An analysis of side chain interactions and pair correlations within antiparallel β-sheets : the differences between backbone hydrogen-bonded and non-hydrogen-bonded residue pairs

Cross-strand pair correlations are calculated for residue pairs in antiparallel β-sheet for two cases: pairs whose backbone atoms are hydrogen bonded together (H-bonded site) and pairs which are not (non-H-bonded site). The statistics show that this distinction is important. When glycine is located on the edge of a sheet, it shows a 3:1 preference for the H-bonded site. Thestrongest observed correlations are for pairs of disulfide-bonded cystines, many of which adopt a close-packed conformation with each cystine in a spiral conformation of opposite chirality to its partner. It is likely that these pairs are a signature for the family of small, cystine-rich proteins. Most other strong positive and negative correlations involve charged and polar residues. It appears that electrostatic compatibility is the strongest factor affecting pair correlation. Significant correlations are observed for β- and γ-branched residues inthe non-H-bonded site. An examination of the structures showsa directionality in side chain packing. There is a correlation between (1) the directionality in the packing interactions of non-H-bonded β- and γ-branched residue pairs, (2) the handedness of the observed enantiomers of chiral β-branched side chains, and (3) the handedness of the twist of β-sheet. These findings have implications for the formation of β-sheets during protein folding and the mechanism by which the sheet becomes twisted

Cordycepin interferes with 3' end formation in yeast independently of its potential to terminate RNA chain elongation

Cordycepin (3′ deoxyadenosine) is a biologically active compound that, when incorporated during RNA synthesis in vitro, provokes chain termination due to the absence of a 3′ hydroxyl moiety. We were interested in the effects mediated by this drug in vivo and analyzed its impact on RNA metabolism of yeast. Our results support the view that cordycepin-triphosphate (CoTP) is the toxic component that is limiting cell growth through inhibition of RNA synthesis. Unexpectedly, cordycepin treatment modulated 3′ end heterogeneity of ACT1 and ASC1 mRNAs and rapidly induced extended transcripts derived from CYH2 and NEL025c loci. Moreover, cordycepin ameliorated the growth defects of poly(A) polymerase mutants and the pap1-1 mutation neutralized the effects of the drug on gene expression. Our observations are consistent with an epistatic relationship between poly(A) polymerase function and cordycepin action and suggest that a major mode of cordycepin activity reduces 3′ end formation efficiency independently of its potential to terminate RNA chain elongation. Finally, chemical-genetic profiling revealed genome-wide pathways linked to cordycepin activity and identified novel genes involved in poly(A) homeostasis.

Jumping on the omega-3 bandwagon : distinguishing the role of long-chain and short-chain omega-3 fatty acids

Omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA) are almost unanimously recognized for their health benefits, while only limited evidence of any health benefit is currently available specifically for the main precursor of these fatty acids, namely α-linolenic acid (ALA, 18:3n-3). However, both the n-3 LC-PUFA and the short-chain C18 PUFA (i.e., ALA) are commonly referred to as “omega-3” fatty acids, and it is difficult for consumers to recognize this difference. A current gap of many food labelling legislations worldwide allow products containing only ALA and without n-3 LC-PUFA to be marketed as “omega-3 source” and this misleading information can negatively impact the ability of consumers to choose more healthy diets. Within the context of the documented nutritional and health promoting roles of omega-3 fatty acids, we briefly review the different metabolic fates of dietary ALA and n-3 LC-PUFA. We also review food sources rich in n-3 LC-PUFA, some characteristics of LC-PUFA and current industry and regulatory trends. A further objective is to present a case for regulatory bodies to clearly distinguish food products containing only ALA from foods containing n-3 LC-PUFA. Such information, when available, would then avoid misleading information and empower consumers to make a more informed choice in their food purchasing behavior.

Echium oil provides no benefit over linseed oil for (n-3) long-chain PUFA biosynthesis in rainbow trout

The implementation of alternative lipid sources for use in aquaculture is of considerable interest globally. However, the possible benefit of using stearidonic acid (SDA)–rich fish oil (FO) alternatives has led to scientific confusion. Two hundred and forty rainbow trout (Oncorhynchus mykiss) were fed 1 of 4 diets (3 replicate tanks/treatment) containing either FO, linseed oil (LO), echium oil, or mixed vegetable oil (72% LO, 23% sunflower oil, and 6% canola oil) as the dietary lipid source (16.5%) for 73 d to investigate the competition and long-chain PUFA (LC-PUFA) biosynthesis between the fatty acid substrates α-linolenic acid (ALA) and SDA. SDA was more efficiently bioconverted to LC-PUFA compared with ALA. However, when the dietary lipid sources were directly compared, the increased provision of C18 PUFA within the LO diet resulted in no significant differences in (n-3) LC-PUFA content compared with fish fed the other diets. This study therefore shows that, rather than the previously speculated substrate competition, the limiting process in the apparent in vivo (n-3) LC-PUFA biosynthesis appears to be substrate availability. Rainbow trout fed the SDA- and ALA-rich dietary lipid sources subsequently had similar significant reductions in (n-3) LC-PUFA compared with fish fed the FO diet, therefore providing no additional dietary benefit on (n-3) LC-PUFA concentrations.

