Biology subjects

Yang, J.

Publications and source records attributed to Yang, J..

At least 703 records · Page 39Linked to original sources

bioRxiv2022

Biphasic response of CD8 T cell to asparagine restriction maximizes its metabolic fitness and antitumoral functionality

Robust and effective T cell immune surveillance and cancer immunotherapy require properly allocating metabolic resources to sustain energetically costly processes, including growth and cytokine production. Amino acids are major cellular constituents that serve as protein building blocks, energy sources, and signaling molecules. Although T cells can synthesize all nonessential amino acids, including asparagine (Asn), activated CD8 T cells still consume considerable quantities of exogenous Asn. Unexpectedly, Asn restriction on CD8 T cells induced a biphasic response, consisting of sequential actions with opposing effects at two conceptually separated phases after activation. Asn restriction suppressed activation and cell cycle entry in the early phase by depleting the intracellular Asn pool while rapidly engaging an ATF4/NRF2-dependent stress response, conferring robust proliferation and effector function of CD8 T cells in the late phase. Mechanistically, ATF4 and NRF2 activation rendered CD8 T cells to utilize de novo biosynthesis of Asn, consuming less glucose and glutamine but producing more intracellular nucleotides for proliferation. Moreover, NRF2 activation promoted the expression of inflammatory and effector genes to enhance effector functions in CD8 T cells. Accordingly, Asn restriction or overexpression of ATF4 or NRF2 potentiated T cell-mediated antitumoral response in the metabolically restricted tumor microenvironment. Our studies revealed Asn as a critical metabolic node in directing the stress signaling to shape T cell metabolic fitness and effector functions. Asn restriction is a promising and clinically relevant strategy to enhance cancer immunotherapy.

immunology↗

bioRxiv2022

Organs-on-a-Chip Database (OOCDB): A Comprehensive, Systematic and Real-time Organs-on-a-chip Database

Organs-on-a-Chip is a microfluidic microphysiological system that uses microfluidic technology to make high-resolution and real-time imaging analysis on the structure and function of living human cells at the level of tissue and organ in vitro. Compared with the traditional two-dimensional cell culture model and animal model, organs-on-a-chip technology can simulate the pathological and toxicological interactions between different organs or tissues more closely and reflect the collaborative response of multiple organs to drugs. Although lots of organs-on-a-chip-related literature have been published, none of current databases have achieved all the following functionalities yet: searching, downloading and analyzing data and results from literature of organs-on-a-chip. To address this need, we established a database named organs-on-a-chip database (OOCDB), as a platform to integrate information related to organs-on-a-chip from various sources: literature, patents, microarray and transcriptome sequencing raw data, many open access data of organs-on-a-chip and organoids, as well as the data generated in our lab. OOCDB comprises dozens of sub databases and analysis tools and each sub database contains a number of data related to organs-on-a-chip, aiming to provide a comprehensive, systematic and convenient search engine for researchers. In addition, it provides functions such as mathematical modeling, three-dimensional model and citation map to meet the needs of researchers and to promote the development of organs-on-a-chip. The organs-on-a-chip database can be visited at http://www.organchip.cn.

bioinformatics↗

bioRxiv2022

mBAT-combo: a more powerful test to detect gene-trait associations from GWAS data

Gene-based association tests aggregate multiple SNP-trait associations into sets defined by gene boundaries. Since genes have a direct biological link to downstream function, gene-based test results are widely used in post-GWAS analysis. A common approach for gene-based tests is to combine SNPs associations by computing the sum of{chi} 2 statistics. However, this strategy ignores the directions of SNP effects, which could result in a loss of power for SNPs with masking effects (e.g., when the product of the effects of two SNPs and their linkage disequilibrium (LD) correlation is negative). Here, we introduce "mBAT-combo", a new set-based test that is better powered than other methods to detect multi-SNP associations in the context of masking effects. We validate the method through simulations and applications to real data. We find that of 35 blood and urine biomarker traits in the UK Biobank, 34 traits show evidence for masking effects in a total of 4,175 gene-trait pairs, indicating that masking effects in complex traits is common. We further validate the improved power of our method in height, body mass index and schizophrenia with different GWAS sample sizes and show that on average 95.7% of the genes detected only by mBAT-combo with smaller sample sizes can be identified by the single-SNP approach with larger sample sizes (average sample size increased by 1.7-fold). For instance, LRRC4B is significant only in our method for schizophrenia, which has been shown to play a role in presynaptic pathology using genetic fine-mapping and evidence-based synaptic annotations. As a more powerful gene-based method, mBAT-combo is expected to improve the downstream pathway analysis or tissue and cell-type enrichment analysis that takes genes identified from GWAS data as input to understand the biological mechanisms of the trait or disease. Despite our focus on genes in this study, the framework of mBAT-combo is general and can be applied to any set of SNPs to refine trait-association signals hidden in genomic regions with complex LD structures.

