Biology subjects

Zhang, M.

Publications and source records attributed to Zhang, M..

At least 703 records · Page 39Linked to original sources

bioRxiv2020

HDAC6 regulates radiosensitivity of non-small cell lung cancer by promoting degradation of Chk1

We previously discovered that HDAC6 regulates the DNA damage response via modulating the homeostasis of a DNA mismatch repair protein, MSH2, through HDAC6s ubiquitin E3 ligase activity. Here, we have reported HDAC6s second E3 ligase substrate, a critical cell cycle checkpoint protein, Chk1. We have found that HDAC6 and Chk1 directly interact, and that HDAC6 ubiquitinates Chk1 in vivo. Typical Chk1 protein levels fluctuate, peaking at G2 and subsequently resolving via the ubiquitin-proteasome pathway. However, in HDAC6 knockdown cells, Chk1 is constitutively active and fails to resolve post-ionizing radiation (IR), leading to increased radiation sensitivity. Upon IR treatment, a greater proportion of HDAC6 knockdown cells accumulated at G2/M phase when compared with control cells. Depletion or inhibition of Chk1 in HDAC6 knockdown cells renders those cells radiosensitive, suggesting that persistently high level of Chk1 could lead cells to arrest at G2/M phase and eventually, apoptosis. Clinically, we found that high levels of phosphorylated Chk1 (p-Ser317) are associated with a better overall survival in a cohort of non-small cell lung cancer (NSCLC) patients, suggesting a link between active Chk1 and lung cancer development. Overall, our results highlight a novel mechanism of Chk1 regulation at the protein level, and a possible strategy for sensitizing NSCLC to radiation via inhibiting the activity of HDAC6s E3 ligase.

molecular biology↗

bioRxiv2020

MiRNAs profiling and degradome sequencing between the CMS-line N816S and its maintainer line Ning5m during anther development in pepper (Capsicum annuum L.)

Utilization of cytoplasmic male sterility (CMS) is significant for agriculture. MiRNAs are a class of endogenously non-coding small RNAs (21-24 nt) that play key roles in the regulation of various growth and developmental processes in plants. The knowledge miRNA-guided CMS regulation is rather limited in pepper. To better understand the miRNAs involvement and regulatory mechanism of CMS, miRNA libraries from anther of CMS-line N816S and its maintainer line Ning5m were generated by miRNAome sequencing in pepper. A total of 76 differentially expressed miRNAs were detected, of which 18 miRNAs were further confirmed by quantitative real-time PCR (qRT-PCR). In addition, miRNA targets were identified by degradome sequencing. The result showed that 1292 targets that were potentially cleaved by 321 miRNAs (250 conserved miRNAs and 71 novel miRNAs). Gene Ontology (GO) and KEGG pathway analysis indicated that 35 differentially expressed miRNAs might play roles in the regulation of CMS sterility, by cleaving 77 target transcripts, such as MYBs, SPLs, and AFRs, of which targeted by miR156, miR167, miRNA858 family. Nineteen miRNA-cleaved targets were selectively examined by qRT-PCR, and the results showed that there were mostly negative correlations between miRNAs and their targets on the expression level. These findings provide a valuable information to understand miRNAs mechanism during anther development and CMS occurrence in pepper.

plant biology↗

bioRxiv2020

Transposase assisted tagmentation of RNA/DNA hybrid duplexes

Tn5-mediated transposition of double-strand DNA has been widely utilized in various high-throughput sequencing applications. Here, we report that the Tn5 transposase is also capable of direct tagmentation of RNA/DNA hybrids in vitro. As a proof-of-concept application, we utilized this activity to replace the traditional library construction procedure of RNA sequencing, which contains many laborious and time-consuming processes. Results of activity of transposase assisted RNA/DNA hybrids co-tagmentation (termed "ATRAC-seq") are comparable to traditional RNA-seq methods in terms of gene number, gene body coverage and gene expression analysis; at the meantime, ATRAC-seq enables a one-tube library construction protocol and hence is more rapid (within 8 h) and convenient. We expect this tagmentation activity on RNA/DNA hybrids to have broad potentials on RNA biology and chromatin research.