HIV-1 down-modulates γ signaling chain of FcγR in human macrophages : a possible mechanism for inhibition of phagocytosis

HIV-1 infection impairs a number of macrophage effector functions, thereby contributing to development of opportunistic infections and the pathogenesis of AIDS. FcγR-mediated phagocytosis by human monocyte-derived macrophages (MDM) is inhibited by HIV-1 infection in vitro, and the underlying mechanism was investigated in this study. Inhibition of phagocytosis directly correlated with the multiplicity of HIV-1 infection. Expression of surface FcγRs was unaffected by HIV-1 infection, suggesting that inhibition of phagocytosis occurred during or after receptor binding. HIV-1 infection of MDM markedly inhibited tyrosine phosphorylation of the cellular proteins, which occurs following engagement of FcγRs, suggesting a defect downstream of initial receptor activation. FcγR-mediated phagocytosis in HIV-infected MDM was associated with inhibition of phosphorylation of tyrosine kinases from two different families, Hck and Syk, defective formation of Syk complexes with other tyrosine-phosphorylated proteins, and inhibition of paxillin activation. Down-modulation of protein expression but not mRNA of the γ signaling subunit of FcγR (a docking site for Syk) was observed in HIV-infected MDM. Infection of MDM with a construct of HIV-1 in which nef was replaced with the gene for the γ signaling subunit augmented FcγR-mediated phagocytosis, suggesting that down-modulation of γ-chain protein expression in HIV-infected MDM caused the defective FcγR-mediated signaling and impairment of phagocytosis. This study is the first to demonstrate a specific alteration in phagocytosis signal transduction pathway, which provides a mechanism for the observed impaired FcγR-mediated phagocytosis in HIV-infected macrophages and contributes to the understanding of how HIV-1 impairs cell-mediated immunity leading to HIV-1 disease progression.

Trophic responses to nutrient enrichment in a temperate seagrass food chain

Simple ecological models that predict trophic responses to bottom-up forcing are valuable tools for ecosystem managers. Traditionally, theoretical ecologists have used resource-dependent functional responses to explain the modification of food chains exposed to bottom-up perturbations. These models predict alternating positive, negative and zero responses at each trophic level. More recently, ratio-dependent functional response models that predict proportional increases at each level have challenged this paradigm. The present study tested the predictions of the 2 hypotheses empirically by comparing the relative biomasses of 4 trophic levels of an estuarine seagrass food chain in relatively undisturbed, low-nutrient catchments and ‘developed’ catchments subjected to a prolonged period of nutrient enrichment. We found that nutrient-enriched sites had significantly greater biomass of both epiphytic algae and grazing invertebrates; however, the bottom-up forcing of nutrients was attenuated at higher trophic levels (occupied by juvenile and piscivorous fish), with no significant effect of catchment development. This disconnect in the upward cascade of energy may be due to a number of possible reasons including high levels of diversity and omnivory, trophic subsidy within the system or the strength or nature of perturbations. Although the predictions of both hypotheses failed to hold across all trophic groups, ratio dependence was prevalent at the lower levels of the food chain, which has implications for catchment management.

π-Selective stationary phases: (I) Influence of the spacer chain length of phenyl type phases on the aromatic and methylene selectivity of aromatic compounds in reversed phase high performance liquid chromatography

Phenyl type stationary phases of increasing spacer chain length (phenyl, methyl phenyl, ethyl phenyl, propyl phenyl and butyl phenyl, with 0–4 carbon atoms in the spacer chain, respectively) were synthesised and packed in house to determine the impact that the spacer chain length has on the retention process. Two trends in the aromatic selectivity, q_aromatic, were observed, depending on whether the number of carbon atoms in the spacer chain is even or odd. Linear log k′ vs ϕ plots were obtained for each stationary phase and the S coefficient was determined from the gradient of these plots. For the phenyl type phases, the S vs n_c plots of the retention factors of linear polycyclic aromatic hydrocarbons vs the number of rings exhibit a distinct discontinuity that between 3 and 4 rings, which increases with increasing spacer chain length for even phases but decreases for odd phases. Accordingly, we suggest that the retention factors depend differently on the number of carbon atoms in the spacer chain depending on whether this number is even or odd and that this effect is caused by different orientations of the aromatic ring relative to the silica surface.