Biology subjects

Li, S.

Publications and source records attributed to Li, S..

At least 1,297 records · Page 72Linked to original sources

bioRxiv2018

Assembly of Yeast Spindle Pole Body and its Components Revealed by Electron Cryo-Tomography

Spindle pole body (SPB) is the microtubule organizing center (MTOC) in yeast. It plays essential roles during many cellular processes, ranging from mitosis to karyogamy. Here, we used electron cryo-tomography (cryo-ET) and image processing to study SPB and its component purified from the budding yeast. The 3D images and models of SPB at various cell cycle stages were reconstructed by cryo-ET and were analyzed. The results reveal SPB as a cylindrical shaped structure composed of multiple layers. The central layers are arranged with a degree of crystalline order. By using subtomogram averaging methods, we studied the purified \"sheet\" from over-expressed Spc42p. Our analysis of the SPBs and its components provides new insights into the assembly of this organelle and its cellular function as an MTOC.

cell biology↗

bioRxiv2018

Electron Cryo-Tomography Provides Insight into Procentriole Architecture and Assembly Mechanism

Centriole is an essential structure with multiple functions in cellular processes. Centriole biogenesis and homeostasis is tightly regulated. Using electron cryo-tomography (cryoET) we present the structure of procentrioles from Chlamydomonas reinhardtii. We identified a set of non-tubulin components attached to the triplet microtubule (MT), many are at the junctions of tubules likely to reinforce the triplet. We describe structure of the A-C linker that bridges neighboring triplets. We find that POC1 is an integral component of the A-C linker. Its conserved WD40 {beta}-propeller domain provides sites for attachment to other A-C linker components. The twist of A-C linker results in an iris diaphragm-like motion of the triplets in the longitudinal direction of procentriole. Finally, we identified two assembly intermediates at the growing ends of procentriole allowing us to propose a model for the procentriole assembly. Our results provide a comprehensive structural framework for understanding the molecular mechanisms underpinning procentriole biogenesis and assembly.

cell biology↗

bioRxiv2018

D-GPM: a deep learning method for gene promoter methylation inference

BackgroundGene promoter methylation plays a critical role in a wide range of biological processes, such as transcriptional expression, gene imprinting, X chromosome inactivation, etc. Whole-genome bisulfite sequencing generates a comprehensive profiling of the gene methylation levels but is limited by a high cost. Recent studies have partitioned the genes into landmark genes and target genes and suggested that the landmark gene expression levels capture adequate information to reconstruct the target gene expression levels. Moreover, the methylation level of the promoter is usually negatively correlated with its corresponding gene expression. This result inspired us to propose that the methylation level of the promoters might be adequate to reconstruct the promoter methylation level of target genes, which would eventually reduce the cost of promoter methylation profiling.\n\nResultsHere, we developed a deep learning model (D-GPM) to predict the whole-genome promoter methylation level based on the methylation profile of the landmark genes. We benchmarked D-GPM against three machine learning methods, namely, linear regression (LR), regression tree (RT) and support vector machine (SVM), based on two criteria: the mean absolute deviation (MAE) and the Pearson correlation coefficient (PCC). After profiling the methylation beta value (MBV) dataset from the TCGA, with respect to MAE and PCC, we found that D-GPM outperforms LR by 9.59% and 4.34%, RT by 27.58% and 22.96% and SVM by 6.14% and 3.07% on average, respectively. For the number of better-predicted genes, D-GPM outperforms LR in 92.65% and 91.00%, RT in 95.66% and 98.25% and SVM in 85.49% and 81.56% of the target genes.\n\nConclusionsD-GPM acquires the least overall MAE and the highest overall PCC on MBV-te compared to LR, RT, and SVM. For a genewise comparative analysis, D-GPM outperforms LR, RT, and SVM in an overwhelming majority of the target genes, with respect to the MAE and PCC. Most importantly, D-GPM predominates among the other models in predicting a majority of the target genes according to the model distribution of the least MAE and the highest PCC for the target genes.

bioinformatics↗

bioRxiv2018

SmbHLH37 functions antagonistically with SmMYC2 in regulating jasmonate-mediated biosynthesis of phenolic acids in Salvia miltiorrhiza