genetics↗

bioRxiv2022

Phase separation of Myc differentially regulates gene transcription

Dysregulation and enhanced expression of MYC transcription factors (TFs) including MYC and MYCN contribute to the majority of human cancers. For example, MYCN is amplified up to several hundred-fold in high-risk neuroblastoma. The resulting overexpression of N-myc aberrantly activates genes that are not activated at low N-myc levels and drives proliferation and cell survival. Whether increasing N-myc levels simply mediate binding to lower-affinity binding sites in the genome or fundamentally changes the activation process remains unclear. One such activation mechanism that could become important above threshold levels of N-myc is the formation of aberrant transcriptional condensates through phase separation. Phase separation has recently been linked to transcriptional regulation, but how strongly it contributes to gene activation remains unclear. Here we characterized the phase behavior of N-myc and showed that it can form dynamic condensates that bear the hallmarks of transcriptional activity. We tested the contribution of phase separation to N-myc-mediated gene expression by using a chemogenetic tool that allowed us to compare non-phase-separated and phase-separated conditions at identical N-myc levels, which both showed a strong impact on gene expression compared to no N-myc expression. However, we found that only a small fraction of <3% of N-myc-regulated genes is further affected by phase separation, but that these events include the activation of key oncogenes and the repression of tumor suppressors. Indeed, phase separation increases cell survival by [~]15% corroborating the biological effects of the transcriptional changes. However, our results also show that >97% of N-myc-regulated genes are not affected by N-myc phase separation, highlighting that transcription can be activated effectively by diffuse complexes of TFs with the transcriptional machinery.

cell biology↗

bioRxiv2022

Corner flows induced by surfactant-producing bacteria Bacillus subtilis and Pseudomonas fluorescens

Mechanistic understanding of bacterial spreading in soil is critical to control pathogenic contamination of groundwater and soil as well as design bioremediation projects. However, our understanding is currently limited by the lack of direct bacterial imaging in soil conditions. Here, we overcome this limitation by directly observing the spread of bacterial solution in a transparent chamber with varying corner angles designed to replicate soil-like conditions. We show that two common soil bacteria, Bacillus subtilis and Pseudomonas fluorescens, generate flows along sharp corners (< 60{degrees}) by producing surfactants that turn nonwetting solid surfaces into wetting surfaces. We further show that a surfactant-deficient mutant of B. subtilis cannot generate corner flows along sharp corners, confirming that the bacteria-generated corner flows require the production of bacterial surfactants. The speed of biosurfactant-induced corner flow at the sharp corner is about several millimeters per hour, similar to that of bacterial swarming, the fastest mode of known bacterial surface translocation. We further demonstrate that the bacteria-generated corner flow only occurs when the corner angle is less than a critical value, which can be predicted from the contact angle of the bacterial solution. Furthermore, we show that the corner flow has a maximum height due to the roundness or cutoff of corners. The mechanistic understanding and mathematical theories of bacterial spreading presented in this study will help improve predictions of bacterial spreading in soil, where corners are ubiquitous, and facilitate future designs of soil contamination mitigation and other bioremediation projects. ImportanceThe spread of bacterial cells in soil regulates soil biogeochemical cycles, increases the possibility of soil and groundwater contamination, and controls the efficiency of many bacteria-based bioremediation projects. However, mechanistic understanding of bacterial spreading in soil remains incomplete due to a lack of direct or in-situ observations. Here, we simulate confined spaces of soil using a transparent material with similar hydrophobicity as hydrocarbon-covered soil and directly visualize the spread of two common soil bacteria, Bacillus subtilis and Pseudomonas fluorescens. We show that both bacteria can generate vertical flows along sharp corners of the transparent chamber. The velocity of the bacterial corner flow is several millimeters per hour. We further demonstrate that the corner flow was generated by bacteria-produced bio-surfactants, which are soap-like chemicals and turn nonwetting solid surfaces into wetting surfaces. Our results will help improve predictions of bacterial spreading in soil and facilitate designs of soil-related bioremediation projects.

