Biology subjects

Feng, H.

Publications and source records attributed to Feng, H..

At least 109 records · Page 6Linked to original sources

bioRxiv2020

Impact of nitrogen and phosphorus addition on resident soil and root mycobiomes in beech forests

In forest soils, the pools of N and P available for microbes and plants are strongly dependent on soil properties. Here, we conducted a P and N fertilization experiment to disentangle the effects of nutrient availability on soil-residing, root-associated and ectomycorrhizal fungi in beech (Fagus sylvativa) forests differing in P availability. We tested the hypothesis that in P-poor forests, P fertilization leads to enhanced fungal diversity in soil and roots, resulting in enhanced P nutrition of beech and that N fertilization aggravates P shortage, shifting the fungal communities towards nitrophilic species. In response to fertilizer treatments (1x 50 kg ha-1 P, 5x 30 kg ha-1 N within 2 years), the labile P fractions increased in soil and roots, regardless of plant-available P in soil. Root total P decreased in response to N fertilization and root total P increased at the low P site in response to P addition. The relative abundances of ectomycorrhizal fungi, but not their species richness, increased in response to P or N addition in comparison with that of saprotrophic fungi. While some fungal orders (Trechisporales, Atheliales, Cantharellales) were moderately decreased in response to fertilizer treatments, Boletales increased in response to P and Russulaes to N addition. N or P fertilization resulted in functional trade-off, shifting away from saprotrophic towards symbiotrophic potential. Our results suggest that chronic exposure of forest ecosystems to increased nutrient inputs may overcome the resistance of the resident mycobiome structures resulting in nutritional imbalance and loss of forest ecosystem services.

ecology↗

bioRxiv2020

N6-methyladenine DNA demethylase ALKBH1 regulates mammalian axon regeneration

Recent studies have shown that DNA N6-methyladenine (N6-mA) modification is emerging to be a novel and important epigenetic regulator of mammalian gene transcription. Several studies demonstrated DNA N6-mA in human or rodents was regulated by methyltransferase N6AMT1 and demethylase ALKBH1. Moreover, studies in mouse brain or human glioblastoma cells showed that reduced level of N6-mA or higher level of ALKBH1 was correlated with up regulated levels of genes associated with neuronal development. We thus investigated the functional roles of ALKBH1 in sensory axon regeneration. Our results showed that ALKBH1 regulated the level of N6-mA in sensory neurons, and upon peripheral nerve injury ALKBH1 was up regulated in mouse sensory neurons. Functionally, knocking down ALKBH1 in sensory neurons resulted in reduced axon regeneration in vitro and in vivo, which could be rescued by simultaneously knocking down N6AMT1. Moreover, knocking down ALKBH1 led to decreased levels of many neurodevelopment regulatory genes, including neuritin that is well known to enhance axon growth and regeneration. Our study not only revealed a novel physiological function of DNA N6-mA, but also identified a new epigenetic mechanism regulating mammalian axon regeneration. Significance StatementThe study demonstrated that DNA N6-methyladenine (N6-mA) modification played important roles in regulation of sensory axon regeneration, likely through controlling the expression of neurodevelopmental associated genes. The results will add new evidence about the physiological function of DNA N6-mA and its regulatory demethylase ALKBH1 in neurons.

neuroscience↗

bioRxiv2020

Hybrid diffuse optical monitoring of hemodynamic changes following acute cerebral ischemia in a porcine model

