Biology subjects

Hou, H.

Publications and source records attributed to Hou, H..

48 records · Page 3Linked to original sources

bioRxiv2021

Sulfur limitation increases duckweed starch accumulation without compromising growth

Duckweeds contain relatively high levels of starch and are a potential biomass feedstock for biofuel production. Here, the biomass and starch yield of duckweed under three different nutrient-limited conditions were analyzed to investigate possible ways of further increasing the efficiency of starch production. The results showed that sulfur limitation resulted in the highest starch yield, which was 42% and 73% higher than in nitrogen or phosphorus limitation, respectively. The high yield of sulfur-limited duckweed is largely due to the combinations of little effects on biomass and high accumulations of starch. Although nitrogen limitation led to higher starch content (67.4%), it severely reduced biomass production. The photosynthetic performance indicator Fv/Fm was a simple and sensitive indicator of starch content in nutrient-limited duckweed. Taken together, this study demonstrates that sulfur limitation is a simple and efficient way to increase starch yield, highlighting the great potential of duckweed for biofuel production. We report that sulfur limitation is a practical approach to increase starch yields in duckweed without affecting growth or biomass. HighlightsO_LISulfur limitation induces starch production in a duckweed specie. C_LIO_LINitrogen limitation triggers the highest starch content, but limits growth. C_LIO_LISulfur limitation results in the highest starch yield. C_LIO_LIFv/Fm is a rapid and robust proxy of starch content in nutrient-limited duckweed. C_LI

plant biology↗

bioRxiv2020

Template-independent genome editing and repairing correct frameshift disease in vivo

Frameshift mutation caused by small insertions/deletions (indels) often generate truncated and non-functional proteins, which underlies 22% inherited Mendelian disorders in humans. However, there is no efficient in vivo gene therapy strategies available to date, especially in postmitotic systems. Here, we leveraged the non-homologous end joining (NHEJ) mediated non-random editing profiles to compensate the frameshift mutation in a USH1F mouse model - av3j. After treatment by the selected gRNA, about 50% editing products showed reading-frame restoration, and more than 70% targeted hair cells recovered mechanotransduction. In vivo treatment ameliorated the hearing and balance symptoms in homozygous mutant mice. Furthermore, a scale-up analysis of 114 gRNAs targeting 40 frameshift deafness mutations reveals that 65% loci have at least one gRNA with predicted therapeutic potential. Together, our study demonstrates that the NHEJ-mediated frame restoration is a simple and highly efficient therapeutic strategy for small-indel induced frameshift mutations.

neuroscience↗

bioRxiv2020

Efficient storage and analysis of quantitative genomics data with the Dense Depth Data Dump (D4) format and d4tools.

Modern DNA sequencing is used as a readout for diverse assays, with the count of aligned sequences, or "read depth", serving as the quantitative signal for many underlying cellular phenomena. Despite wide use and thousands of datasets, existing formats used for the storage and analysis of read depths are limited with respect to both file size and analysis speed. For example, it is faster to recalculate sequencing depth from an alignment file than it is to analyze the text output from that calculation. We sought to improve on existing formats such as BigWig and compressed BED files by creating the Dense Depth Data Dump (D4) format and tool suite. The D4 format is adaptive in that it profiles a random sample of aligned sequence depth from the input BAM or CRAM file to determine an optimal encoding that often affords reductions in file size, while also enabling fast data access. We show that D4 uses less storage for both RNA-Seq and whole-genome sequencing and offers 3 to 440-fold speed improvements over existing formats for random access, aggregation and summarization. This performance enables scalable downstream analyses that would be otherwise difficult. The D4 tool suite (d4tools) is freely available under an MIT license at: https://github.com/38/d4-format.

