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Du, Y.

Publications and source records attributed to Du, Y..

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Differential gene expression, including Sjfs800, in Schistosoma japonicum females before, during, and after male-female pairing

Schistosomiasis is a prevalent but neglected tropical disease caused by parasitic trematodes of the genus Schistosoma, with the primary disease-causing species being S. haematobium, S. mansoni, and S. japonicum. Male-female pairing of schistosomes is necessary for sexual maturity and the production of a large number of eggs, which are primarily responsible for schistosomiasis dissemination and pathology. Here, we used microarray hybridization, bioinformatics, quantitative PCR, in situ hybridization, and gene silencing assays to identify genes that play critical roles in S. japonicum reproduction biology, particularly in vitellarium development, a process that affects male-female pairing, sexual maturation, and subsequent egg production. Microarray hybridization analyses generated a comprehensive set of genes differentially transcribed before and after male-female pairing. Although the transcript profiles of females were similar 16 and 18 days after host infection, marked gene expression changes were observed at 24 days. The 30 most abundantly transcribed genes on day 24 included those associated with vitellarium development. Among these, genes for female-specific 800 (fs800), eggshell precursor protein, and superoxide dismutase (cu-zn-SOD) were substantially upregulated. Our in situ hybridization results in female S. japonicum indicated that cu-zn-SOD mRNA was highest in the ovary and vitellarium, eggshell precursor protein mRNA was expressed in the ovary, ootype, and vitellarium, and Sjfs800 mRNA was observed only in the vitellarium, localized in mature vitelline cells. Knocking down the Sjfs800 gene in female S. japonicum by approximately 60% reduced the number of mature vitelline cells, decreased rates of pairing and oviposition, and decreased the number of eggs produced in each male-female pairing by about 50%. These results indicate that Sjfs800 is essential for vitellarium development and egg production in S. japonicum and suggest that Sjfs800 regulation may provide a novel approach for the prevention or treatment of schistosomiasis.\n\nAuthor SummarySchistosomiasis is a common but largely unstudied tropical disease caused by parasitic trematodes of the genus Schistosoma. The eggs of schistosomes are responsible for schistosomiasis transmission and pathology, and the production of these eggs is dependent on the pairing of females and males. In this study, we determined which genes in Schistosoma japonicum females were differentially expressed before and after pairing with males, identifying the 30 most abundantly expressed of these genes. Among these 30 genes, we further characterized those in female S. japonicum that were upregulated after pairing and that were related to reproduction and vitellarium development, a process that affects male-female pairing, sexual maturation, and subsequent egg production. We identified three such genes, S. japonicum female-specific 800 (Sjfs800), eggshell precursor protein, and superoxide dismutase, and confirmed that the mRNAs for these genes were primarily localized in reproductive structures. By using gene silencing techniques to reduce the amount of Sjfs800 mRNA in females by about 60%, we determined that Sjfs800 plays a key role in development of the vitellarium and egg production. This finding suggests that regulation of Sjfs800 may provide a novel approach to reduce egg counts and thus aid in the prevention or treatment of schistosomiasis.

genomics

The mitochondrial DNA content can not predict the embryo viability

ObjectiveTo investigate whether the mitochondrial DNA content could predict the embryo viability\n\nDesignRetrospective analysis.\n\nSettingReproductive genetics laboratory\n\nPatient(s)A total of 421 biopsied samples obtained from 129 patients\n\nIntervention(s)Embryo biopsies samples underwent whole genome amplification (WGA) and were tested by next generation sequencing (NGS) and array Comparative Genomic Hybridization (aCGH), 30 samples were selected randomly to undergo quantitative real-time polymerase chain reaction (qPCR).\n\nMain Outcome Measure(s)Those embryos which obtained the consistent chromosome status determined both aCGH and NGS platform were further classified. We investigated the relationship of mtDNA content with several factors including female patient age, embryo morphology, chromosome status, and live birth rate of both blastocysts and blastomeres.\n\nResult(s)A total of 386 (110 blastomeres and 276 blastocysts) out of 399 embryos showed consistent chromosome status outcome. We found no statistically difference was observed in aneuploid and euploid blastocysts (p=0.14), the same phenomenon was observed in aneuploid and euploid blastomeres (p=0.89). Similarly, the mtDNA content was independent of female patient age, embryo morphology and live birth rate.\n\nConclusion(s)The mtDNA content did not provide a reliable prediction of the viability of blastocysts to initiate a pregnancy.