microbiology↗

bioRxiv2022

Clean-PIE: a novel strategy for efficiently constructing precise circRNA with thoroughly minimized immunogenicity to direct potent and durable protein expression

Translatable circular RNAs (circRNAs) are emerging as a crucial molecular format for transient protein expression, with high potential to be an alternative for linear mRNA to reshape the landscape of mRNA pharmaceutical industry. Canonical Anabaena permuted intron-exon (Ana PIE) format that developed by ORNA is an efficient method for RNA circularization, and the engineered circRNAs direct supreme protein expression in eukaryotic cells. However, recent studies revealed that this method may unavoidably result in a remain of immunogenicity in the circRNA products, albeit after thorough RNA purification. In the current study, we develop a novel strategy for efficient generation of circRNA, via the permuted T4Td introns mediated autocatalytically ribozymatic reaction mediated ligation of the flanking segment sequences that concealing in ORF or translation initiation sequence (normally equal to IRES). This strategy universally realizes around 90% circularization effectivity, and the circRNA products can be purified to around 90% purity by our new purification method, and presented thoroughly minimized immunogenicity, thus is termed "Clean-PIE". The purified circRNAs are found to direct potent and durable expression of various proteins in vitro and in vivo. The partly purified Fluc circRNA by HPLC-SEC was found to direct Fluc expression in muscle for no less than 20 days. The highly purified circRNA exhibits much stronger protein expression in vitro and in vivo, and presumed a longer duration. Additionally, the scale-up of RNA circularization with the RNA precursors from 1 L transcription revealed high circularization effectivity (around 90%) and a high productivity of the final circRNA products. Collectively, Clean-PIE is a novel circRNA platform that possesses high circularization effectivity, enabled high RNA purity and thoroughly minimized immunogenicity, as well as scaling-up accessibility and directing extreme durability of protein expression, thus has the potential to develop advanced RNA vaccines and therapeutics in pharmaceutical industrial scale.

molecular biology↗

bioRxiv2022

Identification of cancer-keeping genes as therapeutic targets by finding network control hubs

Finding cancer-driver genes - the genes whose mutations may transform normal cells into cancerous ones - remains a central theme of cancer research. We took a different perspective; instead of considering normal cells, we focused on cancerous cells and genes that maintained abnormal cell growth which we named cancer-keeping genes (CKGs). Intervention in CKGs may rectify aberrant cell growth so that they can be adopted as therapeutic targets for cancer treatment. We developed a novel approach to identifying CKGs by extending the well-established theory of network structural controllability, which aims at finding a control scheme (i.e., a minimal set of non-overlapping control paths covering all nodes) and control nodes (driver genes) that can steer the cell from any state to the designated state. Going beyond driver genes defined by one control scheme, we introduced control-hub genes located in the middle of a control path of every control scheme. Control hubs are essential for maintaining cancerous states and thus can be taken as CKGs. We applied our CKG-based approach to bladder cancer (BLCA) as a case study. All the genes on the cell cycle and p53 pathways in BLCA were identified as CKGs, showing the importance of these genes in cancer and demonstrating the power of our new method. Furthermore, sensitive CKGs that could be easily changed by structural perturbation were better suited as therapeutic targets. Six sensitive CKGs (RPS6KA3, FGFR3, N-cadherin (CDH2), EP300, caspase-1, and FN1) were subjected to small-interferencing-RNA knockdown in two BLCA cell lines to validate their cancer-suppressing effects. Knocking down RPS6KA3 in a mouse model of BLCA significantly inhibited the growth of tumor xenografts in mice. Combined, our results demonstrated the value of CKGs as therapeutic targets for cancer therapy. Key pointsO_LIFocus on genes that maintain aberrant cell growth, named cancer-keeping genes (CKGs). C_LIO_LIDevelop a novel approach for finding CKGs by extending the well-estabilished theory of network structural controllability to total network controllability. C_LIO_LIApply the new method to bladder cancer and experimentally validated the cancer-suppressing function of six CKGs in two bladder cancer cell lines and that of one CKG in bladder cancer mice. C_LI

