Biology subjects

Wu, J.

Publications and source records attributed to Wu, J..

At least 595 records · Page 33Linked to original sources

bioRxiv2022

Oxidative phosphorylation pathway disruption is an alternative pathological mechanism leading to Diamond-Blackfan anemia

Diamond-Blackfan anemia (DBA) is a rare congenital disorder characterized by the failure of erythroid progenitor differentiation; however, the molecular mechanisms leading to erythroid defects remain unclear. By analyzing the transcriptomic profiles of bone marrow from patients with DBA (n = 10), we identified the dysfunction of the oxidative phosphorylation (OXPHOS) pathway as a possible cause of DBA. We established a DBA cell model using differentiating hematopoietic stem progenitor cells in which the OXPHOS pathway was suppressed to completely recapitulate the defects in erythroid progenitor differentiation, ribosome biogenesis, and heme biosynthesis, which are representative characteristics of patients with DBA. Disruption of the OXPHOS pathway led to ribosomal defects and associated erythroid defects via abolishment of the Ran GTPase activating protein RanGAP1, which is pivotal in the RNA transport pathway. The composition of the ribosomal proteins in the established DBA cells was unchanged, but an overall reduction in ribosomal protein levels was observed, leading to an alteration in the translation of a subset of transcripts specific to erythropoiesis. We revealed that the OXPHOS pathway participates in erythropoiesis, particularly at an early stage, and reinforced the relationship between the OXPHOS pathway and erythropoiesis. Coenzyme Q10, an activator of OXPHOS, largely rescued the erythroid defects in DBA cells. Our results reveal that OXPHOS repression is an alternative pathological mechanism leading to DBA, demonstrating its potential as a therapeutic pathway. Key PointsO_LIOxidative phosphorylation (OXPHOS) pathway disruption is an alternative pathological mechanism underlying Diamond-Blackfan anemia (DBA). C_LIO_LISuppression of OXPHOS leads to defects in erythropoiesis and ribosomal biogenesis via the RanGAP1 protein. C_LI

cell biology↗

bioRxiv2022

Real-time denoising of fluorescence time-lapse imaging enables high-sensitivity observations of biological dynamics beyond the shot-noise limit

A fundamental challenge in fluorescence microscopy is the inherent photon shot noise caused by the inevitable stochasticity of photon detection. Noise increases measurement uncertainty, degrades image quality, and limits imaging resolution, speed, and sensitivity. To achieve high-sensitivity imaging beyond the shot-noise limit, we provide DeepCAD-RT, a versatile self-supervised method for effective noise suppression of fluorescence time-lapse imaging. We made comprehensive optimizations to reduce its data dependency, processing time, and memory consumption, finally allowing real-time processing on a two-photon microscope. High imaging signal-to-noise ratio (SNR) can be acquired with 10-fold fewer fluorescence photons. Meanwhile, the self-supervised superiority makes it a practical tool in fluorescence microscopy where ground-truth images for training are hard to obtain. We demonstrated the utility of DeepCAD-RT in extensive experiments, including in vivo calcium imaging of various model organisms (mouse, zebrafish larva, fruit fly), 3D migration of neutrophils after acute brain injury, and 3D dynamics of cortical ATP (adenosine 5-triphosphate) release. DeepCAD-RT will facilitate the morphological and functional interrogation of biological dynamics with minimal photon budget.

biophysics↗

bioRxiv2022

Newly synthesized mRNA escapes translational repression during the acute phase of the mammalian unfolded protein response

