Biology subjects

Kang, X.

Publications and source records attributed to Kang, X..

46 records · Page 3Linked to original sources

bioRxiv2021

phasebook: haplotype-aware de novo assembly of diploid genomes from long reads

Haplotype-aware diploid genome assembly is crucial in genomics, precision medicine, and many other disciplines. Long-read sequencing technologies have greatly improved genome assembly thanks to advantages of read length. However, current long-read assemblers usually introduce disturbing biases or fail to capture the haplotype diversity of the diploid genome. Here, we present phasebook, a novel approach for reconstructing the haplotypes of diploid genomes from long reads de novo. Benchmarking experiments demonstrate that our method outperforms other approaches in terms of haplotype coverage by large margins, while preserving competitive performance or even achieving advantages in terms of all other aspects relevant for genome assembly.

bioinformatics↗

bioRxiv2021

Strainline: full-length de novo viral haplotype reconstruction from noisy long reads

Haplotype-resolved de novo assembly of highly diverse virus genomes is critical in prevention, control and treatment of viral diseases. Current methods either can handle only relatively accurate short read data, or collapse haplotype-specific variations into consensus sequence. Here, we present Strainline, a novel approach to assemble viral haplotypes from noisy long reads without a reference genome. As a crucial consequence, Strainline is the first approach to provide strain-resolved, full-length de novo assemblies of viral quasispecies from noisy third-generation sequencing data. Benchmarking experiments on both simulated and real datasets of varying complexity and diversity confirm this novelty, by demonstrating the superiority of Strainline in terms of relevant criteria in comparison with the state of the art.

bioinformatics↗

bioRxiv2021

A cell wall invertase controls nectar volume and sugar composition

Flowering plants produce nectar to attract pollinators. The main nectar sugars are sucrose, glucose, and fructose, which can vary widely in ratio and concentration across species. Brassica spp. produce a hexose-dominant nectar (high in the monosaccharides glucose and fructose) with very low levels of the disaccharide sucrose. Cell wall invertases (CWINVs) catalyze the irreversible hydrolysis of sucrose into glucose and fructose in the apoplast. We found that BrCWINV4A is highly expressed in the nectaries of Brassica rapa. Moreover, a brcwinv4a null mutant has (1) greatly reduced cell wall invertase activity in the nectaries, and (2) produces a sucrose-rich nectar with little hexose content, but (3) with significantly less volume. These results were recapitulated via exogenous application of an invertase inhibitor to wild-type flowers. Honeybees prefer nectars with some sucrose, but wild-type B. rapa flowers were much more heavily visited than those of brcwinv4a, suggesting that the potentially attractive sucrose-rich nectar of brcwinv4a could not compensate for its low volume. These results cumulatively indicate that BrCWINV4A is not only essential for producing a hexose-rich nectar, but also support a model of nectar secretion in which its hydrolase activity is required for maintaining a high intracellular-to-extracellular sucrose ratio that facilitates the continuous export of sucrose into the apoplast via SWEET9. Extracellular hydrolysis of each sucrose into two hexoses by BrCWINV4A also likely creates the osmotic potential required for nectar droplet formation. In summary, modulation of CWINV activity can at least partially account for naturally occurring differences in nectar volume and sugar composition.

plant biology↗

bioRxiv2020

Stable Polymer Bilayers for Protein Channel Recordings at High Guanidinium Chloride Concentrations

Use of chaotropic reagents is common in biophysical characterization of biomolecules. When the study involves transmembrane protein channels, the stability of the protein channel and supporting bilayer membrane must be considered. In this letter we show that planar bilayers composed of poly(1,2-butadiene)-b-poly(ethylene oxide) diblock copolymer are stable and leak-free at high guanidinium chloride concentrations, in contrast to diphytanoyl phosphatidylcholine bilayers which exhibit deleterious leakage under similar conditions. Further, insertion and functional analysis of channels such as -hemolysin and MspA are straightforward in these polymer membranes. Finally, we demonstrate that -hemolysin channels maintain their structural integrity at 2M guanidinium chloride concentrations using blunt DNA hairpins as molecular reporters.

biophysics↗

bioRxiv2020

lncRNA DLEU2 acts as a miR-181a sponge regulated SEPP1 (may as a biomarker for sarcopenia) to inhibit skeletal muscle differentiation and regeneration

