bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of the gene expression profiles of leukocytes from different isolations
Authors: Xing Yanru , Yang Xi , Chen Haixiao , Zhu Sujun , Xu Jinjin , Chen Yuan , Zeng Juan , Chen Fang , Jiang Hui , Wang Wen-Jing 
Published: June 2019

AbstractBACKGROUNDResearch on peripheral leukocyte gene expression in human health and disease is growing rapidly. However, how to process sample efficiently, simply and stably, and how to reflect human physiological state preferably remains critical issues in large cohort studies.METHODSWe used RNA-seq to explore the differences of gene expression profiles among whole blood (WB) and three groups of leukocytes from buffy coat (BC) extraction, red blood cell (RBC) lysis and peripheral blood mononuclear cell (PBMC) isolation.RESULTSThe residual globin mRNA in leukocytes from RBC lysis (1.00% ±1.23%) and PBMC isolation (0.06% ± 0.03%) was much less than that in leukocytes from BC extraction (17.48% ± 6.95%) and WB (24.46% ± 6.43%), resulting in higher transcriptome mapping rates and larger numbers of detected genes. The expression of 616 genes associated with leukocyte function was slightly higher in leukocytes from RBC lysis than that from BC extraction and WB, but barely detected in leukocytes from PBMC isolation.CONCLUSIONSWe suggest that sample processing based on RBC lysis could allow better applications of gene expression profiling of peripheral leukocytes in large cohort studies.
TulsiPIN: an interologous protein interactome ofOcimum tenuiflorum
Authors: Singh Vikram , Singh Gagandeep , Singh Vikram 
Published: June 2019

AbstractOcimum tenuiflorum, commonly known as holy basil or tulsi, is globally recognized for its multitude of medicinal properties. However, a comprehensive study revealing the complex interplay among its constituent proteins at subcellular level is still lacking. To bridge this gap, a genome scale interologous protein-protein interaction (PPI) network, TulsiPIN, is developed using 49 template plants. The reported network consists of 13, 660 nodes and 327, 409 binary interactions. A high confidence PPI network consisting of 7, 719 nodes having 95, 532 interactions was inferred using domain-domain interaction information along with interolog based statistics, and its reliability was further assessed using functional homogeneity and protein colocalization. 1, 625 vital proteins are predicted by statistically evaluating this high confidence TulsiPIN with two ensembles of corresponding random networks, each consisting of 10, 000 realizations of Erdős-Rényi and Barabási-Albert models. Topological features of TulsiPIN including small-world, scale-free and modular architecture are inspected and found to resemble with other plant PPI networks. Finally, numerous regulatory proteins like transcription factors, transcription regulators and protein kinases are profiled in TulsiPIN and a sub-network of proteins participating in 10 secondary metabolite biosynthetic pathways is studied. We believe, the methodology developed and insights imparted would be useful in understanding regulatory mechanisms in various plant species.
Understanding the functional and structural differences across excitatory and inhibitory neurons
Authors: Minni Sun , Ji-An Li , Moskovitz Theodore , Lindsay Grace , Miller Kenneth , Dipoppa Mario , Yang Guangyu Robert 
Published: June 2019

AbstractOne of the most fundamental organizational principles of the brain is the separation of excitatory (E) and inhibitory (I) neurons. In addition to their opposing effects on post-synaptic neurons, E and I cells tend to differ in their selectivity and connectivity. Although many such differences have been characterized experimentally, it is not clear why they exist in the first place. We studied this question in an artificial neural network equipped with multiple E and I cell types. We found that a deep convolutional recurrent network trained to perform an object classification task was able to capture salient distinctions between E and I neurons. We explored the necessary conditions for the network to develop distinct selectivity and connectivity across cell types. We found that neurons that project to higher-order areas will have greater stimulus selectivity, regardless of whether they are excitatory or not. Sparser connectivity is required for higher selectivity, but only when the recurrent connections are excitatory. These findings demonstrate that the differences observed across E and I neurons are not independent, and can be explained using a smaller number of factors.
The anaerobic digestion microbiome: a collection of 1600 metagenome-assembled genomes shows high species diversity related to methane production
Authors: Campanaro Stefano , Treu Laura , Rodriguez-R Luis M , Kovalovszki Adam , Ziels Ryan M , Maus Irena , Zhu Xinyu , Kougias Panagiotis G. , Basile Arianna , Luo Gang , Schlüter Andreas , Konstantinidis Konstantinos T. , Angelidaki Irini 
Published: June 2019

