Biology subjects

Zhang, N.

Publications and source records attributed to Zhang, N..

16 recordsLinked to original sources

bioRxiv2018

AMON: Annotation of metabolite origins via networks to better integrate microbiome and metabolome data

MotivationUntargeted metabolomics of host-associated samples has yielded insights into mechanisms by which microbes modulate health. However, data interpretation is challenged by the complexity of origins of the small molecules measured, which can come from the host, microbes that live with the host, or from other exposures such as diet or the environment.\n\nResultsWe address this challenge through development of AMON: Annotation of Metabolite Origins via Networks. AMON is an open-source bioinformatics application that can be used to determine the degree to which annotated compounds in the metabolome may have been produced by bacteria present, the host, either (i.e. both the bacteria and host are capable of production), or neither (i.e. neither the human or the fecal microbiome are predicted to be capable of producing the observed metabolite).\n\nAvailability and ImplementationThis software is available at https://github.com/lozuponelab/AMON as well as via pip.\n\nContactcatherine.lozupone@ucdenver.edu

bioinformatics↗

bioRxiv2018

Individual variability in behavior and functional networks predicts vulnerability using a predator scent model of PTSD

Only a minority of individuals who experience traumatic event(s) subsequently develop post-traumatic stress disorder (PTSD). However, whether differences in vulnerability to PTSD result from predisposition or a consequence of trauma exposure remains unclear. A major challenge in differentiating these possibilities is that clinical studies focus on individuals already exposed to traumatic experiences, and do not take into account pre-trauma conditions. Here using the predator scent model of PTSD in rats and a longitudinal design, we measured pre-trauma brain-wide neural circuit functional connectivity (FC), behavioral and corticosterone responses to trauma exposure, and post-trauma anxiety. Individual differences in freezing responses to predator scent exposure correlated with differences in pre-trauma FC in a set of neural circuits, especially in olfactory and stress-related systems, indicating that pre-existing function in these circuits could predispose animals to differential fearful responses to threats. Counterintuitively, rats with the lowest freezing showed more avoidance of the predator scent, a prolonged corticosterone response, and higher anxiety long after exposure. This study provides a comprehensive framework of pre-existing circuit function that determines threat response strategy, which might be directly related to the development of PTSD-like behaviors.

neuroscience↗

bioRxiv2018

Downregulation of insulin-like growth factor binding protein 5 is involved in intervertebral disc degeneration via the ERK signaling pathway

Introduction Introduction Results Discussion Material and methods Conflict of interest References Intervertebral disc degeneration (IDD) is a disease of discs connecting adjoining vertebrae in which structural damage causes the degeneration of the disc and the surrounding area. This disease represents a common cause of back pain, and its treatment is costly and relatively ineffective (Kepler et al., 2013), with patients who do not achieve improvement with conservative management possibly requiring surgery (Lurie et al., 2014; Postacchini, 1996). It has been reported that the central features of IDD are the reduction in the nucleus pulposus (NP) cell population and the loss of extracellular matrix molecules (ECM), which eventually leads to major changes in the ...

molecular biology↗

bioRxiv2018

Divergence in the face of gene flow in two Charadrius plovers along the Chinese coast

Speciation with gene flow is an alternative to the nascence of new taxa in strict allopatric separation. Indeed, many taxa have parapatric distributions at present. It is often unclear if these are secondary contacts, e.g. caused by past glaciation cycles or the manifestation of speciation with gene flow, which hampers our understanding of how different forces drive diversification. Here we studied genetic, phenotypic and ecological aspects of divergence in a pair of incipient species, the Kentish (Charadrius alexandrinus) and the white-faced Plovers (C. dealbatus), shorebirds with parapatric breeding ranges along the Chinese coast. We assessed divergence based on molecular markers with different modes of inheritance and quantified phenotypic and ecological divergence in aspects of morphometric, dietary and climatic niches. These analyses revealed small to moderate levels of genetic and phenotypic distinctiveness with symmetric gene flow across the contact area at the Chinese coast. The two species diverged approximately half a million years ago in dynamical isolation and secondary contact due to cycling sea level changes between the Eastern and Southern China Sea in the mid-late Pleistocene. We found evidence of character displacement and ecological niche differentiation between the two species, invoking the role of selection in facilitating divergence despite gene flow. These findings imply that the ecology can indeed counter gene flow through divergent selection and thus contribute to incipient speciation in these plovers. Furthermore, our study highlights the importance of using integrative datasets to reveal the evolutionary history and underlying mechanisms of speciation.

