Selection of predicted siRNA as potential antiviral therapeutic agent against influenza virus

Influenza virus A (IVA) infection is responsible for recent death worldwide. Hence, there is a need to develop therapeutic agents against the virus. We describe the prediction of short interfering RNA (siRNA) as potential therapeutic molecules for the HA (Haemagglutinin) and NA (Neuraminidase) genes. We screened 90,522 siRNA candidates for HA and 13,576 for NA and selected 1006 and 1307 candidates for HA and NA, respectively based on the proportion of viral sequences that are targeted by the corresponding siRNA, with complete matches. Further short listing to select siRNA with no off-target hits, fulfilling all the guidelines mentioned in approach, provided us 13 siRNAs for haemagglutinin and 13 siRNAs for neuraminidase. The approach of finding siRNA using multiple sequence alignments of amino acid sequences has led to the identification of five conserved amino acid sequences, three in hemagglutinin i.e. RGLFGAIAGFIE, YNAELLV and AIAGFIE and two in neuraminidase i.e. RTQSEC and EECSYP which on reveres translation provided siRNA sequences as potential therapeutic candidates. The approaches used during this study have enabled us to identify potentially therapeutic siRNAs against divergent IVA strains.     

Analysis of glycosylation motifs and glycosyltransferases in Bacteria and Archaea

The process of glycosylation has been studied extensively in prokaryotes but many questions still remain unanswered. Glycosyltransferase is the enzyme which mediates glycosylation and has its preference for the target glycosylation sites as well as for the type of glycosylation i.e. N-linked and O-linked glycosylation. In this study we carried out the bioinformatics analysis of one of the key enzymes of pgl locus from Campylobacter jejuni, known as PglB, which is distributed widely in bacteria and AglB from archaea. Relatively little sequence similarity was observed in the archaeal AglB(s) as compared to those of the bacterial PglB(s). In addition we tried to the answer the question of as to why not all the sequins Asp-X-Ser/Thr have an equal opportunity to be glycosylated by looking at the influence of the neighboring amino acids but no significant conserved pattern of the flanking sites could be identified. The software tool was developed to predict the potential glycosylation sites in autotransporter protein, the virulence factors of gram negative bacteria, and our results revealed that the frequency of glycosylation sites was higher in adhesins (a subclass of autotransporters) relative to the other classes of autotransporters.     

Possible involvement of polyphenols and polyamines in salt tolerance of almond rootstocks

Leaf physiological and biochemical adaptive strategies and more particularly the possible involvement of polyamines and polyphenols in salt stress tolerance were investigated. Three almond rootstocks (GN15, GF677 and bitter almond) were subjected to 0, 25, 50 and 75 mM NaCl for 30 days. The dry mass of leaves, stems and roots decreased with increasing salt concentration in the irrigation solution regardless of genotype. Photosynthetic assimilation rate decreased in the three almond rootstocks, but more so in GF677 and bitter almond. The accumulation of toxic ions was greater in the leaves than in the roots in all genotypes. GN15 accumulated less Na⁺ and Cl⁻ than GF677 and bitter almond. GF677 accumulated polyphenols, but had less anthocyanin and antioxidant activity in its leaves compared to bitter almond. It seems that GN15 was more able to tolerate the excess of toxic ions using anthocyanins which are abundant in its red leaves and free polyamines for a more efficient response to stress. However, most of the antioxidant activity was found in the leaves and was lower in the roots. Given that the upper part of the tree will be of a different cultivar after grafting, this advantage may not be relevant for the tree’s survival. GF677 showed a different antioxidant strategy; it maintained a stable carotenoids content and accumulated polyphenols in its leaves. The three rootstocks used different strategies to deal with the excess of salt in the growth medium.     

