Unusual pattern of bacterial ice nucleation gene evolution

Bacterial ice nucleation activity (INA+ phenotype) can be traced to the product of a single gene, ina. A remarkably sparse distribution of this phenotype within three bacterial genera indicates that the ina gene may have followed an unusual evolutionary path. Southern blot analyses, coupled with assays for ice-nucleating ability, revealed that within four bacterial species an ina gene is present in some strains but absent from others. Results of hybridization experiments using DNA fragments that flank the ina gene suggested that the genotypic dimorphism of ina may be anomalous. A phylogenetic analysis of 16S ribosomal RNA gene sequences from a total of 14 ina+ and ina- bacterial strains indicated that the ina+ bacteria are not monophyletic but instead phylogenetically interspersed among ina- bacteria. The relationships of ina+ bacteria inferred from ina sequence did not coincide with those inferred from the 16S data. These results suggest the possibility of horizontal transfer in the evolution of bacterial ina genes.      

Effects of Paenibacillus nematophilus on the entomopathogenic nematode Heterorhabditis megidis

The insect parasitic nematodes Heterorhabditis spp. are mutualistically associated with entomopathogenic bacteria, Photorhabdus spp. A novel association has been detected between H. megidis isolate EU17 and the endospore-forming bacterium Paenibacillus nematophilus. P. nematophilus sporangia adhere to infective juveniles (IJs) of H. megidis and develop in insect hosts along with the nematodes and their symbiont. We tested the effects of P. nematophilus on H. megidis. The yield and quality (size, energy reserves, and storage survival) of IJs were not affected by co-culture in insects with P. nematophilus. Dispersal of IJs in sand and on agar was inhibited by adhering P. nematophilus sporangia: fewer than 2% of IJs with P. nematophilus sporangia reached the bottom of a sand column, compared to 30% of the control treatment. Sporangia significantly reduced infectivity of H. megidis for wax moth larvae in sand, but not in a close contact (filter paper) assay. The results suggest that P. nematophilus may reduce the transmission potential of H. megidis through impeding the motility of IJs.     

MagicMatch--cross-referencing sequence identifiers across databases

MOTIVATION: At present, mapping of sequence identifiers across databases is a daunting, time-consuming and computationally expensive process, usually achieved by sequence similarity searches with strict threshold values. SUMMARY: We present a rapid and efficient method to map sequence identifiers across databases. The method uses the MD5 checksum algorithm for message integrity to generate sequence fingerprints and uses these fingerprints as hash strings to map sequences across databases. The program, called MagicMatch, is able to cross-link any of the major sequence databases within a few seconds on a modest desktop computer.     

Enzymatic response to cadmium by Impatiens glandulifera: A preliminary investigation

This paper aims to develop our understanding of the effect of cadmium (Cd) on Impatiens glandulifera, a recently identified potential Cd hyperaccumulator. Impatiens glandulifera plants were exposed to three concentrations of Cd (20, 60 and 90 mg/kg) and were sampled at two timepoints (one and seven days) to investigate the stress response of I. glandulifera to Cd. Cd can induce oxidative stress in plants, triggering overproduction of reactive oxygen species (ROS). The level of activity of catalase (CAT) and ascorbate peroxidase (APX), two crucial antioxidant enzymes responsible for detoxifying ROS, were found to increase in a concentration dependent manner. Though there was no change observed in the level of superoxide dismutase (SOD) activity, the activity of glutathione S-transferase (GST), involved in detoxifying and sequestering Cd, increased after exposure to Cd. Cd did not appear to impact the levels of proline and photosynthetic pigments, indicating the plants weren't stressed by the presence of Cd. These results suggest that the rapid response observed in enzyme activity aid the efficacious mitigation of the toxic effects of Cd, preventing significant physiological stress in I. glandulifera.     

