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Biology subjects

Jiang, N.

Publications and source records attributed to Jiang, N..

At least 55 records · Page 3Linked to original sources

MuscleNET: Mapping Electromyography to kinematic and dynamic biomechanical variables by machine learning

ObjectiveThis paper proposes machine learning models for mapping surface electromyography (sEMG) signals to regression of joint angle, joint velocity, joint acceleration, joint torque, and activation torque. ApproachThe regression models, collectively known as MuscleNET, take one of four forms: ANN (Forward Artificial Neural Network), RNN (Recurrent Neural Network), CNN (Convolutional Neural Network), and RCNN (Recurrent Convolutional Neural Network). Inspired by conventional biomechanical muscle models, delayed kinematic signals were used along with sEMG signals as the machine learning models input; specifically, the CNN and RCNN were modeled with novel configurations for these input conditions. The models inputs contain either raw or filtered sEMG signals, which allowed evaluation of the filtering capabilities of the models. The models were trained using human experimental data and evaluated with different individual data. Main resultsResults were compared in terms of regression error (using the root-mean-square) and model computation delay. The results indicate that the RNN (with filtered sEMG signals) and RCNN (with raw sEMG signals) models, both with delayed kinematic data, can extract underlying motor control information (such as joint activation torque or joint angle) from sEMG signals in pick-and-place tasks. The CNNs and RCNNs were able to filter raw sEMG signals. SignificanceAll forms of MuscleNET were found to map sEMG signals within 2 ms, fast enough for real-time applications such as the control of exoskeletons or active prostheses. The RNN model with filtered sEMG and delayed kinematic signals is particularly appropriate for applications in musculoskeletal simulation and biomechatronic device control.

systems biology↗

High-Throughput and High-Dimensional Single Cell Analysis of Antigen-Specific CD8+ T cells

Although critical to T cell function, antigen specificity is often omitted in high-throughput multi-omics based T cell profiling due to technical challenges. We describe a high-dimensional, tetramer-associated T cell receptor sequencing (TetTCR-SeqHD) method to simultaneously profile TCR sequences, cognate antigen specificities, targeted gene-expression, and surface-protein expression from tens of thousands of single cells. Using polyclonal CD8+ T cells with known antigen specificity and TCR sequences, we demonstrated over 98% precision for detecting the correct antigen specificity. We also evaluated gene-expression and phenotypic differences among antigen-specific CD8+ T cells and characterized phenotype signatures of influenza- and EBV-specific CD8+ T cells that are unique to their pathogen targets. Moreover, with the high-throughput capacity of profiling hundreds of antigens simultaneously, we applied TetTCR-SeqHD to identify antigens that preferentially enrich cognate CD8+ T cells in type 1 diabetes patients compared to healthy controls, and discovered a TCR that cross reacts between diabetic and microbiome antigens. TetTCR-SeqHD is a powerful approach for profiling T cell responses.

immunology↗

Complementary Phenotyping of Maize Root Architecture by Root Pulling Force and X-Ray Computed Tomography

The root system is critical for the survival of nearly all land plants and a key target for improving abiotic stress tolerance, nutrient accumulation, and yield in crop species. Although many methods of root phenotyping exist, within field studies one of the most popular methods is the extraction and measurement of the upper portion of the root system, known as the root crown, followed by trait quantification based on manual measurements or 2D imaging. However, 2D techniques are inherently limited by the information available from single points of view. Here, we used X-ray computed tomography to generate highly accurate 3D models of maize root crowns and created computational pipelines capable of measuring 71 features from each sample. This approach improves estimates of the genetic contribution to root system architecture, and is refined enough to detect various changes in global root system architecture over developmental time as well as more subtle changes in root distributions as a result of environmental differences. We demonstrate that root pulling force, a high-throughput method of root extraction that provides an estimate of root biomass, is associated with multiple 3D traits from our pipeline. Our combined methodology can therefore be used to calibrate and interpret root pulling force measurements across a range of experimental contexts, or scaled up as a stand-alone approach in large genetic studies of root system architecture.

plant biology↗

Femtosecond laser microdissection isolating regenerating C. elegans neurons for single cell RNA sequencing

