Organic System Based Evaluation Of Tomato (Solanum Lycopersicum) For Participatory Plant Breeding In Bangladesh

For Participatory breeding program FGD and online survey was conducted with atakeholders to identify key plant traits and a total 32 diverse set of tomato germplasm was evaluated under organic management using Augmented design to better understand horticultural constraints and identify adapted germplasm for further development. Stakeholders rated more number of fruits per plant, nutrition color (lycopene, β carotene), flavor, virus resistances, stronger root, storability as their top breeding priority, safety was the prior quality characters of tomato. The ANOVA indicated significance difference among genotypes, the result indicated the existence of high morphological variation in tomato genotypes grown in organic system based condition. Yield per plant showed significant variation with the quality parameter like lycopene and β-carotene. To screen out suitable cultivars through multivariate analysis and genetic diversity in tomato genotypes based on 17 characters was estimated using Mahalanobis’s D2statistics. Eight different homozygous divergent genotypes were selected from five different clusters using variance ranking among genotypes within cluster

The Impact of Diet and Betel Nut Use on Skin Lesions Associated with Drinking-Water Arsenic in Pabna, Bangladesh

An established exposure–response relationship exists between water arsenic levels and skin lesions. Results of previous studies with limited historical exposure data, and laboratory animal studies suggest that diet may modify arsenic metabolism and toxicity. In this study, we evaluated the effect of diet on the risk of arsenic-related skin lesions in Pabna, Bangladesh. Six hundred cases and 600 controls loosely matched on age and sex were enrolled at Dhaka Community Hospital, Bangladesh, in 2001–2002. Diet, demographic data, and water samples were collected. Water samples were analyzed for arsenic using inductively coupled plasma mass spectroscopy. Betel nut use was associated with a greater risk of skin lesions in a multivariate model [odds ratio (OR) = 1.67; 95% confidence interval (CI), 1.18–2.36]. Modest decreases in risk of skin lesions were associated with fruit intake 1–3 times/month (OR = 0.68; 95%CI, 0.51–0.89) and canned goods at least 1 time/month (OR = 0.41; 95% CI, 0.20–0.86). Bean intake at least 1 time/day (OR = 1.89; 95% CI, 1.11–3.22) was associated with increased odds of skin lesions. Betel nut use appears to be associated with increased risk of developing skin lesions in Bangladesh. Increased intake of fruit and canned goods may be associated with reduced risk of lesions. Increased intake of beans may be associated with an increased risk of skin lesions. The results of this study do not provide clear support for a protective effect of vegetable and overall protein consumption against the development of skin lesions, but a modest benefit cannot be excluded

Prenatal arsenic exposure and DNA methylation in maternal and umbilical cord blood leukocytes

Background: Arsenic is an epigenetic toxicant and could influence fetal developmental programming.Objectives: We evaluated the association between arsenic exposure and DNA methylation in maternal and umbilical cord leukocytes.Methods: Drinking-water and urine samples were collected when women were at 64 28 weeks gestation; the samples were analyzed for arsenic using inductively coupled plasma mass spectrometry. DNA methylation at CpG sites in p16 (n = 7) and p53 (n = 4), and in LINE-1 and Alu repetitive elements (3 CpG sites in each), was quantified using pyrosequencing in 113 pairs of maternal and umbilical blood samples. We used general linear models to evaluate the relationship between DNA methylation and tertiles of arsenic exposure.Results: Mean (\ub1 SD) drinking-water arsenic concentration was 14.8 \ub1 36.2 \u3bcg/L (range: < 1-230 \u3bcg/L). Methylation in LINE-1 increased by 1.36% [95% confidence interval (CI): 0.52, 2.21%] and 1.08% (95% CI: 0.07, 2.10%) in umbilical cord and maternal leukocytes, respectively, in association with the highest versus lowest tertile of total urinary arsenic per gram creatinine. Arsenic exposure was also associated with higher methylation of some of the tested CpG sites in the promoter region of p16 in umbilical cord and maternal leukocytes. No associations were observed for Alu or p53 methylation.Conclusions: Exposure to higher levels of arsenic was positively associated with DNA methylation in LINE-1 repeated elements, and to a lesser degree at CpG sites within the promoter region of the tumor suppressor gene p16. Associations were observed in both maternal and fetal leukocytes. Future research is needed to confirm these results and determine if these small increases in methylation are associated with any health effect

In Utero Arsenic Exposure and Epigenome-Wide Associations in Placenta, Umbilical Artery and Human Umbilical Vein Endothelial Cells