evolutionary biology↗

bioRxiv2018

Transcriptional Profiling of Patient Isolates Identifies a Novel TOR Regulatory Pathway in Cryptococcal Virulence

Human infection with Cryptococcus causes up to a quarter million AIDS-related deaths annually and is the most common cause of non-viral meningitis in the United States. As an opportunistic fungal pathogen, C. neoformans is distinguished by its ability to adapt to diverse host environments including plants, amoeba and mammals. In the present study, comparative transcriptomics of the fungus within human cerebrospinal fluid identified expression profiles representative of low-nutrient adaptive responses. Transcriptomics of fungal isolates from a cohort of HIV/AIDS patients identified a low nutrient-induced gene, an alternative carbon nutrient transporter STL1 associated with poor early fungicidal activity, an important clinical prognostic marker. Mouse modeling and pathway analysis demonstrated a role for STL1 in mammalian pathogenesis and revealed that STL1 expression is regulated by a novel target-of-rapamycin (TOR)-related multi-gene regulatory mechanism involving the CAC2 subunit of the chromatin assembly complex 1, CAF-1. In this pathway, the TOR-related RNA chaperone, VAD1 was found to transcriptionally regulate a cryptococcal homolog of a cytosolic protein Ecm15, in turn, required for nuclear transport of the Cac2 protein. Derepression of STL1 by the CAC2-containing CAF-1 complex was mediated by Cac2 and modulated binding and suppression of the STL1 enhancer element. Derepression of STL1 resulted in enhanced survival and growth of the fungus in the presence of low nutrient, alternative carbon sources, facilitating virulence in mice. The study underscores the utility of ex vivo expression profiling of fungal clinical isolates and provides fundamental genetic understanding of saprophyte adaption to the human host.\n\nAuthor summaryThe fungus Cryptococcus is a fungal pathogen that kills an estimated quarter of a million individuals yearly and is the most common cause of meningitis in the United States. The fungus is carried in about 10% of the adult population and, after re-activation, causes disease in a wide variety of individuals including HIV-infected as well as immunosuppression either from genetic defects or after immune suppressive treatments due to transplant conditioning, cancer therapy or treatment of autoimmune diseases. The fungus is widely carried in the soil and trees and can infect plants, single cell organisms and even dolphins. However, mechanisms for this widespread ability to infect a variety of hosts are poorly understood. The present study identified adaptation to low nutrients as a key property that allows the fungus to infect these diverse hosts and identified a nutrient transporter, STL1 to be associated with a marker of poor clinical outcome in a cohort of HIV/AIDS patients. Understanding molecular mechanisms involved in environmental adaptation may help to design better methods of control and treatment of widely dispersed fungal pathogens such as Cryptococcus.

microbiology↗

bioRxiv2018

Bulk Tissue Cell Type Deconvolution with Multi-Subject Single-Cell Expression Reference

We present MuSiC, a method that utilizes cell-type specific gene expression from single-cell RNA sequencing (RNA-seq) data to characterize cell type compositions from bulk RNA-seq data in complex tissues. When applied to pancreatic islet and whole kidney expression data in human, mouse, and rats, MuSiC outperformed existing methods, especially for tissues with closely related cell types. MuSiC enables characterization of cellular heterogeneity of complex tissues for identification of disease mechanisms.

bioinformatics↗

bioRxiv2018

The Expression of Inflammatory Genes in 3T3-L1 Adipocytes Exhibits a Memory to Stimulation by Macrophage Secretions

