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Long, J.

Publications and source records attributed to Long, J..

At least 37 records · Page 2Linked to original sources

The origin, deployment, and evolution of a plant-parasitic nematode effectorome

Plant-parasitic nematodes constrain global food security. During parasitism, they secrete effectors into the host plant from two types of pharyngeal gland cells. These effectors elicit profound changes in host biology to suppress immunity and establish a unique feeding organ from which the nematode draws nutrition. Despite the importance of effectors in nematode parasitism, there has been no comprehensive identification and characterisation of the effector repertoire of any plant-parasitic nematode. To address this, we advance techniques for gland cell isolation and transcriptional analysis to define a stringent annotation of putative effectors for the cyst nematode Heterodera schachtii at three key life-stages. We define 659 effector gene loci: 293 "known" high-confidence homologs of plant-parasitic nematode effectors, and 366 "novel" effectors with high gland cell expression. In doing so we define a comprehensive "effectorome" of a plant-parasitic nematode. Using this effector definition, we provide the first systems-level understanding of the origin, deployment and evolution of a plant-parasitic nematode effectorome. The robust identification of the comprehensive effector repertoire of a plant-parasitic nematode will underpin our understanding of nematode pathology, and hence, inform strategies for crop protection.

plant biology↗

Global functional connectivity of cognitive control network predicts task-switching performance in older adults

Executive Function (EF) is a complex higher order cognitive process that involves integrating subprocesses of attention, working memory, inhibition, and task switching and known to be one of the first cognitive functions to be affected by age related declines. Global Functional Connectivity (GFC), a measure of whole brain connectivity in brain networks such as the Cognitive Control Network (CCN), has been shown to measure the maintained EF abilities in older adults with cognitive impairment. However, this relationship has not been explored in a sample comprised of mostly cognitively normal older adults nor with the use of an experimental EF task sensitive to sub-processes most sensitive to aging. Task-switch paradigm studies have shown age-related deficits in holding and responding to rule sets while inhibiting another rule set in working memory (i.e., mixing cost). The present study aims to elucidate the relationship seen in EF performance using GFC and leveraging a task-switch paradigm that manipulates response overlap to increase cognitive demands on switching between tasks (e.g., mixing cost). Results show that greater negative DMN GFC coincides with older adults lower mixing costs, not CCN GFC. Findings indicate that DMN GFC, not CCN, may be important for EF performance in older adults.

neuroscience↗

Deletion of sulfate transporter SUL1 extends yeast replicative lifespan via reduced PKA signaling instead of decreased sulfate uptake

The regulation of cellular metabolism and growth in response to nutrient availability is crucial for cell survival and can significantly impact on lifespan. Central to this regulation is a class of transporters that sense and transport specific nutrients and transduce the signal downstream to control genes responsible for growth and survival. In this study, we identified SUL1, a plasma membrane transporter responsible for regulating the entry of extracellular sulfate in Saccharomyces cerevisiae, as a key gene for regulating lifespan. We conducted a systematic analysis to delineate the downstream mechanism underlying the lifespan extension by SUL1 deletion. Surprisingly, we found that the lifespan extending effect of SUL1 deletion is not due to decreased sulfate transport. The SUL1 deletion mutant exhibited decreased PKA signaling, resulting in a series of downstream effects, including increased stress-protective trehalose and glycogen, increased nuclear translocation of MSN2, elevated expression of general stress response genes, enhanced autophagy, and reduced expression of amino acid biosynthetic and ribosomal genes. We demonstrated that the observed increase in lifespan is dependent on MSN2 and autophagy pathways. Our findings exemplify the influence of nutrient signaling rather than the nutrient itself on lifespan regulation and further substantiate the pivotal role of the PKA pathway in this process.

molecular biology↗

Ikzf1 association with Foxp3 for Foxp3-dependent gene repression in Treg cells: induction of autoimmunity and tumor immunity by disrupting the association

