Biology subjects

Chen, L.

Publications and source records attributed to Chen, L..

At least 757 records · Page 42Linked to original sources

bioRxiv2021

Minian: An open-source miniscope analysis pipeline

Miniature microscopes have gained considerable traction for in vivo calcium imaging in freely behaving animals. However, extracting calcium signals from raw videos is a computationally complex problem and remains a bottleneck for many researchers utilizing single-photon in vivo calcium imaging. Despite the existence of many powerful analysis packages designed to detect and extract calcium dynamics, most have either key parameters that are hard-coded or insufficient step-by-step guidance and validations to help the users choose the best parameters. This makes it difficult to know whether the output is reliable and meets the assumptions necessary for proper analysis. Moreover, large memory demand is often a constraint for setting up these pipelines since it limits the choice of hardware to specialized computers. Given these difficulties, there is a need for a low memory demand, user-friendly tool offering interactive visualizations of how altering parameters at each step of the analysis affects data output. Our open-source analysis pipeline, Minian (Miniscope Analysis), facilitates the transparency and accessibility of single-photon calcium imaging analysis, permitting users with little computational experience to extract the location of cells and their corresponding calcium traces and deconvolved neural activities. Minian contains interactive visualization tools for every step of the analysis, as well as detailed documentation and tips on parameter exploration. Furthermore, Minian has relatively small memory demands and can be run on a laptop, making it available to labs that do not have access to specialized computational hardware. Minian has been validated to reliably and robustly extract calcium events across different brain regions and from different cell types. In practice, Minian provides an open-source calcium imaging analysis pipeline with user-friendly interactive visualizations to explore parameters and validate results.

neuroscience↗

bioRxiv2021

Clonal inactivation of telomerase promotes accelerated stem cell differentiation

Telomerase is intimately associated with stem cells and upregulated in cancer, where it serves essential roles through its catalytic action in elongating telomeres, nucleoprotein caps that protect chromosome ends1. Overexpression of the telomerase reverse transcriptase (TERT) enhances cell proliferation through telomere-independent means, yet definitive evidence for such a direct role in stem cell function has yet to be revealed through loss-of-function studies. Here, we show that conditional deletion of TERT in spermatogonial stem cells (SSCs) markedly impairs competitive clone formation. Using lineage-tracing from the Tert locus, we find that TERT-expressing SSCs yield long-lived clones, but that selective TERT-inactivation in SSCs causes accelerated stem cell differentiation thereby disrupting clone formation. This requirement for TERT in clone formation is bypassed by expression of a catalytically inactive TERT transgene and occurs independently of the canonical telomerase complex. TERT inactivation induces a genome-wide reduction in open chromatin evident in purified SSCs, but not in committed progenitor cells. Loss of TERT causes reduced activity of the MYC oncogene and transgenic expression of MYC in TERT-deleted SSCs efficiently rescues clone formation. These data reveal a required catalytic activity-independent role for TERT in preventing stem cell differentiation, forge a genetic link between TERT and MYC and suggest new means by which TERT may promote tumorigenesis.

developmental biology↗

bioRxiv2021

Tetratricopeptide repeat domain 36 protects renal tubular cells from cisplatin-induced apoptosis via maintaining mitochondrial homeostasis

The apoptosis of proximal tubule epithelial cells (PTECs) is a critical event of acute kidney injury (AKI). Tetratricopeptide repeat domain 36 (TTC36) with three tetratricopeptide repeats is evolutionarily conserved across mammals, which functions as a chaperone for heat shock protein 70. We have revealed that TTC36 is specifically expressed in PTECs in our previous work. There are few studies about the role TTC36 played in AKI. Therefore, in this study, we investigated the function of TTC36 in the apoptosis of HK2 cells, which are derived from the human proximal tubule. Firstly, we observed that TTC36 was obviously down-regulated and was negatively related to the kidney damage degree in a mouse model of acute kidney injury established by ischemia/reperfusion. In addition, TTC36 overexpression protected HK2 cells against cisplatin-induced apoptosis. Moreover, we discovered the mechanism that TTC36 mitigated cisplatin-triggered mitochondrial disorder via sustaining the membrane potential of mitochondria and mitochondrial autophagy-related gene expression. Collectively, these results suggested that TTC36 plays a protective role in the cisplatin-induced apoptosis of renal tubular cells through maintaining the mitochondrial potential and mitochondrial autophagy-related gene expression. These observations highlight the essential role of TTC36 in regulating PTEC apoptosis and imply TTC36/mitochondrial homeostasis axis as a potential target for the therapeutic intervention in AKI.