AbstractBackgroundMicroorganisms in biogas reactors are essential for degradation of organic matter and methane production through anaerobic digestion process. However, a comprehensive genome-centric comparison, including relevant metadata for each sample, is still needed to identify the globally distributed biogas community members and serve as a reliable repository.ResultsHere, 134 publicly available datasets derived from different biogas reactors were used to recover 1,635 metagenome-assembled genomes (MAGs) representing different bacterial and archaeal species. All genomes were estimated to be >50% complete and nearly half were ≥90% complete with ≤5% contamination. In most samples, specialized microbial communities were established, while only a few taxa were widespread among the different reactor systems. Metabolic reconstruction of the MAGs enabled the prediction of functional traits related to biomass degradation and methane production from waste biomass. An extensive evaluation of the replication index provided an estimation of the growth rate for microbes involved in different steps of the food chain. The recovery of many MAGs belonging to Candidate Phyla Radiation and other underexplored taxa suggests their specific involvement in the anaerobic degradation of organic matter.ConclusionsThe outcome of this study highlights a high flexibility of the biogas microbiome. The dynamic composition and adaptability to the environmental conditions, including temperatures and a wide range of substrates, were demonstrated. Our findings enhance the mechanistic understanding of anaerobic digestion microbiome and substantially extend the existing repository of genomes. The established database represents a relevant resource for future studies related to this engineered ecosystem.
PEGylated surfaces for the study of DNA-protein interactions by atomic force microscopy
Authors: Akpinar Bernice , Bell Nicholas A. W. , Pyne Alice L.B. , Hoogenboom Bart W. 
Published: June 2019

AbstractDNA-protein interactions are vital to cellular function, with key roles in the regulation of gene expression and genome maintenance. Atomic force microscopy (AFM) offers the ability to visualize DNA-protein interactions at nanometre resolution in near-physiological buffers, but it requires that the DNA be adhered to the surface of a solid substrate. This presents a problem when working at biologically relevant protein concentrations, where protein may be present at large excess in solution; much of the biophysically relevant information can therefore be occluded by non-specific protein binding to the underlying substrate. Here we explore the use of PLLx-b-PEGyblock copolymers to achieve selective adsorption of DNA on a mica surface. Through varying both the number of lysine and ethylene glycol residues in the block copolymers, we show selective adsorption of DNA on mica that is functionalized with a PLL10-b-PEG113/ PLL1000-2000mixture as viewed by AFM imaging in a solution containing high concentrations of streptavidin. We show that this selective adsorption extends to DNA-protein complexes, through the use of biotinylated DNA and streptavidin, and demonstrate that DNA-bound streptavidin can be unambiguously distinguished by in-liquid AFM in spite of an excess of unbound streptavidin in solution.
The full-length transcriptome of Spartina alterniflora reveals the complexity of high salt tolerance in monocotyledonous halophyte
Authors: Ye Wenbin , Wang Taotao , Wei Wei , Lou Shuaitong , Lan Faxiu , Zhu Sheng , Li Qinzhen , Ji Guoli , Lin Chentao , Wu Xiaohui , Ma Liuyin 
Published: June 2019

