Genome-wide analysis revealed sex-specific gene expression in asthmatics.

Global gene-expression analysis has shown remarkable difference between males and females in response to exposure to many diseases. Nevertheless, gene expression studies in asthmatics have so far focused on sex-combined analysis, ignoring inherent variabilities between the sexes, which potentially drive disparities in asthma prevalence. The objectives of this study were to identify (1) sex-specific differentially expressed genes (DEGs), (2) genes that show sex-interaction effects and (3) sex-specific pathways and networks enriched in asthma risk. We analyzed 711 males and 689 females and more than 2.8 million transcripts covering 20 000 genes leveraged from five different tissues and cell types (i.e. epithelial, blood, induced sputum, T cells and lymphoblastoids). Using tissue-specific meta-analysis, we identified 439 male- and 297 female-specific DEGs in all cell types, with 32 genes in common. By linking DEGs to the genome-wide association study (GWAS) catalog and the lung and blood eQTL annotation data from GTEx, we identified four male-specific genes (FBXL7, ITPR3 and RAD51B from epithelial tissue and ALOX15 from blood) and one female-specific gene (HLA-DQA1 from epithelial tissue) that are disregulated during asthma. The hypoxia-inducible factor 1 signaling pathway was enriched only in males, and IL-17 and chemokine signaling pathways were enriched in females. The cytokine-cytokine signaling pathway was enriched in both sexes. The presence of sex-specific genes and pathways demonstrates that sex-combined analysis does not identify genes preferentially expressed in each sex in response to diseases. Linking DEG and molecular eQTLs to GWAS catalog represents an important avenue for identifying biologically and clinically relevant genes.

The fifth leaf and spike organs of barley (Hordeum vulgare L.) display different physiological and metabolic responses to drought stress.

BACKGROUND: Photosynthetic organs of the cereal spike (ear) provide assimilate for grain filling, but their response to drought is poorly understood. In this study, we characterized the drought response of individual organs of the barley spike (awn, lemma, and palea) and compared them with a vegetative organ (fifth leaf). Understanding differences in physiological and metabolic responses between the leaf and spike organs during drought can help us develop high yielding cultivars for environments where terminal drought is prevalent. RESULTS: We exposed barley plants to drought by withholding water for 4 days at the grain filling stage and compared changes in: (1) relative water content (RWC), (2) osmotic potential (Ψs), (3) osmotic adjustment (OA), (4) gas exchange, and (5) metabolite content between organs. Drought reduced RWC and Ψs in all four organs, but the decrease in RWC was greater and there was a smaller change in Ψs in the fifth leaf than the spike organs. We detected evidence of OA in the awn, lemma, and palea, but not in the fifth leaf. Rates of gas exchange declined more rapidly in the fifth leaf than awn during drought. We identified 18 metabolites but, only ten metabolites accumulated significantly during drought in one or more organs. Among these, proline accumulated in all organs during drought while accumulation of the other metabolites varied between organs. This may suggest that each organ in the same plant uses a different set of osmolytes for drought resistance. CONCLUSIONS: Our results suggest that photosynthetic organs of the barley spike maintain higher water content, greater osmotic adjustment, and higher rates of gas exchange than the leaf during drought.

Self-reported race/ethnicity in the age of genomic research: its potential impact on understanding health disparities.

This review explores the limitations of self-reported race, ethnicity, and genetic ancestry in biomedical research. Various terminologies are used to classify human differences in genomic research including race, ethnicity, and ancestry. Although race and ethnicity are related, race refers to a person's physical appearance, such as skin color and eye color. Ethnicity, on the other hand, refers to communality in cultural heritage, language, social practice, traditions, and geopolitical factors. Genetic ancestry inferred using ancestry informative markers (AIMs) is based on genetic/genomic data. Phenotype-based race/ethnicity information and data computed using AIMs often disagree. For example, self-reporting African Americans can have drastically different levels of African or European ancestry. Genetic analysis of individual ancestry shows that some self-identified African Americans have up to 99% of European ancestry, whereas some self-identified European Americans have substantial admixture from African ancestry. Similarly, African ancestry in the Latino population varies between 3% in Mexican Americans to 16% in Puerto Ricans. The implication of this is that, in African American or Latino populations, self-reported ancestry may not be as accurate as direct assessment of individual genomic information in predicting treatment outcomes. To better understand human genetic variation in the context of health disparities, we suggest using "ancestry" (or biogeographical ancestry) to describe actual genetic variation, "race" to describe health disparity in societies characterized by racial categories, and "ethnicity" to describe traditions, lifestyle, diet, and values. We also suggest using ancestry informative markers for precise characterization of individuals' biological ancestry. Understanding the sources of human genetic variation and the causes of health disparities could lead to interventions that would improve the health of all individuals.

