Catch and discardfish species of trawl fisheries in the Iskenderun Bay (Northeastern Mediterranean) with emphasis on lessepsian and chondricthyan species

Fish species in catch and discard of trawl fisheries in and around Iskenderun Bay were examined within the fishing closure period and fishingperiod.The sampling was performed from May 2010 to January 2011 by a commercial trawl vessel.Chondricthyan species composed 49 % of discard catch biomass whileGymnura altavela and Dasyatis pastinacawere dominant in hauls. 27 lessepsian fish species were captured during the study,nine of them beingtarget species for trawl fisheries. In total, 14 of the lessepsian fish species were determined as discard species.In both sampling periods, Equulites klunzingeriand Citharus linguatula contributed to discard fish catch dissimilarity among depth ranges (deeper and shallower than 60 m). E. klunzingerishowed high abundance in discard catch.There were no significant differences in the distribution of the discard fish biomass between the sampling periods (ANOVA test, p>0.05). However, depth range pointed out significantdifferences in discard fish catch composition (p<0.05).Among major commercial fish species of trawl fisheries, Mullus surmuletus and Sparus aurata were not separated as discard in anyhaul by fishermen. Any size of these two species  were included in commercial catch (Total length ranged from 61 to 721 mm)

Synthesis of superlow friction carbon films from highly hydrogenated methane plasmas.

In this study, we investigated the friction and wear performance of diamondlike carbon films (DLC) derived from increasingly hydrogenated methane plasmas. The films were deposited on steel substrates by a plasma-enhanced chemical vapor deposition process at room temperature and the tribological tests were performed in dry nitrogen. Tests results revealed a close correlation between the hydrogen in source gas plasma and the friction and wear coefficients of the DLC films. Specifically, films grown in plasmas with higher hydrogen-to-carbon ratios had much lower friction coefficients and wear rates than did films derived from source gases with lower hydrogen-to-carbon ratios. The lowest friction coefficient (0.003) was achieved with a film derived from 25% methane--75% hydrogen, while a coefficient of 0.015 was found for films derived from pure methane. Similar correlations were observed for wear rates. Films derived from hydrogen-rich plasmas had the least wear, while films derived from pure methane suffered the highest wear. We used a combination of surface analytical methods to characterize the structure and chemistry of the DLC films and worn surfaces

Tribological Behavior of Near-Frictionless Carbon Coatings in High- and Low- Sulfur Diesel Fuels

The sulfur content in diesel fuel has a significant effect on diesel engine emissions, which are currently subject to environmental regulations. It has been observed that engine particulate and gaseous emissions are directly proportional to fuel sulfur content. With the introduction of low-sulfur fuels, significant reductions in emissions are expected. The process of sulfur reduction in petroleum-based diesel fuels also reduces the lubricity of the fuel, resulting in premature failure of fuel injectors. Thus, another means of preventing injector failures is needed for engines operating with low-sulfur diesel fuels. In this study, the authors evaluated a near-frictionless carbon (NFC) coating (developed at Argonne National Laboratory) as a possible solution to the problems associated with fuel injector failures in low-lubricity fuels. Tribological tests were conducted with NFC-coated and uncoated H13 and 52100 steels lubricated with high- and low- sulfur diesel fuels in a high-frequency reciprocating test machine. The test results showed that the NFC coatings reduced wear rates by a factor of 10 over those of uncoated steel surfaces. In low-sulfur diesel fuel, the reduction in wear rate was even greater (i.e., by a factor of 12 compared to that of uncoated test pairs), indicating that the NFC coating holds promise as a potential solution to wear problems associated with the use of low-lubricity diesel fuels

A Cross-Sectional Study of Dietary and Genetic Predictors of Blood Folate Levels in Healthy Young Adults