Jasmonates (JAs) are integral to various defense responses and induce biosynthesis of many secondary metabolites. MYC2, a basic helix-loop-helix (bHLH) transcription factor (TF), acts as a transcriptional activator of JA signaling. MYC2 is repressed by the JASMONATE ZIM-domain (JAZ) proteins in the absence of JA, but de-repressed by the protein complex SCFCOI1 on perception of JA. We previously reported that overexpression of SmMYC2 promotes the production of salvianolic acid B (Sal B) in Salvia miltiorrhiza. However, the responsible molecular mechanism is unclear. Here, we showed that SmMYC2 binds to and activates the promoters of its target genes SmTAT1, SmPAL1, and SmCYP98A14 to activate Sal B accumulations. SmbHLH37, a novel bHLH gene significantly up-regulated by constitutive expression of SmMYC2, was isolated from S. miltiorrhiza for detailed functional characterization. SmbHLH37 forms a homodimer and interacts with SmJAZ3/8. Overexpression of SmbHLH37 substantially decreased yields of Sal B. SmbHLH37 binds to the promoters of its target genes SmTAT1 and SmPAL1 and blocks their expression to suppress the pathway for Sal B biosynthesis. These results indicate that SmbHLH37 negatively regulates JA signaling and functions antagonistically with SmMYC2 in regulating Sal B biosynthesis in S. miltiorrhiza.

plant biology↗

bioRxiv2018

AIDE: annotation-assisted isoform discovery and abundanceestimation from RNA-seq data

Genome-wide accurate identification and quantification of full-length mRNA isoforms is crucial for investigating transcriptional and post-transcriptional regulatory mechanisms of biological phenomena. Despite continuing efforts in developing effective computational tools to identify or assemble full-length mRNA isoforms from second-generation RNA-seq data, it remains a challenge to accurately identify mRNA isoforms from short sequence reads due to the substantial information loss in RNA-seq experiments. Here we introduce a novel statistical method, AIDE (Annotation-assisted Isoform DiscovEry), the first approach that directly controls false isoform discoveries by implementing the testing-based model selection principle. Solving the isoform discovery problem in a stepwise and conservative manner, AIDE prioritizes the annotated isoforms and precisely identifies novel isoforms whose addition significantly improves the explanation of observed RNA-seq reads. We evaluate the performance of AIDE based on multiple simulated and real RNA-seq datasets followed by a PCR-Sanger sequencing validation. Our results show that AIDE effectively leverages the annotation information to compensate the information loss due to short read lengths. AIDE achieves the highest precision in isoform discovery and the lowest error rates in isoform abundance estimation, compared with three state-of-the-art methods Cufflinks, SLIDE, and StringTie. As a robust bioinformatics tool for transcriptome analysis, AIDE will enable researchers to discover novel transcripts with high confidence.

bioinformatics↗

bioRxiv2018

Potent anti-influenza H7 human monoclonal antibody induces separation of hemagglutinin receptor binding head domains

Seasonal influenza virus infections can cause significant morbidity and mortality, but the threat from emergence of a new pandemic influenza strain might have potentially even more devastating consequences. As such, there is intense interest in isolating and characterizing potent neutralizing antibodies that target the hemagglutinin (HA) viral surface glycoprotein. Here, we use cryo-electron microscopy to decipher the mechanism of action of a potent HA head-directed monoclonal antibody bound to an influenza H7 HA. The epitope of the antibody is not solvent accessible in the compact, pre-fusion conformation that typifies all HA structures to date. Instead, the antibody binds between HA head protomers to an epitope that must be partly or transiently exposed in the pre-fusion conformation. The \"breathing\" of the HA protomers is implied by the exposure of this epitope, which is consistent with metastability of class I fusion proteins. This structure likely therefore represents an early structural intermediate in the viral fusion process. Understanding the extent of transient exposure of conserved neutralizing epitopes also may lead to new opportunities to combat influenza that have not been appreciated previously.\n\nAuthor SummaryA transiently exposed epitope on influenza H7 hemagglutinin represents a new target for neutralizing antibodies.

immunology↗

bioRxiv2018

Proteomic Profile of TGF-β1 treated Lung Fibroblasts identifies Novel Markers of Activated Fibroblasts in the Silica Exposed Rat Lung

