LTR_STRUC: a novel search and identification program for LTR retrotransposons

MOTIVATION: Long terminal repeat (LTR) retrotransposons constitute a substantial fraction of most eukaryotic genomes and are believed to have a significant impact on genome structure and function. Conventional methods used to search for LTR retrotransposons in genome databases are labor intensive. We present an efficient, reliable and automated method to identify and analyze members of this important class of transposable elements. RESULTS: We have developed a new data-mining program, LTR_STRUC (LTR retrotransposon structure program) which identifies and automatically analyzes LTR retrotransposons in genome databases by searching for structural features characteristic of such elements. LTR_STRUC has significant advantages over conventional search methods in the case of LTR retrotransposon families having low sequence homology to known queries or families with atypical structure (e.g. non-autonomous elements lacking canonical retroviral ORFs) and is thus a discovery tool that complements established methods. LTR_STRUC finds LTR retrotransposons using an algorithm that encompasses a number of tasks that would otherwise have to be initiated individually by the user. For each LTR retrotransposon found, LTR_STRUC automatically generates an analysis of a variety of structural features of biological interest. AVAILABILITY: The LTR_STRUC program is currently available as a console application free of charge to academic users from the authors.     

In vitro receptor autoradiography: a map for exploring the hypothalamus.

In rabbits and guinea pigs, hypothalamic sites for prostaglandin E2 (PGE2) action were studied by means of in vitro receptor autoradiography. The density of PGE2 binding sites (probably PGE2 receptors) was the highest in the anterior wall of the third ventricle (A3V). This result is consistent in all mammalian species ever studied, suggesting a fundamental role of the A3V in the hypothalamic action of PGE2, such as fever.     

Haloarchaea: worth exploring for their biotechnological potential

Halophilic archaea are unique microorganisms adapted to survive under high salt conditions and biomolecules produced by them may possess unusual properties. Haloarchaeal metabolites are stable at high salt and temperature conditions that are useful for industrial applications. Proteins and enzymes of this group of archaea are functional under salt concentrations at which bacterial counterparts fail to be active. Such properties makes haloarchaeal enzymes suitable for salt-based applications and their use under dehydrating conditions. For example, bacteriorhodopsin or the purple membrane protein present in halophilic archaea has the most recognizable applications in photoelectric devices, artificial retinas, holograms etc. Haloarchaea are also useful for bioremediation of polluted hypersaline areas. Polyhydroxyalkanoates and exopolysccharides produced by these microorganisms are biodegradable and have the potential to replace commercial non-degradable plastics and polymers. Moreover, halophilic archaea have excellent potential to be used as drug delivery systems and for nanobiotechnology by virtue of their gas vesicles and S-layer glycoproteins. Despite of possible applications of halophilic archaea, laboratory-to-industrial transition of these potential candidates is yet to be established.     

Protein aggregation processes: In search of the mechanism

Amyloid formation typically follows a time course in which there is a long lag period followed by a rapid formation of fibrils. In this review, I show that the standard mechanisms of polymerization need to be expanded to consider that the monomeric proteins/peptides involved in amyloid formation are intrinsically disordered and exist as an ensemble of disordered-collapsed states. The review focuses primarily on events which occur in the long lag period defining these as protein folding issues, coupled with formation of oligomers. Experimental methods to explore folding and oligomerization issues over a wide range of protein concentrations using primarily fluorescence and 19F-NMR methods are discussed.     

Cuckoo search epistasis: a new method for exploring significant genetic interactions

The advent of high-throughput sequencing technology has resulted in the ability to measure millions of single-nucleotide polymorphisms (SNPs) from thousands of individuals. Although these high-dimensional data have paved the way for better understanding of the genetic architecture of common diseases, they have also given rise to challenges in developing computational methods for learning epistatic relationships among genetic markers. We propose a new method, named cuckoo search epistasis (CSE) for identifying significant epistatic interactions in population-based association studies with a case–control design. This method combines a computationally efficient Bayesian scoring function with an evolutionary-based heuristic search algorithm, and can be efficiently applied to high-dimensional genome-wide SNP data. The experimental results from synthetic data sets show that CSE outperforms existing methods including multifactorial dimensionality reduction and Bayesian epistasis association mapping. In addition, on a real genome-wide data set related to Alzheimer''s disease, CSE identified SNPs that are consistent with previously reported results, and show the utility of CSE for application to genome-wide data.     

In search of a treatment for Alzheimer's disease and potential immunonosuppresive therapeutic interventions

Alzheimer's disease (AD) is a serious neurodegenerative disease of aging. Recent projections of the dramatic increase in AD incidence worldwide by 2050 reveal its magnitude as a world-wide health crisis and underscore the urgent need to understand the etiology of AD in order to develop therapeutic interventions. A popular debate among scientists has traditionally pitted those in support of Beta amyloid protein as a causative factor ("Baptists") against others who implicate tau hyperphosphorylation ("Tauists"). Considering the significance of Beta amyloid protein and hyperphosphorlyated tau protein aggregates in AD pathology, this article delves into the nature of inflammation associated with these aggregates. Aspects of inflammation focus on microglia, resident immune cells of the CNS that are activated during AD inflammation and are known to play a significant role in pathogenesis. This article discusses the role of microglia, inflammation, and the immune response as a middle ground in the debate between the "Tauists" and the "Baptists" respective positions. It explores recent advances in immunotherapy and supports continued research in and use of immunosuppressive regimens as potential therapeutic interventions for AD.     

In search of the holy replicator

After 40 years of searching for the eukaryotic replicator sequence, it is time to abandon the concept of 'the' replicator as a single genetic entity. Here I propose a 'relaxed replicon model' in which a positive initiator-replicator interaction is facilitated by a combination of several complex features of chromatin. An important question for the future is whether the positions of replication origins are simply a passive result of local chromatin structure or are actively localized to coordinate replication with other chromosomal activities.     

In search of the ideal nose

The proportions of the so-called ideal nasal shape and the operations designed to achieve this have been the subject of innumerable papers. The vast majority of patients in the authors' practices desire a more refined version of the nose and do not want the so-called nosejob look with ideal proportions. A total of 2930 cosmetic rhinoplasties performed over the past 20 years, based on the philosophy of refining the more unrefined features of the nose according to the patients' wishes, have been reviewed, and almost all of these patients were satisfied with the long-term shape of their nose, even though in many cases these noses would be considered less than ideal by some of the newer criteria.