Endoplasmic Reticulum (ER) stress, caused by the accumulation of misfolded proteins in the ER, elicits a homeostatic mechanism known as the Unfolded Protein Response (UPR). The UPR reprograms gene expression to promote adaptation to chronic ER stress. The UPR comprises an acute phase involving inhibition of bulk protein synthesis and a chronic phase of transcriptional induction coupled with the partial recovery of protein synthesis. However, the role of transcriptional regulation in the acute phase of the UPR is not well understood. Here we analyzed the fate of newly synthesized mRNA encoding the protective and homeostatic transcription factor X-box binding protein 1 (XBP1) during this acute phase. We have previously shown that global translational repression induced by the acute UPR was characterized by decreased translation and increased stability of XBP1 mRNA. We demonstrate here that this stabilization is independent of new transcription. In contrast, we show XBP1 mRNA newly synthesized during the acute phase accumulates with long poly(A) tails and escapes translational repression. Inhibition of nascent RNA polyadenylation during the acute phase decreased cell survival with no effect in unstressed cells. Furthermore, during the chronic phase of the UPR, levels of XBP1 mRNA with long poly(A) tails decreased in a manner consistent with co-translational deadenylation. Finally, additional pro-survival, transcriptionally-induced mRNAs show similar regulation, supporting the broad significance of the pre-steady state UPR in translational control during ER stress. We conclude that the biphasic regulation of poly(A) tail length during the UPR represents a previously unrecognized pro-survival mechanism of mammalian gene regulation.

molecular biology↗

bioRxiv2022

A cadherin mutation in Celsr3 linked to Tourette Disorder affects dendritic patterning and excitability of cholinergic interneurons

CELSR3 encodes an atypical protocadherin cell adhesion receptor that was recently identified as a high-risk gene for Tourette disorder. A putative damaging de novo variant was inserted into the mouse genome to generate an amino acid substitution within the fifth cadherin repeat. By contrast to Celsr3 constitutive null animals, mice homozygous for the R774H amino acid substitution are viable and have grossly normal forebrain development. The density of cortical and striatal interneuron subpopulations is normal, but 3D geometric analysis of cortical pyramidal neurons and striatal cholinergic interneurons revealed changes to dendritic patterning and types and distributions of spines. Furthermore, patch clamp recordings in cholinergic interneurons located within the sensorimotor striatum uncovered mild intrinsic hyperexcitability. Despite these changes, Celsr3R774H homozygous mice do not show obvious tic-like stereotypies at baseline nor motor learning impairments, but females exhibited perseverative digging behavior. Our findings show that a human mutation in CELSR3 linked to Tourette disorder is sufficient to alter dendritic patterning in the cortex and striatum and also the intrinsic excitability of cholinergic interneurons.

neuroscience↗

bioRxiv2022

In vitro evolution of Listeria monocytogenes reveals selective pressure for loss of SigB and AgrA function at different incubation temperatures.

The alternative sigma factor B ({sigma}B) contributes to the stress tolerance of the foodborne pathogen Listeria monocytogenes by upregulating the General Stress Response. We previously showed that {sigma}B loss-of-function mutations arise frequently in strains of L. monocytogenes, and suggested that mild stresses might favour the selection of such mutations. In this study, we performed in vitro evolution experiments (IVEE) where L. monocytogenes was allowed to evolve over 30 days at elevated (42{degrees}C) or lower (30{degrees}C) incubation temperatures. Isolates purified throughout the IVEE revealed the emergence of sigB operon mutations at 42{degrees}C. However, at 30{degrees}C independent alleles in the agr locus arose, resulting in the inactivation of the Agr quorum sensing. Colonies of both sigB- and agr- strains exhibited a greyer colouration on 7-days-old agar plates compared with the parental strain. Scanning electron microscopy revealed a more complex colony architecture in the wild type than in the mutant strains. sigB- strains outcompeted the parental strain at 42{degrees}C, but not at 30{degrees}C, whilst agr- strains showed a small increase in competitive fitness at 30{degrees}C. Analysis of 40,080 L. monocytogenes publicly available genome sequences revealed a high occurrence rate of premature stop codons in both the sigB and agrCA loci. An analysis of a local L. monocytogenes strain collection revealed 5 out of 168 strains carrying agrCA alleles. Our results suggest that the loss of {sigma}B or Agr confer an increased competitive fitness in some specific conditions and this likely contributes to the emergence of these alleles in strains of L. monocytogenes. ImportanceTo withstand environmental aggressions L. monocytogenes upregulates a large regulon through the action of the alternative sigma factor B ({sigma}B). However, {sigma}B becomes detrimental for L. monocytogenes growth under mild stresses, which confer a competitive advantage to {sigma}B loss-of-function alleles. Temperatures of 42{degrees}C, a mild stress, are often employed in mutagenesis protocols of L. monocytogenes and promote the emergence of {sigma}B loss-of-function alleles in the sigB operon. In contrast, lower temperatures of 30{degrees}C promote the emergence of Agr loss-of-function alleles, a cell-cell communication mechanism in L. monocytogenes. Our findings demonstrate that loss-of-function alleles emerge spontaneously in laboratory-grown strains. These alleles rise in the population as a consequence of the trade-off between growth and survival imposed by the activation of {sigma}B in L. monocytogenes. Additionally, our results demonstrate the importance of identifying unwanted hitchhiker mutations in newly constructed mutant strains.