genomics↗

bioRxiv2020

Integrated Analysis of Methylome and Transcriptome Following Developmental Atrazine Exposure in Zebrafish Reveals Aberrant Gene-Specific Methylation of Neuroendocrine and Reproductive Pathways

Atrazine (ATZ) is one of the most commonly used herbicides in the United States. Previous studies have hypothesized the role of ATZ as an endocrine disruptor (EDC), and developmental exposure to ATZ has been shown to lead to behavioral and morphological alterations. Specific epigenetic mechanisms responsible for these alterations, however, are yet to be elucidated. In this study, we exposed zebrafish embryos to 0.3, 3, and 30 ppb ({micro}g/L) of ATZ for 72 hours post fertilization. We performed whole-genome bisulfite sequencing (WGBS) to assess the effects of developmental ATZ exposure on DNA methylation in female fish brains. The number of differentially methylated genes (DMG) increase with increasing dose of treatments. DMGs are enriched in neurological pathways with extensive methylation changes consistently observed in neuroendocrine and reproductive pathways. To assess the effects of DNA methylation on gene expression, we integrated our data with transcriptomic data. Four genes, namely CHD9, FRAS1, PID1, and PCLO, were differentially expressed and methylated in each dose. Overall, this study identifies specific genes and pathways with aberrant methylation and expression following ATZ exposure as targets to elucidate the molecular mechanisms of ATZ toxicity and presents ATZ-induced site-specific DNA methylation as a potential mechanism driving aberrant gene expression.

pharmacology and toxicology↗

bioRxiv2020

Accurate CNV identification from only a few cells with low GC bias in a single-molecule sequencing platform

A technical problem of characterizing copy number variation of several cells with next-generation sequencing is the whole genome amplification induced bias. The result of CNVs and mosaicism detection is affected by the GC bias. Here, we report a rapid non-WGA sample preparation strategy for a single-molecule sequencing platform GenoCare1600. This approach, combined with a single-molecule sequencing platform that avoids the use of WGA and bridge PCR processes, can provide higher reliability with its lower GC bias. By combining our optimized Tn5-based transposon insertion approach with GenoCare, we successfully detected CNVs as small as 1.29M and mosaicism as small as 20%, which is consistent with next-generation sequencing (NGS) data. Moreover, our GenoCare-TTI protocol showed less GC bias and less Mad of Diff. These results suggest that the optimized TTI approach, together with the GenoCare1600 sequencing platform, is a promising option for CNV characterization from maybe one single cell.

genetics↗

bioRxiv2020

Three genomes of Osteoglossidae shed light on ancient teleost evolution

Osteoglossiformes is a basal clade of teleost, originated from late Jurassic and had seen the process of continental drift. The genomic differences amongst Osteoglossiformes species should reflect the unique evolve history of that time. Here, we presented the chromosome-level genome of Heterotis niloticus which is the only omnivore species of Osteoglossidae spreading in Africa. Together with other two Osteoglossidae species genomes of Arapaima gigas and Scleropages formosus which spread in South America and Australia respectively, we found great evolutionary differences in gene families and transposable elements. Phylogenetic analysis showed that the ancestor of H. niloticus and A. gigas diverged with S. formosus at [~]106.1Mya, consistent with the time of Afro-South American drift and A. gigas speciated from the ancestor of H. niloticus and A. gigas at [~]59.2 Mya, consistent with the separation of Eurasia and North American continents. And we proposed the evolutionary traces of Osteoglossidae species based on comparative genomics analysis and their living geographic habitats. We identified loss of LINEs and LTRs, fast evolutionary rate in parallel to fast pseudogenization rate in H. niloticus and A. gigas comparing to S. formosus during the evolutionary process. We also found notable OR genes contraction in H. niloticus, which might be related to the diet transition. Taken together, we reconstructed the evolutionary process of Osteoglossidae using three representative genomes, providing a possible clue for biogeographic and evolution study of ancient teleost clade.

genomics↗

bioRxiv2020

In vitro activities of the tetrazole SHR8008 compared to itraconazole and fluconazole against Candida and Cryptococcus species

