Catalytically impaired TrpA subunit of tryptophan synthase from Chlamydia trachomatis is an allosteric regulator of TrpB

Intracellular growth and pathogenesis of Chlamydia species is controlled by the availability of tryptophan, yet the complete biosynthetic pathway for l‐Trp is absent among members of the genus. Some representatives, however, preserve genes encoding tryptophan synthase, TrpAB – a bifunctional enzyme catalyzing the last two steps in l‐Trp synthesis. TrpA (subunit α) converts indole‐3‐glycerol phosphate into indole and glyceraldehyde‐3‐phosphate (α reaction). The former compound is subsequently used by TrpB (subunit β) to produce l‐Trp in the presence of l‐Ser and a pyridoxal 5′‐phosphate cofactor (β reaction). Previous studies have indicated that in Chlamydia, TrpA has lost its catalytic activity yet remains associated with TrpB to support the β reaction. Here, we provide detailed analysis of the TrpAB from C. trachomatis D/UW‐3/CX, confirming that accumulation of mutations in the active site of TrpA renders it enzymatically inactive, despite the conservation of the catalytic residues. We also show that TrpA remains a functional component of the TrpAB complex, increasing the activity of TrpB by four‐fold. The side chain of non‐conserved βArg267 functions as cation effector, potentially rendering the enzyme less susceptible to the solvent ion composition. The observed structural and functional changes detected herein were placed in a broader evolutionary and genomic context, allowing identification of these mutations in relation to their trp gene contexts in which they occur. Moreover, in agreement with the in vitro data, partial relaxation of purifying selection for TrpA, but not for TrpB, was detected, reinforcing a partial loss of TrpA functions during the course of evolution.     

Native arbuscular mycorrhizal fungi in the Yungas forests, Argentina

The arbuscular mycorrhizal fungal (AMF) communities from the Yungas forests of Argentina were studied. The AMF species present in the rhizosphere of some dominant native plants (one tree: Alnus acuminata; three herbaceous species: Duchesnea indica, Oxalis conorrhiza, Trifolium aff. repens; and one shrub: Sambucus peruviana) from two sites (Quebrada del Portugués and Narváez Range) of the Yungas forests were isolated, identified and quantified during the four seasons of the year. Twenty-two AMF morphotaxa were found. Spore density of some AMF species at each site varied among seasons. The genera that most contributed to the biodiversity index were Acaulospora for Quebrada del Portugués and Glomus for Narváez Range. High diversity values were observed in the Yungas forests, particularly in the spring (rainy season). We concluded AMF differed in species composition and seasonal sporulation dynamics in the Yungas forests.     

Fine structure and histochemistry of the tail fin ray in teleosts

Summary Ultrastructural and histochemical studies performed on the skeletal elements of the tail fins of six representative species of teleosts enabled the following observations to be made. The electron microscopic pattern of amorphous substance deposition, and the diameter of the collagen fibrils, in lepidotrichia closely resemble those which are typical of cartilage. In addition, lepidotrichia contain chondroitin sulfate AC as the only sulfated glycosaminoglycan, and this glycosaminoglycan shows high levels of interaction with collagen, both features being characteristic of cartilage. Furthermore, the histochemical data presented in this paper suggest that not all of the glycosaminoglycans present in lepidotrichia are bound to protein cores to form proteoglycans. Each actinotrichium consists of a single ultrastructural entity of remarkable width and, thus, is not composed of a bundle of discretely separated collagen fibrils but rather of hyperpolymerized collagen molecules. This aspect differs from the arrangement pattern of all the other interstitial collagens, suggesting that actinotrichia may contain a new type of collagen.To whom offprint requests should be sent     

Open-Phylo: a customizable crowd-computing platform for multiple sequence alignment

Citizen science games such as Galaxy Zoo, Foldit, and Phylo aim to harness the intelligence and processing power generated by crowds of online gamers to solve scientific problems. However, the selection of the data to be analyzed through these games is under the exclusive control of the game designers, and so are the results produced by gamers. Here, we introduce Open-Phylo, a freely accessible crowd-computing platform that enables any scientist to enter our system and use crowds of gamers to assist computer programs in solving one of the most fundamental problems in genomics: the multiple sequence alignment problem.     

Antibacterial metabolites synthesized by psychrotrophic bacteria isolated from cold-freshwater environments

The ability of three psychrotrophic Gram-negative bacilli isolated from Chilean Patagonian cold freshwater rivers to produce bioactive metabolites was evaluated. The strains were isolated from cold waters rivers and identified by their biochemical properties and 16S rRNA gene analysis. The metabolites fractions showing antibacterial activity were obtained by solvent extraction and partially characterized by gas–mass chromatography (GC-MS). Antibacterial activity of the fractions was evaluated by an agar-well diffusion test upon 14 bacterial strains, both Gram positive and Gram negative. Thermal and proteolytic resistances of the antibacterial metabolites fractions were also evaluated. Molecular analysis allows the identification of the three Patagonian strains as Pseudomonas sp. RG-6 (Pseudomonas brenneri 99.6 % identity), Pseudomonas sp. RG-8 (Pseudomonas trivialis 99.6 % identity) and Yersinia sp. RP-3 (Yersinia aldovae 99.5 % identity). These extracts were able to inhibit both Gram-positive and Gram-negative bacteria but not Listeria monocytogenes. The antibacterial activity of the filtrated supernatants was lost at temperatures ≥60 °C, and was not affected by proteinase K treatment. The chemical structure of the active molecule remains to be elucidated, although the GC-MS analysis of the filtrates suggests that compounds like sesquiterpenes derivatives from β-maaliene or δ-selinene could be responsible of this antibacterial activity. Pristine cold freshwater streams showed to be interesting sources of metabolites-producing microorganisms with antibacterial activity.     

