Genome-wide identification and expression analysis of the GRAS gene family under abiotic stresses in wheat (Triticum aestivum L.).

The GRAS transcription factors are multifunctional proteins involved in various biological processes, encompassing plant growth, metabolism, and responses to both abiotic and biotic stresses. Wheat is an important cereal crop cultivated worldwide. However, no systematic study of the GRAS gene family and their functions under heat, drought, and salt stress tolerance and molecular dynamics modeling in wheat has been reported. In the present study, we identified the GRAS gene in Triticum aestivum through systematically performing gene structure analysis, chromosomal location, conserved motif, phylogenetic relationship, and expression patterns. A total of 177 GRAS genes were identified within the wheat genome. Based on phylogenetic analysis, these genes were categorically placed into 14 distinct subfamilies. Detailed analysis of the genetic architecture revealed that the majority of TaGRAS genes had no intronic regions. The expansion of the wheat GRAS gene family was proven to be influenced by both segmental and tandem duplication events. The study of collinearity events between TaGRAS and analogous orthologs from other plant species provided valuable insights into the evolution of the GRAS gene family in wheat. It is noteworthy that the promoter regions of TaGRAS genes consistently displayed an array of cis-acting elements that are associated with stress responses and hormone regulation. Additionally, we discovered 14 miRNAs that target key genes involved in three stress-responsive pathways in our study. Moreover, an assessment of RNA-seq data and qRT-PCR results revealed a significant increase in the expression of TaGRAS genes during abiotic stress. These findings highlight the crucial role of TaGRAS genes in mediating responses to different environmental stresses. Our research delved into the molecular dynamics and structural aspects of GRAS domain-DNA interactions, marking the first instance of such information being generated. Overall, the current findings contribute to our understanding of the organization of the GRAS genes in the wheat genome. Furthermore, we identified TaGRAS27 as a candidate gene for functional research, and to improve abiotic stress tolerance in the wheat by molecular breeding.

Epidemiology of viral acute lower respiratory infections in a community-based cohort of rural north Indian children.

BACKGROUND: In India, community-based acute lower respiratory infections (ALRI) burden studies are limited, hampering development of prevention and control strategies. METHODS: We surveyed children <10 years old at home weekly from August 2012-August 2014, for cough, sore throat, rhinorrhoea, ear discharge, and shortness of breath. Symptomatic children were assessed for ALRI using World Health Organization definitions. Nasal and throat swabs were obtained from all ALRI cases and asymptomatic controls and tested using polymerase chain reaction for respiratory syncytial virus (RSV), human metapneumovirus (hMPV), parainfluenza viruses (PIV), and influenza viruses (IV). We estimated adjusted odds ratios (aOR) using logistic regression to calculate etiologic fractions (EF). We multiplied agent-specific ALRI incidence rates by EF to calculate the adjusted incidence as episodes per child-year. RESULTS: ALRI incidence was 0.19 (95% confidence interval (CI) = 0.18-0.20) episode per child-year. Association between virus and ALRI was strongest for RSV (aOR = 15.9; 95% CI = 7.3-34.7; EF = 94%) and least for IV (aOR = 4.6; 95% CI = 2.0-10.6; EF = 78%). Adjusted agent-specific ALRI incidences were RSV (0.03, 95% CI = 0.02-0.03), hMPV (0.02, 95% CI = 0.01-0.02), PIV (0.02, 95% CI = 0.01-0.02), and IV (0.01, 95% CI = 0.01-0.01) episode per child-year. CONCLUSIONS: ALRI among children in rural India was high; RSV was a significant contributor.

Evaluation of case definitions for estimation of respiratory syncytial virus associated hospitalizations among children in a rural community of northern India.

BACKGROUND: The burden estimation studies for respiratory syncytial virus (RSV) have been based on varied case definitions, including case-definitions designed for influenza surveillance systems. We used all medical admissions among children aged 0-59 months to study the effect of case definitions on estimation of RSV-associated hospitalizations rates. METHODS: The hospital-based daily surveillance enrolled children aged 0-59 months admitted with acute medical conditions from July 2009-December 2012, from a well-defined rural population in Ballabgarh in northern India. All study participants were examined and nasal and throat swabs taken for testing by real-time polymerase chain reaction (RT-PCR) for RSV and influenza virus. Clinical data were used to retrospectively evaluate World Health Organization (WHO) case definitions (2011) commonly used for surveillance of respiratory pathogens, ie, acute respiratory illness (WHO-ARI), severe ARI (SARI) and influenza-like illness (ILI), for determination of RSV-associated hospitalization. RSV-associated hospitalization rates adjusted for admissions at non-study hospitals were calculated. FINDINGS: Out of 505 children enrolled, 82 (16.2%) tested positive for RSV. Annual incidence rates of RSV-associated hospitalization per 1000 children were highest among infants aged 0-5 months (15.2; 95% confidence interval (CI) 8.3-26.8), followed by ages 6-23 months (5.3, 95% CI 3.2-8.7) and lowest among children 24-59 months (0.5, 95% CI 0.1-1.5). The RSV positive children were more likely to have signs of respiratory distress like wheeze, chest in-drawing, tachypnea, and crepitation compared to RSV-negative based on bivariate comparisons. Other less commonly seen signs of respiratory distress, ie, nasal flaring, grunting, accessory muscle usage were also significantly associated with being RSV positive. Compared to the estimated RSV hospitalization rate based on all medical hospitalizations, the WHO-ARI case definition captured 86% of the total incidence, while case definitions requiring fever like ILI and SARI underestimated the incidence by 50-80%. CONCLUSIONS: Our study suggests that RSV is a substantial cause of hospitalization among children aged <24months especially those aged <6 months. The WHO-ARI case definition appeared to be the most suitable screening definition for RSV surveillance because of its high sensitivity.

Rates of respiratory virus-associated hospitalization in children aged <5 years in rural northern India.

OBJECTIVES: Though respiratory viruses are thought to cause substantial morbidity globally in children aged <5 years, the incidence of severe respiratory virus infections in children is unknown in India where 20% of the world's children live. METHODS: During August 2009-July 2011, prospective population-based surveillance was conducted for hospitalizations of children aged <5 years in a rural community in Haryana State. Clinical data and respiratory specimens were collected. Swabs were tested by RT-PCR for influenza and parainfluenza viruses, respiratory syncytial virus (RSV), human metapneumovirus, coronaviruses, and adenovirus. Average annual hospitalization incidence was calculated using census data and adjusted for hospitalizations reported to occur at non-study hospitals according to a community healthcare utilization survey. RESULTS: Of 245 hospitalized children, respiratory viruses were detected among 98 (40%), of whom 92 (94%) had fever or respiratory symptoms. RSV accounted for the highest virus-associated hospitalization incidence (34.6/10,000, 95% CI 26.3-44.7) and 20% of hospitalizations. There were 11.8/10,000 (95% CI 7.9-18.4) influenza-associated hospitalizations (7% of hospitalizations). RSV and influenza virus detection peaked in winter (November-February) and rainy seasons (July), respectively. CONCLUSION: Respiratory viruses were associated with a substantial proportion of hospitalizations among young children in a rural Indian community. Public health research and prevention in India should consider targeting RSV and influenza in young children.