Our understanding of nerve regeneration can be enhanced by delineating its underlying molecular activities at single neuron resolution in small model organisms such as Caenorhabditis elegans. Existing cell isolation techniques cannot isolate regenerating neurons from the nematode. We present femtosecond laser microdissection (fs-LM), a new single cell isolation method that dissects intact cells directly from living tissue by leveraging the micron-scale precision of fs-laser ablation. We show that fs-LM facilitated sensitive and specific gene expression profiling by single cell RNA-sequencing, while mitigating the stress related transcriptional artifacts induced by tissue dissociation. Single cell RNA-sequencing of fs-LM isolated regenerating C. elegans neurons revealed transcriptional program leading to successful regeneration in wild-type animals or regeneration failure in animals lacking DLK-1/p38 kinase. The ability of fs-LM to isolate specific neurons based on phenotype of interest allowed us to study the molecular basis of regeneration heterogeneity displayed by neurons of the same type. We identified gene modules whose expression patterns were correlated with axon regrowth rate at a single neuron level. Our results establish fs-LM as a highly specific single cell isolation method ideal for precision and phenotype-driven studies.

bioengineering↗

SARS-CoV-2 susceptibility of cell lines and substrates commonly used in diagnosis and isolation of influenza and other viruses

Coinfection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other viruses is inevitable as the COVID-19 pandemic continues. This study aimed to evaluate cell lines commonly used in virus diagnosis and isolation for their susceptibility to SARS-CoV-2. While multiple kidney cell lines from monkeys were susceptible and permissive to SARS-CoV-2, many cell types derived from human, dog, mink, cat, mouse, or chicken were not. Analysis of MDCK cells, which are most commonly used for surveillance and study of influenza viruses, demonstrated that they were insusceptible to SARS-CoV-2 and that the cellular barrier to productive infection was due to low expression level of the angiotensin converting enzyme 2 (ACE2) receptor and lower receptor affinity to SARS-CoV-2 spike, which could be overcome by over-expression of canine ACE2 in trans. Moreover, SARS-CoV-2 cell tropism did not appear to be affected by a D614G mutation in the spike protein.

microbiology↗

X-ray microscopy enables multiscale high-resolution 3D imaging of plant cells, tissues, and organs

Capturing complete internal anatomies of plant organs and tissues within their relevant morphological context remains a key challenge in plant science. While plant growth and development are inherently multiscale, conventional light, fluorescence, and electron microscopy platforms are typically limited to imaging of plant microstructure from small flat samples that lack direct spatial context to, and represent only a small portion of, the relevant plant macrostructures. We demonstrate technical advances with a lab-based X-ray microscope (XRM) that bridge the imaging gap by providing multiscale high-resolution 3D volumes of intact plant samples from the cell to whole plant level. Serial imaging of a single sample is shown to provide sub-micron 3D volumes co-registered with lower magnification scans for explicit contextual reference. High quality 3D volume data from our enhanced methods facilitate more sophisticated and effective computational segmentation and analyses than have previously been employed for X-ray based imaging. Advances in sample preparation make multimodal correlative imaging workflows possible, where a single resin-embedded plant sample is scanned via XRM to generate a 3D cell-level map, and then used to identify and zoom in on sub-cellular regions of interest for high resolution scanning electron microscopy. In total, we present the methodologies for use of XRM in the multiscale and multimodal analysis of 3D plant features using numerous economically and scientifically important plant systems.

plant biology↗

SARS-CoV-2 spike D614G variant confers enhanced replication and transmissibility

During the evolution of SARS-CoV-2 in humans a D614G substitution in the spike (S) protein emerged and became the predominant circulating variant (S-614G) of the COVID-19 pandemic1. However, whether the increasing prevalence of the S-614G variant represents a fitness advantage that improves replication and/or transmission in humans or is merely due to founder effects remains elusive. Here, we generated isogenic SARS-CoV-2 variants and demonstrate that the S-614G variant has (i) enhanced binding to human ACE2, (ii) increased replication in primary human bronchial and nasal airway epithelial cultures as well as in a novel human ACE2 knock-in mouse model, and (iii) markedly increased replication and transmissibility in hamster and ferret models of SARS-CoV-2 infection. Collectively, our data show that while the S-614G substitution results in subtle increases in binding and replication in vitro, it provides a real competitive advantage in vivo, particularly during the transmission bottle neck, providing an explanation for the global predominance of S-614G variant among the SARS-CoV-2 viruses currently circulating.

microbiology↗

Reverse-transcription recombinase-aided amplification assay for H5 subtype avian influenza virus

