Biology subjects

Yan, L.

Publications and source records attributed to Yan, L..

At least 109 records · Page 6Linked to original sources

bioRxiv2020

Genomic Architecture of Cells in Tissues (GeACT): Study of Human Mid-gestation Fetus

By circumventing cellular heterogeneity, single cell omics have now been widely utilized for cell typing in human tissues, culminating with the undertaking of human cell atlas aimed at characterizing all human cell types. However, more important are the probing of gene regulatory networks, underlying chromatin architecture and critical transcription factors for each cell type. Here we report the Genomic Architecture of Cells in Tissues (GeACT), a comprehensive genomic data base that collectively address the above needs with the goal of understanding the functional genome in action. GeACT was made possible by our novel single-cell RNA-seq (MALBAC-DT) and ATAC-seq (METATAC) methods of high detectability and precision. We exemplified GeACT by first studying representative organs in human mid-gestation fetus. In particular, correlated gene modules (CGMs) are observed and found to be cell-type-dependent. We linked gene expression profiles to the underlying chromatin states, and found the key transcription factors for representative CGMs. HighlightsO_LIGenomic Architecture of Cells in Tissues (GeACT) data for human mid-gestation fetus C_LIO_LIDetermining correlated gene modules (CGMs) in different cell types by MALBAC-DT C_LIO_LIMeasuring chromatin open regions in single cells with high detectability by METATAC C_LIO_LIIntegrating transcriptomics and chromatin accessibility to reveal key TFs for a CGM C_LI

genomics↗

bioRxiv2020

A Cryptic Site of Vulnerability on the Receptor Binding Domain of the SARS-CoV-2 Spike Glycoprotein

SARS-CoV-2 is a zoonotic virus that has caused a pandemic of severe respiratory disease--COVID-19-- within several months of its initial identification. Comparable to the first SARS-CoV, this novel coronaviruss surface Spike (S) glycoprotein mediates cell entry via the human ACE-2 receptor, and, thus, is the principal target for the development of vaccines and immunotherapeutics. Molecular information on the SARS-CoV-2 S glycoprotein remains limited. Here we report the crystal structure of the SARS-CoV-2 S receptor-binding-domain (RBD) at a the highest resolution to date, of 1.95 [A]. We identified a set of SARS-reactive monoclonal antibodies with cross-reactivity to SARS-CoV-2 RBD and other betacoronavirus S glycoproteins. One of these antibodies, CR3022, was previously shown to synergize with antibodies that target the ACE-2 binding site on the SARS-CoV RBD and reduce viral escape capacity. We determined the structure of CR3022, in complex with the SARS-CoV-2 RBD, and defined a broadly reactive epitope that is highly conserved across betacoronaviruses. This epitope is inaccessible in the "closed" prefusion S structure, but is accessible in "open" conformations. This first-ever resolution of a human antibody in complex with SARS-CoV-2 and the broad reactivity of this set of antibodies to a conserved betacoronavirus epitope will allow antigenic assessment of vaccine candidates, and provide a framework for accelerated vaccine, immunotherapeutic and diagnostic strategies against SARS-CoV-2 and related betacoronaviruses. HIGHLIGHTSHigh resolution structure of the SARS-CoV-2 Receptor-Binding-Domain (RBD). Recognition of the SARS-CoV-2 RBD by SARS-CoV antibodies. Structure of the SARS-COV-2 RBD in complex with antibody CR3022. Identification of a cryptic site of vulnerability on the SARS-CoV-2 Spike.

immunology↗

bioRxiv2020

Structure of RNA-dependent RNA polymerase from 2019-nCoV, a major antiviral drug target

A novel coronavirus (2019-nCoV) outbreak has caused a global pandemic resulting in tens of thousands of infections and thousands of deaths worldwide. The RNA-dependent RNA polymerase (RdRp, also named nsp12), which catalyzes the synthesis of viral RNA, is a key component of coronaviral replication/transcription machinery and appears to be a primary target for the antiviral drug, remdesivir. Here we report the cryo-EM structure of 2019-nCoV full-length nsp12 in complex with cofactors nsp7 and nsp8 at a resolution of 2.9-[A]. Additional to the conserved architecture of the polymerase core of the viral polymerase family and a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain featured in coronaviral RdRp, nsp12 possesses a newly identified {beta}-hairpin domain at its N-terminal. Key residues for viral replication and transcription are observed. A comparative analysis to show how remdesivir binds to this polymerase is also provided. This structure provides insight into the central component of coronaviral replication/transcription machinery and sheds light on the design of new antiviral therapeutics targeting viral RdRp. One Sentence SummaryStructure of 2019-nCov RNA polymerase.