Candida and Cryptococcus are the main pathogens of clinical fungal infection associated with high morbidity and mortality. SHR8008 (in fact, this is the only official name in China and it is called VT-1161 by FDA) is a novel tetrazole agent that selectively inhibits fungal CYP51A compared to mammalian cytochrome P450 enzymes to achieve a better antifungal effect. The in vitro activities of SHR8008 and its comparators itraconazole and fluconazole were determined in 127 Candida and 50 Cryptococcus strains isolated from Chinese patients in the last 2 years by Invasive Fungal Infection Group. The MICs of SHR8008 and other triazoles were measured by the Clinical and Laboratory Standards Institute guidelines M27-E4. For Candida spp., SHR8008 (geometric mean MIC=0.078 g/mL) was 6.5-fold and 11.2-fold more potent than itraconazole and fluconazole, respectively. There is a good correlation of MICs between SHR8008 and itraconazole/fluconazole. The MIC values of SHR8008 against Candida glabrata and Candida tropicalis were significantly lower than those of fluconazole, while for Candida albicans and Candida parapsilosis, the differences between SHR8008 and fluconazole were not statistically significant, either. For Cryptococcus spp., SHR8008 (geometric mean MIC=0.024 g/mL) was 21.7-fold and 104.5-fold more potent than itraconazole and fluconazole, respectively. Against the seven Cryptococcus neoformans isolates with elevated fluconazole MICs ([≥]8g/mL based on the MIC90 value for this azole), SHR8008 maintained potent activity, with MICs ranging between 0.031 and 0.5 g/mL. The results showed that tetrazole SHR8008 was more promising in the treatment of Candida and Cryptococcus infection than itraconazole and fluconazole.

microbiology↗

bioRxiv2020

Diversified Learning Environment Alleviates Learning Impairment Caused by Contextual Stress

Environment is capable of affecting our learning ability. Existing studies reported that learning ability can be enhanced by enriched environment and impaired by stressful context. However, it is still unclear whether diversified environment can reverse or ameliorate the learning difficulty caused by stressful context. In this study, several behavioral tasks were designed to test the role of diversified environment in active avoidance learning. In the present study, sound-cued active avoidance (two-way shuttle box) acted as learning paradigm. Multiple shuttle boxes with the identical size but different designs were employed to mimic diversified environment in learning tasks. Mild but inevitable foot shocking was adopted to increase animals stress to certain context. To quantify the depression/anxiety level of animals, open field test, forced swimming test, light-dark box test, and elevated plus maze were performed. The following findings were reported. First, diversified learning environment could improve learning ability in active avoidance, as manifested by higher successful rate and sharper learning curve. Second, elevating the stress level of animal to a certain context could noticeably reduce its performance in active avoidance learning. Third, the learning impairment attributed to stressful context can be improved by training in diversified environments. Thus, as revealed from the results, learning impairment caused by stressful context can be alleviated by diversified learning environment which may facilitate further medical and education applications.

animal behavior and cognition↗

bioRxiv2020

Characterization of novel Actinobacteriophage Giantsbane reveals potential genomic recombination hotspot and unexpected intra-cluster similarities

Bacteriophages that infect Arthrobacter, a genus of bacteria which play key ecological roles in soil, warrant further study. Giantsbane, a novel Actinobacteriophage, was isolated using Arthrobacter globiformis as a host. Transmission electron microscopy and whole-genome sequencing revealed a Siphoviridae morphology and a genome length of 56,734 bp. Genome annotation identified 94 putative genes, such as a duplicated major tail protein and a major capsid and protease fusion protein. No genes were associated with lysogeny, indicating a lytic phage. Giantsbane was assigned to the phage cluster AU. Batch average nucleotide identity analysis and phylogenetic networks constructed from shared genes revealed unexpected nucleotide and gene content similarities within cluster AU. These findings have resulted in the creation of two new AU subclusters and the resubclustering of three AU bacteriophages. Analysis using Phamerator and MEME identified repeated motifs and a gene cassette present in all evaluated cluster AU phages which may promote recombination. These findings offer the first intra-cluster analysis of cluster AU phages and further our understanding of the relationships between closely related bacteriophages.

genomics↗

bioRxiv2019

Phase separation-mediated formation of condensed GIT/PIX enzyme complex module for compartmentalized signaling