genomics↗

bioRxiv2020

Piezo2 mediates ultrasonic hearing via cochlear outer hair cells in mice

Ultrasonic hearing is exploited for hunting and navigation as in echolocation by microbats and bottleneck dolphins, and for social communication like ultrasonic vocalization by mice and rats. However, the molecular and cellular basis for ultrasonic hearing is not known yet. Here we show that knockout of the mechanosensitive ion channel PIEZO2 in cochlea disrupts the ultrasonic hearing but not the low-frequency hearing in mice, as shown by audiometry and acoustically-associative freezing behavior. Deletion of Piezo2 in the outer hair cells specifically abolishes the associative learning of the mice upon hearing the ultrasonic frequency. Ex vivo cochlear Ca2+ imaging revealed that the ultrasonic transduction requires both PIEZO2 and the hair-cell mechanotransduction channel. Together, our study demonstrates that the outer hair cells are the effector cells with PIEZO2 as an essential molecule for ultrasonic hearing in mice. Significance StatementSome animals have evolved an incredible ability for vocalizing and hearing ultrasonic frequencies that is inaudible for humans (> 20 kHz). For many years, it has been considered that animals hear ultrasonic frequencies with their cochlear hair cells, using the identical set of mechanotransduction molecules in the hair bundles for hearing audible frequencies. Here, we show that the mice lacking the mechanosensitive ion channel PIEZO2 hardly hear ultrasonic frequencies, while can still be sensitive to audible frequencies. Thus, animals may use a partially different mechanism for sensing physiological ultrasound.

neuroscience↗

bioRxiv2020

Single-cell mapper (scMappR): using scRNA-seq to infer cell-type specificities of differentially expressed genes

RNA sequencing (RNA-seq) is widely used to identify differentially expressed genes (DEGs) and reveal biological mechanisms underlying complex biological processes. RNA-seq is often performed on heterogeneous samples and the resulting DEGs do not necessarily indicate the cell types where the differential expression occurred. While single-cell RNA-seq (scRNA-seq) methods solve this problem, technical and cost constraints currently limit its widespread use. Here we present single cell Mapper (scMappR), a method that assigns cell-type specificity scores to DEGs obtained from bulk RNA-seq by integrating cell-type expression data generated by scRNA-seq and existing deconvolution methods. After benchmarking scMappR using RNA-seq data obtained from sorted blood cells, we asked if scMappR could reveal known cell-type specific changes that occur during kidney regeneration. We found that scMappR appropriately assigned DEGs to cell-types involved in kidney regeneration, including a relatively small proportion of immune cells. While scMappR can work with any user supplied scRNA-seq data, we curated scRNA-seq expression matrices for [~]100 human and mouse tissues to facilitate its use with bulk RNA-seq data alone. Overall, scMappR is a user-friendly R package that complements traditional differential expression analysis available at CRAN. HighlightsO_LIscMappR integrates scRNA-seq and bulk RNA-seq to re-calibrate bulk differentially expressed genes (DEGs). C_LIO_LIscMappR correctly identified immune-cell expressed DEGs from a bulk RNA-seq analysis of mouse kidney regeneration. C_LIO_LIscMappR is deployed as a user-friendly R package available at CRAN. C_LI

bioinformatics↗

bioRxiv2020

Impaired Fetal Lung Development can be Rescued by Administration of Extracellular Vesicles Derived from Amniotic Fluid Stem Cells

Incomplete lung development, also known as pulmonary hypoplasia, is a recognized cause of neonatal death and poor outcome for survivors. To date, there is no effective treatment that promotes fetal lung growth and maturation. Herein, we describe a novel stem cell-based approach that enhances fetal lung development via the administration of extracellular vesicles (EVs) derived from amniotic fluid stem cells (AFSCs). In experimental models of pulmonary hypoplasia, administration of AFSC-EVs promoted lung branching morphogenesis and alveolarization, and stimulated pulmonary epithelial cell and fibroblast differentiation. This regenerative ability was confirmed in two models of injured human lung cells, where human AFSC-EVs obtained following good manufacturing practices restored pulmonary epithelial homeostasis. AFSC-EV beneficial effects were exerted via the release of RNA cargo, primarily miRNAs, that regulate the expression of genes involved in fetal lung development. Our findings suggest that AFSC-EVs hold regenerative ability for underdeveloped fetal lungs, demonstrating potential for therapeutic application. One Sentence SummaryFetal lung regeneration via administration of extracellular vesicles derived from amniotic fluid stem cells

