Reduced alphabet for protein folding prediction

What are the key building blocks that would have been needed to construct complex protein folds? This is an important issue for understanding protein folding mechanism and guiding de novo protein design. Twenty naturally occurring amino acids and eight secondary structures consist of a 28‐letter alphabet to determine folding kinetics and mechanism. Here we predict folding kinetic rates of proteins from many reduced alphabets. We find that a reduced alphabet of 10 letters achieves good correlation with folding rates, close to the one achieved by full 28‐letter alphabet. Many other reduced alphabets are not significantly correlated to folding rates. The finding suggests that not all amino acids and secondary structures are equally important for protein folding. The foldable sequence of a protein could be designed using at least 10 folding units, which can either promote or inhibit protein folding. Reducing alphabet cardinality without losing key folding kinetic information opens the door to potentially faster machine learning and data mining applications in protein structure prediction, sequence alignment and protein design. Proteins 2015; 83:631–639. © 2015 Wiley Periodicals, Inc.     

Two steroidal saponins from Camassia cusickii induce L1210 cell death through the apoptotic mechanism.

Two steroidal saponins, tigogenin hexasaccharide-1 (TGHS-1, (25R)-5alpha-spirostan-3beta-yl 4-O-[2-0-[3-O-(alpha-L-rhamnopyranosyl)-beta-D-glucopyranosyl]-3-0-[4-0- (alpha-L-rhamnopyranosyl)-beta-D-glucopyranosyl]-beta-D-glucopyranosyl]-3-D- galactopyranoside) and tigogenin hexasaccharide-2 (TGHS-2, (25R)-5alpha-spirostan-3beta-yl 4-O-[2-0-[3-0-(beta-D-glucopyranosyl)-beta-D-glucopyranosyl]-3-0-[4-0- (alpha-L-rhamnopyranosyl)-beta-D-glucopyranosyl]-beta-D-glucopyranosyl]beta-D-galactopyranoside), were isolated from the fresh bulbs of Camassia cusickii. In murine leukemic L1210 cells, both compounds showed cytotoxicity with an EC50 value of 0.06 microM. The morphological observation revealed that TGHS-1 and TGHS-2 induced shrinkage in cell soma and chromatin condensation, suggesting apoptotic cell death. The cell death was confirmed to be apoptosis by Annexin V binding to phosphatidylserine in the cell membrane and excluding propidium iodide. A typical apoptotic DNA ladder and the cleavage of caspase-3 were observed after treatment with TGHS-1 and TGHS-2. In the presence of both the compounds, cells with sub-G1 DNA content were detected by flow cytometric analysis, indicating that TGHS-1 and TGHS-2 (each EC50 value of 0.1 microM) are the most powerful apoptotic saponins known. These results suggest that TGHS-1 and TGHS-2 induce apoptotic cell death through caspase-3 activation.     

Growth performance and carcass characteristics of Awassi lambs and Shami goat kids fed yeast culture in their finishing diet

Two experiments were completed to examine effects of inclusion of a yeast culture (YC) to a diet based on barley grain and wheat straw on digestibility, growth and meat traits of Awassi lambs and Shami goat kids. Experiment 1 studied effects of YC on apparent digestibility of dry matter (DM), organic matter (OM), crude protein (CP), neutral detergent fiber (NDF), acid detergent fiber (ADF) and N balance in sheep, while experiment 2 studied effects on growth performance and carcass composition of lambs and kids. The same diet was used in both experiments and the YC was added to the diet of treated groups at the level of 12.6 kg YC/tonne of diet. Addition of YC had no effect on apparent digestibility of DM, CP and NDF, but it increased (P<0.05) digestibility of OM and ADF. No differences occurred in N intake, output or retention. Addition of YC did not affect growth rate, or DM intake, in both lambs and kids. YC supplementation to lambs reduced hot carcass weight, cold dressing proportion and total muscle/bone ratio, but increased empty digestive tract weight. There were no changes in back fat thickness, intermuscular fat of the leg muscle, and weights and proportions of carcass cuts. Measures of kids’ carcass characteristics and quality also did not differ. Only cuts of leg and shoulder differed (P<0.05) when calculated as a proportion of the whole carcass cut. Results show that YC supplementation increased digestibility with no effect on growth, feed intake or feed conversion ratio of fattening lambs and kids. However, YC supplementation reduced meat/bone ratio and tissue protein content, but increased fat content in carcasses of fattening Awassi lambs, but not in fattened Shami kids.     

