A molecular evaluation of dengue virus pathogenesis and its latest vaccine strategies

More than one third of the world’s population living in tropical and subtropical areas of the world is at risk of dengue infections and as many as 100 million people are yearly infected. This disease has reemerged during the past 20 years in the form of an epidemic. Dengue is caused by one of four related serotypes of dengue virus and often leads to severe forms of the disease, resulting commonly from secondary infections. Dengue virus is a mosquito borne virus, belongs to the family Flaviviridae and consists of a single stranded positive sense RNA genome. Like other RNA viruses it escapes defense mechanisms and neutralization attempts by mutations, which make it more resistant and adaptable to its environment. Antiviral strategies and vaccine development is thus impaired and hence to date there is no licensed vaccine available for dengue virus. Here we discuss various efforts made towards the identification of potential vaccine targets for dengue as well as various strategies employed by research groups/pharmaceutical companies towards the development of a successful dengue vaccine.     

Calcium Supplements: an Additional Source of Lead Contamination

The risk posed by the quantity of heavy metal lead present in Ca supplements is of grave concern. Some lead levels have been measured up to the extent of regulatory limit set by the United States. Calcium supplements inevitably get contaminated with lead as both are naturally occurring elements having the same charge density. Therefore, it is imperative to indicate the level of this toxic metal in these supplements in order to create awareness among consumers. The calcium in the supplements is derived from natural as well as synthetic/refined sources (chelated or non-chelated). In this study, a sophisticated analytical technique, atomic absorption spectrometer (both with FAAS and GFAAS modes of atomization), was used for the purpose of analyzing Pb contents in 27 commonly used Ca supplements manufactured by different national and multinational companies. The daily intake of lead through these supplements was calculated. Only 10% of the calcium supplements analyzed met the criteria of acceptable Pb levels (1.5 μg/daily dose) in supplements/consumer products set by the United States. It was also found that Pb intake was highest in chelated calcium supplements whereas lowest through calcium supplements with vitamin D formulation. The Pb concentration in calcium supplements was significantly increased (p < 0.001) according to their composition. In order to validate our results from the study conducted, IAEA-certified reference material (animal bone, H-5) was analyzed for Pb levels. The limit of detection of the method used was 0.05 μg/g and a 95% lead recovery of IAEA-certified reference material (animal bone, H-5).     

Decision-making critical amino acids: role in designing peptide vaccines for eliciting Th1 and Th2 immune response

CD4 T cells play a cardinal role in orchestrating immune system. Differentiation of CD4 T cells to Th1 and Th2 effector subsets depends on multiple factors such as relative intensity of interactions between T cell receptor with peptide-major histocompatibility complex, cytokine milieu, antigen dose, and costimulatory molecules. Literature supports the critical role of peptide’s binding affinity to Human Leukocyte Antigens (HLAs) and in the differentiation of naïve CD4 T cells to Th1 and Th2 subsets. However, there exists no definite report addressing very precisely the correlation between physicochemical properties (hydrophobicity, hydrophilicity), pattern, position of amino acids in peptide and their role in skewing immune response towards Th1 and Th2 cells. This may play a significant role in designing peptide vaccines. Hence in the present study, we have evaluated the relationship between amino acid pattern and their influence in differentiation of Th1 and Th2 cells. We have used a data set of 320 peptides, whose role has been already established experimentally in the generation of either Th1 or Th2 immune response. Further, characterization was done based on binding affinity, promiscuity, amino acid pattern and binding conformation of peptides. We have observed that distinct amino acids in peptides elicit either Th1 or Th2 immunity. Consequently, this study signifies that alteration in the sequence and type of selected amino acids in the HLA class II binding peptides can modulate the differentiation of Th1 and Th2 cells. Therefore, this study may have an important implication in providing a platform for designing peptide-based vaccine candidates that can trigger desired Th1 or Th2 response.     

Comparing genomic prediction accuracy from purebred,crossbred and combined purebred and crossbred reference populations in sheep

Background

The accuracy of genomic prediction depends largely on the number of animals with phenotypes and genotypes. In some industries, such as sheep and beef cattle, data are often available from a mixture of breeds, multiple strains within a breed or from crossbred animals. The objective of this study was to compare the accuracy of genomic prediction for several economically important traits in sheep when using data from purebreds, crossbreds or a combination of those in a reference population.

Methods

The reference populations were purebred Merinos, crossbreds of Border Leicester (BL), Poll Dorset (PD) or White Suffolk (WS) with Merinos and combinations of purebred and crossbred animals. Genomic breeding values (GBV) were calculated based on genomic best linear unbiased prediction (GBLUP), using a genomic relationship matrix calculated based on 48 599 Ovine SNP (single nucleotide polymorphisms) genotypes. The accuracy of GBV was assessed in a group of purebred industry sires based on the correlation coefficient between GBV and accurate estimated breeding values based on progeny records.

