The Biogeochemistry of Submerged Soils. * Kirk, G. 2004. * Chichester, UK: John Wiley & Sons, Ltd. {pound}100 (hardcover). 304 pp.

One can learn a lot about thegeochemistry of submerged soils in this book by Kirk. However,it is not, as the title implies, focused on the biogeochemistryof all submerged soils. In Chapter 1 Kirk gives a very briefoverview     

Vascular transport in plants * Holbrook NM, Zwieniecki MA. eds. 2005. * Amsterdam: Elsvier, * Academic Press. {pound}62.99 * (hardback). 564 pp.

This comprehensivecollection of 26 papers on all aspects of function and structureof vascular tissues will be of interest for anyone working inplant structure/function generally, or to specialists dealingwith physiology of water and sugar movement, leaf functions,wood anatomy and ecophysiology. The work of 52 contributors,including the two editors whose     

Seeds handbook: biology, production, processing and storage. 2nd edn. * Desai BB. 2004. * New York: Marcel Dekker.{pound}115 (hardback). 787 pp.

This book comprisesfour parts, the first three as identified in the title, anda fourth described as newer seed biotechnologies. Almost halfof the book is devoted to seed production,     

Development of an immunoenzyme method for detection and quantitative determination of microcystins

An indirect competitive immunoenzyme method for the quantitative estimation of microcystins (MCs) in water (MC-ELISA) using prepared MC-specific polyclonal antibodies was developed. The threshold concentration of the most widespread and highly toxic MC-LR, which was reliably detected using MC-ELISA, was 0.05 ± 0.01 ng/mL; the 50% inhibition concentration was 0.41 ± 0.05 ng/mL; and the concentration range for the quantitative estimation of MC-LR was 0.1–5.0 ng/mL. The MC-ELISA made it possible to detect MC-LR in water at concentrations 10–20 times lower than the World Health Organization guideline level for drinking water and 100–200 times lower than the allowable MC concentrations in water bodies. A group of cross-reacting MCs and nodularin was detected using MC-ELISA. This method can be applied for monitoring MC concentrations in water bodies and drinking water.     

Clusters of nonsolvent water in partially destroyed Saccharomyces cerevisiae yeast cells

The state of water in partially destroyed dry yeast cells has been studied using low-temperature ¹H NMR spectroscopy. It has been shown that the residual water is in the form of clusters of strongly and weakly associated water (SAW and WAW, respectively). Three or more types of SAW different in the chemical shift values have been found. It has been established that the interfacial water poorly dissolves hydrochloric and trifluoroacetic acids as well as DMSO and CD₃CN. Hydrochloric acid on a surface of biomaterials can be separated into HCl and water. This process is stabilized by polar co-solvents (DMSO and CD₃CN) added to the CDCl₃ dispersion medium.     

Household Water Chlorination Reduces Incidence of Diarrhea among Under-Five Children in Rural Ethiopia: A Cluster Randomized Controlled Trial

Background

Household water treatment has been advocated as a means of decreasing the burden of diarrheal diseases among young children in areas where piped and treated water is not available. However, its effect size, the target population that benefit from the intervention, and its acceptability especially in rural population is yet to be determined. The objective of the study was to assess the effectiveness of household water chlorination in reducing incidence of diarrhea among children under-five years of age.

Method

A cluster randomized community trial was conducted in 36 rural neighborhoods of Eastern Ethiopia. Households with at least one child under-five years of age were included in the study. The study compared diarrhea incidence among children who received sodium hypochlorite (liquid bleach) for household water treatment and children who did not receive the water treatment. Generalized Estimation Equation model was used to compute adjusted incidence rate ratio and the corresponding 95% confidence interval.

Result

In this study, the incidence of diarrhea was 4.5 episodes/100 person week observations in the intervention arm compared to 10.4 episodes/100 person week observations in the control arm. A statistically significant reduction in incidence of diarrhea was observed in the intervention group compared to the control (Adjusted IRR = 0.42, 95% CI 0.36–0.48).