Exposure to arsenic early in life has been associated with increased risk of several chronic diseases and is believed to alter epigenetic programming in utero. In the present study, we evaluate the epigenome-wide association of arsenic exposure in utero and DNA methylation in placenta (n = 37), umbilical artery (n = 45) and human umbilical vein endothelial cells (HUVEC) (n = 52) in a birth cohort using the Infinium HumanMethylation450 BeadChip array. Unadjusted and cell mixture adjusted associations for each tissue were examined along with enrichment analyses relative to CpG island location and omnibus permutation tests of association among biological pathways. One CpG in artery (cg26587014) and 4 CpGs in placenta (cg12825509; cg20554753; cg23439277; cg21055948) reached a Bonferroni adjusted level of significance. Several CpGs were differentially methylated in artery and placenta when controlling the false discovery rate (q-value<0.05), but none in HUVEC. Enrichment of hypomethylated CpG islands was observed for artery while hypermethylation of open sea regions were present in placenta relative to prenatal arsenic exposure. The melanogenesis pathway was differentially methylated in artery (Max F P < 0.001), placenta (Max F P < 0.001), and HUVEC (Max F P = 0.02). Similarly, the insulin-signaling pathway was differentially methylated in artery (Max F P = 0.02), placenta (Max F P = 0.02), and HUVEC (Max F P = 0.02). Our results show that prenatal arsenic exposure can alter DNA methylation in artery and placenta but not in HUVEC. Further studies are needed to determine if these alterations in DNA methylation mediate the effect of prenatal arsenic exposure and health outcomes later in life.Keywords: Arsenic, Epigenetics, environmental epigenetics, DNA methylation, Illumina 450K, fetal programming, In-utero exposureKeywords: Arsenic, Epigenetics, environmental epigenetics, DNA methylation, Illumina 450K, fetal programming, In-utero exposur

Arsenic Reduction in Drinking Water and Improvement in Skin Lesions: A Follow-Up Study in Bangladesh

BACKGROUND: Chronic exposure to arsenic is associated with skin lesions. However, it is not known whether reducing arsenic exposure will improve skin lesions. OBJECTIVE: We evaluated the association between reduced arsenic exposures and skin lesion recovery over time. METHODS: A follow-up study of 550 individuals was conducted in 2009-2011 on a baseline population of skin lesion cases (n = 900) previously enrolled in Bangladesh in 2001-2003. Arsenic in drinking water and toenails, and skin lesion status and severity were ascertained at baseline and follow-up. We used logistic regression and generalized estimating equation (GEE) models to evaluate the association between log(10)-transformed arsenic exposure and skin lesion persistence and severity. RESULTS: During the study period, water arsenic concentrations decreased in this population by 41% overall, and 65 individuals who had skin lesions at baseline had no identifiable lesions at follow-up. In the adjusted models, every log(10) decrease in water arsenic and toenail arsenic was associated with 22% [odds ratio (OR) = 1.22; 95% CI: 0.85, 1.78] and 4.5 times (OR = 4.49; 95% CI: 1.94, 11.1) relative increase in skin lesion recovery, respectively. In addition, lower baseline arsenic levels were significantly associated with increased odds of recovery. A log(10) decrease in toenail arsenic from baseline to follow-up was also significantly associated with reduced skin lesion severity in cases over time (mean score change of -5.22 units; 95% CI: -8.61, -1.82). CONCLUSIONS: Reducing arsenic exposure increased the odds that an individual with skin lesions would recover or show less severe lesions within 10 years. Reducing arsenic exposure must remain a public health priority in Bangladesh and in other regions affected by arsenic-contaminated water.This is the publisher’s final pdf. The published article is copyrighted by National Institute of Environmental Health Sciences and can be found at: http://ehp.niehs.nih.gov/. Reproduced with permission from Environmental Health Perspectives.Keywords: Arsenic, Change, Skin lesion, Bangladesh, RecoveryKeywords: Arsenic, Change, Skin lesion, Bangladesh, Recover

