BEAM: a beam search algorithm for the identification of cis-regulatory elements in groups of genes.

The identification of potential protein binding sites (cis-regulatory elements) in the upstream regions of genes is key to understanding the mechanisms that regulate gene expression. To this end, we present a simple, efficient algorithm, BEAM (beam-search enumerative algorithm for motif finding), aimed at the discovery of cis-regulatory elements in the DNA sequences upstream of a related group of genes. This algorithm dramatically limits the search space of expanded sequences, converting the problem from one that is exponential in the length of motifs sought to one that is linear. Unlike sampling algorithms, our algorithm converges and is capable of finding statistically overrepresented motifs with a low failure rate. Further, our algorithm is not dependent on the objective function or the organism used. Limiting the space of candidate motifs enables the algorithm to focus only on those motifs that are most likely to be biologically relevant and enables the algorithm to use direct evaluations of background frequencies instead of resorting to probabilistic estimates. In addition, limiting the space of candidate motifs makes it possible to use computationally expensive objective functions that are able to correctly identify biologically relevant motifs.     

More than Just a Phase: Prions at the Crossroads of Epigenetic Inheritance and Evolutionary Change

A central tenet of molecular biology is that heritable information is stored in nucleic acids. However, this paradigm has been overturned by a group of proteins called “prions.” Prion proteins, many of which are intrinsically disordered, can adopt multiple conformations, at least one of which has the capacity to self-template. This unusual folding landscape drives a form of extreme epigenetic inheritance that can be stable through both mitotic and meiotic cell divisions. Although the first prion discovered—mammalian PrP—is the causative agent of debilitating neuropathies, many additional prions have now been identified that are not obviously detrimental and can even be adaptive. Intrinsically disordered regions, which endow proteins with the bulk property of “phase-separation,” can also be drivers of prion formation. Indeed, many protein domains that promote phase separation have been described as prion-like. In this review, we describe how prions lie at the crossroads of phase separation, epigenetic inheritance, and evolutionary adaptation.     

A peptidyl derivative of [3H]aniline as a sensitive, stable, protease substrate.

A peptidyl derivative of [³H]aniline, Gly-Gly-Arg-[³H]anilide, can be used as a substrate in a convenient and sensitive assay procedure for trypsin, urokinase, and plasminogen activator from transformed cells. The extent of hydrolysis can be determined simply by selective extraction of the product [³H]aniline into an organic phase containing a scintillant. (The uncleaved peptide is not appreciably soluble in this phase and is not counted.) The reaction is of comparable sensitivity to fluorimetric assays, but has the advantage that no cleanup of the biological sample is required, since it is far less subject to interference from fluorescence quenching. Other peptidyl anilides should be useful for assaying proteolytic enzymes with widely varying specificities.     

Drug protein interaction at the molecular level: A study of sulphonamide carbonic anhydrase complexes

The molecular mechanism of drug action has been studied by X-ray diffraction analysis of human carbonic anhydrase I complexed with two different sulphonamides. The acetazolamide and amino benzene sulphonamide are found to bind to the catalytically essential zinc ion thereby inhibiting the function of the enzyme. The inhibitor molecules are stabilized in the active site of the protein by van der Waals interaction with a number of protein side chain groups.     

Genome-wide profiling of sperm DNA methylation in relation to buffalo (Bubalus bubalis) bull fertility

The DNA methylation pattern in spermatozoa of buffalo bulls of different fertility status was investigated. Spermatozoa isolated DNA from two groups of buffalo bulls (n = 5), selected based on their artificial insemination–generated conception rate data followed by IVF efficiency, were studied for global methylation changes using a custom-designed 180 K buffalo (Bubalus bubalis) CpG island/promoter microarray. A total of 96 individual genes with another 55 genes covered under CpG islands were found differentially methylated in sperm of high-fertile and subfertile buffalo bulls. Important genes associated with biological processes, cellular components, and functions were identified to be differentially methylated in buffalo bulls with differential fertility status. The identified differentially methylated genes were found to be involved in germ cell development, spermatogenesis, capacitation, and embryonic development. The observations hint that methylation defects of sperm DNA may play a crucial role in determining the fertility of breeding bulls. This growing field of sperm epigenetics will be of great benefit in understanding the graded fertility conditions of breeding bulls in commercial livestock production system.     

Health Risk Assessment of Domestic Roof Water Harvesting Using Failure Mode and Effects Analysis: Evidence from Nagaur,Rajasthan, India

This article is crafted around assessment and analysis of health risks associated with domestic rooftop water harvesting in India, with the prime objective of bringing to the forefront the deterrent issues and challenges in rainwater harvesting in general and domestic rooftop water harvesting in particular. This is based on a study on health risk assessment of a domestic rooftop water harvesting project conducted in the Nagaur district of Rajasthan, India, providing a critical reflection and exemplifying the prevalent scenario in the arid regions of the world. The methodology used for deriving the conclusions is failure mode and effects analysis. A set of risks were graded according to their severity based on their risk priority number scores evolved, including various contaminants polluting the harvested rainwater. The findings bear implications for planning of reconstructive changes to be incorporated and thus providing the necessary outlook for effective alleviation of the deterrents and make rainwater harvesting the premium solution for realization of the Millennium Development Goals by providing access to safe drinking water to the populace chiefly in the developing countries where the problem of scarce safe water is grave.