6-4-2. Further, cross-linked α-syn oligomers show resistance towards denaturant like urea and SDS treatment and remain fully functional as internal standard in an aggregation-specific enzyme-linked immunosorbent assay (ELISA) despite prior incubation with urea. We propose that FA cross-linked α-syn oligomers could serve as important calibrators to facilitate comparative and standardized α-syn biomarker studies going forward.
Characterization and function of medium and large extracellular vesicles from plasma and urine by surface antigens and Annexin V
Authors: Igami Ko , Uchiumi Takeshi , Ueda Saori , Kamioka Kazuyuki , Setoyama Daiki , Gotoh Kazuhito , Akimoto Masaru , Matsumoto Shinya , Kang Dongchon 
Published: April 2019

AbstractMedium/large extracellular vesicles (m/lEVs) are released by most cell types and are involved in multiple basic biological processes. Analysis of m/lEV levels in blood or urine may help unravel pathophysiological findings in many diseases. However, it remains unclear how many naturally-occurring m/lEV subtypes exist as well as how their characteristics and functions differ from one another. Here, we identified m/lEVs pelleted from plasma and urine samples by differential centrifugation and showed by flow cytometry that they typically possessed diameters between 200 nm and 800 nm. Using proteomic profiling, we identified several proteins involved in m/lEV biogenesis including adhesion molecules, peptidases and exocytosis regulatory proteins. In healthy human plasma, we could distinguish m/lEVs derived from platelets, erythrocytes, monocytes/macrophages, T and B cells, and vascular endothelial cells using various surface antigens. m/lEVs derived from erythrocytes and monocytes were Annexin V positive. In urine, 50% of m/lEVs were Annexin V negative but contained various membrane peptidases derived from renal tubular villi. Urinary m/lEVs, but not plasma m/lEVs, showed peptidase activity. The method we have developed to characterize cell-derived m/lEVs suggests the possibility of clinical applications.
Predicting and Designing therapeutics against the Nipah virus
Authors: Sen Neeladri , Kanitkar Tejashree Rajaram , Roy Ankit Animesh , Soni Neelesh , Amritkar Kaustubh , Supekar Shreyas , Nair Sanjana , Singh Gulzar , Madhusudhan M.S. 
Published: April 2019

AbstractThough every outbreak of the Nipah Virus has resulted in high mortality rates (>70% in Southeast Asia), there are no licensed drugs against it. In this study we have considered all 9 Nipah proteins as potential therapeutic targets and computationally identified putative peptides (against G, F, and M proteins) and small molecules inhibitors (against F, G, M, N, and P proteins). The computations include extensive homology/ab initio modelling, peptide design and small molecule docking. An important contribution of this study is the increased structural characterization of Nipah proteins by approximately 90% of what is deposited in the PDB. In addition, we have carried out molecular dynamics simulations on all the designed protein-peptide complexes to check for stability and to estimate binding strengths. Details, including atomic coordinates of all the proteins and their ligand bound complexes, can be accessed at http://cospi.iiserpune.ac.in/Nipah. Our strategy was to tackle the development of therapeutics on a proteome wide scale and the lead compounds identified could be attractive starting points for drug development. To this end, we have designed 4 peptide inhibitors and predicted 70 small molecules (13 with high confidence) against 3 and 5 Nipah proteins respectively. To counter the threat of drug resistance, we have analyzed the sequences of the viral strains from different outbreaks, to check whether they would be sensitive to the binding of the proposed inhibitors.Author SummaryNipah virus infections have killed 72-86% of the infected individuals in Bangladesh and India. The infections are spread via bodily secretions of bats, pigs and other infected individuals. Even though, the disease was first detected in the human population in 1998, there are no approved drugs/vaccines against it. In this study, we have tried to model the 3D structures of the Nipah virus proteins. We have then used these models to design/predict small inhibitory molecules that would bind them and prevent their function. We have also analyzed the different strains of the virus to identify conservation patterns of amino acids in the proteins, which in turn informs us of the efficacy of the drugs. The designed/docked compounds as well as the protein models are freely accessible for experimental validation and hypothesis testing.
Selective brain hypothermia ameliorates focal cerebral ischemia-reperfusion injury via inhibiting Fis1 in rats
Authors: Tang Yanan , Chen Huailong , Sun Xiaopeng , Qin Weiwei , Shi Fei , Sun Lixin , Xu Xiaona , Zhang Gaofeng , Wang Mingshan 
Published: April 2019

AbstractMitochondrial immoderate fission induces neuronal apoptosis following focal cerebral ischemia-reperfusion (I/R) injury. With fewer complications, selective brain hypothermia (SBH) is considered an effective treatment against neuronal injury after stroke. However, the specific mechanism by which SBH influences mitochondrial fission remains unknown. Mitochondrial fission 1 protein (Fis1), a key factor of the mitochondrial fission system, regulates mitochondrial dynamics. This study aimed to investigate whether SBH regulates Fis1 expression in focal cerebral I/R injury. In this study, rat middle cerebral artery occlusion (MCAO) models were established. After 2 h of occlusion, cold saline or normal saline was pumped into rats in different groups through the carotid artery, followed by restoration of blood perfusion. Cortical and rectal temperatures showed that the cold saline treatment achieved SBH. Cerebral I/R injury increased neurological deficit scores (NDS); neuronal apoptosis; Fis1 protein and mRNA expression; cytosolic cytochrome c (cyto-Cyto c) protein expression at 6, 24 and 48 h postreperfusion; and cerebral infarct volumes at 24 h postreperfusion. Interestingly, SBH inhibited Fis1 protein and mRNA expression, blocked cyto-Cyto c protein expression, preserved neuronal cell integrity, and reduced neuronal apoptosis. However, normal saline treatment rarely resulted in positive outcomes. Based on these results, SBH inhibited Fis1 expression, thus ameliorating focal cerebral I/R injury in rats.