Biology subjects

Zhu, S.

Publications and source records attributed to Zhu, S..

At least 217 records · Page 12Linked to original sources

bioRxiv2019

Towards Practical and Robust DNA-based Data Archiving by Codec System Named ‘Yin-Yang’

DNA is a promising data storage medium due to its remarkable durability and space-efficient storage. Early bit-to-base transcoding schemes have primarily pursued information density, at the expense however of introducing biocompatibility challenges or at the risk of decoding failure. Here, we propose a robust transcoding algorithm named the "Yin-Yang Codec" (YYC), using two rules to encode two binary bits into one nucleotide, to generate DNA sequences highly compatible with synthesis and sequencing technologies. We encoded two representative file formats and stored them in vitro as 200-nt oligo pools and in vivo as an ~54-kb DNA fragment in yeast cells. Sequencing results show that YYC exhibits high robustness and reliability for a wide variety of data types, with an average recovery rate of 99.94% at 104 molecule copies and an achieved recovery rate of 87.53% at 100 copies. In addition, the in vivo storage demonstration achieved for the first time an experimentally measured physical information density of 198.8 EB per gram of DNA (44% of the theoretical maximum for DNA).

synthetic biology↗

bioRxiv2019

Establishing Rod-Shape from Spherical, Peptidoglycan-Deficient Bacterial Spores

Chemical-induced spores of the Gram-negative bacterium Myxococcus xanthus are peptidoglycan (PG)-deficient. It is unclear how these spherical spores germinate into rod-shaped, walled cells without preexisting PG templates. We found that germinating spores first synthesize PG randomly on spherical surfaces. MglB, a GTPase-activating protein, forms a cluster that surveys the status of PG growth and stabilizes at one future cell pole. Following MglB, the Ras family GTPase MglA localizes to the second pole. MglA directs molecular motors to transport the bacterial actin homolog MreB and the Rod PG synthesis complexes away from poles. The Rod system establishes rod-shape by elongating PG at nonpolar regions. Thus, the interaction between GTPase, cytoskeletons and molecular motors provides a mechanism for the de novo establishment of rod-shape in bacteria. SignificanceSpheres and rods are among the most common shapes adopted by walled bacteria, in which the peptidoglycan (PG) cell wall largely determines cell shape. When induced by chemicals, rod-shaped vegetative cells of the Gram-negative bacterium Myxococcus xanthus thoroughly degrade their PG and shrink into spherical spores. As these spores germinate, rod-shaped cells are rebuilt without preexisting templates, which provides a rare opportunity to visualize de novo PG synthesis and bacterial morphogenesis. In this study, we investigated how spherical spores germinate into rods and elucidated a system for rod-shape morphogenesis that includes the Rod PG synthesis system, a GTPase-GAP pair, the MreB cytoskeleton and a molecular motor.

microbiology↗

bioRxiv2019

Deglycosylation of isoflavone C-glucoside puerarin by combination of two recombinant bacterial enzymes and 3-oxo-glucose.