cell biology↗

bioRxiv2021

WRKY33-mediated indole glucosinolate metabolic pathway confers host resistance against Alternaria brassicicola

The tryptophan (Trp)-derived plant secondary metabolites, including camalexin, 4-hydroxy-indole-3-carbonylnitrile (4OH-ICN), and indole glucosinolate (IGS), show broad-spectrum antifungal activity. However, the upstream regulators of these metabolic pathways among different plant species in response to fungus infection are rarely studied. In this study, our results revealed a positive role of WRKY33 in host resistance to Alternaria brassicicola by directly regulating the transcription of genes involved in the biosynthesis and atypical hydrolysis of IGS both in Arabidopsis and Chinese kale. Indole-3-yl-methylglucosinolate (I3G) and 4-methoxyindole-3-yl-methylglucosinolate (4MI3G) are the main components of IGS. WRKY33 induces the expression of MYB51 and CYP83B1 which promotes the biosynthesis of I3G, the precursor of 4MI3G. Moreover, it also directly activates the expression of CYP81F2, IGMT1, and IGMT2 to drive side chain modification of I3G to produce 4MI3G, which is in turn hydrolyzed by PEN2. However, Chinese kale showed a more severe symptom than Arabidopsis when infected by Alternaria brassicicola. Comparative analyses of the origin and evolution of Trp-metabolism indicate that the loss of camalexin biosynthesis in Brassica crops during evolution might attenuate the resistance of crops to Alternaria brassicicola. As a result, IGS metabolic pathway mediated by WRKY33 becomes essential for Chinese kale to deter Alternaria brassicicola. Our results highlight the differential regulation of Trp-derived camalexin and IGS biosynthetic pathways in plant immunity between Arabidopsis and Brassica crops. One-sentence SummaryPathogen-responsive WRKY33 directly regulates indole glucosinolates biosynthesis and atypical hydrolysis, conferring to host resistance to Alternaria brassicicola in Arabidopsis and Brassica crops.

plant biology↗

bioRxiv2021

Developmental and Intergenerational Landscape of Human Circulatory Lipidome and its Association with Obesity Risk

Lipids play a vital role in human health and development, but changes to their circulatory levels during gestation and in early life are poorly understood. Here we present the first developmental and intergenerational landscape of the human circulatory lipidome, derived by profiling of 480 lipid species representing 25 lipid classes, in mothers and their offspring (n=2491). Levels of 66% of the profiled lipids increased in maternal circulation during gestation, while cord blood had higher concentrations of acylcarnitines and lysophospholipids. The offspring lipidome at age six years revealed striking similarities with postnatal maternal lipidome (adult) in its lipid composition and concentrations. Comparison of lipids associated with child and maternal adiposity identified a 92% overlap, implying intergenerational similarities in the lipid signatures of obesity risk. We also catalogued lipid signatures linked with maternal adiposity during gestation and offspring birthweight, and validated (>70% overlap) the findings in an independent birth-cohort (n=1935).

systems biology↗

bioRxiv2021

A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines

The human genome contains more than 200,000 gene isoforms. However, different isoforms can be highly similar, and with an average length of 1.5kb remain difficult to study with short read sequencing. To systematically evaluate the ability to study the transcriptome at a resolution of individual isoforms we profiled 5 human cell lines with short read cDNA sequencing and Nanopore long read direct RNA, amplification-free direct cDNA, PCR-cDNA sequencing. The long read protocols showed a high level of consistency, with amplification-free RNA and cDNA sequencing being most similar. While short and long reads generated comparable gene expression estimates, they differed substantially for individual isoforms. We find that increased read length improves read-to-transcript assignment, identifies interactions between alternative promoters and splicing, enables the discovery of novel transcripts from repetitive regions, facilitates the quantification of full-length fusion isoforms and enables the simultaneous profiling of m6A RNA modifications when RNA is sequenced directly. Our study demonstrates the advantage of long read RNA sequencing and provides a comprehensive resource that will enable the development and benchmarking of computational methods for profiling complex transcriptional events at isoform-level resolution.