Conclusion

Expanding access to household water chlorination can help to substantially reduce child morbidity and achieve millennium development goal until reliable access to safe water is achieved.

Trial Registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT01376440","term_id":"NCT01376440"}}NCT01376440     

Field observations on the influence of low water velocities on drifting of Bulinus globosus

The influence of water velocities of less than 30 cm/s on drifting of Bulinus globosus in a natural stream was investigated. It is shown that although a low water velocity does not sweep away adhering snails, it carries away snails releasing their hold and crawling along the water surface in search of new food sources. A low water velocity therefore assists considerably to the spreading of a snail species. Vegetation was found to have a decisive impact on local water velocity conditions by reducing the current and creating protected pockets. Upstream migration was found not to be common among Bulinus globosus. In addition, evidence for snail drifting under natural conditions within well established Schistosoma haematobium transmission sites is presented.     

Survival and HLA-B*57 in HIV/HCV Co-Infected Patients on Highly Active Antiretroviral Therapy (HAART)

Background and aims

HLA class I alleles, in particular HLA-B*57, constitute the most consistent host factor determining outcomes in untreated HCV- and HIV-infection. In this prospective cohort study, we analysed the impact of HLA class I alleles on all-cause mortality in patients with HIV-, HCV- and HIV/HCV- co-infection receiving HAART.

Methods

In 2003 HLA-A and B alleles were determined and patients were prospectively followed in 3-month intervals until 2013 or death. HLA-A and B alleles were determined by strand-specific oligonucleotide hybridisation and PCR in 468 Caucasian patients with HCV- (n=120), HIV- (n=186) and HIV/HCV-infection (n=162). All patients with HIV-infection were on HAART. In each patient group, HLA class I-associated survival was analysed by Kaplan-Meier method and Cox regression analysis.

Results

At recruitment the proportion of patients carrying a HLA-B*57 allele differed between HIV- (12.9%) and HCV-infection (4.2%). Kaplan Meier analysis revealed significantly increased mortality in HLA-B*57-positive patients with HIV-infection (p=0.032) and HIV/HCV-co-infection (p=0.004), which was apparently linked to non-viral infections. Cox logistic regression analysis confirmed HLA-B*57 (p=0.001), serum gamma-glutamyltranspeptidase (p=0.003), serum bilirubin (p=0.022) and CD4 counts (p=0.041) as independent predictors of death in HIV-infected patients.

Conclusion

Differences in the prevalence of HLA-B*57 at study entry between HIV- and HCV- infected patients may reflect immune selection in the absence of antiviral therapy. When patients were treated with HAART, however, HLA-B*57 was associated with increased mortality and risk to die from bacterial infections and sepsis, suggesting an ambiguous role of HLA-B*57 for survival in HIV/HCV infection depending on the circumstances.     

Prediction of drought-resistant genes in Arabidopsis thaliana using SVM-RFE

Background

Identifying genes with essential roles in resisting environmental stress rates high in agronomic importance. Although massive DNA microarray gene expression data have been generated for plants, current computational approaches underutilize these data for studying genotype-trait relationships. Some advanced gene identification methods have been explored for human diseases, but typically these methods have not been converted into publicly available software tools and cannot be applied to plants for identifying genes with agronomic traits.

Methodology

In this study, we used 22 sets of Arabidopsis thaliana gene expression data from GEO to predict the key genes involved in water tolerance. We applied an SVM-RFE (Support Vector Machine-Recursive Feature Elimination) feature selection method for the prediction. To address small sample sizes, we developed a modified approach for SVM-RFE by using bootstrapping and leave-one-out cross-validation. We also expanded our study to predict genes involved in water susceptibility.

