Biology subjects

Tang, X.

Publications and source records attributed to Tang, X..

15 recordsLinked to original sources

bioRxiv2018

A prognostic signature for lower-grade gliomas based on expression of long noncoding RNAs

Diffuse low-grade and intermediate-grade gliomas (together known as lower-grade gliomas, WHO grade II and III) develop in the supporting glial cells of brain and are the most common types of primary brain tumor. Despite a better prognosis for lower-grade gliomas, 70% of patients undergo high-grade transformation within 10 years, stressing the importance of better prognosis. Long non-coding RNAs (lncRNAs) are gaining attention as potential biomarkers for cancer diagnosis and prognosis. We have developed a computational model, UVA8, for prognosis of lower-grade gliomas by combining lncRNA expression, Cox regression and L1-LASSO penalization. The model was trained on a subset of patients in TCGA. Patients in TCGA, as well as a completely independent validation set (CGGA) could be dichotomized based on their risk score, a linear combination of the level of each prognostic lncRNA weighted by its multivariable cox regression coefficient. UVA8 is an independent predictor of survival and outperforms standard epidemiological approaches and previous published lncRNA-based predictors as a survival model. Guilt-by-association studies of the lncRNAs in UVA8, all of which predict good outcome, suggest they have a role in suppressing interferon stimulated response and epithelial to mesenchymal transition. The expression levels of 8 lncRNAs can be combined to produce a prognostic tool applicable to diverse populations of glioma patients. The 8 lncRNA (UVA8) based score can identify grade II and grade III glioma patients with poor outcome and thus identify patients who should receive more aggressive therapy at the outset.

genomics↗

bioRxiv2018

Identification of the bacterial biosynthetic gene clusters of the oral microbiome illuminates the unexplored social language of bacteria during health and disease

Small molecules are the primary communication media of the microbial world. Recent bioinformatics studies, exploring the biosynthetic gene clusters (BGCs) which produce many small molecules, have highlighted the incredible biochemical potential of the signaling molecules encoded by the human microbiome. Thus far, most research efforts have focused on understanding the social language of the gut microbiome, leaving crucial signaling molecules produced by oral bacteria, and their connection to health versus disease, in need of investigation. In this study, a total of 4,915 BGCs were identified across 461 genomes representing a broad taxonomic diversity of oral bacteria. Sequence similarity networking provided a putative product class for over 100 unclassified novel BGCs. The newly identified BGCs were cross-referenced against 254 metagenomes and metatranscriptomes derived from individuals with either good oral health, dental caries, or periodontitis. This analysis revealed 2,473 BGCs, which were differentially represented across the oral microbiomes associated with health versus disease. Co-abundance network analysis identified numerous inverse correlations between BGCs and specific oral taxa. These correlations were present in health, but greatly reduced in dental caries, which may suggest a defect in colonization resistance. Finally, corroborating mass spectrometry identified several compounds with homology to products of the predicted BGC classes. Together, these findings greatly expand the number of known biosynthetic pathways present in the oral microbiome and provide an atlas for experimental characterization of these abundant, yet poorly understood, molecules and socio-chemical relationships, which impact the development of caries and periodontitis, two of the worlds most common chronic diseases.\n\nIMPORTANCEThe healthy oral microbiome is symbiotic with the human host, importantly providing colonization resistance against potential pathogens. Dental caries and periodontitis are two of the worlds most common and costly chronic infectious diseases, and are caused by a localized dysbiosis of the oral microbiome. Bacterially produced small molecules, often encoded by BGCs, are the primary communication media of bacterial communities, and play a crucial, yet largely unknown, role in the transition from health to dysbiosis. This study provides a comprehensive mapping of the BGC repertoire of the human oral microbiome and identifies major differences in health compared to disease. Furthermore, BGC representation and expression is linked to the abundance of particular oral bacterial taxa in health versus dental caries and periodontitis. Overall, this study provides a significant insight into the chemical communication network of the healthy oral microbiome, and how it devolves in the case of two prominent diseases.

microbiology↗

bioRxiv2018

Morphological profile determines the frequency of spontaneous calcium events in astrocytic processes

