Identification and distribution of insertion sequences of Paracoccus solventivorans

Three novel insertion sequences (ISs) (ISPso1, ISPso2, and ISPso3) of the soil bacterium Paracoccus solventivorans DSM 11592 were identified by transposition into entrapment vector pMEC1. ISPso1 (1,400 bp) carries one large open reading frame (ORF) encoding a putative basic protein (with a DDE motif conserved among transposases [Tnps] of elements belonging to the IS256 family) with the highest levels of similarity with the hypothetical Tnps of Rhodospirillum rubrum and Sphingopyxis macrogoltabida. ISPso2 (832 bp) appeared to be closely related to ISPpa2 of Paracoccus pantotrophus DSM 11072 and IS1248 of Paracoccus denitrificans PdX22, both of which belong to the IS427 group (IS5 family). These elements contain two overlapping ORFs and a putative frameshift motif (AAAAG) responsible for production of a putative transframe Tnp. ISPso3 (1,286 bp) contains a single ORF, whose putative product showed homology with Tnps of ISs classified as members of a distinct subgroup of the IS5 group of the IS5 family. The highest levels of similarity were observed with ISSsp126 of Sphingomonas sp. and IS1169 of Bacteroides fragilis. Analysis of the distribution of ISs of P. solventivorans revealed that ISPso2-like elements are the most widely spread of the elements in nine species of the genus PARACOCCUS: ISPso1 and ISPso3 are present in only a few paracoccal strains, which suggests that they were acquired by lateral transfer. Phylogenetic analysis of Tnps of the novel ISs and their closest relatives showed their evolutionary relationships and possible directions of lateral transfer between various bacterial hosts.     

3D-Hit: fast structural comparison of proteins

3D-Hit is a fast scanning method for detecting structural similarities between proteins. The algorithm is based on a hashing function, which decomposes proteins into segments of 13 residues. The scanning procedures start with assigning a set of similar segments from the database to each segment in the query protein. These initial hits are expanded by two iterations of structural superposition of larger segments of 99 and 299 residues. The method generates an alignment for the query protein by concatenating partial structural alignments.     

Progesterone is a suppressor of apoptosis in bovine luteal cells

Progesterone is suggested to be a suppressor of apoptosis in bovine luteal cells. Fas antigen (Fas) is a cell surface receptor that triggers apoptosis in sensitive cells. Furthermore, apoptosis is known to be controlled by the bcl-2 gene/protein family and caspases. This study was undertaken to determine whether intraluteal progesterone (P4) is involved in Fas L-mediated luteal cell death in the bovine corpus luteum (CL) in vitro. Moreover, we studied whether an antagonist of P4 influences gene expression of the bcl-2 family and caspase-3 and the activity of caspase-3 in the bovine CL. Luteal cells obtained from the cows in the midluteal phase of the estrous cycle (Days 8-12 of the cycle) were exposed to a specific P4 antagonist (onapristone [OP], 10(-4) M) with or without 100 ng/ml Fas L. Although Fas L alone did not show a cytotoxic effect, treatment of the cells with OP alone or in combination with Fas L resulted in killing of 30% and 45% of the cells, respectively (P <0.05). DNA fragmentation was observed in the cells treated with Fas L in the presence of OP. The inhibition of P4 action by OP increased the expression of Fas mRNA (P <0.01); however, it did not affect bax or bcl-2 mRNA expression (P >0.05). Moreover, OP stimulated expression of caspase-3 mRNA (P <0.01). The overall results indirectly show that intraluteal P4 suppresses apoptosis in bovine luteal cells through the inhibition of Fas and caspase-3 mRNA expression and inhibition of caspase-3 activation.     

Genetic Organization of the Basic Replicon of Plasmid pMTH4 of a Facultatively Methylotrophic Bacterium <Emphasis Type="Italic">Paracoccus methylutens</Emphasis> DM12

Two functional regions within the basic replicon of plasmid pMTH4 of Paracoccus methylutens DM12 have been distinguished that are responsible for the replication of the plasmid (REP) and its stabilization (STA). In the REP region, a gene encoding the putative replication initiation protein RepA has been identified, with the highest similarity to the replication protein of plasmid pALC1 (Paracoccus alcaliphilus). The potential origin of replication (oriV), consisting of five long repeated sequences (iterons) as well as putative DnaA and IHF boxes, has been localized in the promoter region of the gene repA. The STA region was found to ensure stability for heterogeneous plasmid pABW3 that is unstable itself in paracocci. The mini-STA region (850 bp) contains two short open reading frames, one of which shows similarity to the RelB protein of Escherichia coli. Our investigations suggest that the stabilizing system of pMTH4 is based on the toxin and antidote principle.     

Subcellular sites for bacterial protein export

Most bacterial proteins destined to leave the cytoplasm are exported to extracellular compartments or imported into the cytoplasmic membrane via the highly conserved SecA‐YEG pathway. In the present studies, the subcellular distributions of core components of this pathway, SecA and SecY, and of the secretory protein pre‐AmyQ, were analysed using green fluorescent protein fusions, immunostaining and/or immunogold labelling techniques. It is shown that SecA, SecY and (pre‐)AmyQ are located at specific sites near and/or in the cytoplasmic membrane of Bacillus subtilis. The localization patterns of these proteins suggest that the Sec machinery is organized in spiral‐like structures along the cell, with most of the translocases organized in specific clusters along these structures. However, this localization appears to be independent of the helicoidal structures formed by the actin‐like cytoskeletal proteins, MreB or Mbl. Interestingly, the specific localization of SecA is dynamic, and depends on active translation. Moreover, reducing the phosphatidylglycerol phospholipids content in the bacterial membrane results in delocalization of SecA, suggesting the involvement of membrane phospholipids in the localization process. These data show for the first time that, in contrast to the recently reported uni‐ExPortal site in the coccoïd Streptococcus pyogenes, multiple sites dedicated to protein export are present in the cytoplasmic membrane of rod‐shaped B. subtilis.     

