Diversification and Distribution of Ruminant Chlamydia abortus Clones Assessed by MLST and MLVA

Chlamydia abortus, an obligate intracellular bacterium, is the most common infectious cause of abortion in small ruminants worldwide and has zoonotic potential. We applied multilocus sequence typing (MLST) together with multiple-locus variable-number tandem repeat analysis (MLVA) to genotype 94 ruminant C. abortus strains, field isolates and samples collected from 1950 to 2011 in diverse geographic locations, with the aim of delineating C. abortus lineages and clones. MLST revealed the previously identified sequence types (STs) ST19, ST25, ST29 and ST30, plus ST86, a recently-assigned type on the Chlamydiales MLST website and ST87, a novel type harbouring the hemN_21 allele, whereas MLVA recognized seven types (MT1 to MT7). Minimum-spanning-tree analysis suggested that all STs but one (ST30) belonged to a single clonal complex, possibly reflecting the short evolutionary timescale over which the predicted ancestor (ST19) has diversified into three single-locus variants (ST86, ST87 and ST29) and further, through ST86 diversification, into one double-locus variant (ST25). ST descendants have probably arisen through a point mutation evolution mode. Interestingly, MLVA showed that in the ST19 population there was a greater genetic diversity than in other STs, most of which exhibited the same MT over time and geographical distribution. However, the evolutionary pathways of C. abortus STs seem to be diverse across geographic distances with individual STs restricted to particular geographic locations. The ST30 singleton clone displaying geographic specificity and represented by the Greek strains LLG and POS was effectively distinguished from the clonal complex lineage, supporting the notion that possibly two separate host adaptations and hence independent bottlenecks of C. abortus have occurred through time. The combination of MLST and MLVA assays provides an additional level of C. abortus discrimination and may prove useful for the investigation and surveillance of emergent C. abortus clonal populations.     

129-Derived Mouse Strains Express an Unstable but Catalytically Active DNA Polymerase Iota Variant

Mice derived from the 129 strain have a nonsense codon mutation in exon 2 of the polymerase iota (Polι) gene and are therefore considered Polι deficient. When we amplified Polι mRNA from 129/SvJ or 129/Ola testes, only a small fraction of the full-length cDNA contained the nonsense mutation; the major fraction corresponded to a variant Polι isoform lacking exon 2. Polι mRNA lacking exon 2 contains an open reading frame, and the corresponding protein was detected using a polyclonal antibody raised against the C terminus of the murine Polι protein. The identity of the corresponding protein was further confirmed by mass spectrometry. Although the variant protein was expressed at only 5 to 10% of the level of wild-type Polι, it retained de novo DNA synthesis activity, the capacity to form replication foci following UV irradiation, and the ability to rescue UV light sensitivity in Polι^−/− embryonic fibroblasts derived from a new, fully deficient Polι knockout (KO) mouse line. Furthermore, in vivo treatment of 129-derived male mice with Velcade, a drug that inhibits proteasome function, stabilized and restored a substantial amount of the variant Polι in these animals, indicating that its turnover is controlled by the proteasome. An analysis of two xeroderma pigmentosum-variant (XPV) cases corresponding to missense mutants of Polη, a related translesion synthesis (TLS) polymerase in the same family, similarly showed a destabilization of the catalytically active mutant protein by the proteasome. Collectively, these data challenge the prevailing hypothesis that 129-derived strains of mice are completely deficient in Polι activity. The data also document, both for 129-derived mouse strains and for some XPV patients, new cases of genetic defects corresponding to the destabilization of an otherwise functional protein, the phenotype of which is reversible by proteasome inhibition.     

