Biology subjects

He, H.

Publications and source records attributed to He, H..

At least 163 records · Page 9Linked to original sources

bioRxiv2020

Thioproline formation as a driver of formaldehyde toxicity in Escherichia coli

Formaldehyde (HCHO) is a reactive carbonyl compound that formylates and cross-links proteins, DNA, and small molecules. It is of specific concern as a toxic intermediate in the design of engineered pathways involving methanol oxidation or formate reduction. The high interest in engineering these pathways is not, however, matched by engineering-relevant information on precisely why HCHO is toxic or on what damage-control mechanisms cells deploy to manage HCHO toxicity. The only well-defined mechanism for managing HCHO toxicity is formaldehyde dehydrogenase-mediated oxidation to formate, which is counterproductive if HCHO is a desired pathway intermediate. We therefore sought alternative HCHO damage-control mechanisms via comparative genomic analysis. This analysis associated homologs of the Escherichia coli pepP gene with HCHO-related one-carbon metabolism. Furthermore, deleting pepP increased the sensitivity of E. coli to supplied HCHO but not other carbonyl compounds. PepP is a proline aminopeptidase that cleaves peptides of the general formula X-Pro-Y, yielding X + Pro-Y. HCHO is known to react spontaneously with cysteine to form the close proline analog thioproline (thiazolidine-4-carboxylate), which is incorporated into proteins and hence into proteolytic peptides. We therefore hypothesized that thioproline-containing peptides are toxic and that PepP cleaves these aberrant peptides. Supporting this hypothesis, PepP cleaved the model peptide Ala-thioproline-Ala as efficiently as Ala-Pro-Ala in vitro and in vivo, and deleting pepP increased sensitivity to supplied thioproline. Our data thus (i) provide biochemical genetic evidence that thioproline formation contributes substantially to HCHO toxicity and (ii) make PepP a candidate damage-control enzyme for engineered pathways having HCHO as an intermediate.

biochemistry↗

bioRxiv2020

Calculation of fungal and bacterial inorganic nitrogen immobilization rates in soil

Microbial inorganic nitrogen (N) immobilization is an important mechanism in the retention of N in soils. However, as a result of the high diversity and complexity of soil microorganisms, there is still no effective approach to measuring the respective immobilization rates of inorganic N by fungi and bacteria, which are the two dominant microbial communities in soils. We propose a mathematical framework, combining the experimentally measurable gross inorganic N immobilization rate and proxies for fungal and bacterial inorganic N immobilization rates, to quantify the respective immobilization rates of inorganic N by fungal and bacterial communities in soil. Our approach will help to unravel the mechanisms of N retention in soils.Competing Interest StatementThe authors have declared no competing interest.View Full Text

microbiology↗

bioRxiv2020

Altered Sensorimotor-to-Transmodal Hierarchical Organization in Schizophrenia

For decades, schizophrenia has been primarily conceptualized as a disorder of high-order cognitive functions with deficits in executive brain regions. Yet due to the increasing reports of early sensory processing deficit, recent models focus more on the developmental effects of impaired sensory process on high-order functions. The present study examined whether this pathological interaction relates to an overarching system-level imbalance, specifically a disruption in macroscale hierarchy affecting integration and segregation of unimodal and transmodal networks. We applied a novel combination of connectome gradient and stepwise connectivity analysis to resting-state functional magnetic resonance imaging (rsfMRI) to characterize the sensorimotor-to-transmodal cortical hierarchy organization (96 patients vs. 122 controls). Using these techniques, we demonstrated compression of the cortical hierarchy organization in schizophrenia, with a prominent compression from the sensorimotor region and a less prominent compression from the frontal-parietal region, resulting in a diminished separation between sensory and fronto-parietal cognitive systems. Further analyses suggested reduced differentiation related to atypical functional connectome transition from unimodal to transmodal brain areas. Specifically, we found hypo-connectivity within unimodal regions and hyper-connectivity between unimodal regions and frontoparietal and ventral attention regions along the classical sensation-to-cognition continuum established in prior neuroanatomical work. The compression of cortical hierarchy organization represents a novel and integrative system-level substrate underlying the pathological interaction of early sensory and cognitive function in schizophrenia. This abnormal cortical hierarchy organization suggests cascaded impairments stemming from the disrupted somatosensory-motor system and inefficient integration of bottom-up sensory information with attentional demands and executive control processes partially account for high-level cognitive deficits characteristic of schizophrenia.