biochemistry↗

bioRxiv2020

The Pathogenicity of 2019 Novel Coronavirus in hACE2 Transgenic Mice

Severe acute respiratory syndrome CoV-2 (SARS-CoV-2) caused the Corona Virus Disease 2019 (COVID-19) cases in China has become a public health emergency of international concern (PHEIC). Based on angiotensin converting enzyme 2 (ACE2) as cell entry receptor of SARS-CoV, we used the hACE2 transgenic mice infected with SARS-CoV-2 to study the pathogenicity of the virus. Weight loss and virus replication in lung were observed in hACE2 mice infected with SARS-CoV-2. The typical histopathology was interstitial pneumonia with infiltration of significant lymphocytes and monocytes in alveolar interstitium, and accumulation of macrophages in alveolar cavities. Viral antigens were observed in the bronchial epithelial cells, alveolar macrophages and alveolar epithelia. The phenomenon was not found in wild type mice with SARS-CoV-2 infection. The pathogenicity of SARS-CoV-2 in hACE2 mice was clarified and the Kochs postulates were fulfilled as well, and the mouse model may facilitate the development of therapeutics and vaccines against SARS-CoV-2.

microbiology↗

bioRxiv2020

Single cell atlas of trisomy 21 cerebral cortex

Down syndrome (DS) is one of the most common human birth defects caused by trisomy 21 (T21), leading to a variety of cognitive impairments. The cellular composition of human brain has been explored using single cell RNA sequencing in both physiological and pathological conditions. However, the cellular heterogeneity of human brain with chromosome aneuploidy is largely unknown. Here, we profiled the transcriptome of 36046 cells in cerebral cortex of T21 human fetus, covering frontal lobe, parietal lobe, occipital lobe and temporal lobe. Intriguingly, we detected several genes positively associated with neurons maturation was dysregulated in T21 frontal cortex (HIC2, POU2F2, ZGLP1 and FOXK1). To share, explore and utilized the data resources of T21 cerebral cortex, we developed a comprehensive platform named T21atlas, composing of two functional modules (T21cluster and T21talk). Overall, our study provides, as far as we know, the first single cell atlas for T21 cerebral cortex, which could promote our understanding of the molecular mechanism of DS at an unprecedented resolution and could potentially facilitate the development of novel clinical therapeutics against T21.

neuroscience↗

bioRxiv2019

Boron alters carboxyl group binding capacity and Al transport pathway to relieve Al toxicity

Boron (B) is indispensable for plant growth and has been reported in the mitigation of aluminum (Al) toxicity in different plants. This study unraveled the efficacy of B in reducing the toxicity of Al to trifoliate orange seedlings in a hydroponic experiment. In the current study, B supply had a positive effect on root length and plant growth-related parameters, and attenuated Al-induced inhibition of plasma membrane H+-ATPase activity. The results of XPS and SEM-EDS revealed that B reduces the Al accumulation in root cell wall (CW), especially acts on pectin fractions (alkali-soluble pectin), accompanied by suppressing the pectin synthesis, inhibiting pectin methylesterase (PME) activity and PME expression. Furthermore, B application inhibits NRAT1 expression while increases ALS1 expression, which are responsible for restraining Al transport from external cells to the cytoplasm and accelerating Al divert to vacuoles, and the results can be further demonstrated by TEM-EDS analysis. Taken together, our results indicated that B mainly promotes the efflux of H+ by regulating the plasma membrane H+-ATPase activity, futhur reduce the demethylation of pectin to weaken Al binding ability to carboxyl. More importantly, B alleviated some of the toxic effects of Al by decreasing the deposition of Al in cytoplasm and compartmentalizes Al into vacuoles. One-sentence summaryBoron can reduce the binding amount of carboxyl group to Al in pectin, decreasing the deposition of Al in cytoplasm and compartmentalizes Al into vacuoles, thereby reduce the toxicity of Al to plants..

