A Two-Step Procedure for Obtaining Highly Purified Particulate Guanylate Cyclase From Rat Lung

Abstract

Cuanylate cyclase (CTP pyrophosphate lyase (cyclizing), EC 4.6.1.21, the enzyme catalyzing the formation of cyclic CMP, from GTP, exists in both soluble and membrane-bound forms.1-6 These enzymes have been implicated as key regulatory components in a variety of biological events such as secretion7-10, and smooth muscle relaxation.11-14 Understanding the role these enzymes play in cellular regulation is predicated upon obtaining purified preparations of guanylate cyclase. Several procedures for purifying the soluble enzyme to apparent homogeneity from a variety of tissues have been reported.15-19 The particulate enzyme has been purified to apparent homogeneity from sea urchin sperm20,21 but, to date, homogeneous preparations of particulate guanylate cyclase from mammalian tissues have not been obtained. Here we report our efforts in purifying particulate guanylate cyclase about 8,200- to 52,000-fold from homogenates of rat lung. Portions of this work have appeared in abstract form.     

Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus

Background

Elucidating the process of speciation requires an in-depth understanding of the evolutionary history of the species in question. Studies that rely upon a limited number of genetic loci do not always reveal actual evolutionary history, and often confuse inferences related to phylogeny and speciation. Whole-genome data, however, can overcome this issue by providing a nearly unbiased window into the patterns and processes of speciation. In order to reveal the complexity of the speciation process, we sequenced and analyzed the genomes of 10 wild pigs, representing morphologically or geographically well-defined species and subspecies of the genus Sus from insular and mainland Southeast Asia, and one African common warthog.

Results

Our data highlight the importance of past cyclical climatic fluctuations in facilitating the dispersal and isolation of populations, thus leading to the diversification of suids in one of the most species-rich regions of the world. Moreover, admixture analyses revealed extensive, intra- and inter-specific gene-flow that explains previous conflicting results obtained from a limited number of loci. We show that these multiple episodes of gene-flow resulted from both natural and human-mediated dispersal.

Conclusions

Our results demonstrate the importance of past climatic fluctuations and human mediated translocations in driving and complicating the process of speciation in island Southeast Asia. This case study demonstrates that genomics is a powerful tool to decipher the evolutionary history of a genus, and reveals the complexity of the process of speciation.     

Antimicrobial activities of Gloriosa superba Linn (Colchicaceae) extracts

The methanol extract of the rhizomes of Gloriosa superba Linn (Colchicaceae) and its subsequent fractions in different solvent systems were screened for antibacterial and antifungal activities. Excellent antifungal sensitivity was expressed by the n-butanol fraction against Candida albicans and Candida glaberata (up to 90%) and against Trichophyton longifusus (78%) followed by the chloroform fraction against Microsporum canis (80%). In the antibacterial bioassay, the crude extract and subsequent fractions showed mild to moderate antibacterial activities. Chloroform fraction displayed highest antibacterial sensitivity against Staphylococcus aureous (88%) followed by the crude extract (59%). The total phenol content of the crude extract and fractions of the plant expressed no significant correlation with the antimicrobial activities.     

Novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) and Other Coronaviruses: A Genome-wide Comparative Annotation and Analysis

Molecular and Cellular Biochemistry - Novel strain of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) causes mild to severe respiratory illness. The early symptoms may be fever, dry...     

Quantitative interpretation of cell rolling velocity distribution

Leukocyte rolling adhesion, facilitated by selectin-mediated interactions, is a highly dynamic process in which cells roll along the endothelial surface of blood vessel walls to reach the site of infection. The most common approach to investigate cell-substrate adhesion is to analyze the cell rolling velocity in response to shear stress changes. It is assumed that changes in rolling velocity indicate changes in adhesion strength. In general, cell rolling velocity is studied at the population level as an average velocity corresponding to given shear stress. However, no statistical investigation has been performed on the instantaneous velocity distribution. In this study, we first developed a method to remove systematic noise and revealed the true velocity distribution to exhibit a log-normal profile. We then demonstrated that the log-normal distribution describes the instantaneous velocity at both the population and single-cell levels across the physiological flow rates. The log-normal parameters capture the cell motion more accurately than the mean and median velocities, which are prone to systematic error. Lastly, we connected the velocity distribution to the molecular adhesion force distribution and showed that the slip-bond regime of the catch-slip behavior of the P-selectin/PSGL-1 interaction is responsible for the variation of cell velocity.     

An efficient algorithmic approach for mass spectrometry-based disulfide connectivity determination using multi-ion analysis

Background

Determining the disulfide (S-S) bond pattern in a protein is often crucial for understanding its structure and function. In recent research, mass spectrometry (MS) based analysis has been applied to this problem following protein digestion under both partial reduction and non-reduction conditions. However, this paradigm still awaits solutions to certain algorithmic problems fundamental amongst which is the efficient matching of an exponentially growing set of putative S-S bonded structural alternatives to the large amounts of experimental spectrometric data. Current methods circumvent this challenge primarily through simplifications, such as by assuming only the occurrence of certain ion-types (b-ions and y-ions) that predominate in the more popular dissociation methods, such as collision-induced dissociation (CID). Unfortunately, this can adversely impact the quality of results.

Method

We present an algorithmic approach to this problem that can, with high computational efficiency, analyze multiple ions types (a, b, b ^o , b ^* , c, x, y, y ^o , y ^* , and z) and deal with complex bonding topologies, such as inter/intra bonding involving more than two peptides. The proposed approach combines an approximation algorithm-based search formulation with data driven parameter estimation. This formulation considers only those regions of the search space where the correct solution resides with a high likelihood. Putative disulfide bonds thus obtained are finally combined in a globally consistent pattern to yield the overall disulfide bonding topology of the molecule. Additionally, each bond is associated with a confidence score, which aids in interpretation and assimilation of the results.

Results

The method was tested on nine different eukaryotic Glycosyltransferases possessing disulfide bonding topologies of varying complexity. Its performance was found to be characterized by high efficiency (in terms of time and the fraction of search space considered), sensitivity, specificity, and accuracy. The method was also compared with other techniques at the state-of-the-art. It was found to perform as well or better than the competing techniques. An implementation is available at: http://tintin.sfsu.edu/~whemurad/disulfidebond.

Conclusions

This research addresses some of the significant challenges in MS-based disulfide bond determination. To the best of our knowledge, this is the first algorithmic work that can consider multiple ion types in this problem setting while simultaneously ensuring polynomial time complexity and high accuracy of results.

     

Soybeans as bioreactors for biopharmaceuticals and industrial proteins

Plants present various advantages for the production of biomolecules, including low risk of contamination with prions, viruses and other pathogens, scalability, low production costs, and available agronomical systems. Plants are also versatile vehicles for the production of recombinant molecules because they allow protein expression in various organs, such as tubers and seeds, which naturally accumulate large amounts of protein. Among crop plants, soybean is an excellent protein producer. Soybean plants are also a good source of abundant and cheap biomass and can be cultivated under controlled greenhouse conditions. Under containment, the plant cycle can be manipulated and the final seed yield can be maximized for large-scale protein production within a small and controlled area. Exploitation of specific regulatory sequences capable of directing and accumulating recombinant proteins in protein storage vacuoles in soybean seeds, associated with recently developed biological research tools and purification systems, has great potential to accelerate preliminary characterization of plant-derived biopharmaceuticals and industrial macromolecules. This is an important step in the development of genetically engineered products that are inexpensive and safe for medicinal, food and other uses.