scholarly journals Early transcriptome analysis of the brown streak virus–cassava pathosystem provides molecular insights into virus susceptibility and resistance

2017 ◽  
Author(s):  
Ravi B. Anjanappa ◽  
Devang Mehta ◽  
Michal J. Okoniewski ◽  
Alicja Szabelska ◽  
Wilhelm Gruissem ◽  
...  
Keyword(s):  
Time Course ◽  
Meta Analysis ◽  
Sub Saharan Africa ◽  
Resistant Variety ◽  
Streak Virus ◽  
Rna Seq ◽  
Transcriptional Responses ◽  
Callose Deposition ◽  
Cassava Varieties ◽  
Brown Streak

SUMMARYCassava brown streak viruses (CBSVs) are responsible for significant cassava yield losses in eastern sub–Saharan Africa. In the present work, we inoculated CBSV–susceptible and –resistant cassava varieties with a mixed infection of CBSVs using top-cleft grafting. Virus titres in grafted scions were monitored in a time course experiment in both varieties. We performed RNA-seq of the two cassava varieties at the earliest time-point of full infection in the susceptible scions. Genes encoding proteins in RNA silencing and salicylic acid pathways were regulated in the susceptible cassava variety but transcriptional changes were limited in the resistant variety. After infection, genes related to callose deposition at plasmodesmata were regulated and callose deposition was significantly reduced in the susceptible cassava variety. We also show that β–1,3–glucanase enzymatic activity is differentially regulated in the susceptible and resistant varieties. The differences in transcriptional responses to CBSV infection indicate that resistance involves callose deposition at plasmodesmata but does not trigger typical anti-viral defence responses. A meta-analysis of the current RNA-seq dataset and selected, previously reported, host–potyvirus and virus-cassava RNA-seq datasets revealed comparable host responses across pathosystems only at similar time points after infection or infection of a common host.HIGHLIGHTOur results suggest that resistance to CBSV in cassava involves callose deposition at the plasmodesmata and our meta-analysis of multiple virus-crop RNA-seq studies suggests that conserved responses across different host-virus systems are limited and depend greatly on time after infection.

scholarly journals PAL1 gene of the phenylpropanoid pathway increases resistance to the Cassava brown streak virus in cassava

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Siji Kavil ◽  
Gerald Otti ◽  
Sophie Bouvaine ◽  
Andrew Armitage ◽  
Midatharahally N. Maruthi
Keyword(s):  
Phenylpropanoid Pathway ◽  
Streak Virus ◽  
Rna Seq ◽  
Cassava Brown Streak Virus ◽  
Cassava Brown Streak Disease ◽  
Chalcone Synthase Genes ◽  
Increased Susceptibility ◽  
Cassava Varieties ◽  
Brown Streak

Abstract Background The phenylalanine ammonia lyase genes play crucial role in plant response to biotic and abiotic stresses. In this study, we characterized the role of PAL genes in increasing resistance to the Cassava brown streak virus that causes the economically important cassava brown streak disease (CBSD) on cassava in Africa. Methods The whole transcriptomes of eight cassava varieties differing in resistance to CBSD were obtained at 1, 5 and 8 weeks after CBSV infection. Results Analysis of RNA-Seq data identified the overexpression of PAL1, PAL2, cinnamic acid and two chalcone synthase genes in CBSD-resistant cassava varieties, which was subsequently confirmed by RT-qPCR. The exogenous application of Acibenzolar-S-Methyl induced PAL1 gene expression to enhance resistance in the susceptible var. Kalawe. In contrast, the silencing of PAL1 by RNA interference led to increased susceptibility of the resistant var. Kaleso to CBSD. Conclusions PAL1 gene of the phenylpropanoid pathway has a major role in inducing resistance to CBSD in cassava plants and its early induction is key for CBSD resistance.

scholarly journals Photoperiodically driven transcriptome-wide changes in the hypothalamus reveal transcriptional differences between physiologically contrasting seasonal life-history states in migratory songbirds

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Aakansha Sharma ◽  
Subhajit Das ◽  
Sayantan Sur ◽  
Jyoti Tiwari ◽  
Khushboo Chaturvedi ◽  
...  
Keyword(s):  
Life History ◽  
Time Course ◽  
Light Exposure ◽  
Degradation Pathway ◽  
Apolipoprotein A1 ◽  
Mrna Levels ◽  
Rna Seq ◽  
Transcriptional Responses ◽  
Migratory Songbirds ◽  
Short Days