Incidence and nature of testicular toxicity findings in pharmaceutical development

BACKGROUND : Testicular toxicity (TT) is a sporadic and challenging issue in pharmaceutical drug development. Efforts to develop TT screening assays or biomarkers have been overshadowed by consortium efforts to predict drug‐induced toxicities such as hepatic injury, which are encountered more frequently. METHODS : To gauge the current state of the field and to prioritize future TT activities, the International Life Sciences Institute‐Health and Environmental Sciences Institute Developmental and Reproductive Toxicology (DART) Technical Committee sponsored a survey to better understand the incidence and nature of TT findings encountered during drug development. RESULTS : Highlights from the 16 survey respondents include: (1) Although preclinical TT was encountered relatively infrequently, half of the participants observed repeated problems with TT during pharmaceutical development, (2) despite control measures such as use of sexually mature animals to diminish confounding effects of spurious lesions, interpretation of TT remains a challenge, (3) “traditional” evaluation tools such as hormonal monitoring and newer approaches such as ‐omics are utilized to investigate testicular changes, and (4) an understanding of the risk and relevance of TT findings is achieved through joint consideration of factors such as species specificity, potential mode of action, and safety margins. CONCLUSIONS : TT remains a relatively uncommon but persistent challenge in pharmaceutical development. Although current preclinical TT approaches appear to be effective in limiting the occurrence of pharmaceutical candidate attrition in clinical trials, improved biomarker or screening platforms would allow companies to identify TT at an earlier stage, thus decreasing the time and resources expended on safety evaluation of pharmaceutical candidates. Birth Defects Res (Part B) 92: 511–525, 2011. © 2011 Wiley Periodicals, Inc.     

Messenger RNA and microRNA profiling during early mouse EB formation

Embryonic stem (ES) cells can be induced to differentiate into embryoid bodies (EBs) in a synchronised manner when plated at a fixed density in hanging drops. This differentiation procedure mimics post-implantation development in mouse embryos and also serves as the starting point of protocols used in differentiation of stem cells into various lineages. Currently, little is known about the potential influence of microRNAs (miRNAs) on mRNA expression patterns during EB formation. We have measured mRNA and miRNA expression in developing EBs plated in hanging drops until day 3, when discrete structural changes occur involving their differentiation into three germ layers. We observe significant alterations in mRNA and miRNA expression profiles during this early developmental time frame, in particular of genes involved in germ layer formation, stem cell pluripotency and nervous system development. Computational target prediction using Pictar, TargetScan and miRBase Targets reveals an enrichment of binding sites corresponding to differentially and highly expressed miRNAs in stem cell pluripotency genes and a neuroectodermal marker, Nes. We also find that members of let-7 family are significantly down-regulated at day 3 and the corresponding up-regulated genes are enriched in let-7 seed sequences. These results depict how miRNA expression changes may affect the expression of mRNAs involved in EB formation on a genome-wide scale. Understanding the regulatory effects of miRNAs during EB formation may enable more efficient derivation of different cell types in culture.     

Low-dimensional trade-offs fail to explain richness and structure in species-rich plant communities

Mathematical models and ecological theory suggest that low-dimensional life history trade-offs (i.e. negative correlation between two life history traits such as competition vs. colonisation) may potentially explain the maintenance of species diversity and community structure. In the absence of trade-offs, we would expect communities to be dominated by ‘super-types’ characterised by mainly positive trait expressions. However, it has proven difficult to find strong empirical evidence for such trade-offs in species-rich communities. We developed a spatially explicit, rule-based and individual-based stochastic model to explore the importance of low-dimensional trade-offs. This model simulates the community dynamics of 288 virtual plant functional types (PFTs), each of which is described by seven life history traits. We consider trait combinations that fit into the trade-off concept, as well as super-types with little or no energy constraints or resource limitations, and weak PFTs, which do not exploit resources efficiently. The model is parameterised using data from a fire-prone, species-rich Mediterranean-type shrubland in southwestern Australia. We performed an exclusion experiment, where we sequentially removed the strongest PFT in the simulation and studied the remaining communities. We analysed the impact of traits on performance of PFTs in the exclusion experiment with standard and boosted regression trees. Regression tree analysis of the simulation results showed that the trade-off concept is necessary for PFT viability in the case of weak trait expression combinations such as low seed production or small seeds. However, species richness and diversity can be high despite the presence of super-types. Furthermore, the exclusion of super-types does not necessarily lead to a large increase in PFT richness and diversity. We conclude that low-dimensional trade-offs do not provide explanations for multi-species co-existence contrary to the prediction of many conceptual models.     

Notes on Scleroderma,Puff balls and Geastrum of Azad Jammu and Kashmir,Pakistan

Six species of mushrooms allied to the Family Sclerodermataceae, Lycoperdaceae and Geastraceae have been described for the first time from Azad Jammu and Kashmir. These are Scleroderma aurantium, Calvatia verrucosia sp. nov., Lycoperdon pedicellaton sp. nov. L. sphaericon sp. nov., L. echinulaton sp. nov., and Geastrum heptaplex sp. nov.