Biology subjects

Yu, J.

Publications and source records attributed to Yu, J..

At least 505 records · Page 28Linked to original sources

bioRxiv2019

Coupling Day Length Data and Genomic Prediction tools for Predicting Time-Related Traits under Complex Scenarios

Genomic selection (GS) has proven to be an efficient tool for predicting crop-rank performance of untested genotypes; however, when the traits have intermediate optima (phenology stages) this implementation might not be the most convenient. GS might deliver high rank correlations but incurring in serious bias. Days to heading (DTH) is a crucial development stage in rice for regional adaptability with significant impact in yield potential. The objectives of this research consisted in the development of a method that accurately predicts time related traits like DTH in unobserved environments. For this, we developed an implementation that incorporate day length information (DL) in the prediction process for two relevant scenarios: CV0, predicting tested genotypes in unobserved environments (C method); and CV00, predicting untested genotypes in unobserved environments (CB method). The use of DL has advantages over weather data since it can be determined in advance just by knowing the location and planting date. The proposed methods showed that DL information significantly helps to improve the predictive ability of DTH in unobserved environments. Under CV0, the C method returned an root-mean-square-error (RMSE) of 3.9 days, a Pearson Correlation (PC) of 0.98 and the differences between the predicted and observed environmental means (EMD) ranged between -4.95 and 4.67 days. For CV00, the CB method returned an RMSE of 7.3 days, a PC of 0.93 and the EMD ranged between -6.4 and 4.1 days while the conventional GS implementation produced an RMSE of 18.1 days, a PC of 0.41 and the EMD ranged between -31.5 and 28.7 days.

genomics↗

bioRxiv2019

The Ciliary Lumen Accommodates Passive Diffusion and Vesicle Trafficking in Cytoplasmic-Ciliary Transport

Transport of membrane and cytosolic proteins into the primary cilium is essential for its role in cellular signaling. Using single molecule microscopy, we mapped the movement of membrane and soluble proteins at the base of the primary cilium. In addition to the well-known intraflagellar transport (IFT) route, we identified two new pathways within the lumen of the primary cilium - passive diffusional and vesicle transport routes - that are adopted by proteins for cytoplasmic-cilium transport in live cells. Independent of the IFT path, approximately half of IFT motors (KIF3A) and cargo (-tubulin) take the passive diffusion route and more than half of membrane-embedded G protein coupled receptors (SSTR3 and HTR6) use RAB8A-regulated vesicles to transport into and inside cilia. Furthermore, ciliary lumen transport is the preferred route for membrane proteins in the early stages of ciliogenesis and inhibition of SSTR3 vesicle transport completely blocks ciliogenesis. Furthermore, clathrin-mediated, signal-dependent internalization of SSTR3 also occurs through the ciliary lumen. These transport routes were also observed in Chlamydomonas reinhardtii flagella, suggesting their conserved roles in trafficking of ciliary proteins.

biophysics↗

bioRxiv2019

Enrichment in conservative amino acid changes among fixed and standing missense variations in slow evolving proteins

Proteins were first used in the early 1960s to discover the molecular clock dating method and remain in common usage today in phylogenetic inferences based on neutral variations. To avoid substitution saturation, it is necessary to use slow evolving genes. However, it remains unclear whether fixed and standing missense changes in such genes may qualify as neutral. Here, based on the evolutionary rates as inferred from identity scores between orthologs in human and Macaca monkey, we found that the fraction of conservative amino acid mismatches between species was significantly higher in slow evolving proteins. We also examined the single nucleotide polymorphisms (SNPs) by using the 1000 genomes project data and found that missense SNPs in slow evolving proteins also had higher fraction of conservative changes, especially for common SNPs, consistent with more natural selection for SNPs, particularly rare ones, in fast evolving proteins. These results suggest that fixed and standing missense variations in slow evolving proteins are more likely to be neutral and hence better qualified for use in phylogenetic inferences.

evolutionary biology↗

bioRxiv2019

Does deliberation really need more effort than intuition? A test using event-related brain potential