ecology

Group ICA for Identifying Biomarkers in Schizophrenia: ‘Adaptive’ Networks via Spatially Constrained ICA Show More Sensitivity to Group Differences than Spatio-temporal Regression

Brain functional networks identified from fMRI data can provide potential biomarkers for brain disorders. Group independent component analysis (GICA) is popular for extracting brain functional networks from multiple subjects. In GICA, different strategies exist for reconstructing subject-specific networks from the group-level networks. However, it is unknown whether these strategies have different sensitivities to group differences and abilities in distinguishing patients. Among GICA, spatio-temporal regression (STR) and spatially constrained ICA approaches such as group information guided ICA (GIG-ICA) can be used to propagate components (indicating networks) to a new subject that is not included in the original subjects. In this study, based on the same a priori network maps, we reconstructed subject-specific networks using these two methods separately from resting-state fMRI data of 151 schizophrenia patients (SZs) and 163 healthy controls (HCs). We investigated group differences in the estimated functional networks and the functional network connectivity (FNC) obtained by each method. The networks were also used as features in a cross-validated support vector machine (SVM) for classifying SZs and HCs. We selected features using different strategies to provide a comprehensive comparison between the two methods. GIG-ICA generally showed greater sensitivity in statistical analysis and better classification performance (accuracy 76.45{+/-}8.9%, sensitivity 0.74{+/-}0.11, specificity 0.79{+/-}0.11) than STR (accuracy 67.45{+/-}8.13%, sensitivity 0.65{+/-}0.11, specificity 0.71{+/-}0.11). Importantly, results were also consistent when applied to an independent dataset including 82 HCs and 82 SZs. Our work suggests that the functional networks estimated by GIG-ICA are more sensitive to group differences, and GIG-ICA is promising for identifying image-derived biomarkers of brain disease.

neuroscience

Synergistic antifungal effect of amphotericin B-loaded PLGA nanoparticles based ultrasound against C. albicans biofilms

C. albicans is human opportunistic pathogens that cause superficial and life-threatening infections. An important reason for the failure of current antifungal drugs is related to biofilm formation mostly associated with implanted medical device. The present study aims to investigate the synergistic antifungal efficacy of low-frequency and low-intensity ultrasound combined with amphotericin B-loaded PLGA nanoparticles (AmB-NPs) on C.albicans biofilms. AmB-NPs were prepared by a double emulsion method and demonstrated the lower toxicity than free AmB, after which biofilms were established and treated with ultrasound and AmB-NPs separately or jointly in vitro and in vivo. The results demonstrated the activity, biomass, and proteinase and phospholipase activities of biofilms were decreased significantly after the combination treatment of AmB-NPs with 42 KHz ultrasound irradiation at an intensity of 0.30 W/cm2 for 15 min compared to the control, the AmB alone or the ultrasound alone treatment (P < 0.01), and the morphology of biofilms was altered remarkably after jointly treatment under CLSM observation and detection, especially thickness thinning and structure loosing. Furthermore, the same synergistic effects were proved in a subcutaneous catheter biofilm rat model. The result of colony forming units of catheter fungus loading exhibited a significant reduction after AmB-NPs and ultrasound jointly treatment for 7 days continuous therapy, and the CLSM images revealed that the biofilm on the catheter surface was substantially eliminated. Our study may provide a new noninvasive, safe and effective application to C.albicans biofilm infection therapy.

microbiology

Sequencing of the MHC region defines HLA-DQA1 as the major independent risk for anti-citrullinated protein antibodies (ACPA)-positive rheumatoid arthritis in Han population