Rapid screening for stroke in pre-hospital settings may improve patient outcomes by allowing early deployment of thrombolytic therapies. Near-infrared hybrid diffuse optical screening devices may fill this need. This study seeks to determine whether hybrid diffuse optical measurements can measure hemodynamic changes associated with cerebral ischemia within the first few hours of the onset of acute ischemia in a large animal model. A hybrid diffuse optical device combining of near-infrared spectroscopy (NIRS) and diffuse correlation spectroscopy (DCS) was fabricated to measure total hemoglobin concentration (HbT), tissue oxygen saturation (StO2) and blood flow index (BFI). Cerebral ischemia was induced by ligation of the bilateral common carotid arteries (CCA) in five miniature pigs. Additionally, a fatal stroke was induced in two pigs by injecting 5ml air emboli into both CCA. Cerebral hemodynamic parameters were monitored continuously throughout the study with the hybrid optical device. Relative changes BFI showed the good repeatability both of the ligation and fatal stroke experiments. During bilateral CCA ligation, the BFI decreased by up to about 66% of baseline values; during the fatal stroke experiment, the BFI decreased by up to about 95%, with a temporal resolution of 20 seconds. To the best of our knowledge, there are not existing methods which can measure the cerebral ischemia within the first few hours of the onset noninvasively. The MRI scanning was conducted at 24 h post injury. However, the images showed no abnormality. The results show the hybrid diffuse optical method can immediately measure the hemodynamic changes of miniature pigs in the first few hours of each single cerebral ischemia onset, and the BFI may be the promising biomarker to distinguish the cerebral ischemia and cerebral death.

neuroscience↗

bioRxiv2020

An improved Nicotiana benthamiana strain for aphid and whitefly research

Nicotiana benthamiana is used extensively as a platform for transient gene expression and as a model system for studying plant-virus interactions. However, many tobacco-feeding generalist herbivores, including Myzus persicae (green peach aphid), Bemisia tabaci (whitefly), Macrosiphum euphorbiae (potato aphid), Heliothis virescens (tobacco budworm), Trichoplusia ni (cabbage looper), and Helicoverpa zea (corn earworm), grow poorly on N. benthamiana, limiting its utility for research on plant-insect interactions. Using CRISPR/Cas9, we generated knockout mutations in two N. benthamiana acylsugar acyltransferases, ASAT1 and ASAT2, which contribute to the biosynthesis of insect-deterrent acylsucroses. Whereas asat1 mutations reduced the abundance of two predominant acylsucroses, asat2 mutations caused almost complete depletion of foliar acylsucroses. The tested hemipteran and lepidopteran species survived, gained weight, and/or reproduced significantly better on asat2 mutant plants than on wildtype N. benthamiana. Furthermore, both asat1 and asat2 mutations reduced the water content and increased the temperature of leaves, indicating that foliar acylsucroses can protect against desiccation. Two experiments demonstrated the utility of the N. benthamiana asat2 mutant line for insect bioassays. Transmission of turnip mosaic virus by M. persicae was significantly improved by an asat2 mutation. Tobacco rattle virus constructs were used for virus-induced gene silencing of acetylcholinesterase, squalene synthase, toll-like receptor 7, and tubulin-specific chaperon D genes in B. tabaci, an experiment that would have been difficult with wild-type N. benthamiana due to high insect mortality. Additionally, the absence of acylsugars in asat2 mutant lines will simplify transient expression assays for the functional analysis of acylsugar biosynthesis genes from other Solanaceae.

plant biology↗

bioRxiv2020

Leveraging expression from multiple tissues using sparse canonical correlation analysis (sCCA) and aggregate tests improves the power of transcriptome-wide association studies (TWAS)