bioinformatics↗

bioRxiv2022

Structural basis for CDC42 and RAC activation by the dual specificity GEF DOCK10

Dedicator of cytokinesis 10 (DOCK10) is a guanine nucleotide exchange factor (GEF) belonging to the DOCK family that activate RHO GTPases. DOCK10 controls amoeboid migration and IL-4 induced B cell activation. Recent structural studies of the catalytic DHR2 domains of DOCK-family GEFs DOCK2 and DOCK9 in the presence of nucleotide-free RAC and CDC42 respectively, have revealed a conserved mechanism of nucleotide exchange distinct from the large family of Dbl homology (DH) GEFs. Less is known from a biochemical and structural perspective, about DOCK10. We have determined the crystal structure of the apo-state of the DHR2 domain of DOCK10 (DOCK10DHR2), which provides the first structural model for the apo-state of a DHR2 domain for the entire DOCK family. It demonstrates the conformational changes within DOCK10DHR2 on engaging the GTPase, and associated induced conformational changes of the GTPase required to stimulate nucleotide release. We also report on the unexpected dual specificity of DOCK10DHR2 which directly interacts with RAC and CDC42 and induces the nucleotide exchange of both in vitro. This dual specificity is unique to DOCK10 within its evolutionarily related D subfamily. Structural studies of DOCK10DHR2 in complex with RAC revealed an intriguing 2:1 stoichiometry between DOCK10DHR2 and the GTPase, that differs from the canonical 1:1 stoichiometry for all other known DOCK-GTPase complexes. This was confirmed in solution using a variety of biophysical techniques. The identification of a novel mode of interaction between DOCK10DHR2 and the RAC GTPase provides new insights into how DOCK family GEFs discriminate between CDC42, RAC and RHOA.

biochemistry↗

bioRxiv2022

Disruption of CFAP418 interaction with lipids causes abnormal membrane-associated cellular processes in retinal degenerations

Syndromic ciliopathies and retinal degenerations are large heterogeneous groups of genetic diseases. CFAP418 is a causative gene of both disorders, and its protein sequence is evolutionarily conserved. However, the pathogenic mechanism caused by CFAP418 mutations is largely unknown. Here, we employed affinity purification coupled with mass spectrometry and quantitative lipidomic, proteomic, and phosphoproteomic approaches to address the molecular function of CFAP418 in mouse retinas. We showed that CFAP418 bound to lipid metabolism precursor phosphatidic acid (PA) and mitochondrion-specific lipid cardiolipin but did not form a tight and static complex with proteins. Loss of Cfap418 led to membrane lipid imbalance and protein-membrane association alteration, which subsequently caused mitochondrial defects and membrane remodeling abnormalities in multiple vesicular trafficking pathways. Loss of Cfap418 also increased the activity of PA-binding protein kinase C. Our results indicate that membrane lipid imbalance is a new pathological mechanism underlying syndromic ciliopathies and retinal degenerations, which is associated with other known causative genes for these diseases, such as RAB28 and BBS genes.

cell biology↗

bioRxiv2022

Site-specific C-terminal fluorescent labeling of Tau protein

Formation of Tau protein aggregates in neurons is a pathological hallmark of several neurodegenerative diseases, including Alzheimers disease. Fluorescently-labeled Tau protein is therefore useful to study the aggregation of these pathological proteins and to identify potential therapeutic targets. Conventionally, cysteine residues are used for labeling Tau proteins, however, the full-length Tau isoform contains two cysteine residues in the microtubule-binding region, which are implicated in Tau aggregation by forming intermolecular disulfide bonds. In order to prevent the fluorescent label from disturbing the microtubule binding region, we developed a strategy to fluorescently label Tau at its C-terminus while leaving cysteine residues unperturbed. We took advantage of a Sortase A-mediated transpeptidation approach to bind a short peptide (GGGH6-Alexa647) with a His-tag and a covalently attached Alexa 647 fluorophore to the C-terminus of Tau. This reaction relies on the presence of a Sortase recognition motif (LPXTG), which we attached to the C-terminus of recombinantly expressed Tau. We determined the possible effects of the resulting C-terminal modification on the secondary structure of Tau protein, its aggregation kinetics, and fibril morphology compared to the unlabeled native Tau protein in vitro. The results showed no significant differences between the native and C-terminally labeled Tau monomer with regard to aggregation kinetics, secondary structure, and morphology.

