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Combustible renewable energy can be an effective instrument to confirm sustainable development in reducing CO2 emissions to Gross Domestic Product (GDP) per capita in developing countries. However, connecting to some developing regions, the main research question is to what extent, in EU post-communist fast-developing countries (Visegrad Countries/Czech Republic, Slovakia, Hungary, Poland), will meeting the climate change preferences affect the use of biomass for energy and waste incineration, and how will this affect GDP growth? In addition, of course, what the Balkan countries can learn from this is also very important. The study investigates the relationship between GDP per capita, CO2 emissions, and Combustible Energy and Waste Consumption (CEWC). According to the Hausman test, the regression model along with random effect is the appropriate method for panel-balanced data as of 2008 to 2020 concerning Balkan countries. The data was divided into three categories: 10 Balkan countries, 4 countries without access to the sea (Kosovo, Bosnia and Herzegovina, Serbia, and Macedonia), and Visegrad countries. The study discovered a substantial positive influence of CEWC on GDP per capita and a significant negative influence of CO2 emissions. The cointegration test confirms the cointegration of all three variables. This means that all three variables have a long-term relationship concerning the sense of each three forms of the chosen panel. The Granger causality findings shows the variables have a two-way causative relationship. The biomass energy use can dramatically hamper GDP growth in Visegrad and less developed Balkan countries without sea water, due to low energy productivity and a lack of technical innovation. The study recommended that instead of using energy production from simple biomass, these countries can use other circular, platform-based models to prevent unexpected rises in CO2 emissions and achieve Green House Gas (GHG) reductions. Therefore, this should be given more attention when setting climate and renewable energy policy targets, because they can significantly slow down economic growth. [ABSTRACT FROM AUTHOR]

Switchgrass (Panicum virgatum L.) has been identified as a potential feedstock for cellulosic ethanol production in United States for its high biomass yield and adaptation to marginal lands. Composition of the cell wall plays an important role in bioethanol conversion. A total of 209 pseudo‐F1 testcross progenies obtained from a biparental cross, AP13 × VS16, were grown at three locations from 2008 to 2011. Near‐infrared spectroscopy was used to estimate cell wall composition from biomass harvested at maturity. A linkage map of the pseudo‐F1 testcross was constructed with 8,757 SNPs developed by genotyping‐by‐sequencing. Quantitative trait loci (QTL) analysis was performed on eight lignocellulosic traits, namely, klason lignin, sugar, glucose, xylose, hexose, ethanol, hexosoic ethanol, and cell wall ethanol conversion percentage. A total of 327 QTL were recorded for the eight lignocellulosic traits. We have identified 111 major regions in the switchgrass genome that underlie these lignocellulosic traits. Scanning of the genome sequence for genes flanking the QTL peaks, we identified 45 important genes that are involved in lignin biosynthesis, carbohydrate and sugar metabolism, and other biological and cellular functions. Identification of valuable genes associated with QTL along with pleotropic effects of the significant number of QTL suggests that simultaneous selection and genetic improvement of these traits are possible using marker‐assisted selection. [ABSTRACT FROM AUTHOR]

Background We hypothesized that drinking water, sanitation, handwashing (WSH), and nutritional interventions would improve environmental enteric dysfunction (EED), a potential contributor to stunting. Methods Within a subsample of a cluster-randomized, controlled trial in rural Bangladesh, we enrolled pregnant women in 4 arms: control, WSH, child nutrition counseling plus lipid-based nutrient supplements (N), and nutrition plus WSH (N+WSH). Among the birth cohort, we measured biomarkers of gut inflammation (myeloperoxidase, neopterin), permeability (alpha-1-antitrypsin, lactulose, mannitol), and repair (regenerating gene 1β) at median ages 3, 14, and 28 months. Analysis was intention-to-treat. Results We assessed 1512 children. At age 3 months, compared to controls, neopterin was reduced by nutrition (–0.21 log nmol/L; 95% confidence interval [CI], –.37, –.05) and N+WSH (–0.20 log nmol/L; 95% CI, –.34, –.06) interventions; similar reductions were observed at 14 months. At 3 months, all interventions reduced lactulose and mannitol (–0.60 to –0.69 log mmol/L). At 28 months, myeloperoxidase was elevated in the WSH and nutrition arms (0.23–0.27 log ng/mL) and lactulose was higher in the WSH arm (0.30 log mmol/L; 95% CI,.07,.53). Conclusions Reductions in permeability and inflammation at ages 3 and 14 months suggest that the interventions promoted healthy intestinal maturation; however, by 28 months, the WSH and nutrition arms showed elevated EED biomarkers. These results underscore the importance of developing a better understanding of EED pathophysiology and targeting interventions early in childhood, when they are likely to have the largest benefit to intestinal health. Clinical Trials Registration NCT01590095. [ABSTRACT FROM AUTHOR]

Switchgrass (Panicum virgatum L.), a native warm‐season perennial grass, is being considered as a feedstock for biofuel production in the United States. To expedite its genetic improvement and enhance genetic gain per selection cycle, application of marker‐assisted selection is indispensable. A high‐density linkage map was constructed in a pseudo‐F1 testcross mapping population of AP13×VS16, consisting of 349 progenies. A total of 8,757 single nucleotide polymorphism (SNP) markers generated through genotype‐by‐sequencing (GBS) were used to construct the linkage map. The total map length spans up to 2,540.2 cM with the marker density of one marker in every 0.25–0.34 cM. Spring green‐up (SG), days to flowering (FL), and the vegetative growth period (VP) data were analyzed and used for quantitative trait loci (QTL) mapping. The population showed significant variations and exhibited transgressive segregation for SG, FL, and VP. QTL analyses were performed using trait mean of each year and location along with BLUP (best linear unbiased prediction) values of the traits. A total of 35, 37, and 34 QTL for SG, FL, and VP, respectively, were identified. Phenotypic variability explained by each QTL ranged from 11.29% to 27.85%. The additive genetic effects of individual QTL ranged from −1.81 to 2.40, −6.12 to 7.58, and −16.01 to 6.38 for SG, FL, and VP, respectively. Comparing major QTL regions in the switchgrass genome, 20 candidate genes were identified which were reported to be involved in growth‐, development‐, and flowering‐related traits in switchgrass. High‐density linkage map of tetraploid switchgrass. Major QTL for spring green up, flowering, and vegetative growth period identified on each chromosome except 3N, 4N, 4K, and 8K. [ABSTRACT FROM AUTHOR]

