Unexpected diversity of chlorite dismutases: a catalytically efficient dimeric enzyme from Nitrobacter winogradskyi

Chlorite dismutase (Cld) is a unique heme enzyme catalyzing the conversion of ClO(2)(-) to Cl(-) and O(2). Cld is usually found in perchlorate- or chlorate-reducing bacteria but was also recently identified in a nitrite-oxidizing bacterium of the genus Nitrospira. Here we characterized a novel Cld-like protein from the chemolithoautotrophic nitrite oxidizer Nitrobacter winogradskyi which is significantly smaller than all previously known chlorite dismutases. Its three-dimensional (3D) crystal structure revealed a dimer of two identical subunits, which sharply contrasts with the penta- or hexameric structures of other chlorite dismutases. Despite a truncated N-terminal domain in each subunit, this novel enzyme turned out to be a highly efficient chlorite dismutase (K(m) = 90 μM; k(cat) = 190 s(-1); k(cat)/K(m) = 2.1 × 10(6) M(-1) s(-1)), demonstrating a greater structural and phylogenetic diversity of these enzymes than was previously known. Based on comparative analyses of Cld sequences and 3D structures, signature amino acid residues that can be employed to assess whether uncharacterized Cld-like proteins may have a high chlorite-dismutating activity were identified. Interestingly, proteins that contain all these signatures and are phylogenetically closely related to the novel-type Cld of N. winogradskyi exist in a large number of other microbes, including other nitrite oxidizers.     

Diarylheptanoids from Green Alder Bark and Their Potential for DNA Protection

Nine diarylheptanoids, 1 – 9 , catechin ( 11 ), and a phenolic glucoside, 10 , were isolated from the bark of green alder (Alnus viridis). Four of the isolated compounds, i.e., 2, 5, 8, 10 , are new. The structures of 1 – 11 were determined on the basis of spectroscopic data. All isolated compounds were evaluated for their in vitro protective effects on chromosome aberrations in peripheral human lymphocytes using cytokinesis‐block micronucleus (CBMN) assay. Almost all of them exerted a pronounced effect of decreasing DNA damage of human lymphocytes, acting stronger than the known synthetic protector amifostine.     

Genetic variation and relationship of alfalfa populations and their progenies based on RAPD markers

The aim of investigation was to evaluate genetic variation and relationship among alfalfa populations and their offspring, with minimal cost, by using DNA marker analysis. RAPD analysis was performed on bulked DNA samples of five alfalfa parental populations and their progenies: 20 F1 populations from reciprocal diallel crosses and five S1 populations from self-pollination. Twenty primers generated 217 bands, ranging in size from 300 to 6000 bp, with the average number of bands per primer of 10.85 and polymorphism information content of 0.246. Percentage of polymorphic loci, effective number of alleles, expected heterozygosity and Shannon’s information index were used to estimate genetic variation. Higher diversity was observed in F1 progeny populations, while genetic variation in parental populations and S1 progenies remained similar. The genetic relatedness of alfalfa populations was analysed by UPGMA and Bayesian model-based clustering approach. In both types of analysis selfpollinated progenies were grouped. Furthermore, the hybrid offspring where Zuzana, and RSI 20 were maternal parents were placed in separate groups. The results indicate that use of RAPD markers on bulked DNA samples can be fast and cost-effective way for differentiation of alfalfa parental populations and their offspring, as well as for evaluation of their genetic relationships.     

A Scoping Review of Published Research on the Relinquishment of Companion Animals

Globally, large populations of companion animals are relinquished each year. The purpose of this scoping review was to identify all published research investigating companion-animal relinquishment to map out and evaluate research gaps, needs, and opportunities. A comprehensive search strategy was implemented in 4 online databases, identified citations were screened, and relevant articles were procured and characterized. From 6,848 unique citations identified, 192 were confirmed relevant, including 115 primary-research articles and 77 reviews and commentaries. The majority of these articles originated from the United States (131; 68.2%); 74 (38.5%) of them have been published since 2006. Among the primary-research articles, 84 (73.0%) investigated reasons for companion-animal relinquishment. The most commonly studied reasons were aggressive companion-animal behaviors (49; 58.3%); moving, rental, or housing issues (45; 53.6%); and caretaker personal issues (42; 50.0%). Only 17 primary-research articles investigated interventions to prevent companion-animal relinquishment. The quantity of research into reasons for relinquishment highlights an opportunity for future knowledge-synthesis activities in this area, including systematic review and meta-analysis. In comparison, the limited research into interventions identifies a priority for new research.     

Systematic Detection of Internal Symmetry in Proteins Using CE-Symm

Symmetry is an important feature of protein tertiary and quaternary structures that has been associated with protein folding, function, evolution, and stability. Its emergence and ensuing prevalence has been attributed to gene duplications, fusion events, and subsequent evolutionary drift in sequence. This process maintains structural similarity and is further supported by this study. To further investigate the question of how internal symmetry evolved, how symmetry and function are related, and the overall frequency of internal symmetry, we developed an algorithm, CE-Symm, to detect pseudo-symmetry within the tertiary structure of protein chains. Using a large manually curated benchmark of 1007 protein domains, we show that CE-Symm performs significantly better than previous approaches. We use CE-Symm to build a census of symmetry among domain superfamilies in SCOP and note that 18% of all superfamilies are pseudo-symmetric. Our results indicate that more domains are pseudo-symmetric than previously estimated. We establish a number of recurring types of symmetry–function relationships and describe several characteristic cases in detail. With the use of the Enzyme Commission classification, symmetry was found to be enriched in some enzyme classes but depleted in others. CE-Symm thus provides a methodology for a more complete and detailed study of the role of symmetry in tertiary protein structure [availability: CE-Symm can be run from the Web at http://source.rcsb.org/jfatcatserver/symmetry.jsp. Source code and software binaries are also available under the GNU Lesser General Public License (version 2.1) at https://github.com/rcsb/symmetry. An interactive census of domains identified as symmetric by CE-Symm is available from http://source.rcsb.org/jfatcatserver/scopResults.jsp].     

Genetic diversity of 15 STR loci in a population of Montenegro

Genetic diversity and forensic parameters based on 15AmpFlSTR Identifiler short tandem repeat (STR) loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA) were evaluated in a sample of 101 unrelated, autochthonous adults from Montenegro. After applying Bonferroni correction, the agreement with Hardy-Weinberg equilibrium (HWE) was confirmed for all loci with the exception of D5S818 (chi2 test) and D21S11 (exact test). The combined power of discrimination (PD) and the combined power of exclusion (PE) for the 15 studied loci were 0.9999999999999999844 and 0.99999382, respectively. According to measures of within-population genetic diversity, D2S1338, D18S51 and FGA may be considered as the most variable and most informative markers for forensic testing and population genetic analyses out of the 15 analysed loci in a population of Montenegro. D5S818 showed to be the least variable and together with TPOX, the least informative. Interpopulation comparisons were carried out and levels of genetic differentiation between population of Montenegro and five South-eastern European populations (Kosovo Albanians, Serbians from Vojvodina province, Macedonians, Bosnians and Croatians) were evaluated. The most differentiated population in relation to Montenegro is a population of Kosovo Albanians as suggested by both AMOVA and coefficients of genetic differentiation (F(ST) and R(ST)).