We performed liquid chromatography-tandem mass spectrometry (LC-MS/MS) on control and TGF-{beta}1-exposed rat lung fibroblasts to identify proteins differentially expressed between cell populations. A total of 1648 proteins were found to be differentially expressed in response to TGF-{beta}1 treatment and 196 proteins were expressed at [≥] 1.2 fold relative to control. Guided by these results, we next determined whether similar changes in protein expression were detectable in the rat lung after chronic exposure to silica dust. Of the five proteins selected for further analysis, we found that levels of all proteins were markedly increased in the silica-exposed rat lung, including the proteins for the very low density lipoprotein receptor (VLDLR) and the transmembrane (type I) heparin sulfate proteoglycan called syndecan 2 (SDC2). Because VLDLR and SDC2 have not, to our knowledge, been previously linked to the pathobiology of silicosis, we next examined whether knockdown of either gene altered responses to TGF-{beta}1 in MRC-5 lung fibroblasts. Interestingly, we found knockdown of either VLDLR or SDC2 dramatically reduced collagen production to TGF-{beta}1, suggesting that both proteins might play a novel role in myofibroblast biology and pathogenesis of silica-induced pulmonary fibrosis. In summary, our findings suggest that performing LC-MS/MS on TGF-{beta}1 stimulated lung fibroblasts can uncover novel molecular targets of activated myofibroblasts in silica-exposed lung.\n\nHighlightsWe identified 196 proteins differentially expressed between control and TGF-{beta}1 treated fibroblastsby LC-MS/MS.\n\nSeveral proteins identified by LC-MS/MS were also found to be differentially expressed in whole lung tissues and isolated fibroblasts after chronic exposure to silica dust, including the very low density lipoprotein receptor (VLDLR) and the transmembrane type I heparan sulfate proteoglycan called syndecan 2\n\nKnockdown of SDC2 or VLDLR markedly inhibited collagen production in MRC-5 fibroblasts, suggesting a novel pathogenic role for these proteins in myofibroblast biology.

pharmacology and toxicology↗

bioRxiv2018

Combating viral contaminants in CHO cells by engineering STAT1 mediated innate immunity

Viral contamination in biopharmaceutical manufacturing can lead to shortages in the supply of critical therapeutics. To facilitate the protection of bioprocesses, we explored the basis for the susceptibility of CHO cells, the most commonly used cell line in biomanufacturing, to RNA virus infection. Upon infection with certain ssRNA and dsRNA viruses, CHO cells fail to generate a significant interferon (IFN) response. Nonetheless, the downstream machinery for generating IFN responses and its antiviral activity is intact in these cells: treatment of cells with exogenously-added type I IFN or poly I:C prior to infection limited the cytopathic effect from Vesicular stomatitis virus (VSV), Encephalomyocarditis virus (EMCV), and Reovirus-3 virus (Reo-3) in a STAT1-dependent manner. To harness the intrinsic antiviral mechanism, we used RNA-Seq to identify two upstream repressors of STAT1: Gfi1 and Trim24. By knocking out these genes, the engineered CHO cells exhibited increased resistance to the prototype RNA viruses tested. Thus, omics-guided engineering of mammalian cell culture can be deployed to increase safety in biotherapeutic protein production among many other biomedical applications.

bioengineering↗

bioRxiv2018

Inhibition of nucleotide synthesis mediates replicative senescence of human mammary epithelial cells

Cellular senescence is a mechanism by which cells permanently withdraw from the cell cycle in response to stresses including telomere shortening, DNA damage, or oncogenic signaling. Senescent cells contribute to both age-related degeneration and hyperplastic pathologies, including cancer. In culture, normal human epithelial cells enter senescence after a limited number of cell divisions, known as replicative senescence. Here, to investigate how metabolic pathways regulate replicative senescence, we used LC-MS-based metabolomics to analyze senescent primary human mammary epithelial cells (HMECs). We did not observe significant changes in glucose uptake or lactate secretion in senescent HMECs. However, analysis of intracellular metabolite pool sizes indicated that senescent cells exhibit depletion of metabolites from nucleotide synthesis pathways. Furthermore, stable isotope tracing with 13C-labeled glucose or glutamine revealed a dramatic blockage of flux of these two metabolites into nucleotide synthesis pathways in senescent HMECs. To test whether cellular immortalization would reverse these observations, we expressed telomerase in HMECs. In addition to preventing senescence, telomerase expression maintained metabolic flux from glucose into nucleotide synthesis pathways. Finally, we investigated whether inhibition of nucleotide synthesis in proliferating HMECs is sufficient to induce senescence. In proliferating HMECs, both pharmacological and genetic inhibition of ribonucleotide reductase regulatory subunit M2 (RRM2), a rate-limiting enzyme in dNTP synthesis, induced premature senescence with concomitantly decreased metabolic flux from glucose into nucleotide synthesis. Taken together, our results suggest that nucleotide synthesis inhibition plays a causative role in the establishment of replicative senescence in HMECs.