The present study aims at investigating the actual situation prevailing in Bangladesh in respect to quality control and management system of different pesticides. The most commonly used pesticides for insect-pests control of vegetables are diazinon, malathion and fenitrothion. In connection with the quality control and assessment of pesticides, samples of diazinon, malathion and fenitrothion were collected from different sources of formulation/repackaging factories existing in Bangladesh and tested in the laboratory. Analytical results of those samples indicated that quality of pesticides collected from factory premises found comparatively better than that of field samples. Field experiments with collected pesticides were conducted on brinjal to find out the effectiveness of 4-different treatments having 4-different doses of each pesticide to control brinjal soot and fruit borer (BSFB) at flowering and fruiting stage. The treatment of fenitrothion was the best with lowest shoot infestation (5.57%) and found superior to control BSFB than all other pesticide treatments. [ABSTRACT FROM AUTHOR]

Abstract. A simple method for the normalisation of cDNA libraries is presented. The method has been used to normalise barley and wheat endosperm libraries. Gene probes for transcripts present at different frequencies in the primary library were used to evaluate the effectiveness of the normalisation process. [ABSTRACT FROM AUTHOR]

In the case of developing countries, it is not clear which crisis management tools will ensure sustainable development in a sustainable and environmentally friendly way, as well as reducing CO2 emissions in addition to ensuring GDP growth. The next analysis discusses the details of this issue. The study explores the connection between per capita GDP, emission of CO2, combustible energy, and waste consumption. The Hausman test ratifies that the regression model with the fixed effect is the proper method for the panel balanced data from 1990 to 2019 in the selected 13 countries of the EU. This study ordered the data into three categories (for 13 selected countries, the top nine EU countries (in GDP), and Visegrad countries (Hungary, Slovakia, Czech Republic and Poland)). The study found a significant positive effect of combustible energy and waste consumption and the negative impact of CO2 emission on GDP per capita. The cointegration test confirms that all three variables are cointegrated. This implies a long-term link among all three variables in the context of all three types of the selected panel. The Granger causality results ensure that there is a two-way cause–effect relation between the variables. The study strongly recommends that developed European Union countries (the top nine EU countries) increase energy production from biomass-based renewable energy and waste to stimulate economic growth. The same strategy was not recommended in the Visegrad countries because of the much lower GDP growth due to the N-shaped Kuznets curve. In these countries, it is advisable to avoid unexpected increases in CO2 emissions from biomass and fossil fuel-burning, to achieve greenhouse gas reductions using other circular, platform-based models instead of simple biomass energy production. Due to the low level of energy efficiency and the lack of application of technological innovation, the energy use of biomass can significantly slow down GDP growth in less developed EU countries (such as the V4 countries). [ABSTRACT FROM AUTHOR]

A lack of adaptive capacities for climate change prevents poor farmers from diversifying agricultural production in Bangladesh's drought-resilient areas. Climate change adaptation strategies can reduce the production risk relating to unforeseen climatic shocks and increase farmers' food, income, and livelihood security. This paper investigates rice farmers' adaptive capacities to adapt climate change strategies to reduce the rice production risk. The study collected 400 farm-level micro-data of rice farmers with the direct cooperation of Rajshahi District. The survey was conducted during periods between June and July of 2020. Rice farmers' adaptive capacities were estimated quantitatively by categorizing the farmers as high, moderate, and low level adapters to climate change adaptation strategies. In this study, a Cobb–Douglas production function was used to measure the effects of farmers' adaptive capacities on rice production. The obtained results show that farmers are moderately adaptive in terms of adaptation strategies on climate change and the degree of adaptation capacities. Agronomic practices such as the quantity of fertilizer used, the amount of labor, the farm's size, and extension contacts have a substantial impact on rice production. This study recommends that a farmer more significantly adjusts to adaptation strategies on climate change to reduce rice production. These strategies will help farmers to reduce the risk and produce higher quality rice. Consequently, rice farmers should facilitate better extension services and change the present agronomic practice to attain a higher adaptation status. It can be very clearly seen that low adaptability results in lower rice yields. [ABSTRACT FROM AUTHOR]

Background: A number of studies have detected relationships between weather and diarrhea. Few have investigated associations with specific enteric pathogens. Understanding pathogen-specific relationships with weather is crucial to inform public health in low-resource settings that are especially vulnerable to climate change. Objectives: Our objectives were to identify weather and environmental risk factors associated with diarrhea and enteropathogen prevalence in young children in rural Bangladesh, a population with high diarrheal disease burden and vulnerability to weather shifts under climate change. Methods: We matched temperature, precipitation, surface water, and humidity data to observational longitudinal data from a cluster-randomized trial that measured diarrhea and enteropathogen prevalence in children 6 months-5.5 years from 2012–2016. We fit generalized additive mixed models with cubic regression splines and restricted maximum likelihood estimation for smoothing parameters. Results: Comparing weeks with 30°C versus 15°C average temperature, prevalence was 3.5% higher for diarrhea, 7.3% higher for Shiga toxin-producing Escherichia coli (STEC), 17.3% higher for enterotoxigenic E. coli (ETEC), and 8.0% higher for Cryptosporidium. Above-median weekly precipitation (median: 13mm; range: 0-396mm) was associated with 29% higher diarrhea (adjusted prevalence ratio 1.29, 95% CI 1.07, 1.55); higher Cryptosporidium, ETEC, STEC, Shigella, Campylobacter, Aeromonas, and adenovirus 40/41; and lower Giardia, sapovirus, and norovirus prevalence. Other associations were weak or null. Discussion: Higher temperatures and precipitation were associated with higher prevalence of diarrhea and multiple enteropathogens; higher precipitation was associated with lower prevalence of some enteric viruses. Our findings emphasize the heterogeneity of the relationships between hydrometeorological variables and specific enteropathogens, which can be masked when looking at composite measures like all-cause diarrhea. Our results suggest that preventive interventions targeted to reduce enteropathogens just before and during the rainy season may more effectively reduce child diarrhea and enteric pathogen carriage in rural Bangladesh and in settings with similar meteorological characteristics, infrastructure, and enteropathogen transmission. Author summary: Location-specific weather factors influence the fate, transport, and transmission of enteropathogens that cause diarrhea. We sought to identify hydrometeorological risk factors associated with childhood diarrhea and specific enteropathogens in rural Bangladesh. In this setting, higher temperatures and precipitation were associated with higher diarrhea in children under 5 years old and with several enteropathogens including bacteria, viruses, and parasites. Higher precipitation was associated with the lower prevalence of some enteric viruses. Our data suggest that interventions targeted to reduce pathogen transmission just before and during the rainy season might be most effective to reduce diarrhea in this setting. [ABSTRACT FROM AUTHOR]