biophysics↗

bioRxiv2022

HIV proviral genetic diversity, compartmentalization and inferred dynamics in lung and blood during long-term suppressive antiretroviral therapy

The lung is an understudied site of HIV persistence. We isolated 882 subgenomic proviral sequences by single-genome approaches from blood and lung from nine individuals on long-term suppressive antiretroviral therapy (ART), and characterized genetic diversity and compartmentalization using formal tests. Consistent with clonal expansion as a driver of HIV persistence, identical sequences comprised between 9% to 86% of within-host datasets, though their location (blood vs. lung) followed no consistent pattern. The majority (77%) of participants harbored at least one sequence shared across blood and lung, supporting the migration of clonally-expanded cells between sites. No participant exhibited genetic compartmentalization so obvious that it was visually apparent in a phylogeny. When formal tests were applied however, two (22%) participants showed modest yet significant support for compartmentalization when analysis was restricted to distinct proviruses per site. This increased to four participants (44%) when considering all within-host sequences. Thus, while a minority of individuals harbor somewhat distinctive proviral populations in blood and lung, these can simply be due to unequal distributions of clonally-expanded sequences. Importantly, the extent of lung proviral diversity on ART strongly reflected that in blood (Spearman {rho} = 0.98, p < 0.0001), confirming blood as a strong indicator of total body proviral diversity. Analysis of on-ART proviral diversity in context of pre-therapy viral diversity in two participants revealed marked differences in proviral longevity and dynamics. Whereas one participants proviral pool was rich in ancestral sequences that recapitulated more of HIVs within-host evolutionary history, the others largely comprised more contemporary sequences, including ones that re-seeded the reservoir during a three-year treatment interruption. Results highlight the genetic complexity of proviruses persisting in lung and blood during ART, and the uniqueness of each individuals proviral composition. Individualized HIV remission and cure strategies may be needed to overcome these challenges. Author SummaryHIV persists in the body despite long-term suppressive antiretroviral therapy. Much of our knowledge about the HIV reservoir comes from studying proviruses in blood, but a fundamental question is whether these are distinct from those in tissues. The lung could theoretically engender genetically distinctive HIV populations, but this remains understudied. Our analysis of nearly 900 proviral sequences from blood and lung of nine individuals with HIV receiving long-term therapy revealed substantial within-host heterogeneity, yet some common patterns. Identical sequences (consistent with clonal expansion of infected cells) were observed in everyone, though at different (9-86%) frequencies. Recovery of shared sequences across blood and lung was common (77% of participants). Fewer than half of participants exhibited blood-lung genetic compartmentalization, and only modestly so. Moreover, when present, compartmentalization was often attributable to differential distribution of identical sequences, not the presence of genetically distinctive populations, across sites. Results also revealed marked inter-individual differences in proviral dynamics, as evidenced by the proportion of persisting proviruses that represented ancestral versus more recently-circulating viral sequences. Critically, the extent of within-host proviral diversity in blood correlated strongly with that in lung, indicating that despite inter-individual heterogeneity, blood is a strong indicator of proviral diversity elsewhere in the body.

molecular biology↗

bioRxiv2022

SMAD4 suppresses colitis-associated carcinoma through inhibition of CCL20/CCR6-mediated inflammation

Background & AimsChronic inflammation in the colon is a predisposing factor for colon cancer. We previously reported that colon epithelial cell silencing of Smad4, the central downstream mediator of TGF{beta} family signaling, increased epithelial expression of inflammatory genes, including the chemokine CCL20, and increased susceptibility to colitis-associated cancer. Here, we examine the role of the chemokine/receptor pair CCL20/CCR6 in mediating colitis-associated colon carcinogenesis induced by SMAD4 loss. MethodsMice with conditional, epithelial-specific Smad4 loss with and without germline deletion of the Ccr6 gene were subjected to three rounds of dextran sodium sulfate and followed for up to 3 months. Tumors were quantified histologically, and immune cell populations were analyzed by flow cytometry and immunostaining. ResultsIn humans, SMAD4 expression inversely correlated with CCL20 expression. Smad4 loss in mouse colon epithelium led to enlarged gut-associated lymphoid tissues and recruitment of specific immune cell subsets to the mouse colon epithelium and underlying stroma, particularly Treg, Th17, and dendritic cells. Loss of CCR6 abrogated these immune responses and significantly reduced the incidence of colitis-associated tumors observed with loss of SMAD4 alone. ConclusionsRegulation of mucosal inflammation is a critical role of SMAD4 signaling within the colon epithelium and central to its tumor suppressor function in the colon. A key downstream node in this regulation is suppression of CCL20 signaling by the epithelium to CCR6 in immune cells. Loss of SMAD4 in the colon epithelium increases CCL20 expression and chemoattraction of CCR6+ immune cells, contributing to greater susceptibility to colon cancer.