genomics↗

bioRxiv2021

Potential transmission chains of variant B.1.1.7 and co-mutations of SARS-CoV-2

The presence of SARS-CoV-2 mutants, including the emerging variant B.1.1.7, has raised great concerns in terms of pathogenesis, transmission, and immune escape. Characterizing SARS-CoV-2 mutations, evolution, and effects on infectivity and pathogenicity is crucial to the design of antibody therapies and surveillance strategies. Here we analyzed 454,443 SARS-CoV-2 spike genes/proteins and 14,427 whole-genome sequences. We demonstrated that the early variant B.1.1.7 may not have evolved spontaneously in the United Kingdom or within human populations. Our extensive analyses suggested that Canidae, Mustelidae or Felidae, especially the Canidae family (for example, dog) could be a possible host of the direct progenitor of variant B.1.1.7. An alternative hypothesis is that the variant was simply yet to be sampled. Notably, the SARS-CoV-2 whole genome represents a large number of potential co-mutations with very strong statistical significances (p value<E- 44). In addition, we used an experimental SARS-CoV-2 reporter replicon system to introduce the dominant co-mutations NSP12_c14408t, 5UTR_c241t, and NSP3_c3037t into the viral genome, and to monitor the effect of the mutations on viral replication. Our experimental results demonstrated that the co-mutations significantly attenuated the viral replication. The study provides valuable clues for discovering the transmission chains of variant B.1.1.7 and understanding the evolutionary process of SARS-CoV-2.

microbiology↗

bioRxiv2021

Dendritic GABAergic inhibition controlled by Shh signaling-dependent stellate cell pool is critical for motor learning

Cerebellar inhibitory interneurons are important regulators of neural circuit activity for diverse motor and non-motor functions. The molecular layer interneurons (MLI), consisting of basket cells (BCs) and stellate cells (SCs), provide dendritic and somatic inhibitory synapses onto Purkinje cells, respectively. They are sequentially generated in an inside-out pattern from Pax2+ immature interneurons which migrate from the prospective white matter to the ML of the cortex. However, little is known as to how MLI subtype identities and pool sizes are determined, nor are their contributions to motor learning well understood. Here, we show that GABAergic progenitors fated to generate both BCs and SCs respond to the Shh signal. Conditional abrogation of Shh signaling inhibited proliferation of GABAergic progenitors and reduced the number of Pax2+ cells, whereas persistent Shh pathway activation increased their numbers. These changes, however, did not affect early-born BC numbers but selectively altered the SC pool size. Moreover, genetic depletion of GABAergic progenitors when BCs are actively generated also resulted in a specific reduction of SCs, suggesting that the specification of MLI subtypes is independent of Shh signaling and their birth order and likely occurs after Pax2+ cells settle into their laminar positions in an inside-out sequence. Mutant mice with reduced SC numbers displayed decreased dendritic inhibitory synapses and neurotransmission onto Purkinje cells, resulting in an impaired acquisition of eyeblink conditioning. These findings also reveal an essential role of Shh signaling-dependent SCs in regulating inhibitory dendritic synapses and motor learning.

neuroscience↗

bioRxiv2021

Portrait of a genus: the genetic diversity of Zea

Maize is a globally valuable commodity and one of the most extensively studied genetic model organisms. However, we know surprisingly little about the extent and potential utility of the genetic variation found in the wild relatives of maize. Here, we characterize a high-density genomic variation map from ~700 genomes encompassing maize and all wild taxa of the genus Zea, identifying over 65 million single nucleotide polymorphisms (SNPs), 8 million Insertion/Deletion (InDel) polymorphisms, and over one thousand novel inversions. The variation map reveals evidence of selection within taxa displaying novel adaptations such as perenniality and regrowth. We focus in detail on evidence of convergent adaptation in highland teosinte and temperate maize. This study not only indicates the key role of hormone related pathways in highland adaptation and flowering time related pathways in high latitude adaptation, but also identifies significant overlap in the genes underlying adaptations to both environments. To show how this data can identify useful genetic variants, we generated and characterized novel mutant alleles for two flowering time candidate genes. This work provides the most extensive sampling to date of the genetic diversity inherent in the genus Zea, resolving questions on evolution and identifying adaptive variants for direct use in modern breeding.

