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Achieving crop stress tolerance and improvement--an overview of genomic techniques

Rasool S, Ahmad P, Rehman MU, Arif A, Anjum NA

Appl Biochem Biotechnol, 2015 Dec;177(7):1395-408.
PMID: 26440315 DOI: 10.1007/s12010-015-1830-9

The inexorable exposure of plants to the combinations of abiotic stresses has affected the worldwide food supply. The crop improvement against these abiotic stresses has been captivating approach to increase the yield and enhance the stress tolerance. By using traditional and modern breeding methods, the characters that confer tolerance to these stresses were accomplished. No doubt genetic engineering and molecular breeding have helped in comprehending the intricate nature of stress response. Understanding of abiotic stress-involved cellular pathways provides vital information on such responses. On the other hand, genomic research for crop improvement has raised new assessments in breeding new varieties against abiotic stresses. Interpretation of responses of the crop plants under stress is of great significance by studying the main role of crops in food and biofuel production. This review presents genomic-based approaches revealing the complex networks controlling the mechanisms of abiotic stress tolerance, and the possible modes of assimilating information attained by genomic-based approaches due to the advancement in isolation and functional analysis of genes controlling the yield and abiotic stress tolerance are discussed.
Fulltext Identification and Comparative Analysis of H2O2-Scavenging Enzymes (Ascorbate Peroxidase and Glutathione Peroxidase) in Selected Plants Employing Bioinformatics Approaches

Ozyigit II, Filiz E, Vatansever R, Kurtoglu KY, Koc I, Öztürk MX, et al.

Front Plant Sci, 2016;7:301.
PMID: 27047498 DOI: 10.3389/fpls.2016.00301

Among major reactive oxygen species (ROS), hydrogen peroxide (H2O2) exhibits dual roles in plant metabolism. Low levels of H2O2 modulate many biological/physiological processes in plants; whereas, its high level can cause damage to cell structures, having severe consequences. Thus, steady-state level of cellular H2O2 must be tightly regulated. Glutathione peroxidases (GPX) and ascorbate peroxidase (APX) are two major ROS-scavenging enzymes which catalyze the reduction of H2O2 in order to prevent potential H2O2-derived cellular damage. Employing bioinformatics approaches, this study presents a comparative evaluation of both GPX and APX in 18 different plant species, and provides valuable insights into the nature and complex regulation of these enzymes. Herein, (a) potential GPX and APX genes/proteins from 18 different plant species were identified, (b) their exon/intron organization were analyzed, (c) detailed information about their physicochemical properties were provided, (d) conserved motif signatures of GPX and APX were identified, (e) their phylogenetic trees and 3D models were constructed, (f) protein-protein interaction networks were generated, and finally (g) GPX and APX gene expression profiles were analyzed. Study outcomes enlightened GPX and APX as major H2O2-scavenging enzymes at their structural and functional levels, which could be used in future studies in the current direction.
Salvia officinalis L. Methanolic Extract Reduces Lead and Nicotine-Induced Sperm Quality Degeneration in Male Rats

Ammar Aldaddou W, Aljohani ASM, Adewale Ahmed I, Al-Wabel NA, El-Ashmawy IM

Chem Biodivers, 2023 Jul;20(7):e202300115.
PMID: 37236909 DOI: 10.1002/cbdv.202300115

Most heavy metals and industrial chemicals such as nicotine and lead cause harm to the reproduction process through a decrease in sperm motility, fertilization process, and sperm binding to the oocyte. Salvia officinalis L. (sage) has been reported to enhance serum testosterone levels and other certain biochemical enzymes. Thus, the current study is aimed at evaluating the potential health benefits of S. officinalis L. methanol extract on lead and nicotine hydrogen tartrate-induced sperm quality degeneration in male rats and also identifying some of the non-polar volatile bioactive compounds that might be attributed to the bioactivity of S. officinalis extract using gas chromatography-mass spectrometry (GC/MS). In the study, fifty-four mature male albino rats of about 220-250 g [were divided randomly and equally into 9 groups (n=6)]. Sperm quality degeneration was induced through the oral administration of 1.5 g/L of lead acetate in drinking water or peritoneal injection of 0.50 mg/kg (animal weight) nicotine hydrogen tartrate for sixty days. Two doses (200 & 400 mg/kg b.w.) of S. officinalis L. were used. The rats were anesthetized after the experimental period and then sacrificed. Blood samples were collected while the epididymis, testicle, and accessory sex organs (prostates and seminal vesical) were taken for histopathological studies. Twelve major compounds were identified through the GC/MS analysis of S. officinalis L. methanol extract. Lead and nicotine toxicity had a great effect on the rats' sperm quality causing a significant (p<0.05) decrease in the quantity of sperm and sperm motility as well as an upsurge in the abnormalities of the sperm and a reduction in the length & diameter of seminiferous tubules and size & weight of sexual organs (accessory sex glands, epididymis, and testis). The administration of S. officinalis L. methanol extract, however, had a positive impact on the sexual organ weights, semen quality & quantity, and rats' fertility, thus, ameliorating the adversative effects of both lead and nicotine. Further evaluation and isolation of the bioactive components are recommended as potential drug leads.
Fulltext Rasch Modeling and Multilevel Confirmatory Factor Analysis for the Usability of the Impact of Event Scale-Revised (IES-R) during the COVID-19 Pandemic

Aljaberi MA, Lee KH, Alareqe NA, Qasem MA, Alsalahi A, Abdallah AM, et al.