Conclusions

We analyzed the top 10 genes predicted to be involved in water tolerance. Seven of them are connected to known biological processes in drought resistance. We also analyzed the top 100 genes in terms of their biological functions. Our study shows that the SVM-RFE method is a highly promising method in analyzing plant microarray data for studying genotype-phenotype relationships. The software is freely available with source code at http://ccst.jlu.edu.cn/JCSB/RFET/.     

The plant cell wall. * Rose JKC, ed 2003. * Oxford: CRC Press. {pound}99.50 (hardback). * 381 pp.

Cell walls have long been recognized as important and uniquefeatures of plant cells, contributing not only to the architectureof plant organs but also to the control of growth, to the exclusionof pathogens and to the production and transmission of signallingmolecules. Gross measurements of plant cell composition establishedlong ago that the plant devotes a large     

The R* rule and energy flux in a plant-nutrient ecosystem

The R* rule predicts that the species that can survive in steady state at the lowest level of limiting resource, R*, excludes all other species. Simple models indicate that this concept is not necessarily consistent with Lotka's conjecture that an ecological system should evolve towards a state of maximum power, Max(G), where G is the power, or rate of biomass production of the system. To explore the relationship in detail, we used a published model of a plant-nutrient system in which a plant can use various strategies, S, of allocation of energy between foliage, roots, and wood. We found that the allocation strategy, S_MinR*, that leads to , where is a limiting nutrient in soil pore water in our model (and equivalent to R* in Tilman's notation), is the same as the strategy, S_{MaxG_root}, for which energy flux to roots is maximized. However, that allocation strategy is different from the strategy, S_MaxG, that produces maximum power, or maximum photosynthetic rate, for the plant system, Max(G). Hence, we conclude that and Max(G) should not necessarily co-occur in an ecological system. We also examined which strategy, S_fit, was fittest; that is, eliminated any other strategies, when allowed to compete. The strategy S_fit differed from S_MinR*, S_MaxG, and S_{MaxG_root}, which we demonstrated mathematically. We also considered the feasible situation in which a plant is able to positively influence external nutrient input to the system. Under such conditions, the strategy, S_{MaxG_root}, that maximizes energy flux to roots was the same as the strategy, S_MaxR*, that leads to maximum concentration of available nutrient in soil pore water, , and not same as S_MinR*, for .     

Involvement of miR164- and miR167-mediated target gene expressions in responses to water deficit in cassava

Cassava (Manihot esculenta Crantz) is an important crop and it is significantly affected by water stress. The computational analysis of cis-regulatory elements in promoter regions of 21 drought-responsive miRNA gene families and 35 miRNA-target genes in cassava indicated some elements relevant to drought stress responses. To investigate the role of miRNAs and target genes in responses to a water deficit in cassava in more detail, in vitro plantlets were subjected to an imitated water deficit by 40 % polyethylene glycol. Using RT-qPCR, the differential expression of the cassava miR164/MesNAC and miR167/MesARF6/8 were observed to be associated with changes in the leaf shape, stomatal closure, and relative water content. The modified 5′-RNA ligase-mediated rapid amplification of cDNA-end (5’RLM-RACE) experiment confirmed MesNAC and MesARF8 as the in vivo-target genes of miR164 and miR167, respectively, in cassava leaf. The possible functions of miR164 and miR167-target genes in response to water deficit are discussed.     

An introduction to plant structure and development * Beck CB. 2005. * Cambridge, UK: Cambridge University Press. {pound}30.00 (hardback). 464 pp.

This book has beenwritten primarily as a text for a senior plant anatomy course.The initial phrase ‘An introduction to’ is somewhatmisleading as a student would need to have some elementary knowledgeof botany as well as cell structure and physiology to followthe information and the ideas without difficulty. The authordoes     

Arsenic in Drinking Water and Mortality for Cancer and Chronic Diseases in Central Italy, 1990-2010

Background

In several volcanic areas of Italy, arsenic levels exceed European regulatory limits (10 μg/L in drinking water). There is still uncertainty about health risks from arsenic at low-medium doses (<100 μg/L).

