Genomic and physiological analysis reveals versatile metabolic capacity of deep-sea <Emphasis Type="Italic">Photobacterium phosphoreum</Emphasis> ANT-2200

Bacteria of the genus Photobacterium thrive worldwide in oceans and show substantial eco-physiological diversity including free-living, symbiotic and piezophilic life styles. Genomic characteristics underlying this variability across species are poorly understood. Here we carried out genomic and physiological analysis of Photobacterium phosphoreum strain ANT-2200, the first deep-sea luminous bacterium of which the genome has been sequenced. Using optical mapping we updated the genomic data and reassembled it into two chromosomes and a large plasmid. Genomic analysis revealed a versatile energy metabolic potential and physiological analysis confirmed its growth capacity by deriving energy from fermentation of glucose or maltose, by respiration with formate as electron donor and trimethlyamine N-oxide (TMAO), nitrate or fumarate as electron acceptors, or by chemo-organo-heterotrophic growth in rich media. Despite that it was isolated at a site with saturated dissolved oxygen, the ANT-2200 strain possesses four gene clusters coding for typical anaerobic enzymes, the TMAO reductases. Elevated hydrostatic pressure enhances the TMAO reductase activity, mainly due to the increase of isoenzyme TorA1. The high copy number of the TMAO reductase isoenzymes and pressure-enhanced activity might imply a strategy developed by bacteria to adapt to deep-sea habitats where the instant TMAO availability may increase with depth.     

Probing the roles of two tryptophans surrounding the unique zinc coordination site in lipase family I.5

A unique zinc domain found in all of the identified members of the lipase family I.5 is surrounded by two conserved tryptophans (W61 and W212). In this study, we investigated the role of these hydrophobic residues in thermostability and thermoactivity of the lipase from Bacillus thermocatenulatus (BTL2) taken as the representative of the family. Circular dichroism spectroscopy revealed that the secondary structure of BTL2 is conserved by the tryptophan mutations (W61A, W212A, and W61A/W212A), and that W61 is located in a more rigid and less solvent exposed region than is W212. Thermal denaturation and optimal activity analyses pointed out that zinc induces thermostability and thermoactivity of BTL2, in which both tryptophans W61 and W212 play contributing roles. Molecular explanations describing the roles of these tryptophans were pursued by X‐ray crystallography of the open form of the W61A mutant and molecular dynamics simulations which highlighted a critical function for W212 in zinc binding to the coordination site. This study reflects the potential use of hydrophobic amino acids in vicinity of metal coordination sites in lipase biocatalysts design. Proteins 2016; 84:129–142. © 2015 Wiley Periodicals, Inc.     

In the Pursuit of the Predatory Behavior of Borophagines (Mammalia,Carnivora, Canidae): Inferences from Forelimb Morphology

Here, we perform an ecomorphological study on the major bones (humerus, radius, and ulna) of the carnivoran forelimb using three-dimensional geometric morphometrics. More specifically, we test the association between forelimb morphology and predatory behavior. Our results suggest that the main morphological adaptions of carnivorans to different predatory behaviors relate to: (i) the capacity to perform long and efficient runs as in pounce/pursuit and pursuit predators; (ii) the ability to maneuver as in occasional predators; and (iii) the capacity to exert and resist large loads as in ambushing predators. We used borophagine canids as a case study, given the controversy on the predatory behavior of this extinct subfamily. Our results indicate that borophagines displayed a limited set of adaptions towards efficient running, including reduced joint mobility in both the elbow and the wrist, aspects in which they resemble the living canids. Furthermore, they had forelimbs as powerful as those of the extant ambushing carnivorans (i.e., most felids). This combination of traits suggests that the predatory behavior of borophagines was unique among carnivorans, as it was not fully equivalent to any of the living species.     

Benzyl propionate synthesis by fed-batch esterification using commercial immobilized and lyophilized Cal B lipase

Bioprocess and Biosystems Engineering - In this work, a fed-batch approach was adopted to overcome propionic acid lipase inactivation effects in the benzyl propionate direct esterification mediated...     

An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity

Whole genome sequences (WGS) greatly increase our ability to precisely infer population genetic parameters, demographic processes, and selection signatures. However, WGS may still be not affordable for a representative number of individuals/populations. In this context, our goal was to assess the efficiency of several SNP genotyping strategies by testing their ability to accurately estimate parameters describing neutral diversity and to detect signatures of selection. We analysed 110 WGS at 12× coverage for four different species, i.e., sheep, goats and their wild counterparts. From these data we generated 946 data sets corresponding to random panels of 1K to 5M variants, commercial SNP chips and exome capture, for sample sizes of five to 48 individuals. We also extracted low‐coverage genome resequencing of 1×, 2× and 5× by randomly subsampling reads from the 12× resequencing data. Globally, 5K to 10K random variants were enough for an accurate estimation of genome diversity. Conversely, commercial panels and exome capture displayed strong ascertainment biases. Besides the characterization of neutral diversity, the detection of the signature of selection and the accurate estimation of linkage disequilibrium (LD) required high‐density panels of at least 1M variants. Finally, genotype likelihoods increased the quality of variant calling from low coverage resequencing but proportions of incorrect genotypes remained substantial, especially for heterozygote sites. Whole genome resequencing coverage of at least 5× appeared to be necessary for accurate assessment of genomic variations. These results have implications for studies seeking to deploy low‐density SNP collections or genome scans across genetically diverse populations/species showing similar genetic characteristics and patterns of LD decay for a wide variety of purposes.     

Age,growth, and reproductive biology of the Atlantic spadefish Chaetodipterus faber in southern Brazil

Ichthyological Research - This is the first study to investigate the age, growth and reproductive biology of the Atlantic spadefish Chaetodipterus faber in southern Brazil. A total of 625...     

Understanding and predicting frost‐induced tropical tree mortality patterns

Extreme climatic and weather events are increasing in frequency and intensity across the world causing episodes of widespread tree mortality in many forested ecosystems. However, we have a limited understanding about which local factors influence tree mortality patterns, restricting our ability to predict tree mortality, especially within topographically complex tropical landscapes with a matrix of mature and secondary forests. We investigated the effects of two major local factors, topography and forest successional type, on climate‐induced tropical tree mortality patterns using an observational and modeling approach. The northernmost Neotropical dry forest endured an unprecedented episode of frost‐induced tree mortality after the historic February 2011 cold wave hit northwestern Mexico. In a moderately hilly landscape covering mature and secondary tropical dry forests, we surveyed 454 sites for the presence or absence of frost‐induced tree mortality. In addition, across forty‐eight 1 ha plots equally split into the two forest types, we examined 6,981 woody plants to estimate a frost‐disturbance severity metric using the density of frost‐killed trees. Elevation is the main factor modulating frost effects regardless of forest type. Higher occurrence probabilities of frost‐induced tree mortality at lowland forests can be explained by the strong influence of elevation on temperature distribution since heavier cold air masses move downhill during advective frosts. Holding elevation constant, the probability of frost‐induced tree mortality in mature forests was twice that of secondary forests but severity showed the opposite pattern, suggesting a cautious use of occurrence probabilities of tree mortality to infer severity of climate‐driven disturbances. Extreme frost events, in addition to altering forest successional pathways and ecosystem services, likely maintain and could ultimately shift latitudinal and altitudinal range margins of Neotropical dry forests.