The ever increasing number of sequences in protein databases usually turns out large numbers of homologs in sequence similarity searches. While information from homology can be very useful for functional prediction based on amino acid conservation, many of these homologs usually have high levels of identity among themselves, which hinders multiple sequence alignment (MSA) computation and, especially, visualization. More generally, high redundancy reduces the usability of a protein set in machine learning applications and biases statistical analyses. We developed an algorithm to identify redundant sequence homologs that can be culled producing a streamlined FASTA file. As a difference from other automatic approaches that only aggregate sequences with high identity, our method clusters near-full length homologs allowing for lower sequence identity thresholds. Our method was fully tested and implemented in a web application called FASTA Herder, publicly available at http://www.ogic.ca/projects/fh/orain.html .

Abstract A cyclodextrin glycosyltransferase (CGTase) from an alkaliphilic Bacillus sp. strain, isolated from Cuban soil, was purified with Sephadex G-50 with a yield of 66.5%. The CGTase was stable over a very wide pH range, 6.0–10, at 25°C and was most active at pH 7.5. The enzyme exhibited an optimum temperature of 60°C and was stable to 50°C for at least 8 h. The T 50 value – defined as the temperature at which 50% of the initial activity was retained–was 63°C in this enzyme. The influence of substrate or product concentration on the initial rate of CD production was studied, and the kinetic parameters were determined. The analysis of kinetic parameters K m and V max was obtained by the action of CGTase on the starch of corn with respect to β-CD, and the values were 4.1 g/L and 5.2 μM β-CD/min ml, respectively. The purified CGTase from Bacillus sp. could be used for an efficient cyclodextrin (CD) production which is the significant yield of γ- CDs.

Autophagy is an evolutionarily conserved self-digestion process for the quality control of intracellular entities in eukaryotes. In the past few years, mounting evidence indicates that microRNAs (miRNAs)-mediated post-transcriptional regulation of gene expression represents an integral part of the autophagy regulatory network and may have a substantial effect on autophagy-related physiological and pathological conditions including cancer. Herein, we examine some of the molecular mechanisms by which miRNAs manipulate the autophagic machinery to maintain cellular homeostasis and their biological outputs during cancer development. A better understanding of interaction between miRNAs and cellular autophagy may ultimately benefit future cancer diagnostic and anticancer therapeutics.

Abstract We analytically compute the long-term orbital variations of a test particle orbiting a central body acted upon by an incident monochromatic plane gravitational wave. We assume that the characteristic size of the perturbed two-body system is much smaller than the wavelength of the wave. Moreover, we also suppose that the wave's frequency ν g is much smaller than the particle's orbital one n b. We make neither a priori assumptions about the direction of the wavevector k ̂ nor on the orbital configuration of the particle. While the semi-major axis a is left unaffected, the eccentricity e, the inclination I, the longitude of the ascending node Ω, the longitude of pericenter ϖ and the mean anomaly ℳ undergo non-vanishing long-term changes of the form d Ψ / d t = F ( K i j ; e , I , Ω , ω ) , Ψ = e , I , Ω , ϖ , ℳ , where K i j , i , j = 1 , 2 , 3 are the coefficients of the tidal matrix K. Thus, in addition to the variations of its orientation in space, the shape of the orbit would be altered as well. Strictly speaking, such effects are not secular trends because of the slow modulation introduced by K and by the orbital elements themselves: they exhibit peculiar long-term temporal patterns which would be potentially of help for their detection in multidecadal analyses of extended data records of planetary observations of various kinds. In particular, they could be useful in performing independent tests of the inflation-driven ultra-low gravitational waves whose imprint may have been indirectly detected in the Cosmic Microwave Background by the Earth-based experiment BICEP2. Our calculation holds, in general, for any gravitationally bound two-body system whose orbital frequency n b is much larger than the frequency ν g of the external wave, like, e.g., extrasolar planets and the stars orbiting the Galactic black hole. It is also valid for a generic perturbation of tidal type with constant coefficients over timescales of the order of the orbital period of the perturbed particle.

Abstract The activation of aromatic diaryl isoxazoles with strong electron-withdrawing groups, such as the nitro, triflyl, and the phenylsulfonyl groups, at the 4-position has enabled the first regio- and diastereoselective difluoromethylation at the 5-position of isoxazoles by nucleophilic addition using (difluoromethyl) trimethylsilane, Me3SiCF2H, to provide difluoromethylated isoxazolines in good yields. Conjugated styryl-4-nitroisoxazoles were also nicely converted into the corresponding CF2H adducts with high regio- and excellent diastereoselectivities. Since the trifluoromethylated analogs of the corresponding diaryl-isoxazolines are effective ectoparasiticides, represented by fluralaner, should a series of difluoromethylated isoxazolines be obtained, they would be of great importance as promising drug candidates in this field.

Rat CD39, a membrane-bound ectonucleoside triphosphate diphosphohydrolase that hydrolyzes extracellular nucleoside tri- and diphosphates, is anchored to the membrane by two transmembrane domains at the two ends of the molecule. The transmembrane domains are important for enzymatic activity, as mutants lacking one or both of these domains have a fraction of the enzymatic activity of the wild-type CD39. We investigated the interactions between the transmembrane domains by using a strain of yeast that requires surface expression of CD39 for growth. Random mutagenesis of selected amino acid residues in the N-terminal transmembrane domain revealed that the presence of charged amino acids at these positions prevents expression of functional protein. Rescue of the growth of these mutants by complementary mutations on selected residues of the C-terminal transmembrane domain indicates that there is contact between particular faces of the transmembrane domains.