cancer biology↗

bioRxiv2022

Robust genome editing via modRNA-based Cas9 or base editor in human pluripotent stem cells

CRISPR systems have revolutionized biomedical research because they offer an unprecedented opportunity to explore the application of genome editing in human pluripotent stem cells (hPSCs). Due to the inherent simplicity of CRISPR systems, requiring a Cas protein and its corresponding single guide RNA (sgRNA), they are more widely adopted and used for diverse biomedical research than their predecessors (zinc finger nucleases and TALENs). However, a bottleneck of applying CRISPR systems in hPSCs is how to deliver CRISPR effectors easily and efficiently into hPSCs. Herein, we developed modified mRNA (modRNA) based CRIPSR systems that utilized Cas9 or base editor (ABE8e) modRNA for genome editing of hPSCs via simple lipid-based transfection. We have achieved 71.09% {+/-} 9.13% and 68.53% {+/-} 3.81% gene knockout (KO) efficiency with Cas9 modRNA and ABE8e modRNA, respectively, which is significantly higher than plasmid-based systems. In summary, we demonstrate that our non-integrating modRNA based CRISPR methods hold great promise as the more efficient and accessible techniques for genome editing of hPSCs.

bioengineering↗

bioRxiv2022

Nucleotide resolution genetic mapping in pigs by publicly accessible whole genome imputation

Genetic mapping to identify genes and alleles associated with or causing economically important quantitative trait variation in livestock animals such as pigs is a major goal in the genetic improvement animals. Despite recent advances in high throughput genotyping technologies, resolution of genetic mapping in pigs remains poor due in part to the low density of genotyped variant sites. In this study, we overcame this limitation by developing a reference haplotype panel for pigs based on 2,259 whole genome sequenced animals representing 44 pig breeds. We optimized the imputation procedure to achieve an average concordance rate in excess of 97%, non-reference concordance rate 91%, and r2 0.89. We demonstrated that genotype imputation using this resource can dramatically improve resolution of genetic mapping. Finally, we developed a public web server (swimgeno.org) to allow the pig genetics community to fully utilize this resource. We expect the resource and server to significantly facilitate genetic mapping and accelerate genetic improvement in pigs.

genomics↗

bioRxiv2022

Larger cerebral cortex is genetically correlated with greater frontal area and dorsal thickness

Human cortical expansion has occurred non-uniformly across the brain. We assessed the genetic architecture of cortical global expansion and regionalization by comparing two sets of genome-wide association studies of 24 cortical regions with and without adjustment for global measures (i.e. total surface area, mean cortical thickness) using a genetically-informed parcellation in 32,488 adults. We found 393 and 756 significant loci with and without adjusting for globals, respectively, among which 8% and 45% loci were associated with more than one region. Results from analyses without adjustment for globals recounted loci associated with global measures. Genetic factors that contribute to total surface area of the cortex particularly expand anterior/frontal regions, whereas those contributing to thicker cortex predominantly increase dorsal/frontal-parietal thickness. Interactome-based analyses revealed significant overlap of global and regional genetic modules, enriched for neurodevelopmental and immune system pathways. Consideration of global measures is important in understanding the genetic variants underlying cortical morphology.

neuroscience↗

bioRxiv2022

Genomic insights into the adaptive and convergent evolution of Leuciscus waleckii inhabiting extremely alkaline environments