physiology↗

bioRxiv2019

Cyniclomyces guttulatus is an opportunistic pathogen in rabbits with coccidiosis

Cyniclomyces guttulatus is a common inhabitant of the gastrointestinal tract in rabbits, and large numbers are often present in feces of diarrheic rabbits. However, its relation with rabbit diarrhea has not been clearly identified. We isolated a C. guttulatus Zhejiang strain from a rabbit with severe diarrhea and optimized the culture conditions in YPG medium. The sequenced 18S and 26S ribosomal DNA fragments were 1559bp and 632bp, respectively, and showed 99.8% homology with the 18S ribosomal sequence of the NRRL Y-17561 isolate from the dog and 100% homology with the 26S ribosomal sequence of the DPA-CGR1 and CGDPA-GP1 isolates from the rabbit and guinea pig. Our isolate was not pathogenic to healthy SPF rabbits. Instead, rabbits inoculated with the yeast had a slightly better body weight gain and higher food intake. Rabbits co-inoculated with C. guttulatus and the coccidian, E. intestinalis developed more severe coccidiosis as shown by clinical signs, and decreased body weight gain, diarrhea and death, associated with significantly higher fecal output of C. guttulatus vegetative cells but lower coccidian oocysts output than the rabbits inoculated with C. guttulatus or E. intestinalis alone. We also surveyed the prevalence of C. guttulatus in rabbits and found a positive rate of 83% in Zhejiang province. Our results indicate that C. guttulatus alone is not pathogenic to healthy rabbits, but could become an opportunistic pathogen when the digestive tract is damaged by other pathogens such as coccidia. Author summaryCyniclomyces guttulatus, a commensal yeast in rabbit gastrointestinal tract, is very commonly seen in diarrhea cases. However, it is unclear whether it causes or is a co-cause of diarrhea with other pathogens. Here, a C. guttulatus Zhejiang strain was firstly isolated from a rabbit with severe diarrhea and the culture conditions in YPG medium were optimized. Then, it was identified in morphology and molecular. It was agreed with the previous description in morphology and showed a closer phylogenetic relationship with other strains originated from herbivores than those from the carnivore. Finally, the C. guttulatus Zhejiang strain was inoculated to SPF rabbits singly or co-inoculated with Eimeria intestinalis. All of the results in animal assays show C. guttulatus alone is not pathogenic but seems a probiotic microorganism in rabbits. However, it could become an opportunistic pathogen when the digestive tract is damaged by other pathogens such as coccidia.

microbiology↗

bioRxiv2019

Single-cell multiomics sequencing reveals the functional regulatory landscape of early embryos

Extensive epigenetic reprogramming occurs during preimplantation embryo development and is accompanied by zygotic genome activation (ZGA) and first cell fate specification. Recent studies using single-cell epigenome sequencing techniques have provided global views of the dynamics of different epigenetic layers during this period. However, it remains largely unclear how the drastic epigenetic reprogramming contributes to transcriptional regulatory network. Here, we developed a single-cell multiomics sequencing technology (scNOMeRe-seq) that enables profiling of genome-wide chromatin accessibility, DNA methylation and RNA expression in the same individual cell with improved performance compared to that of earlier techniques. We applied this method to analyze the global dynamics of different molecular layers and their associations in mouse preimplantation embryos. We found that global DNA methylation remodeling facilitates the reconstruction of genetic lineages in early embryos and revealed that the gradual increases in heterogeneity among blastomeres are driven by asymmetric cleavage. Allele-specific DNA methylation pattern is maintained throughout preimplantation development and is accompanied by allele-specific associations between DNA methylation and gene expression in the gene body that are inherited from oocytes and sperm. Through integrated analyses of the collective dynamics between gene expression and chromatin accessibility, we constructed a ZGA-associated regulatory network and revealed coordination among multiple epigenetic layers, transcription factors (TFs) and repeat elements that instruct the proper ZGA process. Moreover, we found that inner cell mass (ICM)/trophectoderm (TE) lineage-associated cis-regulatory elements are stepwise activated in blastomeres during post-ZGA embryo stages. TE lineage-specific TFs play dual roles in promoting the TE program while repressing the ICM program, thereby separating the TE lineage from the ICM lineage. Taken together, our findings not only depict the first single-cell triple-omics map of chromatin accessibility, DNA methylation and RNA expression during mouse preimplantation development but also enhance the fundamental understanding of epigenetic regulation in early embryos.

