The advantage of functional prediction based on clustering of yeast genes and its correlation with non-sequence based classifications.

Sequence similarity is probably the most widely used tool to infer functional linkage between proteins. The fully sequenced, much researched, genome of Saccharomyces cerevisiae gives us on opportunity to compare and statistically quantify computational methods based on sequence similarity, which aim to detect such linkage. In addition, the amount of data regarding Saccharomyces Cerevisiae genes and proteins, which is not directly based on sequence is rapidly increasing. Consequently, it allows investigation of the connections and correlation between classification based on these types of data and that based solely on sequence similarity. In this work we start with a simple clustering algorithm to cluster genes based on the BLAST E-score of their similarity. We analyze how well one can infer function from these clusters and for how many of the genes that are currently unknown one can suggest a prediction. Given these parameters, we show that even a simple algorithm achieves better results than simply considering the BLAST output of matching genes. In the second part of the paper, we show that there is a highly significant correlation (p-value < 10(-4) for the vast majority of the experiments) between the aforementioned clusters and other types of classifications. Namely, we show that a pair of genes being clustered together is correlated with these genes having similar expression patterns in DNA array experiments and with the encoded proteins being involved in protein-protein interactions. Although this correlation is highly significant, it is, of course, not strong enough to be, by itself, a tool for predicting co-regulation of genes or interaction of proteins. We discuss possible explanations for this correlation. Furthermore, the statistical evaluation of these results should be considered when developing tools that are aimed at making such predictions.     

A Model for Shaping Membrane Sheets by Protein Scaffolds

Membranes of peripheral endoplasmic reticulum form intricate morphologies consisting of tubules and sheets as basic elements. The physical mechanism of endoplasmic-reticulum shaping has been suggested to originate from the elastic behavior of the sheet edges formed by linear arrays of oligomeric protein scaffolds. The heart of this mechanism, lying in the relationships between the structure of the protein scaffolds and the effective intrinsic shapes and elastic properties of the sheets’ edges, has remained hypothetical. Here we provide a detailed computational analysis of these issues. By minimizing the elastic energy of membrane bending, we determine the effects of a rowlike array of semicircular arclike membrane scaffolds on generation of a membrane fold, which shapes the entire membrane surface into a flat double-membrane sheet. We show, quantitatively, that the sheet’s edge line tends to adopt a positive or negative curvature depending on the scaffold’s geometrical parameters. We compute the effective elastic properties of the sheet edge and analyze the dependence of the equilibrium distance between the scaffolds along the edge line on the scaffold geometry.     

Antibacterial effects of the tellurium compound OTD on E. coli isolates

The antibacterial effects of a new organo-tellurium compound [Octa-O-bis-(R,R)-tartarate ditellurane (OTD)] on Escherichia coli isolates as a model are shown. OTD was found to be a bactericidal drug. It exhibits inhibition zones on a protein-rich agar medium but not in a protein-poor medium unless a thiol is added. When applied at the lag phase, OTD inhibits more efficiently than at the log phase. Thiols enhance the efficiency at the log phase. OTD inhibits biofilm formation of E. coli. X-ray microanalysis demonstrated damage caused to the Na⁺/K⁺ pumps and leakage of potassium and phosphorous. Scanning electron microscopy demonstrated an incomplete surface of the bacterial cell wall with a concavity in the center that looks like a hole. Transmission electron microscopy demonstrated severe damage, such as depletion, perforation, and holes in the inner membrane. These results indicate for the first time that the new tellurium compound has antibacterial activities.     

Kinematics of swimming garter snakes (Thamnophis sirtalis).

We investigate the kinematics of swimming garter snakes (Thamnophis sirtalis) using a novel nonlinear regression-based digitization method to establish quantitative statistical support for non-constant wavelengths in the undulatory pattern exhibited by swimming snakes. We find that in swimming snakes, the growth of the amplitude of the propulsive wave head-to-tail is strongly correlated (p < 0.005) with the head-to-tail growth in the wavelength. We investigate correlations between kinematic parameters and steady swimming speed, and find a very strong positive correlation between swimming speed and undulation frequency. We furthermore find a statistically well-supported positive correlation between swimming speed and both the initial amplitude of the propulsive wave at the head and the degree of amplitude growth from head to tail.     