C-Glucosides are resistant to glycoside hydrolase activity because the anomeric carbon of glucose is directly connected to aglycone via carbon-carbon bonding. A human intestinal bacterium strain PUE related to Dorea species can metabolize the isoflavone C-glucoside puerarin (daidzein 8-C-glucoside) to daidzein and glucose by more than three bacterial enzymes which have not been well-characterized. We previously reported that 3\"-oxo-puerarin is an essential reaction intermediate in enzymatic puerarin degradation and characterized a bacterial enzyme of DgpB-C complex which cleaved the C-glycosidic bond in 3\"-oxo-puerarin. However, the exact enzyme catalyzing the oxidation of C-3\" hydroxyl in puerarin has not been identified, and the other metabolite corresponding to the precursor of D-glucose, derived from the sugar moiety in 3\"-oxo-puerarin in the cleaving reaction catalyzed by the DgpB-C complex, remains unknown.\n\nIn this study, we demonstrated that recombinant DgpA, a Gfo/Idh/MocA family oxidoreductase, catalyzed puerarin oxidation in the presence of 3-oxo-glucose as the hydride accepter. In addition, enzymatic C-deglycosylation of puerarin was achieved by a combination of recombinant DgpA, DgpB-C complex, and 3-oxo-glucose. Furthermore, the metabolite derived from the sugar moiety in 3\"-oxo-puerarin cleaving reaction catalyzed by DgpB-C complex was characterized as 1,5-anhydro-D-erythro -hex-1-en-3-ulose, suggesting that the C-glycosidic linkage is cleaved through a {beta}-elimination like mechanism.\n\nImportanceOne important role of the gut microbiota is to metabolize dietary nutrients and supplements such as flavonoid glycosides. Ingested glycosides are metabolized by intestinal bacteria to more absorbable aglycones and further degradation products which show beneficial effects in humans. Although numerous glycoside hydrolases that catalyze O-deglycosylation have been reported, enzymes responsible for C-deglycosylation are still limited. In this study, we characterized enzymes involved in C-deglycosylation of puerarin from a human intestinal bacterium PUE. To our knowledge, this is the first report of the expression, purification and characterization of an oxidoreductase involved in C-glucoside degradation. This study provides new insights for the elucidation of mechanisms of enzymatic C-deglycosylation.

biochemistry↗

bioRxiv2019

De Novo Protein Design for Novel Folds using Guided Conditional Wasserstein Generative Adversarial Networks (gcWGAN)

MotivationFacing data quickly accumulating on protein sequence and structure, this study is addressing the following question: to what extent could current data alone reveal deep insights into the sequence-structure relationship, such that new sequences can be designed accordingly for novel structure folds?\n\nResultsWe have developed novel deep generative models, constructed low-dimensional and generalizable representation of fold space, exploited sequence data with and without paired structures, and developed ultra-fast fold predictor as an oracle providing feedback. The resulting semi-supervised gcWGAN is assessed with the oracle over 100 novel folds not in the training set and found to generate more yields and cover 3.6 times more target folds compared to a competing data-driven method (cVAE). Assessed with structure predictor over representative novel folds (including one not even part of basis folds), gcWGAN designs are found to have comparable or better fold accuracy yet much more sequence diversity and novelty than cVAE. gcWGAN explores uncharted sequence space to design proteins by learning from current sequence-structure data. The ultra fast data-driven model can be a powerful addition to principle-driven design methods through generating seed designs or tailoring sequence space.\n\nAvailabilityData and source codes will be available upon request.\n\nContactyshen@tamu.edu\n\nSupplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2019

Generation and quality control of maternal plasma lipidomics data associated with preterm birth

Preterm birth is not only one of the most common causes of infant deaths but also a great risk for them to have severe subsequent health problems. The causes of preterm birth may be due to a combination of genetic and environmental factors, however, it remains largely unknown. Here we report an untargeted lipidomics dataset of plasma specimens from 258 pregnant women at the stage of twelve to twenty-five gestational weeks. Among them, 44 had extremely to very preterm births, 54 had moderate preterm births, 71 had late preterm births and 89 had full-term deliveries. The metabolomic profiling was generated with an UPLC-MS in both the positive and negative mode, and putative identification of all the metabolites was provided by searching against online databases. The quality assessment performed on quality control samples showed that the data is reproducible, robust and reliable. Both the raw data files, the raw and processed data matrix were available on MetaboLights, which may be used as a valuable validation dataset for new findings and a test dataset for novel algorithms.

systems biology↗

bioRxiv2019

Evaluation of five cell-free DNA isolation kits for plasma

Cell-free DNA (cfDNA) has been widely used in prenatal test and cancer diagnosis nowadays. The cost- and time-effective isolation kits are needed especially in large-scale clinical application. Here, we compared three domestic kits: VAHTS Serum/Plasma Circulating DNA kit (VZ), MagPure Gel Pure DNA mini kit (MG) and Serum/Plasma Circulating DNA Kit (TG), together with QIAamp Circulating Nucleic Acid Kit (QC) and QIAamp DNA Blood Mini Kit (QD) in cfDNA isolation. cfDNA was isolated from the pooled samples with spike-in fragments, qPCR was conducted to quantify the spike-in fragments recovery. The results indicated that all of the five kits could isolate cfDNA with different efficiency. The VZ kit had an efficiency as high as 90 percent, which is comparable to QC kit. The libraries were constructed using the isolated cfDNAs, quantified by Qubit and analyzed by 2100 bioanalyzer. Both showed the libraries were qualified. Finally, cffDNAs were detected by qPCR targeting SRY gene using libraries from pregnant women bearing male fetuses. All five kits could isolate cffDNAs that could be detected by qPCR. Our results provided more choices in wide-scale clinical application of cfDNA-based non-invasive genetic tests.