Intuition and deliberation are two strategies for problem-solving and decision-making. It is commonly believed that deliberation requires more effort than intuition. However, to date, neural evidence approving or disapproving this point is scarce. To explore this issue, we asked participants to play two well-matched games requiring either deliberation or intuition. Using event-related brain potential (ERP) technique, we found: (1) Deliberation elicited more deflective ERP than intuition during -1000 ~ -500 ms before the response, which is consistent with the common belief. (2) More importantly, intuition evoked more deflective ERP than deliberation during 550 ~ 650 ms after the onset of the stimulus, which suggests that intuition may need more effort than deliberation at early stage, contradicting the common belief.

neuroscience↗

bioRxiv2019

The Chinese chestnut genome: a reference for species restoration

Forest tree species are increasingly subject to severe mortalities from exotic pests, diseases, and invasive organisms, accelerated by climate change. Forest health issues are threatening multiple species and ecosystem sustainability globally. While sources of resistance may be available in related species, or among surviving trees, introgression of resistance genes into threatened tree species in reasonable time frames requires genome-wide breeding tools. Asian species of chestnut (Castanea spp.) are being employed as donors of disease resistance genes to restore native chestnut species in North America and Europe. To aid in the restoration of threatened chestnut species, we present the assembly of a reference genome with chromosome-scale sequences for Chinese chestnut (C. mollissima), the disease-resistance donor for American chestnut restoration. We also demonstrate the value of the genome as a platform for research and species restoration, including new insights into the evolution of blight resistance in Asian chestnut species, the locations in the genome of ecologically important signatures of selection differentiating American chestnut from Chinese chestnut, the identification of candidate genes for disease resistance, and preliminary comparisons of genome organization with related species.

genomics↗

bioRxiv2019

Volumetric two-photon imaging in live cells and embryos via axially gradient excitation

Two-photon microscopy(TPM) that features subcellular resolution, intrinsic optical sectioning ability, and deep penetration in sample is a powerful tool of bioimaging. However, the process of layer-by-layer scanning to form a 3D image inherently limits the volumetric imaging speed and significantly increases the phototoxicity. Here we develop a gradient TPM technique that enables rapid volumetric imaging by only acquiring two 2D images. By sequentially exciting the specimen with two axially elongated two-photon beams with complementary gradient intensities, the axial positions of fluorophores can be decoded from the intensity ratio of the paired images. We achieve an axial localization accuracy of 0.728 {+/-} 0.657 m, which is sufficient for rapid 3D subcellular imaging. We demonstrate the flexibility of the gradient TPM on a variety of sparsely labelled samples, including bead phantoms, mouse brain tissues, live macrophages and live nematode embryos. The results show that, compared with conventional TPM, the 3D imaging speed increases 6 folds while the photobleaching and photodamage are extremely reduced.

bioengineering↗

bioRxiv2019

Ibuprofen-mediated potential inhibition of biofilm development and quorum sensing in Pseudomonas aeruginosa

Pseudomonas aeruginosa is one of the leading causes of opportunistic and hospital-acquired infections worldwide. The infection with P. aeruginosa is frequently linked with clinical treatment difficulties given drug resistance and abuse of antibiotics. Ibuprofen, a widely used non-steroidal anti-inflammatory drug, has been previously reported to exert antimicrobial activity, although the specific mechanism of its action requires additional investigation. Given the regulation effects on quorum sensing (QS), we hypothesized that inhibition of P. aeruginosa with ibuprofen is linked with the QS systems. First, we assessed the action of ibuprofen in P. aeruginosa by measuring CFU. The antimicrobial activity of ibuprofen was evaluated by crystal violent staining and acridine orange staining at various drug concentrations (0, 50, 75, and 100 g/mL). Moreover, the effect of ibuprofen on different QS virulence factors, such as pyocyanin, elastase, protease, and rhamnolipids, was assessed revealing a concentration-dependent decrease (P<0.05). The effect of ibuprofen was confirmed by liquid chromatography/mass spectrometry analysis of 3-oxo-C12-HSL and C4-HSL production. In addition, qRT-PCR results identified significant suppression of Las and Rhl gene expression after 18 hours of treatment with ibuprofen (P<0.05), with the most significant suppression observed at the concentration of 75 g/mL. Functional complementation with exogenous 3-oxo-C12-HSL and C4-HSL suggested that C4-HSL can recover the production of virulence factors and biofilm formation in P. aeruginosa. Molecular docking of ibuprofen with QS-associated proteins revealed high binding affinity. In summary, the results suggest that ibuprofen is a candidate drug for the treatment of clinical infections with P. aeruginosa.