developmental biology↗

bioRxiv2019

Genome-wide association analyses identify variants in IRF4 associated with Acute Myeloid Leukemia and Myelodysplastic Syndrome susceptibility

The role of common genetic variation in susceptibility to acute myeloid leukemia (AML), and myelodysplastic syndrome (MDS), a group of rare clonal hematologic disorders characterized by dysplastic hematopoiesis and high mortality, remains unclear. We performed AML and MDS genome-wide association studies (GWAS) in the DISCOVeRY-BMT cohorts (2309 cases and 2814 controls). Association analysis based on subsets (ASSET) was used to conduct a summary statistics SNP-based analysis of MDS and AML subtypes. For each AML and MDS case and control we used PrediXcan to estimate the component of gene expression determined by their genetic profile and correlate this imputed gene expression level with risk of developing disease in a transcriptome-wide association study (TWAS). ASSET identified an increased risk for de novo AML and MDS (OR=1.38, 95% CI, 1.26-1.51, Pmeta=2.8x10-12) in patients carrying the T allele at rs12203592 in Interferon Regulatory Factor 4 (IRF4), a transcription factor which regulates myeloid and lymphoid hematopoietic differentiation. Our TWAS analyses showed increased IRF4 gene expression is associated with increased risk of de novo AML and MDS (OR=3.90, 95% CI, 2.36-6.44, Pmeta =1.0x10-7). The identification of IRF4 by both GWAS and TWAS contributes valuable insight on the role of genetic variation in AML and MDS susceptibility.

genomics↗

bioRxiv2019

Development of equations for converting random-zero to automated oscillometric blood pressure values

ObjectiveThis study aimed to collect data to compare blood pressure values between random-zero sphygmomanometers and automated oscillometric devices and generate equations to convert blood pressure values from one device to the other.\n\nMethodsOmron HEM-907, a widely used automated oscillometric device in many epidemiologic surveys and cohort studies, was compared here with random-zero sphygmomanometers. Two hundred and one participants aged 40-79 years (37% men) were enrolled and randomly assigned to one of two groups with blood pressure measurement first taken by automated oscillometric devices or by random-zero sphygmomanometers. The study design enabled comparisons of blood pressure values between random-zero sphygmomanometers and two modes of this automated oscillometric device - automated and manual, and assessment of effects of measurement order on blood pressure values.\n\nResultsAmong all participants, mean blood pressure levels were lowest when measured with random-zero sphygmomanometers compared with both modes of automated oscillometric devices. Several variables, including age and gender, were found to contribute to the blood pressure differences between random-zero sphygmomanometers and automated oscillometric devices. Equations were developed using multiple linear regression after taking those variables into account to convert blood pressure values by random-zero sphygmomanometers to automated oscillometric devices.\n\nConclusionEquations developed in this study could be used to compare blood pressure values between epidemiologic and clinical studies or identify shift of blood pressure distribution over time using different devices for blood pressure measurements.

epidemiology↗

bioRxiv2019

Mechanics of allostery: contrasting the induced fit and population shift scenarios