The transcription factor Foxp3 specifically expressed in regulatory T (Treg) cells controls Treg function by repressing some genes and activating others. We have shown here that the transcription factor Ikzf1 associates with Foxp3 via its exon 5 (called IkE5) and that conditional deletion of IkE5 up-regulated the genes, including Ifng, normally repressed by Foxp3 upon TCR stimulation. IkE5-deletion in Treg cells indeed incurred IFN-{gamma} overproduction, which destabilized Foxp3 expression and impaired suppressive function, consequently producing fatal systemic autoimmune diseases and evoking strong anti-tumor immunity. In addition, pomalidomide, which degrades IKZF1 and IKZF3, induced IFN-{gamma} overproduction in human Treg cells. Mechanistically, the Foxp3/Ikzf1/Ikzf3 complex exerted gene-repressing function by competing with epigenetic co-activators, such as p300 and NFAT1, for binding to the target gene loci via chromatin remodeling. Collectively, the association of Ikzf1 with Foxp3 is essential for repressive function of Foxp3, and can be targeted to control autoimmunity and tumor immunity.

immunology↗

A robust method for the rapid generation of nanobodies.

Nanobody refers to the variable domain of heavy-chain-only antibodies. The distinctive advantages of nanobodies including small size, feasible expression in Escherichia coli (E. coli), and superior stability make them promising tools for applications in scientific research and therapies. So far, the screening and expression of nanobodies are mainly following similar methods used for conventional antibodies, suffering from amplification-caused losses of the diversity of libraries and requirements of subcloning of interests into the expression vector. Here, based on the unique properties of nanobodies, we developed an integrated method to screen and express nanobodies simultaneously with no bias of the library diversity. The library of nanobodies was cloned and secretively expressed into the culture medium. Target specifical binding nanobodies were isolated through 1-3 rounds of dilution and regrown steps in a way following the Poisson distribution to ensure no positive clones were dismissed, while the population of positive clones increased by more than 10 folds upon each round of dilution. Ultimately, 5 nanobodies against the death domain receptor 5 (DR5) and 5 nanobodies against the Pyrococcus furiosus (Pfu) DNA polymerase were produced directly out of their immunized libraries, respectively. Additionally, our approach allowed nanobody screening even without any specialized instruments/devices, demonstrating general applicability in the routine production of monoclonal nanobodies for diverse biomedical applications.

biochemistry↗

Monkeypox virus quadrivalent mRNA vaccine induces antibody responses and cellular immunity and protects mice against Vaccinia virus

There is an urgent need for efficient and safe vaccines against the monkeypox virus (MPXV) in response to the rapidly spreading monkeypox epidemic. In the age of COVID-19, mRNA vaccines have been highly successful and emerged as platforms enabling rapid development and large-scale preparation. Here, we have developed two MPXV quadrivalent mRNA vaccines, named mRNA-A-LNP and mRNA-B-LNP, based on two IMVs (A29L and M1R) and two EEVs (A35R and B6R). By administering mRNA-A-LNP and mRNA-B-LNP intramuscularly twice, mice have induced MPXV-specific IgG antibodies and potent Vaccinia virus (VACV)-specific neutralizing antibodies. Additionally, it elicited durable MPXV-specific killer memory T-cell immunity as well as memory B-cell immunity in mice. Furthermore, the passive transfer of sera from mRNA-A-LNP and mRNA-B-LNP-immunized mice protected nude mice against the VACV challenge. In addition, two doses of mRNA-A-LNP and mRNA-B-LNP were also protective against the VACV challenge in mice. Overall, our results demonstrated that mRNA-A-LNP and mRNA-B-LNP appear to be safe and effective vaccine candidates against monkeypox epidemics, as well as against outbreaks caused by other orthopoxviruses, including the smallpox virus.

immunology↗

Cereblon controls the timing of muscle differentiation in Ciona embryos

Thalidomide has a dark history as a teratogen, but in recent years it has been shown to function as a chemotherapeutic agent. Thalidomide binds cereblon, a component of E3 ubiquitin ligase complex and modifies its degradation targets. Despite these insights, remarkably little is known about the normal function of cereblon in development. Here, we employ the simple proto-vertebrate model, Ciona intestinalis, to address this question. We observed a "hotspot" of Crbn expression in the developing tail muscles and identify its enhancer containing both Myod activator sites and a Snail repressive element. Overexpression of Crbn in tail muscles decreases expression of contractility genes. We suggest that this reduction is due to premature degradation of Tbx6. Drug inhibition studies using lenalidomide, a derivative of thalidomide, lead to a striking increase of Crbn expression. This autofeedback regulation could be induced by neomorphic degradation of Snail, contributing to the efficacy of lenalidomide in treating metastatic melanoma. In summary, our analysis of Crbn suggests that its normal function in Ciona is to time expression of contractility genes during muscle differentiation thereby ensuring coordination of tail morphogenesis and hatching of swimming tadpoles.