evolutionary biology↗

bioRxiv2021

CNAHap: a germline haplotyping method using tumor allele-specific copy number alteration

Haplotype phasing is indispensable to study human genetics. The pervasiveness of large copy number variant segments in solid tumors brings possibilities to resolve long germline phasing blocks utilizing allele imbalance in tumor data. Although there exist such studies, none of them provide easy-use software based on availability and usability. Herein, we present a novel tool, CNAHap, to determine the allele-specific copy number in tumor and then phase germline variants according to the imbalanced alleles in tumor genomes. We also provide interactive web interfaces to visualize the copy number and phase landscape from CNAHap. On in silico datasets, CNAHap demonstrates higher allele-specific copy number calling accuracy than the benchmark tool and generates long phasing blocks. As a case study on Hepatocellular carcinoma, CNAHap successfully generates huge phase blocks with the averages of N50 and N90 as 25M and 7M, respectively, and finds the Olfactory receptor family is recurrent amplified. Our results illustrate the efficacy of CNAHap in determining tumor allele-specific copy numbers and their long germline haplotypes. CNAHap is available at https://github.com/bowentan/CNAHap and the CNAHap visualization web interfaces are hosted at bio.oviz.org.

bioinformatics↗

bioRxiv2021

Occurrence of COVID-19 symptoms during SARS-CoV-2 infection defines waning of humoral immunity

Approximately half of the SARS-CoV-2 infections occur without apparent symptoms, raising questions regarding long-term humoral immunity in asymptomatic individuals. Plasma levels of immunoglobulin G (IgG) and M (IgM) against the viral spike or nucleoprotein were determined for 25,091 individuals enrolled in a surveillance program in Wuhan, China. We compared 405 asymptomatic individuals with 459 symptomatic COVID-19 patients. The well-defined duration of the SARS-CoV-2 endemic in Wuhan allowed a side-by-side comparison of antibody responses following symptomatic and asymptomatic infections without subsequent antigen re-exposure. IgM responses rapidly declined in both groups. However, both the prevalence and durability of IgG responses and neutralizing capacities correlated positively with symptoms. Regardless of sex, age, and body weight, asymptomatic individuals lost their SARS-CoV-2-specific IgG antibodies more often and rapidly than symptomatic patients. These findings have important implications for immunity and favour immunization programs including individuals after asymptomatic infections. One-Sentence SummaryPrevalence and durability of SARS-CoV-2-specific IgG responses and neutralizing capacities correlate with COVID-19 symptoms.

immunology↗

bioRxiv2021

Deep neural network analysis employing diffusion basis spectrum imaging metrics as classifiers improves prostate cancer detection and grading

Structural and cellular complexity of prostatic histopathology limits the accuracy of noninvasive detection and grading of prostate cancer (PCa). We addressed this limitation by employing a novel diffusion basis spectrum imaging (DBSI) to derive structurally-specific diffusion fingerprints reflecting various underlying prostatic structural and cellular components. We further developed diffusion histology imaging (DHI) by combining DBSI-derived structural fingerprints with a deep neural network (DNN) algorithm to more accurately classify different histopathological features and predict tumor grade in PCa. We examined 243 patients suspected with PCa using in vivo DBSI. The in vivo DBSI-derived diffusion metrics detected coexisting prostatic pathologies distinguishing inflammation, PCa, and benign prostatic hyperplasia. DHI distinguished PCa from benign peripheral and transition zone tissues with over 95% sensitivity and specificity. DHI also demonstrated over 90% sensitivity and specificity for Gleason score noninvasively. We present DHI as a novel diagnostic tool capable of noninvasive detection and grading of PCa. One sentence summaryDiffusion histology imaging noninvasively and accurately detects and grades prostate cancer.

bioinformatics↗

bioRxiv2021

Divergent epigenetic profiles from two differentially impacted wild populationsof estuarine cordgrass (Sporobolus alterniflorus)