Background We evaluated the impact of low-cost water, sanitation, and handwashing (WSH) and child nutrition interventions on enteropathogen carriage in the WASH Benefits cluster-randomized controlled trial in rural Bangladesh. Methods We analyzed 1411 routine fecal samples from children 14 ± 2 months old in the WSH (n = 369), nutrition counseling plus lipid-based nutrient supplement (n = 353), nutrition plus WSH (n = 360), and control (n = 329) arms for 34 enteropathogens using quantitative polymerase chain reaction. Outcomes included the number of co-occurring pathogens; cumulative quantity of 4 stunting-associated pathogens; and prevalence and quantity of individual pathogens. Masked analysis was by intention-to-treat. Results Three hundred twenty-six (99.1%) control children had 1 or more enteropathogens detected (mean, 3.8 ± 1.8). Children receiving WSH interventions had lower prevalence and quantity of individual viruses than controls (prevalence difference for norovirus: –11% [95% confidence interval {CI}, –5% to –17%]; sapovirus: –9% [95% CI, –3% to –15%]; and adenovirus 40/41: –9% [95% CI, –2% to –15%]). There was no difference in bacteria, parasites, or cumulative quantity of stunting-associated pathogens between controls and any intervention arm. Conclusions WSH interventions were associated with fewer enteric viruses in children aged 14 months. Different strategies are needed to reduce enteric bacteria and parasites at this critical young age. [ABSTRACT FROM AUTHOR]

Hundreds of millions of children in low- and middle-income countries are exposed to chronic stressors, such as poverty, poor sanitation and hygiene, and sub-optimal nutrition. These stressors can have physiological consequences for children and may ultimately have detrimental effects on child development. This study explores associations between biological measures of chronic stress in early life and developmental outcomes in a large cohort of young children living in rural Bangladesh. We assessed physiologic measures of stress in the first two years of life using measures of the hypothalamic-pituitary-adrenal (HPA) axis (salivary cortisol and glucocorticoid receptor gene methylation), the sympathetic-adrenal-medullary (SAM) system (salivary alpha-amylase, heart rate, and blood pressure), and oxidative status (F2-isoprostanes). We assessed child development in the first two years of life with the MacArthur-Bates Communicative Development Inventories (CDI), the WHO gross motor milestones, and the Extended Ages and Stages Questionnaire (EASQ). We compared development outcomes of children at the 75th and 25th percentiles of stress biomarker distributions while adjusting for potential confounders using generalized additive models, which are statistical models where the outcome is predicted by a potentially non-linear function of predictor variables. We analyzed data from 684 children (49% female) at both 14 and 28 months of age; we included an additional 765 children at 28 months of age. We detected a significant relationship between HPA axis activity and child development, where increased HPA axis activity was associated with poor development outcomes. Specifically, we found that cortisol reactivity (coefficient −0.15, 95% CI (−0.29, −0.01)) and post-stressor levels (coefficient −0.12, 95% CI (−0.24, −0.01)) were associated with CDI comprehension score, post-stressor cortisol was associated with combined EASQ score (coefficient −0.22, 95% CI (−0.41, −0.04), and overall glucocorticoid receptor methylation was associated with CDI expression score (coefficient −0.09, 95% CI (−0.17, −0.01)). We did not detect a significant relationship between SAM activity or oxidative status and child development. Our observations reveal associations between the physiological evidence of stress in the HPA axis with developmental status in early childhood. These findings add to the existing evidence exploring the developmental consequences of early life stress. • We measured stress biomarkers and development in young children in Bangladesh. • We evaluated biomarkers from multiple stress systems. • We used generalized additive models to flexibly assess correlations. • Hypothalamic-pituitary-adrenal axis markers were associated with child development. [ABSTRACT FROM AUTHOR]

Background: Pneumonia is the leading cause of death in children globally with the majority of these deaths observed in resource-limited settings. Globally, the annual incidence of clinical pneumonia in under-five children is approximately 152 million, mostly in the low- and middle-income countries. Of these, 8.7% progressed to severe pneumonia requiring hospitalization. However, data to predict children at the greatest risk to develop severe pneumonia from pneumonia are limited. Method: Secondary data analysis was performed after extracting relevant data from a prospective cluster randomized controlled clinical trial; children of either sex, aged two months to five years with pneumonia or severe pneumonia acquired in the community were enrolled over a period of three years in 16 clusters in urban Dhaka city. Results: The analysis comprised of 2,597 children aged 2–59 months. Of these, 904 and 1693 were categorized as pneumonia (controls) and severe pneumonia (cases), respectively based on WHO criteria. The median age of children was 9.2 months (inter quartile range, 5.1–17.1) and 1,576 (60%) were male. After adjustment for covariates, children with temperature ≥38°C, duration of illness ≥3 days, male sex, received prior medical care and severe stunting showed a significantly increased likelihood of developing severe pneumonia compared to those with pneumonia. Severe pneumonia in children occurred more often in older children who presented commonly from wealthy quintile families, and who often sought care from private facilities in urban settings. Conclusion and recommendation: Male sex, longer duration of illness, fever, received prior medical care, and severe stunting were significantly associated with development of WHO-defined severe childhood pneumonia in our population. The results of this study may help to develop interventions target to reduce childhood morbidity and mortality of children suffering from severe pneumonia. [ABSTRACT FROM AUTHOR]