Obesity is characterized by increased output of inflammatory compounds from adipose tissue. Whilst the relative contribution of adipocytes and resident macrophages to this phenomenon is debated, there is no doubt that the secretions of each cell type can stimulate the expression of inflammatory genes in the other. We hypothesized that mechanisms must exist to prevent an escalating positive feedback loop between the two cell types, so that after an initial exposure to macrophage secretions, adipocytes would become desensitized to subsequent inflammatory stimulation.\n\nWe used microarrays to investigate the response of 3T3-L1 adipocytes to macrophage secretions (macrophage conditioned medium, MCM). MCM caused a rapid (<4 hours) and high amplitude (over 100-fold) rise in the expression of several inflammatory genes. For some genes, generally cytokines, expression returned to basal levels within 24 h following removal of the MCM, but other transcripts, notably those for acute phase proteins and extracellular matrix remodeling proteins, remained highly expressed even during the washout period.\n\nUnexpectedly, some cytokine genes (e.g., iNOS, IL-6) showed an enhanced expression to a second exposure of MCM, illustrating that the transcriptome response of 3T3-L1 adipocytes retains a memory to the first stimulus. We characterized the parameters that give rise to the memory phenomenon, finding that additional stimuli do not augment or abrogate the effect. The memory is preserved for several days after the initial exposure and it is not due to a change in sensitivity to the MCM but, rather, a change in the capacity of the signal-target system. The possible mechanisms of the memory are discussed, along with the physiological ramifications should the phenomenon be replicated in vivo.

biochemistry↗

bioRxiv2018

Stalk-mediated communication in the dynein motor domain

The movement of a molecular motor protein along a cytoskeletal track requires communication between enzymatic, polymer-binding, and mechanical elements. Such communication is particularly complex and not well understood in the dynein motor, an ATPase that is comprised of a ring of six AAA domains, a large mechanical element (linker) spanning over the ring, and a microtubule-binding domain (MTBD) that is separated from the AAA ring by a ~135 [A] coiled-coil stalk. We identified mutations in the stalk that disrupt directional motion, have microtubule-independent hyperactive ATPase activity, and nucleotide-independent low affinity for microtubules. Cryo-electron microscopy structures of a mutant that uncouples ATPase activity from directional movement reveal that nucleotide-dependent conformational changes occur normally in one half of the AAA ring, but are disrupted in the other half. The large-scale linker conformational change observed in the wild-type protein is also inhibited, revealing that this conformational change is not required for ATP hydrolysis. These results demonstrate an essential role of the stalk in regulating motor activity and coupling conformational changes across the two halves of the AAA ring.

biochemistry↗

bioRxiv2018

Implementation of CRISPR-Cas13a system in fission yeast and its repurposing for precise RNA editing

In contrast to genome editing that introduces genetic changes at DNA level, disrupting or editing genes transcripts provides a distinctive approach to perturb a genetic system, offering benefits complementary to classic genetic approaches. To develop a new toolset for manipulation of RNA, we first implemented a member of type VI CRISPR systems, Cas13a from Leptotrichia shahii (LshCas13a) in Schizosaccharomyces pombe, an important model organism employed by biologists to study key cellular mechanisms conserved from yeast to humans. While it was shown to knock down targeted endogenous genes transcripts, differently from previous studies in E. coli, no collateral cleavage of other non-specific RNA by activated Cas13a-crRNA complex was detected in fission yeast. Second, we engineered a RNA-editing system by tethering an inactive form of LshCas13a (dCas13) to the catalytic domain of human Adenosine Deaminase Act on RNA 2 (hADAR2d), which was shown to be programmable with crRNA to target messenger RNAs and precisely edit specific nucleotide residues. We optimized the system parameters using a dual-florescence reporter and demonstrated its utility in editing of randomly selected endogenous genes transcripts. Our engineered RNA-editing system enables a new toolset for transcriptomic manipulation that is widely applicable in basic genetic and biotechnological research.

synthetic biology↗

bioRxiv2018

The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies

Multiple nuclear markers provide genetic polymorphism data for molecular systematics and population genetic studies. They are especially required for the coalescent-based analyses that can be used to accurately estimate species trees and infer population demographic histories. However, in avian evolutionary studies, these powerful coalescent-based methods are hindered by the lack of a sufficient number of markers. In this study, we designed PCR primers to amplify 136 nuclear protein-coding loci (NPCLs) by scanning the published Red Junglefowl (Gallus gallus) and Zebra Finch (Taeniopygia guttata) genomes. To test their utility, we amplified these loci in 41 bird species representing 23 Aves orders. The sixty-three best-performing NPCLs, based on high PCR success rates, were selected which had various mutation rates and were evenly distributed across 17 avian autosomal chromosomes and the Z chromosome. To test phylogenetic resolving power of these markers, we conducted a Neoavian phylogenies analysis using 63 concatenated NPCL markers derived from 48 whole genomes of birds. The resulting phylogenetic topology, to a large extent, is congruence with results resolved by previous whole genome data. To test the level of intraspecific polymorphism in these makers, we examined the genetic diversity in four populations of the Kentish Plover (Charadrius alexandrinus) at 17 of NPCL markers chosen at random. Our results showed that these NPCL markers exhibited a level of polymorphism comparable with mitochondrial loci. Therefore, this set of pan-avian nuclear protein-coding loci has great potential to facilitate studies in avian phylogenetics and population genetics.