Since 1998, the U.S. has mandated folic acid (FA) fortification of certain grain products to reduce the risk of neural tube defects. Folate intake and red blood cell (RBC) folate concentrations increased substantially post-intervention, although recent studies raise concerns about the level of ongoing benefit. This study investigated blood folate level determinants in healthy young adults, including intake of naturally occurring food folate, synthetic FA, and the interaction of naturally occurring food folate with a common missense variant in the FOLH1 gene thought to affect absorption. Participants (n = 265) completed the Diet History Questionnaire II, RBC folate testing, and were genotyped for the 484T>C FOLH1 variant. Men reported significantly greater intake of all folate sources except for supplemental FA, but RBC folate levels did not significantly differ by sex. Synthetic FA was a stronger predictor of RBC folate than naturally occurring food folate. In the largest racial group, synthetic FA and the interaction of FOLH1 genotype with naturally occurring food folate significantly predicted RBC folate, with the overall model accounting for 13.8% of the variance in RBC folate levels. Blood folate levels rely on a complex interaction of natural and synthetic folate intake as well as FOLH1 genotype

The ϕ6 Cystovirus Protein P7 Becomes Accessible to Antibodies in the Transcribing Nucleocapsid: A Probe for Viral Structural Elements

Protein P7 is a component of the cystovirus viral polymerase complex. In the unpackaged procapsid, the protein is situated in close proximity to the viral directed RNA polymerase, P2. Cryo-electron microscopy difference maps from the species ϕ6 procapsid have demonstrated that P7 and P2 likely interact prior to viral RNA packaging. The location of P7 in the post-packaged nucleocapsid (NC) remains unknown. P7 may translocate closer to the five-fold axis of a filled procapsid but this has not been directly visualized. We propose that monoclonal antibodies (Mabs) can be selected that serve as probe- reagents for viral assembly and structure. A set of Mabs have been isolated that recognize and bind to the ϕ6 P7. The antibody set contains five unique Mabs, four of which recognize a linear epitope and one which recognizes a conformational epitope. The four unique Mabs that recognize a linear epitope display restricted utilization of Vκ and VH genes. The restricted genetic range among 4 of the 5 antibodies implies that the antibody repertoire is limited. The limitation could be the consequence of a paucity of exposed antigenic sites on the ϕ6 P7 surface. It is further demonstrated that within ϕ6 nucleocapsids that are primed for early-phase transcription, P7 is partially accessible to the Mabs, indicating that the nucleocapsid shell (protein P8) has undergone partial disassembly exposing the protein’s antigenic sites

Three-Dimensional Structure of the Enveloped Bacteriophage Φ12: An Incomplete T = 13 Lattice Is Superposed on an Enclosed T = 1 Shell

BACKGROUND:Bacteriophage phi12 is a member of the Cystoviridae, a unique group of lipid containing membrane enveloped bacteriophages that infect the bacterial plant pathogen Pseudomonas syringae pv. phaseolicola. The genomes of the virus species contain three double-stranded (dsRNA) segments, and the virus capsid itself is organized in multiple protein shells. The segmented dsRNA genome, the multi-layered arrangement of the capsid and the overall viral replication scheme make the Cystoviridae similar to the Reoviridae. METHODOLOGY/PRINCIPAL FINDINGS:We present structural studies of cystovirus phi12 obtained using cryo-electron microscopy and image processing techniques. We have collected images of isolated phi12 virions and generated reconstructions of both the entire particles and the polymerase complex (PC). We find that in the nucleocapsid (NC), the phi12 P8 protein is organized on an incomplete T = 13 icosahedral lattice where the symmetry axes of the T = 13 layer and the enclosed T = 1 layer of the PC superpose. This is the same general protein-component organization found in phi6 NC's but the detailed structure of the entire phi12 P8 layer is distinct from that found in the best classified cystovirus species phi6. In the reconstruction of the NC, the P8 layer includes protein density surrounding the hexamers of P4 that sit at the 5-fold vertices of the icosahedral lattice. We believe these novel features correspond to dimers of protein P7. CONCLUSIONS/SIGNIFICANCE:In conclusion, we have determined that the phi12 NC surface is composed of an incomplete T = 13 P8 layer forming a net-like configuration. The significance of this finding in regard to cystovirus assembly is that vacancies in the lattice could have the potential to accommodate additional viral proteins that are required for RNA packaging and synthesis

