Biology subjects

Zhou, T.

Publications and source records attributed to Zhou, T..

At least 217 records · Page 12Linked to original sources

bioRxiv2020

The branched chain aminotransferase IlvE promotes growth, stress resistance, and pathogenesis of Listeria monocytogenes

The bacterial plasma membrane is a key interface during pathogen-host interactions, and membrane composition enhances resistance against host antimicrobial defenses. Branched chain fatty acids (BCFAs) are the major plasma membrane component in the intracellular Gram-positive pathogen Listeria monocytogenes (Lm) and BCFA metabolism is essential for Lm growth and virulence. BCFA synthesis requires branched chain amino acids (BCAAs), and the BCAA Isoleucine (Ile) is a necessary substrate for the predominant membrane anteiso-BCFAs (ai-BCFAs) as well as an environmental signal for virulence regulation in Lm. In this study, we explored how two proteins that metabolize or sense Ile contribute to Lm growth, BCFA metabolism, and virulence. The IlvE aminotransferase incorporates Ile into ai-BCFAs, while CodY is an Ile-sensing regulator that coordinates BCAA synthesis and virulence gene expression. Analysis of deletion mutants lacking IlvE ({Delta}ilvE) or CodY ({Delta}codY) revealed a major role for IlvE under nutrient restriction and stress conditions. Cultures of the {Delta}ilvE mutant contained proportionally less ai-BCFAs relative to wild type, while of the {Delta}codY mutant had a lower proportion of ai-BCFAs in stationary phase, despite containing more cell-associated Ile. Both {Delta}ilvE and {Delta}codY mutants required exogenous Ile for optimal growth, but the {Delta}ilvE mutant had an absolute requirement for Valine and Leucine when Ile was absent. IlvE was also necessary for resistance to membrane stress, cell-to-cell spread, infection of primary macrophages, and virulence in mice. Our findings implicate IlvE as an integral aspect of Lm stress resistance and emphasize the central importance of Ile in Lm growth and virulence.

microbiology↗

bioRxiv2020

IL4-driven microglia modulate stress resilience through BDNF-dependent neurogenesis

Adult neurogenesis in the dentate gyrus of the hippocampus is regulated by specific groups of microglia and is functionally implicated in behavioral responses to stress. However, the role of microglia in modulating hippocampal neurogenesis in stress responses remains poorly understood. Here we investigated the effects of IL4-driven Arg1+ microglia in the restoration of hippocampal neurogenesis and conferment of stress resilience. We found that low IL4 levels in the hippocampus of mice was associated with greater stress vulnerability and, conversely, overexpression of IL4 in the hippocampus induced a large number of Arg1+ microglia and ameliorated stress-induced depressive-like behaviors. Knockdown of microglial IL4 receptors in the hippocampus of mice exacerbated the stress-induced inflammatory response and abolished the antidepressant effects of IL4 overexpression. Enhancement or inhibition of IL4 signaling in hippocampal microglia modulated neurogenesis, and blockade of neurogenesis abolished the resilience to stress-induced depression. We further show that IL4-activated microglia is associated with upregulation of BDNF levels and neurogenesis. Taken together, our findings suggest that IL4-driven microglia in the hippocampus trigger BDNF-dependent neurogenesis in response to chronic stress, helping protect against depressive-like symptoms. These findings identify the modulation of a specific microglial phenotype as a treatment strategy for mood disorders. In BriefZhang et al. show that IL4-induced Arg1+ microglia restore hippocampal neurogenesis and promote resilience against stress in mice by increasing BDNF levels. Targeting microglia with immunomodulatory factors may be a strategy for treating mood disorders. HighlightsO_LIVulnerability to stress in mice is associated with reduced IL4 signaling in the hippocampus C_LIO_LIBrain-derived IL4 promotes adult hippocampal neurogenesis and stress resistance by driving Arg1+ microglia C_LIO_LIIL4-driven Arg1+ microglia enhance hippocampal neurogenesis via a BDNF-dependent pathway C_LI

neuroscience↗

bioRxiv2020

Subcortical magnocellular visual system facilities object recognition by processing topological property

