The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird

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Levansucrase from Halomonas smyrnensis AAD6T: first halophilic GH-J clan enzyme recombinantly expressed,purified, and characterized

Fructans, homopolymers of fructose produced by fructosyltransferases (FTs), are emerging as intriguing components in halophiles since they are thought to be associated with osmotic stress tolerance and overall fitness of microorganisms and plants under high-salinity conditions. Here, we report on the full characterization of the first halophilic FT, a levansucrase from Halomonas smyrnensis AAD6^T (HsLsc; EC 2.4.1.10). The encoding gene (lsc) was cloned into a vector with a 6xHis Tag at its C-terminus, then expressed in Escherichia coli. The purified recombinant enzyme (47.3 kDa) produces levan and a wide variety of fructooligosaccharides from sucrose, but only in the presence of high salt concentrations (> 1.5 M NaCl). HsLsc showed Hill kinetics and pH and temperature optima of 5.9 and 37 °C, respectively. Interestingly, HsLsc was still very active at salt concentrations close to saturation (4.5 M NaCl) and was selectively inhibited by divalent cations. The enzyme showed high potential in producing novel saccharides derived from raffinose as both fructosyl donor and acceptor and cellobiose, lactose, galactose, and ʟ-arabinose as fructosyl acceptors. With its unique biochemical characteristics, HsLsc is an important enzyme for future research and potential industrial applications in a world faced with drought and diminishing freshwater supplies.

     

Fast phylogenetic inference from typing data

Background

Microbial typing methods are commonly used to study the relatedness of bacterial strains. Sequence-based typing methods are a gold standard for epidemiological surveillance due to the inherent portability of sequence and allelic profile data, fast analysis times and their capacity to create common nomenclatures for strains or clones. This led to development of several novel methods and several databases being made available for many microbial species. With the mainstream use of High Throughput Sequencing, the amount of data being accumulated in these databases is huge, storing thousands of different profiles. On the other hand, computing genetic evolutionary distances among a set of typing profiles or taxa dominates the running time of many phylogenetic inference methods. It is important also to note that most of genetic evolution distance definitions rely, even if indirectly, on computing the pairwise Hamming distance among sequences or profiles.

Results

We propose here an average-case linear-time algorithm to compute pairwise Hamming distances among a set of taxa under a given Hamming distance threshold. This article includes both a theoretical analysis and extensive experimental results concerning the proposed algorithm. We further show how this algorithm can be successfully integrated into a well known phylogenetic inference method, and how it can be used to speedup querying local phylogenetic patterns over large typing databases.

     

Vertical segregation of age-0 and age-1+ polar cod (<Emphasis Type="Italic">Boreogadus saida</Emphasis>) over the annual cycle in the Canadian Beaufort Sea

The offshore marine ecosystem of the Canadian Beaufort Sea faces the double pressure of climate change and industrialization. Polar cod (Boreogadus saida) is a pivotal forage species in this ecosystem, accounting for 95 % of the pelagic fish assemblage. Its vertical distribution over the annual cycle remains poorly documented. Hydroacoustic records from 2006 to 2012 were analysed to test the hypothesis that age-0 polar cod segregate vertically from larger congeners. Trawls and ichthyoplankton nets validated the acoustic signal. Fish length, weight, and biomass were estimated from new regressions of target strength and weight on standard length. Polar cod were vertically segregated by size in all months, with small age-0 juveniles in the epipelagic (<100 m) layer and larger age-1+ deeper in the water column. From December to March, the biomass of age-1+ peaked in a mesopelagic layer between 200 and 400 m. With increasing irradiance from April to July, the mesopelagic layer deepened and extended to 600 m. Starting in July, age-0 polar cod formed an epipelagic scattering layer that persisted until November. From September onward, age-0 left the epipelagic layer to join small age-1+ in the upper mesopelagic layer. Low biomass in the mesopelagic layer from February to September likely resulted from large polar cod settling on the seafloor to avoid diving marine mammals. Longer ice-free seasons, warmer sea-surface temperatures, or an oil spill at the surface would likely impact epipelagic age-0, while mesopelagic age-1+ would be vulnerable to an eventual oil plume spreading over and above the seafloor.     

An evaluation of active acoustic methods for detection of marine mammals in the Canadian Beaufort Sea

A commercially available fisheries sonar was mounted on an icebreaker and evaluated during an environmental baseline study in the Canadian Beaufort Sea, to determine the applicability of active acoustic monitoring (AAM) for marine mammal detection by comparing marine mammal observer (MMO) visual sightings and active acoustic detections. During 170 h of simultaneous MMO and AAM, 115 bowhead whales (Balaena mysticetus) and four beluga whales (Delphinapterus leucas) were visually sighted by MMOs, while 59 sonar detections of bowhead whales occurred using AAM. The fisheries sonar detected 92% of the cetaceans observed within 2,000 m. Additional observations of ringed seals (Pusa hispida) and bearded seals (Erignathus barbatus) were recorded both by MMOs and AAM. Comparative results indicate that a commercially available active acoustic system can consistently detect marine mammals within varying ranges dictated by water column properties. Shallow environments and strong pycnoclines currently present challenges to AAM.     

Synthesis and evaluation of original amidoximes as antileishmanial agents

An original series of amidoxime derivatives was synthesized using manganese(III) acetate, Buchwald–Hartwig and Heck reactions. Two amidoximes (39 and 52) showed interesting in vitro activities toward Leishmania donovani promastigotes, exhibiting 8.3 and 8.8 μM IC₅₀ values. Moreover, the cytotoxicity of these compounds was evaluated on human THP1 cells, giving access to the corresponding selectivity index. Among the 25 tested compounds, amidoximes 38 and 39 and diamidoximes 50 and 52 exhibited a better selectivity index than pentamidine used as a drug compound reference.     

Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes

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Statistical Distance as a Measure of Physiological Dysregulation Is Largely Robust to Variation in Its Biomarker Composition

Physiological dysregulation may underlie aging and many chronic diseases, but is challenging to quantify because of the complexity of the underlying systems. Recently, we described a measure of physiological dysregulation, D_M, that uses statistical distance to assess the degree to which an individual’s biomarker profile is normal versus aberrant. However, the sensitivity of D_M to details of the calculation method has not yet been systematically assessed. In particular, the number and choice of biomarkers and the definition of the reference population (RP, the population used to define a “normal” profile) may be important. Here, we address this question by validating the method on 44 common clinical biomarkers from three longitudinal cohort studies and one cross-sectional survey. D_Ms calculated on different biomarker subsets show that while the signal of physiological dysregulation increases with the number of biomarkers included, the value of additional markers diminishes as more are added and inclusion of 10-15 is generally sufficient. As long as enough markers are included, individual markers have little effect on the final metric, and even D_Ms calculated from mutually exclusive groups of markers correlate with each other at r~0.4-0.5. We also used data subsets to generate thousands of combinations of study populations and RPs to address sensitivity to differences in age range, sex, race, data set, sample size, and their interactions. Results were largely consistent (but not identical) regardless of the choice of RP; however, the signal was generally clearer with a younger and healthier RP, and RPs too different from the study population performed poorly. Accordingly, biomarker and RP choice are not particularly important in most cases, but caution should be used across very different populations or for fine-scale analyses. Biologically, the lack of sensitivity to marker choice and better performance of younger, healthier RPs confirm an interpretation of D_M physiological dysregulation and as an emergent property of a complex system.