The H5 subtype Avian Influenza Virus has caused huge economic losses to the poultry industry and is a threat to human health. A rapid and simple test is needed to confirm infection in suspected cases during disease outbreaks. In this study, we developed a reverse-transcription recombinase-aided amplification assay for the detection of H5 subtype avian influenza virus. Assays were performed at a single temperature (39{degrees}C), and the results were obtained within 20 min. The assay showed no cross-detection with Newcastle disease virus or infectious bronchitis virus. The analytical sensitivity was 103 RNA copies per reaction at a 95% confidence interval according to probit regression analysis, with 100% specificity. Compared with published reverse-transcription quantitative real-time polymerase chain reaction assays, the {kappa} value of the reverse transcription recombinase-aided amplification assay in 365 avian clinical samples was 0.970 (p < 0.001). The sensitivity for avian clinical sample detection was 94.44% (95%CI, 70.63% - 99.71%), and the specificity was 100% (95%CI, 98.64% - 100%). These results indicated that our reverse-transcription recombinase-aided amplification assay may be a valuable tool for detecting H5 subtype avian influenza virus.

molecular biology↗

An Antioxidant Enzyme Therapeutic for COVID-19

The COVID-19 pandemic has taken a significant toll on people worldwide, and there are currently no specific antivirus drugs or vaccines. We report herein a therapeutic based on catalase, an antioxidant enzyme that can effectively breakdown hydrogen peroxide and minimize the downstream reactive oxygen species, which are excessively produced resulting from the infection and inflammatory process. Catalase assists to regulate production of cytokines, protect oxidative injury, and repress replication of SARS-CoV-2, as demonstrated in human leukocytes and alveolar epithelial cells, and rhesus macaques, without noticeable toxicity. Such a therapeutic can be readily manufactured at low cost as a potential treatment for COVID-19.

biochemistry↗

Flocked swab might be one main reason causing the high false-negative rate in COVID-19 screening----the advantages of a novel silicone swab

RNA testing using RT-PCR can provide direct evidence for diagnoses of COVID-19 which has brought unexpected disasters and changes to our human society. However, the absorption of cotton swab for RNA lysates may lead to a low concentration of detectable RNA, which might be one of the main reasons for the unstable positive detecting rate. We designed and manufactured a kind of silicone swab with concave-convex structure, and further compared the effects of silicone and cotton swab on RNA extraction. Principal component analysis and Paired Wilcoxcon test suggested that a higher RNA concentration and A260/A280 would be obtained using silicone swab. The results indicated that our silicone swab had a more excellent ability to sample than the cotton swab, characterized by the higher quantity and quality of extracted RNA. Thus, we advised that the current cotton swabs need to be improved urgently in COVID-19 diagnoses and the process of "sample collection" and "sample pre-processing" must be standardized and emphasized. HighlightsThe current cotton swabs need to be improved urgently in COVID-19 screening.

microbiology↗

Characterization of xyloglucan-specific fucosyltransferase activity in Golgi-enriched microsomal preparations from wheat seedlings

Xyloglucan (XyG) is a major hemicellulosic polymer in primary cell walls of dicotyledonous plants but represents only a minor constituent of cell walls from graminaceous monocotyledons (Poaceae). Our current information on XyG biosynthesis in vitro comes exclusively from studies on dicotyledonous plants. While XyG has been reported in grass cell walls, there are no studies of XyG biosynthesis in vitro in grasses. In this report, we investigated XyG structure and biosynthesis in etiolated wheat seedlings and showed that their walls contain small amounts (4-14%) of XyG. Furthermore, structural analysis using electrospray ionization mass spectrometry (ESI-MS) and high pH anion exchange chromatography (HPAEC) revealed that wheat XyG may be of XXGGG-type. Interestingly, detergent extracts from root microsomes were able to fucosylate tamarind XyG in vitro in a similar way as fucosyltransferase activity from Arabidopsis thaliana (AtFUT1) and pea (PsFUT1). Endoglucanase digestion of the [14C]fucosylated-tamarind XyG formed by the wheat fucosyltransferase activity released radiolabeled oligosaccharides that co-eluted with authentic fucoslyated XyG oligosaccharides (XXFG and XLFG). Although wheat fucosyltransferase activity was low, it appeared to be specific to XyG and required divalent ions (Mg2+ or Mn2+) for full activity. Together, these results suggest that the XyG fucosylation mechanism is conserved between monocots and dicots.