Transcriptome-wide association studies (TWAS) test the association between traits and genetically predicted gene expression levels. The power of a TWAS depends in part on the strength of the correlation between a genetic predictor of gene expression and the causally relevant gene expression values. Consequently, TWAS power can be low when expression quantitative trait locus (eQTL) data used to train the genetic predictors have small sample sizes, or when data from causally relevant tissues are not available. Here, we propose to address these issues by integrating multiple tissues in the TWAS using sparse canonical correlation analysis (sCCA). We show that sCCA-TWAS combined with single-tissue TWAS using an aggregate Cauchy association test (ACAT) outperforms traditional single-tissue TWAS. In empirically motivated simulations, the sCCA+ACAT approach yielded the highest power to detect a gene associated with phenotype, even when expression in the causal tissue was not directly measured, while controlling the Type I error when there is no association between gene expression and phenotype. For example, when gene expression explains 2% of the variability in outcome, and the GWAS sample size is 20,000, the average power difference between the ACAT combined test of sCCA features and single-tissue, versus single-tissue combined with Generalized Berk-Jones (GBJ) method, single-tissue combined with S-MultiXcan or summarizing cross-tissue expression patterns using Principal Component Analysis (PCA) approaches was 5%, 8%, and 38%, respectively. The gain in power is likely due to sCCA cross-tissue features being more likely to be detectably heritable. When applied to publicly available summary statistics from 10 complex traits, the sCCA+ACAT test was able to increase the number of testable genes and identify on average an additional 400 additional gene-trait associations that single-trait TWAS missed. Our results suggest that aggregating eQTL data across multiple tissues using sCCA can improve the sensitivity of TWAS while controlling for the false positive rate.Author summary Transcriptome-wide association studies (TWAS) can improve the statistical power of genetic association studies by leveraging the relationship between genetically predicted transcript expression levels and an outcome. We propose a new TWAS pipeline that integrates data on the genetic regulation of expression levels across multiple tissues. We generate cross-tissue expression features using sparse canonical correlation analysis and then combine evidence for expression-outcome association across cross- and single-tissue features using the aggregate Cauchy association test. We show that this approach has substantially higher power than traditional single-tissue TWAS methods. Application of these methods to publicly available summary statistics for ten complex traits also identifies associations missed by single-tissue methods.View Full Text

genetics↗

bioRxiv2020

Wide field-of-view volumetric imaging by a mesoscopic scanning oblique plane microscopy with switchable objective lens

Conventional light sheet fluorescence microscopy (LSFM), or selective plane illumination microscopy (SPIM), enables high resolution 3D imaging over a large volume by using two orthogonally aligned objective lenses to decouple excitation and emission. The recent development of oblique plane microscopy (OPM) simplifies LSFM design with only one single objective lens, by using off-axis excitation and remote focusing. However, most reports on OPM has a limited microscopic field of view (FOV), typically within 1×1 mm2. Our goal is to overcome the limitation with a new variant of OPM to achieve mesoscopic FOV. We implemented an optical design of mesoscopic scanning OPM to allow using low numerical aperture (NA) objective lens. The angle of the intermediate image before the remote focusing system was increased by a demagnification under Scheimpflug condition such that the light collecting efficiency in the remote focusing system was significantly improved. We characterized the 3D resolutions and FOV by imaging fluorescence microspheres, and demonstrated the volumetric imaging on intact whole zebrafish larvae, mouse cortex, and multiple Caenorhabditis elegans (C. elegans). We demonstrate a mesoscopic FOV up to ~6× 5×0.6 mm3 volumetric imaging, the largest reported FOV by OPM so far. The angle of the intermediate image plane is independent of the magnification. As a result, the system is highly versatile, allowing simple switching between different objective lenses with low (10x, NA 0.3) and median NA (20x, NA 0.5). Detailed microvasculature in zebrafish larvae, mouse cortex, and neurons in C. elegans are clearly visualized in 3D. The proposed mesoscopic scanning OPM allows using low NA objective such that centimeter-level FOV volumetric imaging can be achieved. With the extended FOV, simple sample mounting protocol, and the versatility of changeable FOVs/resolutions, our system will be ready for the varieties of applications requiring in vivo volumetric imaging over large length scales.Competing Interest StatementThe authors have declared no competing interest.View Full Text

bioengineering↗

bioRxiv2020

YTHDF2 is essential for spermatogenesis and fertility through mediating a wave of transcript transition during spermatogonial differentiation