molecular biology↗

bioRxiv2022

cLD: Rare-variant disequilibrium between genomic regions identifies novel genomic interactions

Linkage disequilibrium (LD) is a fundamental concept in genetics; critical for studying genetic associations and molecular evolution. However, LD measurements are only reliable for common genetic variants, leaving low-frequency variants unanalyzed. In this work, we introduce cumulative LD (cLD), a stable statistic that captures the rare-variant LD between genetic regions, which reflects more biological interactions between variants, in addition to lack of recombination. We derived the theoretical variance of cLD using delta methods to demonstrate its higher stability than LD for rare variants. This property is also verified by bootstrapped simulations using real data. In application, we find cLD reveals an increased genetic association between genes in 3D chromatin interactions, a phenomenon recently reported negatively by calculating standard LD between common variants. Additionally, we show that cLD is higher between gene pairs reported in interaction databases, identifies unreported protein-protein interactions, and reveals interacting genes distinguishing case/control samples in association studies.

bioinformatics↗

bioRxiv2022

The brassinosteroid biosynthesis gene TaD11-2A controls grain size and its elite haplotype improves wheat grain yields

Brassinosteroids (BRs) control many important agronomic traits, therefore the manipulation of BR components could improve crop productivity and performance. However, the potential effects of BR-related genes on yield-related traits and stress tolerance in wheat (Triticum aestivum L.) remain poorly understood. Here, we identified TaD11 genes in wheat (rice D11 orthologs) that encoded enzymes involved in BR biosynthesis. TaD11 genes were highly expressed in roots (Zadoks scale: Z11) and grains (Z75), while expression was significantly suppressed by exogenous BR (24-epiBL). Ectopic expression of TaD11-2A rescued the abnormal panicle structure and plant height (PH) of the cpb1 mutant, and also increased endogenous BR levels, resulting in improved grain yields and grain quality in rice. Natural variations in TaD11-2A were associated with significant differences in yield-related traits, including PH, grain width (GW), 1000-grain weight (TGW), and grain yield per plant (GYPP), and its favorable haplotype, TaD11-2A-HapI was subjected to positive selection during wheat breeding. Additionally, TaD11-2A influenced root length and salt tolerance in rice and wheat at seedling stages. These results indicated the important role of BR TaD11 biosynthetic genes in controlling grain size and root length, and also highlighted their potential in the molecular biological analysis of wheat. HighlightThe brassinosteroid biosynthesis gene TaD11-2A regulates grain size and root length and its haplotype favorably improves grain yields and salt tolerance in wheat.

plant biology↗

bioRxiv2022

Bile Acid Restrained T Cell Activation Explains Cholestasis Aggravated Hepatitis B Virus Infection

Cholestasis is a common complication of Hepatitis B Virus (HBV) infection, characterized by increased intrahepatic and plasma bile acid levels. Cholestasis was found negatively associated with hepatitis outcome, however; the exact mechanism by which cholestasis impact on anti-viral immunity and impede HBV clearance remains elusive. Here, we found that cholestatic mice are featured with dysfunctional T cell response, and bile acids inhibit the activation and metabolic reprogramming of CD4+ T cells. Mechanistically, bile acids disrupt intracellular calcium homeostasis via inhibiting mitochondria calcium uptake and elevating cytoplasmic Ca2+ concentration of CD4+ T cells, leading to STIM1 and ORAIL1 decoupling and impaired store-operated Ca2+ entry which is essential for NFAT signaling and T cell activation. Moreover, in a transgenic mouse model of HBV infection, it was confirmed that cholestasis compromised T cells activation resulting in poor viral clearance. Collectively, our results suggest that bile acids play pivotal roles in anti-HBV infection via controlling T cells activation and metabolism, and that targeting regulation of bile acids may be a therapeutic strategy for host virus defense.