Objectives

A large population-based study using an administrative cohort of residents in the Viterbo province (Central Italy), chronically exposed to low-medium arsenic levels via drinking water, was investigated to evaluate the effects of a lifetime exposure to arsenic on mortality from cancers and chronic diseases.

Methods

The study population consisted of 165,609 residents of 17 municipalities, followed from 1990 until 2010. Average individual arsenic exposure at the first residence (As_I) was estimated through a space-time modeling approach using residential history and arsenic concentrations from water supply. A time-dependent Cumulative Arsenic dose Indicator (CAI) was calculated, accounting for daily water intake and exposure duration. Mortality Hazard Ratios (HR) were estimated by gender for different diseases using Cox proportional models, adjusting for individual and area-level confounders. A flexible non-parametric approach was used to investigate dose-response relationships.

Results

Mean As_I exposure was 19.3 μg/L, and average exposure duration was 39.5 years. Associations of As_I and CAI indicators with several diseases were found, with greatest risks found for lung cancer in both sexes (HR = 2.61 males; HR = 2.09 females), myocardial infarction, peripheral arterial disease and COPD in males (HR = 2.94; HR = 2.44; HR = 2.54 respectively) and diabetes in females (HR = 2.56). For lung cancer and cardiovascular diseases dose-response relationship is modelled by piecewise linear functions revealing effects even for doses lower than 10 μg/L, and no threshold dose value was identified as safe for health.

Conclusions

Results provide new evidence for risk assessment of low-medium concentrations of arsenic and contribute to the ongoing debate about the threshold-dose of effect, suggesting that even concentrations below 10 μg/L carry a mortality risk. Policy actions are urgently needed in areas exposed to arsenic like in the Viterbo province, to comply with current EU regulations.     

Effects of Source- versus Household Contamination of Tubewell Water on Child Diarrhea in Rural Bangladesh: A Randomized Controlled Trial

Background

Shallow tubewells are the primary drinking water source for most rural Bangladeshis. Fecal contamination has been detected in tubewells, at low concentrations at the source and at higher levels at the point of use. We conducted a randomized controlled trial to assess whether improving the microbiological quality of tubewell drinking water by household water treatment and safe storage would reduce diarrhea in children <2 years in rural Bangladesh.

Methods

We randomly assigned 1800 households with a child aged 6-18 months (index child) into one of three arms: chlorine plus safe storage, safe storage and control. We followed households with monthly visits for one year to promote the interventions, track their uptake, test participants’ source and stored water for fecal contamination, and record caregiver-reported child diarrhea prevalence (primary outcome). To assess reporting bias, we also collected data on health outcomes that are not expected to be impacted by our interventions.

Findings

Both interventions had high uptake. Safe storage, alone or combined with chlorination, reduced heavy contamination of stored water. Compared to controls, diarrhea in index children was reduced by 36% in the chlorine plus safe storage arm (prevalence ratio, PR = 0.64, 0.55-0.73) and 31% in the safe storage arm (PR = 0.69, 0.60-0.80), with no difference between the two intervention arms. One limitation of the study was the non-blinded design with self-reported outcomes. However, the prevalence of health outcomes not expected to be impacted by water interventions did not differ between study arms, suggesting minimal reporting bias.

Conclusions

Safe storage significantly improved drinking water quality at the point of use and reduced child diarrhea in rural Bangladesh. There was no added benefit from combining safe storage with chlorination. Efforts should be undertaken to implement and evaluate long-term efforts for safe water storage in Bangladesh.