An analysis approach to identify specific functional sites in orthologous proteins using sequence and structural information: Application to neuroserpin reveals regions that differentially regulate inhibitory activity

The analysis of sequence conservation is commonly used to predict functionally important sites in proteins. We have developed an approach that first identifies highly conserved sites in a set of orthologous sequences using a weighted substitution‐matrix‐based conservation score and then filters these conserved sites based on the pattern of conservation present in a wider alignment of sequences from the same family and structural information to identify surface‐exposed sites. This allows us to detect specific functional sites in the target protein and exclude regions that are likely to be generally important for the structure or function of the wider protein family. We applied our method to two members of the serpin family of serine protease inhibitors. We first confirmed that our method successfully detected the known heparin binding site in antithrombin while excluding residues known to be generally important in the serpin family. We next applied our sequence analysis approach to neuroserpin and used our results to guide site‐directed polyalanine mutagenesis experiments. The majority of the mutant neuroserpin proteins were found to fold correctly and could still form inhibitory complexes with tissue plasminogen activator (tPA). Kinetic analysis of tPA inhibition, however, revealed altered inhibitory kinetics in several of the mutant proteins, with some mutants showing decreased association with tPA and others showing more rapid dissociation of the covalent complex. Altogether, these results confirm that our sequence analysis approach is a useful tool that can be used to guide mutagenesis experiments for the detection of specific functional sites in proteins. Proteins 2015; 83:135–152. © 2014 Wiley Periodicals, Inc.     

The Banker Plant Method in Biological Control

In the banker plant method, long-lasting rearing units for beneficials are created in the crop by distributing plants infested with herbivores or carrying other food items, such as pollen. The method has been widely investigated over many years and used to aid establishment, development and dispersal of beneficial organisms employed in biological control. In this review, we refine the definition of the banker plant method based on previous concepts and studies and offer the term “banker plant system” to describe the unit that is purposefully added to or established in a crop for control of pests in greenhouses or open field. The three basic elements of a banker plant system (banker plant, food source, beneficials) are discussed and illustrated with examples, and the diversity of banker plant systems (classified by target pest) used or investigated is documented. The benefits of using banker plant systems, such as low cost, increased freshness of beneficials, possibility for preventive control and for integration within IPM frameworks, make the method an interesting plant protection option with potential to enhance adoption of biological control in pest management programs.     

Planulation,larval biology,and early growth of the deep‐sea soft corals Gersemia fruticosa and Duva florida (Octocorallia: Alcyonacea)

Abstract. Although the reproductive biology and early life‐history stages of deep‐sea corals are poorly understood, such data are crucial for their conservation and management. Here, we describe the timing of larval release, planula behavior, metamorphosis, settlement, and early juvenile growth of two species of deep‐sea soft corals from the northwest Atlantic. Live colonies of Gersemia fruticosa maintained under flow‐through laboratory conditions released 79 planulae (1.5–2.5 mm long) between April and early June 2007. Peak planulation in G. fruticosa coincided with peaks in the chlorophyll concentration and deposition rates of planktic matter. Metamorphosis and settlement occurred 3–70 d post‐release. The eight primary mesenteries typically appeared within 24 h, and primary polyps grew to a height of ～6–10 mm and a stalk diameter of ～1 mm within 2–3 months. Planulae of Duva florida (1.5–2.5 mm long) were extracted surgically from several colonies and were successfully reared in culture. Primary polyps reached a height of ～3–4 mm within 2–3 months. No budding of primary polyps was observed in either species over 11–13 months of monitoring, suggesting a very slow growth rate.     

Effect of consumption of food cooked in aluminium or stainless-steel pots on Bangladeshi children with calcium-deficient rickets: an eight month trial

The putative role of aluminium intake in young Bangladeshi children (1.5 to 4 years of age) with calcium-deficient rickets was evaluated in a non randomised controlled eight month trial. The effects of aluminium or stain-less-steel cooking pots on bone metabolism were assessed by measuring blood calcium, phosphorus, alkaline phosphatase, parathyroid hormone, 1,25 dihydroxy vitamin D, aminoterminal propeptide of type 1 collagen (PINP), cross-linked carboxyterminal telopeptide of type 1 collagen (ICTP), aluminium and albumin, and by analysis of wrist radiographs. In both groups, blood alkaline phosphatase, 1,25 dihydroxy vitamin D and aluminium decreased significantly, while serum albumin increased (p < 0.01). These results suggest that the nutrition may well be of major importance, whereas the role of aluminium appears to be insignificant.