Rank-based genome-wide analysis reveals the association of ryanodine receptor-2 gene variants with childhood asthma among human populations.

BACKGROUND: The standard approach to determine unique or shared genetic factors across populations is to identify risk alleles in one population and investigate replication in others. However, since populations differ in DNA sequence information, allele frequencies, effect sizes, and linkage disequilibrium patterns, SNP association using a uniform stringent threshold on p values may not be reproducible across populations. Here, we developed rank-based methods to investigate shared or population-specific loci and pathways for childhood asthma across individuals of diverse ancestry. We performed genome-wide association studies on 859,790 SNPs genotyped in 527 affected offspring trios of European, African, and Hispanic ancestry using publically available asthma database in the Genotypes and Phenotypes database. RESULTS: Rank-based analyses showed that there are shared genetic factors for asthma across populations, more at the gene and pathway levels than at the SNP level. Although the top 1,000 SNPs were not shared, 11 genes (RYR2, PDE4D, CSMD1, CDH13, ROBO2, RBFOX1, PTPRD, NPAS3, PDE1C, SEMA5A, and CTNNA2) mapped by these SNPs were shared across populations. Ryanodine receptor 2 (RYR2, a statin response-related gene) showed the strongest association in European (p value=2.55×10(-7)) and was replicated in African (2.57×10(-4)) and Hispanic (1.18 × 10(-3)) Americans. Imputation analyses based on the 1000 Genomes Project uncovered additional RYR2 variants associated with asthma. Network and functional ontology analyses revealed that RYR2 is an integral part of dermatological or allergic disorder biological networks, specifically in the functional classes involving inflammatory, eosinophilic, and respiratory diseases. CONCLUSION: Our rank-based genome-wide analysis revealed for the first time an association of RYR2 variants with asthma and replicated previously discovered PDE4D asthma gene across human populations. The replication of top-ranked asthma genes across populations suggests that such loci are less likely to be false positives and could indicate true associations. Variants that are associated with asthma across populations could be used to identify individuals who are at high risk for asthma regardless of genetic ancestry.

Evaluation of In Vivo Antidiarrheal Activities of 80% Methanol Extract and Solvent Fractions of Peels of Colocasia esculenta (Araceae).

Background: Diarrhea is the common gastrointestinal disorder accounting for 2.5 billion episodes and 1.5 million deaths annually. Limitations and inaccessibility of currently available medications are the main problem associated with treatment of diarrhea. Hence, medicinal plants are usually preferred to manage diarrhea because they may contain constituents with high activity and fewer side effects. Even though the dose, safety, and efficacy of Colocasia esculenta (L.) Schott are not substantiated scientifically, several societies use it for the treatment of diarrhea. Objective: This study was targeted at exploring the in vivo antidiarrheal activities of 80% methanol extract and solvent fractions of peels of Colocasia esculenta (L.) Schott in Swiss albino mice. Methods: The plant was collected and extracted with 80% methanol, followed by fractionation with distilled water, chloroform, and diethyl ether. Castor oil-induced diarrhea, enteropooling, and motility tests were used to evaluate antidiarrheal activity. The test groups received graded doses of 100 mg/kg, 200 mg/kg, and 400 mg/kg. Negative controls received 10 ml/kg of 2% Tween 80 while positive controls received loperamide (3 mg/kg) or atropine (5 mg/kg). Results: The crude and solvent fractions of the plant extract have induced significant effects in reduction of the number and weight of wet stools at all tested doses. However, delay in onset of diarrhea was observed only at 400 mg/kg (P < 0.001) for both crude extract and solvent fractions. In antienteropooling test, 80% methanol extract and solvent fractions have significantly reduced the weight and volume of intestinal contents, especially at 200 mg/kg and 400 mg/kg. Regarding the antimotility test, the crude extract reduced motility at all tested doses, whereas the solvent fractions reduced intestinal motility mainly at 400 mg/kg (P < 0.001). Conclusion: The study has revealed that the 80% methanol extract and solvent fractions of the plant possess antidiarrheal activities supporting the traditional antidiarrheal claims of the plant.

Phytolacca Dodecandra (L' Herit) (Phytolaccaceae) Methanol Root Extract Protects Liver from Acetaminophen-Induced Injury in Rats.

