A two-stage pruning algorithm for likelihood computation for a population tree

We have developed a pruning algorithm for likelihood estimation of a tree of populations. This algorithm enables us to compute the likelihood for large trees. Thus, it gives an efficient way of obtaining the maximum-likelihood estimate (MLE) for a given tree topology. Our method utilizes the differences accumulated by random genetic drift in allele count data from single-nucleotide polymorphisms (SNPs), ignoring the effect of mutation after divergence from the common ancestral population. The computation of the maximum-likelihood tree involves both maximizing likelihood over branch lengths of a given topology and comparing the maximum-likelihood across topologies. Here our focus is the maximization of likelihood over branch lengths of a given topology. The pruning algorithm computes arrays of probabilities at the root of the tree from the data at the tips of the tree; at the root, the arrays determine the likelihood. The arrays consist of probabilities related to the number of coalescences and allele counts for the partially coalesced lineages. Computing these probabilities requires an unusual two-stage algorithm. Our computation is exact and avoids time-consuming Monte Carlo methods. We can also correct for ascertainment bias.     

Mycobacterium avium subspecies paratuberculosis diagnosis and geno-typing: genomic insights

Effective control of paratuberculosis and investigations of potential link to Crohn's disease have been hampered by the lack of effective assays for easy and accurate diagnosis of Mycobacterium avium subspecies paratuberculosis (Map). Map is extremely fastidious and depends on iron chelator (Mycobactin). Map strains from humans and sheep are very difficult to isolate and may require years to emerge. Therefore, small numbers of Map isolates have been maintained in available collections. This situation has limited the study of biodiversity of Map. Though, much is known about environmental and host factors that contribute to paratuberculosis disease, but little is known about bacterial genetic mechanism of infection. Diagnostic and strain typing markers still demand improvements. Complete genome sequence of Map K10 strain is available in public domain for comparative genomics with other mycobacteria and clinical isolates of Map. It is anticipated that the genome sequence will help in carrying molecular diagnosis and strain typing with respect to Map forward at rapid pace. This paper reviews the current diagnostic and strain typing markers, which may be useful in typing of clinical isolates in near future.     

Efficient synthesis of 3,3-diheteroaromatic oxindole analogues and their in vitro evaluation for spermicidal potential

Syntheses of 3,3-diheteroaromatic oxindole derivatives has been achieved by coupling indole-2,3-dione (isatin) with differently substituted indoles and pyrrole in presence of I₂ in i-PrOH. The in vitro spermicidal potentials and the mode of spermicidal action of the synthesized analogues were evaluated and the derivative, 3,3-bis (5-methoxy-1H-indol-3-yl) indolin-2-one (3d) exhibited most significant activity.     

Design,synthesis and bioactivity of catechin/epicatechin and 2-azetidinone derived chimeric molecules

A new class of chimeric molecules have been developed. These are based on polyphenols like catechin and epicatechin and monocyclic β-lactams. The two units are joined via a triazole linker using the ‘Click Chemistry’ conditions. The compounds showed good to weak antibacterial activity against Escherichia coli as well as moderate inhibition of RNase A.     

In vivo protein tyrosine nitration in S. cerevisiae: Identification of tyrosine-nitrated proteins in mitochondria

Protein tyrosine nitration (PTN) is a selective post-translational modification often associated with pathophysiological conditions. Although yeast cells lack of mammalian nitric oxide synthase (NOS) orthologues, still it has been shown that they are capable of producing nitric oxide (NO). Our studies showed that NO or reactive nitrogen species (RNS) produced in flavohemoglobin mutant (Δyhb1) strain along with the wild type strain (Y190) of Saccharomyces cerevisiae can be visualized using specific probe 4,5-diaminofluorescein diacetate (DAF-2DA). Δyhb1 strain of S. cerevisiae showed bright fluorescence under confocal microscope that proves NO or RNS accumulation is more in absence of flavohemoglobin. We further investigated PTN profile of both cytosol and mitochondria of Y190 and Δyhb1 cells of S. cerevisiae using two-dimensional (2D) gel electrophoresis followed by western blot analysis. Surprisingly, we observed many immunopositive spots both in cytosol and in mitochondria from Y190 and Δyhb1 using monoclonal anti-3-nitrotyrosine antibody indicating a basal level of NO or nitrite or peroxynitrite is produced in yeast system. To identify proteins nitrated in vivo we analyzed mitochondrial proteins from Y190 strains of S. cerevisiae. Among the eight identified proteins, two target mitochondrial proteins are aconitase and isocitrate dehydrogenase that are involved directly in the citric acid cycle. This investigation is the first comprehensive study to identify mitochondrial proteins nitrated in vivo.     

Cep78 controls centrosome homeostasis by inhibiting EDD‐DYRK2‐DDB1VprBP

The centrosome plays a critical role in various cellular processes including cell division and cilia formation, and deregulation of centrosome homeostasis is a hallmark feature of many human diseases. Here, we show that centrosomal protein of 78 kDa (Cep78) localizes to mature centrioles and directly interacts with viral protein R binding protein (VprBP). Although VprBP is a component of two distinct E3 ubiquitin ligases, EDD‐DYRK2‐DDB1^VprBP and CRL4^VprBP, Cep78 binds specifically to EDD‐DYRK2‐DDB1^VprBP and inhibits its activity. A pool of EDD‐DYRK2‐DDB1^VprBP is active at the centrosome and mediates ubiquitination of CP110, a novel centrosomal substrate. Deregulation of Cep78 or EDD‐DYRK2‐DDB1^VprBP perturbs CP110 ubiquitination and protein stability, thereby affecting centriole length and cilia assembly. Mechanistically, ubiquitination of CP110 entails its phosphorylation by DYRK2 and binding to VprBP. Cep78 specifically impedes the transfer of ubiquitin from EDD to CP110 without affecting CP110 phosphorylation and binding to VprBP. Thus, we identify Cep78 as a new player that regulates centrosome homeostasis by inhibiting the final step of the enzymatic reaction catalyzed by EDD‐DYRK2‐DDB1^VprBP.