A Country on the Verge of Malaria Elimination – The Kingdom of Saudi Arabia

Significant headway has been made in the global fight against malaria in the past decade and as more countries enter the elimination phase, attention is now focused on identifying effective strategies to shrink the malaria map. Saudi Arabia experienced an outbreak of malaria in 1998, but is now on the brink of malaria elimination, with just 82 autochthonous cases reported in 2012. A review of published and grey literature was performed to identify the control strategies that have contributed to this achievement. The number of autochthonous malaria cases in Saudi Arabia decreased by 99.8% between 1998 and 2012. The initial steep decline in malaria cases coincided with a rapid scaling up of vector control measures. Incidence continued to be reported at low levels (between 0.01 and 0.1 per 1,000 of the population) until the adoption of artesunate plus sulfadoxine-pyrimethamine as first line treatment and the establishment of a regional partnership for a malaria-free Arabian Peninsula, both of which occurred in 2007. Since 2007, incidence has decreased by nearly an order of magnitude. Malaria incidence is now very low, but a high proportion of imported cases, continued potential for autochthonous transmission, and an increased proportion of cases attributable to Plasmodium vivax all present challenges to Saudi Arabia as they work toward elimination by 2015.     

iSCHRUNK – In Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models of Genome-scale Metabolic Networks

Accurate determination of physiological states of cellular metabolism requires detailed information about metabolic fluxes, metabolite concentrations and distribution of enzyme states. Integration of fluxomics and metabolomics data, and thermodynamics-based metabolic flux analysis contribute to improved understanding of steady-state properties of metabolism. However, knowledge about kinetics and enzyme activities though essential for quantitative understanding of metabolic dynamics remains scarce and involves uncertainty. Here, we present a computational methodology that allow us to determine and quantify the kinetic parameters that correspond to a certain physiology as it is described by a given metabolic flux profile and a given metabolite concentration vector. Though we initially determine kinetic parameters that involve a high degree of uncertainty, through the use of kinetic modeling and machine learning principles we are able to obtain more accurate ranges of kinetic parameters, and hence we are able to reduce the uncertainty in the model analysis. We computed the distribution of kinetic parameters for glucose-fed E. coli producing 1,4-butanediol and we discovered that the observed physiological state corresponds to a narrow range of kinetic parameters of only a few enzymes, whereas the kinetic parameters of other enzymes can vary widely. Furthermore, this analysis suggests which are the enzymes that should be manipulated in order to engineer the reference state of the cell in a desired way. The proposed approach also sets up the foundations of a novel type of approaches for efficient, non-asymptotic, uniform sampling of solution spaces.     

The Impact of Artemisinin Combination Therapy and Long-Lasting Insecticidal Nets on Forest Malaria Incidence in Tribal Villages of India, 2006–2011

Introduction

New tools for malaria control, artemisinin combination therapy (ACT) and long-lasting insecticidal nets (LLINs) were recently introduced across India. We estimated the impact of universal coverage of ACT and ACT plus LLINs in a setting of hyperendemic, forest malaria transmission.

Methods

We reviewed data collected through active and passive case detection in a vaccine trial cohort of 2,204 tribal people residing in Sundargarh district, Odisha between 2006 and 2011. We compared measures of transmission at the village and individual level in 2006–2009 versus 2010–2011 after ACT (in all villages) and LLINs (in three villages) were implemented.

Results

During 2006–2009 malaria incidence per village ranged from 156–512 per 1000 persons per year and slide prevalence ranged from 28–53%. Routine indoor residual spray did not prevent seasonal peaks of malaria. Post-intervention impact in 2010–2011 was dramatic with ranges of 14–71 per 1000 persons per year and 6–16% respectively. When adjusted for village, ACT alone decreased the incidence of malaria by 83% (IRR 0.17, 95%CI: 0.10, 0.27) and areas using ACT and LLINs decreased the incidence of malaria by 86% (IRR 0.14, 95%CI: 0.05, 0.38). After intervention, the age of malaria cases, their parasite density, and proportion with fever at the time of screening increased.

Conclusions

ACT, and LLINs along with ACT, effectively reduced malaria incidence in a closely monitored population living in a forest ecotype. It is unclear whether LLINs were impactful when prompt and quality antimalarial treatment was available. In spite of universal coverage, substantial malaria burden remained.     

In Silico Analysis of Crop Science： Report on the First China-UK Workshop on Chips, Computers and Crops

A workshop on ＂Chips, Computers and Crops＂ was held in Hangzhou, China during September 26-27, 2008. The main objective of the workshop was to bring together China and UK scientists from mathematics, bioinformatics and plant molecular biology communities to exchange ideas, enhance awareness of each others＇ fields, explore synergisms and make recommendations on fruitful future directions in crop science. Here we describe the contributions to the workshop, and examine some conceptual issues that lie at the foundations and future of crop systems biology.     