Phytolacca dodecandra (L' Herit), or 'Endod', is one of the widely known medicinal plants in Ethiopia. Berries of the endod have been used as a detergent for centuries. The present study was aimed to test the hepatoprotective effects of the plant against acetaminophen (APAP)-induced liver injury in rats. Mice of either sex were used for oral acute toxicity tests and APAP-induced lethality tests. Hepatoprotective experiments were done on male rats using 2 g/kg of APAP to induce liver damage. Liver enzymes, total bilirubin (TB), and lipid profile were determined. Liver tissues were also examined histopathologically to see a morphologic change in the control and experiment groups. The protective effect of the plant extract was also tested through sodium pentobarbital (SPB)-induced sleeping time. A significant increase in serum levels of liver enzymes, TB, low-density lipoprotein (LDL), and triglycerides (TGs) was seen from oral administration of 2 g/kg APAP. Total cholesterol (TC) and high-density lipoprotein (HDL) levels were decreased. Serum levels of all parameters were reversed to normal after administration of silymarin 100 mg/kg and, 100, 200, and 400 mg/kg doses of the extract. A significant dose-dependent hepatoprotective effect of Phytolacca dodecandra Methanol Root Extract (PDME) was seen in terms of LDL. Histopathological investigations and SPB-induced sleeping time confirmed the findings of biochemical analysis. The findings of the present study indicate that PDME protected the liver from APAP injury.

Prevalence of childhood stunting and determinants in low and lower-middle income African countries: Evidence from standard demographic and health survey.

INTRODUCTION: Undernutrition poses a significant global public health challenge, adversely affecting childhood cognitive and physical development while increasing the risk of disease and mortality. Stunting, characterized by impaired growth and development in children due to insufficient psychological stimulation, frequent infections, and inadequate nutrition, remains a critical issue. Although economic growth alone cannot fully address the prevalence of stunting, there exists a robust correlation between a country's income level and childhood stunting rates. Countries with higher incomes tend to have lower rates of childhood stunting. Notably, while childhood stunting is declining worldwide, it remains persistent in Africa. Consequently, this study aims to assess the prevalence of childhood stunting and its determinants in low- and lower-middle-income African countries. METHOD: This study conducted a secondary analysis of standard demographic and health surveys in low- and lower-middle-income African countries spanning the period from 2010 to 2022. The analysis included a total sample of 204,214 weighted children under the age of five years. To identify the determinants of stunting, we employed a multilevel mixed-effect model, considering the three levels of variables. The measures of association (fixed effect) were determined using the adjusted odds ratio at a 95% confidence interval. Significance was declared when the association between the outcome variable and the explanatory variable had a p-value less than 0.05. RESULT: In low and lower-middle-income African countries, 31.28% of children under five years old experience stunting, with a 95% confidence interval ranging from 31.08% to 31.48%. The results from a multilevel mixed-effect analysis revealed that 24 months or more of age of child, male gender, low and high birth weight, low and high maternal BMI, no and low maternal education, low household wealth index, multiple (twin or triplet) births, rural residence, and low income of countries were significantly associated with childhood stunting. CONCLUSION: Stunting among children under five years of age in low- and lower-middle-income African countries was relatively high. Individual, community, and country-level factors were statistically associated with childhood stunting. Equally importantly, with child, maternal, and community factors of stunting, the income of countries needs to be considered in providing nutritional interventions to mitigate childhood stunting in Africa.

Prevalence of timely complementary feeding initiation and associated factors among mothers having children aged 6-24 months in rural north-central Ethiopia: Community based cross-sectional study.

BACKGROUND: Complementary foods are defined as any solid or liquid foods other than breast milk offered to children. Timely initiation of complementary foods during infancy is necessary for growth and development. The first two years of life are important period for rapid physical, cognitive and social development that requires optimal nutrition. Currently, there is no study done in this rural community about timely initiation of complementary feeding. OBJECTIVE: The main aim of this study was to assess the prevalence of timely initiation of complementary feeding among mothers having children aged 6-24 months in Farta district, rural Ethiopia. METHODS: A community-based cross-sectional study was employed from December 2020 to February 2021 among 570 mothers by using multi-stage sampling techniques. Data were collected using a structured interviewer-administered questionnaire and entered into Epi Data 4.6 then transferred to Statistical Package for Social Science version 25 for analysis. Bivariate and multivariable logistic regression analysis with a 95% confidence interval carried out to determine the association between explanatory and the outcome variables. A P-value of < 0.05 was considered statistically significant. RESULTS: The prevalence of timely initiation of complementary feeding among mothers having children aged 6-24 months was 51.9%. Institutionaldelivery [(AOR = 2.10, 95% CI: (1.31-3.32)],Keeping livestock [(AOR = 2.21, 95% CI: (1.35, 3.65)], Postnatal follow up [(AOR = 0.60, 95% CI:(0.36, 0.77)],merchants [(AOR = 4.58; 95% CI:1.99, 10.55)], and daily labourer [(AOR = 2.88, 95% CI:(1.50-5.51)] were statistically associated with timely initiation of complementary feeding. CONCLUSION: This finding revealed that the prevalence of timely initiation of complementary feeding is still low. Factors affecting timely initiations of complementary feeding were home delivery, unable to attend postnatal care follow-up, being housewife and farmers. All health professionals including health extension workers should give special attention to advising and counseling for mothers and their husbands about timely initiation of complementary feeding.