Trial Registration

ClinicalTrials.gov NCT01350063     

Solvated helical backbones: x-ray diffraction study of Boc-Ala-Leu-Aib-Ala-Leu-Aib-OMe.H2O

A second example of insertion of a water molecule into the helical backbone of an apolar peptide is presented here and compared to a similar occurrence in a longer peptide with the same type of sequence of residues, i.e., Boc-Aib-(Ala-Leu-Aib)3-OMe. The backbone of the title compound assumes an approximate 3(10)-helical form with three 4----1 hydrogen bonds. In the place of a fourth 4----1 hydrogen bond, a water molecule is inserted between O(1) and N(4), and acts as a bridge by forming hydrogen bonds N(4) ... W(1) (2.95 A) and W(1) ... O(1) (2.81 A). The water molecule participates in a third hydrogen bond with a neighboring peptide molecule, W(1) ... O(4) (2.91 A). The insertion of the water molecule causes the apolar peptide to mimic an amphiphilic helix. Crystals grown from ethyl acetate/petroleum ether (reported here) or from methanol/water solution are in space group P2(1)2(1)2(1) with a = 12.024(4) A, b = 15.714(6) A, c = 21.411(7) A, Z = 4 and dcalc = 1.124 g/cm3 for C32H58N6O9.H2O. The overall agreement factor R is 6.3% for 2707 reflections observed with intensities greater than 3 sigma(F) and the resolution is 0.90 A.     

HLA Allele E*01:01 Is Associated with a Reduced Risk of EBV-Related Classical Hodgkin Lymphoma Independently of HLA-A*01/*02

Background

An inefficient immune response against Epstein-Barr virus (EBV) infection is related to the pathogenesis of a subgroup of classical Hodgkin lymphomas (cHL). Some EBV immune-evasion mechanisms target HLA presentation, including the non-classical HLA-E molecule. HLA-E can be recognized by T cells via the TCR, and it also regulates natural killer (NK) cell signaling through the inhibitory CD94/NKG2A receptor. Some evidences indicate that EBV-infected B-cells promote the proliferation of NK subsets bearing CD94/NKG2A, suggesting a relevant function of these cells in EBV control. Variations in CD94/NKG2A-HLA-E interactions could affect NK cell-mediated immunity and, consequently, play a role in EBV-driven transformation and lymphomagenesis. The two most common HLA-E alleles, E*01:01 and E*01:03, differ by a single amino acid change that modifies the molecule function. We hypothesized that the functional differences in these variants might participate in the pathogenicity of EBV.

Aim

We studied two series of cHL patients, both with EBV-positive and-negative cases, and a cohort of unrelated controls, to assess the impact of HLA-E variants on EBV-related cHL susceptibility.

Results

We found that the genotypes with at least one copy of E*01:01 (i.e., E*01:01 homozygous and heterozygous) were underrepresented among cHL patients from both series compared to controls (72.6% and 71.6% vs 83%, p = 0.001). After stratification by EBV status, we found low rates of E*01:01-carriers mainly among EBV-positive cases (67.6%). These reduced frequencies are seen independently of other factors such as age, gender, HLA-A*01 and HLA-A*02, HLA alleles positively and negatively associated with the disease (adjusted OR = 0.4, p = 0.001). Furthermore, alleles from both HLA loci exert a cumulative effect on EBV-associated cHL susceptibility.

Conclusions

These results indicate that E*01:01 is a novel protective genetic factor in EBV-associated cHL and support a role for HLA-E recognition on the control of EBV infection and lymphomagenesis.     

A randomised controlled trial of ion-exchange water softeners for the treatment of eczema in children

Background

Epidemiological studies and anecdotal reports suggest a possible link between household use of hard water and atopic eczema. We sought to test whether installation of an ion-exchange water softener in the home can improve eczema in children.

Methods and Findings

This was an observer-blind randomised trial involving 336 children (aged 6 months to 16 years) with moderate/severe atopic eczema. All lived in hard water areas (≥200 mg/l calcium carbonate). Participants were randomised to either installation of an ion-exchange water softener plus usual eczema care, or usual eczema care alone. The primary outcome was change in eczema severity (Six Area Six Sign Atopic Dermatitis Score, SASSAD) at 12 weeks, measured by research nurses who were blinded to treatment allocation. Analysis was based on the intent-to-treat population. Eczema severity improved for both groups during the trial. The mean change in SASSAD at 12 weeks was −5.0 (20% improvement) for the water softener group and −5.7 (22% improvement) for the usual care group (mean difference 0.66, 95% confidence interval −1.37 to 2.69, p = 0.53). No between-group differences were noted in the use of topical corticosteroids or calcineurin inhibitors.