The Self-Limiting Dynamics of TGF-β Signaling In Silico and In Vitro,with Negative Feedback through PPM1A Upregulation

The TGF-β/Smad signaling system decreases its activity through strong negative regulation. Several molecular mechanisms of negative regulation have been published, but the relative impact of each mechanism on the overall system is unknown. In this work, we used computational and experimental methods to assess multiple negative regulatory effects on Smad signaling in HaCaT cells. Previously reported negative regulatory effects were classified by time-scale: degradation of phosphorylated R-Smad and I-Smad-induced receptor degradation were slow-mode effects, and dephosphorylation of R-Smad was a fast-mode effect. We modeled combinations of these effects, but found no combination capable of explaining the observed dynamics of TGF-β/Smad signaling. We then proposed a negative feedback loop with upregulation of the phosphatase PPM1A. The resulting model was able to explain the dynamics of Smad signaling, under both short and long exposures to TGF-β. Consistent with this model, immuno-blots showed PPM1A levels to be significantly increased within 30 min after TGF-β stimulation. Lastly, our model was able to resolve an apparent contradiction in the published literature, concerning the dynamics of phosphorylated R-Smad degradation. We conclude that the dynamics of Smad negative regulation cannot be explained by the negative regulatory effects that had previously been modeled, and we provide evidence for a new negative feedback loop through PPM1A upregulation. This work shows that tight coupling of computational and experiments approaches can yield improved understanding of complex pathways.     

In vitro Hardening – The Role of Ventilation on Acclimation Stress in Kniphofia leucocephala

Culture-induced phenotypes, which are caused by conditions in vitro, may result in poor survival of plantlets during acclimatisation. In vitro hardening of these phenotypes, however, may reduce the stress incurred with transplantation by inducing morphological or anatomical differences. Despite morphological differences, however, ventilated plantlets of Kniphofia leucocephala incurred stress of a similar magnitude to the controls as indicated by similar reductions in PSII photochemical efficiency (F _v/F _m). Thus, in vitro hardening in this species does not improve its capacity to tolerate environmental stresses during acclimatisation.     

The Effect of Fixed Orthodontic Appliances and Fluoride Mouthwash on the Oral Microbiome of Adolescents – A Randomized Controlled Clinical Trial

While the aesthetic effect of orthodontic treatment is clear, the knowledge on how it influences the oral microbiota and the consequential effects on oral health are limited. In this randomized controlled clinical trial we investigated the changes introduced in the oral ecosystem, during and after orthodontic treatment with fixed appliances in combination with or without a fluoride mouthwash, of 10–16.8 year old individuals (N = 91). We followed several clinical parameters in time, in combination with microbiome changes using next-generation sequencing of the bacterial 16S rRNA gene. During the course of our study, the oral microbial community displayed remarkable resilience towards the disturbances it was presented with. The effects of the fluoride mouthwash on the microbial composition were trivial. More pronounced microbial changes were related to gingival health status, orthodontic treatment and time. Periodontal pathogens (e.g. Selenomonas and Porphyromonas) were highest in abundance during the orthodontic treatment, while the health associated Streptococcus, Rothia and Haemophilus gained abundance towards the end and after the orthodontic treatment. Only minor compositional changes remained in the oral microbiome after the end of treatment. We conclude that, provided proper oral hygiene is maintained, changes in the oral microbiome composition resulting from orthodontic treatment are minimal and do not negatively affect oral health.     

In Silico Identification and Experimental Validation of Insertion–Deletion Polymorphisms in Tomato Genome

Comparative analysis of the genome sequences of Solanum lycopersicum variety Heinz 1706 and S. pimpinellifolium accession LA 1589 using MUGSY software identified 145 695 insertion–deletion (InDel) polymorphisms. A selected set of 3029 candidate InDels (≥2 bp) across the entire tomato genome were subjected to PCR validation, and 82.4% could be verified. Of 2272 polymorphic InDels between LA 1589 and Heinz 1706, 61.6, 45.2, and 31.6% were polymorphic in 8 accessions of S. pimpinellifolium, 4 accessions of S. lycopersicum var. cerasiforme, and 10 varieties of S. lycopersicum, respectively. Genetic distance was 0.216 in S. pimpinellifolium, 0.202 in S. lycopersicum var. cerasiforme, and 0.108 in S. lycopersicum. The data suggested a reduction of genetic variation from S. pimpinellifolium to S. lycopersicum var. cerasiforme and S. lycopersicum. Cluster analysis showed that the 8 accessions of S. pimpinellifolium were in one group, whereas 4 accessions of S. lycopersicum var. cerasiforme and 10 varieties of S. lycopersicum were in the same group.     