Switchgrass (Panicum virgatum L.) is a promising candidate species for sustainable biofuel feedstock production on marginal land. Soil salinity is one of the significant factors that limits sustainable agricultural production worldwide including a substantial reduction in biomass yield of switchgrass. This study was designed to assess genetic variation in lowland switchgrass and identify genomic regions contributing to an increased level of salinity tolerance using a subset (550 pseudo F2) of a nested association mapping (NAM) population. Salinity tolerance was evaluated based on salt injury score (SIS) using a 1 to 9 scale (1 = the most tolerant, 9 = the most sensitive) and stress tolerance index (STI) calculated from plant height measurements. Substantial variation among NAMfamilies and genotypes within families was observed (p < .05) for SIS. However, no variation was evident among NAM families and genotypes within families for STI. The switchgrass plant accessions EG 1104-1, and EG 1104-2 displayed a high level of salinity tolerance based on SIS which can be used as source material for cultivar development. A total of five quantitative trait loci (QTL) associated with SIS were detected by composite interval mapping on four chromosomes 2B, 6B, 7B, and 9B. The phenotypic variation explained by an individual QTL ranged from 1.4 to 6.5%. The additive genetic effects of individual QTL ranged from -0.07 to 0.63. Homologs of five candidate genes were identified, which were reported to be associated with salinity tolerance. [ABSTRACT FROM AUTHOR]

Background: Previously, we demonstrated that a water, sanitation, handwashing, and nutritional intervention improved linear growth and was unexpectedly associated with shortened childhood telomere length (TL) (Lin et al., 2017). Here, we assessed the association between TL and growth. Methods: We measured relative TL in whole blood from 713 children. We reported differences between the 10th percentile and 90th percentile of TL or change in TL distribution using generalized additive models, adjusted for potential confounders. Results: In cross-sectional analyses, long TL was associated with a higher length-for-age Z score at age 1 year (0.23 SD adjusted difference in length-for-age Z score [95% CI 0.05, 0.42; FDR-corrected p-value = 0.01]). TL was not associated with other outcomes. Conclusions: Consistent with the metabolic telomere attrition hypothesis, our previous trial findings support an adaptive role for telomere attrition, whereby active TL regulation is employed as a strategy to address 'emergency states' with increased energy requirements such as rapid growth during the first year of life. Although short periods of active telomere attrition may be essential to promote growth, this study suggests that a longer overall initial TL setting in the first 2 years of life could signal increased resilience against future telomere erosion events and healthy growth trajectories. [ABSTRACT FROM AUTHOR]

Rapid urbanization has led to a growing sanitation crisis in urban areas of Bangladesh and potential exposure to fecal contamination in the urban environment due to inadequate sanitation and poor fecal sludge management. Limited data are available on environmental fecal contamination associated with different exposure pathways in urban Dhaka. We conducted a cross-sectional study to explore the magnitude of fecal contamination in the environment in low-income, high-income, and transient/floating neighborhoods in urban Dhaka. Ten samples were collected from each of 10 environmental compartments in 10 different neighborhoods (4 low-income, 4 high-income and 2 transient/floating neighborhoods). These 1,000 samples were analyzed with the IDEXX-Quanti-Tray technique to determine most-probable-number (MPN) of E. coli. Samples of open drains (6.91 log10 MPN/100 mL), surface water (5.28 log10 MPN/100 mL), floodwater (4.60 log10 MPN/100 mL), produce (3.19 log10 MPN/serving), soil (2.29 log10 MPN/gram), and street food (1.79 log10 MPN/gram) had the highest mean log10E. coli contamination compared to other samples. The contamination concentrations did not differ between low-income and high-income neighborhoods for shared latrine swabs, open drains, municipal water, produce, and street foodsamples. E. coli contamination levels were significantly higher (p <0.05) in low-income neighborhoods compared to high-income for soil (0.91 log10 MPN/gram, 95% CI, 0.39, 1.43), bathing water (0.98 log10 MPN/100 mL, 95% CI, 0.41, 1.54), non-municipal water (0.64 log10 MPN/100 mL, 95% CI, 0.24, 1.04), surface water (1.92 log10 MPN/100 mL, 95% CI, 1.44, 2.40), and floodwater (0.48 log10 MPN/100 mL, 95% CI, 0.03, 0.92) samples. E. coli contamination were significantly higher (p<0.05) in low-income neighborhoods compared to transient/floating neighborhoods for drain water, bathing water, non-municipal water and surface water. Future studies should examine behavior that brings people into contact with the environment and assess the extent of exposure to fecal contamination in the environment through multiple pathways and associated risks. [ABSTRACT FROM AUTHOR]

• Different Physical of SrRu 2 X 2 (X = P, Ge, As)) have been studied. • All of the three compounds are stable in nature. • All of the compounds possess a mixture of ionic, covalent and metallic bonds. • All the compounds possess low thermal conductivity and Debye temperature. • All compounds possess the high melting temperature. We have studied the physical properties containing structural, elastic, mechanical, electronic, optical and thermodynamic properties of recently discovered SrRu 2 X 2 (X = P, Ge, As) type compounds. All the calculations have been performed by the first-principles method depend on the density functional theory (DFT) with generalized gradient approximation (GGA). For all phases the optimized lattice parameters show a good agreement with the available experimental data. The elastic constants for all compounds are positive which ensures that all phases possess the mechanical stability in nature. The calculated values of Pugh's ratio and Poisson's ratio refer the brittle nature of SrRu 2 P 2 and SrRu 2 Ge 2 and ductility behaviors of SrRu 2 As 2. The zero value of the Universal anisotropy index A U and also the zero value of the percentage of anisotropy in compression and shear (A B and A G) represent the pure isotropic compounds. For any others values compound processes the anisotropic characteristics. The calculated values of A U, A B and A G ensure that all these phases have anisotropic characteristics in nature. The values of Vickers hardness indicate that the rigidity decreases in the order of SrRu 2 Ge 2 >SrRu 2 P 2 >SrRu 2 As 2. Since the conduction band and valence band are overlapped at the Fermi level so the band structure analysis ensures the metallic character of all these phases. The analysis of Mulliken population and charge density ensure the existing of ionic and covalent bonds in these phases. The investigation of dielectric function also ensures the metallic behavior of these compounds. The thermodynamic study provides the Debye temperature of SrRu 2 P 2 , SrRu 2 Ge 2 and SrRu 2 As 2 are 363.86 K, 334.92 K and 329.83 K correspondingly. [ABSTRACT FROM AUTHOR]