developmental biology↗

bioRxiv2020

Alternative polyadenylation is a determinant of oncogenic Ras function

Alternative polyadenylation of pre-mRNA has been recently shown to play important roles in development and cancer. Activating mutations in the Ras oncogene are common drivers of many human cancers but the mechanisms by which they cooperate with alternative polyadenylation are not known. By exploiting the genetics of C. elegans, we identified cfim-1/CFIm25, a subunit of the alternative polyadenylation machine, as a key determinant of hyperactive Ras function. Ablation of cfim-1 increased penetrance of multivulva phenotype in let-60/Ras gain-of-function (gf) mutant through shortening of transcripts at the 3 untranslated region, including p21 activated kinase pak-1/PAK1 and multidrug transporter mrp-5/ABCC1. Depletion of CFIm25 in human KRAS-driven cancer cells resulted in a similar shortening of 3 untranslated regions in the PAK1 and ABCC1 transcripts, which caused an epithelial-to-mesenchymal transition and increased cell migration. Exploiting the mechanisms by which alternative polyadenylation affects activated oncogene output could offer novel approaches for the treatment of Ras-driven tumors.

cancer biology↗

bioRxiv2020

The pregnant myometrium is epigenetically activated at contractility-driving gene loci prior to the onset of labor in mice

During gestation, uterine smooth muscle cells transition from a state of quiescence to one of contractility, but the molecular mechanisms underlying this transition at a genomic level are not well-known. To better understand these events, we evaluated the epigenetic landscape of the mouse myometrium during pregnancy, labor and post-partum. We established gestational timepoint-specific enrichment profiles involving histone H3K27 acetylation (H3K27ac), H3K4 tri-methylation (H3K4me3), and RNA polymerase II (RNAPII) occupancy by chromatin immunoprecipitation sequencing (ChIP-seq), as well as gene expression profiles by total RNA-sequencing (RNA-seq). Our findings reveal that 533 genes, including known contractility-driving genes (Gja1, Fos, Oxtr, Ptgs2), are upregulated during active labor due to an increase in transcription at gene bodies. Their promoters and putative intergenic enhancers, however, are epigenetically activated by H3K27ac as early as day 15, four days prior to the onset of active labor on day 19. In fact, we find that the majority of genome-wide H3K27ac or H3K4me3 peaks identified during active labor are present in the myometrium on day 15. Despite the early presence of H3K27ac at labor-associated genes, both an increase in non-coding enhancer RNA (eRNA) production, and in recruitment of RNAPII to corresponding genes occur during active labor, at labor upregulated gene loci. Our findings indicate that epigenetic activation of the myometrial genome precedes active labor by at least four days in the mouse model, suggesting the myometrium is poised for rapid activation of contraction-associated genes in order to exit the state of quiescence.

genomics↗

bioRxiv2019

Structural insight into the mechanism of 4-aminoquinolines selectivity for the alpha2A-adrenoceptor

2A-adrenoceptor (AR) is a potential target for the treatment of degenerative diseases of the central nervous system, and 2A-AR agonists are one of the most effective drugs for this condition. However, the lack of high selectivity for 2A-AR subtype of traditional drugs greatly limits their clinic usage. In this study, a series of homobivalent 4-aminoquinolines conjugated by two 4-aminoquinoline moieties via varying alkane linker length (C2-C12) were characterized for their affinities for each 2-AR subtype. Subsequently, docking, molecular dynamics and mutagenesis were applied to uncover the molecular mechanism. Most 4-aminoquinolines (4-aminoquinoline monomer, C2-C6, C8-C10) were selective for the 2A-AR over 2B- and 2C-ARs. Besides, the affinities are of similar linker length-dependence for each 2-AR subtype. Among all the compounds tested, C10 has the highest affinity for the 2A-AR (pKi=-7.45{+/-}0.62), which is 12-fold and 60-fold selective over 2B-AR and 2C-AR, respectively. Docking and molecular dynamics studies suggest that C10 simultaneously interacts with an orthosteric and an "allosteric site" of the 2A-AR. The mutation of F205, which is situated at the orthosteric binding pocket decreases the affinity by 2-fold. The potential allosteric residues include Ser90, Asn93, Glu94 and W99. The specificity of C10 for the 2A-AR and the potential orthosteric and allosteric binding sites proposed in this study provide valuable guidance for the development of novel 2A-AR subtype selective compounds.

pharmacology and toxicology↗

bioRxiv2019

Remodeling gut microbiota by Streptococcus thermophilus 19 attenuates inflammation in septic mice