The Magnocellular (M) visual pathway is known as a fast route to convey coarse information and facilitates object recognition by initiating top-down processes. It is unclear what exact properties M pathway conveys to accelerate visual object processing. Previous studies suggest that visual systems are highly sensitive to the perception of topological property (TP), which remains unchanged under various shape changes, and the TP is probably processed through a fast subcortical pathway. Here we hypothesize that a subcortical M system contributes to the fast object recognition by processing TP first. We first demonstrate that the facilitation effect of TP processing on object perception occurs mainly in the M visual system, and then support the subcortical M hypothesis of TP processing by the evidence that the early processing of TP was not affected when cortical function was temporarily damaged by the transcranial magnetic stimulation and when stimuli were biased to M system.

neuroscience↗

bioRxiv2019

Control strategies for the timing of intracellular events

While the timing of intracellular events is essential for many cellular processes, gene expression inside a cell can exhibit substantial cell-to-cell variability, raising the question of how cells ensure precision in the event timing despite such stochasticity. We address this question by analyzing a biologically reasonable model of gene expression in the context of first passage time (FPT), focusing on two experimentally measurable statistics: mean FPT (MFPT) and timing variability (TV). We show that: (1) transcriptional burst size (BS) and burst frequency (BF) can minimize the TV; (2) translational BS monotonically reduces the MFPT to a nonzero low bound and can minimize the TV; (3) the timescale of promoter kinetics can minimize both the MFPT and the TV, depending on the ratio of the off-switching rate over the on-switching rate; and (4) positive feedback regulation of any form can all minimize the TV, whereas negative feedback regulation of transcriptional BF or BS always enhances the TV. These control strategies can have broad implications for diverse cellular processes relying on precise temporal triggering of events.

systems biology↗

bioRxiv2019

A cortico-collicular pathway for motor planning in a memory-dependent perceptual decision task

Survival in a dynamic environment requires animals to plan future actions based on past sensory evidence. However, the neural circuit mechanism underlying this crucial brain function, referred to as motor planning, remains unclear. Here, we employ projection-specific imaging and perturbation methods to investigate the direct pathway linking two key nodes in the motor planning network, the secondary motor cortex (M2) and the midbrain superior colliculus (SC), in mice performing a memory-dependent perceptual decision task. We find dynamic coding of choice information in SC-projecting M2 neurons during motor planning and execution, and disruption of this information by inhibiting M2 terminals in SC selectively impaired decision maintenance. Furthermore, cell-type-specific optogenetic circuit mapping shows that M2 terminals modulate both excitatory and inhibitory SC neurons with balanced synaptic strength. Together, our results reveal the dynamic recruitment of the premotor-collicular pathway as a circuit mechanism for motor planning.

neuroscience↗

bioRxiv2019

RecV recombinase system for spatiotemporally controlled light-inducible genomic modifications.

Brain circuits are composed of vast numbers of intricately interconnected neurons with diverse molecular, anatomical and physiological properties. To allow highly specific targeting of individual neurons for structural and functional studies, we modified three site-specific DNA recombinases, Cre, Dre and Flp, by combining them with a fungal light-inducible protein, Vivid, so that their recombinase activities can be driven by blue light. We generated viral vectors to express these light-inducible recombinases and demonstrated that they can induce genomic modifications in dense or sparse populations of neurons in live mouse brains controlled by one-photon or two-photon light induction. As an important application, we showed that light-inducible recombinases can produce highly targeted, sparse and strong labeling of individual neurons thereby enabling whole-brain morphological reconstruction to identify their axonal projection specificity. In addition to targeting cortical brain areas, we applied the method in deep targets, with a demonstration of functional calcium imaging. These molecular tools enable spatiotemporally-precise, targeted genomic modifications that will greatly facilitate detailed analysis of neural circuits and linking genetic identity, morphology, connectivity and function.