Healthcare (Basel), 2022 Sep 24;10(10).
PMID: 36292305 DOI: 10.3390/healthcare10101858

BACKGROUND: Several instruments are currently used to assess Coronavirus Disease 2019 (COVID-19) -induced psychological distress, including the 22-item Impact of Event Scale-Revised (IES-R). The IES-R is a self-administered scale used to assess post-traumatic stress disorder (PTSD). The current study aimed to examine the construct validity of the IES-R, based on the Rasch model, with COVID-19-related data, as well as to test the multilevel construct validity of the IES-R within and among countries during the pandemic crisis.
METHODS: A multi-country web-based cross-sectional survey was conducted utilizing the 22-item IES-R. A total of 1020 participants enrolled in our survey, of whom 999 were included in the analyses. Data were analyzed using Rasch modeling and multilevel confirmatory factor analysis (MCFA).
RESULTS: The Rasch modeling results of the IES-R demonstrated that the IES-R is a satisfactory instrument with the five-point Likert scale, asserting that its 22 items are significant contributors to assessing PTSD as a unidimensional construct covered by the items of the IES-R. The MCFA confirmed that the 22-item IES-R, with its three factors, including intrusion, avoidance, and hyperarousal, demonstrates adequate construct validity at the within- and among-country levels. However, the results of the Akaike information criterion (AIC) model determined that the 16-item IES-R is better than the 22-item IES-R.
CONCLUSION: The results suggested that the 22-item IES-R is a reliable screening instrument for measuring PTSD related to the COVID-19 pandemic, and can be utilized to provide timely psychological health support, when needed, based on the screening results.
Fulltext A cross-sectional study on the impact of the COVID-19 pandemic on psychological outcomes: Multiple indicators and multiple causes modeling

Aljaberi MA, Alareqe NA, Alsalahi A, Qasem MA, Noman S, Uzir MUH, et al.

PLoS One, 2022;17(11):e0277368.
PMID: 36350838 DOI: 10.1371/journal.pone.0277368

Although the psychological impact of coronavirus disease 2019 (COVID-19) has been evaluated in the literature, further research is needed, particularly on post-traumatic stress disorder (PTSD) and psychological outcomes, is needed. This study aims to investigate the effect of the COVID-19 pandemic on psychological outcomes (depression, anxiety, and insomnia). A cross-sectional study using an online survey was conducted using the following instruments: Impact of Event Scale-Revised (IES-R), Patient Health Questionnaire-9 (PHQ-9), Generalized Anxiety Disorder (GAD-7), and Insomnia Severity Index (ISI). Confirmatory factor analysis (CFA), structural equation model (SEM), multiple indicators and multiple causes (MIMIC) modeling, and differential item functioning (DIF) were performed to analyze the collected data. According to the results, participants with PTSD (n = 360) showed a higher level of depression, anxiety, and insomnia than those without PTSD (n = 639). Among the participants, 36.5% experienced moderate to severe symptoms of depression, and 32.6% had mild depressive symptoms. Moreover, 23.7% of participants experienced moderate to severe anxiety symptoms, and 33.1% had mild anxiety symptoms. In addition, 51.5% of participants experienced symptoms of insomnia. In conclusion, the PTSD caused by COVID-19 is significantly associated with depression, anxiety, and insomnia at the level of latent constructs and observed variables.
Fulltext Comparison of Hematological Parameters and the Associated Factors Among Women with and without Breast Cancer: A Case-Control Study

Abbas AB, Al-Gamei S, Naser A, Al-Oqab A, Alduhami K, Al-Sabri M, et al.

Breast Cancer (Dove Med Press), 2024;16:877-885.
PMID: 39678025 DOI: 10.2147/BCTT.S497313

BACKGROUND: Breast cancer (BC) is the most popular and dangerous cancer, with a high mortality rate. Hematological parameters are often used in routine diagnosis of numerous disorders. Therefore, the study aimed to evaluate hematological parameters amongst women with and without BC.
METHODOLOGY: Briefly, 200 blood samples (100 cases and 100 controls) were collected at Life Center of Breast Cancer Control, Ibb City, Yemen. The whole blood samples were tested immediately for complete blood count (CBC) parameters. Socio-demographic and reproductive characteristics were collected by using a standardized questionnaire. Kolmogorov-Smirnov test, Unpaired t-test, Mann-Whitney test, Fisher's exact test and chi-square test for trends were calculated using GraphPad Prism 8.0.1. P-values ≤0.05 were statistically significant.
RESULTS: The mean and standard deviation (SD) revealed significant differences between BC group and the healthy control group attributed to the variables of age (P<0.0001), weight (P<0.0001), residence (P=0.0218), employment state (P<0.0001), economic state (P=0.0003), education levels (P<0.0001), regular exercise (P<0.0001) and a strict diet (P<0.0008). Marital state, marital age, number of births, and use of contraceptives demonstrated statistical significance (P<0.0001, P=0.0008, P=0.0009, and P<0.0001, respectively). Additionally, Hb, RBCs, WBCs count, neutrophils, lymphocytes and monocytes displayed significant differences (P=0.0393, P=0.0045, P=0.0327, P=0.0441, P=0.0098 and P<0.0001, respectively).
CONCLUSION: Hb, RBCs, WBCs, neutrophils, lymphocytes, monocytes and other parameters scored high points of evidence for BC surveillance. Further studies are required to evaluate hematological parameter differences and biochemical parameters after or during chemotherapy or mastectomy.