Astrocytes express a complex repertoire of intracellular Ca2+ transients (events) that represent a major form of signaling within individual cells and in the astrocytic syncytium. These events have different spatiotemporal profiles, which are modulated by neuronal activity. Spontaneous Ca2+ events appear more frequently in distal astrocytic processes and independently from each other. However, little is known about the mechanisms underlying such subcellular distribution of the Ca2+ events. Here we identify the initiation points of the Ca2+ events within the territory of single astrocytes expressing genetically encoded Ca2+ indicator GCaMP2 in culture or in hippocampal slices. We found that most of the Ca2+ events start in thin distal processes. Our mathematical model demonstrated that a high surface-to-volume (SVR) of the thin processes leads to increased amplitude of baseline Ca2+ fluctuations caused by a stochastic opening of Ca2+ channels in the plasma membrane. Suprathreshold fluctuations trigger Ca2+-induced Ca2+ release (CICR) from the Ca2+ stores by activating inositol 1,4,5-trisphosphate (IP3) receptors. In agreement with the model prediction, the spontaneous Ca2+ events frequency depended on the extracellular Ca2+ concentration. Astrocytic depolarization by high extracellular K+ increased the frequency of the Ca2+ events through activation of voltage-gated Ca2+ channels (VGCC) in cultured astrocytes. Our results suggest that the morphological profile of the astrocytic processes is responsible for tuning of the Ca2+ event frequency. Therefore, the structural plasticity of astrocytic processes can be directly translated into changes in astrocytic Ca2+ signaling. This may be important for both physiological and pathological astrocyte remodeling.\n\nMain pointsO_LIMajority of spontaneous Ca2+ events start in thin astrocytic processes\nC_LIO_LIHigher surface-to-volume ratio of the process is responsible for larger intracellular Ca2+ fluctuations\nC_LIO_LILarger intracellular Ca2+ fluctuations trigger Ca2+-dependent Ca2+ release\nC_LI

neuroscience↗

bioRxiv2018

Distinct timescales of RNA regulators enable the construction of a genetic pulse generator

To build complex genetic networks with predictable behaviours, synthetic biologists use libraries of modular parts that can be characterized in isolation and assembled together to create programmable higher-order functions. Characterization experiments and computational models for gene regulatory parts operating in isolation are routinely employed to predict the dynamics of interconnected parts and guide the construction of new synthetic devices. Here, we individually characterize two modes of RNA-based transcriptional regulation, using small transcription activating RNAs (STARs) and CRISPR interference (CRISPRi), and show how their distinct regulatory timescales can be used to engineer a composed feedforward loop that creates a pulse of gene expression. We use a cell-free transcription-translation system (TXTL) to rapidly characterize the system, and we apply Bayesian inference to extract kinetic parameters for an ODE-based mechanistic model. We then demonstrate in simulation and verify with TXTL experiments that the simultaneous regulation of a single gene target with STARs and CRISPRi leads to a pulse of gene expression. Our results suggest the modularity of the two regulators in an integrated genetic circuit, and we anticipate that construction and modeling frameworks that can leverage this modularity will become increasingly important as synthetic circuits increase in complexity.

synthetic biology↗

bioRxiv2018

Sirt7 regulates circadian phase coherence of hepatic circadian clock via a body temperature/Hsp70-Sirt7-Cry1 axis

The biological clock is generated in the hypothalamic suprachiasmatic nucleus (SCN), which synchronizes peripheral oscillators to coordinate physiological and behavioral activities throughout the body. Disturbance of circadian phase coherence between the central and peripheral could disrupt rhythms and thus cause diseases and aging. Here, we identified hepatic Sirt7 as an early element responsive to light, which ensures the phase coherence in mouse liver. Loss of Sirt7 leads to advanced liver circadian phase; restricted feeding in daytime entrains hepatic clock more rapidly in Sirt7-/- mice compared to wild-types. Molecularly, a light-driven body temperature (BT) oscillation induces rhythmic expression of Hsp70, which binds to and promotes the ubiquitination and proteasomal degradation of Sirt7. Sirt7 rhythmically deacetylates Cry1 on K565/579 and promotes Fbxl3-mediated degradation, thus coupling hepatic clock to the central pacemaker. Together, our data identify a novel BT/Hsp70-Sirt7-Cry1 axis, which transmits biological timing cues from the central to the peripheral and ensures circadian phase coherence in livers.

