Contribution of lateral gene transfer to the gene repertoire of a gut-adapted methanogen

Methanobrevibacter smithii is the most abundant archaeon in the human colon. As most of its neighbors are bacterial species, it is expected that lateral gene acquisition from bacteria might have contributed to the evolution and adaptation of this archaeon. We performed a tree-based genome-wide survey of putative lateral gene transfer products in M. smithii, using a phylogenetic pipeline. Over 15% of the coding genes of M. smithii are inferred to be bacterial in origin, based on this analysis. Laterally acquired genes have had the largest contribution to surface functions, and encode glycosyl-transferases and adhesin-like proteins. In addition, several important ABC transporters, especially metal transporters are of bacterial origin. Thus, bacterial genes contributed to the host-adaptation by allowing a larger variety of surface structures and increasing the efficiency of metal ion uptake in the competitive gut niche.     

Native homing endonucleases can target conserved genes in humans and in animal models

In recent years, both homing endonucleases (HEases) and zinc-finger nucleases (ZFNs) have been engineered and selected for the targeting of desired human loci for gene therapy. However, enzyme engineering is lengthy and expensive and the off-target effect of the manufactured endonucleases is difficult to predict. Moreover, enzymes selected to cleave a human DNA locus may not cleave the homologous locus in the genome of animal models because of sequence divergence, thus hampering attempts to assess the in vivo efficacy and safety of any engineered enzyme prior to its application in human trials. Here, we show that naturally occurring HEases can be found, that cleave desirable human targets. Some of these enzymes are also shown to cleave the homologous sequence in the genome of animal models. In addition, the distribution of off-target effects may be more predictable for native HEases. Based on our experimental observations, we present the HomeBase algorithm, database and web server that allow a high-throughput computational search and assignment of HEases for the targeting of specific loci in the human and other genomes. We validate experimentally the predicted target specificity of candidate fungal, bacterial and archaeal HEases using cell free, yeast and archaeal assays.     

Diagnostic PCR can be used to illuminate meiofaunal diets and trophic relationships

Analysis of the meiofaunal food web is hampered because few prey have features that persist long enough in a predator's digestive tract to allow identification to species. Hence, at least for platyhelminth predators, direct observations of prey preference are almost nonexistent, and where they occur, prey identification is often limited to the phylum level. Studies using an in vitro approach are rare because they are extremely time‐consuming and are subject to the criticism that predators removed from their natural environment may exhibit altered behaviors. Although PCR‐based approaches have achieved wide application in food‐web analysis, their application to meiofaunal flatworms suffers from a number of limitations. Most importantly, the microscopic size of both the predator and prey does not allow for removal of prey material from the digestive tract of the predator, and thus the challenge is to amplify prey sequences in the presence of large quantities of predator sequence. Here, we report on the successful use of prey‐taxon‐specific primers in diagnostic PCR to identify, to species level, specific prey items of 13 species of meiofaunal flatworms. Extension of this method will allow, for the first time, the development of a species‐level understanding of trophic interactions among the meiofauna.     

A theoretical study on the coordination behavior of some phosphoryl,carbonyl and sulfoxide derivatives in lanthanide complexation

The selectivity of phosphoryl P(O)R₃, sulfoxide S(O)R₂, and carbonyl C(O)R₂ (R?=?NH₂, CH₃, OH, and F) derivatives with lanthanide cations (La³⁺, Eu³⁺, Lu³⁺) was studied by density functional theory calculations. Theoretical approaches were also used to investigate energy and the nature of metal–ligand interaction in the model complexes. Atoms in molecules and natural bond orbital (NBO) analyses were accomplished to understand the electronic structure of ligands, L, and the related complexes, L–Ln³⁺. NBO analysis demonstrated that the negative charge on phosphoryl, carbonyl, and sulfoxide oxygen (O_P, O_C, and O_S) has maximum and minimum values when the connected –R groups are –NH₂ and –F. The metal–ligand distance declines as, –F?>?–OH?>?–CH₃?>?–NH₂. Charge density at the bond critical point and on the lanthanide cation in the L–Ln³⁺ complexes varies in the order –F?<?–OH?<?–CH₃?<?–NH₂, due to greater ligand to metal charge transfer, which is well explained by energy decomposition analysis. It was also illustrated that E⁽²⁾ values of Lp(N)?→?σ*(Y–N) vary in the order P=O ? S=O ? C=O and the related values of Lp(N)?→?σ*(Y=O) change as C=O ? S=O ? P=O in (NH₂)_nYO ligands (Y?=?P, C, and S). Trends in the L–Ln³⁺ CP–corrected bond energies are in good accordance with the optimized O_Y?Ln distances. It seems that, comparing the three types of ligands studied, NH₂–substituted are the better coordination ligands.

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Graphical Abstract Density functional theory (B3LYP) calculations were used to compare structural, electronic and energy aspects of lanthanide (La, Eu, Lu) complexes of phosphine derivatives with those of carbonyls and sulfoxides in which the R– groups connected to the P=O, C=O and S=O are –NH₂, –CH₃, –OH and –F.

     

Emulsifier of Arthrobacter RAG-1: chemical and physical properties.

The extracellular emulsifier of Arthrobacter RAG-1 was deproteinized by hot phenol treatment and purified by fractional precipitation with (NH(4))(2)SO(4). The active fraction, precipitating between 30 and 35% saturation [EF-RAG(UET) WA], appeared to be homogeneous by immunodiffusion and sedimentation analysis. EF-RAG(UET) WA had an intrinsic viscosity of 750 cm(3)/g, a sedimentation constant of 6.06S, a diffusion constant of 5.25 x 10(-8) cm(2) s(-1), and a partial molar volume of 0.712 cm(3) g(-1). From these data a weight average molecular weight of 9.76 x 10(5) and a viscosity average molecular weight of 9.88 x 10(5) were calculated. EF-RAG(UET)WA contained 46.7% C, 7.01% H, and 6.06% N. Titration of the nonreducing polymer gave a single inflection point (pK' = 3.05), corresponding to 1.5 mumol of carboxyl groups per mg. Direct estimation of O-ester and hexose content of the highly acidic polymer yielded 0.65 and 0.29 mumol/mg, respectively. Mild alkaline hydrolysis released fatty acids with an average molecular weight of about 231. Strong acid hydrolysis of EF-RAG(UET)WA yielded d-glucose (minor), d-galactosamine (major), and an unidentified amino uronic acid (major).