The strong genetic contribution of the major histocompatibility complex (MHC) to rheumatoid arthritis (RA) susceptibility has been generally attributed to HLA-DRB1. However, due to the high linkage disequilibrium in the MHC region, it is difficult to define the real or/and additional independent genetic risks using the conventional HLA genotyping or chip-based microarray technology. By the capture sequencing of entire MHC region for discovery and HLA-typing for validation in 2,773 subjects of Han ancestry, we identified HLA-DQ1:160D as the strongest independent genetic risk for anti-citrullinated protein antibodies (ACPA)-positive RA in Han population (P = 6.16 x 10-36, OR=2.29). Further stepwise conditional analysis revealed that DR{beta}1:37N has an independent protective effect on ACPA-positive RA (P = 5.81 x 10-16, OR=0.49). The DQ1:160 coding allele DQA1*0303 displayed high impact on joint radiographic severity, especially in patients with early disease and smoking (P = 3.02 x 10-5). Interaction analysis by comparative molecular modeling revealed that the negative charge of DQ1:160D stabilizes the dimer of dimers, leading to an increased T cell activation. The electrostatic potential surface analysis indicated that the negative charged DR{beta}1:37N encoding alleles could bind with epitope P9 arginine, thus may result in a decreased RA susceptibility.\n\nIn this study, we provide the first evidence that HLA-DQA1, instead of HLA-DRB1, is the strongest and independent genetic risk for ACPA-positive RA in Chinese Han population. Our study also illustrates the value of MHC deep sequencing for fine mapping disease risk variants in the MHC region.

genetics

Local membrane charge regulates β2 adrenergic receptor coupling to Gi

G protein coupled receptors (GPCRs) are transmembrane receptors that signal through heterotrimeric G proteins. Lipid modifications anchor G proteins to the plasma membrane; however, little is known about the effect of phospholipid composition on GPCR-G protein coupling. The {beta}2 adrenergic receptor ({beta}2AR) signals through both Gs and Gi in cardiac myocytes where studies suggest that Gi signaling may be cardioprotective. However, Gi coupling is much less efficient than Gs coupling in most cell-based and biochemical assays, making it difficult to study {beta}2AR-Gi interactions. To investigate the role of phospholipid composition on Gs and Gi coupling, we reconstituted {beta}2AR in detergent/lipid mixed micelles and found that negatively charged phospholipids (PS and PG) inhibit {beta}2AR-Gi3 coupling. Replacing negatively charged lipids with neutral lipids (PC or PE) facilitated the formation of a functional {beta}2AR-Gi3 interaction that activated Gi3. Ca2+, known to interact with negatively charged PS, facilitated {beta}2AR-Gi3 interaction in PS. Mutational analysis suggested that Ca2+ interacts with the negatively charged EDGE motif on the carboxyl-terminal end of the N helix of Gi3 and coordinates an EDGE-PS interaction. These results were confirmed in {beta}2AR reconstituted into nanodisc phospholipid bilayers. {beta}2AR-Gi3 interaction was favored in neutral lipids (PE and PC) over negatively charged lipids (PG and PS). In contrast, basal {beta}2AR-Gs interaction was favored in negatively charged lipids over neutral lipids. In negatively-charged lipids, Ca2+ and Mg2+ facilitated {beta}2AR-Gi3 interaction. Taken together, our observations suggest that local membrane charge modulates the interaction between {beta}2AR and competing G protein subtypes.

biochemistry

Inducible formation of leading cells driven by CD44 switching gives rise to collective invasion

Collective invasion into adjacent tissue is a hallmark of luminal breast cancer, with about 20% of cases that eventually undergo metastasis. It remained unclear how less aggressive luminal-like breast cancer transit to invasive cancer. Our study revealed that CD44hi cancer cells are the leading subpopulation in collective invading cancer cells, which could efficiently lead the collective invasion of CD44lo/follower cells. CD44hi/leading subpopulation showed specific gene signature of a cohort of hybrid epithelial/mesenchymal state genes and key functional co-regulators of collective invasion, which was distinct from CD44lo/follower cells. However, the CD44hi/leading cells, in partial-EMT state, were readily switching to CD44lo phenotype along with collective movements and vice versa, which is spontaneous and sensitive to tumor microenvironment. The CD44lo-to-CD44hi conversion is accompanied with a shift of CD44s-to-CD44v, but not corresponding to the conversion of non-CSC-to-CSC. Therefore, the CD44hi leader cells are not a stable subpopulation in breast tumors. This plasticity and ability to generate CD44hi carcinoma cells with enhanced invasion-initiating powers might be responsible for the transition from in situ to invasive behavior of luminal-type breast cancer.\n\nSignificanceNow, the mechanisms involved in local invasion and distant metastasis are still unclear. We identified a switch of CD44 that drives leader cell formation during collective invasion in luminal breast cancer. We provided evidence that interconversions between low and high CD44 states occur frequently during collective invasion. Furthermore, these findings demonstrated that the CD44hi/leader cells featuring partial EMT are inducible and attainable in response to tumor microenvironment. The CD44lo cancer cells are plastic that readily shift to CD44hi state, accompanied with shifts of CD44s-to-CD44v, thereby increasing tumorigenic and malignant potential. There are many \"non-invasiveness\" epithelial/follower cells with reversible invasive potential within an individual tumor, that casting some challenges on molecular targeting therapy.