microbiology↗

bioRxiv2019

Plasma Circular RNA Panel to Diagnose Hepatitis B Virus-Related Hepatocellular Carcinoma

To explore whether plasma circular RNAs (circRNAs) can diagnose hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC), microarray and qPCR were used to identify plasma circRNAs that were increased in HCC patients compared with controls (including healthy controls, chronic hepatitis B, HBV-related liver cirrhosis and HCC patients). A logistic regression model was constructed using a training set (n=313) and then validated using another two independent sets (n=306 and 526, respectively). Area under the receiver operating characteristic curve (AUC) was used to evaluate diagnostic accuracy. We identified a plasma circRNA panel (CircPanel) containing three circRNAs (hsa_circ_0000976, hsa_circ_0007750 and hsa_circ_0139897) that could detect HCC. CircPanel showed a higher accuracy than AFP (alpha-fetoprotein) to distinguish individuals with HCC from controls in all three sets (AUC 0.863 [95% CI 0.819-0.907] vs 0.790 [0.738-0.842], P=0.036 in training set; 0.843 [0.796-0.890] vs 0.747 [0.691-0.804], P=0.011 in validation set 1 and 0.864 [0.830-0.898] vs 0.769 [0.728-0.810], P<0.001 in validation set 2). CircPanel also performed well in detecting Small-HCC (solitary, [≤]3cm), AFP-negative HCC and AFP-negative Small-HCC.\n\nSignificance of this studyWhat is already known about this subject? O_LIThe diagnostic accuracy of alpha-fetoprotein (AFP) in detecting hepatocellular carcinoma (HCC) is unsatisfactory.\nC_LIO_LICircular RNA (circRNA) expression profiles in HCC and adjacent nontumor liver tissues are significantly different.\nC_LIO_LIPlasma circRNAs are enriched, stable and can be biomarkers for various diseases.\nC_LI\n\nWhat are the new findings? O_LIThe expression of circRNAs in the plasma from HCC patients and chronic hepatitis B is significantly different.\nC_LIO_LIPlasma circRNA panel (CircPanel, including hsa_circ_0000976, hsa_circ_0007750 and hsa_circ_0139897) has a higher accuracy than AFP to distinguish individuals with HCC or Small-HCC (solitary, [≤]3cm) from controls (healthy controls, chronic hepatitis B and HBV-related liver cirrhosis).\nC_LIO_LICircPanel also performs well in diagnosing AFP-negative HCC and AFP-negative Small-HCC.\nC_LI\n\nHow might it impact on clinical practice in the foreseeable future? Plasma CircPanel can be a diagnostic biomarker in detecting HCC and improves the diagnostic accuracy.

cancer biology↗

bioRxiv2019

Principles Governing the Dynamics of GABAergic Interneurons in the Barrel Cortex

Information processing in the neocortex is performed by GABAergic interneurons that are integrated with excitatory neurons into precisely structured circuits. To reveal how each neuron type shapes sensory representations, we measured spikes and membrane potential of specific types of neurons in the barrel cortex while mice performed an active, whisker-dependent object localization task. Whiskers were tracked with millisecond precision. Fast-spiking (FS) neurons were activated by touch with short latency and by whisking. FS neurons track thalamic input and provide feedforward inhibition. Somatostatin (SOM)-expressing neurons were also excited by touch, but with a delay (5 ms) compared to excitatory (E) and FS neurons. SOM neurons monitor local excitation and provide feedback inhibition. Vasoactive intestinal polypeptide (VIP)-expressing neurons were not driven by touch but elevated their spike rate during whisking, disinhibiting E and FS neurons. Our data reveal rules of recruitment for specific interneuron types, providing foundations for understanding cortical computations.

neuroscience↗

bioRxiv2019

CRISPR-pass: Gene rescue of nonsense mutations using adenine base editors

A nonsense mutation is a substitutive mutation in a DNA sequence that causes a premature termination during translation and produces stalled proteins resulting in dysfunction of a gene. Although it usually induces severe genetic disorders, there are no definite methods for inducing read-through of premature termination codons (PTCs). Here, we present a targeted tool for bypassing PTCs, named CRISPR-pass that uses CRISPR-mediated adenine base editors. CRISPR-pass, which should be applicable to 95.5% of clinically significant nonsense mutations in the ClinVar database, rescues protein synthesis in patient-derived fibroblasts, suggesting potential clinical utility.