biochemistry↗

LTR_FINDER_parallel: parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons

SummaryAnnotation of plant genomes is still a challenging task due to the abundance of repetitive sequences, especially long terminal repeat (LTR) retrotransposons. LTR_FINDER is a widely used program for identification of LTR retrotransposons but its application on large genomes is hindered by its single threaded processes. Here we report an accessory program that allows parallel operation of LTR_FINDER, resulting up to 8,500X faster identification of LTR elements. It takes only 72 minutes to process the 14.5 Gb bread wheat (Triticum aestivum) genome in comparison to 1.16 years required by the original sequential version.\n\nAvailabilityLTR_FINDER_parallel is freely available at https://github.com/oushujun/LTR_FINDER_parallel.\n\nContactjiangn@msu.edu

genomics↗

RecO impedes RecG-SSB binding to impair the strand annealing recombination pathway in E.coli

Faithful duplication of genomic DNA relies not only on the fidelity of DNA replication itself, but also on fully functional DNA repair and homologous recombination machinery. We report a molecular mechanism responsible for deciding homologous recombinational repair pathways during replication dictated by binding of RecO and RecG to SSB in E.coli. Using a RecG-yfp fusion protein, we found that RecG-yfp foci appeared only in the {Delta}recG, {Delta}recO and {Delta}recA, {Delta}recO double mutants. Surprisingly, foci were not observed in wild-type {Delta}recG, or double mutants where recG and either recF or, separately recR were deleted. In addition, formation of RecG-yfp foci in the {Delta}recO::kanR required wildtype ssb, as ssb-113 could not substitute. This suggests that RecG and RecO binding to SSB is competitive. We also found that the UV resistance of recO alone mutant increased to certain extent by supplementing RecG. In an ssb-113 mutant, RecO and RecG worked following a different pattern. Both RecO and RecG were able to participate in repairing UV damages when grown at permissive temperature, while they could also be involved in making DNA double strand breaks when grown at nonpermissive temperature. So, our results suggested that differential binding of RecG and RecO to SSB in a DNA replication fork in Escherichia coli.may be involved in determining whether the SDSA or DSBR pathway of homologous recombinational repair is used.\n\nAuthor summarySingle strand DNA binding proteins (SSB) stabilize DNA holoenzyme and prevent single strand DNA from folding into non-B DNA structures in a DNA replication fork. It has also been revealed that SSB can also act as a platform for some proteins working in DNA repair and recombination to access DNA molecules when DNA replication fork needs to be reestablished. In Escherichia coli, several proteins working primarily in DNA repair and recombination were found to participate in DNA replication fork resumption by physically interacting with SSB, including RecO and RecG etc. However the hierarchy of these proteins interacting with SSB in Escherichia coli has not been well defined. In this study, we demonstrated a differential binding of RecO and RecG to SSB in DNA replication was used to establish a RecO-dependent pathway of replication fork repair by abolishing a RecG-dependent replication fork repair. We also show that, RecG and RecO could randomly participate in DNA replication repair in the absence of a functional SSB, which may be responsible for the generation of DNA double strand breaks in an ssb-113 mutant in Escherichia coli.

molecular biology↗

Benchmarking Transposable Element Annotation Methods for Creation of a Streamlined, Comprehensive Pipeline

Sequencing technology and assembly algorithms have matured to the point that high-quality de novo assembly is possible for large, repetitive genomes. Current assemblies traverse transposable elements (TEs) and allow for annotation of TEs. There are numerous methods for each class of elements with unknown relative performance metrics. We benchmarked existing programs based on a curated library of rice TEs. Using the most robust programs, we created a comprehensive pipeline called Extensive de-novo TE Annotator (EDTA) that produces a condensed TE library for annotations of structurally intact and fragmented elements. EDTA is open-source and freely available: https://github.com/oushujun/EDTA.

genomics↗

Characterizing grapevine (Vitis spp.) inflorescence architecture using X-ray imaging: implications for understanding cluster density

