Inhibition of heat shock protein 90, a novel RET/PTC1-associated protein, increases radioiodide accumulation in thyroid cells

RET/PTC1 is a rearranged form of the RET tyrosine kinase commonly seen in papillary thyroid carcinomas. It has been shown that RET/PTC1 decreases expression of the sodium/iodide symporter (NIS), the molecule that mediates radioiodide therapy for thyroid cancer. Using proteomic analysis, we identify hsp90 and its co-chaperone p50cdc37 as novel proteins associated with RET/PTC1. Inhibition of hsp90 function with 17-allylamino-17-demothoxygeldanamycin (17-AAG) reduces RET/PTC1 protein levels. Furthermore, 17-AAG increases radioiodide accumulation in thyroid cells, mediated in part through a protein kinase A-independent mechanism. We show that 17-AAG does not increase the total amount of NIS protein or cell surface NIS localization. Instead, 17-AAG increases radioiodide accumulation by decreasing iodide efflux. Finally, the ability of 17-AAG to increase radioiodide accumulation is not restricted to thyroid cells expressing RET/PTC1. These findings suggest that 17-AAG may be useful as a chemotherapeutic agent, not only to inhibit proliferation but also to increase the efficacy of radioiodide therapy in patients with thyroid cancer.     

Whole genome resequencing of tobacco (<Emphasis Type="Italic">Nicotiana tabacum</Emphasis> L.) genotypes and high-throughput SNP discovery

Genome-wide single-nucleotide polymorphisms (SNPs) are highly useful in unraveling genetic insights and are essential to accelerate selections for genetic improvement in tobacco. The discovery of genome-wide SNPs in tobacco is very complex due to its high level of repetitive genome and polyploidy. At present, publicly available genomic data on SNPs are very limited, which warrants the need for high-throughput SNPs for application in tobacco breeding. In this research paper, we describe our efforts on SNP discovery by whole genome resequencing of 18 flue-cured Virginia (FCV) tobacco genotypes and annotation of SNPs in the tobacco genome. A large amount of data of about 225 GB per genotype was generated, with an average read depth of 50× using paired-end next-generation sequencing (NGS) with the HiSeq 2500 platform. The discovery of a large number of SNPs and indels was attempted to assist mapping and, thus, the selection processes to develop superior tobacco breeding lines. Discovered SNPs, their functional annotation, mapping to the reference genome, and their relative positioning in the linkage group are discussed in this paper.     

Paradigm shift – Metabolic transformation of docosahexaenoic and eicosapentaenoic acids to bioactives exemplify the promise of fatty acid drug discovery

Fatty acid drug discovery (FADD) is defined as the identification of novel, specialized bioactive mediators that are derived from fatty acids and have precise pharmacological/therapeutic potential. A number of reports indicate that dietary intake of omega-3 fatty acids and limited intake of omega-6 promotes overall health benefits. In 1929, Burr and Burr indicated the significant role of essential fatty acids for survival and functional health of many organs. In reference to specific dietary benefits of differential omega-3 fatty acids, docosahexaenoic and eicosapentaenoic acids (DHA and EPA) are transformed to monohydroxy, dihydroxy, trihydroxy, and other complex mediators during infection, injury, and exercise to resolve inflammation. The presented FADD approach describes the metabolic transformation of DHA and EPA in response to injury, infection, and exercise to govern uncontrolled inflammation. Metabolic transformation of DHA and EPA into a number of pro-resolving molecules exemplifies a novel, inexpensive approach compared to traditional, expensive drug discovery. DHA and EPA have been recommended for prevention of cardiovascular disease since 1970. Therefore, the FADD approach is relevant to cardiovascular disease and resolution of inflammation in many injury models. Future research demands identification of novel action targets, receptors for biomolecules, mechanism(s), and drug-interactions with resolvins in order to maintain homeostasis.     