developmental biology↗

Regulation of astrocyte lipid metabolism and ApoE secretion by the microglial oxysterol, 25-hydroxycholesterol

Neuroinflammation is a major hallmark of Alzheimers disease and several other neurological and psychiatric disorders and is often associated with dysregulated cholesterol metabolism. Relative to homeostatic microglia, activated microglia express higher levels of Ch25h, an enzyme that hydroxylates cholesterol to produce 25-hydroxycholesterol (25HC). 25HC is an oxysterol with interesting immune roles stemming from its ability to regulate cholesterol biosynthesis. Since astrocytes synthesize cholesterol in the brain and transport it to other cells via apolipoprotein E (ApoE)-containing lipoproteins, we hypothesized that secreted 25HC from microglia may influence lipid metabolism as well as extracellular ApoE derived from astrocytes. Here we show that astrocytes take up externally added 25HC and respond with altered lipid metabolism. 25HC increased extracellular levels of ApoE lipoprotein particles without altering Apoe mRNA expression, due to elevated Abca1 expression via activation of LXRs and decreased ApoE reuptake due to suppressed Ldlr expression via inhibition of SREBP. Astrocytes metabolized 25HC to limit its effects on lipid metabolism via Cyp7b1, an enzyme responsible for 7-hydroxylation of 25HC. Knockdown of Cyp7b1 expression with siRNA prolonged the effects of 25HC on astrocyte lipid metabolism. 25HC also suppressed Srebf2 expression to reduce cholesterol synthesis in astrocytes but did not affect fatty acid levels or the genes required for fatty acid synthesis. We further show that 25HC led to a doubling of the amount of cholesterol esters and their concomitant storage in lipid droplets. Our results suggest an important role for 25HC in regulating astrocyte lipid metabolism.

cell biology↗

Dissecting Mutational Allosteric Effects in Alkaline Phosphatases Associated with Different Hypophosphatasia Phenotypes: An Integrative Computational Investigation

Hypophosphatasia (HPP) is a rare inherited disorder characterized by defective bone mineralization, is highly variable in its clinical phenotype. The disease occurs due to various loss-of-function mutations in ALPL, the gene encoding tissue-nonspecific alkaline phosphatase (TNSALP). In this work, a data-driven and biophysics-based approach for large-scale analysis of ALPL mutations - from nonpathogenic to severe HPPs is proposed. Allosteric molecular signatures of ALPL mutations were determined using an integrated pipeline of synergistic approaches including sequence and energetic-based analysis, structural topology network modeling and elastic network models. Statistical analysis of molecular features computed for the ALPL mutations showed a significant difference between the control and mild and severe HPP phenotypes, and the developed machine learning model suggested that the topological network parameters could serve as is a robust indicator for severe mutations. Molecular dynamics simulations coupled with protein structure network was employed to analyze the effect of single-residue variation on conformational dynamics of TNSALP dimers, and we found that severe disease-associated mutations have a significantly greater effect on allosteric communications. The results of this study suggested that ALPL mutations associated with mild and severe HPPs tend to have different effects on protein stability on local scale and long-range communications caused by network rewiring. By linking disease phenotypes with allosteric molecular signatures, the proposed integrative computational approach elucidates the complex sequence-structure-allostery relationships of ALPL mutations and dissects the role of allosteric effects in the pathogenesis of HPPs. Author SummaryThe understanding of mutational genotype- disease phenotype relationship is a fundamental step for enabling precision medicine. It remains a challenging task to assess the molecular principle of the genotype- phenotype relationship. By focusing on Hypophosphatasia, a rare inherited disorder, as an example, we performed comprehensive analysis of single-amino-acid mutations in the encoded protein of Tissue Nonspecific Alkaline Phosphatase associated in terms of their sequence, structure, and dynamics properties. We further developed a machine learning -based method to classify different disease phenotypes, and the interpretability of the classification model was addressed by the structural-functional analysis of network topological important mutations. Our results highlighted the allosteric propensity of severe mutations, and show the potential allosteric principle of genotype- phenotype relationship.