In allosteric proteins, binding a ligand can affect function at a distant location, for example by changing the binding affinity of a substrate at the active site. The induced fit and population shift models, which differ by the assumed number of stable configurations, explain such cooperative binding from a thermodynamic viewpoint. Yet, understanding what mechanical principles constrain these models remains a challenge. Here we provide an empirical study on 34 proteins supporting the idea that allosteric conformational change generally occurs along a soft elastic mode presenting extended regions of high shear. We argue, based on a detailed analysis of how the energy profile along such a mode depends on binding, that in the induced fit scenario there is an optimal stiffness [Formula] for cooperative binding, where N is the number of residues involved in the allosteric response. We find that the population shift scenario is more robust to mutation affecting stiffness, as binding becomes more and more cooperative with stiffness up to the same characteristic value [Formula], beyond which cooperativity saturates instead of decaying. We confirm numerically these findings in a non-linear mechanical model. Dynamical considerations suggest that a stiffness of order [Formula] is favorable in that scenario as well, supporting that for proper function proteins must evolve a functional elastic mode that is softer as their size increases. In consistency with this view, we find a significant anticorrelation between the stiffness of the allosteric response and protein size in our data set.

biophysics↗

bioRxiv2019

Phanerochaete chrysosporium strain B-22, a parasitic fungus infecting Meloidogyne incognita

We characterized the parasitism by strain B-22 of Phanerochaete chrysosporium on the eggs, second stage juveniles (J2), and adult females of the root-knot nematode (Meloidogyne Incognita). Strain B-22 had a strong lethal effect against M. incognita J2. The highest corrected mortality was 71.9% at 3 x 108 conidia mL-1. The estimated LC50 value was 0.96 x 108 conidia mL-1. Strain B-22 parasitized M. incognita eggs 2 days after treatment, causing the depression and dissolution of egg shells. The fungal spores parasitized J2 by gathering in the body wall, germinating to develop hyphae, and crossing the juvenile cuticle to dissolve it, thereby causing the shrinkage and deformation of the juvenile body wall. The spores and hyphae also attacked adult females, causing the shrinkage and dissolution of their bodies and leakage of contents in 5 days. Results of greenhouse experiments showed that different concentrations of P. chrysosporium effectively controlled different life stages of M. incognita and root knot symptoms in tomato plants. Moreover, the control efficacy increased with increasing conidial concentration; the best results were achieved with 3 x 108 cfu mL-1. In the roots, the highest inhibition rate was 84.61% for adult females, 78.91% for juveniles, 84.25% for the egg mass, and 79.48% for the gall index. The highest juvenile inhibition rate was 89.18% in the soil. Meanwhile, strain B-22 improved the plant growth. Thus, P. chrysosporium strain B-22 is safe for tomato plants while effectively parasitizing M. incognita, making it a promising biocontrol agent against M. incognita.

pathology↗

bioRxiv2019

Effectiveness of Genomic Selection by Response to Selection for Winter Wheat Variety Improvement

The genomic revolution opened up the possibility for predicting un-tested phenotypes in schemes commonly referred as genomic selection (GS). Considering the practicality of applying GS in the line development stage of a hard red winter (HRW) wheat variety development program (VDP), effectiveness of GS was evaluated by prediction accuracy, as well as by the response to selection across field seasons that demonstrated challenges for crop improvement under significant climate variability. Important breeding targets for HRW wheat improvement in the southern Great Plains of USA, including Grain Yield, Kernel Weight, Wheat Protein content, and Sodium Dodecyl Sulfate (SDS) Sedimentation Volume as a rapid test for predicting bread-making quality, were used to estimate GSs effectiveness across harvest years from 2014 (drought) to 2016 (normal). In general, nonparametric algorithms RKHS and RF produced higher accuracies in both same-year/environment cross validations and cross-year/environment predictions, for the purpose of line selection in this bi-parental doubled haploid (DH) population. Further, the stability of GS performance was greatest for SDS Sedimentation Volume but least for Wheat Protein content. To ensure long-term genetic gain, our study on selection response suggested that across this sample of environmental variability, and though there are cases where phenotypic selection (PS) might be still preferential, training conducted under drought stress or in suboptimal conditions could still provide an encouraging prediction outcome, when selection decisions were made in normal conditions. However, it is not advisable to use training information collected from a normal field season to predict trait performance under drought conditions. Further, the superiority of response to selection was most evident if the training population can be optimized. Core IdeasO_LIPrediction performance for winter wheat grain yield and end-use quality traits. C_LIO_LIPrediction accuracy evaluated by cross validations significantly overestimated. C_LIO_LINon-parametric algorithms outperform, when considering cross-year predictions. C_LIO_LIStrategically designing training population improves response to selection. C_LIO_LIResponse to selection varied across growing seasons/environments. C_LI

plant biology↗

bioRxiv2018

Somatic LINE-1 retrotransposition in cortical neurons of Rett patients and healthy individuals