molecular biology↗

bioRxiv2019

TAF1-gene editing impairs Purkinje cell morphology and function

TAF1 intellectual disability syndrome is an X-linked disorder caused by loss-of-function mutations in the TAF1 gene. How these mutations cause dysmorphology, hypotonia, intellectual and motor defects is unknown. Mouse models which have embryonically targeted TAF1 have failed, possibly due to TAF1 being essential for viability, preferentially expressed in early brain development, and intolerant of mutation. Novel animal models are valuable tools for understanding neuronal pathology. Here, we report the development and characterization of a novel animal model for TAF1 ID syndrome in which the TAF1 gene is deleted in embryonic rats using clustered regularly interspaced short palindromic repeats (CRISPR) associated protein 9 (Cas9) technology and somatic brain transgenesis mediated by lentiviral transduction. Rat pups, post-natal day 3, were subjected to intracerebroventricular (ICV) injection of either gRNA-control or gRNA-TAF1 vectors. Rats were subjected to a battery of behavioral tests followed by histopathological analyses of brains at post-natal day 14 and day 35. TAF1-edited rats exhibited behavioral deficits at both the neonatal and juvenile stages of development. Deletion of TAF1 lead to a hypoplasia and loss of the Purkinje cells. Abnormal motor symptoms in TAF1-edited rats were associated with irregular cerebellar output caused by changes in the intrinsic activity of the Purkinje cells. Immunostaining revealed a reduction in the expression of the CaV3.1 T-type calcium channel. This animal model provides a powerful new tool for studies of neuronal dysfunction in conditions associated with TAF1 abnormalities and should prove useful for developing therapeutic strategies to treat TAF1 ID syndrome. Significance StatementIntellectual disability (ID) syndrome is an X-linked rare disorder caused by loss-of-function mutations in the TAF1 gene. There is no animal model for understanding neuronal pathology and to facilitate development of new therapeutics for this X-linked intellectual disability syndrome. Novel animal models are valuable tools for understanding neuronal pathology and to facilitate development of new therapeutics for diseases. Here we developed a novel animal model for TAF1 ID syndrome in which the TAF1 gene is deleted by CRISPR-Cas9 editing and lentiviral transduction. This animal model provides a powerful new tool for studies of neuronal dysfunction associated with TAF1 abnormalities and should prove useful for developing therapeutic strategies to treat TAF1 ID syndrome.

neuroscience↗

bioRxiv2019

Mitochondrial volume fraction controls translation of nuclear-encoded mitochondrial proteins

Mitochondria are dynamic in their size and morphology yet must also precisely control their protein composition according to cellular energy demand. This control is particularly complicated for mitochondria, as they must coordinate gene expression from both the nuclear and mitochondrial genome. We have found that cells are able to use this dynamic morphology to post-transcriptionally coordinate protein expression with the metabolic demands of the cell through enhanced mRNA localization to the mitochondria. As yeast switch to respiratory metabolism, they increase their mitochondrial volume fraction that is, the ratio of mitochondrial volume to intracellular volume which drives the localization of nuclear-encoded mitochondrial mRNAs to the surface of the mitochondria. Through artificial tethering experiments, we show that this mitochondrial localization is sufficient to increase protein production, whereas sequestering mRNAs away from the mitochondrial surface decreases protein production, and those cells are deficient in growth in respiratory conditions. Furthermore, we find that this mRNA sensitivity to mitochondrial volume fraction is driven by the speed of translation downstream of the mitochondrial targeting sequence (MTS), as local ribosome stalling through a stretch of polyprolines in the nascent peptide can drive constitutive localization of mRNAs to the mitochondria. This points to a mechanism by which organelle volume fraction provides feedback to regulate organelle-specific gene expression through mRNA localization while potentially circumventing the need to directly coordinate with the nuclear genome.

cell biology↗

bioRxiv2019

Pleiotropic Meta-Analysis of Cognition, Education, and Schizophrenia Differentiates Roles of Early Neurodevelopmental and Adult Synaptic Pathways