The dynamic and reversible regulation roles of m6A modification, and the characterization of m6A readers have provided new insights into spermatogenesis at post-transcriptional level. YTHDF2 has been reported to recognize and mediate the m6A-containing transcripts decay during the mouse oocyte mature, embryonic stem cell differentiation, neural development, and zebrafish maternal-to-zygotic transition. However, the roles of YTHDF2 in mammalian spermatogenesis are uncertain. Here, we generated germ cell-specific Ythdf2 mutants (Ythdf2-vKO) at a C57BL/6J background, and demonstrated that YTHDF2 was essential for mouse spermatogenesis and fertility. Ythdf2-vKO provided oligoasthenoteratozoospermia (OAT) phenotype with increased apoptosis in germ cells. High-throughput RNA-seq of the testis tissue showed the failure of the degradation of a wave of YTHDF2 target mRNA. Interestingly, RNA-seq analysis combined with our previous single-cell transcriptomics data of mouse spermatogenesis pointed out the failure of a wave of transcript transition during the spermatogenesis of Ythdf2-vKO, which was confirmed by gene expression analysis of diplotene spermatocytes and round spermatids obtained through fluorescence-activated cell sorting using qPCR. Our study demonstrates the fundamental role of YTHDF2 during mouse spermatogenesis and provides a potential candidate for the diagnosis of male infertility with OAT syndrome. Author summaryMale infertility is becoming a worldwide health problem. Male gamete is generated through spermatogenesis, which is a complicated developmental process with dynamic transcriptome changes. RNA m6A modification has been reported as the most prominently internal mRNA modification, which control the tune of gene expression through mRNA splicing, export, translation and decay. RNA m6A modification is catalyzed by "writers", and could be removed by "erasers". The m6A modification enzymes are reported to play important roles during spermatogenesis. Given that the biological function of m6A modification are mediated through its "readers", its readers might be proposed to be involved in the regulation of spermatogenesis. YTHDF2, as a reader of m6A modification, has been reported to mediate the m6A-containing transcripts decay. To explore the roles of YTHDF2 in spermatogenesis, we used germ cell-specific mutation strategy to knock out the mouse Ythdf2. The mutants provided oligoasthenoteratozoospermia phenotype. Our study demonstrate that YTHDF2 is essential for mouse spermatogenesis. YTHDF2 could be a potential candidate for the diagnosis of oligoasthenoteratozoospermia syndrome.

genetics↗

bioRxiv2020

A dual role for Axin in establishing the anterior-posterior axis in the early sea urchin embryo

The activation of Wnt/{beta}-catenin (cWnt) signaling at the future posterior end of early embryos is a highly conserved mechanism for initiating pattern formation along the anterior-posterior (AP) axis in bilaterians. Moreover, in many bilaterian taxa, in addition, to activation of cWnt signaling at the posterior end, inhibition of cWnt signaling at the anterior end is required for normal development of anterior structures. In most cases, inhibition of cWnt signaling at the anterior end occurs around gastrulation and it is typically mediated by secreted factors that block signal transduction through the cWnt cell surface receptor-ligand complex. This phenomenon has been fairly well characterized, but the emerging role for intracellular inhibition of cWnt signaling in future anterior blastomeres--in cleavage stage embryos--to regulate correct AP patterning is less well understood. To investigate this process in an invertebrate deuterostome embryo we studied the function of Axin, a critical negative regulator of cWnt signaling, during early sea urchin embryogenesis. Sea urchin Axin is ubiquitously expressed in early embryos and by the blastula stage the expression of the gene becomes restricted to the posterior end of the embryo. Strikingly, knockdown of Axin protein levels using antisense Axin morpholinos (MO) led to ectopic nuclearization of {beta}-catenin and activation of endomesoderm gene expression in anterior blastomeres in early embryos. These embryos developed a severely posteriorized phenotype that could be fully rescued by co-injection of Axin MO with wild-type Axin mRNA. Axin is known to negatively regulate cWnt by its role in mediating {beta}-catenin stability within the destruction complex. Consistent with this function overexpression of Axin by mRNA injection led to the downregulation of nuclear {beta}-catenin, inhibition of endomesoderm specification and a strong anteriorization of embryos. Axin has several well-defined domains that regulate its interaction with {beta}-catenin and the key regulators of the destruction complex, Adenomatous Polyposis Coli (APC), Glycogen Synthase Kinase 3{beta}(GSK-3{beta}), and Dishevelled (Dvl). Using Axin constructs with single deletions of the binding sites for these proteins we showed that only the GSK-3{beta}binding site on Axin is required for its inhibition of cWnt in the sea urchin embryo. Strikingly, overexpression of the GSK-3{beta}-binding domain alone led to embryos with elevated levels of endomesoderm gene expression and a strongly posteriorized phenotype. These results indicated that Axin has a critical global role in inhibiting cWnt signaling in the early sea urchin embryo, and moreover, that the interaction of Axin with GSK-3{beta}is critical for this inhibition. These results also add to the growing body of evidence that Axin plays a global function in suppressing cWnt signaling in early embryos and indicates that modulation of Axin function may be a critical early step during patterning of the AP axis during bilaterian development