evolutionary biology↗

bioRxiv2017

Retrosplenial cortex and its role in spatial cognition

Retrosplenial cortex (RSC) is a region within the posterior neocortical system, heavily interconnected with an array of brain networks, both cortical and subcortical, that is engaged by a myriad of cognitive tasks. Although there is no consensus as to its precise function, evidence from both human and animal studies clearly points to a role in spatial cognition. However, the spatial processing impairments that follow RSC damage are not straightforward to characterise, leading to difficulties in defining the exact nature of its role. In the present article we review this literature and classify the types of ideas that have been put forward into three broad, somewhat overlapping classes: (i) Learning of landmark location, stability and permanence; (ii) Integration between spatial reference frames, and (iii) Consolidation and retrieval of spatial knowledge (\"schemas\"). We evaluate these models and suggest ways to test them, before briefly discussing whether the spatial function may be a subset of a more general function in episodic memory.

animal behavior and cognition↗

bioRxiv2017

Cholecystokinin release triggered by presynaptic NMDA receptors produces LTP and sound-sound associative memory formation

Memory is stored in neural networks via changes in synaptic strength mediated in part by NMDA-dependent long-term potentiation (LTP). There is evidence that entorhinal cortex enables neocortical neuroplasticity through cholecystokinin (CCK)-containing neocortical projections. Here we show that a CCKB antagonist blocks high-frequency stimulation (HFS)-induced LTP in the auditory cortex, whereas local infusion of CCK induces LTP. CCK-/- mice lacked neocortical LTP and showed deficits in a cue-cue associative learning paradigm; administration of CCK rescued associative learning. HFS of CCK-containing entorhino-neocortical projection neurons in anesthetized mice enabled cue-cue associative learning. Furthermore, when one cue was pre-conditioned to footshock, the mouse showed a freezing response to the other cue, indicating that the mice had formed an association. HFS-induced neocortical LTP was completely blocked by either NMDA antagonist or CCK-BR antagonist, while application of either NMDA or CCK induced LTP after low-frequency stimulation (LFS). Moreover, in the presence of CCK LTP was still induced, even after blockade of NMDA receptors. Local application of NMDA induced CCK release in the neocortex. To identify how NMDA receptor switches LTP, a stimulation protocol of 25 pulse-pairs was adopted to replace HFS; NMDA-dependent LTP was induced with the inter-pulse intervals between 10 and 100 ms, but not with those of 5 and 200 ms. LTP-mediated plasticity was linked to localization of the NMDA receptor subunit NR2a on cortical CCK terminals originating in the entorhinal cortex. These novel findings suggest that presynaptic NMDA receptors on CCK terminals control the release of CCK, which enables neocortical LTP and formation of cue-cue associative memory.\n\nOne Sentence SummaryPresynaptic NMDA receptors switches the release of CCK from entorhinal neurons, which enables neocortical LTP and formation of sound-sound associative memory.

neuroscience↗

bioRxiv2017

Integrative DNA copy number detection and genotyping from sequencing and array-based platforms

MotivationCopy number variations (CNVs) are gains and losses of DNA segments and have been associated with disease. Many large-scale genetic association studies are performing CNV analysis using whole exome sequencing (WES) and whole genome sequencing (WGS). In many of these studies, previous SNP-array data are available. An integrated cross-platform analysis is expected to improve resolution and accuracy, yet there is no tool for effectively combining data from sequencing and array platforms. The detection of CNVs using sequencing data alone can also be further improved by the utilization of allele-specific reads.\n\nResultsWe propose a statistical framework, integrated Copy Number Variation detection algorithm (iCNV), which can be applied to multiple study designs: WES only, WGS only, SNP array only, or any combination of SNP and sequencing data. iCNV applies platform specific normalization, utilizes allele specific reads from sequencing and integrates matched NGS and SNP-array data by a Hidden Markov Model (HMM). We compare integrated two-platform CNV detection using iCNV to naive intersection or union of platforms and show that iCNV increases sensitivity and robustness. We also assess the accuracy of iCNV on WGS data only, and show that the utilization of allele-specific reads improve CNV detection accuracy compared to existing methods.\n\nAvailabilityhttps://github.com/zhouzilu/iCNV\n\nContactnzh@wharton.upenn.edu, zhouzilu@mail.med.upenn.edu\n\nSupplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2017