systems biology↗

bioRxiv2018

Genetic Determinants of Cortical Structure (Thickness, Surface Area and Volumes) among Disease Free Adults in the CHARGE Consortium

Cortical thickness, surface area and volumes (MRI cortical measures) vary with age and cognitive function, and in neurological and psychiatric diseases. We examined heritability, genetic correlations and genome-wide associations of cortical measures across the whole cortex, and in 34 anatomically predefined regions. Our discovery sample comprised 22,822 individuals from 20 cohorts within the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium and the United Kingdom Biobank. Significant associations were replicated in the Enhancing Neuroimaging Genetics through Meta-analysis (ENIGMA) consortium, and their biological implications explored using bioinformatic annotation and pathway analyses. We identified genetic heterogeneity between cortical measures and brain regions, and 161 genome-wide significant associations pointing to wnt/{beta}-catenin, TGF-{beta} and sonic hedgehog pathways. There was enrichment for genes involved in anthropometric traits, hindbrain development, vascular and neurodegenerative disease and psychiatric conditions. These data are a rich resource for studies of the biological mechanisms behind cortical development and aging.

genetics↗

bioRxiv2018

Absence of SIV-specific CD8+ T cells in germinal centers may set the stage for persistent infection

CD8+ T cells play an important role in controlling of HIV and SIV infections. However, these cells are largely excluded from B cell follicles where HIV and SIV producing cells concentrate during chronic infection. It is not known, however, if antigen-specific CD8+ T cells are excluded gradually as pathogenesis progresses from early to chronic phase, or this phenomenon occurs from the beginning infection. In this study we determined that SIV-specific CD8+ T cells were largely excluded from follicles during early infection, we also found that within follicles, they were entirely absent in 60% of the germinal centers (GCs) examined. Furthermore, levels of SIV-specific CD8+ T cells in follicular but not extrafollicular areas significantly correlated inversely with levels of viral RNA+ cells. In addition, subsets of follicular SIV-specific CD8+ T cells were activated and proliferating and expressed the cytolytic protein perforin. These studies suggest that a paucity of SIV-specific CD8+ T cells in follicles and complete absence within GCs during early infection may set the stage for the establishment of persistent chronic infection.\n\nAuthor SummaryA paucity of SIV-specific CD8+ T cells in lymphoid follicles and complete absence within most follicular germinal centers during early infection may set the stage for the establishment of persistent chronic infection.

immunology↗

bioRxiv2018

Planar cell polarity pathway and development of the human visual cortex

The radial unit hypothesis provides a framework for global (proliferation) and regional (distribution) expansion of the primate cerebral cortex. Using principal component analysis (PCA), we have identified cortical regions with shared variance in their surface area and cortical thickness, respectively, segmented from magnetic resonance images obtained in 23,800 participants. We then carried out meta-analyses of genome-wide association studies of the first two principal components for each phenotype. For surface area (but not cortical thickness), we have detected strong associations between each of the components and single nucleotide polymorphisms in a number of gene loci. The first (global) component was associated mainly with loci on chromosome 17 (9.5e-32 [≤] p [≤] 2.8e-10), including those detected previously as linked with intracranial volume and/or general cognitive function. The second (regional) component captured shared variation in the surface area of the primary and adjacent secondary visual cortices and showed a robust association with polymorphisms in a locus on chromosome 14 containing Disheveled Associated Activator of Morphogenesis 1 (DAAM1; p=2.4e-34). DAAM1 is a key component in the planar-cell-polarity signaling pathway. In follow-up studies, we have focused on the latter finding and established that: (1) DAAM1 is highly expressed between 12th and 22nd post-conception weeks in the human cerebral cortex; (2) genes co-expressed with DAAM1 in the primary visual cortex are enriched in mitochondria-related pathways; and (3) volume of the lateral geniculate nucleus, which projects to regions of the visual cortex staining for cytochrome oxidase (a mitochondrial enzyme), correlates with the surface area of the visual cortex in major-allele homozygotes but not in carriers of the minor allele. Altogether, we speculate that, in concert with thalamocortical input to cortical subplate, DAAM1 enables migration of neurons to cytochrome-oxidase rich regions of the visual cortex, and, in turn, facilitates regional expansion of this set of cortical regions during development.

neuroscience↗

bioRxiv2018

Tenuivirus uses a molecular bridge strategy to overcome insect midgut barriers for virus persistent transmission