Processing of metacaspase into a cytoplasmic catalytic domain mediating cell death in Leishmania major

Metacaspases are cysteine peptidases that could play a role similar to caspases in the cell death programme of plants, fungi and protozoa. The human protozoan parasite Leishmania major expresses a single metacaspase (LmjMCA) harbouring a central domain with the catalytic dyad histidine and cysteine as found in caspases. In this study, we investigated the processing sites important for the maturation of LmjMCA catalytic domain, the cellular localization of LmjMCA polypeptides, and the functional role of the catalytic domain in the cell death pathway of Leishmania parasites. Although LmjMCA polypeptide precursor form harbours a functional mitochondrial localization signal (MLS), we determined that LmjMCA polypeptides are mainly localized in the cytoplasm. In stress conditions, LmjMCA precursor forms were extensively processed into soluble forms containing the catalytic domain. This domain was sufficient to enhance sensitivity of parasites to hydrogen peroxide by impairing the mitochondrion. These data provide experimental evidences of the importance of LmjMCA processing into an active catalytic domain and of its role in disrupting mitochondria, which could be relevant in the design of new drugs to fight leishmaniasis and likely other protozoan parasitic diseases.     

Molecular typing of Bordetella parapertussis isolates circulating in Pakistan

Although a whole-cell pertussis vaccine was introduced in Pakistan in 1980, little is known about the pertussis prevalence and circulating strains in Pakistan. The aim of this study was to analyze Bordetella parapertussis isolates circulating between 2005 and 2009 in Pakistan and to compare them with those found in other countries during different periods. A total of 59 (7.35%) B.?parapertussis isolates from 802 subjects (median age, 3?years) from Pakistan, with pertussis-like symptoms were investigated. We carried out genotyping and DNA microarray analyses on these isolates and compared them with some international isolates of B.?parapertussis. We found that the allele for pertactin (prn) found in strains studied from Pakistan was identical to the predominant type found in Europe. We showed that B.?parapertussis isolates circulating in Pakistan are part of the same pulsed-field gel electrophoresis group to those circulating in Finland during the period of 1982-2007. Finally, microarray analysis confirmed that the isolates collected in Pakistan, were quite similar to international strains. Overall, these results confirm that B.?parapertussis is extremely monomorphic. The high isolation rate of B.?parapertussis (7.35%) compared to Bordetella pertussis (0.5%) may suggest that the whole-cell vaccine used in Pakistan is effective against B.?pertussis (0.5% infections detected), but much less so against B.?parapertussis.     

Combination therapy with KRAS siRNA and EGFR inhibitor AZD8931 suppresses lung cancer cell growth in vitro

Lung cancer is a leading cause of cancer-related deaths worldwide, with less than a 5-year survival rate for both men and women. Epidermal growth factor receptor (EGFR) and Kirsten rat sarcoma oncogene (KRAS) signaling pathways play a critical role in the proliferation and progression of various cancers, including lung cancer. Genetic studies have shown that amplification, over-expression, or mutation of EGFR is an early and major molecular event in many human tumors. KRAS mutation is a negative factor in various cancer, including non-small-cell lung cancer, and complicates therapeutic approaches with adjuvant chemotherapy and anti-EGFR directed therapies. This article is dedicated to evaluating the synergistic effect of a novel EGFR inhibitor AZD8931 and KRAS small interfering RNA (siRNA) on the proliferation and apoptosis of lung adenocarcinoma cancer cells. A549 lung cancer cells were treated with KRAS siRNA and the EGFR inhibitor alone or in combination. The cytotoxic effects of KRAS siRNA and te EGFR inhibitor were determined usingMTT assay, and induction of apoptosis was determined by FACS analysis. Suppression of KRAS, Her-2, and EGFR expression by treatments was measured by qRT-PCR and western blotting. KRAS siRNA and the EGFR inhibitor significantly reduced the proliferation of A549 cells as well as KRAS and EGFR mRNA levels 24 hr after treatment. The results also indicated that the silencing of KRAS and EGFR has synergistic effects on the induction of apoptosis on the A549 cells. These results indicated that KRAS and EGFR might play important roles in the progression of lung cancer and could be potential therapeutic targets for treatment of lung cancer.     

Life cycle assessment of retaining wall backfilled with shredded tires

Purpose

This life cycle assessment (LCA) study compares energy consumption, greenhouse gas emissions, and environmental damages for two methods of constructing retaining structures, a traditional method involving a retaining wall backfilled with sand, and an alternative method involving a retaining wall backfilled with shredded tires.