BackgroundSarcopenia is a serious public health problem. The ceRNA network has been demonstrated vital in the development of skeletal muscle, but there is currently no effective method to assess the risk of sarcopenia. The purpose of this research is to create and authenticate a ceRNA pathway based on a predictive model of sarcopenia. MethodsA clinical prediction model for sarcopenia was established using the RNAs (validated by clinical data) that are co-differentially expressed in the database, and a ceRNA network was constructed. The correlation analysis of each element in the ceRNA network was performed according to the clinical samples and the GTEX database, and the possible key ceRNA pathways were screened. C2C12 mouse myoblast Cells experiments were used to verify these ceRNA pathways. FindingsBased on four molecular markers of SEPP1, SV2A, GOT1 and GFOD1, we developed a new model for predicting sarcopenia with well accuracy, and constructed a ceRNA network accordingly. Clinical sample showed that the expression levels of lncDLEU2, SEPP1, and miR-181a were closely related to the risk of sarcopenia. The C2C12 mouse myoblast cells were cultivated to verify that lncDLEU2 inhibits muscle proliferation and differentiation by acting as a miR-181a sponge regulated SEPP1. InterpretationOur research developed a highly accurate prediction tool for the risk of sarcopenia. These findings suggest that lncDLEU2-miR-181a-SEPP1 pathway inhibits muscle differentiation and regeneration. This pathway may uncover some new therapeutic targets for the treatment of sarcopenia caused by aging.

bioinformatics↗

bioRxiv2020

Optimization of multiplexed CRISPR/Cas9 system for highly efficient genome editing in Setaria viridis

In recent years, Setaria viridis has been developed as a model plant to better understand the C4 photosynthetic pathway in major crops. With the increasing availability of genomic resources for S. viridis research, highly efficient genome editing technologies are needed to create genetic variation resources for functional genomics. Here, we developed a protoplast assay to rapidly optimize the multiplexed CRISPR/Cas9 system in S. viridis. Targeted mutagenesis efficiency was further improved by an average of 1.4-fold with the exonuclease, Trex2. Distinctive mutation profiles were found in the Cas9_Trex2 samples with 94% of deletions larger than 10bp, and less than 1% of mutations being insertions. Further analyses indicated that 52.2% of deletions induced by Cas9_Trex2, as opposed to 3.5% by Cas9 alone, were repaired through microhomology-mediated end joining (MMEJ) rather than the canonical NHEJ DNA repair pathway. Combined with the robust agrobacterium-mediated transformation method with more than 90% efficiency, the multiplex CRISPR/Cas9_Trex2 system was demonstrated to induce targeted mutations in two tightly linked genes, svDrm1a and svDrm1b, at the frequency ranging from 73% to 100% in T0 plants. These mutations were transmitted to at least 60% of the transgene-free T1 plants with 33% of them containing bi-allelic or homozygous mutations in both genes. This highly efficient multiplex CRISPR/Cas9_Trex2 system makes it possible to create a large mutant resource for S. viridis in a rapid and high throughput manner, and has the potential to be widely applicable in achieving more predictable MMEJ-mediated mutations in many plant species.

plant biology↗

bioRxiv2020

From graph topology to ODE models for gene regulatory networks

A gene regulatory network can be described at a high level by a directed graph with signed edges, and at a more detailed level by a system of ordinary differential equations (ODEs). The former qualitatively models the causal regulatory interactions between ordered pairs of genes, while the latter quantitatively models the time-varying concentrations of mRNA and proteins. This paper clarifies the connection between the two types of models. We propose a property, called the constant sign property, for a general class of ODE models. The constant sign property characterizes the set of conditions (system parameters, external signals, or internal states) under which an ODE model is consistent with a signed, directed graph. If the constant sign property for an ODE model holds globally for all conditions, then the ODE model has a single signed, directed graph. If the constant sign property for an ODE model only holds locally, which may be more typical, then the ODE model corresponds to different graphs under different sets of conditions. In addition, two versions of constant sign property are given and a relationship between them is proved. As an example, the ODE models that capture the effect of cis-regulatory elements involving protein complex binding, based on the model in the GeneNetWeaver source code, are described in detail and shown to satisfy the global constant sign property with a unique consistent gene regulatory graph. Even a single gene regulatory graph is shown to have many ODE models of GeneNetWeaver type consistent with it due to combinatorial complexity and continuous parameters. Finally the question of how closely data generated by one ODE model can be fit by another ODE model is explored. It is observed that the fit is better if the two models come from the same graph.