Discovery of Dihydrochalcone as Potential Lead for Alzheimer’s Disease: In Silico and In Vitro Study

By the virtual screening method we have screened out Dihydrochalcone as a top-lead for the Alzheimer’s disease using the database of about 32364 natural compounds. The binding affinity of this ligand to amyloid beta (A) fibril has been thoroughly studied by computer simulation and experiment. Using the Thioflavin T (ThT) assay we have obtained the inhibition constant IC50 M. This result is in good agreement with the estimation of the binding free energy obtained by the molecular mechanic-Poisson Boltzmann surface area method and all-atom simulation with the force field CHARMM 27 and water model TIP3P. Cell viability assays indicated that Dihydrochalcone could effectively reduce the cytotoxicity induced by A. Thus, both in silico and in vitro studies show that Dihydrochalcone is a potential drug for the Alzheimers disease.     

Adolescents with Type 1 Diabetes – The Impact of Gender,Age, and Health-Related Functioning on Eating Disorder Psychopathology

Objective

To investigate correlates of eating disorder psychopathology in adolescent males and females with type 1 diabetes.

Method

A total of 105 adolescents with type 1 diabetes (42% males), aged 12–20 years, were recruited from the Norwegian Childhood Diabetes Registry in this population-based study. All participants were interviewed with the Child Eating Disorder Examination. Additionally, the Brief Illness Perception Questionnaire, the Adolescent Coping Orientation for Problem Experiences and the Beliefs about Medicines Questionnaire were administered to assess health-related functioning. Clinical data were obtained from the Norwegian Childhood Diabetes Registry.

Results

Significant gender differences were demonstrated in the pattern of correlates of eating disorder pathology. Among females, eating disorder psychopathology was significantly associated with body mass index adjusted for age and gender, age, insulin restriction, coping, illness perceptions, and perceptions of insulin concern. In a regression model, age, illness perceptions, and insulin restriction remained significantly associated with eating disorder psychopathology, explaining 48% of the variance. None of the variables were associated with eating disorder psychopathology among males.

Discussion

Greater clinical awareness of illness perceptions, attitudes toward insulin, and insulin restriction may potentially decrease the risk of developing eating disorders among female adolescents with type 1 diabetes, and the subsequent increased morbidity and mortality associated with comorbid type 1 diabetes and eating disorders.     

Impact of Malaria Control on Mortality and Anemia among Tanzanian Children Less than Five Years of Age, 1999–2010

Background

Mainland Tanzania scaled up multiple malaria control interventions between 1999 and 2010. We evaluated whether, and to what extent, reductions in all-cause under-five child mortality (U5CM) tracked with malaria control intensification during this period.

Methods

Four nationally representative household surveys permitted trend analysis for malaria intervention coverage, severe anemia (hemoglobin <8 g/dL) prevalence (SAP) among children 6–59 months, and U5CM rates stratified by background characteristics, age, and malaria endemicity. Prevalence of contextual factors (e.g., vaccination, nutrition) likely to influence U5CM were also assessed. Population attributable risk percentage (PAR%) estimates for malaria interventions and contextual factors that changed over time were used to estimate magnitude of impact on U5CM.

Results

Household ownership of insecticide-treated nets (ITNs) rose from near zero in 1999 to 64% (95% CI, 61.7–65.2) in 2010. Intermittent preventive treatment of malaria in pregnancy reached 26% (95% CI, 23.6–28.0) by 2010. Sulfadoxine-pyrimethamine replaced chloroquine in 2002 and artemisinin-based combination therapy was introduced in 2007. SAP among children 6–59 months declined 50% between 2005 (11.1%; 95% CI, 10.0–12.3%) and 2010 (5.5%; 95% CI, 4.7–6.4%) and U5CM declined by 45% between baseline (1995–9) and endpoint (2005–9), from 148 to 81 deaths/1000 live births, respectively. Mortality declined 55% among children 1–23 months of age in higher malaria endemicity areas. A large reduction in U5CM was attributable to ITNs (PAR% = 11) with other malaria interventions adding further gains. Multiple contextual factors also contributed to survival gains.

Conclusion

Marked declines in U5CM occurred in Tanzania between 1999 and 2010 with high impact from ITNs and ACTs. High-risk children (1–24 months of age in high malaria endemicity) experienced the greatest declines in mortality and SAP. Malaria control should remain a policy priority to sustain and further accelerate progress in child survival.     