AbstractWe investigated time course of photoperiodically driven transcriptional responses in physiologically contrasting seasonal life-history states in migratory blackheaded buntings. Birds exhibiting unstimulated winter phenotype (photosensitive state; responsive to photostimulation) under 6-h short days, and regressed summer phenotype (photorefractory state; unresponsiveness to photostimulation) under 16-h long days, were released into an extended light period up to 22 h of the day. Increased tshβ and dio2, and decreased dio3 mRNA levels in hypothalamus, and low prdx4 and high il1β mRNA levels in blood confirmed photoperiodic induction by hour 18 in photosensitive birds. Further, at hours 10, 14, 18 and 22 of light exposure, the comparison of hypothalamus RNA-Seq results revealed transcriptional differences within and between states. Particularly, we found reduced expression at hour 14 of transthyretin and proopiomelanocortin receptor, and increased expression at hour 18 of apolipoprotein A1 and carbon metabolism related genes in the photosensitive state. Similarly, valine, leucine and isoleucine degradation pathway genes and superoxide dismutase 1 were upregulated, and cocaine- and amphetamine-regulated transcript and gastrin-releasing peptide were downregulated in the photosensitive state. These results show life-history-dependent activation of hypothalamic molecular pathways involved in initiation and maintenance of key biological processes as early as on the first long day.

scholarly journals Systematic evaluation of transcriptomic disease risk and diagnostic biomarker overlap between COVID-19 and tuberculosis: a patient-level meta-analysis

2020 ◽  
Author(s):  
Dylan Sheerin ◽  
Abhimanyu ◽  
Xutao Wang ◽  
W Evan Johnson ◽  
Anna Coussens
Keyword(s):  
Gene Expression ◽  
Disease Risk ◽  
Meta Analysis ◽  
Risk Scores ◽  
Systematic Evaluation ◽  
Rna Seq ◽  
Sequencing Data ◽  
Transcriptional Responses ◽  
Patient Level ◽  
Gene Expression Signatures

AbstractBackgroundThe novel coronavirus, SARS-CoV-2, has increased the burden on healthcare systems already strained by a high incidence of tuberculosis (TB) as co-infection and dual presentation are occurring in syndemic settings. We aimed to understand the interaction between these diseases by profiling COVID-19 gene expression signatures on RNA-sequencing data from TB-infected individuals.MethodsWe performed a systematic review and patient-level meta-analysis by querying PubMed and pre-print servers to derive eligible COVID-19 gene expression signatures from human whole blood (WB), PBMCs or BALF studies. A WB influenza dataset served as a control respiratory disease signature. Three large TB RNA-seq datasets, comprising multiple cohorts from the UK and Africa and consisting of TB patients across the disease spectrum, were chosen to profile these signatures. Putative “COVID-19 risk scores” were generated for each sample in the TB datasets using the TBSignatureProfiler package. Risk was stratified by time to TB diagnosis in progressors and contacts of pulmonary and extra-pulmonary TB. An integrative analysis between TB and COVID-19 single-cell RNA-seq data was performed and a population-level meta-analysis was conducted to identify shared gene ontologies between the diseases and their relative enrichment in COVID-19 disease severity states.Results35 COVID-19 gene signatures from nine eligible studies comprising 98 samples were profiled on TB RNA-seq data from 1181 samples from 853 individuals. 25 signatures had significantly higher COVID-19 risk in active TB (ATB) compared with latent TB infection (p <0·005), 13 of which were validated in two independent datasets. FCN1- and SPP1-expressing macrophages enriched in BALF during severe COVID-19 were identified in circulation during ATB. Shared perturbed ontologies included antigen presentation, epigenetic regulation, platelet activation, and ROS/RNS production were enriched with increasing COVID-19 severity. Finally, we demonstrate that the overlapping transcriptional responses may complicate development of blood-based diagnostic signatures of co-infection.InterpretationOur results identify shared dysregulation of immune responses in COVID-19 and TB as a dual risk posed by co-infection to COVID-19 severity and TB disease progression. These individuals should be followed up for TB in the months subsequent to SARS-CoV-2 diagnosis.

Morphological Changes in the Brain of Acutely Ill and Weight-Recovered Patients with Anorexia Nervosa

2014 ◽  
Vol 42 (1) ◽  
pp. 7-18 ◽  
Author(s):  
Jochen Seitz ◽  
Katharina Bühren ◽  
Georg G. von Polier ◽  
Nicole Heussen ◽  
Beate Herpertz-Dahlmann ◽  
...  
Keyword(s):  
Anorexia Nervosa ◽  
Cognitive Deficits ◽  
Time Course ◽  
Morphological Changes ◽  
Meta Analysis ◽  
Short Term ◽  
Clinical Prognosis ◽  
Qualitative Review ◽  
Brain Changes ◽  
The Brain