immunology↗

bioRxiv2022

The impact of the soluble protein fraction and kernel hardness on wheat flour starch digestibility

Wheat is the staple crop for 35% of the worlds population, providing a major source of calories for much of the worlds population. Starch is the main source of energy in wheat flour, but the digestibility of wheat starch varies greatly between different flours and wheat products. This has relevance from a health perspective because wheat starch products that are rapidly digested and elicit large post-prandial glucose peaks are associated with a host of cardiac and metabolic disorders. In this study, we investigate the impact of protein on starch digestion in three commercially sourced flours with different grain hardness. Grain hardness impacted on flour particle size, but not significantly on starch digestion. A soluble extract of wheat proteins was found to dramatically reduce starch digestion, even following gastric proteolysis. Proteomic analysis revealed that this soluble extract was enriched in proteinaceous -amylase inhibitors which were partially degraded during gastric proteolysis. Therefore, we conclude that the soluble proteins of wheat flour have a significant contribution towards retarding starch digestion, even following gastric digestion.

biochemistry↗

bioRxiv2022

Duration reproduction under memory pressure: Modeling the roles of visual memory load in duration encoding and reproduction

Duration estimates are often biased by the sampled statistical context, yielding the classical central-tendency effect, i.e., short durations are over- and long duration underestimated. Most studies of the central-tendency bias have primarily focused on the integration of the sensory measure and the prior information, without considering any cognitive limits. Here, we investigated the impact of cognitive (visual working-memory) load on duration estimation in the duration encoding and reproduction stages. In four experiments, observers had to perform a dual, attention-sharing task: reproducing a given duration (primary) and memorizing a variable set of color patches (secondary). We found an increase in memory load (i.e., set size) during the duration-encoding stage to increase the central-tendency bias, while shortening the reproduced duration in general; in contrast, increasing the load during the reproduction stage prolonged the reproduced duration, without influencing the central tendency. By integrating an attentional-sharing account into a hierarchical Bayesian model, we were able to predict both the general over- and underestimation and the central-tendency effects observed in all four experiments. The model suggests that memory pressure during the encoding stage increases the sensory noise, which elevates the central-tendency effect. In contrast, memory pressure during the reproduction stage only influences the monitoring of elapsed time, leading to a general duration over-reproduction without impacting the central tendency.

neuroscience↗

bioRxiv2022

Lyophilized mRNA-lipid nanoparticles vaccine with long-term stability and high antigenicity against SARS-CoV-2

Advanced mRNA vaccines play vital roles against SARS-CoV-2. However, due to their poor stability, most current mRNA delivery platforms need to be stored at -20{degrees}C or -70{degrees}C, which severely limits their distribution. Herein, we present lyophilized SARS-CoV-2 mRNA-lipid nanoparticle vaccines, which can be stored at room temperature with long-term thermostability. In the in vivo Delta virus challenge experiment, lyophilized Delta variant mRNA vaccine successfully protected mice from infection and cleared the virus. Lyophilized omicron mRNA vaccine enabled to elicit both potent humoral and cellular immunity. In booster immunization experiments in mice and old monkeys, lyophilized omicron mRNA vaccine could effectively increase the titers of neutralizing antibodies against wild-type coronavirus and omicron variants. In humans, lyophilized omicron mRNA vaccine as a booster shot could also engender excellent immunity and had less severe adverse events. This lyophilization platform overcomes the instability of mRNA vaccines without affecting their bioactivity, and significantly improved their accessibility, particularly in remote regions.

immunology↗

bioRxiv2022

Whole-Brain Map of Top-down afferent Inputs to Nucleus Accumbens of the Mouse

Nucleus accumbens (NAc) is an important part of basal ganglia and receives major transsynaptic inputs from medial prefrontal cortex (mPFC), basolateral amygdala nucleus (BL) and hippocampus (HPC). The neural circuits formed by mPFC, BL, HPC with NAc are closely related to diverse brain functions such as decision-making, social behavior, reward seeking behavior and aggressive behavior. However, a lack of information about network structure of NAc top-down afference has limited our understanding of mechanisms of these functions. Here, we systematically analyzed whole brain patterns of inputs to mPFC/HPC/BL-NAc projectors via using (TRIO) labeling strategy. We found that the upstream input patterns between mPFC-core and mPFC-shell projections, BL-core and BL-shell projections, HPC-core and HPC-shell projections were similar. The projections from mPFC and BL to NAc receive a wide range of inputs, while the projections from HPC to NAc receive convergent inputs. Furthermore, all of mPFC/HPC/BL-NAc projectors receive considerable inputs from respective local regions. This study lays a foundation for further analysis of complex NAc functional mechanisms.