Background: Shorter childhood telomere length (TL) and more rapid TL attrition are widely regarded as manifestations of stress. However, the potential effects of health interventions on child TL are unknown. We hypothesized that a water, sanitation, handwashing (WSH), and nutritional intervention would slow TL attrition during the first two years of life. Methods: In a trial in rural Bangladesh (ClinicalTrials.gov, NCT01590095), we randomized geographical clusters of pregnant women into individual water treatment, sanitation, handwashing, nutrition, combined WSH, combined nutrition plus WSH (N + WSH), or control arms. We conducted a substudy enrolling children from the control arm and the N + WSH intervention arm. Participants and outcome assessors were not masked; analyses were masked. Relative TL was measured at 1 and 2 years after intervention, and the change in relative TL was reported. Analysis was intention-to-treat. Findings: Between May 2012 and July 2013, in the overall trial, we randomized 720 geographical clusters of 5551 pregnant women to a control or an intervention arm. In this substudy, after 1 year of intervention, we assessed a total of 662 children (341 intervention and 321 control) and 713 children after 2 years of intervention (383 intervention and 330 control). Children in the intervention arm had significantly shorter relative TL compared with controls after 1 year of intervention (difference -163 base pairs (bp), p=0.001). Between years 1 and 2, TL increased in the intervention arm (+76 bp) and decreased in the controls (-23 bp) (p=0.050). After 2 years, there was no difference between the arms (p=0.305). Interpretation: Our unexpected finding of increased telomere attrition during the first year of life in the intervention group suggests that rapid telomere attrition during this critical period could reflect the improved growth in the intervention group, rather than accumulated stress. Funding: The Bill and Melinda Gates Foundation [ABSTRACT FROM AUTHOR]

The article presents the study that explores on the evolutionary paths of Vitrella and Chromera nuclear genomes to understand the intracellular parasitism in Apicomplexa and its evolution from photosynthetic algae.

Background: Cholera infection continues to be a threat to global public health. The current cholera pandemic associated with Vibrio cholerae El Tor has now been ongoing for over half a century. Methodology/Principal Findings: Thirty-eight V. cholerae El Tor isolates associated with a cholera outbreak in 2009 from the Chandigarh region of India were characterised by a combination of microbiology, molecular typing and whole-genome sequencing. The genomic analysis indicated that two clones of V. cholera circulated in the region and caused disease during this time. These clones fell into two distinct sub-clades that map independently onto wave 3 of the phylogenetic tree of seventh pandemic V. cholerae El Tor. Sequence analyses of the cholera toxin gene, the Vibrio seventh Pandemic Island II (VSPII) and SXT element correlated with this phylogenetic position of the two clades on the El Tor tree. The clade 2 isolates, characterized by a drug-resistant profile and the expression of a distinct cholera toxin, are closely related to the recent V. cholerae isolated elsewhere, including Haiti, but fell on a distinct branch of the tree, showing they were independent outbreaks. Multi-Locus Sequence Typing (MLST) distinguishes two sequence types among the 38 isolates, that did not correspond to the clades defined by whole-genome sequencing. Multi-Locus Variable-length tandem-nucleotide repeat Analysis (MLVA) identified 16 distinct clusters. Conclusions/Significance: The use of whole-genome sequencing enabled the identification of two clones of V. cholerae that circulated during the 2009 Chandigarh outbreak. These clones harboured a similar structure of ICEVchHai1 but differed mainly in the structure of CTX phage and VSPII. The limited capacity of MLST and MLVA to discriminate between the clones that circulated in the 2009 Chandigarh outbreak highlights the value of whole-genome sequencing as a route to the identification of further genetic markers to subtype V. cholerae isolates. Author Summary: Vibrio cholerae is a diarrheal pathogen that is responsible for substantial morbidity and mortality worldwide. Historically, seven pandemics of cholera have been recognized, with classical biotype strains associated with the sixth and the El Tor biotype with the seventh (current) pandemic. Recently multi-drug resistant El Tor variants expressing classical cholera toxin have replaced the original El Tor strains in many epidemics, and are sometimes associated with more severe diarrhea leading to a higher mortality rate. In regions that experience recurrent cholera outbreaks, such as Northern India, it is important to understand the nature of the circulating strains and establish how they are related to the strains circulating globally. Here, we have demonstrated that whole- genome sequencing is a valuable method to characterize V. cholerae isolates that circulated during the 2009 outbreak in the Northern Indian city of Chandigarh. Through comparative genomic analysis, we identified two clones that circulated during a single outbreak. Importantly, these clones contain significant differences in the structure of the cholera toxin gene and the Vibrio seventh pandemic island II. Our findings demonstrate the limitations of current molecular typing techniques and the importance of surveillance with whole-genome sequencing for identifying V. cholerae clades with distinct genomic signatures. [ABSTRACT FROM AUTHOR]

Background: Cholera infection continues to be a threat to global public health. The current cholera pandemic associated with Vibrio cholerae El Tor has now been ongoing for over half a century. Methodology/Principal Findings: Thirty-eight V. cholerae El Tor isolates associated with a cholera outbreak in 2009 from the Chandigarh region of India were characterised by a combination of microbiology, molecular typing and whole-genome sequencing. The genomic analysis indicated that two clones of V. cholera circulated in the region and caused disease during this time. These clones fell into two distinct sub-clades that map independently onto wave 3 of the phylogenetic tree of seventh pandemic V. cholerae El Tor. Sequence analyses of the cholera toxin gene, the Vibrio seventh Pandemic Island II (VSPII) and SXT element correlated with this phylogenetic position of the two clades on the El Tor tree. The clade 2 isolates, characterized by a drug-resistant profile and the expression of a distinct cholera toxin, are closely related to the recent V. cholerae isolated elsewhere, including Haiti, but fell on a distinct branch of the tree, showing they were independent outbreaks. Multi-Locus Sequence Typing (MLST) distinguishes two sequence types among the 38 isolates, that did not correspond to the clades defined by whole-genome sequencing. Multi-Locus Variable-length tandem-nucleotide repeat Analysis (MLVA) identified 16 distinct clusters. Conclusions/Significance: The use of whole-genome sequencing enabled the identification of two clones of V. cholerae that circulated during the 2009 Chandigarh outbreak. These clones harboured a similar structure of ICEVchHai1 but differed mainly in the structure of CTX phage and VSPII. The limited capacity of MLST and MLVA to discriminate between the clones that circulated in the 2009 Chandigarh outbreak highlights the value of whole-genome sequencing as a route to the identification of further genetic markers to subtype V. cholerae isolates. [ABSTRACT FROM AUTHOR]