ABSTRACTSpartina alterniflora (Spartina) is the only halophyte in the salt marsh. However, the molecular basis of its high salt tolerance remains elusive. In this study, we used PacBio full-length single molecule long-read sequencing and RNA-seq to elucidate the transcriptome dynamics of high salt tolerance in Spartina by salt-gradient experiments (0, 350, 500 and 800 mM NaCl). We systematically analyzed the gene expression diversity and deciphered possible roles of ion transporters, protein kinases and photosynthesis in salt tolerance. Moreover, the co-expression network analysis revealed several hub genes in salt stress regulatory networks, including protein kinases such as SaOST1, SaCIPK10 and three SaLRRs. Furthermore, high salt stress affected the gene expression of photosynthesis through down-regulation at the transcription level and alternative splicing at the post-transcriptional level. In addition, overexpression of two Spartina salt-tolerant genes SaHSP70-I and SaAF2 in Arabidopsis significantly promoted the salt tolerance of transgenic lines. Finally, we built the SAPacBio website for visualizing the full-length transcriptome sequences, transcription factors, ncRNAs, salt-tolerant genes, and alternative splicing events in Spartina. Overall, this study sheds light on the high salt tolerance mechanisms of monocotyledonous-halophyte and demonstrates the potential of Spartina genes for engineering salt-tolerant plants.
Organotypic slice culture model demonstrates interneuronal spreading of alpha-synuclein aggregates
Authors: Elfarrash Sara , Jensen Nanna Møller , Ferreira Nelson , Betzer Cristine , Thevathasan Jervis Vermal , Diekmann Robin , Adel Mohamed , Omar Nisreen Mansour , Boraie Mohamed Z. , Gad Sabry , Ries Jonas , Kirik Deniz , Nabavi Sadegh , Jensen Poul Henning 
Published: June 2019

AbstractHere we describe the use of an organotypic hippocampal slice model for studying α-synuclein aggregation and inter-neuronal spreading initiated by injection of preformed α-synuclein filaments (PFFs). PFF injection at dentate gyrus templates the endogenous α-synuclein to form aggregates in axons and cell bodies that spread to CA3 and CA1 regions. Aggregates were insoluble and phosphorylated at serine 129, recapitulating Lewy pathology features found in Parkinson’s disease and other synucleinopathies. The spreading of the aggregates were favoring the anterograde direction in the slice model. The model allowed development of slices expressing only serine-129 phosphorylation-deficient human α-synuclein (S129G) using adeno-associated viral (AAV) vector in α-synuclein knockout slices. Processes of aggregation and spreading of α-synuclein were thereby shown to be independent of phosphorylation at serine 129. We provide methods and highlight crucial steps for PFF microinjection and characterization of aggregate formation and spreading. Slices derived from genetically engineered mice or manipulated by using viral vectors allow testing of hypotheses on mechanisms involved in formation of α-synuclein aggregates and their prion-like spreading.
Extreme tolerance of Paramecium to acute injury induced by γ rays
Authors: Wang Ye , Duan Xiaopeng , Hu Yiping 
Published: June 2019

AbstractDue to the wide use of nuclear energy, nuclear radiation threat is increasing day by day. However, methods for protection against nuclear radiation are limited and not effective. Therefore, it is necessary to develop an effective method for protection and therapy against injury caused by radiation. According to the law of biological evolution, one of the most primitive eukaryotes, Paramecium, could be tolerant to ionizing radiations, in a way similar to or better than Ramazzottius varieornatus and Bdelloids rotifer. Therefore, in the present study, the anti-radiation effects of Paramecium were explored, which could be applicable to human beings. Paramecium was found to be tolerant to 60Co γ rays, and its half lethal dose (LD50) was approximately 3000 Gy, which is 60 times more than that of human beings. The GSPATT00021409001 and GSPATT00016349001 genes were significantly up-regulated, which might play a role in DNA binding and nuclear transport, and thus, could function in DNA protection or repair. The biological function of the two genes and their effects in humans need to be explored in future studies.
Connecting gene regulatory relationships to neurobiological mechanisms of brain disorders
Authors: Sey Nancy Y. A , Fauni Harper , Ma Won , Won Hyejung 
Published: June 2019