neuroscience↗

bioRxiv2019

Meiotic viral attenuation through an ancestral apoptotic pathway

The programmed release of apoptogenic proteins from mitochondria is a core event of apoptosis, though ancestral roles of this phenomenon are not known. In mammals, one such apoptogenic protein is Endonuclease G (EndoG), a conserved nuclease that fragments the DNA of dying cells. In this work, we show that budding yeast executes meiotically programmed mitochondrial release of an EndoG homologue, Nuc1, during sporulation. In contrast to EndoGs ostensible pro-death function during apoptosis, Nuc1 mitochondrial release attenuates the cytosolic dsRNA mycovirus, Killer, protecting spores from a lethal accumulation of its encoded toxin. Our identification of cell-protective viral attenuation as a target of this rudimentary apoptotic pathway illuminates a primordial role for mitochondrial release of EndoG.\n\nOne Sentence SummaryYeast sporulation induces release of mitochondrial endonuclease G to accomplish viral attenuation.

genetics↗

bioRxiv2019

Computation of stationary distributions in stochastic models of cellular processes with molecular memory

AbstractModeling stochastic dynamics of intracellular processes has long rested on Markovian (i.e., memoryless) hypothesis. However, many of these processes are non-Markovian (i.e., memorial) due to, e.g., small reaction steps involved in synthesis or degradation of a macroscopic molecule. When interrogating aspects of a cellular network by experimental measurements (e.g., by singlemolecule and single-cell measurement technologies) of network components, a key need is to develop efficient approaches to simulate and compute joint distributions of these components. To cope with this computational challenge, we develop two efficient algorithms: stationary generalized Gillespie algorithm and stationary generalized finite state projection, both being established based on a stationary generalized chemical master equation. We show how these algorithms can be combined in a streamlined procedure for evaluation of non-Markovian effects in a general cellular network. Stationary distributions are evaluated in two models of constitutive and bursty gene expressions as well as a model of genetic toggle switch, each considering molecular memory. Our approach significantly expands the capability of stochastic simulation to investigate gene regulatory network dynamics, which has the potential to advance both understanding of molecular systems biology and design of synthetic circuits.\n\nAuthor summaryCellular systems are driven by interactions between subsystems via time-stamped discrete events, involving numerous components and reaction steps and spanning several time scales. Such biochemical reactions are subject to inherent noise due to the small numbers of molecules. Also, they could involve several small steps, creating a memory between individual events. Delineating these molecular stochasticity and memory of biomolecular networks are continuing challenges for molecular systems biology. We present a novel approach to compute the probability distribution in stochastic models of cellular processes with molecular memory based on stationary generalized chemical master equation. We map a stochastic system with memory onto a Markovian model with effective reaction propensity functions. This formulation enables us to efficiently develop algorithms under the Markovian framework, and thus systematically analyze how molecular memories regulate stochastic behaviors of biomolecular networks. Here we propose two representative algorithms: stationary generalized Gillespie algorithm and stationary generalized finite state projection algorithm. The former generate realizations with Monte Carlo simulation, but the later compute approximations of the probability distribution by solving a truncated version of stochastic process. Our approach is demonstrated by applying it to three different examples from systems biology: generalized birth-death process, a stochastic toggle switch model, and a 3-stage gene expression model.

systems biology↗

bioRxiv2018

IL-25 induces beige fat to improve metabolic homeostasis via macrophage and innervation

