The misuse of terms in scientific literature

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Solving biclustering with a GRASP-like metaheuristic: two case-study on gene expression analysis

The explosion of "omics" data over the past few decades has generated an increasing need of efficiently analyzing high-dimensional gene expression data in several different and heterogenous contexts, such as for example in information retrieval, knowledge discovery, and data mining. For this reason, biclustering, or simultaneous clustering of both genes and conditions has generated considerable interest over the past few decades. Unfortunately, the problem of locating the most significant bicluster has been shown to be NP-complete. We have designed and implemented a GRASP-like heuristic algorithm to efficiently find good solutions in reasonable running times, and to overcome the inner intractability of the problem from a computational point of view. Experimental results on two datasets of expression data are promising indicating that this algorithm is able to find significant biclusters, especially from a biological point of view

Molecular dynamics analysis of the structural properties of the transglutaminases of Kutzneria albida and Streptomyces mobaraensis

The microbial transglutaminase (TGase) from Streptomyces mobaraensis (MTGase) is widely used for industrial applications. However, in the last decades, TGases from other bacteria have been described. We focused our attention on TGase, from Kutzneria albida (KalbTGase), recently characterized as more selective than MTGase and proposed for applications in drug delivery. By comparison of the crystallographic structures, the volume of the catalytic site results smaller in KalbTGase. We compared KalbTGase and MTGase structural flexibility by molecular dynamics (MD) simulations at different conditions. KalbTGase is more rigid than MTGase at 300 K, but the catalytic site has a preserved conformation in both structures. Preliminary studies at higher temperatures suggest that KalbTGase acquires enhanced conformational flexibility far from the active site region. The volume of the catalytic active site pocket of KalbTGase at room temperature is smaller than that of MTGase, and decreases at 335 K, remaining stable after further temperature increase. On the contrary, in MTGase the pocket volume continues to decrease as the temperature increases. Overall, the results of our study suggest that at room temperature the enhanced specificity of KalbTGase could be related to a more closed catalytic pocket and lower flexibility than MTGase. Moreover, by preliminary results at higher temperature, KalbTGase structural flexibility suggests an adaptability to different substrates not recognized at room temperature. Lower adaptability of MTGase at higher temperature with a reduction of the catalytic pocket, instead, suggests a reduction of its activity

Global Diversification, Industrial Diversification, and Firm Value

Using a sample of 27,287 firm-years over the period of 1983-1993 we document an increasing trend in both the incidence and level of global diversification over time. This trend does not, however, reflect a substitution of global for industrial diversification. Global diversification results in average valuation discounts of the same magnitude as those for industrial diversification. Analysis of the changes in excess value associated with changes in diversification status reveals that increases in global diversification reduce excess value, while reductions in global diversification increase excess value

HINT, a code for understanding the interaction between biomolecules: a tribute to Donald J. Abraham

A long-lasting goal of computational biochemists, medicinal chemists, and structural biologists has been the development of tools capable of deciphering the molecule–molecule interaction code that produces a rich variety of complex biomolecular assemblies comprised of the many different simple and biological molecules of life: water, small metabolites, cofactors, substrates, proteins, DNAs, and RNAs. Software applications that can mimic the interactions amongst all of these species, taking account of the laws of thermodynamics, would help gain information for understanding qualitatively and quantitatively key determinants contributing to the energetics of the bimolecular recognition process. This, in turn, would allow the design of novel compounds that might bind at the intermolecular interface by either preventing or reinforcing the recognition. HINT, hydropathic interaction, was a model and software code developed from a deceptively simple idea of Donald Abraham with the close collaboration with Glen Kellogg at Virginia Commonwealth University. HINT is based on a function that scores atom–atom interaction using LogP, the partition coefficient of any molecule between two phases; here, the solvents are water that mimics the cytoplasm milieu and octanol that mimics the protein internal hydropathic environment. This review summarizes the results of the extensive and successful collaboration between Abraham and Kellogg at VCU and the group at the University of Parma for testing HINT in a variety of different biomolecular interactions, from proteins with ligands to proteins with DNA

Solvent-dependent termination, size and stability in polyynes synthesis by laser ablation in liquids