molecular biology↗

bioRxiv2018

Genetically modified pigs are protected from classical swine fever virus

Classical swine fever (CSF) caused by classical swine fever virus (CSFV) is among the most detrimental diseases, and leads to significant economic losses in the swine industry. Despite efforts by many government authorities try to stamp out the disease from national pig populations, the disease remains widespread. Here, antiviral small hairpin RNAs (shRNAs) were selected and then inserted at the porcine ROSA26 (pROSA26) locus via a CRISPR/Cas9-mediated knock-in strategy. Finally, anti-CSFV transgenic (TG) pigs were produced by somatic nuclear transfer (SCNT). Importantly, in vitro and in vivo viral challenge assays demonstrated that these TG pigs could effectively limit the growth of CSFV and reduced CSFV-associated clinical signs and mortality, and the disease resistance was stably transmitted to F1-generation. The use of these TG pigs can improve the well-being of livestock and substantially reduce virus-related economic losses. Additionally, this antiviral approach may provide a reference for future antiviral research.\n\nAuthor summaryClassical swine fever (CSF), caused by classical swine fever virus (CSFV), and is a highly contagious, often fatal porcine disease with significant economic losses. Due to its economic importance to the pig industry, the biology and pathogenesis of CSFV have been investigated extensively. Despite efforts by many government authorities to stamp out the disease from national pig populations, the disease remains widespread in some regions and seems to be waiting for the reintroduction and the next round of disease outbreaks. These highlight the necessity and urgency of developing more effective approaches to eradicate the challenging CSFV. In this study, we successfully produced anti-CSFV transgenic pigs and confirmed that these transgenic pigs could effectively limit the growth of CSFV in vivo and in vitro and that the disease resistance traits in the TG founders can be stably transmitted to their F1-generation offspring. This study suggests that these TG pigs can improve the well-being of livestock and contribute to offer potential benefits over commercial vaccination. The use of these TG pigs can improve the well-being of livestock and substantially reduce CSFV-related economic losses.

genomics↗

bioRxiv2018

Hazard detection with monocular bioptic telescopes in a driving simulator

ABSTRACT\n\nPurpose: Recently we developed a driving simulator paradigm to evaluate detection of road hazards when using a bioptic telescope and conducted an initial study using normally-sighted observers with simulated vision loss. We now extend our investigation to quantifying the extent to which visually impaired bioptic users are able to use their fellow (non-telescope) eye to compensate for the ring scotoma of a monocular bioptic telescope. We tested the hypothesis that detection rates would be higher in binocular viewing (fellow eye could potentially compensate) than monocular viewing (fellow eye patched so it could not compensate) for pedestrian hazards present in the scene only while the telescope was being used.\n\nMethods: Sixteen bioptic telescope users (17-80 y) completed six test drives, including three with binocular viewing interleaved between three with monocular viewing. While driving, they used their own monocular bioptic telescopes to read information on highway road signs (n = 71) and pressed the horn when they saw a pedestrian hazard (n = 50). Twenty-six of the pedestrians were programed to appear, run on the road ahead of the driver for 1s within the ring scotoma and then disappear, within the period when participants were reading signs through the bioptic. The timing of the head movement to look into and out of the bioptic was determined and events were then categorized by whether or not the pedestrian hazard was present in the scene only while using the bioptic.\n\nResults: When pedestrian hazards were in the scene only while subjects were using the bioptic to read a sign, detection rates were significantly higher in binocular than monocular viewing (68% vs. 40%). However, when pedestrians when subjects had a brief view of the pedestrian either beforeor after looking through the bioptic, then detection rates did not differ in binocular and monocular viewing (78% vs. 79%). By comparison, when not using the bioptic detection rates were higher (> 90%) and reaction times were shorter (without 0.95 s vs. with 1.25 s)\n\nConclusions: Our results suggest that under binocular viewing conditions the fellow eye was able to compensate for the ring scotoma to a certain extent when subjects used a monocular telescope to read road signs; however, performance was not as good as without the bioptic.