Comparison of measures of marker informativeness for ancestry and admixture mapping.

BACKGROUND: Admixture mapping is a powerful gene mapping approach for an admixed population formed from ancestral populations with different allele frequencies. The power of this method relies on the ability of ancestry informative markers (AIMs) to infer ancestry along the chromosomes of admixed individuals. In this study, more than one million SNPs from HapMap databases and simulated data have been interrogated in admixed populations using various measures of ancestry informativeness: Fisher Information Content (FIC), Shannon Information Content (SIC), F statistics (FST), Informativeness for Assignment Measure (In), and the Absolute Allele Frequency Differences (delta, δ). The objectives are to compare these measures of informativeness to select SNP markers for ancestry inference, and to determine the accuracy of AIM panels selected by each measure in estimating the contributions of the ancestors to the admixed population. RESULTS: FST and In had the highest Spearman correlation and the best agreement as measured by Kappa statistics based on deciles. Although the different measures of marker informativeness performed comparably well, analyses based on the top 1 to 10% ranked informative markers of simulated data showed that In was better in estimating ancestry for an admixed population. CONCLUSIONS: Although millions of SNPs have been identified, only a small subset needs to be genotyped in order to accurately predict ancestry with a minimal error rate in a cost-effective manner. In this article, we compared various methods for selecting ancestry informative SNPs using simulations as well as SNP genotype data from samples of admixed populations and showed that the In measure estimates ancestry proportion (in an admixed population) with lower bias and mean square error.

Drought response in the spikes of barley: gene expression in the lemma, palea, awn, and seed.

The photosynthetic organs of the barley spike (lemma, palea, and awn) are considered resistant to drought. However, there is little information about gene expression in the spike organs under drought conditions. We compared response of the transcriptome of the lemma, palea, awn, and seed to drought stress using the Barley1 Genome Array. Barley plants were exposed to drought treatment for 4 days at the grain-filling stage by withholding water. At the end of the stress, relative water content of the lemma, palea, and awn dropped from 85% to 60%. Nevertheless, the water content of the seed only decreased from 89% to 81%. Transcript abundance followed the water status of the spike organs; the awn had more drought-regulated genes followed by lemma and palea, and the seed showed very little change in gene expression. Despite expressing more drought-associated genes, many genes for amino acid, amino acid derivative, and carbohydrate metabolism, as well as for photosynthesis, respiration, and stress response, were down-regulated in the awn compared with the lemma, palea, and seed. This suggests that the lemma and the palea are more resistant to drought stress compared with the awn.

The Lem2 gene promoter of barley directs cell- and development-specific expression of gfp in transgenic plants.

Transgenic approaches to combating fungal pathogens, such as Fusarium graminearum, require the targeting of antifungal gene expression in tissues of developing seed spikes of cereal grains, especially lemmas and epicarps. The Lem2 gene of barley encodes a lectin-like protein that is strongly up-regulated by salicylic acid and is preferentially expressed in lemmas, paleas (lemma/palea) and coleoptiles. Transient expression studies have indicated that the proximal -75/+70 region (relative to the transcription start site) determines organ specificity. In the present study, Golden Promise barley stably transformed with Morex Lem2 promoter/gfp reporter constructs displayed cell- and development-specific expression of gfp (green fluorescent protein gene). This expression corresponded to the expression seen in Northern blots of Morex organs. Under the full-length promoter, strong GFP fluorescence was observed in the lemma/palea, glumes, coleoptile, auricle and ligule. Weak GFP fluorescence was also observed in the rachis, tips of primary leaves and the leaf sheath. Unexpectedly, strong expression occurred in the epicarp, even though Lem2 is not expressed in this organ in Morex. Studies showed that the Lem2 promoter is more highly methylated in the epicarp than in the lemma of Morex. In the lemma/palea, gfp underwent a temporal shift in expression from the mesophyll to specialized epidermal cork cells. Similar to the lemma/palea, expression in the leaf sheath was localized in the cork cells. Progressive 5' deletions of the promoter to nucleotide -75 gradually reduced the level of gfp expression, but tissue- and cell-specific expression was retained.