bioinformatics↗

bioRxiv2019

Revaluation of magnetic properties of Magneto, MagR and αGFP-TRPV1/GFP-ferritin

ABSTRACT AND INTRODUCTIONMagnetic control of neuronal activity offers many obvious advantages over electric, optogenetic and chemogenetic manipulations. A recent series of highly visible papers reported the development of magnetic actuators (i.e., Magneto, MagR and GFP-TRPV1/GFP-ferritin) that appeared to be effective in controlling neuronal firing1-3, yet their action mechanisms seem to conflict with the principles of physics4. We found that neurons expressing Magneto, MagR and GFP-TRPV1/GFP-ferritin did not respond to magnetic stimuli with any membrane depolarization (let alone action potential firing), although these neurons frequently generated spontaneous action potentials. Because the previous study did not establish the precise temporal correlation between magnetic stimuli and action potentials in recorded neurons1-3, the reported magnetically-evoked action potentials are likely to represent mismatched spontaneous firings.

neuroscience↗

bioRxiv2019

Time Series Experiment Design Under One-Shot Sampling: The Importance of Condition Diversity

Many biological data sets are prepared using one-shot sampling, in which each individual organism provides only one sample. Time series therefore do not follow trajectories of individuals over time. However, samples collected at different times from individuals grown/raised under the same conditions share the same perturbations of the biological processes, and hence behave as surrogates for multiple samples from a single individual at different times. This implies the importance of growing/raising individuals under multiple conditions if one-shot sampling is used. This paper models the condition effect explicitly by correlated perturbations in the variations driving the expression dynamics, quantifies the performance of the generalized likelihood-ratio test for network structure, and illustrates the difficulty in network reconstruction under one-shot sampling when the condition effect is absent.

systems biology↗

bioRxiv2019

Combined Transcriptomics and Proteomics Forecast Analysis for Potential Genes Regulating the Columbian Plumage Color in Chickens

BackgroundColoration is one of the most recognizable characteristics in chickens, and clarifying the coloration mechanisms will help us understand feather color formation. \"Yufen I\" is an commercial egg-laying chicken breed in China, that was developed by a three-line cross using lines H, N and D. Columbian plumage is a typical feather character of the \"Yufen I\" H line. To elucidate the molecular mechanism underlying pigmentation of Columbian plumage, this study utilizes the technology of high-throughput sequencing to compare the transcriptome and proteome differences in different feather follicular tissue, including the dorsal neck with black and white striped feather follicles (Group A) and the ventral neck with white feather follicles (Group B) in the \"Yufen I\" H line.\n\nResultsIn this study, we identified a total of 21,306 genes and 5203 proteins in chicken feather follicles. Among these, 209 genes and 382 proteins were differentially expressed in two different locations, Group A and Group B, respectively. A total of 8 differentially expressed genes (DEGs) and 9 differentially expressed proteins (DEPs) were found to be involved in the melanogenesis pathway. Besides, a specifically expressed MED23 gene and a differential expressed GNAQ protein were involved in melanin synthesis. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis mapped 190 DEGs and 322 DEPs, to 175 and 242 pathways, respectively, and there were 166 pathways correlated with both DEGs and DEPs. 49 DEPs/DEGs overlapped and were enriched for 12 pathways. Transcriptomic and proteomic analyses revealed that the following pathways were activated: melanogenesis, cardiomycete adrenergic, calcium and the cGMP-PKG. The expression of DEGs was validated by real-time quantitative polymerase chain reaction (qRT-PCR) that was similar to that of RNA-seq. In addition, we found that MED23, FZD10, WNT7B and WNT11 genes expression peaked at approximately 8 weeks in the \"Yufen I\" H line, which is consistent with the molting cycle. As both the groups showed significant differences in terms of expression of the genes studied, this study opens up avenues for study in the future to assess their exact function in color of plumage.\n\nConclusionThese common DEGs and DEPs were enriched in the melanogenesis pathway. The MED23 and GNAQ were also reported to have a crucial part synthesis of melanin. In addition, this study is the first to reveal variations in gene and protein in the \"Yufen I\" H line during Columbian feather color development, and discover principal genes and proteins that would aid in the functional genomics studies in future. The results of the present study provide a significant conceptual basis for the \"Yufen I\" H line future breeding schemes and provide a basis for research on the mechanisms of feather pigmentation.

molecular biology↗