neuroscience↗

bioRxiv2018

Roles of motion perception and visual acuity for driving hazard perception

PURPOSEThere are many visually impaired people who can drive legally with bioptic telescope. Drawing on the experience of drivers with reduced vision, this study investigated the role of motion perception and visual acuity in driving, under simulated low visual acuity.\n\nMETHODSTwenty normally sighted participants took part in a driving hazard perception (HP) test, in four different conditions: with/without motion interruption and with/without simulated low visual acuity. In interrupted motion conditions a mask frame was inserted between every frame of the driving videos. In simulated low visual acuity conditions, participants wore glasses with diffusing filters that lowered their visual acuity to 20/120 on average. Participants response time, hazard detection rates, and HP scores, which combined response time and detection rate, were compared.\n\nRESULTSRepeated measure ANOVA revealed that the HP scores significantly declined from 20.46 to 16.82 due to the motion mask (F(1,19) = 9.343, p = 0.006). However, simulated low visual acuity did not affect HP scores (F(1,19) = 1.807, p = 0.195). The interaction between vision and mask was not significant (F(1,19) = 1. 295, p = 0.269). The decline in score was mostly due to significant decrease in detection rate, from 0.80 to 0.64, due to the motion mask (F(1,19) = 16.686, p = 0.001).\n\nCONCLUSIONSIn this experimental setting, human observers relied largely on motion information for detecting driving hazards, rather than high visual acuity. This finding might help explain how visually impaired drivers can compensate for their impaired vision during driving.

neuroscience↗

bioRxiv2018

Colonization of phosphate-solubilizing Pseudomonas sp. strain P34-L in the wheat rhizosphere and its effects on wheat growth and the expression of phosphate transporter gene TaPT4 in wheat

The ability to colonize the rhizosphere is an important basics requirement for field application of plant growth-promoting rhizobacteria (PGPR) strains. There are complex signal exchanges and mutual recognition between microbes and plants. In this study, phosphate-solubilizing Pseudomonas sp. P34, a PGPR strain with affinity to wheat, was isolated from the wheat rhizosphere by wheat germ agglutinin (WGA). The plasmid pTR102 harboring the luciferase luxAB gene was transferred into P34 to create P34-L. The labeled strain was used to track the temporal and spatial characteristics of colonization in wheat rhizosphere and its effects on wheat development. The transcript level of phosphate transporter gene TaPT4, a phosphorus deficiency indicator gene, in wheat roots was monitored by quantitative reverse-transcription PCR. The experimental results indicated that there was a high density of stain P34-L within the top 8-cm depth of the wheat rhizosphere on day 36 of wheat growth. The strain could survive in the wheat rhizosphere for a long time, and colonize new spaces in wheat rhizosphere following the extension of wheat roots. Compared with uninoculated wheat plants, those inoculated with P34-L showed significantly increased phosphorus accumulation in leaves, seedling fresh and dry weight, root fresh and dry weight, total root length, and number of root tips, forks, crossings, which showed a great value of application of the strain on wheat production by promoting the root growth and dry matter accumulation. Strain P34-L down-regulated the transcript level of TaPT4 in wheat roots, which means a well phosphorus supplementation environment was established by P34-L.\n\nImportanceMany PGPR strains often failed to achieve the desired effects when applied in the field. One major reason for the failure is lack of a special affinity between a certain strain and the target host plant, so those strains have low competitive ability with the indigenous microorganism, and unable to survive constantly in rhizosphere. In this work, a new technique to isolate wheat-specific phosphate-solubilizing PGPR strain by WGA was established. The isolate P34 was confirmed can colonize the wheat rhizosphere, and have significantly ability in promoting phosphorus absorption and wheat growth by luminescence labeling techniques. Furthermore, the phosphate-solubilizing ability of this affinity PGPR strain was verified in gene level by quantitative reverse-transcription PCR. These results lay a firm foundation for further research on the relationships between PGPR and their host plants. Meanwhile, this work supplied a potential ideal biofertilizer producing strain for sustainable agriculture.