Cells compartmentalize enzymes for broad physiological functions such as efficient metabolic reactions and spatiotemporally controlled signaling. A given enzyme or enzyme complex can participate in multiple cellular processes in response to different signal inputs by forming different cellular compartments. Here, we demonstrate that association of GIT1 and {beta}-Pix, a pair of GTPase regulatory enzymes involved in diverse cellular processes, leads to autonomous condensation of the complex via phase separation without additional scaffolding molecules. The atomic structure of the GIT/PIX complex reveals the molecular basis governing the phase separation-mediated condensation of the GIT1/{beta}-Pix complex. Importantly, the GIT1/{beta}-Pix condensates can function as a versatile modular membrane-less organelle- like structure for distinct cellular compartmentalization by binding to upstream proteins such as Paxillin in focal adhesions, Shank3 in neuronal synapses, and Scribble in cellular junctions. Thus, phase separation-mediated formation of condensed enzyme complexes provides a powerful way of dynamically concentrating limited amounts of cooperating enzymes to specific cellular compartments for optimal signaling.

cell biology↗

bioRxiv2019

Reward produces learning of a consciously inaccessible feature

Reward has significant impacts on behavior and perception. Most past work in associative reward learning has used distinct visual cues to associate with different reward values. Thus, it remains unknown to what extent the learned associations depend on the consciousness. Here we resolved this issue by using an inter-ocular suppression paradigm with the monetary rewarding and non-rewarding cues identical to each other except for the eye-of-origin. Thus, the reward coding system cannot rely on the consciousness to select the reward-associated cue. Surprisingly, the targets in the rewarded eye broke into awareness faster than those in the non-rewarded eye. We further revealed that producing this effect required both attention and inter-ocular suppression. These findings suggest that the humans reward coding system can produce two different types of reward-based learning. One is independent of the consciousness yet fairly consuming attentional resource. The other one results from volitional selections guided by top-down attention.

neuroscience↗

bioRxiv2019

Seasonal Variation in the Internet Searches for Cancer Recurrence: An Infodemiological Study

BackgroundWhile few clinical and epidemiological studies have assessed how seasonality affects cancer recurrence, it has not been studied with the utility of the internet data. In this study, we aim to test whether cancer recurrence presents seasonality on a population level, utilizing internet search query data. MethodsThis infodemiological study used Google Trends to find query data for the term "cancer recurrence" from January 01, 2004, to December 31, 2018 in the USA, the UK, Canada, and Australia. Time series seasonal decomposition and the cosinor analysis were used to analyze and describe the seasonal trends for cancer recurrence. ResultsA general upward trend in UK and northern hemisphere were observed. Statistically significant seasonal trends on "cancer recurrence" in the USA (p=1.33x10-5), the UK (p=0.012), and northern hemisphere (p=5.67x10-7) were revealed by cosinor analysis, with a peak in early summer and nadir in early winter. Besides, a seasonal variation was also found in Australia (p=2.3x10-4), with a peak in late summer and nadir in late winter. ConclusionsThe evidence from internet search query data showed a seasonal variation in cancer recurrence, with a peak in early summer(northern hemisphere)/late summer(southern hemisphere). Besides, the relative search volume of "cancer recurrence" appeared a general upward trend in UK and northern hemisphere in recent years.

cancer biology↗

bioRxiv2019

ERP sources in middle cingulate and precuneus differentiate Parkinson's patients from healthy controls and lingual gyri sources reflect human recombinant EPO effects in a Flanker task

We used EEG source analysis to identify which cortical areas were involved in the automatic and controlled processes of inhibitory control on a flanker task and compared the potential efficacy of recombinant-human erythropoietin (rHuEPO) on the performance of Parkinson s Disease patients. The samples were 18 medicated PD patients (nine of them received rHuEPO in addition to their usual anti-PD medication through random allocation and the other nine patients were on their regular anti-PD medication only) and 9 age and education-matched healthy controls (HCs) who completed the flanker task with simultaneous EEG recordings. N1 and N2 event-related potential (ERP) components were identified and a low-resolution tomography (LORETA) inverse solution was employed to localize the neural generators. Reaction times and errors were increased for the incongruent flankers for PD patients compared to controls. EEG source analysis identified an effect of rHuEPO on the lingual gyri for the early N1 component. N2-related sources in middle cingulate and precuneus were associated with the inhibition of automatic responses evoked by incongruent stimuli differentiated PD and HCs. From our results rHuEPO, seems to mediate an effect on N1 sources in lingual gyri but not on behavioural performance. N2-related sources in middle cingulate and precuneus evoked by incongruent stimuli differentiated PD and HCs.