neuroscience↗

bioRxiv2022

3D Printable High Performance Conducting Polymer Hydrogel for All-Hydrogel Bioelectronics

Owing to the unique combination of electrical conductivity and tissue-like mechanical properties, conducting polymer hydrogels have emerged as a promising candidate for bioelectronic interfacing with biological systems. However, despite the recent advances, the development of hydrogels with both excellent electrical and mechanical properties in physiological environments remains a lingering challenge. Here, we report a bi-continuous conducting polymer hydrogel (BC-CPH) that simultaneously achieves high electrical conductivity (over 11 S cm-1), stretchability (over 400%) and fracture toughness (over 3,300 J m-2) in physiological environments, and is readily applicable to advanced fabrication methods including 3D printing. Enabled by the BC-CPH, we further demonstrate multi-material 3D printing of monolithic all-hydrogel bioelectronic interfaces for long-term electrophysiological recording and stimulation of various organs. This study may offer promising materials and a platform for future bioelectronic interfacing.

bioengineering↗

bioRxiv2022

Rapid deep widefield neuron finder driven by virtual calcium imaging data

Widefield microscope provides optical access to multi-millimeter fields of view and thousands of neurons in mammalian brains at video rate. However, calcium imaging at cellular resolution has been mostly contaminated by tissue scattering and background signals, making neuronal activities extraction challenging and time-consuming. Here we present a deep widefield neuron finder (DeepWonder), which is fueled by simulated calcium recordings but effectively works on experimental data with an order of magnitude faster speed and improved inference accuracy than traditional approaches. The efficient DeepWonder accomplished fifty-fold signal-to-background ratio enhancement in processing terabytes-scale cortex-wide recording, with over 14000 neurons extracted in 17 hours in workstation-grade computing resources compared to nearly week-long processing time with previous methods. DeepWonder circumvented the numerous computational resources and could serve as a guideline to massive data processing in widefield neuronal imaging.

bioengineering↗

bioRxiv2022

Types of cis- and trans-gene regulation of expression quantitative trait loci across human tissues

Expression quantitative trait loci (eQTLs) have been identified for most genes in the human genome across tissues and cell types. While most of the eQTLs are near the associated genes, some can be far away or on different chromosomes, with the regulatory mechanisms largely unknown. Here, we study cis- and trans-regulation by eQTLs on protein-coding genes and long noncoding RNAs (lncRNAs) across nearly 50 tissues and cell types. Specifically, we constructed trios consisting of an eQTL, its cis-gene and trans-gene and inferred the regulatory relationships with causal network inference. We identify multiple types of regulatory networks for trios: across all the tissues, more than half of the trios are inferred to be conditionally independent, where the two genes are conditionally independent given the genotype of the eQTL (gene 1 [<-] eQTL [->] gene 2). Around 1.5% of the trios are inferred to be mediation (eQTL [->] mediator [->] target), around 1.3% fully connected among the three nodes, and just a handful v-structures (eQTL [->] gene 1 [<-] gene 2). Unexpectedly, across the tissues, on average more than half of the mediation trios have the trans-gene as the mediator. Most of the mediators (cis and trans) are tissue specific, and cis-gene mediators are significantly enriched for protein-coding genes, whereas trans-gene mediators have a similar distribution of protein-coding genes and lncRNAs to the whole genome.

genomics↗

bioRxiv2022

Single-molecule nanopore dielectrophoretic trapping of α-Synuclein with lipid membranes