developmental biology↗

bioRxiv2020

Population sequencing enhances understanding of tea plant evolution

Tea is an economically important plant characterized by a large genome size and high heterozygosity and species diversity. In this study, we assembled a 3.26 Gb high-quality chromosome-scale genome for tea using the Longjing 43 cultivar of Camellia sinensis var. sinensis. Population resequencing of 139 tea accessions from around the world was used to investigate the evolution of tea and to reveal the phylogenetic relationships among tea accessions. With the spread of tea cultivation, hybridization has increased the heterozygosity and wide-ranging gene flow among tea populations. Population genetics and transcriptomics analyses revealed that during domestication, the selection for disease resistance and flavor in C. sinensis var. sinensis populations has been stronger than that in C. sinensis var. assamica populations. The data compiled in this study provide new resources for the marker assisted breeding of tea and are a basis for further research on the genetics and evolution of tea.

genomics↗

bioRxiv2020

The dominance hierarchy of the female Yunnan snub-nosed monkeys (Rhinopithecus bieti)

Dominance hierarchies are common in social mammals, especially primates. The formation of social hierarchies is conducive to solving the problem of the allocation of scarce resources among individuals. From August 2015 to July 2016, we observed a wild, provisioned Yunnan snub-nosed monkey (Rhinopithecus bieti) group at Xiangguqing in Baimaxueshan National Nature Reserve, Yunnan Province, China. Aggressive and submissive behaviors were used to investigate dominance hierarchies between female individuals in the same one-male unit (OMU), and the grooming reciprocity index was used to detect reciprocal relationships between these females within the OMU. The results showed that loose social hierarchies exist among the females in each OMU, and more dominant individuals have higher grooming incomes. These results are consistent with the aggressive-submissive hypothesis and the resource control hypothesis.

animal behavior and cognition↗

bioRxiv2020

Inactivation of LCN2/EGR1 Promotes Oligodendrocyte Progenitor Cell Differentiation and Remyelination after White Matter Injury

The insufficient remyelination due to the impaired oligodendrocyte precursor cell differentiation and maturation is highly associated with irreversible white matter injury and neurological deficits. Consequently, inhibitory components and microenvironment for remyelination might serve as potential therapeutic targets for treating white matter injury after acute central nervous system injury and neurodegeneration diseases. Lipocalin-2 was recently reported to corelate with white matter in both atypical, acute white matter injured disease subarachnoid hemorrhage and typical, chronic white matter injured disease multiple sclerosis. To elucidate the role and underlying mechanism of Lipocalin-2 in oligodendrocyte precursor cell differentiation and remyelination, we used genetic inhibition and a constitutive conditional knockout model with subarachnoid hemorrhage or multiple sclerosis. We found that the genetic inhibition of the increase in Lipocalin-2 promoted oligodendrocyte precursor cell differentiation, remyelination, and functional recovery after subarachnoid hemorrhage or multiple sclerosis. Unexpectedly, the inhibition of Lipocalin-2 did not reduce glial activation and inflammation. Lipocalin-2 was shown to activate Early Growth Response Protein 1 in oligodendrocyte precursor cells, which is partly regulated by its receptor SLC22A17. In the conditional knockout of Early Growth Response Protein 1 in oligodendrocyte precursor cells, we discovered enhanced oligodendrocyte precursor cell differentiation in developing and injured white matter; consistently, the specific inactivation of Early Growth Response Protein 1 promoted remyelination and neurological recovery after subarachnoid hemorrhage or multiple sclerosis. Thus, we propose that following white matter injury in humans, the increase in Lipocalin-2 activates Early Growth Response Protein 1 and consequently impair oligodendrocyte precursor cell differentiation and myelin repair. Our results suggest that therapies specifically inactivating Lipocalin-2/ Early Growth Response Protein 1 signal in oligodendroglial lineage cells could represent a novel strategy to enhance differentiation and remyelination in white matter injury patients.