In recent years there has been a growing interest in sp-carbon chains as possible novel nanostructures. An example of sp-carbon chains are the so-called polyynes, characterized by the alternation of single and triple bonds that can be synthesized by pulsed laser ablation in liquid (PLAL) of a graphite target. In this work, by exploiting different solvents in the PLAL process, e.g. water, acetonitrile, methanol, ethanol, and isopropanol, we systematically investigate the solvent role in polyyne formation and stability. The presence of methyland cyano-groups in the solutions influences the termination of polyynes, allowing to detect, in addition to hydrogen-capped polyynes up to HC22H, methyl-capped polyynes up to 18 carbon atoms (i.e. HCnCH3) and cyanopolyynes up to HC12CN. The assignment of each species was done by UV-Vis spectroscopy and supported by density functional theory simulations of vibronic spectra. In addition, surface-enhanced Raman spectroscopy allowed to observe differences, due to different terminations (hydrogen, methyl-and cyano group), in the shape and positions of the characteristic Raman bands of the size-selected polyynes. The evolution in time of each polyyne has been investigated evaluating the chromatographic peak area, and the effect of size, terminations and solvents on polyynes stability has been individuated.Comment: 13 pages, 5 figures. Supporting Information of this article is available in the end of this manuscrip

Amino acid transport in thermophiles: characterization of an arginine-binding protein in Thermotoga maritima. 2. Molecular organization and structural stability

ABC transport systems provide selective passage of metabolites across cell membranes and typically require the presence of a soluble binding protein with high specificity to a specific ligand. In addition to their primary role in nutrient gathering, the binding proteins associated with bacterial transport systems have been studied for their potential to serve as design scaffolds for the development of fluorescent protein biosensors. In this work, we used Fourier transform infrared spectroscopy and molecular dynamics simulations to investigate the physicochemical properties of a hyperthermophilic binding protein from Thermotoga maritima. We demonstrated preferential binding for the polar amino acid arginine and experimentally monitored the significant stabilization achieved upon binding of ligand to protein. The effect of temperature, pH, and detergent was also studied to provide a more complete picture of the protein dynamics. A protein structure model was obtained and molecular dynamic experiments were performed to investigate and couple the spectroscope observations with specific secondary structural elements. The data determined the presence of a buried ẞ-sheet providing significant stability to the protein under all conditions investigated. The specific amino acid residues responsible for arginine binding were also identified. Our data on dynamics and stability will contribute to our understanding bacterial binding protein family members and their potential biotechnological applications

Amino acid transport in thermophiles: characterization of an arginine-binding protein in Thermotoga maritima. 2. Molecular organization and structural stability

ABC transport systems provide selective passage of metabolites across cell membranes and typically require the presence of a soluble binding protein with high specificity to a specific ligand. In addition to their primary role in nutrient gathering, the binding proteins associated with bacterial transport systems have been studied for their potential to serve as design scaffolds for the development of fluorescent protein biosensors. In this work, we used Fourier transform infrared spectroscopy and molecular dynamics simulations to investigate the physicochemical properties of a hyperthermophilic binding protein from Thermotoga maritima. We demonstrated preferential binding for the polar amino acid arginine and experimentally monitored the significant stabilization achieved upon binding of ligand to protein. The effect of temperature, pH, and detergent was also studied to provide a more complete picture of the protein dynamics. A protein structure model was obtained and molecular dynamic experiments were performed to investigate and couple the spectroscope observations with specific secondary structural elements. The data determined the presence of a buried ẞ-sheet providing significant stability to the protein under all conditions investigated. The specific amino acid residues responsible for arginine binding were also identified. Our data on dynamics and stability will contribute to our understanding bacterial binding protein family members and their potential biotechnological applications

Resources and tools for rare disease variant interpretation

: Collectively, rare genetic disorders affect a substantial portion of the world's population. In most cases, those affected face difficulties in receiving a clinical diagnosis and genetic characterization. The understanding of the molecular mechanisms of these diseases and the development of therapeutic treatments for patients are also challenging. However, the application of recent advancements in genome sequencing/analysis technologies and computer-aided tools for predicting phenotype-genotype associations can bring significant benefits to this field. In this review, we highlight the most relevant online resources and computational tools for genome interpretation that can enhance the diagnosis, clinical management, and development of treatments for rare disorders. Our focus is on resources for interpreting single nucleotide variants. Additionally, we present use cases for interpreting genetic variants in clinical settings and review the limitations of these results and prediction tools. Finally, we have compiled a curated set of core resources and tools for analyzing rare disease genomes. Such resources and tools can be utilized to develop standardized protocols that will enhance the accuracy and effectiveness of rare disease diagnosis