We characterized grapevine inflorescence architecture (the rachis and all branches without berries) to describe variation among 10 wild Vitis species, assess phylogenetic signals underlying inflorescence architecture traits, and interpret this variation in the context of breeding objectives. Three-dimensional X-ray tomography scans of grapevine inflorescences were used to measure geometric traits and inflorescence topology using persistent homology, a mathematical approach that can comprehensively measure and compare shapes. We simulated potential space available for berry growth within a given inflorescence architecture by evaluating expanding spheres attached to pedicels, referred to as "berry potential." Lastly, we performed phylogenetic analysis and mapped trait variation. We detected wide variation in inflorescence architecture features among Vitis species. Hierarchical clustering and correlation analyses revealed relationships among traits. Multivariate analyses identify traits contributing the most to variation and distinguish between species with high accuracy. Phylogenetic analyses revealed 12 morphological traits with strong phylogenetic signal. Morphometric analysis uncovered novel differences in inflorescence architecture among clades and between Vitis species. Cluster density is an important trait for assessing crop quality and forecasting yield; analyses presented here can be used to tease apart subtle, heritable features and environmental influences on this major agronomic trait.

plant biology↗

Mapping the lineage relationship between CXCR5+ and CXCR5- CD4+ T cells in HIV infected human lymph nodes

CXCR5 is a key surface marker expressed on follicular helper T (TFH) cells. We report here B cell help functionality in a population of CD4+ T cells isolated from primary human lymph nodes (LN) that lacked CXCR5 expression. This CXCR5- subset is distinguished from other CXCR5- CD4+ T cells by high PD-1 expression. Accumulation of CXCR5-PD-1+ T cells correlated with peripheral CD4+ T cell depletion and an increase in T-bet+ B cells in the LN, highlighting these atypical CD4+ T cells as a key component of lymphoid dysregulation during chronic HIV infection. By interrogating the phenotypic heterogeneity, functional capacity, TCR repertoire, transcriptional profile, and epigenetic state of CXCR5-PD-1+ T cells, we showed that CXCR5-PD-1+ T cells are related to CXCR5+PD-1+ T cells and provided evidence for the down regulation of CXCR5 following cell division as one mechanism for the absence of CXCR5 expression. Notably, CXCR5-PD-1+ T cells exhibited a migratory transcriptional program and contributed to circulating CXCR5-PD-1+ T cells with B cell help functionality in the peripheral blood. Thus, these data link LN pathology to circulating T cells and expand the current understanding on T cell diversity in the regulation of B cell responses during chronic inflammation. O_LIHigh dimensional profiling of activated CD4+ T cells in HIV infected lymph nodes revealed an accumulation of a CXCR5 negative subset. C_LIO_LICXCR5-PD-1+CD4+ T cells exhibited TFH-like protein expression and function. C_LIO_LICXCR5-PD-1+CD4+ T cells are related to TFH cells by clonal lineage and epigenetic similarity. C_LIO_LICXCR5-PD-1+CD4+ T cells upregulate a migratory gene program and contribute to circulating T cells with B cell help functionality C_LI

immunology↗

High-throughput determination of the antigen specificities of T cell receptors in single cells

We present tetramer-associated T-cell receptor sequencing (TetTCR-Seq), a method to link T cell receptor (TCR) sequences to their cognate antigens in single cells at high throughput. Binding is determined using a library of DNA-barcoded antigen tetramers that is rapidly generated by in vitro transcription and translation. We applied TetTCR-Seq to identify patterns in TCR cross-reactivity with cancer neo-antigens and to rapidly isolate neo-antigen-specific TCRs with no cross-reactivity to the wild-type antigen.

immunology↗

A conserved morphogenetic mechanism for epidermal ensheathment of nociceptive sensory neurites

Interactions between epithelial cells and neurons influence a range of sensory modalities including taste, touch, and smell. Vertebrate and invertebrate keratinocytes/keratinocyte-like epidermal cells ensheath peripheral arbors of somatosensory neurons, including nociceptors, yet the developmental origins and functional roles of this ensheathment are largely unknown. Here, we describe an evolutionarily conserved morphogenetic mechanism for epidermal ensheathment of somatosensory neurites. We found that somatosensory neurons in Drosophila and zebrafish induce formation of epidermal sheaths, which wrap neurites of different types of neurons to different extents. Neurites induce formation of plasma membrane phosphatidylinositol 4,5-bisphosphate microdomains at nascent sheaths, followed by a filamentous actin network, and recruitment of junctional proteins that likely form autotypic junctions to seal sheaths. Finally, blocking epidermal sheath formation destabilized dendrite branches and reduced nociceptive sensitivity in Drosophila. Epidermal somatosensory neurite ensheathment is thus a deeply conserved cellular process that contributes to the morphogenesis and function of nociceptive sensory neurons.

neuroscience↗