Objective: Acute anorexia nervosa (AN) leads to reduced gray (GM) and white matter (WM) volume in the brain, which however improves again upon restoration of weight. Yet little is known about the extent and clinical correlates of these brain changes, nor do we know much about the time-course and completeness of their recovery. Methods: We conducted a meta-analysis and a qualitative review of all magnetic resonance imaging studies involving volume analyses of the brain in both acute and recovered AN. Results: We identified structural neuroimaging studies with a total of 214 acute AN patients and 177 weight-recovered AN patients. In acute AN, GM was reduced by 5.6% and WM by 3.8% compared to healthy controls (HC). Short-term weight recovery 2–5 months after admission resulted in restitution of about half of the GM aberrations and almost full WM recovery. After 2–8 years of remission GM and WM were nearly normalized, and differences to HC (GM: –1.0%, WM: –0.7%) were no longer significant, although small residual changes could not be ruled out. In the qualitative review some studies found GM volume loss to be associated with cognitive deficits and clinical prognosis. Conclusions: GM and WM were strongly reduced in acute AN. The completeness of brain volume rehabilitation remained equivocal.

scholarly journals Disentangling transcriptional responses in plant defense against arthropod herbivores

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Alejandro Garcia ◽  
M. Estrella Santamaria ◽  
Isabel Diaz ◽  
Manuel Martinez
Keyword(s):  
Regulatory Networks ◽  
Pieris Rapae ◽  
Meta Analysis ◽  
Plant Response ◽  
Plant Responses ◽  
Transcriptional Responses ◽  
Crop Species ◽  
Physiological Processes ◽  
Meta Analyses ◽  
Plant Herbivore

AbstractThe success in the response of a plant to a pest depends on the regulatory networks that connect plant perception and plant response. Meta-analyses of transcriptomic responses are valuable tools to discover novel mechanisms in the plant/herbivore interplay. Considering the quantity and quality of available transcriptomic analyses, Arabidopsis thaliana was selected to test the ability of comprehensive meta-analyses to disentangle plant responses. The analysis of the transcriptomic data showed a general induction of biological processes commonly associated with the response to herbivory, like jasmonate signaling or glucosinolate biosynthesis. However, an uneven induction of many genes belonging to these biological categories was found, which was likely associated with the particularities of each specific Arabidopsis-herbivore interaction. A thorough analysis of the responses to the lepidopteran Pieris rapae and the spider mite Tetranychus urticae highlighted specificities in the perception and signaling pathways associated with the expression of receptors and transcription factors. This information was translated to a variable alteration of secondary metabolic pathways. In conclusion, transcriptomic meta-analysis has been revealed as a potent way to sort out relevant physiological processes in the plant response to herbivores. Translation of these transcriptomic-based analyses to crop species will permit a more appropriate design of biotechnological programs.

scholarly journals Predictors of lost to follow up from antiretroviral therapy among adults in sub-Saharan Africa: a systematic review and meta-analysis

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Hafte Kahsay Kebede ◽  
Lillian Mwanri ◽  
Paul Ward ◽  
Hailay Abrha Gesesew
Keyword(s):  
Risk Factors ◽  
Systematic Review ◽  
Meta Analysis ◽  
Sub Saharan Africa ◽  
Hiv Care ◽  
Care Services ◽  
Validity Assessment ◽  
Sub Saharan ◽  
Lost To Follow Up

Abstract Background It is known that ‘drop out’ from human immunodeficiency virus (HIV) treatment, the so called lost-to-follow-up (LTFU) occurs to persons enrolled in HIV care services. However, in sub-Saharan Africa (SSA), the risk factors for the LTFU are not well understood. Methods We performed a systematic review and meta-analysis of risk factors for LTFU among adults living with HIV in SSA. A systematic search of literature using identified keywords and index terms was conducted across five databases: MEDLINE, PubMed, CINAHL, Scopus, and Web of Science. We included quantitative studies published in English from 2002 to 2019. The Joanna Briggs Institute Meta-Analysis of Statistics Assessment and Review Instrument (JBI-MAStARI) was used for methodological validity assessment and data extraction. Mantel Haenszel method using Revman-5 software was used for meta-analysis. We demonstrated the meta-analytic measure of association using pooled odds ratio (OR), 95% confidence interval (CI) and heterogeneity using I2 tests. Results Thirty studies met the search criteria and were included in the meta-analysis. Predictors of LTFU were: demographic factors including being: (i) a male (OR = 1.2, 95% CI 1.1–1.3, I2 = 59%), (ii) between 15 and 35 years old (OR = 1.3, 95% CI 1.1–1.3, I2 = 0%), (iii) unmarried (OR = 1.2, 95% CI 1.2–1.3, I2 = 21%), (iv) a rural dweller (OR = 2.01, 95% CI 1.5–2.7, I2 = 40%), (v) unemployed (OR = 1.2, 95% CI 1.04–1.4, I2 = 58%); (vi) diagnosed with behavioral factors including illegal drug use(OR = 13.5, 95% CI 7.2–25.5, I2 = 60%), alcohol drinking (OR = 2.9, 95% CI 1.9–4.4, I2 = 39%), and tobacco smoking (OR = 2.6, 95% CI 1.6–4.3, I2 = 74%); and clinical diagnosis of mental illness (OR = 3.4, 95% CI 2.2–5.2, I2 = 1%), bed ridden or ambulatory functional status (OR = 2.2, 95% CI 1.5–3.1, I2 = 74%), low CD4 count in the last visit (OR = 1.4, 95% CI 1.1–1.9, I2 = 75%), tuberculosis co-infection (OR = 1.2, 95% CI 1.02–1.4, I2 = 66%) and a history of opportunistic infections (OR = 2.5, 95% CI 1.7–2.8, I2 = 75%). Conclusions The current review identifies demographic, behavioral and clinical factors to be determinants of LTFU. We recommend strengthening of HIV care services in SSA targeting the aforementioned group of patients. Trial registration Protocol: the PROSPERO Registration Number is CRD42018114418