Many persistent transmitted plant viruses, including Rice stripe tenuivirus (RSV), cause serious damages to crop productions in China and worldwide. Although many reports have indicated that successful insect-mediated virus transmission depends on proper virus-insect vector interactions, the mechanism(s) controlling interactions between viruses and insect vectors for virus persistent transmission remained poorly understood. In this study, we used RSV and its small brown planthopper (SBPH) vector as a working model to elucidate the molecular mechanism controlling RSV virion entrance into SBPH midgut for persistent transmission. We have now demonstrated that this non-enveloped Tenuivirus uses its non-structural glycoprotein NSvc2 as a helper component to bridge the specific interaction between virion and SBPH midgut cells, leading to overcome SBPH midgut barriers for virus persistent transmission. In the absence of this glycoprotein, purified RSV virion is not capable of entering SBPH midgut cells. In RSV-infected cells, glycoprotein NSvc2 is processed into two mature proteins: an amino-terminal protein NSvc2-N and a carboxyl-terminal protein NSvc2-C. We determined that NSvc2-N interacted with RSV virion and bound directly to midgut lumen surface via its N-glycosylation sites. Upon recognition by midgut cells, the midgut cells underwent endocytosis followed by compartmentalizing RSV virion and NSvc2 into early and then late endosomes. The acidic condition inside the late endosome triggered conformation change of NSvc2-C and caused cell membrane fusion via its highly conserved fusion loop motifs, leading to the release of RSV virion from endosome into cytosol. In summary, our results showed for the first time that a rice Tenuivirus uses a molecular bridge strategy to ensure proper interactions between virus and insect midgut for successful persistent transmission.\n\nAuthor summaryOver 75% of the known plant viruses are insect transmitted. Understanding how plant viruses interacted with their insect vectors during virus transmission is one of the key steps to manage virus diseases worldwide. Both the direct and indirect virus-insect vector interaction models have been proposed for virus non-persistent and semi-persistent transmission. However, the indirect virus-vector interaction mechanism during virus persistent transmission has not been reported previously. In this study, we developed a new reverse genetics technology and demonstrated that the circulative and propagative transmitted Rice stripe tenuivirus utilizes a glycoprotein NSvc2 as a helper component to ensure a specific interaction between Tenuivirus virion and midgut cells of small brown planthopper (SBPH), leading to conquering the midgut barrier of SBPH. This is the first report of a helper component mediated-molecular bridge mechanism for virus persistent transmission. These new findings and our new model on persistent transmission expand our understanding of molecular mechanism(s) controlling virus-insect vector interactions during virus transmission in nature.

pathology↗

bioRxiv2018

Assessing 16S marker gene survey data analysis methods using mixtures of human stool sample DNA extracts.

BackgroundAnalysis of 16S rRNA marker-gene surveys, used to characterize prokaryotic microbial communities, may be performed by numerous bioinformatic pipelines and downstream analysis methods. However, there is limited guidance on how to decide between methods, appropriate data sets and statistics for assessing these methods are needed. We developed a mixture dataset with real data complexity and an expected value for assessing 16S rRNA bioinformatic pipelines and downstream analysis methods. We generate an assessment dataset using a two-sample titration mixture design. The sequencing data were processed using multiple bioinformatic pipelines, i) DADA2 a sequence inference method, ii) Mothur a de novo clustering method, and iii) QIIME with open-reference clustering. The mixture dataset was used to qualitatively and quantitatively assess count tables generated using the pipelines.\n\nResultsThe qualitative assessment was used to evalute features only present in unmixed samples and titrations. The abundance of Mothur and QIIME features specific to unmixed samples and titrations were explained by sampling alone. However, for DADA2 over a third of the unmixed sample and titration specific feature abundance could not be explained by sampling alone. The quantitative assessment evaluated pipeline performance by comparing observed to expected relative and differential abundance values. Overall the observed relative abundance and differential abundance values were consistent with the expected values. Though outlier features were observed across all pipelines.\n\nConclusionsUsing a novel mixture dataset and assessment methods we quantitatively and qualitatively evaluated count tables generated using three bioinformatic pipelines. The dataset and methods developed for this study will serve as a valuable community resource for assessing 16S rRNA marker-gene survey bioinformatic methods.

bioinformatics↗

bioRxiv2018

Generation of Highly Diverse Peptide Library by Linear-double-stranded DNA Based AND Logic Computation in Mammalian Cells