neuroscience↗

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

The structures of natively assembled clathrin coated vesicles

Vesicle trafficking by clathrin coated vesicles (CCVs) is one of the major mechanisms by which proteins and nutrients are absorbed by the cell and transported between organelles. The individual proteins comprising the coated vesicles include clathrin heavy chain, clathrin light chain, and a variety of adaptor protein complexes. Much is known about the structures of the individual CCV components, but data are lacking about the structures of the fully assembled complexes together with membrane and in complex with cargo. Here we determined the structures of natively assembled CCVs in a variety of geometries. We show that the adaptor {beta}2-appendages crosslink adjacent CHC {beta}-propellers and that the appendage densities reside almost exclusively in CCV hexagonal faces. We resolve how AP2 and other associated factors in hexagonal faces form an assembly hub with an extensive web of interactions between neighboring {beta}-propellers and propose a structural model that explains how adaptor binding can direct the formation of pentagonal and hexagonal faces.

biophysics↗

bioRxiv2019

Neural Encoding for Human Visual Cortex with Deep Neural Networks Learning "What" and "Where"

Neural encoding, a crucial aspect to understand human brain information processing system, aims to establish a quantitative relationship between the stimuli and the evoked brain activities. In the field of visual neuroscience, with the ability to explain how neurons in primary visual cortex work, population receptive field (pRF) models have enjoyed high popularity and made reliable progress in recent years. However, existing models rely on either the inflexible prior assumptions about pRF or the clumsy parameter estimation methods, severely limiting the expressiveness and interpretability. In this paper, we propose a novel neural encoding framework by learning "what" and "where" with deep neural networks. The modeling approach involves two separate aspects: the spatial characteristic ("where") and feature selection ("what") of neuron populations in visual cortex. Specifically, we use the receptive field estimation and multiple features regression to learn these two aspects respectively, which are implemented simultaneously in a deep neural network. The two forms of regularizations: sparsity and smoothness, are also adopted in our modeling approach, so that the receptive field can be estimated automatically without prior assumptions about shapes. Furthermore, an attempt is made to extend the voxel-wise modeling approach to multi-voxel joint encoding models, and we show that it is conducive to rescuing voxels with poor signal-to-noise characteristics. Extensive empirical results demonstrate that the method developed herein provides an effective strategy to establish neural encoding for human visual cortex, with the weaker prior constraints but the higher encoding performance. Author summaryCharacterizing the quantitative relationship between the stimuli and the evoked brain activities usually involves learning the spatial characteristic ("where") and feature selection ("what") of neuron populations. As an effective strategy, we propose a novel end-to-end "what" and "where" architecture to perform neural encoding. The proposed modeling approach consists of receptive field estimation and multiple features regression, which learns "where" and "what" simultaneously in a deep neural network. Different from previous methods, we use the sparsity and smoothness regularizations in the deep neural network to guide the receptive field estimation, so that the receptive field for each voxel can be estimated automatically. Moreover, in consideration of computational similarities between adjacent voxels, we made an attempt to extend the proposed modeling approach to multi-voxel joint encoding models, improving the encoding performance of voxels with poor signal-to-noise characteristics. Empirical evaluations show that the proposed method outperforms other baselines to achieve the state-of-the-art performance.

neuroscience↗

bioRxiv2019

Characterization of Isoforms of the Ovine Granulocyte Colony Stimulating Factor

The granulocyte colony-stimulating factor (GCSF) regulates the maturation, proliferation, and differentiation of precursor cells of neutrophilic granulocytes, and has been widely studied in several species. To investigate the function of variants of sheep GCSF (sGCSF), this study compared difference in their mRNA expression levels. Both the activity and mRNA expression level of GCSFv2 were higher than those of GCSFv1. Their sequences were aligned, which showed that they had the highest homology with bovine GCSF. Then, predicted ovine GCSF isoforms and their constant C-terminals were cloned and expressed, which were stably expressed in mammalian cells. After purification, all GCSF functions were different both in vitro and in vivo, and the GCSF C-terminal was best. These results indicated that the ability to stimulate both the proliferation and differentiation of progenitor cells and to activate the maturation of neutrophils could be used for research of efficacious non-antibiotic protein drugs. Furthermore, GCSF can be used as candidate target of genetic breeding to specifically improve sheep immunity.