Temporal transitions of spontaneous brain activity in awake rats

Spontaneous brain activity, typically investigated using resting-state fMRI (rsfMRI), provides a measure of inter-areal resting-state functional connectivity (RSFC). Previous rsfMRI studies mainly focused on spatial characteristics of RSFC, but the temporal relationship between RSFC patterns is still elusive. Particularly, it remains unknown whether separate RSFC patterns temporally fluctuate in a random manner, or transit in specific orders. Here we investigated temporal transitions between characteristic RSFC patterns in awake rats and humans. We found that transitions between RSFC patterns were reproducible and significantly above chance, suggesting that RSFC pattern transitions were nonrandom. The organization of RSFC pattern transitions in rats was analyzed using graph theory. Pivotal RSFC patterns in transitions were identified including hippocampal, thalamic and striatal networks. This study has revealed nonrandom temporal relationship between characteristic RSFC patterns in both rats and humans. It offers new insights into understanding the spatiotemporal dynamics of spontaneous activity in the mammalian brain.

neuroscience↗

bioRxiv2017

Simultaneous GCaMP6-based Fiber Photometry and fMRI in Rats

Understanding the relationship between neural and vascular signals is essential for interpretation of functional MRI (fMRI) results with respect to underlying neuronal activity. Simultaneously measuring neural activity using electrophysiology with fMRI has been highly valuable in elucidating the neural basis of the blood oxygenation-level dependent (BOLD) signal. However, this approach is also technically challenging due to the electromagnetic interference that is observed in electrophysiological recordings during MRI scanning. Recording optical correlates of neural activity, such as calcium signals, avoids this issue, and has opened a new avenue to simultaneously acquire neural and BOLD signals. The present study is the first to demonstrate the feasibility of simultaneously and repeatedly acquiring calcium and BOLD signals in animals using a genetically encoded calcium indicator, GCaMP6. This approach was validated with a visual stimulation experiment, during which robust increases of both calcium and BOLD signals in the superior colliculus were observed. In addition, repeated measurement in the same animal demonstrated reproducible calcium and BOLD responses to the same stimuli. Taken together, simultaneous GCaMP6-based fiber photometry and fMRI recording presents a novel, artifact-free approach to simultaneously measuring neural and fMRI signals. Furthermore, given the cell-type specificity of GCaMP6, this approach has the potential to mechanistically dissect the contributions of individual neuron populations with respect to BOLD signal, and ultimately reveal its underlying neural mechanisms.

neuroscience↗

bioRxiv2017

Accounting For Technical Noise In Single-Cell RNA Sequencing Analysis

Recent technological breakthroughs have made it possible to measure RNA expression at the single-cell level, thus paving the way for exploring expression heterogeneity among individual cells. Current single-cell RNA sequencing (scRNA-seq) protocols are complex and introduce technical biases that vary across cells, which can bias downstream analysis without proper adjustment. To account for cell-to-cell technical differences, we propose a statistical framework, TASC (Toolkit for Analysis of Single Cell RNA-seq), an empirical Bayes approach to reliably model the cell-specific dropout rates and amplification bias by use of external RNA spike-ins. TASC incorporates the technical parameters, which reflect cell-to-cell batch effects, into a hierarchical mixture model to estimate the biological variance of a gene and detect differentially expressed genes. More importantly, TASC is able to adjust for covariates to further eliminate confounding that may originate from cell size and cell cycle differences. In simulation and real scRNA-seq data, TASC achieves accurate Type I error control and displays competitive sensitivity and improved robustness to batch effects in differential expression analysis, compared to existing methods. TASC is programmed to be computationally efficient, taking advantage of multi-threaded parallelization. We believe that TASC will provide a robust platform for researchers to leverage the power of scRNA-seq.

bioinformatics↗