NGSmethDB: a database for next-generation sequencing single-cytosine-resolution DNA methylation data

Next-generation sequencing (NGS) together with bisulphite conversion allows the generation of whole genome methylation maps at single-cytosine resolution. This allows studying the absence of methylation in a particular genome region over a range of tissues, the differential tissue methylation or the changes occurring along pathological conditions. However, no database exists fully addressing such requirements. We propose here NGSmethDB (http://bioinfo2.ugr.es/NGSmethDB/gbrowse/) for the storage and retrieval of methylation data derived from NGS. Two cytosine methylation contexts (CpG and CAG/CTG) are considered. Through a browser interface coupled to a MySQL backend and several data mining tools, the user can search for methylation states in a set of tissues, retrieve methylation values for a set of tissues in a given chromosomal region, or display the methylation of promoters among different tissues. NGSmethDB is currently populated with human, mouse and Arabidopsis data, but other methylomes will be incorporated through an automatic pipeline as soon as new data become available. Dump downloads for three coverage levels (1, 5 or 10 reads) are available. NGSmethDB will be useful for experimental researchers, as well as for bioinformaticians, who might use the data as input for further research

Opioidergic and dopaminergic modulation of cost/benefit decision-making in Long Evans Rats

Eating disorders are associated with impaired decision-making and dysfunctional reward-related neurochemistry. The present study examined the potential contributions of dopamine and opioid signaling to these processes using two different decision-making tasks. In one task, Long Evans Rats chose between working for a preferred food (high-carbohydrate banana-flavored sucrose pellets) by lever pressing on a progressive-ratio schedule of reinforcement vs. obtaining less preferred laboratory chow that was concurrently available. In a second (effort-free) task, rats chose between the same two reinforcers when they were both available freely. Rats were trained in these tasks before receiving haloperidol (0.00, 0.05, 0.10 mg/kg, intraperitoneally (i.p.)) or naloxone (0.0, 1.5, 3.0 mg/kg, i.p.). In the first task, haloperidol decreased breakpoint, lever presses, number of reinforcers earned, and increased chow intake, whereas naloxone decreased breakpoint and number of reinforcers earned but had no effect on chow consumption. In the effort-free task, haloperidol reduced intakes of both foods without affecting preference, whereas naloxone selectively reduced the consumption of banana-pellets. The present findings support converging evidence suggesting that DA signaling affects processes more closely related to appetitive motivation, leaving other components of motivation unchanged. By contrast, opioid signaling appears to mediate aspects of hedonic feeding by selectively altering intakes of highly palatable foods. For preferred foods, both appetitive and consummatory aspects of food intake were altered by opioid receptor antagonism. Our findings argue against a general suppression of appetite by either compound, as appetite manipulations have been shown to unselectively alter intakes of both types of food regardless of the task employed

CpGislandEVO: A Database and Genome Browser for Comparative Evolutionary Genomics of CpG Islands

Hypomethylated, CpG-rich DNA segments (CpG islands, CGIs) are epigenome markers involved in key biological processes. Aberrant methylation is implicated in the appearance of several disorders as cancer, immunodeficiency, or centromere instability. Furthermore, methylation differences at promoter regions between human and chimpanzee strongly associate with genes involved in neurological/psychological disorders and cancers. Therefore, the evolutionary comparative analyses of CGIs can provide insights on the functional role of these epigenome markers in both health and disease. Given the lack of specific tools, we developed CpGislandEVO. Briefly, we first compile a database of statistically significant CGIs for the best assembled mammalian genome sequences available to date. Second, by means of a coupled browser front-end, we focus on the CGIs overlapping orthologous genes extracted from OrthoDB, thus ensuring the comparison between CGIs located on truly homologous genome segments. This allows comparing the main compositional features between homologous CGIs. Finally, to facilitate nucleotide comparisons, we lifted genome coordinates between assemblies from different species, which enables the analysis of sequence divergence by direct count of nucleotide substitutions and indels occurring between homologous CGIs. The resulting CpGislandEVO database, linking together CGIs and single-cytosine DNA methylation data from several mammalian species, is freely available at our website.This work was supported by the Spanish Government [BIO2008-01353 to José L. Oliver and BIO2010-20219 to Michael Hackenberg], Basque country “AE” grant (to Guillermo Barturen) and Erasmus internships (to Stefanie Geisen, Francisco Dios, and E. J. Maarten Hamberg)