neuroscience↗

bioRxiv2019

Behaviour and cold hardiness of the purple stem borer in winter, colonizing more northerly latitudes

To escape or alleviate low temperatures in winter, insects have evolved many behavioral and physiological strategies. The rice pest insect, the purple stem borer, Sesamia inferens (Walker) is currently reported to be expanding their northern distributions and causing damage to summer maize in Xinxiang, China. However, their method of coping with the lower temperature in the new northern breeding area in winter is largely unknown. This paper investigates the overwinter site of S. inferens, and identifies the cold hardiness of larvae collected from a new breeding area in winter and explores a potential distribution based on low temperature threshold and on species distribution model, MaxEnt. The results show that the overwintering location of the S. inferens population is more likely to be underground with increasing latitude and,in the north, with the temperature decreasing, the larvae gradually moved down the corn stalk and drilled completely underground by February 18th. Those who were still above ground were all winterkilled. The cold hardiness test shows the species is a moderate freeze-tolerant one, and Supercooling Points (SCP), Freezing Points (FP) and mortality rate during the middle of winter (January, SCP: -7.653, FP: -6.596) were significantly lower than early winter (October) or late winter (March). Distribution in the new expansion area was predicted and the survival probability area was below N 35{degrees} for the Air Lower Lethal Temperature (ALLT50) and below N 40{degrees} for the Underground Lower Lethal Temperature (ULLT50), The suitable habitat areas for S. inferens with MaxEnt were also below N 40{degrees}. This study suggests the overwinter strategies have led to the colonization of up to a five degree more northerly overwintering latitude. This behavior of S. inferens could help maize producers to propose a control method to increase pest mortality by extracting the maize stubble after harvest.

animal behavior and cognition↗

bioRxiv2019

Mice with GNAO1 R209H Movement Disorder Variant Display Hyperlocomotion Alleviated by Risperidone

Neurodevelopmental disorder with involuntary movements (NEDIM, OMIM: 617493) is a severe, early onset neurological condition characterized by a delay in psychomotor development, hypotonia, and hyperkinetic involuntary movements. Heterozygous de novo mutations in the GNAO1 gene cause NEDIM. Go, the gene product of GNAO1, is the alpha subunit of Go, a member of the heterotrimeric Gi/o family of G-proteins. Go is found abundantly throughout the brain but the pathophysiological mechanisms linking Go functions to clinical manifestations of GNAO1-related disorders are still poorly understood. One of the most common mutant alleles among the GNAO1 encephalopathies is the c.626G>A or p.Arg209His (R209H) mutation. We developed heterozygous knock-in Gnao1+/R209H mutant mice using CRISPR/Cas9 methodology to assess whether a mouse model could replicate aspects of the NEDIM clinical pattern. Mice carrying the R209H mutation exhibited increased locomotor activity and a modest gait abnormality at 8-12 weeks. In contrast to mice carrying other mutations in Gnao1, the Gnao1+/R209H mice did not show enhanced seizure susceptibility. Levels of protein expression in multiple brain regions were unchanged from WT mice but the nucleotide exchange rate of mutant R209H Go was 9 times faster than WT. The atypical neuroleptic risperidone has shown efficacy in a patient with the R209H mutation. It also alleviated the hyperlocomotion phenotype observed in our mouse model but suppressed locomotion in WT mice as well. In this study, we show that Gnao1+/R209H mice mirror elements of the patient phenotype and respond to an approved pharmacological agent.