Discrete limbal epithelial stem cell populations mediate corneal homeostasis and wound healing

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Theoretical Analysis of Membrane Tension in Moving Cells

Lateral tension in cell plasma membranes plays an essential role in regulation of a number of membrane-related intracellular processes and cell motion. Understanding the physical factors generating the lateral tension and quantitative determination of the tension distribution along the cell membrane is an emerging topic of cell biophysics. Although experimental data are accumulating on membrane tension values in several cell types, the tension distribution along the membranes of moving cells remains largely unexplored. Here we suggest and analyze a theoretical model predicting the tension distribution along the membrane of a cell crawling on a flat substrate. We consider the tension to be generated by the force of actin network polymerization against the membrane at the cell leading edge. The three major factors determining the tension distribution are the membrane interaction with anchors connecting the actin network to the lipid bilayer, the membrane interaction with cell adhesions, and the force developing at the rear boundary due to the detachment of the remaining cell adhesion from the substrate in the course of cell crawling. Our model recovers the experimentally measured values of the tension in fish keratocytes and their dependence on the number of adhesions. The model predicts, quantitatively, the tension distribution between the leading and rear membrane edges as a function of the area fractions of the anchors and the adhesions.     

Conformation and protein interactions of intramolecular DNA and phosphorothioate four-way junctions

The objectives of this study are to evaluate the structure and protein recognition features of branched DNA four-way junctions in an effort to explore the therapeutic potential of these molecules. The classic immobile DNA 4WJ, J1, is used as a matrix to design novel intramolecular junctions including natural and phosphorothioate bonds. Here we have inserted H2-type mini-hairpins into the helical termini of the arms of J1 to generate four novel intramolecular four-way junctions. Hairpins are inserted to reduce end fraying and effectively eliminate potential nuclease binding sites. We compare the structure and protein recognition features of J1 with four intramolecular four-way junctions: i-J1, i-J1(PS1), i-J1(PS2) and i-J1(PS3). Circular dichroism studies suggest that the secondary structure of each intramolecular 4WJ is composed predominantly of B-form helices. Thermal unfolding studies indicate that intramolecular four-way junctions are significantly more stable than J1. The T_m values of the hairpin four-way junctions are 25.2° to 32.2°C higher than the control, J1. With respect to protein recognition, gel shift assays reveal that the DNA-binding proteins HMGBb1 and HMGB1 bind the hairpin four-way junctions with affinity levels similar to control, J1. To evaluate nuclease resistance, four-way junctions are incubated with DNase I, exonuclease III (Exo III) and T5 exonuclease (T5 Exo). The enzymes probe nucleic acid cleavage that occurs non-specifically (DNase I) and in a 5ʹ→3ʹ (T5 Exo) and 3ʹ→5ʹ direction (Exo III). The nuclease digestion assays clearly show that the intramolecular four-way junctions possess significantly higher nuclease resistance than the control, J1.     

A Transporter Interactome Is Essential for the Acquisition of Antimicrobial Resistance to Antibiotics

Awareness of the problem of antimicrobial resistance (AMR) has escalated and drug-resistant infections are named among the most urgent problems facing clinicians today. Our experiments here identify a transporter interactome and portray its essential function in acquisition of antimicrobial resistance. By exposing E. coli cells to consecutive increasing concentrations of the fluoroquinolone norfloxacin we generated in the laboratory highly resistant strains that carry multiple mutations, most of them identical to those identified in clinical isolates. With this experimental paradigm, we show that the MDTs function in a coordinated mode to provide an essential first-line defense mechanism, preventing the drug reaching lethal concentrations, until a number of stable efficient alterations occur that allow survival. Single-component efflux transporters remove the toxic compounds from the cytoplasm to the periplasmic space where TolC-dependent transporters expel them from the cell. We postulate a close interaction between the two types of transporters to prevent rapid leak of the hydrophobic substrates back into the cell. The findings change the prevalent concept that in Gram-negative bacteria a single multidrug transporter, AcrAB-TolC type, is responsible for the resistance. The concept of a functional interactome, the process of identification of its members, the elucidation of the nature of the interactions and its role in cell physiology will change the existing paradigms in the field. We anticipate that our work will have an impact on the present strategy searching for inhibitors of AcrAB-TolC as adjuvants of existing antibiotics and provide novel targets for this urgent undertaking.