Bromodomain‐dependent stage‐specific male genome programming by Brdt

Male germ cell differentiation is a highly regulated multistep process initiated by the commitment of progenitor cells into meiosis and characterized by major chromatin reorganizations in haploid spermatids. We report here that a single member of the double bromodomain BET factors, Brdt, is a master regulator of both meiotic divisions and post‐meiotic genome repackaging. Upon its activation at the onset of meiosis, Brdt drives and determines the developmental timing of a testis‐specific gene expression program. In meiotic and post‐meiotic cells, Brdt initiates a genuine histone acetylation‐guided programming of the genome by activating essential genes and repressing a ‘progenitor cells’ gene expression program. At post‐meiotic stages, a global chromatin hyperacetylation gives the signal for Brdt's first bromodomain to direct the genome‐wide replacement of histones by transition proteins. Brdt is therefore a unique and essential regulator of male germ cell differentiation, which, by using various domains in a developmentally controlled manner, first drives a specific spermatogenic gene expression program, and later controls the tight packaging of the male genome.     

Lipid transport function is the main target of oral oleoylethanolamide to reduce adiposity in high-fat-fed mice

We evaluated the biological basis of reduced fat gain by oleoylethanolamide (OEA) in high-fat-fed mice and sought to determine how degradation of OEA affected its efficiency by comparing its effects to those of KDS-5104, a nonhydrolyzable lipid OEA analog. Mice were given OEA or KDS-5104 by the oral route (100 mg/kg body weight). Sixty-eight variables per mouse, describing six biological processes (lipid transport, lipogenesis, energy intake, energy expenditure, endocannabinoid signaling, and glucose metabolism), spanning gene expression of biochemical and physiological parameters were examined to determine the primary target whereby OEA reduces fat gain. Although KDS-5104 but not OEA was resistant to fatty acid amide hydrolase hydrolysis, OEA was degraded by an unidentified hydrolysis system in the liver. Nevertheless, both compounds equally decreased body fat pads after 5 weeks (20%; P < 0.05). The six biological functions constructed from the 68 initial variables predicted up to 58% of adipose fat variations. Lipid transport appeared central to the explanation for body fat deposition (16%; P < 0.0001), in which decreased expression of the FAT/CD36 gene was the component most related to adipose depots. Lipid transport appears to be a determinant player in the OEA fat-lowering response, with adipose tissue FAT/CD36 expression being the most relevant bioindicator of OEA action.     

Cyclodipeptide synthases, a family of class-I aminoacyl-tRNA synthetase-like enzymes involved in non-ribosomal peptide synthesis

Cyclodipeptide synthases (CDPSs) belong to a newly defined family of enzymes that use aminoacyl-tRNAs (aa-tRNAs) as substrates to synthesize the two peptide bonds of various cyclodipeptides, which are the precursors of many natural products with noteworthy biological activities. Here, we describe the crystal structure of AlbC, a CDPS from Streptomyces noursei. The AlbC structure consists of a monomer containing a Rossmann-fold domain. Strikingly, it is highly similar to the catalytic domain of class-I aminoacyl-tRNA synthetases (aaRSs), especially class-Ic TyrRSs and TrpRSs. AlbC contains a deep pocket, highly conserved among CDPSs. Site-directed mutagenesis studies indicate that this pocket accommodates the aminoacyl moiety of the aa-tRNA substrate in a way similar to that used by TyrRSs to recognize their tyrosine substrates. These studies also suggest that the tRNA moiety of the aa-tRNA interacts with AlbC via at least one patch of basic residues, which is conserved among CDPSs but not present in class-Ic aaRSs. AlbC catalyses its two-substrate reaction via a ping-pong mechanism with a covalent intermediate in which L-Phe is shown to be transferred from Phe-tRNA(Phe) to an active serine. These findings provide insight into the molecular bases of the interactions between CDPSs and their aa-tRNAs substrates, and the catalytic mechanism used by CDPSs to achieve the non-ribosomal synthesis of cyclodipeptides.     

fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios

MOTIVATION: Genetic studies focus on increasingly larger genomic regions of both extant and ancient DNA, and there is a need for simulation software to match these technological advances. We present here a new coalescent-based simulation program fastsimcoal, which is able to quickly simulate a variety of genetic markers scattered over very long genomic regions with arbitrary recombination patterns under complex evolutionary scenarios. Availability and Implementation: fastsimcoal is a C++ program compiled for Windows, MacOsX and Linux platforms. It is freely available at cmpg.unibe.ch/software/fastsimcoal/, together with its detailed user manual and example input files.     