Beige fat dissipates energy and functions as a defense against cold and obesity, but the underlying mechanisms remain unclear. We found that the signaling of interleukin (IL)-25 including its cognate receptor, IL-17 receptor B (IL-17RB), increased in adipose tissue upon cold and {beta}3-adrenoceptor agonist stimulation. IL-25 induced the browning effect in white adipose tissue (WAT) by releasing IL-4, 13 and promoting alternative activation of macrophages to regulate innervation, which characterized as tyrosine hydroxylase (TH) up-regulation to produce more catecholamine including norepinephrine. Blockade of IL-4R and depletion of macrophages with clodronate-loaded liposomes in vivo significantly impaired the browning of WAT. Obese mice administered with IL-25 were protected from obesity on a high-fat diet and the subsequent metabolic disorders, and the process involved the uncoupling protein 1 (UCP1)-mediated thermogenesis. In conclusion, the activation of IL-25 signaling on beige fat might play a therapeutic potential for obesity and its associated metabolic disorders.

biochemistry↗

bioRxiv2018

Intraflagellar transport protein 74 is essential for mouse spermatogenesis and male fertility by regulating axonemal microtubule assembly in mice

IFT74 is a component of the core intraflagellar transport (IFT) complex, a bidirectional movement of large particles along the axoneme microtubules for cilia formation. In this study, we investigated its role in sperm flagella formation and discovered that mice deficiency in IFT74 in male germ cells were infertile associated with low sperm counts and immotile sperm. The few developed spermatozoa displayed misshaped heads and short tails. Transmission electron microscopy revealed abnormal flagellar axoneme in the seminiferous tubules where sperm are made. Clusters of unassembled microtubules were present in the spermatids. Testicular expression levels of IFT27, IFT57, IFT81, IFT88 and IFT140 were significantly reduced in the mutant mice, with the exception of IFT20 and IFT25. The levels of ODF2 and SPAG16L proteins were also not changed. However, the processed AKAP4 protein, a major component of the fibrous sheath, a unique structure of sperm tail, was significantly reduced. Our study demonstrates that IFT74 is essential for mouse sperm formation, probably through assembly of the core axoneme and fibrous sheath, and highlights a potential genetic factor (IFT74) that contributes to human infertility in men.

developmental biology↗

bioRxiv2018

Stochastic temporal timing for intracellular events to cross dynamically fluctuating thresholds

Fractional killing, which is a significant impediment to successful chemotherapy, is observed even in a population of genetically identical cancer cells exposed to apoptosis-inducing agents. This phenomenon arises not from genetic mutation but from cell-to-cell variation in the activation timing and level of the proteins that regulate apoptosis. To understand the mechanism behind the phenomenon, we formulate complex fractional killing processes as a first-passage time (FPT) problem with a stochastically fluctuating boundary. Analytical calculations are performed for the FPT distribution in a toy model of stochastic p53 gene expression, where the cancer cell is killed only when the p53 expression level crosses an activity apoptotic threshold. Counterintuitively, we find that threshold fluctuations can effectively enhance cellular killing by significantly decreasing the mean time that the p53 protein reaches the threshold level for the first time. Moreover, faster fluctuations lead to the killing of more cells. These qualitative results imply that dynamic variability in threshold is an unneglectable stochastic source, and can be taken as a strategy for combating fractional killing of cancer cells.

systems biology↗

bioRxiv2018

BodyMap transcriptomes reveal unique circular RNA features across tissue types and developmental stages

Circular RNAs (circRNAs) are a novel class of regulatory RNAs. Here, we present a comprehensive investigation of circRNA expression profiles across 11 tissues and 4 developmental stages in rats, along with cross-species analyses in humans and mice. Although positively correlated, circRNAs exhibit higher tissue specificity than cognate mRNAs. Also, genes with higher expression levels exhibit a larger fraction of spliced circular transcripts than their linear counterparts. Intriguingly, while we observed a monotonic increase of circRNA abundance with age in the rat brain, we further discovered a dynamic, age-dependent pattern of circRNA expression in the testes that is characterized by a dramatic increase with advancing stages of sexual maturity and a decrease with aging. The age-sensitive testicular circRNAs are highly associated with spermatogenesis, independent of cognate mRNA expression. The tissue/age implications of circRNAs suggest that they present unique physiological functions rather than simply occurring as occasional by-products of gene transcription.