Genotype-environment interactions and their translational implications.

Organisms frequently encounter different environmental conditions. The physiological and behavioral responses to these conditions depend on the genetic make up of individuals. Genotype generally remains constant from one environment to another, although occasional spontaneous mutations may occur which cause it to change. However, when the same genotype is subjected to different environments, it can produce a wide range of phenotypes. These phenotypic variations are attributable to the effect of the environment on the expression and function of genes influencing the trait. Changes in the relative performance of genotypes across different environments are referred to as genotype-environment interactions (GEI). A general argument for research on the impact of GEI in common diseases is that it provides insights into disease processes at the population, individual and molecular levels. In humans, GEI is complicated by multiple factors including phenocopies, genocopies, epigenetics and imprinting. A better understanding of GEI is essential if patients are to make informed health choices guided by their genomic information. In this article, we clarify the role of the environment on phenotype, we describe how human population structure can obscure the resolution of GEI and we discuss how emerging biobanks across the globe can be coordinated to further our understanding of genotype-phenotype associations within the context of varying environment.

A proximal upstream sequence controls tissue-specific expression of Lem2, a salicylate-inducible barley lectin-like gene.

The lemma and palea (lemma/palea), which form the husk of barley (Hordeum vulgare L.) seeds, constitutively express high levels of defense-related genes, relative to leaves [Abebe et al. (2004) Crop Sci 44:942-950]. One of these genes, Lem2, is expressed mainly in the lemma/palea and coleoptile and is strongly upregulated by salicylic acid (SA) and its functional analog 2,6-dichloroisonicotinic acid . Induction by SA was rapid, occurring within 4 h of treatment. However, Lem2 is not responsive to methyl jasmonate (MeJA) or wounding and is downregulated by drought, dehydration, and abscisic acid. These results suggest that Lem2 is involved in systemic acquired resistance. Sequence analysis showed that LEM2 is a jacalin-related lectin (JRL)-like protein with two domains. Consistent with northern and western blot data, transient expression analyses using Lem2::gfp constructs showed strong expression in lemmas and a trace expression in leaves. Successive 5' deletions of the 1,414 bp upstream region gradually weakened promoter strength, as measured by real-time PCR. Promoter deletion studies also revealed that the -75/+70 region (containing the TATA box, 5' UTR, and a SA-response element) determines tissue specificity and that the distal promoter region simply enhances expression. Southern analysis indicated that Morex barley has at least three copies of the Lem2 gene arranged in tandem on chromosome 5(1H) Bin 02, near the short arm telomere. Lem2 is not present in the barley cultivars Steptoe, Harrington, Golden Promise, and Q21861.

Tolerance of mannitol-accumulating transgenic wheat to water stress and salinity.

Previous work with model transgenic plants has demonstrated that cellular accumulation of mannitol can alleviate abiotic stress. Here, we show that ectopic expression of the mtlD gene for the biosynthesis of mannitol in wheat improves tolerance to water stress and salinity. Wheat (Triticum aestivum L. cv Bobwhite) was transformed with the mtlD gene of Escherichia coli. Tolerance to water stress and salinity was evaluated using calli and T(2) plants transformed with (+mtlD) or without (-mtlD) mtlD. Calli were exposed to -1.0 MPa of polyethylene glycol 8,000 or 100 mM NaCl. T(2) plants were stressed by withholding water or by adding 150 mM NaCl to the nutrient medium. Fresh weight of -mtlD calli was reduced by 40% in the presence of polyethylene glycol and 37% under NaCl stress. Growth of +mtlD calli was not affected by stress. In -mtlD plants, fresh weight, dry weight, plant height, and flag leaf length were reduced by 70%, 56%, 40%, and 45% compared with 40%, 8%, 18%, and 29%, respectively, in +mtlD plants. Salt stress reduced shoot fresh weight, dry weight, plant height, and flag leaf length by 77%, 73%, 25%, and 36% in -mtlD plants, respectively, compared with 50%, 30%, 12%, and 20% in +mtlD plants. However, the amount of mannitol accumulated in the callus and mature fifth leaf (1.7-3.7 micromol g(-1) fresh weight in the callus and 0.6-2.0 micromol g(-1) fresh weight in the leaf) was too small to protect against stress through osmotic adjustment. We conclude that the improved growth performance of mannitol-accumulating calli and mature leaves was due to other stress-protective functions of mannitol, although this study cannot rule out possible osmotic effects in growing regions of the plant.