biophysics↗

Sucrose-dependence of sugar uptake, quorum sensing and virulence of the rice blight pathogen Xanthomonas oryzae pv. oryzae

Withdrawal StatementThe authors have withdrawn their manuscript owing to potential issues with the qRT-PCR data and issues with accessing some of the raw data from one of the authors (FAIR principle requirements). Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

plant biology↗

Spatial modulation of individual behaviors enables collective decision-making during bacterial group migration

Coordination of individuals with diversity often requires sophisticated communications and high-order computational abilities. Microbial populations can exhibit diverse individualistic behaviors and yet can engage in collective migratory patterns with a spatially sorted arrangement of phenotypes following a self-generated attractant gradient. However, its unclear how individual bacteria without complex computational abilities can achieve the consistent group performance and determine their positions in the group while facing spatiotemporally dynamic stimuli. Here, we investigate the statistics of bacterial run-and-tumble trajectories during group migration. We discover that, despite of the constant migrating speed as a group, the individual drift velocity exhibits a spatially dependent structure that decreases from the back to the front of the group. The spatial modulation of individual stochastic behaviors constrains cells in the group, ensuring the coherent population movement with ordered patterns of phenotypes. These results reveal a simple computational principle for emergent collective behaviors from heterogeneous individuals.

microbiology↗

Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis

The plant male germline undergoes DNA methylation reprogramming, which methylates genes de novo and thereby alters gene expression and facilitates meiosis. Why reprogramming is limited to the germline and how specific genes are chosen is unknown. Here, we demonstrate that genic methylation in the male germline, from meiocytes to sperm, is established by germline-specific siRNAs transcribed from transposons with imperfect sequence homology. These siRNAs are synthesized by meiocyte nurse cells (tapetum) via activity of the tapetum-specific chromatin remodeler CLASSY3. Remarkably, tapetal siRNAs govern germline methylation throughout the genome, including the inherited methylation patterns in sperm. Finally, we demonstrate that these nurse cell-derived siRNAs (niRNAs) silence germline transposons, thereby safeguarding genome integrity. Our results reveal that tapetal niRNAs are sufficient to reconstitute germline methylation patterns and drive extensive, functional methylation reprogramming analogous to piRNA-mediated reprogramming in animal germlines. O_FIG O_LINKSMALLFIG WIDTH=186 HEIGHT=200 SRC="FIGDIR/small/428150v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@1e985c0org.highwire.dtl.DTLVardef@4c065corg.highwire.dtl.DTLVardef@1358a5forg.highwire.dtl.DTLVardef@f9c03_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

Multiplexed Imaging Analysis of the Tumor-Immune Microenvironment Reveals Predictors of Outcome in Triple-Negative Breast Cancer

Triple-negative breast cancer, the poorest-prognosis breast cancer subtype, lacks clinically approved biomarkers for patient risk stratification and treatment management. Prior literature has shown that interrogation of the tumor-immune microenvironment may be a promising approach for the discovery of methods to fill these gaps. Recently developed high-dimensional tissue imaging technology, such as multiplexed ion beam imaging, provide spatial context to protein expression in the microenvironment, allowing in-depth characterization of cellular processes. We demonstrate that profiling the functional proteins involved in cell-to-cell interactions in the microenvironment can predict recurrence and overall survival. We highlight the immunological relevance of the immunoregulatory proteins PD-1, PD-L1, IDO, and Lag3 by tying interactions involving them to recurrence and survival. Multivariate analysis reveals that our methods provide additional prognostic information compared to clinical variables. In this work, we present a computational pipeline for the examination of the tumor-immune microenvironment using multiplexed ion-beam imaging that produces interpretable results, and is generalizable to other cancer types.

cancer biology↗

Momilactone B inhibits Arabidopsis growth and development via disruption of ABA and auxin signaling