Sepsis is a life-threatening organ dysfunction caused by a dysregulated host response to infection and is the leading cause of death in burn patients. Streptococcus thermophilus 19 is a highly effective probiotic, with well-studied health benefits, but its role in protecting viscera against injury caused by sepsis and the underlying mechanism is poorly understood. The goal of this study was to evaluate protection potency of S. thermophilus against inflammation in mice and evaluate the influence of sepsis and S. thermophilus on microbial community. We tested the utility of S. thermophilus 19 in attenuating inflammation in vitro and vivo of LPS-induced sepsis mouse model. We also evaluated the influence of sepsis and S. thermophilus on microbial community. In vitro, S. thermophilus 19 decrease the expression of inflammatory factors. Additionally, in a lipopolysaccharide-induced septic mouse model, mice administered the probiotic 19 was highly resistant to Lps and exhibited decreased expression of inflammatory factors compared to Lps-treated control mice. A MiSeq-based sequence analysis revealed that gut microbiota alterations in mice intraperitoneally injected with 1 mg/ml LPS were mitigated by the administration of oral probiotics 19. Together these findings indicate that S. thermophilus 19 may be a new avenue for interventions against inflammation caused by sepsis and other systemic inflammatory diseases. In an analysis of the gut microbiota of the all group mice, we found that sepsis is associated with gut microbiota and probiotics attenuate the inflammation through remodeling gut microbiota. ImportanceSepsis is life-threatening organ dysfunction which is the leading cause of death in burn patients. Although our understanding of sepsis has increased substantially in recent years, its still reported to be the leading cause of death in seriously ill patients. Evidences showed that gut microbiota play an important role in sepsis. Moreover, probiotics have been used to prevent numbers of gut health disorders and alleviate inflammation associated with some human diseases by promoting changes in the gut microbiota composition. Hence, to investigate the mechanism of probiotics in the treatment of sepsis has emerged. The significance of our research is in identifying the role of gut microbiota in sepsis and found an effective probiotic that reduces inflammation, S. thermophilus 19, and investigating the therapeutic effect and mechanism of S. thermophilus 19 on sepsis, which might be a new avenue for interventions against inflammation caused by sepsis and other systemic inflammatory diseases.

microbiology↗

bioRxiv2018

Neural Correlates of Optimal Multisensory Decision Making

Perceptual decisions are often based on multiple sensory inputs whose reliabilities rapidly vary over time, yet little is known about how our brain integrates these inputs to optimize behavior. Here we show multisensory evidence with time-varying reliability can be accumulated near optimally, in a Bayesian sense, by simply taking time-invariant linear combinations of neural activity across time and modalities, as long as the neural code for the sensory inputs is close to an invariant linear probabilistic population code (ilPPC). Recordings in the lateral intraparietal area (LIP) while macaques optimally performed a vestibular-visual multisensory decision-making task revealed that LIP population activity reflects an integration process consistent with the ilPPC theory. Moreover, LIP accumulates momentary evidence proportional to vestibular acceleration and visual velocity which are encoded in sensory areas with a close approximation to ilPPCs. Together, these results provide a remarkably simple and biologically plausible solution to optimal multisensory decision making.

neuroscience↗

bioRxiv2018

Using molecular ecological network analysis to explore the effects of chemotherapy on intestinal microbial communities of colorectal cancer patients

Intestinal microbiota is now widely known to be key roles in the nutrition uptake, metabolism, and the regulation of human immune responses. However, we do not know how changes the intestinal microbiota in response to the chemotherapy. In this study, we used network-based analytical approaches to explore the effects of five stages of chemotherapy on the intestinal microbiota of colorectal cancer patients. The results showed that chemotherapy greatly reduced the alpha diversity and changed the specie-specie interaction networks of intestinal microbiota, proved by the network size, network connectivity and modularity. The OTU167 and OTU8 from the genus Fusobacterium and Bacteroides were identified as keystone taxa by molecular ecological networks in the first two stages of chemotherapy, and were significantly correlated with tumor makers (P < 0.05). Five stages of chemotherapy did not make the intestinal micro-ecosystem regain a steady state, because of the lower alpha diversity and more complicated ecological networks compared to the healthy individuals. Furthermore, combing the changes of ecological networks with the tumor markers, the intestinal microbiota was closely linked with clinical chemotherapeutic effects.\n\nImportanceA deeply understanding of the role of intestinal microbiota contributes to help us find path forward for improving the prognosis of colorectal cancer patients. In addition, diet or probiotics interventions will be a possible attempt to improve the clinical chemotherapeutic effects for colorectal cancer patients.

microbiology↗