DNA-encoded peptide libraries are ideal functional peptide discovery platforms for their extremely large capacity. However, its still difficult to build high content peptide library in intact mammalian cells, which offer advantages associated with appropriate protein modification, proper protein folding, and natural status of membrane protein. Our previous work established linear-double-stranded DNAs (ldsDNAs) as innovative biological parts to implement AND gate genetic circuits in mammalian cell line. In the current study, we employ ldsDNA with terminal NNK degenerate codons as AND gate input to build highly diverse peptide library in mammalian cells. This ldsDNA-based AND gate (LBAG) peptide strategy is easy to conduct, only PCR reaction and cell transfection experiments are needed. High-throughput sequencing (HTS) results reveal that our new LBAG strategy could generate peptide library with both amino acid sequence and peptide length diversities. Moreover, by a mammalian cell two-hybrid system, we pan an MDM2 protein interacting peptide through the LBAG peptide library. Our work establishes ldsDNA as biological parts for building highly diverse peptide library in mammalian cells.

bioengineering↗

bioRxiv2018

SigLASSO: a LASSO approach jointly optimizing sampling likelihood and cancer mutation signatures

Multiple mutational processes drive carcinogenesis, leaving characteristic signatures on tumor genomes. Determining the active signatures from the full repertoire of potential ones can help elucidate mechanisms underlying cancer initiation and development. This task in-volves decomposing the counts of cancer mutations, tabulated according to their trinucleotide context, into a linear combination of known mutational signatures. We formulate it as an optimization problem and develop sigLASSO, a software tool, to carry it out efficiently. (An R package implementation is available at github.com/gersteinlab/siglasso). sigLASSO features four key aspects: (1) It jointly optimizes the likelihood of sampling and signature fitting, by explicitly adding multinomial sampling into the overall objective function. This is particularly important when mutation counts are low and sampling variance is high, such as in exome sequencing. (2) sigLASSO uses L1 regularization to parsimoniously assign signatures to mutation profiles, leading to sparse and more biologically interpretable solutions resembling previously well-characterized results. (3) sigLASSO fine-tunes model complexity, informed by the scale of the data and biological-knowledge based priors. In particular, instead of hard thresholding and choosing a priori a discrete subset of active signatures, sigLASSO allows continuous priors, which can be effectively learned from auxiliary information. (4) Because of this, sigLASSO can assess model uncertainty and abstain from making certain assignments in low-confidence contexts. Finally, to evaluate sigLASSO signature assignments in comparison to other approaches, we develop a set of reasonable expectations (e.g. sparsity, the ability to abstain, and robustness to noise) that we apply consistently in a variety of contexts.

bioinformatics↗

bioRxiv2018

The immune cell landscape in kidneys of lupus nephritis patients

Lupus nephritis is a potentially fatal autoimmune disease, whose current treatment is ineffective and often toxic. To gain insights into disease mechanisms, we analyzed kidney samples from lupus nephritis patients and healthy controls using single-cell RNA-seq. Our analysis revealed 21 subsets of leukocytes active in disease, including multiple populations of myeloid, T, NK and B cells, demonstrating both pro-inflammatory and resolving responses. We found evidence of local activation of B cells correlated with an age-associated B cell signature, and of progressive stages of monocyte differentiation within the kidney. A clear interferon response was observed in most cells. Two chemokine receptors, CXCR4 and CX3CR1, were broadly expressed, pointing to potential therapeutic targets. Gene expression of immune cells in urine and kidney was highly correlated, suggesting urine may be a surrogate for kidney biopsies. Our results provide a first comprehensive view of the complex network of leukocytes active in lupus nephritis kidneys.

immunology↗

bioRxiv2018

CRISPR-Cas12b-assisted nucleic acid detection platform

Rapid molecular diagnostic technology is very useful in many areas, including public health, environmental testing and criminal investigation. We recently showed that Cas12a had trans-cleavage activity upon collateral single-stranded DNA (ssDNA), with which the HOLMES platform (one-HOur Low-cost Multipurpose highly Efficient System) was developed. Here, we combine the thermophilic Cas12b, which also has the ssDNA trans-cleavage activity, with Loop-Mediated Isothermal Amplification (LAMP), and create HOLMESv2. In HOLMESv2, LAMP amplification and Cas12b trans-cleavage can be integrated into a one-step system with a constant temperature, which therefore brings much convenience in nucleic acid detection. Moreover, we also simplify the RNA detection procedures in HOLMESv2, using an RNA-dependent DNA polymerase for amplification and therefore omitting an extra reverse transcription step.\n\nOne Sentence SummaryWe combine LAMP and Cas12b to develop HOLMESv2 for conveniently detecting target nucleic acid in a one-step approach.

molecular biology↗