Synthesis and evaluation of 2-amino-8-alkoxy quinolines as MCHr1 antagonists. Part 3

Prior SAR studies on 2-amino-8-alkoxyquinoline MCHr1 antagonists demonstrated that compounds with acyclic amide-containing sidechains displayed exceptional binding and functional potency, but negligible CNS penetration. Related analogs with acyclic benzylamine-containing sidechains showed greatly improved CNS exposure, but suffered in functional potency. In this report, we demonstrate that cyclization of these benzylic amine sidechains affords compounds that combine the best elements of potency and CNS penetration among this class of antagonists. This is exemplified by compound 21, which has sub-nanomolar MCHr1 binding affinity, good functional potency, and excellent CNS exposure over 24h.     

Molecular insights into the phylogeny of Blapstinina (Coleoptera: Tenebrionidae: Opatrini)

The monophyly of the North and South American endemic subtribe Blapstinina (Tenebrionidae: Opatrini) is tested through phylogenetic analyses using five molecular markers [nuclear ribosomal 28S (28S), cytochrome oxidase subunit II (COII), arginine kinase (ArgK), carbamoyl-phosphate synthetase domain of rudimentary (CAD), wingless (wg)]. Representatives of several opatrinoid subtribes were taken into consideration, including other geographically overlapping endemic genera, namely Ammodonus, Ephalus and Pseudephalus (all previously considered representatives of Ammobiina). A comparative study of morphology was performed to assess resulting phylogenetic hypotheses. Analyses support the monophyly of Blapstinina; however, they also strongly indicate that Ammodonus should be included within the subtribe. Mecysmus is nested within Blapstinus and therefore, a new synonymy, Blapstinus (= Mecysmus syn.n. ), and the following combinations are introduced: Blapstinus advena comb.n. , B. angustus comb.r. , B. laticollis comb.n. , B. parvulus comb.n. , B. tenuis comb.n. Morphological analysis showed a close affiliation between Ephalus and Pseudephalus. Based on these results, Pseudephalus is synonymized with Ephalus [Ephalus (= Pseudephalus syn.n. )], and the following combination is introduced: Ephalus brevicornis comb.n. Recovered topologies also strongly support transferring Ephalus stat.n. into Opatrina, making the distribution of Opatrina amphi-Atlantic.     

Plasma amino acids indicate glioblastoma with ATRX loss

Glioblastoma (GB) is the most common primary brain tumour in adults. The lack of molecular biomarker, non-specific symptoms and fast growth rate often result in a significant delay in diagnosis. Despite multimodal treatment, the prognosis remains poor. Here, we verified the hypothesis that amino acids (AA) regulating the critical metabolic pathways necessary for maintenance, growth, reproduction, and immunity of an organism, may constitute a favourable target in GB biomarker research. We measured the plasma amino acids levels in 18 GB patients and 15 controls and performed the quantitative and qualitative metabolomic analysis of free AA applying high-performance liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QTOF-MS). We present both the raw data and the results of our statistical analysis. The majority of AA were lowered in the study group in comparison to the control group. Five of these (arginine, glutamic acid, glutamine, glycine, and histidine) differed significantly (all p < 10^–5 and AUC > 0.9). Plasma levels of leucine and phenylalanine decreased in the case of GB with lost alpha-thalassemia/mental retardation X-linked (ATRX) expression on immunohistochemistry (p = 0.003 and 0.045, respectively). We demonstrated for the first time that certain plasma-free AA levels of GB patients were significantly different from those in healthy volunteers. Target profiling of plasma-free AA, identified utilizing LC-QTOF-MS, may present prognostic value by indicating GB patients with lost ATRX expression. The on-going quest for glioma biomarkers still aims to determine the detailed metabolic profile and evaluate its impact on therapy and prognosis.

     

A comparative study on the sensitivity of Cyprinus carpio muscle and liver FBPase toward AMP and calcium

The activity of fructose-1,6-bisphosphatase (FBPase; EC 3.1.3.11) isozymes is influenced by AMP, Ca2+ and by reversible interactions with subcellular structures. In contrast to mammalian and avian isozymes, the kinetic properties of FBPases from ectothermal vertebrates are not fully described. To get some insight into mechanism of glycogen resynthesis in ectothermal vertebrates we examined the features of FBPases isolated from Cyprinus carpio skeletal muscle and liver. To investigate the evolutionary origin of the sensitivity of FBPase to effectors, we performed a phylogenetic analysis of known animal amino acids sequences of the enzyme. Based on our findings, we hypothesize that the high, mammalian-like, sensitivity of FBPase to Ca2+ is not essential for controlling the stability of glyconeogenic complex in striated muscles, instead it ensures the precise regulation of mitochondrial metabolism during prolonged Ca2+ elevation in contracting muscle fibers. Comparison of the kinetic properties of vertebrate and insect FBPases suggests that the high sensitivity of muscle isozyme to inhibitors has arisen as an adaptation enabling coordination of energy metabolism in warm-blooded animals.