Mounting evidence supports that LINE-1 (L1) retrotransposition can occur postzygotically in healthy and diseased human tissues, contributing to genomic mosaicism in the brain and other somatic tissues of an individual. However, the genomic distribution of somatic L1Hs (Human-specific LINE-1) insertions and their potential impact on carrier cells remain unclear. Here, using a PCR-based targeted bulk sequencing approach, we profiled 9,181 somatic insertions from 20 postmortem tissues from five Rett patients and their matched healthy controls. We identified and validated somatic L1Hs insertions in both cortical neurons and non-brain tissues. In Rett patients, somatic insertions were significantly depleted in exons--mainly contributed by long genes--than healthy controls, implying that cells carrying MECP2 mutations might be defenseless against a second exonic L1Hs insertion. We observed a significant increase of somatic L1Hs insertions in the brain compared with non-brain tissues from the same individual. Compared to germline insertions, somatic insertions were less sense-depleted to transcripts, indicating that they underwent weaker selective pressure on the orientation of insertion. Our observations demonstrate that somatic L1Hs insertions contribute to genomic diversity and MECP2 dysfunction alters their genomic patterns in Rett patients. Author SummaryHuman-specific LINE-1 (L1Hs) is the most active autonomous retrotransposon family in the human genome. Mounting evidence supports that L1Hs retrotransposition occurs postzygotically in the human brain cells, contributing to neuronal genomic diversity, but the extent of L1Hs-driven mosaicism in the brain is debated. In this study, we profiled genome-wide L1Hs insertions among 20 postmortem tissues from Rett patients and matched controls. We identified and validated somatic L1Hs insertions in both cortical neurons and non-brain tissues, with a higher jumping activity in the brain. We further found that MECP2 dysfunction might alter the genomic pattern of somatic L1Hs in Rett patients.

genomics↗

bioRxiv2018

Enhancer Reprogramming Confers Dependence on Glycolysis and IGF signaling in KMT2D Mutant Melanoma

Epigenetic modifiers have emerged as important regulators of tumor progression. We identified histone methyltransferase KMT2D as a potent tumor-suppressor through an in vivo epigenome-focused pooled RNAi screen in melanoma. KMT2D harbors frequent somatic point mutations in multiple tumor types. How these events contribute to tumorigenesis and whether they impart therapeutic vulnerability are poorly understood. To address these questions, we generated a genetically engineered mouse model of melanoma based on conditional and melanocyte-specific deletion of KMT2D. We demonstrate KMT2D as a bona fide tumor suppressor which cooperates with activated BRAF. KMT2D-deficient tumors showed substantial reprogramming of key metabolic pathways including glycolysis. Glycolysis enzymes, intermediate metabolites and glucose consumption rate were aberrantly upregulated in KMT2D mutant cells. The pharmacological inhibition of glycolysis reduced proliferation and tumorigenesis preferentially in KMT2D mutant cells. Mechanistically, KMT2D loss caused drastic reduction of H3K4me1-marked active enhancer states. Loss of distal enhancer and subsequent reduction in expression of IGFBP5 activated IGF1R-AKT to increase glycolysis in KMT2D-deficient cells. We conclude that KMT2D loss promotes tumorigenesis by facilitating increased usage of glycolysis pathway for enhanced biomass needs via enhancer reprogramming. Our data imply that inhibition of glycolysis or IGFR pathway could be a potential therapeutic strategy in KMT2D mutant tumors.