neuroscience↗

bioRxiv2018

Modeling RNA-binding protein specificity in vivo by precisely registering protein-RNA crosslink sites

RNA-binding proteins (RBPs) regulate post-transcriptional gene expression by recognizing short and degenerate sequence elements in their target transcripts. Despite the expanding list of RBPs with in vivo binding sites mapped genomewide using crosslinking and immunoprecipitation (CLIP), defining precise RBP binding specificity remains challenging. We previously demonstrated that the exact protein-RNA crosslink sites can be mapped using CLIP data at single-nucleotide resolution and observed that crosslinking frequently occurs at specific positions in RBP motifs. Here we have developed a computational method, named mCross, to jointly model RBP binding specificity while precisely registering the crosslinking position in motif sites. We applied mCross to 112 RBPs using ENCODE eCLIP data and validated the reliability of the resulting motifs by genome-wide analysis of allelic binding sites also detected by CLIP. We found that the prototypical SR protein SRSF1 recognizes GGA clusters to regulate splicing in a much larger repertoire of transcripts than previously appreciated.

molecular biology↗

bioRxiv2018

Mesenchymal stem cells protect retinal ganglion cells from degeneration via mitochondrial donation

Retinal ganglion cell (RGC) degeneration is extremely hard to repair or regenerate and is often coupled with mitochondrial dysfunction. Mesenchymal stem cells (MSCs)-based treatment has been demonstrated beneficial for RGC against degeneration. However, underlying mechanisms of MSC-provided RGC protection are largely unknown other than neuropectective paracrine actions. In this study, we sought to investigate whether mitochondrial donation can preserve RGC functions, in a mitochondrial Ndufs4 deficient mouse model of RGC degeneration. The results revealed intravitreal transplanted by induced pluripotent stem cell derived-MSCs (iPSC-MSC) could donate their mitochondria through crossing inner limited membrane to host RGCs. Furthermore, the donated mitochondria effectively protected against RGC death and largely preserved retinal function in Ndufs4-KO mice. Importantly, the protective effects of mitochondrial donation from MSCs were associated with management of pro-inflammatory cytokines. Our data identified a novel role of MSCs-mitochondrial donation in protection of RGC from degeneration, and highlight a viable therapeutic strategy by manipulating stem cell mitochondrial donation for the treatment of retina degeneration in future.

cell biology↗

bioRxiv2018

Osteoblastic PLEKHO1 contributes to joint inflammation in rheumatoid arthritis

Osteoblasts participating in the inflammation regulation gradually obtain concerns. However, its role in joint inflammation of rheumatoid arthritis (RA) is largely unknown. Pleckstrin homology domain-containing family O member 1 (PLEKHO1) was previously identified as a negative regulator of osteogenic lineage activity. Here we demonstrated that PLEKHO1 was highly expressed in osteoblasts of articular specimens from RA patients and inflammatory arthritis mice. Genetic deletion of osteoblastic Plekho1 ameliorated joint inflammation in mice with collagen-induced arthritis (CIA) and K/BxN serum-transfer arthritis (STA), whereas overexpressing Plekho1 only within osteoblasts in CIA and STA mice demonstrated exacerbated local inflammation. Further in vitro studies indicated that PLEKHO1 was required for TRAF2-mediated RIP1 ubiquitination to activate NF-kB for inducing inflammatory cytokines production in osteoblasts. Moreover, osteoblastic PLEKHO1 inhibition improved joint inflammation and attenuated bone formation reduction in CIA mice and non-human primate arthritis model. These data strongly suggest that highly expressed PLEKHO1 in osteoblast mediates joint inflammation in RA. Targeting osteoblastic PLEKHO1 may exert dual therapeutic action of alleviating joint inflammation and promoting bone formation in RA.