The lipid--Synuclein (-Syn) interaction plays a crucial role in the pathogenesis of Parkinsons disease. Here, we trap -Syn at a conjunction of an -hemolysin (HL) single nanopore-lipid to investigate the folding and unfolding kinetics of -Syn in a lipidic environment. The hybridized -Syn is generated through a reaction between a 5-thiol-modified nucleotide oligo (dC30) and the -Syn mutant (A140C). Owing to an applied voltage, single-molecule hybridized -Syn can be trapped at the single nanopore. The trapping events are associated with dielectrophoretic force. The folding and unfolding events of -Syn can be observed at the pore-membrane junction through interpretation of blockade current amplitudes and dwell time. This can be related to the protein quaternary structure influenced by the -Syn-membrane interaction, allowing further analysis of -Syn conformational dynamics. We studied how disease associated metal ions (Cu2+, Zn2+) modulate folding and unfolding of -Syn at the interface of the membranes and pore, and how -helical peptidomimetics stabilize the helical conformation of -Syn in the presence of a membrane. These studies aid our understanding of the complexity of the interaction of -Syn, lipid membranes and metal ions, and in using peptidomimetics, a new strategy against -Syn toxicity and aggregation is advanced.

biochemistry↗

bioRxiv2022

Reference-based comparison of adaptive immune receptor repertoires

B- and T-cell receptor (immune) repertoires can represent an individuals immune history. While current repertoire analysis methods aim to discriminate between health and disease states, they are typically based on only a limited number of parameters (e.g., clonal diversity, germline usage). Here, we introduce immuneREF: a quantitative multi-dimensional measure of adaptive immune repertoire (and transcriptome) similarity that allows interpretation of immune repertoire variation by relying on both repertoire features and cross-referencing of simulated and experimental datasets. immuneREF is implemented in an R package and was validated based on detection sensitivity of immune repertoires with known similarities and dissimilarities. To quantify immune repertoire similarity landscapes across health and disease, we applied immuneREF to >2400 datasets from individuals with varying immune states (healthy, [autoimmune] disease and infection [Covid-19], immune cell population). Importantly we discovered, in contrast to the current paradigm, that blood-derived immune repertoires of healthy and diseased individuals are highly similar for certain immune states, suggesting that repertoire changes to immune perturbations are less pronounced than previously thought. In conclusion, immuneREF implements population-wide analysis of immune repertoire similarity and thus enables the study of the adaptive immune response across health and disease states.

systems biology↗

bioRxiv2022

Conserved Untranslated Regions of Multipartite Viruses: Natural Markers of Novel Viral Genomic Components and Tags of Viral Evolution

Viruses with split genomes are categorized as being either segmented or multipartite according to whether their genomic segments occur in single or different virions. Some complexity will exist, in that inherited "core" vital segments viruses may renew the others once host and environmental alterations keep driving viral evolution. Despite this uncertainty, empirical observations have been made across the split genomes in the untranslated regions (UTRs) on the short or long stretches of conserved or identical sequences. In this study, we describe a methodology that combines RNA and small RNA sequencing, conventional BLASTx, and iterative BLASTn of UTRs to detect viral genomic components even if they encode orphan genes (ORFans). Within the phylum Kitrinoviricota, novel putative multipartite viruses and viral genomic components were annotated using data obtained from our sampling or publicly available sources. The novel viruses, as extensions or intermediate nodes, enriched the information of the evolutionary networks. Furthermore, the diversity of novel genomic components emphasized the evolutionary roles of reassortment and recombination, as well as genetic deletion, strongly supporting the genomic complexity. These data also suggest insufficient knowledge of these genomic components for categorizing some extant viral taxa. The relative conservation of UTRs at the genome level may explain the relationships between monopartite and multipartite viruses and how the multipartite viruses can have a life strategy involving multiple host cells. Author summaryThe current workflows for virus identification are largely based on high-throughput sequencing and coupled protein sequence homology-dependent analysis methods and tools. However, for viruses with split genomes, the identification of genomic components whose deduced protein sequences are not homologous to known sequences is inadequate. Furthermore, many plant-infecting multipartite viruses contain conserved UTRs across their genomic components. Based on this, we propose a practical method of UTR-backed iterative BLASTn (UTR-iBLASTn) to explore the components with ORFans and study virus evolution using the UTRs as signals. These shed light on viral "dark matter"--unknown/omitted genomic components of segmented/multipartite viruses from different kingdoms and hosts, and the origins of these components.

microbiology↗