bioinformatics↗

bioRxiv2018

Stationary Equations for Non-Markovian Biochemical Systems

We develop a new approach for stochastic analysis of biochemical reaction systems with arbitrary distributions of waiting times between reaction events. Specifically, we derive a stationary generalized chemical master equation for a non-Markovian reaction network. Importantly, this equation allows to transform the original non-Markovian problem into a Markovian one by introducing a mean reaction propensity function for every reaction in the network. Furthermore, we derive a stationary generalized linear noise approximation for the non-Markovian system, which is convenient to the direct estimation of the stationary noise in state variables. These derived equations can have broad applications, and exemplars of two representative non-Markovian models provide evidence of their applicability.

systems biology↗

bioRxiv2018

NudCL2 is an Hsp90 cochaperone to regulate sister chromatid cohesion by stabilizing cohesin subunits

Sister chromatid cohesion plays a key role in ensuring precise chromosome segregation during mitosis, which is mediated by the multisubunit complex cohesin. However, the molecular regulation of cohesin subunits stability remains unclear. Here, we show that NudCL2 (NudC-like protein 2) is essential for the stability of cohesin subunits by regulating Hsp90 ATPase activity in mammalian cells. Depletion of NudCL2 induces mitotic defects and premature sister chromatid separation and destabilizes cohesin subunits that interact with NudCL2. Similar defects are also observed upon inhibition of Hsp90 ATPase activity. Interestingly, ectopic expression of Hsp90 efficiently rescues the protein instability and functional deficiency of cohesin induced by NudCL2 depletion, but not vice versa. Moreover, NudCL2 not only binds to Hsp90, but also significantly modulates Hsp90 ATPase activity and promotes the chaperone function of Hsp90. Taken together, these data suggest that NudCL2 is a previously undescribed Hsp90 cochaperone to modulate sister chromatid cohesion by stabilizing cohesin subunits, providing a hitherto unrecognized mechanism that is crucial for faithful chromosome segregation during mitosis.

cell biology↗

bioRxiv2018

Structural survey of HIV-1-neutralizing antibodies targeting Env trimer delineates epitope categories and suggests vaccine templates

HIV-1 broadly neutralizing antibodies are desired for their therapeutic potential and as templates for vaccine design. Such antibodies target the HIV-1-envelope (Env) trimer, which is shielded from immune recognition by extraordinary glycosylation and sequence variability. Recognition by broadly neutralizing antibodies thus provides insight into how antibody can bypass these immune-evasion mechanisms. Remarkably, antibodies neutralizing >25% of HIV-1 strains have now been identified that recognize all major exposed surfaces of the prefusion-closed Env trimer. Here we analyzed all 206 broadly neutralizing antibody-HIV-1 Env complexes in the PDB with resolution suitable to define their interaction chemistries. These segregated into 20 antibody classes based on ontogeny and recognition, and into 6 epitope categories (V1V2, glycan-V3, CD4-binding site, silent face center, fusion peptide, and subunit interface) based on recognized Env residues. We measured antibody neutralization on a 208-isolate panel and analyzed features of paratope and B cell ontogeny. The number of protruding loops, CDR H3 length, and level of somatic hypermutation for broadly HIV-1 neutralizing antibodies were significantly higher than for a comparison set of non-HIV-1 antibodies. For epitope, the number of independent sequence segments was higher (P < 0.0001), as well as the glycan component surface area (P = 0.0005). Based on B cell ontogeny, paratope, and breadth, the CD4-binding site antibody IOMA appeared to be a promising candidate for lineage-based vaccine design. In terms of epitope-based vaccine design, antibody VRC34.01 had few epitope segments, low epitope-glycan content, and high epitope-conformational variability, which may explain why VRC34.01-based design is yielding promising vaccine results.

bioinformatics↗

bioRxiv2018

Epitope-based vaccine design yields fusion peptide-directed antibodies that neutralize diverse strains of HIV-1