A case-control study of GST polymorphisms and arsenic related skin lesions

BACKGROUND: Polymorphisms in GSTT1, GSTM1 and GSTP1 impact detoxification of carcinogens by GSTs and have been reported to increase susceptibility to environmentally related health outcomes. Individual factors in arsenic biotransformation may influence disease susceptibility. GST activity is involved in the metabolism of endogenous and exogenous compounds, including catalyzing the formation of arsenic-GSH conjugates. METHODS: We investigated whether polymorphisms in GSTT1, GSTP1 and GSTM1 were associated with risk of skin lesions and whether these polymorphisms modify the relationship between drinking water arsenic exposure and skin lesions in a case control study of 1200 subjects frequency matched on age and gender in community clinics in Pabna, Bangladesh in 2001–2002. RESULTS AND DISCUSSION: GSTT1 homozygous wildtype status was associated with increased odds of skin lesions compared to the null status (OR1.56 95% CI 1.10–2.19). The GSTP1 GG polymorphism was associated with greater odds of skin lesions compared to GSTP1 AA, (OR 1.86 (95%CI 1.15–3.00). No evidence of effect modification by GSTT1, GSTM1 or GSTP1 polymorphisms on the association between arsenic exposure and skin lesions was detected. CONCLUSION: GSTT1 wildtype and GSTP1 GG are associated with increased risk of skin lesions

Named entity extraction in historical Australian newspaper text

Theoretical thesis.Bibliography: pages 58-62.1. Introduction -- 2. Literature review -- 3. Name entity recognition on Trove newspaper text -- 4. Document classiffcation on Trove newspaper texts -- 5. Discussion -- 6. Conclusion -- Bibliography.A Named Entity Recognition (NER) objective is to extract and to classify atomic entities in text such as proper names (Names and locations), temporal expressions and other specific notation identification. In this project, we will apply NER methods to historical newspaper text taken from the Trove archive in the National Library of Australia. We will present an evaluation of various available NER systems on a hand-annotated sample of newspaper text. We will then present the result of applying the system to the whole corpus of text. Even when the occurrence of a given name is known across a large data set, there may be many individuals who share that name; this is particularly evident in the Trove corpus since it spans a long time period (1803-1959). In the second part of this project we will develop methods to try to classify different individuals with the same name. In particular, we will classify names as either Politician, Entertainer or other based on the documents that they occur in.Mode of access: World wide web1 online resource (ix, 62 pages) graphs, table

Arsenic exposure and global DNA methylation

Background: It has been hypothesized that inorganic arsenic (iAs), an important environmental carcinogen of global public health significance, induces epigenetic changes including aberrant DNA methylation. Both DNA methylation and arsenic metabolism require S-adenosylmethionine (SAM) as the methyl donor. This competitive demand between arsenic metabolism and DNA methylation for SAM may decrease the percentage of methylated CpG dinucleotides throughout the genome. Arsenic has been shown to produce global hypomethylation in both in vitro and animal models. However, few studies have investigated the effect of iAs exposure on genomic DNA methylation in humans. Methods: We evaluated the relationship between iAs and DNA methylation in maternal and cord blood samples collected as part of a pilot study that recruited 52 pregnant women before their 28th week of gestational age in Serajdikhan, Bangladesh. Of the 52 women recruited into this pilot study, cord blood was successfully collected from 29 of the 44 births attended. DNA was extracted using the Puregene DNA isolation kit (Gentra Systems, Minneapolis, MN). DNA was shipped to University of Milan where genomic DNA was subjected to bisulfite modification and global methylation content was determined by PCR-pyrosequencing analysis for LINE-1 and Alu repeated elements. This technique measures the percentage of methylation in three specific CpG positions in LINE-1 and in three specific CpG positions in Alu repeated elements that are present in several thousand copies in a single genome. Maternal exposure to iAs was measured in drinking water samples collected at the time of enrolment using ICP-MS. Results: Drinking water iAs ranged from &lt;1 to 734 \u3bcg/L and the average percent methylation of global LINE-1 and ALU repeats was 78.5% (range: 74.93-88.0%) and 24.57% (range: 20.9-25.9%), respectively. Separate linear regression models evaluated the relationship between the average for LINE-1 and Alu and drinking water arsenic while controlling for exposure to environmental tobacco smoke and chewing betel nuts. We observed that drinking water iAs was associated with decreased methylation at average LINE-1 repeated elements (\u3b2 = -2.35; SE: 1.07, P-value = 0.04) and for average Alu in cord blood samples (\u3b2 = -0.67, SE: 0.031, P-value = 0.04). However, no association was observed when DNA methylation was measured in maternal blood. This suggests that the fetus may be the most susceptible to epigenetic effects of iAs exposure. Conclusion: While the biological significance of these findings remains unclear, these results support the concept that arsenic exposure results in global genomic hypomethylation. We are currently analyzing additional samples to confirm the results of this pilot study