molecular biology↗

bioRxiv2019

Identification of porcine RUNX1 as an LPS-dependent gene expression regulator in PBMCs by Super deepSAGE sequencing of multiple tissues

Genome-wide identification of gene expression regulators may facilitate our understanding of the transcriptome constructed by gene expression profiling experiment. These regulators may be selected as targets for genetic manipulations in farm animals. In this study, we developed a gene expression profile of 76,000+ unique transcripts for 224 porcine samples from 28 normal tissues collected from 32 animals using Super deepSAGE (serial analysis of gene expression by deep sequencing) technology. Excellent sequencing depth has been achieved for each multiplexed library, and principal component analysis showed that duplicated samples from the same tissues cluster together, demonstrating the high quality of the Super deepSAGE data. Comparison with previous research indicated that our results not only have excellent reproducibility but also have greatly extended the coverage of the sample types as well as the number of genes. Clustering analysis discovered ten groups of genes showing distinct expression patterns among those samples. Binding motif over representative analysis identified 41 regulators responsible for the regulation of these gene clusters. Finally, we demonstrate a potential application of this dataset to infectious and immune research by identifying an LPS-dependent transcription factor, runt-related transcription factor 1 (RUNX1), in peripheral blood mononuclear cells (PBMCs). The selected genes are specifically responsible for the transcription of toll-like receptor 2 (TLR2), lymphocyte-specific protein tyrosine kinase (LCK), vav1 oncogene (VAV1), and other 32 genes. These genes belong to the T and B cell signaling pathways, making them potential novel targets for the diagnostic and therapy of bacterial infections and other immune disorders.

genomics↗

bioRxiv2019

PALM-Seq: simultaneous sequencing of cell-free long RNA and small RNA

Cell-free RNA, including both long RNA and small RNA, has been considered important for its biological functions and potential clinical usage, but the major challenge is to effectively sequence them at the same time. Here we present PolyAdenylation Ligation Mediated-Seq (PALM-Seq), an integrated sequencing method for cell-free long and small RNA. Through terminal modification and addition of 3 polyadenylation and 5 adaptor, we could get mRNA, long non-coding RNA, microRNA, tRNA, piRNA and other RNAs in a single library. With target RNA depletion, all these RNAs could be sequenced with relatively low depth. Using PALM-Seq, we identified pregnant-related mRNAs, long non-coding RNAs and microRNAs in female plasma. We also applied PALM-Seq to sequence RNA from amniotic fluids, leukocytes and placentas, and could find RNA signatures associated with specific sample type. PALM-Seq provides an integrated, cost-effective and simple method to characterize the landscape of cell-free RNA, and can stimulate further progress in cell-free RNA study and usage.

molecular biology↗

bioRxiv2019

A database for ITS2 sequences from nematodes

Marker gene surveys have a wide variety of applications in species identification, population genetics, and molecular epidemiology. As these methods expand to new types of organisms and additional markers beyond 16S and 18S rRNA genes, comprehensive databases are a critical requirement for proper analysis of these data. Here we present an ITS2 rDNA database for maker gene surveys of both free-living and parasitic nematode populations and the software used to build the database. This is an important resource for researchers working on nematodes and also provides a tool to create ITS2 databases for any given taxonomy.\n\nAvailability and ImplementationThe database is available as an interactive web app at https://cooperia.chgi.ucalgary.ca/Nematode_ITS2/. The full database can also be downloaded from zenodo https://doi.org/10.5281/zenodo.3235802, and the open source software used to create the database, markerDB is available at https://github.com/ucvm/markerDB/releases/latest.