A central goal of HIV-1-vaccine research is the elicitation of antibodies capable of neutralizing diverse primary isolates of HIV-1. Here we show that focusing the immune response to exposed N-terminal residues of the fusion peptide, a critical component of the viral entry machinery and the epitope of antibodies elicited by HIV-1 infection, through immunization with fusion peptide-coupled carriers and prefusion-stabilized envelope trimers, induces cross-clade neutralizing responses. In mice, these immunogens elicited monoclonal antibodies capable of neutralizing up to 31% of a cross-clade panel of 208 HIV-1 strains. Crystal and cryo-electron microscopy structures of these antibodies revealed fusion peptide-conformational diversity as a molecular explanation for the cross-clade neutralization. Immunization of guinea pigs and rhesus macaques induced similarly broad fusion peptide-directed neutralizing responses suggesting translatability. The N terminus of the HIV-1-fusion peptide is thus a promising target of vaccine efforts aimed at eliciting broadly neutralizing antibodies.

immunology↗

bioRxiv2018

Congenital glaucoma with anterior segment dysgenesis in individuals with biallelic CPAMD8 variants

PurposeCongenital glaucoma is a significant cause of irreversible blindness. In some instances glaucoma is associated with developmental abnormalities of the ocular anterior segment, which can impair drainage of aqueous humor, leading to an increase in intraocular pressure.\n\nMethodsGenome sequencing was performed on a parent-proband congenital glaucoma trio, with exome sequencing of 79 additional individuals with suspected primary congenital glaucoma.\n\nResultsWe describe a unique ocular anterior segment dysgenesis associated with congenital glaucoma in four individuals from three unrelated families. In each case, disease was associated with compound heterozygous variants in CPAMD8, a gene of unknown function recently associated with ocular anterior segment dysgenesis, myopia, and ectopia lentis. CPAMD8 expression was highest in neural crest-derived tissues of the adult anterior segment, suggesting that CPAMD8 variation may cause malformation of key drainage structures and the development of high intraocular pressure and glaucoma.\n\nConclusionsThis study reveals a unique genetic cause of childhood glaucoma, and expands the phenotypic spectrum of CPAMD8-associated ocular disease.

genetics↗

bioRxiv2018

SPORTS1.0: a tool for annotating and profiling non-coding RNAs optimized for rRNA- and tRNA- derived small RNAs

High-throughput RNA-seq has revolutionized the process of small RNA (sRNA) discovery, leading to a rapid expansion of sRNA categories. In addition to the previously well-characterized sRNAs such as microRNAs (miRNAs), Piwi-interacting RNA (piRNAs), and small nucleolar RNA (snoRNAs), recent emerging studies have spotlighted on tRNA-derived sRNAs (tsRNAs) and rRNA-derived sRNAs (rsRNAs) as new categories of sRNAs that bear versatile functions. Since existing software and pipelines for sRNA annotation are mostly focused on analyzing miRNAs or piRNAs, here we developed the sRNA annotation pipeline optimized for rRNA- and tRNA- derived sRNAs (SPORTS1.0). SPORTS1.0 is optimized for analyzing tsRNAs and rsRNAs from sRNA-seq data, in addition to its capacity to annotate canonical sRNAs such as miRNAs and piRNAs. Moreover, SPORTS1.0 can predict potential RNA modification sites based on nucleotide mismatches within sRNAs. SPORTS1.0 is precompiled to annotate sRNAs for a wide range of 68 species across bacteria, yeast, plant, and animal kingdoms, while additional species for analyses could be readily expanded upon end users input. For demonstration, by analyzing sRNA datasets using SPORTS1.0, we reveal that distinct signatures are present in tsRNAs and rsRNAs from different mouse cell types. We also find that compared to other sRNA species, tsRNAs bear the highest mismatch rate which is consistent with their highly modified nature. SPORTS1.0 is an open-source software and can be publically accessed at https://github.com/junchaoshi/sports1.0.

bioinformatics↗