Pseudomonas putida AlkA and AlkB Proteins Comprise Different Defense Systems for the Repair of Alkylation Damage to DNA – In Vivo,In Vitro,and In Silico Studies

Alkylating agents introduce cytotoxic and/or mutagenic lesions to DNA bases leading to induction of adaptive (Ada) response, a mechanism protecting cells against deleterious effects of environmental chemicals. In Escherichia coli, the Ada response involves expression of four genes: ada, alkA, alkB, and aidB. In Pseudomonas putida, the organization of Ada regulon is different, raising questions regarding regulation of Ada gene expression. The aim of the presented studies was to analyze the role of AlkA glycosylase and AlkB dioxygenase in protecting P. putida cells against damage to DNA caused by alkylating agents. The results of bioinformatic analysis, of survival and mutagenesis of methyl methanesulfonate (MMS) or N-methyl-N’-nitro-N-nitrosoguanidine (MNNG) treated P. putida mutants in ada, alkA and alkB genes as well as assay of promoter activity revealed diverse roles of Ada, AlkA and AlkB proteins in protecting cellular DNA against alkylating agents. We found AlkA protein crucial to abolish the cytotoxic but not the mutagenic effects of alkylans since: (i) the mutation in the alkA gene was the most deleterious for MMS/MNNG treated P. putida cells, (ii) the activity of the alkA promoter was Ada-dependent and the highest among the tested genes. P. putida AlkB (PpAlkB), characterized by optimal conditions for in vitro repair of specific substrates, complementation assay, and M13/MS2 survival test, allowed to establish conservation of enzymatic function of P. putida and E. coli AlkB protein. We found that the organization of P. putida Ada regulon differs from that of E. coli. AlkA protein induced within the Ada response is crucial for protecting P. putida against cytotoxicity, whereas Ada prevents the mutagenic action of alkylating agents. In contrast to E. coli AlkB (EcAlkB), PpAlkB remains beyond the Ada regulon and is expressed constitutively. It probably creates a backup system that protects P. putida strains defective in other DNA repair systems against alkylating agents of exo- and endogenous origin.     

Impact of soil salinity on the plant-growth – promoting and biological control abilities of root associated bacteria

The effectiveness of plant growth – promoting bacteria is variable under different biotic and abiotic conditions. Abiotic factors may negatively affect the beneficial properties and efficiency of the introduced PGPR inoculants. The aim of this study was to evaluate the effect of plant growth – promoting rhizobacteria on plant growth and on the control of foot and root rot of tomatoes caused by Fusarium solani under different soil salinity conditions. Among the five tested strains, only Pseudomonas chlororaphis TSAU13, and Pseudomonas extremorientalis TSAU20 were able to stimulate plant growth and act as biological controls of foot and root rot disease of tomato. The soil salinity did not negatively affect the beneficial impacts of these strains, as they were able to colonize and survive on the roots of tomato plants under both saline and non-saline soil conditions. The improved plant height and fruit yield of tomato was also observed for plants inoculated with P. extremorientalis TSAU20. Our results indicated that, saline condition is not crucial factor in obtaining good performance with respect to the plant growth stimulating and biocontrol abilities of PGPR strains. The bacterial inoculant also enhanced antioxidant enzymes activities thereby preventing ROS induced oxidative damage in plants, and the proline concentrations in plant tissue that play an important role in plant stress tolerance.     

The Impact of DMARD and Anti-TNF Therapy on Functional Characterization of Short-Term T-Cell Activation in Patients with Rheumatoid Arthritis – A Follow-Up Study

Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by a systemic dysfunction of T-cells. In this study we tested the impact of DMARD and anti-TNF agents on short-term activation characteristics of T-cells. We enrolled 12 patients with newly diagnosed RA (naïve RA) who were treated with methothrexate (MTX) and glucocorticsteroid (GCS) and 22 patients with established RA non responding to conventional DMARD therapy who were treated with different anti-TNF agents. Nine healthy volunteers served as controls. Blood samples were taken at baseline, then at 4^th and 8^th week of therapy. The characteristics of several intracellular activation processes during short-term activation of T-cells including cytoplasmic Ca²⁺ level, mitochondrial Ca²⁺ level, reactive oxygen species (ROS) and nitric oxide (NO) generation were determined by a novel flow-cytometry technique. At baseline, the tested processes were comparable to controls in naïve RA. During GCS therapy, cytoplasmic Ca²⁺ level and ROS generation decreased. After the addition of MTX to GCS cytoplasmic Ca²⁺ level became comparable to controls, while ROS generation decreased further. In DMARD non responders, cytoplasmic Ca²⁺ level was higher than controls at baseline. The cytoplasmic Ca²⁺ level became comparable to controls and ROS generation decreased during each of the three anti-TNF-α agent therapies. Mitochondrial Ca²⁺ level and NO generation were unaltered in all of the patient groups. These results indicate that intracellular machinery is affected in T-cells of RA patients. This may alter the behavior of T-cells during activation. Different therapeutic approaches may modulate the abnormal T-cell functions.