cell biology↗

bioRxiv2018

LRScaf: Improving Draft Genomes Using Long Noisy Reads

BackgroundThe advent of Third Generation Sequencing (TGS) technologies opens the door to improve genome assembly. Long reads are promised to enhance the quality of fragmental draft assemblies constructed from Next Generation Sequencing (NGS) technologies. To date, a few of algorithms, i.e., SSPACE-LongRead, OPERA-LG, SMIS, npScarf, DBG2OLC, Unicycler, and LINKS, have been released that are capable of improving draft assemblies. However, hybrid assembly on large genomes is still challenging.\n\nResultsWe develop a scalable and computationally efficient scaffolder, Long Reads Scaffolder (LRScaf), that is capable of boosting assembly contiguity to a large extent using long reads. In our experiment, our method significantly improves the contiguity of human draft assemblies, increasing the NG50 value of CHM1 from 127.5 Kb to 10.4 Mb using 20-fold coverage PacBio dataset and the NG50 value of NA12878 from 115.7 Kb to 17.4 Mb using 35-fold coverage Nanopore dataset. The run time for the scaffolding procedure using LRScaf is the shortest in all cases of our experiment. Compared with the run time of SSPACE-LongRead, LRScaf is faster 300 times for S. cerevisiae and 2,300 times for D. melanogaster. The peak RAM of LRScaf, by contrast, is more efficient than LINKS in our test. For the rice case, the peak RAM of LINKS (877.72 Gb) is about 196 times higher than LRScaf. For the experiment of human assembly, the peak RAM of LINKS is beyond the capacity of system memory (1 Tb) whereas LRScaf takes 20.28 and 41.20 Gb on CHM1 and NA12878 datasets.\n\nConclusionsThe new method, LRScaf, yields the best or at least moderate contiguity and accuracy of scaffolds in the shortest run time compared with the state-of-the-art methods. Furthermore, it offers a new opportunity for the hybrid assembly of large genomes.

bioinformatics↗

bioRxiv2018

Mouse Models of GNAO1-Associated Movement Disorder: Allele- and sex-specific differences in phenotypes

Background\n\nInfants and children with dominant de novo mutations in GNAO1 exhibit movement disorders, epilepsy, or both. Children with loss-of-function (LOF) mutations exhibit Epileptiform Encephalopathy 17 (EIEE17). Gain-of-function (GOF) mutations or those with normal function are found in patients with Neurodevelopmental Disorder with Involuntary Movements (NEDIM). There is no animal model with a human mutant GNAO1 allele.\n\nObjectives\n\nHere we develop a mouse model carrying a human GNAO1 mutation and determine whether clinical features of the GNAO1 mutation including movement disorder would be evident in the mouse model.\n\nMethods\n\nA mouse Gnao1 knock-in GOF mutation (G203R) was created by CRISPR/Cas9 methods. The resulting offspring and littermate controls were subjected to a battery of behavioral tests. A previously reported GOF mutant mouse knock-in (Gnao1+/G184S) was also studied for comparison.\n\nResults\n\nGnao1+/G203R mutant mice are viable and gain weight comparably to controls. Homozygotes are non-viable. Grip strength was decreased in both males and females. Male Gnao1+/G203R mice were strongly affected in movement assays (RotaRod and DigiGait) while females were not. Male Gnao1+/G203R mice also showed enhanced seizure propensity in the pentylenetetrazole kindling test. Mice with a G184S GOF knock-in also showed movement-related behavioral phenotypes but females were more strongly affected than males.\n\nConclusions\n\nGnao1+/G203R mice phenocopy children with heterozygous GNAO1 G203R mutations, showing both movement disorder and a relatively mild epilepsy pattern. This mouse model should be useful in mechanistic and preclinical studies of GNAO1-related movement disorders.

animal behavior and cognition↗