cancer biology↗

bioRxiv2018

Co-Expression Network-based Analysis associated with potato initial resistance

RNA sequencing (RNA-seq) providing genome-wide expression datasets has been successfully used to study gene expression patterns and regulation mechanism among multiple samples. Gene co-expression networks (GCNs) studies within or across species showed that coordinated genes in expression patterns are often functionally related. For potatoes, a large amount of publicly available transcriptome datasets have been generated but an optimal GCN detecting expression patterns in different genotypes, tissues and environmental conditions, is lacking. We constructed a potato GCN using 16 published RNA-Seq datasets covering 11 cultivars from native habitat worldwide. The correlations of gene expression were assessed pair-wisely and biologically meaningful gene modules which are highly connected in GCN were identified. One of the primitively native-farmer-selected cultivars in the Andes, ssp.Andigena, had relative far distance in gene expression patterns with other modern varieties. GCN in further enriched 134 highly and specifically co-expressed genes in ssp.Andigena associated with potato disease and stress resistance, which underlying the dramatic shift in evolutionary pressures during potato artificial domestication. In total, the network was consisted of into 14 gene models that involves in a variety of plant processes, which sheds light on how gene modules organized intra- and inter-varieties in the context of evolutionary divergence and provides a basis of information resource for potato gene functional studies.

plant biology↗

bioRxiv2018

Differential responses of antioxidants and dehydrin expression in two switchgrass (Panicum virgatum) cultivars contrasting in drought tolerance

Drought stress is a major limiting factor for plant growth and development in many regions of the world. This study was designed to investigate antioxidant metabolism and dehydrin expression responses to drought stress in two switchgrass cultivars (drought tolerant Alamo, and drought sensitive Dacotah) contrasting in drought tolerance. The plants were subjected to well-watered [100% evapotranspiration (ET)] or drought stress (30%-50% ET) conditions for up to 24 d in growth chambers. Drought stress decreased leaf relative water content (RWC), increased leaf electrolyte leakage (EL), leaf malondialdehyde (MDA) content in two cultivars, but Alamo exhibited higher leaf RWC level, lower leaf EL and MDA when compared to Dacotah at 24 d of drought treatment. Drought stress also increased superoxide dismutase (SOD), catalase (CAT) and ascorbate peroxidase (APX) activities in two cultivars, Alamo had relatively higher SOD, CAT and APX activities and greater abundance of SOD and APX isozymes than Dacotah at 24 d of drought treatment. Alamo had higher abundance of 55 KDa and 18 KDa dehydrin accumulation than Dacotah under drought treatment. Relative genes expression level of PvCAT1, PvAPX2, PvERD and PvPIP1;5 in Alamo were significantly higher than Dacotah at 24 d of drought treatment. These results suggest that increase in antioxidant enzymes and accumulation of dehydrin were highly related with switchgrass drought tolerance. Antioxidant enzyme activity, isozyme expression and dehydrin abundance could provide a useful screening tool to identify relative drought tolerance in switchgrass cultivars.

plant biology↗

bioRxiv2018

Phylodynamics of rapidly adapting pathogens: extinction and speciation of a Red Queen

Rapidly evolving pathogens like influenza viruses can persist by accumulating antigenic novelty fast enough to evade the adaptive immunity of the host population, yet without continuous accumulation of genetic diversity. This dynamical state is often compared to the Red Queen evolving as fast as it can just to maintain its foothold in the host population: Accumulation of antigenic novelty is balanced by the build-up of host immunity. Such Red Queen States (RQS) of continuous adaptation in large rapidly mutating populations are well understood in terms of Traveling Wave (TW) theories of population genetics. Here we shall make explicit the mapping of the established Multi-strain Susceptible-Infected-Recovered (SIR) model onto the TW theory and demonstrate that a pathogen can persist in RQS if cross-immunity is long-ranged and its population size is large populations allowing for rapid adaptation. We then investigate the stability of this state focusing on the rate of extinction and the rate of \"speciation\" defined as antigenic divergence of viral strains beyond the range of cross-inhibition. RQS states are transient, but in a certain range of evolutionary parameters can exist for the time long compared to the typical time to the most recent common ancestor (TMRCA). In this range the steady TW is unstable and the antigenic advance of the lead strains relative to the typical co-circulating viruses tends to oscillate. This results in large fluctuations in prevalence that facilitate extinction. We shall demonstrate that the rate of TW fission into antigenically uncoupled viral populations is related to fluctuations of TMRCA and construct a \"phase diagram\" identifying different regimes of viral phylodynamics as a function of evolutionary parameters.

evolutionary biology↗