The effects of urbanization on watershed ecosystems present critical challenges to modern survival. Organisms in urbanized areas experience high rates of evolutionary change, but genetic adaptation alone cannot mitigate the rapid and severe effects of urbanization on biodiversity. Highly resilient, foundation species are key to maintaining an ecosystems integrity in the face of urban stressors. However, the rapid collapse and disappearance of watershed ecosystems calls into question the extent to which we can rely on such species for their services. Our research investigates the molecular mechanisms by which the foundation ecosystems provider, Sporobolus alterniflorus, adapts to life in an urbanized environment. To elucidate these mechanisms, we quantified changes in global DNA methylation (% 5-mC) as a result of acute heat stress. Specimens from two differentially impacted populations across an urban to suburban geographical transect formed the basis of this study. These two populations of Sporobolus alterniflora exhibit inverse global DNA methylation patterns when exposed to the same acute heat stress. Our findings suggest that epigenetic mechanisms, such as DNA methylation, control rapid and transient adaptation, in the form of differential stress responses, to distinct environment challenges. Highlights for manuscript submissionO_LI{blacksquare} estuarine grasses native to the Bronx River, NY face stresses associated with low dissolved oxygen and urbanization C_LIO_LI{blacksquare} differentially impacted populations of estuarine grasses exhibit inverse global DNA methylation profiles in response to acute heat stress C_LIO_LI{blacksquare} DNA methylation may represent a mechanism by which plants transiently respond to environmental stressors, and this may represent a form of rapid adaptive evolution C_LIO_LI{blacksquare} stress priming by transgenerational epigenetic modification may enhance fitness in grasses native to the heavily impacted Bronx River estuary C_LI

plant biology↗

bioRxiv2021

Benchtop Carbon Fiber Microelectrode Array Fabrication Toolkit

BackgroundConventional neural probes are primarily fabricated in a cleanroom, requiring the use of multiple expensive and highly specialized tools. New methodWe propose a cleanroom "light" fabrication process of carbon fiber neural electrode arrays that can be learned quickly by an inexperienced cleanroom user. This carbon fiber electrode array fabrication process requires just one cleanroom tool, a parylene-c deposition machine, that can be learned quickly or outsourced to a commercial processing facility at marginal cost. Our fabrication process also includes hand-populating printed circuit boards, insulation, and tip optimization. ResultsThe three different tip optimizations explored here (Nd:YAG laser, blowtorch, and UV laser) result in a range of tip geometries and 1kHz impedances, with blowtorched fibers resulting in the lowest impedance. While previous experiments have proven laser and blowtorch electrode efficacy, this paper also shows UV laser cut fibers can record neural signals in vivo. Comparison with existing methodsExisting carbon fiber arrays either do not have individuated electrodes in favor of bundles or require cleanroom fabricated guides for population and insulation. The proposed arrays use only tools that can be used at a benchtop for fiber population. ConclusionsThis carbon fiber electrode array fabrication process allows for quick customization of bulk array fabrication at a reduced price compared to commercially available probes.

bioengineering↗

bioRxiv2021

Genetic Susceptibility to Enteric Fever in Experimentally Challenged Human Volunteers

BackgroundInfection with Salmonella enterica serovars Typhi and Paratyphi A cause an estimated 14 million cases of enteric fever annually. Here the controlled nature of challenge studies is exploited to identify genetic variants associated with enteric fever susceptibility. MethodsHuman challenge participants were genotyped by Illumina OmniExpress-24 BeadChip array (n=176) and/or transcriptionally profiled by RNA-sequencing (n=178). ResultsTwo SNPs within CAPN14 and MIATNB were identified with p<10-5 for association with development of symptoms or bacteraemia following oral S. Typhi or S. Paratyphi A challenge. Imputation of classical human leukocyte antigen (HLA) types from genomic and transcriptomic data identified HLA-B*27:05, previously associated with non-typhoidal Salmonella-induced reactive arthritis, as the HLA type most strongly associated with enteric fever susceptibility (p=0.012). Genes related to the unfolded protein response and heat shock were over-represented in HLA-B*27:05+ participants following challenge (p=0.01). Furthermore, intracellular replication of S. Typhi is higher in C1R cells transfected with HLA-B*27:05 (p=0.02). ConclusionThese data suggest that activation of the unfolded protein response by HLA-B*27:05 misfolding may create an intracellular environment conducive to S. Typhi replication, increasing susceptibility to enteric fever.