Background Alternative splicing (AS) of precursor mRNA (pre-mRNA) is an important gene regulation process that potentially regulates many physiological processes in plants, including the response to abiotic stresses such as salt stress. Results To analyze global changes in AS under salt stress, we obtained high-coverage (∼200 times) RNA sequencing data from Arabidopsis thaliana seedlings that were treated with different concentrations of NaCl. We detected that ∼49% of all intron-containing genes were alternatively spliced under salt stress, 10% of which experienced significant differential alternative splicing (DAS). Furthermore, AS increased significantly under salt stress compared with under unstressed conditions. We demonstrated that most DAS genes were not differentially regulated by salt stress, suggesting that AS may represent an independent layer of gene regulation in response to stress. Our analysis of functional categories suggested that DAS genes were associated with specific functional pathways, such as the pathways for the responses to stresses and RNA splicing. We revealed that serine/arginine-rich (SR) splicing factors were frequently and specifically regulated in AS under salt stresses, suggesting a complex loop in AS regulation for stress adaptation. We also showed that alternative splicing site selection (SS) occurred most frequently at 4 nucleotides upstream or downstream of the dominant sites and that exon skipping tended to link with alternative SS. Conclusions Our study provided a comprehensive view of AS under salt stress and revealed novel insights into the potential roles of AS in plant response to salt stress. [ABSTRACT FROM AUTHOR]

Background Metastasis accounts for the majority of deaths from cancer. Although tumor microenvironment has been shown to have a significant impact on the initiation and/or promotion of metastasis, the mechanism remains elusive. We previously reported that HCT-8 colon cancer cells underwent a phenotypic transition from an adhesive epithelial type (E-cell) to a rounded dissociated type (R-cell) via soft substrate culture, which resembled the initiation of metastasis. The objective of current study was to investigate the molecular and metabolic mechanisms of the E-R transition. Methods Global gene expressions of HCT-8 E and R cells were measured by RNA Sequencing (RNAseq); and the results were further confirmed by real-time PCR. Reactive oxygen species (ROS), anoikis resistance, enzyme activity of aldehyde dehydrogenase 3 family, member A1 (ALDH3A1), and in vitro invasion assay were tested on both E and R cells. The deformability of HCT-8 E and R cells was measured by atomic force microscopy (AFM). To study the in vivo invasiveness of two cell types, athymic nude mice were intra-splenically injected with HCT-8 E or R cells and sacrificed after 9 weeks. Incidences of tumor development and metastasis were histologically evaluated and analyzed with Fisher's exact test. Results Besides HCT-8, E-R transition on soft substrates was also seen in three other cancer cell lines (HCT116, SW480 colon and DU145 prostate cancer). The expression of some genes, such as ALDH3A1, TNS4, CLDN2, and AKR1B10, which are known to play important roles in cancer cell migration, invasion, proliferation and apoptosis, were increased in HCT-8 R cells. R cells also showed higher ALDH3A1 enzyme activity, higher ROS, higher anoikis resistance, and higher softness than E cells. More importantly, in vitro assay and in vivo animal models revealed that HCT-8 R cells were more invasive than E cells. Conclusions Our comprehensive comparison of HCT-8 E and R cells revealed differences of molecular, phenotypical, and mechanical signatures between the two cell types. To our knowledge, this is the first study that explores the molecular mechanism of E-R transition, which may greatly increase our understanding of the mechanisms of cancer mechanical microenvironment and initiation of cancer metastasis. [ABSTRACT FROM AUTHOR]

Traditional DNA sequencing methods are inefficient, lack the ability to discern the least abundant viral sequences, and ineffective for determining the extent of variability in viral populations. Here, populations of single-stranded DNA plant begomoviral genomes and their associated beta- and alpha-satellite molecules (virus-satellite complexes) (genus, Begomovirus; family, Geminiviridae) were enriched from total nucleic acids isolated from symptomatic, field-infected plants, using rolling circle amplification (RCA). Enriched virus-satellite complexes were subjected to Illumina-Next Generation Sequencing (NGS). CASAVA and SeqMan NGen programs were implemented, respectively, for quality control and for de novo and reference-guided contig assembly of viral-satellite sequences. The authenticity of the begomoviral sequences, and the reproducibility of the Illumina-NGS approach for begomoviral deep sequencing projects, were validated by comparing NGS results with those obtained using traditional molecular cloning and Sanger sequencing of viral components and satellite DNAs, also enriched by RCA or amplified by polymerase chain reaction. As the use of NGS approaches, together with advances in software development, make possible deep sequence coverage at a lower cost; the approach described herein will streamline the exploration of begomovirus diversity and population structure from naturally infected plants, irrespective of viral abundance. This is the first report of the implementation of Illumina-NGS to explore the diversity and identify begomoviral-satellite SNPs directly from plants naturally-infected with begomoviruses under field conditions. [ABSTRACT FROM AUTHOR]

Eukaryotic genomes encode hundreds of RNA-binding proteins, yet the functions of most of these proteins are unknown. In a genetic study of stress signal transduction in Arabidopsis, we identified a K homology (KH)-domain RNA-binding protein, HOS5 (High Osmotic Stress Gene Expression 5), as required for stress gene regulation and stress tolerance. HOS5 was found to interact with FIERY2/RNA polymerase II (RNAP II) carboxyl terminal domain (CTD) phosphatase-like 1 (FRY2/CPL1) both in vitro and in vivo. This interaction is mediated by the first double-stranded RNA-binding domain of FRY2/CPL1 and the KH domains of HOS5. Interestingly, both HOS5 and FRY2/CPL1 also interact with two novel serine-arginine (SR)-rich splicing factors, RS40 and RS41, in nuclear speckles. Importantly, FRY2/CPL1 is required for the recruitment of HOS5. In fry2 mutants, HOS5 failed to be localized in nuclear speckles but was found mainly in the nucleoplasm. hos5 mutants were impaired in mRNA export and accumulated a significant amount of mRNA in the nuclei, particularly under salt stress conditions. Arabidopsis mutants of all these genes exhibit similar stress-sensitive phenotypes. RNA-seq analyses of these mutants detected significant intron retention in many stress-related genes under salt stress but not under normal conditions. Our study not only identified several novel regulators of pre-mRNA processing as important for plant stress response but also suggested that, in addition to RNAP II CTD that is a well-recognized platform for the recruitment of mRNA processing factors, FRY2/CPL1 may also recruit specific factors to regulate the co-transcriptional processing of certain transcripts to deal with environmental challenges. [ABSTRACT FROM AUTHOR]