cancer biology

A novel maize gene, glossy6 involved in epicuticular wax deposition and drought tolerance

Epicuticular waxes, long-chain hydrocarbon compounds, form the outermost layer of plant surfaces in most terrestrial plants. The presence of epicuticular waxes protects plants from water loss and other environmental stresses. Cloning and characterization of genes involved in the regulation, biosynthesis, and extracellular transport of epicuticular waxes on to the surface of epidermal cells have revealed the molecular basis of epicuticular wax accumulation. However, intracellular trafficking of synthesized waxes to the plasma membrane for cellular secretion is poorly understood. Here, we characterized a maize glossy (gl6) mutant that exhibited decreased epicuticular wax load, increased cuticle permeability, and reduced seedling drought tolerance relative to wild type. We combined an RNA-sequencing based mapping approach (BSR-Seq) and chromosome walking to identify the gl6 candidate gene, which was confirmed via the analysis of multiple independent mutant alleles. The gl6 gene represents a novel maize glossy gene containing a conserved, but uncharacterized domain. Functional characterization suggests that the GL6 protein may be involved in the intracellular trafficking of epicuticular waxes, opening a door to elucidating the poorly understood process by which epicuticular wax is transported from its site of biosynthesis to the plasma membrane.\n\nSIGNIFICANCE STATEMENTPlant surface waxes provide an essential protective barrier for terrestrial plants. Understanding the composition and physiological functions of surface waxes, as well as the molecular basis underlying wax accumulation on plant surfaces provides opportunities for the genetic optimization of this protective layer. Genetic studies have identified genes involved in wax biosynthesis, extracellular transport, as well as spatial and temporal regulation of wax accumulation. In this study, a maize mutant, gl6 was characterized that exhibited reduced wax load on plant surfaces, increased water losses, and reduced seedling drought tolerance compared to wild type controls. The gl6 gene is a novel gene harboring a conserved domain with an unknown function. Quantification and microscopic observation of wax accumulation as well as subcellular localization of the GL6 protein provided evidence that gl6 may be involved in the intracellular trafficking of waxes, opening a door for studying this necessary yet poorly understood process for wax loading on plant surfaces.

plant biology

Temporal Small RNA Expression Profiling Under Drought Reveals a Potential Regulatory Role of snoRNAs in Drought Responses of Maize

Small RNAs (sRNAs) are short noncoding RNAs that play roles in many biological processes, including drought responses in plants. However, how the expression of sRNAs dynamically changes with the gradual imposition of drought stress in plants is largely unknown. We generated time-series sRNA sequence data from maize seedlings under drought stress and under well-watered conditions at the same time points. Analyses of length, functional annotation, and abundance of 736,372 non-redundant sRNAs from both drought and well-watered data, as well as genome copy number and chromatin modifications at the corresponding genomic regions, revealed distinct patterns of abundance, genome organization, and chromatin modifications for different sRNA classes of sRNAs. The analysis identified 6,646 sRNAs whose regulation was altered in response to drought stress. Among drought-responsive sRNAs, 1,325 showed transient down-regulation by the seventh day, coinciding with visible symptoms of drought stress. The profiles revealed drought-responsive microRNAs, as well as other sRNAs that originated from ribosomal RNAs (rRNAs), splicing small nuclear RNAs, and small nucleolar RNAs (snoRNA). Expression profiles of their sRNA derivers indicated that snoRNAs might play a regulatory role through regulating stability of rRNAs and splicing small nuclear RNAs under drought condition.