AbstractDespite being clinically distinguishable, many neuropsychiatric disorders display a remarked level of genetic correlation and overlapping symptoms. Deciphering neurobiological mechanisms underlying potential shared genetic etiology is challenging because (1) most common risk variants reside in the non-coding region of the genome, and (2) a genome-wide framework is required to compare genome-wide association studies (GWAS) having different power. To address these challenges, we developed a platform, Hi-C coupled MAGMA (H-MAGMA), that converts SNP-level summary statistics into gene-level association statistics by assigning non-coding SNPs to their cognate genes based on chromatin interactions. We applied H-MAGMA to five psychiatric disorders and four neurodegenerative disorders to interrogate biological pathways, developmental windows, and cell types implicated for each disorder. We found that neuropsychiatric disorder-associated genes coalesce at the level of developmental windows (mid-gestation) and cell-type specificity (excitatory neurons). On the contrary, neurodegenerative disorder-associated genes show more diverse cell type specific, and increasing expression over time, consistent with the age-associated elevated risk of developing neurodegenerative disorders. Genes associated with Alzheimer’s disease were not only highly expressed in microglia, but also subject to microglia and oligodendrocyte-specific dysregulation, highlighting the importance of understanding the cellular context in which risk variants exert their effects. We also obtained a set of pleiotropic genes that are shared across multiple psychiatric disorders and may form the basis for common neurobiological susceptibility. Pleiotropic genes are associated with neural activity and gene regulation, with selective expression in corticothalamic projection neurons. These results show how H-MAGMA adds to existing frameworks to help identify the neurobiological basis of shared and distinct genetic architecture of brain disorders.
Topographic specificity of alpha power during auditory spatial attention
Authors: Deng Yuqi , Choi Inyong , Shinn-Cunningham Barbara 
Published: June 2019

AbstractVisual and somatosensory spatial attention both induce parietal alpha (7-14 Hz) oscillations whose topographical distribution depends on the direction of spatial attentional focus. In the auditory domain, contrasts of parietal alpha power for leftward and rightward attention reveal a qualitatively similar lateralization; however, it is not clear whether alpha lateralization changes monotonically with the direction of auditory attention as it does for visual spatial attention. In addition, most previous studies of alpha oscillation did not consider subject-specific differences in alpha frequency, but simply analyzed power in a fixed spectral band. Here, we recorded electroencephalography in human subjects when they directed attention to one of five azimuthal locations. After a cue indicating the direction of an upcoming target sequence of spoken syllables (yet before the target began), alpha power changed in a task specific manner. Subject-specific peak alpha frequencies differed consistently between frontocentral electrodes and parieto-occipital electrodes, suggesting multiple neural generators of task-related alpha. Parieto-occipital alpha increased over the hemisphere ipsilateral to attentional focus compared to the contralateral hemisphere, and changed systematically as the direction of attention shifted from far left to far right. These results showing that parietal alpha lateralization changes smoothly with the direction of auditory attention as in visual spatial attention provide further support to the growing evidence that the frontoparietal attention network is supramodal.
Exploring the role of the various methionine residues in the Escherichia coli CusB adapter protein
Authors: Meir Aviv , Walke Gulshan , Schwerdtfeger Fabian , Gevorkyan-Airapetov Lada , Ruthstein Sharon 
Published: June 2019

AbstractThe dissemination of resistant pathogenic microbes has become one of the most challenging problems that modern medicine has faced. Developing novel drugs based on new molecular targets that previously were not targeted, is therefore the highest priority in antibiotics research. One approach that has been recently suggested is to inhibit copper transporters in prokaryotic systems. Copper is required for many biological pathways, but sometimes it can harm the cell. Pathogenic systems have a highly sophisticated copper-regulation network; therefore, a better understanding of how this network operates at the molecular level should assist in developing the next generation of antibiotics. The CusB protein is part of the CusCBA periplasmic Cu(I) efflux system in Gram-negative bacteria, and it was recently reported to play a key role in the functioning of the whole CusCBA system, in which conformational changes as well as the assembly/disassembly process control the opening of the transporter. More knowledge of the underlying mechanism is needed to attain a full understanding of CusB functioning, which is associated with targeting specific and crucial residues in CusB. Here, we combine in-vitro structural measurements, which used EPR spectroscopy and UV-Vis measurements, with cell experiments to explore the role of the various methionine residues in CusB. We targeted two methionine residues (M227 and M241) that are essential for the proper function of CusB.
Degradation of miR-466d-3p by JEV NS3 facilitates viral replication and IL-1β expression
Authors: Jiang Hui , Zhao Caiquan , Bai Zhuofang , Meng Yanqing , Qin Tian , Wang Xiao , Wang Guojun , Cui Min , Ye Jing , Cao Shengbo , Li Guangpeng , Yang Yang 
Published: June 2019