Liability to schizophrenia is inversely correlated with general cognitive ability at both the phenotypic and genetic level. Paradoxically, a modest but consistent positive genetic correlation has been reported between schizophrenia and educational attainment, despite the strong positive genetic correlation between cognitive ability and educational attainment. Here we leverage published GWAS in cognitive ability, education, and schizophrenia to parse biological mechanisms underlying these results. Association analysis based on subsets (ASSET), a pleiotropic meta-analytic technique, allowed jointly associated loci to be identified and characterized. Specifically, we identified subsets of variants associated in the expected (\"Concordant\") direction across all three phenotypes (i.e., greater risk for schizophrenia, lower cognitive ability, and lower educational attainment); these were contrasted with variants demonstrating the counterintuitive (\"Discordant\") relationship between education and schizophrenia (i.e., greater risk for schizophrenia and higher educational attainment). ASSET analysis revealed 235 independent loci associated with cognitive ability, education and/or schizophrenia at p<5x10-8. Pleiotropic analysis successfully identified more than 100 loci that were not significant in the input GWASs, and many of these have been validated by larger, more recent single-phenotype GWAS. Leveraging the joint genetic correlations of cognitive ability, education, and schizophrenia, we were able to dissociate two distinct biological mechanisms: early neurodevelopmental pathways that characterize concordant allelic variation, and adulthood synaptic pruning pathways that were linked to the paradoxical positive genetic association between education and schizophrenia. Further, genetic correlation analyses revealed that these mechanisms contribute not only to the etiopathogenesis of schizophrenia, but also to the broader biological dimensions that are implicated in both general health outcomes and psychiatric illness.

genetics↗

bioRxiv2019

O-GlcNAc transferase suppresses necroptosis and liver fibrosis

Over a billion people suffer from chronic liver diseases worldwide, which often leads to fibrosis and then cirrhosis. Treatments for fibrosis remain experimental, in part because no unifying mechanism has been identified that initiates liver fibrosis. Here we report that O-linked {beta}-N-acetylglucosamine (O-GlcNAc) modification protects against hepatocyte necroptosis and initiation of liver fibrosis. Decreased O-GlcNAc levels were seen in patients with liver cirrhosis and in mice with ethanol-induced liver injury. Liver-specific O-GlcNAc transferase (OGT) knockout (OGT-LKO) mice exhibited ballooning degeneration and elevated circulating alanine aminotransferase (ALT) levels at an early age and progressed to liver fibrosis and portal inflammation by 10 weeks of age. OGT-deficient hepatocytes underwent excessive necroptosis and exhibited elevated protein expression levels of receptor-interacting protein kinase 3 (RIPK3) and mixed lineage kinase domain-like (MLKL), which are key mediators of necroptosis. Furthermore, glycosylation of RIPK3 by OGT reduced RIPK3 protein stability. Taken together, these findings identify OGT as a key suppressor of hepatocyte necroptosis and OGT-LKO mice may serve as an effective spontaneous genetic model of liver fibrosis.

physiology↗

bioRxiv2018

Targeting the CaV - interaction yields a selective antagonist of the N-type CaV2.2 channel with broad antinociceptive efficacy

Inhibition of voltage-gated calcium (CaV) channels is a potential therapy for many neurological diseases including chronic pain. Neuronal CaV1/CaV2 channels are composed of , {beta} and 2{delta} subunits. The {beta}-subunits of CaV channels are cytoplasmic proteins that increase the surface expression of the pore-forming subunit of CaV. We targeted the high-affinity protein-protein interface of CaV{beta}s pocket within the CaV-subunit. Structure-based virtual screening of 50,000 small molecule library docked to the {beta}-subunit led to the identification of 2-(3,5-dimethylisoxazol-4-yl)-N-((4-((3-phenylpropyl)amino)quinazolin-2-yl)methyl)acetamide (compound 45). This small molecule bound to CaV{beta} and inhibited its coupling with N-type voltage-gated calcium (CaV2.2) channels, leading to a reduction in CaV2.2 currents in rat dorsal root ganglion (DRG) sensory neurons, decreased pre-synaptic localization of CaV2.2 in vivo, decreased frequency of spontaneous excitatory post-synaptic potentials (sEPSC), and inhibited release of the nociceptive neurotransmitter calcitonin gene related peptide (CGRP) from spinal cord. 45 was antinociceptive in naive animals and reversed allodynia and hyperalgesia in models of acute (post-surgical) and neuropathic (spinal nerve ligation, chemotherapy- and gp120-induced peripheral neuropathy, and genome-edited neuropathy) pain. 45 did not cause akinesia or motor impairment, a common adverse effect of CaV2.2 targeting drugs, when injected into the brain. 45, a quinazoline analog, represents a novel class of CaV2.2-targeting compounds that may serve as probes to interrogate CaV-{beta} function and ultimately be developed as a non-opioid therapeutic for chronic pain.