genetics↗

bioRxiv2019

Proprioception is subject-specific and improved without performance feedback

Accumulating evidence indicates that the humans proprioception map appears subject-specific. However, whether the idiosyncratic pattern persists across time with good within-subject consistency has not been quantitatively examined. Here we measured the proprioception by a hand visual-matching task in multiple sessions over two days. We found that people improved their proprioception when tested repetitively without performance feedback. Importantly, despite the reduction of average error, the spatial pattern of proprioception errors remained idiosyncratic. Based on individuals proprioceptive performance, a standard convolutional neural network classifier could identify people with good accuracy. We also found that subjects baseline proprioceptive performance could not predict their motor performance in a visual trajectory-matching task even though both tasks require accurate mapping of hand position to visual targets in the same workspace. Using a separate experiment, we not only replicated these findings but also ruled out the possibility that performance feedback during a few familiarization trials caused the observed improvement in proprioception. We conclude that the conventional proprioception test itself, even without feedback, can improve proprioception but leave the idiosyncrasy of proprioception unchanged.

neuroscience↗

bioRxiv2019

Function of ex vivo stimulated Natural killer T cells from patients with chronic HIV-1 infection

Natural killer T (NKT) cells are innate immune cells that are responsible for the first line of antiviral defense, through crosstalk with downstream antigen-presenting cells, natural killer cells, and adaptive immune cells. Previous studies have indicated that NKT cell function is severely impaired in patients with chronic HIV-1 infection. It was reported that alpha-galactosylceramide, a potent agonist antigen for NKT cells, failed to trigger the expansion of NKT cells, or the production of anti-viral cytokines by NKT cells from HIV-1 infected patients in an in vitro assay, in which peripheral blood mononuclear cells (PBMCs) were cultured in the presence of alpha-galactosylceramide. In this study, we stimulated banked peripheral blood mononuclear cells from HIV-1-infected patients with dendritic cells (DC) generated ex vivo and loaded with alpha-galactosylceramide. The results showed that NKT cells were expanded in HIV infected subjects except in patients with advanced AIDS. Expanded NKT cells were capable of producing antiviral cytokines. Our results indicate that NKT cells in HIV infected individuals are potential targets for therapeutic intervention.

immunology↗

bioRxiv2019

Low-disturbance farming regenerates healthy critical zone towards sustainable agriculture

Intensive conventional farming has degraded farmland topsoil and seriously threaten food and environment security globally. Although low-disturbance practices have been widely adapted to restore soil health, whether this measure in a long run can potentially recover the critical deep soil to meet sustainable intensification of crop production are still unclear. Here we compared soil microbiome, physicochemical parameters along 3-m deep soil profiles, and crop yield in Northeast China subjected to ten years of farming practices at 3 levels of disturbance, including conventional tillage (CT), no-tillage without stover mulching (NTNS), and no-tillage with stover mulching (NTSM). We found that low-disturbance practices (NTNS and NTSM) promoted the ability of the deep soil to retain water, nitrogen and salt-extractable organic, regenerated whole-soil microbial diversity and metabolic function, improved topsoil organic carbon stock and corn yield in the drought year, showed the potential to reduce energy consumption and greenhouse gas emissions, thus regenerating highly efficient, sustainable agriculture.

ecology↗

bioRxiv2019

Model reconstruction from Small angle X-ray Scattering data using deep learning methods

We present an algorithm based on a deep learning method for model reconstruction from small angle X-ray scattering (SAXS) data. An auto-encoder for protein 3D models was trained to compress 3D shape information into vectors of a 200-dimensional latent space, and the vectors are optimized using genetic algorithms to build 3D models that are consistent with the scattering data. The algorithm was implemented using Python with the TensorFlow framework and tested with experimental data, demonstrating capacity and robustness of accurate model reconstruction even without using prior model size information.\n\nSynopsisA deep learning method based on the auto-encoder framework for model reconstruction from small angle scattering data

bioinformatics↗

bioRxiv2019

Targeting the Cx43 Carboxyl Terminal H2 Domain Preserves Left Ventricular Function Following Ischemia-Reperfusion Injury