Results

The accuracy of GBV for Merino sires increased with a larger purebred Merino reference population, but decreased when a large purebred Merino reference population was augmented with records from crossbred animals. The GBV accuracy for BL, PD and WS breeds based on crossbred data was the same or tended to decrease when more purebred Merinos were added to the crossbred reference population. The prediction accuracy for a particular breed was close to zero when the reference population did not contain any haplotypes of the target breed, except for some low accuracies that were obtained when predicting PD from WS and vice versa.

Conclusions

This study demonstrates that crossbred animals can be used for genomic prediction of purebred animals using 50 k SNP marker density and GBLUP, but crossbred data provided lower accuracy than purebred data. Including data from distant breeds in a reference population had a neutral to slightly negative effect on the accuracy of genomic prediction. Accounting for differences in marker allele frequencies between breeds had only a small effect on the accuracy of genomic prediction from crossbred or combined crossbred and purebred reference populations.     

Enhanced Phytoremediation of Cadmium-Contaminated Soil by Parthenium hysterophorus Plant: Effect of Gibberellic Acid (GA3) and Synthetic Chelator,Alone and in Combinations

The roles of gibberellic acid (GA₃) and ethylenediaminetetraacetic acid (EDTA) in phytoremediation of cadmium (Cd)-contaminated soil by Parthenium hysterophorus plant was investigated. GA₃ (10^?9, 10^?7, and 10^?5M) was applied as a foliar spray. EDTA was added to soil in a single dose (160 mg/kg soil) and split doses (40 mg/kg soil, four split doses). GA₃ and EDTA were used separately and in various combinations. P. hysterophorus was selected due to its fast growth and unpalatable nature to herbivores to reduce the entrance of metal into the food chain. The Cd phytoextraction potential of the P. hysterophorus plant was evaluated for the first time. Cd significantly reduced plant growth and dry biomass (DBM). GA₃ alone increased the plant growth and biomass in Cd-contaminated soil, whereas EDTA reduced it. GA₃ in combination with EDTA significantly increased the growth and biomass. The highest significant DBM was found in treatment T3 (10^?5M GA₃). All treatments of GA₃ or EDTA significantly enhanced the plant Cd uptake and accumulation compared with control (C1). The highest significant root and stem Cd concentrations were found in the combination treatment T11 (GA₃ 10^?5M + EDTA split doses), whereas in leaves it was found in the EDTA treatments. Cd concentration in plant parts increased in the order of stem < leaves < roots. The combination treatment T9 (GA₃ 10^?7M + EDTA split doses) showed the significantly highest total Cd accumulation (8 times greater than control C1, i.e., only Cd used). The GA₃ treatments accumulated more than 50% of the total Cd in the roots, whereas the EDTA treatments showed more than 50% in the leaves. Root dry biomass showed a positive and significant correlation with Cd accumulation. GA₃ is environment friendly as compared with EDTA. Therefore, further investigation of GA₃ is recommended for phytoremediation research for the remediation of metal-contaminated soil.     

Genetic alterations in gastric precancerous lesions

To investigate the occurrence of 17p (p53) loss of heterozygosity (LOH) and increased 4N or aneuploidy in gastric precancerous lesions (GPL), and their association with Helicobacter pylori (H pylori) infection. A total of 78 gastric mucosal biopsy specimens, including 10 normal mucosa and 68 gastric precancerous lesions [chronic atrophic gastritis (CAG, n = 20), intestinal metaplasia (IM, n = 12), low grade dysplasia (LGD, n = 15), and high grade dysplasia (HGD, n = 21)] were studied using PCR and flow cytometry. A modified Giemsa staining technique was used to detect H pylori. The study was performed in Erzurum Numune Hospital between 2007 and 2009. 17p (p53) LOH was observed in (1/20) 5% of CAG, in (2/12) 16% of IM, in (3/15) 20% of LGD and in (11/21) 53% of HGD. There was correlation between prevalence of 17p (p53) LOH and histological type of GPL (P = 0.004). Similarly, increased 4N or aneuploidy was detected in (1/20) 5% of CAG, in (1/12) 8% of IM, in (2/15) 13% of LGD and in (9/21) 43% of HGD. The correlation was found between aneuploidy and histological type of GPL (P = 0.009). However, there was no correlation between presence of H pylori infection in histological type of GPL (P = 0.921). On the other hand, a significant association was found between increased 4N or aneuploidy and 17p (p53) LOH in all of GPL (P = 0.0001). However, there was no statistically significant association between H pylori infection and 17p (p53) LOH or increased 4N/aneuplody in GPL. 17p (p53) LOH and increased 4N or aneuploidy are closely related to the early stages of gastric carcinogenesis.