neuroscience↗

bioRxiv2018

Two Contrasting Classes of Nucleolus-Associated Domains in Mouse Fibroblast Heterochromatin

In interphase eukaryotic cells, almost all heterochromatin is located adjacent to the nucleolus or to the nuclear lamina, thus defining Nucleolus-Associated Domains (NADs) and Lamina-Associated Domains (LADs), respectively. Here, we determined the first genome-scale map of murine NADs in mouse embryonic fibroblasts (MEFs) via deep sequencing of chromatin associated with purified nucleoli. We developed a Bioconductor package called NADfinder and demonstrated that it identifies NADs more accurately than other peak-calling tools, due to its critical feature of chromosome-level local baseline correction. We detected two distinct classes of NADs. Type I NADs associate frequently with both the nucleolar periphery and with the nuclear lamina, and generally display characteristics of constitutive heterochromatin, including late DNA replication, enrichment of H3K9me3 and little gene expression. In contrast, Type II NADs associate with nucleoli but do not overlap with LADs. Type II NADs tend to replicate earlier, display greater gene expression, and are more often enriched in H3K27me3 than Type I NADs. The nucleolar associations of both classes of NADs were confirmed via DNA-FISH, which also detected Type I but not Type II probes enriched at the nuclear lamina. Interestingly, Type II NADs are enriched in distinct gene classes, notably factors important for differentiation and development. In keeping with this, we observed that a Type II NAD is developmentally regulated, present in MEFs but not in undifferentiated embryonic stem (ES) cells.

genomics↗

bioRxiv2018

Regrowth-delay Body as a Bacterial Subcellular Structure marking multidrug tolerant Persisters

Bacteria have long been recognized to be capable of entering a phenotypically non-growing persister state, in which the cells exhibit an extended regrowth lag and a multidrug tolerance, thus posing a great challenge in treating infectious diseases. Owing to their non-inheritability, low abundance of existence, lack of metabolic activities, and high heterogeneity, properties of persisters remain poorly understood. Here, we report our accidental discovery of a hitherto unreported subcellular structure that we term the regrowth-delay body, which is formed only in non-growing bacterial cells and sequesters multiple key proteins. As of now, this structure, that dissolves when the cell resumes growth, is the most distinguishable subcellular structure marking persisters. Our studies also indicate that persisters exhibit different depth of persistence, as determined by the status of their regrowth-delay bodies. Our findings imply that suppressing the formation and/or promoting the dissolution of regrowth-delay bodies could be viable strategies for eradicating persisters.

microbiology↗

bioRxiv2018

Stable biphasic interfaces for open microfluidic platforms

We present an open microfluidic platform that enables stable flow of an organic solvent over an aqueous solution. The device features apertures connecting a lower aqueous channel to an upper solvent compartment that is open to air, enabling easy removal of the solvent for analysis. We have previously shown that related open biphasic systems enable steroid hormone extraction from human cells in microscale culture and secondary metabolite extraction from microbial culture; here we build on our prior work by determining conditions under which the system can be used with extraction solvents of ranging polarities, a critical feature for applying this extraction platform to diverse classes of metabolites. We develop an analytical model that predicts the limits of stable aqueous-organic interfaces based on analysis of Laplace pressure. With this analytical model and experimental testing, we developed generalized design rules for creating stable open microfluidic biphasic systems with solvents of varying densities, aqueous-organic interfacial tensions, and polarities. The stable biphasic interfaces afforded by this device will enable on-chip extraction of diverse metabolite structures and novel applications in microscale biphasic chemical reactions.

bioengineering↗