This study explores microbial community structure in managed aquifer recharge (MAR) systems across both laboratory and field scales. Two field sites, the Taif River (Taif, Saudi Arabia) and South Platte River (Colorado), were selected as geographically distinct MAR systems. Samples derived from unsaturated riverbed, saturated-shallow-infiltration (depth, 1 to 2 cm), and intermediate- infiltration (depth, 10 to 50 cm) zones were collected. Complementary laboratory-scale sediment columns representing low (0.6 mg/liter) and moderate (5 mg/liter) dissolved organic carbon (DOC) concentrations were used to further query the influence of DOC and depth on microbial assemblages. Microbial density was positively correlated with the DOC concentration, while diversity was negatively correlated at both the laboratory and field scales. Microbial communities derived from analogous sampling zones in each river were not phylogenetically significantly different on phylum, class, genus, and species levels, as determined by 16S rRNA gene pyrosequencing, suggesting that geography and season exerted less sway than aqueous geochemical properties. When field-scale communities derived from the Taif and South Platte River sediments were grouped together, principal coordinate analysis revealed distinct clusters with regard to the three sample zones (unsaturated, shallow, and intermediate saturated) and, further, with respect to DOC concentration. An analogous trend as a function of depth and corresponding DOC loss was observed in column studies. Canonical correspondence analysis suggests that microbial classes Betaproteobacteria and Gammaproteobacteria are positively correlated with DOC concentration. Our combined analyses at both the laboratory and field scales suggest that DOC may exert a strong influence on microbial community composition and diversity in MAR saturated zones. [ABSTRACT FROM AUTHOR]

Dormancy in underground vegetative buds of Canada thistle, an herbaceous perennial weed, allows escape from current control methods and contributes to its invasive nature. In this study, ∼65 % of root sections obtained from greenhouse propagated Canada thistle produced new vegetative shoots by 14 days post-sectioning. RNA samples obtained from sectioned roots incubated 0, 24, 48, and 72 h at 25°C under 16:8 h light-dark conditions were used to construct four MID-tagged cDNA libraries. Analysis of in silico data obtained using Roche 454 GS-FLX pyrosequencing technologies identified molecular networks associated with paradormancy release in underground vegetative buds of Canada thistle. Sequencing of two replicate plates produced ∼2.5 million ESTs with an average read length of 362 bases. These ESTs assembled into 67358 unique sequences (21777 contigs and 45581 singlets) and annotation against the Arabidopsis database identified 15232 unigenes. Among the 15232 unigenes, we identified processes enriched with transcripts involved in plant hormone signaling networks. To follow-up on these results, we examined hormone profiles in roots, which identified changes in abscisic acid (ABA) and ABA metabolites, auxins, and cytokinins post-sectioning. Transcriptome and hormone profiling data suggest that interaction between auxin- and ABA-signaling regulate paradormancy maintenance and release in underground adventitious buds of Canada thistle. Our proposed model shows that sectioning-induced changes in polar auxin transport alters ABA metabolism and signaling, which further impacts gibberellic acid signaling involving interactions between ABA and FUSCA3. Here we report that reduced auxin and ABA-signaling, in conjunction with increased cytokinin biosynthesis post-sectioning supports a model where interactions among hormones drives molecular networks leading to cell division, differentiation, and vegetative outgrowth. [ABSTRACT FROM AUTHOR]

To identify genes involved in the response to the fire blight pathogen Erwinia amylovora in apple (Malus×domestica), expression profiles were investigated using an apple oligo (70-mer) array representing 40, 000 genes. Blossoms of a fire blight-susceptible apple cultivar Gala were collected from trees growing in the orchard, placed on a tray in the laboratory, and spray-inoculated with a suspension of E. amylovora at a concentration of 108 cfu ml−1. Uninoculated detached flowers served as controls at each time point. Expression profiles were captured at three different time points post-inoculation at 2, 8, and 24 h, together with those at 0 h (uninoculated). A total of about 3500 genes were found to be significantly modulated in response to at least one of the three time points. Among those, a total of 770, 855, and 1002 genes were up-regulated, by 2-fold, at 2, 8, and 24 h following inoculation, respectively; while, 748, 1024, and 1455 genes were down-regulated, by 2-fold, at 2, 8, and 24 h following inoculation, respectively. Over the three time points post-inoculation, 365 genes were commonly up-regulated and 374 genes were commonly down-regulated. Both sets of genes were classified based on their functional categories. The majority of up-regulated genes were involved in metabolism, signal transduction, signalling, transport, and stress response. A number of transcripts encoding proteins/enzymes known to be up-regulated under particular biotic and abiotic stress were also up-regulated following E. amylovora treatment. Those up- or down-regulated genes encode transcription factors, signaling components, defense-related, transporter, and metabolism, all of which have been associated with disease responses in Arabidopsis and rice, suggesting similar response pathways are involved in apple blossoms. [ABSTRACT FROM PUBLISHER]

Thellungiella parvula is related to Arabidopsis thaliana and is endemic to saline, resource-poor habitats, making it a model for the evolution of plant adaptation to extreme environments. Here we present the draft genome for this extremophile species. Exclusively by next generation sequencing, we obtained the de novo assembled genome in 1,496 gap-free contigs, closely approximating the estimated genome size of 140 Mb. We anchored these contigs to seven pseudo chromosomes without the use of maps. We show that short reads can be assembled to a near-complete chromosome level for a eukaryotic species lacking prior genetic information. The sequence identifies a number of tandem duplications that, by the nature of the duplicated genes, suggest a possible basis for T. parvula's extremophile lifestyle. Our results provide essential background for developing genomically influenced testable hypotheses for the evolution of environmental stress tolerance. [ABSTRACT FROM AUTHOR]

The blind subterranean mole rat (Spalax ehrenbergi superspecies) is a model animal for survival under extreme environments due to its ability to live in underground habitats under severe hypoxic stress and darkness. Here we report the transcriptome sequencing of Spalax galili, a chromosomal type of S. ehrenbergi. cDNA pools from muscle and brain tissues isolated from animals exposed to hypoxic and normoxic conditions were sequenced using Sanger, GS FLX, and GS FLX Titanium technologies. Assembly of the sequences yielded over 51,000 isotigs with homology to ,12,000 mouse, rat or human genes. Based on these results, it was possible to detect large numbers of splice variants, SNPs, and novel transcribed regions. In addition, multiple differential expression patterns were detected between tissues and treatments. The results presented here will serve as a valuable resource for future studies aimed at identifying genes and gene regions evolved during the adaptive radiation associated with underground life of the blind mole rat. [ABSTRACT FROM AUTHOR]