genetics↗

bioRxiv2021

Multiple nucleotide polymorphism DNA markers for the accurate evaluation of genetic variations

DNA markers are an essential tool for the detection and evaluation of genetic variations, a central theme in genetics and biology. Effective markers must be highly reproducible, polymorphic, accurate and efficient to profile. We developed multiple dispersed nucleotide polymorphism (MNP) DNA marker and an efficient MNP genotyping method called MNP-Seq. The MNP marker was 17.48% more polymorphic than the highly polymorphic marker of microsatellites on a collection of hybrid rice plants. When applied to genotype more than 80,000 individual MNP markers of diploid rice and polyploidy hybrid cotton varieties which were notoriously difficult to genotype accurately, MNP-Seq finished in two days and achieved accuracies of 99.999% and 99.988%, respectively. We adopted MNP-Seq to reveal the ubiquitous, albeit subtle and neglected, genetic heterogeneities in homonyms of Nipponbare rice, a popular model organism for plant biology. This result raised a question on the consistency of the published results using the model plant. We also used MNP-Seq to accurately and efficiently determine the identities of plant varieties, a key but difficult problem for the protection of plant intellectual property rights. While being applied to plants in the current study, the MNP marker and MNP-Seq are general and readily applicable to similar problems in animals and micro-organisms.

molecular biology↗

bioRxiv2021

A role for the Erk MAPK pathway in modulating SAX-7/L1CAM-dependent locomotion in Caenorhabditis elegans

L1CAMs are immunoglobulin cell adhesion molecules that play important roles in the development and function of the nervous system. In addition to being associated with autism and schizophrenia spectrum disorders, impaired L1CAM function also underlies the X-linked L1 syndrome, which encompasses a group of neurological conditions, including spastic paraplegia and congenital hydrocephalus. Previous studies on both vertebrate and invertebrate L1CAMs established conserved roles that include axon guidance, dendrite morphogenesis, synapse development, and maintenance of neural architecture. We previously identified a genetic interaction between the C. elegans L1CAM encoded by the sax-7 gene and RAB-3, a GTPase that functions in synaptic neurotransmission; rab-3; sax-7 animals exhibit synthetic locomotion abnormalities and neuronal dysfunction. In this study, we examine the significance of this genetic interaction and show that this synergism also occurs when loss of SAX-7 is combined with mutants of other genes encoding key players of the synaptic vesicle cycle. In contrast, sax-7 does not interact with genes that function in synaptogenesis. These findings suggest a post-developmental role for sax-7 in the regulation of synaptic activity. To further assess this possibility, we conducted electrophysiological recordings and ultrastructural analyses at neuromuscular junctions. Lastly, we performed a forward genetic screen for suppressors of the rab-3; sax-7 synthetic phenotypes, uncovering a role for the Mitogen-activated Protein Kinase (MAPK) pathway in promoting coordinated locomotion.

genetics↗

bioRxiv2021

Hypothalamic perineuronal nets are regulated by sex and dietary interventions

Perineuronal nets (PNNs) are widely present in the hypothalamus, and are thought to provide physical protection and ion buffering for neurons, and regulate their synaptic plasticity and intracellular signaling. Recent evidence indicates that PNNs in the mediobasal hypothalamus plays an important role in the regulation of glucose homeostasis. However, whether and how hypothalamic PNNs are regulated are not fully understood. In the present study, we examined whether PNNs in various hypothalamic regions in mice can be regulated by sex, gonadal hormones, dietary interventions, or their interactions. We demonstrated that gonadal hormones are required to maintain normal PNNs in the arcuate nucleus of hypothalamus in both male and female mice. In addition, PNNs in the terete hypothalamic nucleus display a sexual dimorphism with females higher than males, and high-fat diet feeding increases terete PNNs only in female mice but not in male mice. On the other hand, PNNs in other hypothalamic regions are not influenced by sex, gonadal hormones or dietary interventions. In summary, we demonstrated that hypothalamic PNNs are regulated in a region-specific manner and these results provide a framework to further investigate the potential functions of PNNs in regulating energy/glucose homeostasis at the interplay of sex, gonadal hormones and diets.

neuroscience↗