microbiology↗

bioRxiv2018

A large-scale whole-genome sequencing analysis reveals highly specific genome editing by both Cas9 and Cpf1 nucleases in rice

Targeting specificity has been an essential issue for applying genome editing systems in functional genomics, precise medicine and plant breeding. Understanding the scope of off-target mutations in Cas9 or Cpf1-edited crops is critical for research and regulation. In plants, only limited studies had used whole-genome sequencing (WGS) to test off-target effects of Cas9. However, the cause of numerous discovered mutations is still controversial. Furthermore, WGS based off-target analysis of Cpf1 has not been reported in any higher organism to date. Here, we conducted a WGS analysis of 34 plants edited by Cas9 and 15 plants edited by Cpf1 in T0 and T1 generations along with 20 diverse control plants in rice, a major food crop with a genome size of ~380 Mb. The sequencing depth ranged from 45X to 105X with reads mapping rate above 96%. Our results clearly show that most mutations in edited plants were created by tissue culture process, which caused ~102 to 148 single nucleotide variations (SNVs) and ~32 to 83 insertions/deletions (indels) per plant. Among 12 Cas9 single guide RNAs (sgRNAs) and 3 Cpf1 CRISPR RNAs (crRNAs) assessed by WGS, only one Cas9 sgRNA resulted in off-target mutations in T0 lines at sites predicted by computer programs. Moreover, we cannot find evidence for bona fide off-target mutations due to continued expression of Cas9 or Cpf1 with guide RNAs in T1 generation. Taken together, our comprehensive and rigorous analysis of WGS big data across multiple sample types suggests both Cas9 and Cpf1 nucleases are very specific in generating targeted DNA modifications and off-targeting can be avoided by designing guide RNAs with high specificity.

molecular biology↗

bioRxiv2017

Boosting ATM Activity Promotes Longevity in Nematodes and Mice

DNA damage accumulates with age1. However, whether and how robust DNA repair machinery promotes longevity is elusive. Here, we demonstrate that activation of ataxia-telangiectasia mutated (ATM) via low dose of chloroquine (CQ) promotes DNA damage clearance, rescues age-related metabolic shift, and extends lifespan in nematodes and mice. Molecularly, ATM phosphorylates SIRT6 deacetylase and thus prevents MDM2-mediated ubiquitination and proteasomal degradation. Extra copies of Sirt6 in Atm-/- mice extend lifespan, accompanied with restored metabolic homeostasis. In a progeria mouse model with low ATM protein level and DNA repair capacity, the treatment with CQ ameliorates premature aging features and extends lifespan. Thus, our data highlights a pro-longevity role of ATM, for the first time establishing direct causal links between robust DNA repair machinery and longevity, and providing therapeutic strategy for progeria and age-related metabolic diseases.

molecular biology↗

bioRxiv2017

PANOPLY: A computational method for identification of promising drugs for a patient based on multidimensional data

PurposeThe majority of cancer patients receive treatments that are minimally informed by omics data. We propose a precision medicine computational framework (PANOPLY: Precision cancer genomic report: single sample inventory) to identify and prioritize drug targets and cancer therapy regimens.\n\nMethodsThe PANOPLY approach integrates clinical data with germline and somatic features obtained from multi-omics platforms, and apply machine learning, and network analysis approaches in the context of the individual patient and matched controls. The PANOPLY workflow employs four steps (i) selection of matched controls to the case of interest (ii) identification of case-specific genomic events (iii) identification of suitable drugs using the driver-gene network and random forest analyses and (iv) provide an integrated multi-omics case report of the patient with prioritization of anti-cancer drugs.\n\nResultsThe PANOPLY workflow can be executed on a stand-alone virtual machine and is also available for download as an R package. We applied the method to an institutional breast cancer neoadjuvant chemotherapy study which collected clinical and genomic data as well as patient-derived xenografts (PDXs) to investigate the prioritization offered by PANOPLY. In a chemotherapy-resistant PDX model, we found that that the prioritized drug, olaparib, was more effective than placebo in treating the tumor (P < 0.05). We also applied PANOPLY to in-house and publicly accessible multi-omics tumor datasets with therapeutic response or survival data available.\n\nConclusionPANOPLY shows promise as a means to prioritize drugs based on clinical and multi-omics data for an individual cancer patient. Additional studies are needed to confirm this approach.