The genome of Thellungiella parvula, a halophytic relative of Arabidopsis (Arabidopsis thaliana), is being assembled using Roche-454 sequencing. Analyses of a 10-Mb scaffold revealed synteny with Arabidopsis, with recombination and inversion and an uneven distribution of repeat sequences. T. parvula genome structure and DNA sequences were compared with orthologous regions from Arabidopsis and publicly available bacterial artificial chromosome sequences from Thellungiella salsuginea (previously Thellungiella halophila). The three-way comparison of sequences, from one abiotic stress-sensitive species and two tolerant species, revealed extensive sequence conservation and microcolinearity, but grouping Thellungiella species separately from Arabidopsis. However, the T. parvula segments are distinguished from their T. salsuginea counterparts by a pronounced paucity of repeat sequences, resulting in a 30% shorter DNA segment with essentially the same gene content in T. parvula. Among the genes is SALT OVERLY SENSITIVE1 (SOS1), a sodium/proton antiporter, which represents an essential component of plant salinity stress tolerance. Although the SOS1 coding region is highly conserved among all three species, the promoter regions show conservation only between the two Thellungiella species. Comparative transcript analyses revealed higher levels of basal as well as salt-induced SOS1 expression in both Thellungiella species as compared with Arabidopsis. The Thellungiella species and other halophytes share conserved pyrimidine-rich 5' untranslated region proximal regions of SOS1 that are missing in Arabidopsis. Completion of the genome structure of T. parvula is expected to highlight distinctive genetic elements underlying the extremophile lifestyle of this species. [ABSTRACT FROM AUTHOR]

Triticeae contains hundreds of species of both annual and perennial types. Although substantial genomic tools are available for annual Triticeae cereals such as wheat and barley, the perennial Triticeae lack sufficient genomic resources for genetic mapping or diversity research. To increase the amount of sequence information available in the perennial Triticeae, three expressed sequence tag (EST) libraries were developed and annotated for Pseudoroegneria spicata, a mixture of both Elymus wawawaiensis and E. lanceolatus, and a Leymus cinereus × L. triticoides interspecific hybrid. The ESTs were combined into unigene sets of 8 780 unigenes for P. spicata, 11 281 unigenes for Leymus, and 7 212 unigenes for Elymus. Unigenes were annotated based on putative orthology to genes from rice, wheat, barley, other Poaceae, Arabidopsis, and the non-redundant database of the NCBI. Simple sequence repeat (SSR) markers were developed, tested for amplification and polymorphism, and aligned to the rice genome. Leymus EST markers homologous to rice chromosome 2 genes were syntenous on Leymus homeologous groups 6a and 6b (previously 1b), demonstrating promise for in silico comparative mapping. All ESTs and SSR markers are available on an EST information management and annotation database (http://titan.biotec.uiuc.edu/triticeae/). [ABSTRACT FROM AUTHOR]

Many aspects of photosynthetic gene expression are posttranscriptionally regulated in C4 plants. To determine if RbcS mRNA untranslated regions (UTRs) in themselves could confer any characteristic C4 expression patterns, 5' - and 3' -UTRs of AhRbcS1 mRNA from the C4 dicot amaranth were linked to a gusA reporter gene. These were constitutively transcribed from a cauliflower mosaic virus promoter and assayed for posttranscriptional expression patterns in transgenic lines of the C4 dicot Flaveria bidentis. Three characteristic C4 expression patterns were conferred by heterologous AhRbcS1 UTRs in transgenic F. bidentis. First, the AhRbcS1 UTRs conferred strong translational enhancement of gusA expression, relative to control constructs lacking these UTRs. Second, while the UTRs did not appear to confer tissue-specific expression when analyzed by β-glucuronidase activity assays, differences in gusA mRNA accumulation were observed in leaves, stems, and roots. Third, the AhRbcS1 UTRs conferred preferential gusA expression (enzyme activity and gusA mRNA accumulation) in leaf bundle sheath cells. AhRbcS1 UTR-mediated translational enhancement was also observed in transgenic C3 plants (tobacco [Nicotiana tabacum]) and in in vitro translation extracts. These mRNAs appear to be translated with different efficiencies in C4 versus C3 plants, indicating that processes determining overall translational efficiency may vary between these two categories of higher plants. Our findings suggest that the AhRbcS1 5' -UTR functions as a strong translational enhancer in leaves and other tissues, and may work synergistically with the 3' -UTR to modulate overall levels of Rubisco gene expression in different tissues and cell types of C4 plants. [ABSTRACT FROM AUTHOR]

Gene sequences encoding gibberellin (GA) biosynthetic and catabolic enzymes were isolated from ‘Himalaya’ barley. These genes account for most of the enzymes required for the core pathway of GA biosynthesis as well as for the first major catabolic enzyme. By means of DNA gel blot analysis, we mapped coding sequences to chromosome arms in barley and wheat using barley-wheat chromosome addition lines, nulli-tetrasomic substitution and ditelosomic lines of wheat. These same sequences were used to identify closely related sequences from rice, which were mapped in silico, thereby allowing their syntenic relationship with map locations in barley and wheat to be investigated. Determination of the chromosome arm locations for GA metabolic genes provides a framework for future studies investigating possible identity between GA metabolic genes and dwarfing genes in barley and wheat. [ABSTRACT FROM AUTHOR]

Mycobacterium vaccae is a rapidly growing, nontuberculous Mycobacterium species that is generally not considered a human pathogen and is of major pharmaceutical interest as an immunotherapeutic agent. We report here the annotated genome sequence of the M. vaccae type strain, ATCC 25954. [ABSTRACT FROM AUTHOR]

Mycobacterium fortuitum is a member of the rapidly growing nontuberculous mycobacteria (NTM). It is ubiquitous in water and soil habitats, including hospital environments. M. fortuitum is increasingly recognized as an opportunistic nosocomial pathogen causing disseminated infection. Here we report the genome sequence of M. fortuitum subsp, fortuitum type strain DSM46621. [ABSTRACT FROM AUTHOR]