bioinformatics↗

bioRxiv2019

Assessment of the gene expression profiles of leukocytes from different isolations

BACKGROUNDResearch on peripheral leukocyte gene expression in human health and disease is growing rapidly. However, how to process sample efficiently, simply and stably, and how to reflect human physiological state preferably remains critical issues in large cohort studies.\n\nMETHODSWe used RNA-seq to explore the differences of gene expression profiles among whole blood (WB) and three groups of leukocytes from buffy coat (BC) extraction, red blood cell (RBC) lysis and peripheral blood mononuclear cell (PBMC) isolation.\n\nRESULTSThe residual globin mRNA in leukocytes from RBC lysis (1.00% {+/-}1.23%) and PBMC isolation (0.06% {+/-} 0.03%) was much less than that in leukocytes from BC extraction (17.48% {+/-} 6.95%) and WB (24.46% {+/-} 6.43%), resulting in higher transcriptome mapping rates and larger numbers of detected genes. The expression of 616 genes associated with leukocyte function was slightly higher in leukocytes from RBC lysis than that from BC extraction and WB, but barely detected in leukocytes from PBMC isolation.\n\nCONCLUSIONSWe suggest that sample processing based on RBC lysis could allow better applications of gene expression profiling of peripheral leukocytes in large cohort studies.

molecular biology↗

bioRxiv2019

The full-length transcriptome of Spartina alterniflora reveals the complexity of high salt tolerance in monocotyledonous halophyte

Spartina alterniflora (Spartina) is the only halophyte in the salt marsh. However, the molecular basis of its high salt tolerance remains elusive. In this study, we used PacBio full-length single molecule long-read sequencing and RNA-seq to elucidate the transcriptome dynamics of high salt tolerance in Spartina by salt-gradient experiments (0, 350, 500 and 800 mM NaCl). We systematically analyzed the gene expression diversity and deciphered possible roles of ion transporters, protein kinases and photosynthesis in salt tolerance. Moreover, the co-expression network analysis revealed several hub genes in salt stress regulatory networks, including protein kinases such as SaOST1, SaCIPK10 and three SaLRRs. Furthermore, high salt stress affected the gene expression of photosynthesis through down-regulation at the transcription level and alternative splicing at the post-transcriptional level. In addition, overexpression of two Spartina salt-tolerant genes SaHSP70-I and SaAF2 in Arabidopsis significantly promoted the salt tolerance of transgenic lines. Finally, we built the SAPacBio website for visualizing the full-length transcriptome sequences, transcription factors, ncRNAs, salt-tolerant genes, and alternative splicing events in Spartina. Overall, this study sheds light on the high salt tolerance mechanisms of monocotyledonous-halophyte and demonstrates the potential of Spartina genes for engineering salt-tolerant plants.

plant biology↗

bioRxiv2019

Chromosome level draft genomes of the fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae), an alien invasive pest in China

The fall armyworm (FAW), Spodoptera frugiperda (J.E. Smith) is a severely destructive pest native to the Americas, but has now become an alien invasive pest in China, and causes significant economic loss. Therefore, in order to make effective management strategies, it is highly essential to understand genomic architecture and its genetic background. In this study, we assembled two chromosome scale genomes of the fall armyworm, representing one male and one female individual procured from Yunnan province of China. The genome sizes were identified as 542.42 Mb with N50 of 14.16 Mb, and 530.77 Mb with N50 of 14.89 Mb for the male and female FAW, respectively. We predicted about 22,201 genes in the male genome. We found the expansion of cytochrome P450 and glutathione s-transferase gene families, which are functionally related to the intensified detoxification and pesticides tolerance. Further population analyses of corn strain (C strain) and rice strain (R strain) revealed that the Chinese fall armyworm was most likely invaded from Africa. These strain information, genome features and possible invasion source described in this study will be extremely important for making effective strategies to manage the fall armyworms.