neuroscience↗

bioRxiv2019

Structural variation, functional differentiation and expression characteristics of the AP2/ERF gene family and its response to cold stress and methyl jasmonate in Panax ginseng C.A. Meyer

The APETALA2/Ethylene Responsive Factor (AP2/ERF) gene family has been shown to play a crucial role in plant growth and development, stress responses and secondary metabolite biosynthesis. Nevertheless, little is known about the gene family in ginseng (Panax ginseng), an important traditional medicinal herb in Asia and North America. Here, we report the systematic analysis of the gene family present in ginseng using several transcriptomic databases. A total of 189 putative AP2/ERF genes, defined as PgERF001 through PgERF189. The 93 PgERF genes that have the complete AP2 domain in their open reading frames were classified into five subfamilies, DREB, ERF, AP2, RAV and Soloist. The DREB subfamily and ERF subfamily were further clustered four and six groups, respectively, compared to the 12 groups of these subfamilies found in Arabidopsis. Gene ontology categorized these 397 transcripts of the 189 PgERF genes into eight functional subcategories, suggesting their functional differentiation and they have been especially enriched for the nucleic acid binding transcription factor activity subcategory. The expression activity and networks of the 397 PgERF transcripts have substantially diversified across tissues, developmental stages and genotypes. Then, the expression change of six PgERF genes randomly selected from DREB subfamily, i.e., PgERF073, PgERF079, PgERF110, PgERF115, PgERF120 and PgERF128 responding to cold stress suggesting that DREB subfamily genes played an important role in cold resistance of ginseng. Finally, we studied the responses of the PgERF genes to methyl jasmonate (MeJA). 288 (72.5%) of the 397 PgERF gene transcripts responded to the MeJA treatment, with 136 up-regulated and 152 down-regulated, indicating that most members of the PgERF gene family are responsive to MeJA. These results provide resources and knowledge necessary for family-wide functional analysis of the PgERF genes in ginseng and related species.

genomics↗

bioRxiv2019

Nuclear GAPDH signaling mediates pathological cardiac hypertrophy

Here we report that stress-induced nuclear translocation of GAPDH mediates heart hypertrophy via Brahma-Related-Gene-1 (BRG1)-associated chromatin remodelling. In response to pressure overload elicited by transverse aortic constriction, we observed nuclear translocation of GAPDH in the mouse heart. We also demonstrated a robust nuclear localization of GAPDH in cardiomyocytes from patients with dilated hypertrophic cardiomyopathy, whereas negligible GAPDH in the nucleus in control subjects. This is the first demonstration of disease-associated nuclear GAPDH directly in living patients. Using immunohistochemical methods and a pharmacological way that selectively blocks GAPDH nuclear translocation (RR compound), we proved the causal involvement of GAPDH cysteine-150 modification in this translocation in Gq-induced cell model for heart hypertrophy. Accordingly, both pharmacological and genetic interventions proved that the same mechanism played a causal role for heart hypertrophy and dysfunction in vivo. We discovered that, upon nuclear translocation, GAPDH augmented the protein interaction of BRG1 and histone deacetylase 2 (HDAC2), which further facilitated the Myh7/Myh6 isoform ratio from the mature to immature status, an essential mechanism for heart hypertrophy. Beyond medical implications, we provide a novel mechanism of stress-induced reversion of a cellular phenotype from adult to fetal state, which is mediated by a "moonlighting" function of GAPDH.

molecular biology↗

bioRxiv2019

Variation in the life history strategy of cells underlies tumor’s functional diversity