BackgroundCT1 is a 25 amino acid therapeutic peptide incorporating the Zonula Occludens-1 (ZO-1)-binding domain of connexin43 (Cx43) that is currently in Phase III clinical testing for healing chronic skin wounds. In preclinical studies in mice, we reported that CT1 reduces arrhythmias and improves ventricular function following cardiac injury, effects that were accompanied by increases in PKC{varepsilon} phosphorylation of Cx43 at serine 368 (pS368). In this study, we undertake a systematic characterization of the molecular mode-of-action of CT1 in mitigating the effects of ischemia reperfusion injury on ventricular contractile function.\n\nMethods and ResultsTo determine the basis of CT1-mediated increases in pS368 we undertook tandem mass spectrometry of reactants in an in vitro assay of PKC{varepsilon} phosphorylation, identifying an interaction between negatively charged amino acids in the CT1 Asp-Asp-Leu-Glu-Iso sequence and positively charged lysines (Lys345, Lys346) in a short -helical sequence (H2) within the Cx43 CT domain. In silico modeling provided further support of the specificity of this interaction, leading us to conclude that CT1 has potential to directly interact with both Cx43 and ZO-1. Using surface plasmon resonance, thermal shift and phosphorylation assays, we characterized a series of CT1 variant peptides, identifying sequences competent to interact with either ZO-1 PDZ2 or the Cx43 CT, but with limited or no ability to bind both polypeptides. Based on this analysis, it was found that only those peptides competent to interact with Cx43, but not ZO-1 alone, resulted in increased pS368 phosphorylation in vitro and in vivo. Moreover, in a mouse model of global ischemia reperfusion injury we determined that pre-ischemic infusion only with those peptides competent to bind Cx43 preserved left ventricular (LV) contractile function following injury. Interestingly, a short 9 amino acid (MW=1110) Cx43-binding variant of the original 25 amino acid CT1 sequence demonstrated potent LV-protecting effects when infused either before or after ischemic injury.\n\nConclusionsInteraction of CT1 with the Cx43 CT, but not ZO-1 PDZ2, explains cardioprotection mediated by this therapeutic peptide. Pharmacophores targeting the Cx43 carboxyl terminus could provide a novel translational approach to preservation of ventricular function following ischemic injury.

cell biology↗

bioRxiv2019

Probing apoptosis signaling proteins in single living cells for precision efficacy evaluation of anti-cancer drugs

In vitro efficacy evaluation is critical for anti-cancer drug development and precision cancer treatment. Conventional methods, which mainly rely on cell viability and large cell populations, suffer from apparent disadvantages, such as signaling pathway-nonspecific, failing to reflect the real sensitivity of the patient, tedious and time-consuming. Herein, we present a new analytical tool, termed single-cell plasmonic immunosandwich assay (scPISA), for precision efficacy evaluation of anti-cancer drugs. It allows for facilely probing individual signaling proteins as well as protein-protein complexes in single living cells. Based on this approach, two apoptosis signaling proteins, cytochrome C (Cyt C) and caspase-3, were proposed as apoptosis indicators, while three new parameters were proposed as criteria for quantitative efficacy evaluation. Using two typical cytotoxic drugs, actinomycin D (Act D) and staurosporine (STS), as model drugs, the evaluation was found to be consistent among the indicators and parameters. Metformin, a potential anti-cancer drug, was then evaluated using this approach. Interestingly, metformin alone was found to be a less effective anti-cancer drug but its combination with Act D dramatically improved the overall efficacy. The scPISA approach exhibited several unique strengths over conventional assays, including comprehensive and self-consistent evaluation, signaling pathway-specific, simple procedure and high speed. Thus, it holds great promise for personalized drug screening and precision medicine.

cancer biology↗

bioRxiv2019

Keratin-Based Epidermal Green Autofluorescence is a Common Biomarker of Organ Injury

It is critical to discover biomarkers for non-invasive evaluation of the levels of inflammation and oxidative stress in human body - two key pathological factors in numerous diseases. Our study has indicated keratin 1-based epidermal autofluorescence (AF) as a biomarker of this type: Inducers of both inflammation and oxidative stress dose-dependently increased epidermal green AF with polyhedral structure in mice, with the AF intensity being highly associated with the dosages of the inducers. Lung cancer also induced increased epidermal green AF of mice, which was mediated by inflammation. Significant and asymmetrical increases in green AF intensity with polyhedral structure were found in the Dorsal Index Fingers skin of acute ischemic stroke (AIS) patients. While the AF intensity of the subjects with high risk for developing AIS, ischemic stroke patients in recovery phase and lung cancer patients was significantly higher than that of healthy controls, both AF intensity and AF asymmetry of these four groups were markedly lower than those of the AIS patients, which have shown promise for AIS diagnosis. Several lines of evidence have indicated K1 as an origin of the AF, e.g., K1 siRNA administration attenuated the oxidative stress-induced AF increase of mice. Collectively, our study has indicated K1-based epidermal AF as a biomarker for non-invasive evaluation of the levels of inflammation and oxidative stress in the body. These findings have established a basis for novel keratins AF-based biomedical imaging technology for non-invasive, efficient and economic diagnosis and screening of such inflammation- and oxidative stress-associated diseases as AIS.