In competition for limited resources, many plants release allelochemicals to inhibit the growth of neighboring plants. Momilactone B (MB) is a major allelochemical produced by rice (Oryza sativa), however its mode of action is currently unknown. We used Arabidopsis (Arabidopsis thaliana) as a model system to evaluate potential mechanisms underlying the inhibitory effects of MB on seed germination, seedling establishment and root growth through the use of confocal microscopy and the examination of transcriptional responses in MB-treated seedlings. In response to MB treatment, transcript levels for genes encoding several key ABA biosynthetic enzymes and signaling components, including the transcription factor ABA-INSENSITIVE 4 (ABI4), were dramatically increased. Additionally, ABA insensitive 4 (abi4) mutant seedlings exhibited reduced susceptibility to exogenously-provided MB. Although the transcript levels of DELLA genes, which negatively regulate GA signaling, were significantly increased upon MB exposure, exogenous GA application did not reverse the inhibitory effects of MB on Arabidopsis germination and seedling development. Moreover, a reduction in seedling root meristematic activity, associated with reduced expression of auxin biosynthetic genes and efflux transporters, and apparent lowered auxin content, was observed in MB-treated root tips. Exogenous auxin applications partially rescued the inhibitory effects of MB observed in root growth. Our results indicate that MB suppresses Arabidopsis seed germination and root growth primarily via disruption of ABA and auxin signaling. These findings underscore the crucial roles played by phytohormones in mediating responses to allelochemical exposure. One-sentence summaryMomilactone B, the key allelochemical of rice, inhibits Arabidopsis growth and development via disruption of ABA and auxin signaling, suggesting the crucial roles of phytohormones in plant allelopathy

plant biology↗

Single cell transcriptome of CD8+ T cells in multiple cancers reveals comprehensive exhaustion associated mechanisms

T cell exhaustion is one of the main reasons of tumor immune escape. Using single cell transcriptome data of CD8+ T cells in multiple cancers, we identified different cell types, in which Pre_exhaust and exhausted T cells participated in negative regulation of immune system process. By analyzing the co-expression network patterns and differentially expressed genes of Pre_exhaust, exhausted and effector T cells, we identified 35 genes related to T cell exhaustion, which high GSVA scores were associated with significantly poor prognosis in various cancers. In the differentially expressed genes, RGS1 showed the greatest fold change in Pre_exhaust and exhausted cells of three cancers compared with effector T cells, and high expression of RGS1 was also associated with poor prognosis in various cancers. Additionally, RGS1 protein was upregulated significantly in tumor tissues in the immunohistochemistry verification. Furthermore, RGS1 displayed positive correlation with the 35 genes, especially highly correlated with PDCD1, CTLA4, HAVCR2 and TNFRSF9 in CD8+ T cells and cancer tissues, indicating important roles of RGS1 in CD8+ T cell exhaustion. Considering the GTP-hydrolysis activity of RGS1 and significantly high mRNA and protein expression in cancer tissues, we speculated that RGS1 potentially mediate the T cell retention to lead to the persistent antigen stimulation, resulting in T cell exhaustion. In conclusion, our findings suggest that RGS1 is a new marker and promoting factor for CD8+ T cell exhaustion, and provide theoretical basis for research and immunotherapy of exhausted cells.

cancer biology↗

Lymph node follicle formation and vaccination responses reconstituted in vitro in a human Organ Chip

Lymphoid follicles (LFs) are responsible for generation of adaptive immune responses in secondary lymphoid organs and form ectopically during chronic inflammation. A human model of LF formation would provide a tool to understand LF development and an alternative to non-human primate models for preclinical evaluation of vaccines. Here, we show that primary human blood B- and T-lymphocytes autonomously assemble into ectopic LFs when cultured in a three-dimensional (3D) extracellular matrix gel within an organ-on-a-chip microfluidic device. Dynamic fluid flow is required for LF formation and prevention of lymphocyte autoactivation. These germinal center-like LFs contain B cells expressing Activation-Induced Cytidine Deaminase and exhibit plasma cell (PC) differentiation upon activation. To explore their utility for vaccine testing, autologous monocyte-derived dendritic cells were integrated into LF Chips. The human LF chips demonstrated improved antibody responses to split virion influenza vaccination compared to 2D cultures, which were enhanced by addition of a squalene-in-water emulsion adjuvant, and this was accompanied by increases in LF size and number. When inoculated with commercial influenza vaccine, PC formation and production of anti-hemagglutinin IgG were observed, as well as secretion of cytokines similar to those observed in vaccinated humans over clinically relevant timescales.