Classical r- vs. K-selection theory describes the trade-offs between high reproductive output and competitiveness and guides research in evolutionary ecology1-5. While its impact has waned in the recent past, cancer evolution may rekindle it6-10. Indeed, solid tumors are an ideal theater for r- and K-selection and, hence, a good testing ground for ideas on life-history strategy evolution11,12. In this study, we impose r- or K-selection on HeLa cells to obtain strongly proliferative r cells and highly competitive K cells. RNA-seq analysis indicates that phenotypic trade-offs in r and K cells are associated with distinct patterns of expression of genes involved in the cell cycle, adhesion, apoptosis, and contact inhibition. Both empirical observations and simulations based on an ecological competition model show that the trade-off between cell proliferation and competitiveness can evolve adaptively and rapidly in naive cell lines. It is conceivable that the contrasting selective pressure may operate in a realistic ecological setting of actual tumors. When the r and K cells are mixed in vitro, they exhibit strikingly different spatial and temporal distributions in the resultant cultures. Thanks to this niche separation, the fitness of the entire tumor increases. Our analyses of life-history trade-offs are pertinent to evolutionary ecology as well as cancer biology.

evolutionary biology↗

bioRxiv2019

Polarly localized EccE1is required for ESX-1 function and stabilization of ESX-1 membrane proteins in Mycobacterium tuberculosis

Mycobacterium tuberculosis is a slow-growing intracellular bacterium with the ability to induce host cell death and persist indefinitely in the human body. This pathogen uses the specialized ESX-1 secretion system to secrete virulence factors and potent immunogenic effectors required for disease progression. ESX-1 is a multi-subunit apparatus with a membrane complex that is predicted to form a pore in the cytoplasmic membrane. In M. tuberculosis this complex is composed of five membrane proteins: EccB1, EccCa1, EccCb1, EccD1, EccE1. In this study, we have characterized the membrane component EccE1 and found that deletion of eccE1 lowers the levels of EccB1, EccCa1 and EccD1 thereby abolishing ESX-1 secretion and attenuating M. tuberculosis ex vivo. Surprisingly, secretion of EspB was not affected by loss of EccE1. Furthermore, EccE1 was found to be a membrane- and cell-wall associated protein that needs the presence of other ESX-1 components to assemble into a stable complex at the poles of M. tuberculosis. Overall, this investigation provides new insights into the role of EccE1 and its localization in M. tuberculosis.\n\nIMPORTANCETuberculosis (TB), the worlds leading cause of death of humans from an infectious disease, is caused by the intracellular bacterium Mycobacterium tuberculosis. The development of successful strategies to control TB requires better understanding of the complex interactions between the pathogen and human host. We investigated the contribution of EccE1, a membrane protein, to the function of the ESX-1 secretion system, the major virulence determinant of M. tuberculosis. By combining genetic analysis of selected mutants with eukaryotic cell biology and proteomics, we demonstrate that EccE1 is critical for ESX-1 function, secretion of effector proteins and pathogenesis. Our research improves knowledge of the molecular basis of M. tuberculosis virulence and enhances our understanding of pathogenesis.

microbiology↗

bioRxiv2019

Epidermal green autofluorescence intensity is significantly associated with the serum levels of multiple cytokines of LPS-exposed mice

Inflammation plays various crucial pathological and physiological roles, in which a number of pro-inflammatory and anti-inflammatory cytokines are important mediators. It is of great scientific and clinical significance to search for non-invasive approaches for evaluating cytokine levels in the blood. Our previous study reported that epidermal green autofluorescence (AF) intensity of LPS-exposed mice is highly correlated with LPS doses. In our current study, we determined if epidermal green AF intensity is associated with the serum levels of various cytokines in the LPS-exposed mice. We found that both epidermal green AF intensity and LPS doses are significantly associated with the serum levels of key cytokines including interleukin-1{beta} (IL-1{beta}), IL-6 and IL-10. Both epidermal green AF intensity and LPS doses are also significantly associated with the pro-inflammatory factors including IL-2, IL-12(p40), monocyte chemoattractant protein-1 (MCP-1), MIP-1, MIP-1{beta}, and regulated on activation, normal T cell expressed and secreted (RANTES/CCL5), as well as anti-inflammatory factors including IL-5 and granulocyte colony stimulating factor (G-CSF). Our findings have suggested that detection of epidermal green AF intensity may become first approach for non-invasive evaluation of certain cytokine levels in human body, which could profoundly enhance our capacity to evaluate inflammation levels for monitoring health state, disease state and therapeutic effects.

immunology↗