Conclusions

Water softeners provided no additional benefit to usual care in this study population. Small but statistically significant differences were found in some secondary outcomes as reported by parents, but it is likely that such improvements were the result of response bias, since participants were aware of their treatment allocation. A detailed report for this trial is also available at http://www.hta.ac.uk.

Trial registration

Current Controlled Trials ISRCTN71423189 Please see later in the article for the Editors'' Summary     

Molecular ecotoxicology of plants. Ecological Studies Vol. 170. * Sandermann H. ed. 2004. * Berlin: Springer. $89{middle dot}95 (hard cover). 241 pp.

Googling the term‘molecular ecotoxicology’ results in less than 1000hits compared to more than 8·5 million for ‘moleculargenetics’. Hence, we are dealing with a rather new orless well-defined and less propagated field of science. Springer'sbook Molecular ecotoxicology of plants edited by H. Sandermannmay therefore fill a gap and it is unique in focusing on plants.A first introductory chapter sets the stage and tries to definethe term for a broad     

Protective Effect of HLA-B*5701 and HLA-C -35 Genetic Variants in HIV-Positive Caucasians from Northern Poland

Aim of the Study

Association of two HLA class I variants with HIV-1 pretreatment viremia, CD4+ T cell count at the care-entry and CD4+ T cell nadir.

Methods

414 HIV-positive Caucasians (30% women) aged 19-73 years were genotyped for HLA-C -35 (rs9264942) and HLA-B*5701 variants. HIV-1 viral load, as well as CD4+ T cell count at care-entry and nadir, were compared across alleles, genotypes and haplotypes.

Results

HLA-C -35 C/C genotype was found in 17.6% patients, C/T genotype in 48.1%, and T/T genotype in 34.3% patients. HLA-B*5701 variant was present in 5.8% of studied population. HIV plasma viremia in the group with C allele was significantly lower (p=0.0002) compared to T/T group [mean:4.66 log (SD:1.03) vs. 5.07 (SD:0.85) log HIV-RNA copies/ml, respectively], while CD4+ T cell count at baseline was notably higher among C allele carriers compared to T/T homozygotes [median: 318 (IQR:127-537) cells/μl vs. median: 203 (IQR:55-410) cells/μl, respectively] (p=0.0007). Moreover, CD4+ T cell nadir among patients with C allele [median: 205 (IQR:83.5-390) cells/μl] was significantly higher compared to T/T group [median: 133 (IQR:46-328) cells/μl] (p=0.006). Among cases with HLA-B*5701 allele, significantly lower pretreatment viremia and higher baseline CD4+ T cell count were found (mean: 4.08 [SD: 1.2] vs. mean: 4.84 [SD:0.97] log HIV-RNA copies/ml, p=0.003 and 431 vs. 270 cells/μl, p=0.04, respectively) compared to HLA-B*5701 negative individuals. The lowest viremia (mean: 3.85 log [SD:1.3]) HIV-RNA copies/ml and the highest baseline and nadir CD4+ T cell [median: 476 (IQR:304-682) vs. median: 361 (IQR: 205-574) cells/μl, respectively) were found in individuals with HLA-B*5701(+)/HLA-C –35 C/C haplotype.

Conclusions

HLA-C -35 C and HLA-B*5701 allele exert a favorable effect on the immunological (higher baseline and nadir CD4+ T cell count) and virologic (lower pretreatment HIV viral load) variables. This protective effect is additive for the compound HLA-B*5701(+)/HLA-C -35 C/C haplotype.