Structural Studies of the Tandem Tudor Domains of Fragile X Mental Retardation Related Proteins FXR1 and FXR2

Expansion of the CGG trinucleotide repeat in the 5′-untranslated region of the FMR1, fragile X mental retardation 1, gene results in suppression of protein expression for this gene and is the underlying cause of Fragile X syndrome. In unaffected individuals, the FMRP protein, together with two additional paralogues (Fragile X Mental Retardation Syndrome-related Protein 1 and 2), associates with mRNA to form a ribonucleoprotein complex in the nucleus that is transported to dendrites and spines of neuronal cells. It is thought that the fragile X family of proteins contributes to the regulation of protein synthesis at sites where mRNAs are locally translated in response to stimuli.Here, we report the X-ray crystal structures of the non-canonical nuclear localization signals of the FXR1 and FXR2 autosomal paralogues of FMRP, which were determined at 2.50 and 1.92 Å, respectively. The nuclear localization signals of the FXR1 and FXR2 comprise tandem Tudor domain architectures, closely resembling that of UHRF1, which is proposed to bind methylated histone H3K9.The FMRP, FXR1 and FXR2 proteins comprise a small family of highly conserved proteins that appear to be important in translational regulation, particularly in neuronal cells. The crystal structures of the N-terminal tandem Tudor domains of FXR1 and FXR2 revealed a conserved architecture with that of FMRP. Biochemical analysis of the tandem Tudor doamins reveals their ability to preferentially recognize trimethylated peptides in a sequence-specific manner

Crystal Structure of TDRD3 and Methyl-Arginine Binding Characterization of TDRD3, SMN and SPF30

SMN (Survival motor neuron protein) was characterized as a dimethyl-arginine binding protein over ten years ago. TDRD3 (Tudor domain-containing protein 3) and SPF30 (Splicing factor 30 kDa) were found to bind to various methyl-arginine proteins including Sm proteins as well later on. Recently, TDRD3 was shown to be a transcriptional coactivator, and its transcriptional activity is dependent on its ability to bind arginine-methylated histone marks. In this study, we systematically characterized the binding specificity and affinity of the Tudor domains of these three proteins quantitatively. Our results show that TDRD3 preferentially recognizes asymmetrical dimethylated arginine mark, and SMN is a very promiscuous effector molecule, which recognizes different arginine containing sequence motifs and preferentially binds symmetrical dimethylated arginine. SPF30 is the weakest methyl-arginine binder, which only binds the GAR motif sequences in our library. In addition, we also reported high-resolution crystal structures of the Tudor domain of TDRD3 in complex with two small molecules, which occupy the aromatic cage of TDRD3

Structural Basis for Specific Binding of Human MPP8 Chromodomain to Histone H3 Methylated at Lysine 9

. MPP8 binding to methylated H3K9 is suggested to recruit the H3K9 methyltransferases GLP and ESET, and DNA methyltransferase 3A to the promoter of the E-cadherin gene, mediating the E-cadherin gene silencing and promote tumor cell motility and invasion. MPP8 contains a chromodomain in its N-terminus, which is used to bind the methylated H3K9. HP1, a chromodomain containing protein that binds to methylated H3K9 as well. The structure also reveals that the human MPP8 chromodomain forms homodimer, which is mediated via an unexpected domain swapping interaction through two β strands from the two protomer subunits.Our findings reveal the molecular mechanism of selective binding of human MPP8 chromodomain to methylated histone H3K9. The observation of human MPP8 chromodomain in both solution and crystal lattice may provide clues to study MPP8-mediated gene regulation furthermore