genomics

A legacy role for DNA binding of Lon protects against genotoxic stress

DNA binding proteins are essential for cellular life, but persistently bound complexes have toxic consequences. Here we show that the proteotoxic responsive bacterial protease Lon clears proteins from DNA to promote genotoxic stress resistance. Purified Lon binds DNA and degrades neighboring bound proteins, while a fully active DNA-blind Lon variant does not. This variant can degrade substrates as normal during unstressed growth, complements pleotropic phenotypes of {Delta}lon, including proteotoxic resilience, but remains sensitive to genotoxic stresses and fails to degrade proteins efficiently during DNA damage. Transposon sequencing reveals that {Delta}lon is vulnerable to loss of protein-DNA eviction factors and we use dynamic nucleoid occupancy profiling to show that chromosome-wide protein turnover relies on Lon DNA binding. Finally, disrupting Lon binding to mitochondria genomes also results in genotoxic stress sensitivity, consistent with the bacterial ancestry of this organelle. We propose that clearance of persistent proteins from DNA by Lon originated in free-living -proteobacteria and maintained during the evolution of mitochondria. SummaryDNA binding by the Lon protease protects against genotoxic damage in a manner preserved from bacteria to mitochondria.

microbiology

MECP2 duplication and mutations impair NSCs differentiation via miR-197 regulated ADAM10

How MECP2 (Methyl-CpG-binding protein 2) duplication affects cortex development remains elusive. We found that elevated MeCP2 expression promotes neurogenesis during cortex development in Tg(MECP2) mouse brain. Ectopic expression of MeCP2 in NPCs inhibits ADAM10 and hence compromises the NOTCH pathway during NPC differentiation. MeCP2 up-regulates miR-197 to down-regulate ADAM10. The enhanced NPC differentiation/migration in Tg(MECP2) embryonic brain can be repressed by overexpression of ADAM10 or a miR-197 inhibitor.\n\nConsistently, the reduced neurogenesis induced by three rare MeCP2 missense mutations (H371R, E394K, G428S) identified in a Han Chinese autism spectrum disorders (ASD) cohort, can be reversed by miR-197 both in vitro and in vivo. Our results revealed that a regulatory axis involving MeCP2, miR-197, ADAM10, and NOTCH signaling is critical for neurogenesis, which is affected by both MeCP2 duplication and mutation.

developmental biology

Bradyrhizobium diazoefficiens USDA 110-Glycine max interactome provides candidate proteins associated with symbiosis

Although the legume-rhizobium symbiosis is a most important biological process, there is a limited knowledge about the protein interaction network between host and symbiont. Using interolog and domain-based approaches, we constructed an inter-species protein interactome with 5115 protein-protein interactions between 2291 Glycine max and 290 Bradyrhizobium diazoefficiens USDA 110 proteins. The interactome was validated by expression pattern analysis in nodules, GO term semantic similarity, and co-expression analysis. One sub-network was further confirmed using luciferase complementation image assay. In the G. max-B. diazoefficiens interactome, bacterial proteins are mainly ion channel and transporters of carbohydrates and cations, while G. max proteins are mainly involved in the processes of metabolism, signal transduction, and transport. We also identified the top ten highly interacting proteins (hubs) for each of the two species. KEGG pathway analysis for each hub showed that two 14-3-3 proteins (SGF14g and SGF14k) and five heat shock proteins in G. max are possibly involved in symbiosis, and ten hubs in B. diazoefficiens may be important symbiotic effectors. Subnetwork analysis showed that 18 symbiosis-related SNARE proteins may play roles in regulating bacterial ion channels, and SGF14g and SGF14k possibly regulate the rhizobium dicarboxylate transport protein DctA. The predicted interactome and symbiosis proteins provide a valuable basis for understanding the molecular mechanism of root nodule symbiosis in soybean.

bioinformatics

The critical role of ASD-related gene CNTNAP3 in regulating synaptic development and social behavior in mice