genomics↗

bioRxiv2019

Age-dependent sexual dimorphism in the adult human gut microbiota

A decade of studies has established the importance of the gut microbiome in human health. In spite of sex differences in the physiology, lifespan, and prevalence of many age-associated diseases, sex and age disparities in the gut microbiota have been little studied. Here we show age-related sex differences in the adult gut microbial composition and functionality in two community-based cohorts from Northern China and the Netherlands. Consistently, women harbour a more diverse and stable microbial community across broad age ranges, whereas men exhibit a more variable gut microbiota strongly correlated with age. Reflecting the sex-biased age-gut microbiota interaction patterns, sex differences observed in younger adults are considerably reduced in the elderly population. Our findings highlight the age- and sex-biased differences in the adult gut microbiota across two ethnic population and emphasize the need for considering age and sex in studies of the human gut microbiota.

genomics↗

bioRxiv2019

Pharmacodynamics of linezolid-plus-fosfomycin against vancomycin-susceptible and -resistant enterococci in vitro and in vivo of a Galleria mellonella larval infection model

ObjectiveTo explore the in vitro and in vivo antibacterial activity of linezolid/fosfomycin combination against vancomycin-susceptible and -resistant enterococci (VSE and VRE), providing theoretical basis for the treatment of VRE.\n\nMethodsThe checkerboard method and time-kill curve study were used to evaluate the synergistic effect of linezolid combined with fosfomycin against VSE and VRE. The transmission electron microscopy (TEM) was employed to observe the bacterial cell morphology followed by each drug alone and in combination, elucidating the possible result of antibiotic combination therapy. The Galleria mellonella infection model was constructed to demonstrate the in vivo efficacy of linezolid plus fosfomycin for VSE and VRE infection.\n\nResultsThe fractional inhibitory concentration index (FICI) values of all strains suggested that linezolid showed synergy or additivity in combination with fosfomycin against five of the six strains. Time-kill experiments demonstrated that the combination of linezolid-fosfomycin at 1xMIC or 2xMIC led to higher degree of bacterial killing without regrowth for all isolates tested than each monotherapy. TEM imaging showed that the combination treatment damaged the bacterial cell morphology more obviously than each drug alone. In the Galleria mellonella infection model, the enhanced survival rate of the combination treatment was revealed compared to linezolid monotherapy (P<0.05).\n\nConclusionsOur data manifest that the combination of linezolid and fosfomycin may be a possible therapeutic regimen for VRE infection. The combination displays excellent bacterial killing and inhibits amplification of fosfomycin-resistant subpopulations.

pharmacology and toxicology↗

bioRxiv2019

Leveraging Endogenous ADAR for Programmable Editing on RNA

Nucleic acid editing carries enormous potential for biological research and the development of therapeutics. Current tools for DNA or RNA editing rely on introducing exogenous proteins into living organisms, which is subject to potential risks or technical barriers due to possible aberrant effector activity, delivery limits and immunogenicity. Here, we report a programmable approach that employs a short RNA to leverage endogenous ADAR (Adenosine Deaminase Acting on RNA) proteins for targeted RNA editing. We engineered an RNA that is partially complementary to the target transcript to recruit native ADAR1 or ADAR2 to change adenosine to inosine at a specific site. We designated this new method as LEAPER (Leveraging Endogenous ADAR for Programmable Editing on RNA) and the ADAR-recruiting RNA as arRNA. arRNA, either expressed from plasmid or viral vector, or synthesized as an oligonucleotide, could achieve desirable editing. LEAPER has a manageable off-target rate on the targeted transcripts and rare global off-targets. We demonstrated that LEAPER could restore p53 function by repairing a specific cancer-relevant point mutation. Moreover, LEAPER could apply to a broad spectrum of cell types including multiple human primary cells, and it restored the -L-iduronidase catalytic activity in Hurler syndrome patient-derived primary fibroblasts without evoking innate immune responses. As a single molecule system akin to RNAi, LEAPER enables precise and efficient RNA editing, offering the transformative potential for basic research and therapeutics.