bioinformatics↗

bioRxiv2017

Transcriptome Deconvolution of Heterogeneous Tumor Samples with Immune Infiltration

Transcriptomic deconvolution in cancer and other heterogeneous tissues remains challenging. Available methods lack the ability to estimate both component-specific proportions and expression profiles for individual samples. We present DeMixT, a new tool to deconvolve high dimensional data from mixtures of more than two components. DeMixT implements an iterated conditional mode algorithm and a novel gene-set-based component merging approach to improve accuracy. In a series of experimental validation studies and application to TCGA data, DeMixT showed high accuracy. Improved deconvolution is an important step towards linking tumor transcriptomic data with clinical outcomes. An R package, scripts and data are available: https://github.com/wwylab/DeMixT/.

bioinformatics↗

bioRxiv2016

Chimeras Link to Tandem Repeats and Transposable Elements in Tetraploid Hybrid Fish

The formation of the allotetraploid hybrid lineage (4nAT) encompasses both distant hybridization and polyploidization processes. The allotetraploid offspring have two sets of sub-genomes inherited from both parental species and therefore it is important to explore its genetic structure. Herein, we construct a bacterial artificial chromosome library of allotetraploids, and then sequence and analyze the full-length sequences of 19 bacterial artificial chromosomes. Sixty-eight DNA chimeras are identified, which are divided into four models according to the distribution of the genomic DNA derived from the parents. Among the 68 genetic chimeras, 44 (64.71%) are linked to tandem repeats (TRs) and 23 (33.82%) are linked to transposable elements (TEs). The chimeras linked to TRs are related to slipped-strand mispairing and double-strand break repair while the chimeras linked to TEs are benefit from the intervention of recombinases. In addition, TRs and TEs are linked not only with the recombinations, but also with the insertions/deletions of DNA segments. We conclude that DNA chimeras accompanied by TRs and TEs coordinate a balance between the sub-genomes derived from the parents which reduces the genomic shock effects and favors the evolutionary and adaptive capacity of the allotetraploidization. It is the first report on the relationship between formation of the DNA chimeras and TRs and TEs in the polyploid animals.

genetics↗

bioRxiv2016

UNC-5 (UNC5) Regulates the Length and Number of Processes that Caenorhabditis elegans Neurons Can Develop

Neurons extend processes that vary in number, length, and direction of outgrowth. Extracellular cues help determine outgrowth patterns. In Caenorhabditis elegans, neurons respond to the extracellular UNC-6 (netrin) cue via UNC-40 (DCC) and UNC-5 (UNC5) receptors. Previously we presented evidence that UNC-40 asymmetric localization at the plasma membrane is self-organizing and that UNC-40 can localize and mediate outgrowth at randomly selected sites. We also postulate that the process is statistically dependent, i.e. if the probability of outgrowth at one site changes then the probability at another site(s) must also change. Over time, the direction of outgrowth activity fluctuates across the membrane. A probability distribution describes the likelihood of outgrowth in each direction. Random walk modeling predicts that the degree to which the direction of outgrowth fluctuations affects the outward displacement of the membrane. We predict that extracellular cues create patterns of outgrowth by differentially affecting the degree to which the direction of outgrowth activity fluctuates along the membrane. This produces different rates of outgrowth along the surface and creates patterns of extension. Here we present evidence that UNC-5 (UNC5) receptor activity regulates UNC-40 asymmetric localization and the patterning of outgrowth. We show that unc-5 mutations alter UNC-40 asymmetric localization and the patterns of outgrowth that neurons develop. Genetic interactions suggest UNC-5 acts through the UNC-53 (NAV2) cytoplasmic protein to regulate UNC-40 asymmetric localization in response to both the UNC-6 and EGL-20 (wnt) extracellular cues.

neuroscience↗