biophysics↗

bioRxiv2019

Novel risk genes and mechanisms implicated by exome sequencing of 2,572 individuals with pulmonary arterial hypertension

Group 1 pulmonary arterial hypertension (PAH) is a rare disease with high mortality despite recent therapeutic advances. Pathogenic remodeling of pulmonary arterioles leads to increased pulmonary pressures, right ventricular hypertrophy and heart failure. Mutations in bone morphogenetic protein receptor type 2 and other risk genes predispose to disease, but the vast majority of non-familial cases remain genetically undefined. To identify new risk genes, we performed exome sequencing in a large cohort from the National Biological Sample and Data Repository for PAH. By statistical association of rare deleterious variants, we found tissue kallikrein 1 and gamma glutamyl carboxylase as new candidate risk genes for idiopathic PAH associated with a later age-of-onset and relatively moderate disease phenotype compared to bone morphogenetic receptor type 2. Both genes play important roles in vascular hemodynamics and inflammation but have not been implicated in PAH previously. These data suggest new genes, pathogenic mechanisms and therapeutic targets for this lethal vasculopathy.

genetics↗

bioRxiv2019

Primary Studies on the Effect of Microbially Coalbed Methane Enhancement in Suit in the Qinshui Basin

Methods used to yield bio-methane with coal to increase coalbed methane reserves had researched, thus providing a means for improving gas drainage efficiency. One such method utilized to convert coal into gas involves coal biodegradation technology. In order to confirm the practical application of this technology, the experiments were conducted in wells, Z-159, Z-163, Z-167, and Z-7H, in the Qinshui Basin in China, and the duration of the experiments was 32 months. Cl- ion tracer, number changes of Methanogen sp., and coal bed biome evolution indicated that the culture medium diffused in the Z-159 and Z-7H wells. These wells resumed gas production separately. Gasification of coal lasted 635 and 799 days, and yielded 74817 m3 and 251754 m3 coalbed methane in Z-159 and Z-7H wells, respectively. Results demonstrate that coalbed methane enhancement with biogasification of coal is a potential technical to achieve the productivity improvement of coalbed methane wells.

bioengineering↗

bioRxiv2018

The landscapes of DNA methylation associated with the transcriptomic network in laying hens and broilers get insight to embryonic muscle development in chicken

As DNA methylation is one of the key epigenetic mechanisms involved in embryonic development, elucidating its relationship with non-coding RNA and genes is essential for understanding early development. In this study, we performed single-base-resolution bisulfite sequencing together with RNA-seq to explore the genetic basis of embryonic muscle development in chicken. Comparison of methylome profiles between broilers and laying hens revealed that lower methylation in broilers might contribute to muscle development. Differential methylated region (DMR) analysis between two chicken lines showed that the majority of DMRs were hypo-DMRs for broilers. Differential methylated genes were significantly enriched in muscle development-related terms at E13 and E19. Furthermore, by constructing the network of the lncRNAs, we identified a lncRNA, which we named MYH1-AS, that potentially regulated muscle development. These findings reveal an integrative landscape of late period of embryonic myogenesis in chicken and give rise to a comprehensive understanding of epigenetic and transcriptional regulation, in skeletal muscle development. Our study provides a reliable data resource for further muscle studies.

bioinformatics↗

bioRxiv2018

The LIM-Only Protein FHL2 is Involved in Autophagy to Regulate the Development of Skeletal Muscle

Four and a half LIM domain protein 2 (FHL2) is a LIM domain protein expressed in muscle tissue whose deletion is causative of myopathies. Although FHL2 has a confirmed important role in muscle development, its autophagy-related function in muscle differentiation has not been fully determined. To explore the role of FHL2 in autophagy-related muscle regulation, FHL2-silenced and -overexpressing C2C12 mouse cells were examined. Immunofluorescence and co-immunoprecipitation assay findings showed that FHL2 silencing reduced LC3- protein expression and the amount of LC3 that co-immunoprecipitated with FHL2, indicating that FHL2 interacts with LC3- in the formation of autophagosomes. Moreover, the expression of muscle development marker genes such as MyoD1 and MyoG was lower in FHL2-silenced C2C12 cells but not in FHL2-overexpressing C2C12 cells. Electron microscopy analysis revealed large empty autophagosomes in FHL2-silenced myoblasts, while flow cytometry suggested that FHL2 silencing made cells more vulnerable to staurosporine-induced cell death. In conclusion, we propose that FHL2 interacts with LC3- in autophagosome formation to regulate the development of muscle cells.

molecular biology↗