Transient and Persistent Pain Induced Connectivity Alterations in Pediatric Complex Regional Pain Syndrome

Evaluation of pain-induced changes in functional connectivity was performed in pediatric complex regional pain syndrome (CRPS) patients. High field functional magnetic resonance imaging was done in the symptomatic painful state and at follow up in the asymptomatic pain free/recovered state. Two types of connectivity alterations were defined: (1) Transient increases in functional connectivity that identified regions with increased cold-induced functional connectivity in the affected limb vs. unaffected limb in the CRPS state, but with normalized connectivity patterns in the recovered state; and (2) Persistent increases in functional connectivity that identified regions with increased cold-induced functional connectivity in the affected limb as compared to the unaffected limb that persisted also in the recovered state (recovered affected limb versus recovered unaffected limb). The data support the notion that even after symptomatic recovery, alterations in brain systems persist, particularly in amygdala and basal ganglia systems. Connectivity analysis may provide a measure of temporal normalization of different circuits/regions when evaluating therapeutic interventions for this condition. The results add emphasis to the importance of early recognition and management in improving outcome of pediatric CRPS.     

Reciprocal transplantation of the heterotrophic coral Tubastraea coccinea (Scleractinia: Dendrophylliidae) between distinct habitats did not alter its venom toxin composition

Tubastraea coccinea is an azooxanthellate coral species recorded in the Indian and Atlantic oceans and is presently widespread in the southwestern Atlantic with an alien status for Brazil. T. coccinea outcompete other native coral species by using a varied repertoire of biological traits. For example, T. coccinea has evolved potent venom capable of immobilizing and digesting zooplankton prey. Diversification and modification of venom toxins can provide potential adaptive benefits to individual fitness, yet acquired alteration of venom composition in cnidarians is poorly understood as the adaptive flexibility affecting toxin composition in these ancient lineages has been largely ignored. We used quantitative high‐throughput proteomics to detect changes in toxin expression in clonal fragments of specimens collected and interchanged from two environmentally distinct and geographically separate study sites. Unexpectedly, despite global changes in protein expression, there were no changes in the composition and abundance of toxins from coral fragments recovered from either site, and following clonal transplantation between sites. There were also no apparent changes to the cnidome (cnidae) and gross skeletal or soft tissue morphologies of the specimens. These results suggest that the conserved toxin complexity of T. coccinea co‐evolved with innovation of the venom delivery system, and its morphological development and phenotypic expression are not modulated by habitat pressures over short periods of time. The adaptive response of the venom trait to specific predatory regimes, however, necessitates further consideration.     

Fetal gender determination by first-trimester ultrasound in dairy cows under routine herd management in Northwest Spain

Ultrasonography (US) provides detailed visualization of the fetus in early pregnancy in cows, thus allowing for fetal sex determination. The objective of this prospective observational study was to determine the feasibility and accuracy of a single US examination to diagnose fetal sex in dairy cattle under routine reproductive management conditions. For this purpose, 953 Holstein cows at 7-16 weeks of gestation were examined. Gender assignment was performed in 822 cows, while the genitalia could not be clearly visualized in 131 (13.7%) of the fetuses. After calving, it was verified that 99.3% of the diagnoses were accurate. Fetal sex was correctly determined by US in 99.5% of male fetuses and 98.8% of female fetuses. Fetal sex determination was less accurate when conducted before d 55 of gestation. Likewise, it was verified that fetal sex, cow age and ultrasonographic diagnosis section did not have a significant influence (P>0.05) on diagnostic accuracy. With respect to the plane used for diagnosis, the sagittal view was poorly used for early pregnancy diagnosis, whereas the longitudinal and cross-sectional planes were used most frequently. These results demonstrate that US can be routinely applied under farm conditions to accurately determine the fetal sex in cattle between days 51 and 111 of gestation without apparent influence of cow age, US scanning plane or fetal sex. Conversely, days of gestation affected the accuracy and feasibility of US gender determination, showing poorer results when the diagnosis was made before day 55 of gestation.     

A genetic map of an Australian wild Gossypium C genome and assignment of homoeologies with tetraploid cultivated cotton

Genetic diversity for traits such as fibre quality or disease resistance to microorganisms is limited in the elite cotton germplasm; consequently, cotton breeders are looking for novel alleles in the secondary or even in the tertiary gene pools. The wild Australian Gossypium species (tertiary gene pool) represent an alternative source of novel alleles. However, to use these species efficiently, enabling tools are required. Chromosome-specific molecular markers are particularly useful tools to track the transmission of this exotic genetic material into the cultivated cotton during introgression. In this study, we report the construction of a genetic linkage map of the Australian wild C-genome species Gossypium sturtianum. The map, based on an F(2) population of 114 individuals, contains 291 AFLP loci. The map spans 1697 cM with an average distance of 5.8 cM between markers. To associate C-genome chromosomes with the A and D subgenomes of cultivated cotton, 29 SSR and RFLP-STS markers were assigned to chromosomes using cultivated cotton mapped marker information. Polymorphisms were revealed by 51 AFLP primer combinations and 38 RFLP-STS and 115 SSR cotton mapped markers. The utility of transferring RFLP-STS and SSR cotton mapped markers to other Gossypium species shows the usefulness of a comparative approach as a source of markers and for aligning the genetic map of G. sturtianum with the cultivated species in the future. This also indicates that the overall structure of the G. sturtianum linkage groups is similar to that of the A and D subgenomes of cotton at the gross structural level. Applications of the map for the Australia wild C-genome species and cotton breeding are discussed.