Graphite anode surface modification with controlled reduction of specific aryl diazonium salts for improved microbial fuel cells power output

Graphite electrodes were modified with reduction of aryl diazonium salts and implemented as anodes in microbial fuel cells. First, reduction of 4-aminophenyl diazonium is considered using increased coulombic charge density from 16.5 to 200 mC/cm(2). This procedure introduced aryl amine functionalities at the surface which are neutral at neutral pH. These electrodes were implemented as anodes in "H" type microbial fuel cells inoculated with waste water, acetate as the substrate and using ferricyanide reduction at the cathode and a 1000 Ω external resistance. When the microbial anode had developed, the performances of the microbial fuel cells were measured under acetate saturation conditions and compared with those of control microbial fuel cells having an unmodified graphite anode. We found that the maximum power density of microbial fuel cell first increased as a function of the extent of modification, reaching an optimum after which it decreased for higher degree of surface modification, becoming even less performing than the control microbial fuel cell. Then, the effect of the introduction of charged groups at the surface was investigated at a low degree of surface modification. It was found that negatively charged groups at the surface (carboxylate) decreased microbial fuel cell power output while the introduction of positively charged groups doubled the power output. Scanning electron microscopy revealed that the microbial anode modified with positively charged groups was covered by a dense and homogeneous biofilm. Fluorescence in situ hybridization analyses showed that this biofilm consisted to a large extent of bacteria from the known electroactive Geobacter genus. In summary, the extent of modification of the anode was found to be critical for the microbial fuel cell performance. The nature of the chemical group introduced at the electrode surface was also found to significantly affect the performance of the microbial fuel cells. The method used for modification is easy to control and can be optimized and implemented for many carbon materials currently used in microbial fuel cells and other bioelectrochemical systems.     

A global review of the impacts of invasive cats on island endangered vertebrates

Cats are generalist predators that have been widely introduced to the world's ~179 000 islands. Once introduced to islands, cats prey on a variety of native species many of which lack evolved defenses against mammalian predators and can suffer severe population declines and even extinction. As islands house a disproportionate share of terrestrial biodiversity, the impacts of invasive cats on islands may have significant biodiversity impacts. Much of this threatened biodiversity can be protected by eradicating cats from islands. Information on the relative impacts of cats on different native species in different types of island ecosystems can increase the efficiency of this conservation tool. We reviewed feral cat impacts on native island vertebrates. Impacts of feral cats on vertebrates have been reported from at least 120 different islands on at least 175 vertebrates (25 reptiles, 123 birds, and 27 mammals), many of which are listed by the International Union for the Conservation of Nature. A meta‐analysis suggests that cat impacts were greatest on endemic species, particularly mammals and greater when non‐native prey species were also introduced. Feral cats on islands are responsible for at least 14% global bird, mammal, and reptile extinctions and are the principal threat to almost 8% of critically endangered birds, mammals, and reptiles.     

Impacts and management of unowned and owned cats at a seabird colony on Reunion Island (Western Indian Ocean)

Biological Invasions - Cats (Felis catus) introduced on islands have strong impacts on biodiversity, and the main conservation actions to protect native fauna is cat eradication or control (i.e.,...     

Identification and characterization of the first fragment hits for SETDB1 Tudor domain

SET domain bifurcated protein 1 (SETDB1) is a human histone-lysine methyltransferase which is amplified in human cancers and was shown to be crucial in the growth of non-small and small cell lung carcinoma. In addition to its catalytic domain, SETDB1 harbors a unique tandem tudor domain which recognizes histone sequences containing both methylated and acetylated lysines, and likely contributes to its localization on chromatin. Using X-ray crystallography and NMR spectroscopy fragment screening approaches, we have identified the first small molecule fragment hits that bind to histone peptide binding groove of the Tandem Tudor Domain (TTD) of SETDB1. Herein, we describe the binding modes of these fragments and analogues and the biophysical characterization of key compounds. These confirmed small molecule fragments will inform the development of potent antagonists of SETDB1 interaction with histones.     

A DIGE analysis of developing poplar leaves subjected to ozone reveals major changes in carbon metabolism

Tropospheric ozone pollution is described as having major negative effects on plants, compromising plant survival. Carbon metabolism is especially affected. In the present work, the effects of chronic ozone exposure were evaluated at the proteomic level in developing leaves of young poplar plants exposed to 120 ppb of ozone for 35 days. Soluble proteins (excluding intrinsic membrane proteins) were extracted from leaves after 3, 14 and 35 days of ozone exposure, as well as 10 days after a recovery period. Proteins (pI 4 to 7) were analyzed by 2-D DIGE experiments, followed by MALDI-TOF-TOF identification. Additional observations were obtained on growth, lesion formation, and leaf pigments analysis. Although treated plants showed large necrotic spots and chlorosis in mature leaves, growth decreased only slightly and plant height was not affected. The number of abscised leaves was higher in treated plants, but new leaf formation was not affected. A decrease in chlorophylls and lutein contents was recorded. A large number of proteins involved in carbon metabolism were identified. In particular, proteins associated with the Calvin cycle and electron transport in the chloroplast were down-regulated. In contrast, proteins associated with glucose catabolism increased in response to ozone exposure. Other identified enzymes are associated with protein folding, nitrogen metabolism and oxidoreductase activity.