Accumulated genetic evidences indicate that the contactin associated protein-like (CNTNAP) family is implicated in autism spectrum disorders (ASD). In this study, we identified genetic mutations in the CNTNAP3 gene from Chinese Han ASD cohorts and Simons Simplex Collections. We found that CNTNAP3 interacted with synaptic adhesion proteins Neuroligin1 and Neuroligin2, as well as scaffolding proteins PSD95 and Gephyrin. Significantly, we found that CNTNAP3 played an opposite role in controlling the development of excitatory and inhibitory synapses in vitro and in vivo, in which ASD mutants exhibited loss-of-function effects. In this study, we showed that Cntnap3-null mice exhibited deficits in social interaction, spatial learning and prominent repetitive behaviors. These evidences elucidate the pivotal role of CNTNAP3 in synapse development and social behaviors, providing the mechanistic insights for ASD.

neuroscience

ZmCOL3, a CCT-domain containing gene affects maize adaptation as a repressor and upstream of ZmCCT

Flowering time is a vital trait to control the adaptation of flowering plants to different environments. CCT-domain containing genes are considered to play an important role in plants flowering. Among 53 maize CCT family genes, 28 of them were located in the flowering time QTL regions and 16 genes were significant associated with flowering time based on candidate gene-based association mapping analysis. Furthermore, a CCT gene named as ZmCOL3 was validated to be a flowering repressor upstream of ZmCCT which is one of the key genes regulating maize flowering. The overexpressed ZmCOL3 could delay flowering time about 4 days whether in long day or short day conditions. The absent of one cytosine in 3UTR and the present of 551bp fragment in promoter regions are likely the causal polymorphisms which may contribute to the maize adaptation from tropical to temperate regions. ZmCOL3 could transactivate ZmCCT transcription or interfere circadian clock to inhibit flowering which was integrated in the modified model of maize photoperiod pathway.\n\nHighlightMaize CCT genes influence flowering time in different latitude environments and one of them named ZmCOL3 is a flowering time repressor which could transactivate ZmCCT transcription to delay flowering.

genetics

High-throughput fitness profiling of Zika virus E protein reveals different roles for N-linked glycosylation during infection of mammalian and mosquito cells

Zika virus (ZIKV) infection causes Guillain-Barre syndrome and severe birth defects. ZIKV envelope (E) protein is the major viral protein involved in cell receptor binding and entry and therefore considered one of the major determinants in ZIKV pathogenesis. Here, we report a gene-wide mapping of functional residues of ZIKV E protein using a mutant library with changes covering every nucleotide position. By comparing the replication fitness of every viral mutant between mosquito and human cells, we identified that mutations affecting N-linked glycosylation at N154 position display the most divergence. Through characterizing individual mutants, we show that, while ablation of N-linked glycosylation selectively benefits ZIKV infection of mosquito cells by enhancing cell entry, it either had little impact on ZIKV infection on certain human cells or decreased infection through entry factor DC-SIGN. In conclusion, we define the roles of individual residues of ZIKV envelope protein, which contribute to ZIKV replication fitness in human and mosquito cells.\n\nHighlightsO_LIGene-wide mapping of functional residues of E protein in human and mosquito cells.\nC_LIO_LIMutations affecting N-linked glycosylation display the most dramatic difference.\nC_LIO_LIN-linked glycosylation decreases ZIKV entry into mosquito cells.\nC_LIO_LIN-linked glycosylation is important for DC-SIGN mediated infection of human cells.\nC_LI

microbiology

A high-throughput analysis method of microdroplet PCR coupled with fluorescence spectrophotometry

Here we report a novel microdroplet PCR method combined with fluorescence spectrophotometry (MPFS), which allows for qualitative, quantitative and high -throughput detection of multiple DNA targets. In this study, each pair of primers was labeled with a specific fluorophore. Through microdroplet PCR, a target DNA was amplified and labeled with the same fluorophore. After products purification, the DNA products tagged with different fluorophores could be analyzed qualitatively by the fluorescent intensity determination. The relative fluorensence unit was also measured to construct the standard curve and to achieve quantitative analysis. In a reaction, the co -amplified products with different fluorophores could be simultaneously analyzed to achieve high -throughput detection. We used four kinds of GM maize as a model to confirm this theory. The qualitative results revealed high specificity and sensitivity of 0.5% (w / w). The quantitative results revealed that the limit of detection was 103copies and with good repeatability. Moreover, reproducibility assay were further performed using four foodborne pathogenic bacteria. Consequently, the same qualitative, quantitative and high-throughput results were confirmed as the four GM maize.

biochemistry