Methods

Taking into account the extraction and production of the used construction materials, loading, transport and installation, the cumulative energy demand (CED), global warming potential (GWP), acidification potential, Human Health Criteria Air-mobile, aquatic eutrophication potential, ozone depletion potential, and smog potential is determined for each construction method. The seven environmental impact categories are calculated using the software tool, ATHENA® Environmental Impact Estimator (ATHENA® EIE) for Buildings v5.2.0118.

Results and discussion

The seven impact categories were reduced significantly by using shredded tires as retaining wall backfill; this is due to the decrease in the amounts of concrete, reinforcing steel, and fuel quantity consumed by building machines and vehicles transporting construction materials.

Conclusions

The study concludes that in all examined impact categories alternative method provides a larger environmental benefit than the traditional method. Also, the results clearly demonstrate that the use of shredded tires is very effective as a sustainable alternative to retaining structures.

     

Salinity gradient and nutrients as major structuring factors of the phytoplankton communities in salt marshes

This study investigated the major environmental factors structuring, for a year, phytoplankton assemblages in the Sfax saltern (Tunisia): salinity and nutrients. A STATICO analysis based on 11 environmental variables and the abundances of 64 phytoplanktonic species was conducted. STATICO is used to analyze the stable part of the relationships between the environment and species, and then to determine how these relationships change over time. The analysis confirmed that the salinity gradient had a considerable influence on the composition of the phytoplanktonic communities. Bacillariophyceae and Dinophyceae dominated in the least salty ponds, whereas Chlorophyceae and Cyanophyceae dominated in the saltiest ponds, in accordance with the halotolerance level estimated for each species by calculating the optimum salinity and salt tolerance. Nitrogen (N) and phosphorus (P) ions could have a secondary influence on the phytoplankton distribution and its dynamics. Dinophyceae seem to be favored by high ammonium (NH₄ ⁺) concentrations, whereas diatoms seem to be favored by high orthophosphates (PO₄ ^3?) and nitrates (NO₃ ^?) values. The Chlorophyceae Dunalliela salina thrived in the saltiest ponds when the NO₃ ^? concentrations increased.     

Cost-effectiveness of Antivenoms for Snakebite Envenoming in Nigeria

Background

Snakebite envenoming is a major public health problem throughout the rural tropics. Antivenom is effective in reducing mortality and remains the mainstay of therapy. This study aimed to determine the cost-effectiveness of using effective antivenoms for Snakebite envenoming in Nigeria.

Methodology

Economic analysis was conducted from a public healthcare system perspective. Estimates of model inputs were obtained from the literature. Incremental Cost Effectiveness Ratios (ICERs) were quantified as deaths and Disability-Adjusted-Life-Years (DALY) averted from antivenom therapy. A decision analytic model was developed and analyzed with the following model base-case parameter estimates: type of snakes causing bites, antivenom effectiveness to prevent death, untreated mortality, risk of Early Adverse Reactions (EAR), mortality risk from EAR, mean age at bite and remaining life expectancy, and disability risk (amputation). End-user costs applied included: costs of diagnosing and monitoring envenoming, antivenom drug cost, supportive care, shipping/freezing antivenom, transportation to-and-from hospital and feeding costs while on admission, management of antivenom EAR and free alternative snakebite care for ineffective antivenom.

Principal Findings

We calculated a cost/death averted of ($2330.16) and cost/DALY averted of $99.61 discounted and $56.88 undiscounted. Varying antivenom effectiveness through the 95% confidence interval from 55% to 86% yield a cost/DALY averted of $137.02 to $86.61 respectively. Similarly, varying the prevalence of envenoming caused by carpet viper from 0% to 96% yield a cost/DALY averted of $254.18 to $78.25 respectively. More effective antivenoms and carpet viper envenoming rather than non-carpet viper envenoming were associated with lower cost/DALY averted.

Conclusions/Significance

Treatment of snakebite envenoming in Nigeria is cost-effective with a cost/death averted of $2330.16 and cost/DALY averted of $99.61 discounted, lower than the country''s gross domestic product per capita of $1555 (2013). Expanding access to effective antivenoms to larger segments of the Nigerian population should be a considered a priority.