Leuciscus waleckii is widely distributed in Northeast Asia and has high economic value. Different from its freshwater counterparts, the population in Lake Dali Nur has a strong alkalinity tolerance and can adapt to extremely alkaline-saline water with bicarbonate over 50 mmol/L (pH 9.6), thus providing an exceptional model with which to explore the mechanisms of adaptive evolution under extreme alkaline environments. Here, we assembled a high quilty chromosome-level reference genome for L. waleckii from Lake Dali Nur, which provides an important genomic resource for the exploitation of alkaline water fishery resources and adaptive evolution research across teleost fish. Notably, we identified significantly expanded long terminal repeats (LTRs) and long interspersed nuclear elements (LINEs) in L. waleckii compared to other Cypriniformes fish, suggesting their more recent insertion into the L. waleckii genome. We also identified expansions in genes encoding gamma-glutamyltransferase, which possibly underlie the adaptation to extreme environmental stress. Based on the resequencing of 85 L.waleckii individuals from divergent populations, the historical population size of L.waleckii in Lake Dali Nur dramatically expanded in a thousand years approximately 13,000 years ago, and experienced a cliff recession in the process of adapting to the alkaline environment of Lake Dali Nur approximately 6,000 years ago. Genome scans further revealed the significant selective sweep regions from Lake Dali Nur, which harbour a set of candidate genes involved in hypoxia tolerance, ion transport, acid-base regulation and nitrogen metabolism. In particular, 5 alkali population specific nonsynonymous mutations were identified in CA15 gene copies. In addition, two sites with convergent amino acid mutation were detected in the RHCG-a gene among several alkali environment adapted Cypriniformes fish, this mutation may increase the NH3 excretion rate of the RHCG channel. Our findings provide comprehensive insight into the genomic mechanisms of L. waleckii and reveal their adaptative evolution under extreme alkaline environments.

evolutionary biology↗

bioRxiv2022

Delivery of Circular mRNA via Degradable Lipid Nanoparticles against SARS-COV-2 Delta Variant

mRNA vaccines have emerged as a most promising and potent platform in the fight against various diseases including the COVID-19 pandemic. However, the intrinsic instability, varying side effects associated with the delivery systems, and continuous emergence of virus variants highlight the urgent need for the development of stable, safe and efficacious mRNA vaccines. In this study, by screening a panel of proprietary biodegradable ionizable lipidoids, we reported on a novel mRNA vaccine (cmRNA-1130) formed from a biodegradable lipidoid with eight ester bonds in the branched tail (AX4) and synthetic circular mRNA (cmRNA) encoding the trimeric Delta receptor binding domain (RBD) of SARS-CoV-2 spike protein for the induction of robust immune activation. The AX4-based lipid nanoparticles (AX4-LNP) revealed much faster elimination rate from liver and spleen in comparison with commercialized MC3-based LNP (MC3-LNP) and afforded normal level of alanine transferase (ALT), aspartate aminotransferase (AST), and creatinine (CRE) in BALB/c mice. Following intramuscular (IM) administration in BALB/c mice, cmRNA-1130 elicited potent and sustained neutralizing antibodies, RBD-specific CD4+ and CD8+ T effector memory cells (Tem), and Th1-biased T cell activations. cmRNA-1130 vaccine showed excellent stability against 6-month storage at 4 {degrees}C and freezing-thawing cycles. In brief, our study highlights mRNA vaccines based on cmRNA and biodegradable AX4 lipids hold great potential as superb therapeutic platforms for the treatment of varying diseases.

immunology↗

bioRxiv2022

BigNeuron: A resource to benchmark and predict best-performing algorithms for automated reconstruction of neuronal morphology

BigNeuron is an open community bench-testing platform combining the expertise of neuroscientists and computer scientists toward the goal of setting open standards for accurate and fast automatic neuron reconstruction. The project gathered a diverse set of image volumes across several species representative of the data obtained in most neuroscience laboratories interested in neuron reconstruction. Here we report generated gold standard manual annotations for a selected subset of the available imaging datasets and quantified reconstruction quality for 35 automatic reconstruction algorithms. Together with image quality features, the data were pooled in an interactive web application that allows users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and reconstruction data, and benchmarking of automatic reconstruction algorithms in user-defined data subsets. Our results show that image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. By benchmarking automatic reconstruction algorithms, we observed that diverse algorithms can provide complementary information toward obtaining accurate results and developed a novel algorithm to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms. Finally, to aid users in predicting the most accurate automatic reconstruction results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic reconstructions.

bioinformatics↗