Phase Changes in Ni-Ti Under Laser Shock Loading

Near-equiatomic Ni-Ti, known for its shape memory behavior, can decompose to martensitic phases and/or second phase compounds. This phase competition is investigated in NixTi100-x (494Ti3 but no martensite in the AQ state, consistent with resistivity and dilatometry results which showed no hysteresis indicative of first order phase changes over 1.9 K4Ti3 amounts (present in the AQ state) did change upon loading, indicating the importance of shock-induced heating. A thermodynamically complete equation of state (EOS) for NiTi in its B2 (CsCl) structure was generated by ab initio quantum mechanical calculations. This was tested by performing laser-launched flyer experiments, which showed consistency with the theoretical EOS, validating its use in the prediction of dynamic loading histories in the samples during direct drive loading

Optimization of cw sodium laser guide star efficiency

Context: Sodium laser guide stars (LGS) are about to enter a new range of laser powers. Previous theoretical and numerical methods are inadequate for accurate computations of the return flux and hence for the design of the next-generation LGS systems. Aims: We numerically optimize the cw (continuous wave) laser format, in particular the light polarization and spectrum. Methods: Using Bloch equations, we simulate the mesospheric sodium atoms, including Doppler broadening, saturation, collisional relaxation, Larmor precession, and recoil, taking into account all 24 sodium hyperfine states and on the order of 100 velocity groups. Results: LGS return flux is limited by "three evils": Larmor precession due to the geomagnetic field, atomic recoil due to radiation pressure, and transition saturation. We study their impacts and show that the return flux can be boosted by repumping (simultaneous excitation of the sodium D2a and D2b lines with 10-20% of the laser power in the latter). Conclusions: We strongly recommend the use of circularly polarized lasers and repumping. As a rule of thumb, the bandwidth of laser radiation in MHz (at each line) should approximately equal the launched laser power in Watts divided by six, assuming a diffraction-limited spot size.Comment: 15 pages, 12 figures, to be published in Astronomy & Astrophysics, AA/2009/1310

Transcriptional Dynamics and Candidate Genes Involved in Pod Maturation of Common Bean (Phaseolus vulgaris L.)

The authors want to thank the research facilities provided by the Campus de Excelencia Internacional Agroalimentario (CeiA3).Pod maturation of common bean relies upon complex gene expression changes, which in turn are crucial for seed formation and dispersal. Hence, dissecting the transcriptional regulation of pod maturation would be of great significance for breeding programs. In this study, a comprehensive characterization of expression changes has been performed in two common bean cultivars (ancient and modern) by analyzing the transcriptomes of five developmental pod stages, from fruit setting to maturation. RNA-seq analysis allowed for the identification of key genes shared by both accessions, which in turn were homologous to known Arabidopsis maturation genes and furthermore showed a similar expression pattern along the maturation process. Gene- expression changes suggested a role in promoting an accelerated breakdown of photosynthetic and ribosomal machinery associated with chlorophyll degradation and early activation of alpha-linolenic acid metabolism. A further study of transcription factors and their DNA binding sites revealed three candidate genes whose functions may play a dominant role in regulating pod maturation. Altogether, this research identifies the first maturation gene set reported in common bean so far and contributes to a better understanding of the dynamic mechanisms of pod maturation, providing potentially useful information for genomic-assisted breeding of common bean yield and pod quality attributes.Ministerio de Ciencia, Innovacion y Universidades (MCIU/AEI/FEDER, UE) AGL2017-88174-R RTC2017-6198-2 AGL2017-88702-C2-2-RJunta de Andalucia 612

Cell-Free Synthesis of the Mitochondrial ADP/ATP Carrier Protein of Neurospora crassa

ADP/ATP carrier protein was synthesized in heterologous cell-free systems programmed with Neurospora poly(A)-containing RNA and homologous cell-free systems from Neurospora. The apparent molecular weight of the product obtained in vitro was the same as that of the authentic mitochondrial protein. The primary translation product obtained in reticulocyte lysates starts with formylmethionine when formylated initiator methionyl-tRNA (fMet-tRNAfMet) was present. The product synthesized in vitro was released from the ribosomes into the postribosomal supernatant. The evidence presented indicates that the ADP/ATP carrier is synthesized as a polypeptide with the same molecular weight as the mature monomeric protein and does not carry an additional sequence