scholarly journals SPLICE-q: a Python tool for genome-wide quantification of splicing efficiency

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Verônica R. de Melo Costa ◽  
Julianus Pfeuffer ◽  
Annita Louloupi ◽  
Ulf A. V. Ørom ◽  
Rosario M. Piro
Keyword(s):  
Gene Expression ◽  
Cancer Progression ◽  
Time Course ◽  
Progressive Increase ◽  
Rna Seq ◽  
Transcript Processing ◽  
Aberrant Transcript ◽  
Genome Wide ◽  
Splicing Efficiency ◽  
Nascent Rna

Abstract Background Introns are generally removed from primary transcripts to form mature RNA molecules in a post-transcriptional process called splicing. An efficient splicing of primary transcripts is an essential step in gene expression and its misregulation is related to numerous human diseases. Thus, to better understand the dynamics of this process and the perturbations that might be caused by aberrant transcript processing it is important to quantify splicing efficiency. Results Here, we introduce SPLICE-q, a fast and user-friendly Python tool for genome-wide SPLICing Efficiency quantification. It supports studies focusing on the implications of splicing efficiency in transcript processing dynamics. SPLICE-q uses aligned reads from strand-specific RNA-seq to quantify splicing efficiency for each intron individually and allows the user to select different levels of restrictiveness concerning the introns’ overlap with other genomic elements such as exons of other genes. We applied SPLICE-q to globally assess the dynamics of intron excision in yeast and human nascent RNA-seq. We also show its application using total RNA-seq from a patient-matched prostate cancer sample. Conclusions Our analyses illustrate that SPLICE-q is suitable to detect a progressive increase of splicing efficiency throughout a time course of nascent RNA-seq and it might be useful when it comes to understanding cancer progression beyond mere gene expression levels. SPLICE-q is available at: https://github.com/vrmelo/SPLICE-q

Adoption of improved cassava varieties in Nigeria: Insights from DNA fingerprinting versus self-reporting varietal identification approaches

2021 ◽  
pp. 003072702199003
Author(s):  
Patience Ifeyinwa Opata ◽  
Oguejiofor Joseph Okorie ◽  
Juliana Chinasa Iwuchukwu ◽  
Chukwuma Otum Ume ◽  
Oyakhilomen Oyinbo
Keyword(s):  
Measurement Errors ◽  
Empirical Studies ◽  
Sub Saharan Africa ◽  
Limited Attention ◽  
Adoption Studies ◽  
Hidden Hunger ◽  
Varietal Identification ◽  
Sub Saharan ◽  
Cassava Varieties

Much of the empirical studies on crop varietal adoption in Sub-Saharan Africa relied on self-reported adoption in farm-household surveys, which is prone to measurement errors. In addition, farmers’ perceptions of consumption-related varietal traits in adoption studies has received limited attention compared with production-related traits. Using DNA-based and self-reported adoption measures, we analyze the adoption of improved cassava varieties (ICVs) with a focus on the extent of varietal misidentification, the sensitivity of the drivers of adoption to varietal misidentification and the role of farmers’ perceptions of biofortification trait in adoption decisions. We find that the adoption rate of ICVs is relatively high using both DNA-based and self-reported adoption measures, but there is notable misclassification in varietal adoption. We find that the mismatch in DNA-based and self-reported adoption measures leads to some variation in the factors that influence the likelihood and intensity of adoption of ICVs. This suggests that appropriate varietal identification helps in better understanding of the drivers of adoption. In addition, we find that despite the observed varietal misclassification, farmers’ perceptions of biofortification trait is significantly correlated with the probability and intensity of adoption of ICVs using both DNA-based and self-reported varietal identification. This suggests that inclusion of biofortification trait in cassava matters for both the likelihood and extent of adoption of ICVs. The latter lends credence to the emerging policy interests in breeding programs for biofortified crops to address hidden hunger in Nigeria.

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