genomics↗

bioRxiv2019

A spatial cell culture model for predicting chemotherapy dosing strategies

Predicting patient responses to chemotherapy regimens is a major challenge in cancer treatment. To do this requires quantitative mathematical models to predict optimal dose and frequency for a particular drug, and experimental model systems such as three-dimensional organoids that accurately recapitulate the tumor microenvironment and heterogeneity. However, tracking the spatial dynamics of multiple cell types in three-dimensions can be a significant challenge in terms of time and throughput. Here we develop a two-dimensional system that allows for simple tracking of cell populations via fluorescence microscopy for modeling spatial dynamics in tumors. We first develop multiple 4T1 breast cancer cell lines resistant to varying concentrations of doxorubicin, and demonstrate how well mixed and spatially heterogeneous populations expand in a two-dimensional colony. We subject cell populations to varied dose and frequency of chemotherapy and measure colony growth radius and populations. We then build a mathematical model to describe the dynamics of both chemosensitive and chemoresistant populations, where we determine which number of doses can produce the smallest tumor size based on parameters in the system. In the future, this system can be adapted to quickly optimize dosing strategies in the setting of heterogeneous cell types or patient derived cells with varied chemoresistance.

cancer biology↗

bioRxiv2019

Identification of 12 cancer types through genome deep learning

MotivationCancer is a major cause of death worldwide, and an early diagnosis is required for a favorable prognosis. Histological examination is the gold standard for cancer identification; however, there is a large amount of inter-observer variability in histological diagnosis. Numerous studies have shown that cancer genesis is accompanied by an accumulation of harmful mutations within patients genome, potentiating the identification of cancer based on genomic information. We have proposed a method, GDL (genome deep learning), to study the relationship between genomic variations and traits based on deep neural networks with multiple hidden layers and nonlinear transformations. ResultWe analyzed 6,083 samples from 12 cancer types obtained from the TCGA (The Cancer Genome Atlas) and 1,991 healthy samples from the 1000 Genomes project(Genomes Project, et al., 2010). We constructed 12 specific models to distinguish between certain types of cancers and healthy tissues, a specific model that can identify healthy vs diseased tissues, and a mixture model to distinguish between all 12 types of cancer based on GDL. We present the success obtained with GDL when applied to the challenging problem of cancer based on genomic variations and demonstrate state-of-the-art results (97%, 70.08% and 94.70%) for cancer identification. The mixture model achieved a comparable performance. With the development of new molecular and sequencing technologies, we can now collect circulating tumor DNA (ctDNA) from blood and monitor the cancer risk in real time, and using our model, we can also target cancerous tissue that may develop in the future. We developed a new and efficient method for the identification of cancer based on genomic information that offers a new direction for disease diagnosis while providing a new method to predict traits based on that information. Contactchenwenbin@genomics.cn

bioinformatics↗

bioRxiv2019

Gene Panel Sequencing in a Chinese High-risk Breast Cancer Cohort

Currently, over 20 genes have been defined that can confer susceptibility for high-risk breast cancer. Although research has proved the utility of multiple-gene sequencing in the assessment of breast cancer risk, there is little data from China patients. Here, we use a multiple-gene sequencing panel to identify the variant spectrum in Chinese high-risk breast cancer subjects.\n\nA total of 829 Chinese high-risk breast cancer patients participated in the research. The coding regions of 115 hereditary cancer susceptibility genes were sequenced using a next generation sequencing platform. In total, 193 pathogenic variants were identified in 45 genes from 177 patients. The pathogenic variant carrier rate is 21.4%: with 10.5% patients carrying a BRCA1 or BRCA2 mutation only, 10.0% of patients carried non-BRCA gene mutations only, while 1.0% of patients carried both a BRCA1/2 and a non-BRCA gene mutation. Variants of uncertain significance (VUS) totaling 2632 were identified in 115 genes from 787 of 829 patients: 82.5% patients carried more than one VUS, and only 5.1% patients did not carry any VUS. Families carrying pathogenic variants were tracked and adenoma was founded in three of them. Our data provide a comprehensive analysis of potential susceptibility variations of high-risk for breast cancer in a Chinese population. This data will be useful for the comparison of the susceptibility variation spectrum between different populations and to discover potential pathogenic variants to improve the prevention and treatment of high-risk breast cancer.

cancer biology↗