immunology↗

Overexpressing CsGH3.1 and CsGH3.1L reduces susceptibility to Xanthomonas citri subsp. citri by repressing auxin signaling in citrus (Citrus sinensis Osbeck)

The auxin early response gene Gretchen Hagen3 (GH3) plays dual roles in plant development and responses to biotic or abiotic stress. It functions in regulating hormone homeostasis through the conjugation of free auxin to amino acids. In citrus, GH3.1 and GH3.1L play important roles in responding to Xanthomonas citri subsp. citri (Xcc). Here, in Wanjingcheng orange (C. sinensis Osbeck), the overexpression of CsGH3.1 and CsGH3.1L caused increased branching and drooping dwarfism, as well as smaller, thinner and upward curling leaves compared with wild-type. Hormone determinations showed that overexpressing CsGH3.1 and CsGH3.1L decreased the free auxin contents and accelerated the Xcc-induced decline of free auxin levels in transgenic plants. A resistance analysis showed that transgenic plants had reduced susceptibility to citrus canker, and a transcriptomic analysis revealed that hormone signal transduction-related pathways were significantly affected by the overexpression of CsGH3.1 and CsGH3.1L. A MapMan analysis further showed that overexpressing either of these two genes significantly downregulated the expression levels of the annotated auxin/indole-3-acetic acid family genes and significantly upregulated biotic stress-related functions and pathways. Salicylic acid, jasmonic acid, abscisic acid, ethylene and zeatin levels in transgenic plants displayed obvious changes compared with wild-type. In particular, the salicylic acid and ethylene levels involved in plant resistance responses markedly increased in transgenic plants. Thus, the overexpression of CsGH3.1 and CsGH3.1L reduces plant susceptibility to citrus canker by repressing auxin signaling and enhancing defense responses. Our study demonstrates auxin homeostasis potential in engineering disease resistance in citrus.

plant biology↗

Identification of type 2 diabetes loci in 433,540 East Asian individuals

Meta-analyses of genome-wide association studies (GWAS) have identified >240 loci associated with type 2 diabetes (T2D), however most loci have been identified in analyses of European-ancestry individuals. To examine T2D risk in East Asian individuals, we meta-analyzed GWAS data in 77,418 cases and 356,122 controls. In the main analysis, we identified 298 distinct association signals at 178 loci, and across T2D association models with and without consideration of body mass index and sex, we identified 56 loci newly implicated in T2D predisposition. Common variants associated with T2D in both East Asian and European populations exhibited strongly correlated effect sizes. New associations include signals in/near GDAP1, PTF1A, SIX3, ALDH2, a microRNA cluster, and genes that affect muscle and adipose differentiation. At another locus, eQTLs at two overlapping T2D signals act through two genes, NKX6-3 and ANK1, in different tissues. Association studies in diverse populations identify additional loci and elucidate disease genes, biology, and pathways.\n\nType 2 diabetes (T2D) is a common metabolic disease primarily caused by insufficient insulin production and/or secretion by the pancreatic {beta} cells and insulin resistance in peripheral tissues1. Most genetic loci associated with T2D have been identified in populations of European (EUR) ancestry, including a recent meta-analysis of genome-wide association studies (GWAS) of nearly 900,000 individuals of European ancestry that identified >240 loci influencing the risk of T2D2. Differences in allele frequency between ancestries affect the power to detect associations within a population, particularly among variants rare or monomorphic in one population but more frequent in another3,4. Although smaller than studies in European populations, a recent T2D meta-analysis in almost 200,000 Japanese individuals identified 28 additional loci4. The relative contributions of different pathways to the pathophysiology of T2D may also differ between ancestry groups. For example, in East Asian (EAS) populations, T2D prevalence is greater than in European populations among people of similar body mass index (BMI) or waist circumference5. We performed the largest meta-analysis of East Asian individuals to identify new genetic associations and provide insight into T2D pathogenesis.

genetics↗