AbstractPrevious studies revealed that Japanese encephalitis virus (JEV) infection alters the expression of miRNA in central nervous system (CNS). However, the mechanism of JEV infection contributes to the regulation of miRNAs in CNS remain obscure. Here, we found that a global degradation of mature miRNA in mouse brain and neuroblastoma cells after JEV infection. In additional, the integrative analysis of miRNAs and mRNAs suggests that those down-regulated miRNAs are primarily targeted inflammation genes and the miR-466d-3p target the IL-1β which in the middle of those inflammation genes. Transfection of miR-466d-3p decreased the IL-1β expression and inhibited the JEV replication in NA cells. Interestingly, the miR-466d-3p level increased after JEV infection in the presence of cycloheximide, which indicated that viral protein expression reduces miR-466d-3p. Therefore, we generated all the JEV coding protein and demonstrated that NS3 is a potent miRNA suppressor. Furthermore, the NS3 of ZIKA virus, WNV, DENV1 and DENV2 also decreased the expression of miR-466d-3p. The in vitro unwinding assay demonstrated that the NS3 could unwind the pre-miR-466d and induce the disfunction of miRNA. Using computational models and RNA immunoprecipitation assay, we found that arginine-rich domains of NS3 are critical for pre-miRNA binding and the degradation of host miRNAs. Importantly, site-directed mutagenesis of conserved residues revealed that R226G and R202W significantly reduced the binding affinity and degradation of pre-miR-466d. Together, these results extend the helicase of Flavivirus function beyond unwinding duplex RNA to the decay of pre-miRNAs, which provides a new mechanism of NS3 in regulating miRNA pathways and promoting the neuroinflammation.Author SummaryHost miRNAs had been reported to regulate JEV induced inflammation in central nervous system. We found that the NS3 of JEV can reduce most of host miRNA expression. The helicase region of the NS3 specifically binds to precursors of miRNA and lead to incorrect unwinding of precursors of miRNAs which inhibits the function of miRNAs. This observation leads to two major findings. First, we identified the miR-466d-3p targets to the host IL-1β and E protein of JEV, and NS3 degrades the miR-466d-3p to promote the brain inflammation and viral replication. Second, we proved that the arginine on the helicase of NS3 is the main miRNA binding sites, and the miRNA degradation by NS3 was abolished when the R226 and R202 were mutated on the NS3. These findings were also confirmed with NS3 of ZIKA virus, WNV and DENV which could decrease the expression level of miR-466d-3p to enhance the inflammation. Our study provides new insights into the molecular mechanism of encephalitis caused by JEV, and reveals several amino acid sites to further attenuate the JEV vaccine.
Inhibition of Polymerase Chain Reaction: Pathogen-Specific Controls are better than Human Gene Amplification
Authors: Roux Guillaume , Ravel Christophe , Varlet-Marie Emmanuelle , Jendrowiak Rachel , Bastien Patrick , Sterkers Yvon 
Published: June 2019

AbstractPCR inhibition is frequent in medical microbiology routine practice and may lead to false-negative results; however there is no consensus on how to detect it. Pathogen-specific and human gene amplifications are widely used to detect PCR inhibition. We aimed at comparing the value of PCR inhibitor detection using these two methods. We analysed Cp shifts (ΔCp) obtained from qPCRs targeting either the albumin gene or the pathogen-specific sequence used in two laboratory-developed microbiological qPCR assays. 3152 samples including various matrixes were included. Pathogen-specific amplification and albumin qPCR identified 62/3152 samples (2.0 %), and 409/3152 (13.0%) samples, respectively, as inhibited. Only 16 samples were detected using both methods. In addition, the use of the Youden’s index failed to determine adequate Cp thresholds for albumin qPCR, even when we distinguished among the different sample matrixes. qPCR targeting the albumin gene therefore appears not adequate to identify the presence of PCR inhibitors in microbiological PCR assays. Our data may be extrapolated to other heterologous targets and should discourage their use to assess the presence of PCR inhibition in microbiological PCR assays.