Pervasiveness of UVC254-resistant Geobacillus strains in extreme environments

Applied Microbiology and Biotechnology - We have characterized a broad collection of extremophilic bacterial isolates from a deep subsurface mine, compost dumping sites, and several hot spring...     

Amaranthus caudatus lectin with polyproline II fold: conformational and functional transitions and molecular dynamics

Polyproline II (PPII) fold, a peculiar structural element was detected in the Amaranthus caudatus seed lectin (ACL) based on far UV circular dichroism spectrum, conformational transitions of the lectin, and a distinct isodichroic point in thermal denaturation. It was confirmed using PolyprOnline database to estimate the percentage of amino acids contributing to PPII fold and showed the values as 13.5 and 13.9% for PROSS and XTLSSTR, respectively. Investigations of the functional and conformational transitions of ACL during thermal-, pH-, and guanidine hydrochloride (GdnHCl)-induced denaturation were carried out using biochemical and biophysical techniques and molecular dynamics (MD) simulations approach. The lectin got aggregated at 60°C with instantaneous structural alterations. The aggregation-prone regions in ACL were predicted using online servers viz. AGGRESCAN, AmylPred, FoldAmyloid, and Waltz that were represented by Visual Molecular Dynamics tools. Nine conserved regions were identified by these softwares as being ‘hot-spots’ for aggregation. MD simulation studies of the lectin at 60°C revealed increase in radius of gyration. The loss of PPII fold in 2.0 M GdnHCl was reversible. The partially unfolded intermediate of ACL with diminished PPII fold formed at pH 1.0 was stable up to 90°C. The polyproline II fold has been rarely detected in lectins, ACL being the second after the potato lectin.     

Protein bioinformatics and mixtures of bivariate von Mises distributions for angular data

A fundamental problem in bioinformatics is to characterize the secondary structure of a protein, which has traditionally been carried out by examining a scatterplot (Ramachandran plot) of the conformational angles. We examine two natural bivariate von Mises distributions--referred to as Sine and Cosine models--which have five parameters and, for concentrated data, tend to a bivariate normal distribution. These are analyzed and their main properties derived. Conditions on the parameters are established which result in bimodal behavior for the joint density and the marginal distribution, and we note an interesting situation in which the joint density is bimodal but the marginal distributions are unimodal. We carry out comparisons of the two models, and it is seen that the Cosine model may be preferred. Mixture distributions of the Cosine model are fitted to two representative protein datasets using the expectation maximization algorithm, which results in an objective partition of the scatterplot into a number of components. Our results are consistent with empirical observations; new insights are discussed.     

Physiologic determinants of radiation resistance in Deinococcus radiodurans

Immense volumes of radioactive wastes, which were generated during nuclear weapons production, were disposed of directly in the ground during the Cold War, a period when national security priorities often surmounted concerns over the environment. The bacterium Deinococcus radiodurans is the most radiation-resistant organism known and is currently being engineered for remediation of the toxic metal and organic components of these environmental wastes. Understanding the biotic potential of D. radiodurans and its global physiological integrity in nutritionally restricted radioactive environments is important in development of this organism for in situ bioremediation. We have previously shown that D. radiodurans can grow on rich medium in the presence of continuous radiation (6,000 rads/h) without lethality. In this study we developed a chemically defined minimal medium that can be used to analyze growth of this organism in the presence and in the absence of continuous radiation; whereas cell growth was not affected in the absence of radiation, cells did not grow and were killed in the presence of continuous radiation. Under nutrient-limiting conditions, DNA repair was found to be limited by the metabolic capabilities of D. radiodurans and not by any nutritionally induced defect in genetic repair. The results of our growth studies and analysis of the complete D. radiodurans genomic sequence support the hypothesis that there are several defects in D. radiodurans global metabolic regulation that limit carbon, nitrogen, and DNA metabolism. We identified key nutritional constituents that restore growth of D. radiodurans in nutritionally limiting radioactive environments.