Gain of C-Ala enables AlaRS to target the L-shaped tRNAAla

Unlike many other aminoacyl-tRNA synthetases, alanyl-tRNA synthetase (AlaRS) retains a conserved prototype structure throughout biology. While Caenorhabditis elegans cytoplasmic AlaRS (CeAlaRS_c) retains the prototype structure, its mitochondrial counterpart (CeAlaRS_m) contains only a residual C-terminal domain (C-Ala). We demonstrated herein that the C-Ala domain from CeAlaRS_c robustly binds both tRNA and DNA. It bound different tRNAs but preferred tRNA^Ala. Deletion of this domain from CeAlaRS_c sharply reduced its aminoacylation activity, while fusion of this domain to CeAlaRS_m selectively and distinctly enhanced its aminoacylation activity toward the elbow-containing (or L-shaped) tRNA^Ala. Phylogenetic analysis showed that CeAlaRS_m once possessed the C-Ala domain but later lost most of it during evolution, perhaps in response to the deletion of the T-arm (part of the elbow) from its cognate tRNA. This study underscores the evolutionary gain of C-Ala for docking AlaRS to the L-shaped tRNA^Ala.     

Starches from different botanical sources I: Contribution of amylopectin fine structure to thermal properties and enzyme digestibility

Fifteen starches from different botanical sources were selected to study the influence of structural features on thermal properties and enzyme digestibility. Morphological appearance, X-ray diffraction pattern, apparent amylose content, unit-chain length distribution of amylopectin, thermal properties and enzyme digestibility of starch varied with botanical source. It was demonstrated that the distribution of unit-chains of amylopectin significantly correlated with functional properties of the starches. Gelatinization temperature of native and retrograded starches decreased and increased with a relative abundance of unit-chains with an approximate degree of polymerization (DP) of 8–12 and 16–26, respectively (P<0.01). Similar unit-chain lengths also affected the enzyme digestibility of starch granules (P<0.01).     

Human Thg1 displays tRNA-inducible GTPase activity

tRNA^His guanylyltransferase (Thg1) catalyzes the 3′-5′ incorporation of guanosine into position -1 (G-1) of tRNA^His. G-1 is unique to tRNA^His and is crucial for recognition by histidyl-tRNA synthetase (HisRS). Yeast Thg1 requires ATP for G-1 addition to tRNA^His opposite A73, whereas archaeal Thg1 requires either ATP or GTP for G-1 addition to tRNA^His opposite C73. Paradoxically, human Thg1 (HsThg1) can add G-1 to tRNAs^His with A73 (cytoplasmic) and C73 (mitochondrial). As N73 is immediately followed by a CCA end (positions 74–76), how HsThg1 prevents successive 3′-5′ incorporation of G-1/G-2/G-3 into mitochondrial tRNA^His (tRNA_m^His) through a template-dependent mechanism remains a puzzle. We showed herein that mature native human tRNA_m^His indeed contains only G-1. ATP was absolutely required for G-1 addition to tRNA_m^His by HsThg1. Although HsThg1 could incorporate more than one GTP into tRNA_m^Hisin vitro, a single-GTP incorporation prevailed when the relative GTP level was low. Surprisingly, HsThg1 possessed a tRNA-inducible GTPase activity, which could be inhibited by ATP. Similar activity was found in other high-eukaryotic dual-functional Thg1 enzymes, but not in yeast Thg1. This study suggests that HsThg1 may downregulate the level of GTP through its GTPase activity to prevent multiple-GTP incorporation into tRNA_m^His.     

Complexity within an oil palm monoculture: The effects of habitat variability and rainfall on adult dragonfly (Odonata) communities

Recent expansion of oil palm agriculture has resulted in loss of forest habitat and forest-dependent species. However, large numbers of species—particularly insects—can persist within plantations. This study focuses on Odonata (dragonflies and damselflies): a charismatic indicator taxon and a potentially valuable pest control agent. We surveyed adult Odonata populations biannually over three years within an industrial oil palm plantation in Sumatra, Indonesia. We assessed the effects of rainfall (including an El Niño Southern Oscillation-associated drought), the role of roadside ditches, and the importance of understory vegetation on Odonata populations. To assess the impacts of vegetation, we took advantage of a long-term vegetation management experiment that is part of the Biodiversity and Ecosystem Function in Tropical Agriculture (BEFTA) Programme. We found 41 Odonata species, and communities varied between plantation core and roadside edge microhabitats, and between seasons. Abundance was significantly related to rainfall levels four months before surveys, probably indicating the importance of high water levels in roadside ditches for successful larval development. We found no significant effect of the BEFTA understory vegetation treatments on Odonata abundance, and only limited effects on community composition, suggesting that local understory vegetation structure plays a relatively unimportant role in determining communities. Our findings highlight that there are large numbers of Odonata species present within oil palm plantations and suggest that their abundance could potentially be increased by maintaining or establishing waterbodies. As Odonata are predators, this could bring pest control benefits, in addition to enhancing biodiversity within intensive agricultural landscapes.     

The proportion of liver excised in Algerian abattoirs is not a good indicator of Fasciola hepatica infections in local cattle breeds

Clinical and serological investigations on 175 cattle were carried out in 1999 at the slaughterhouse of Jijel, northeastern Algeria, to verify if partial ablation of a liver infected with Fasciola hepatica represents a good epidemiological indicator in the case of fasciolosis, as partial excision of the liver is widespread throughout North African countries. This study was also performed to determine if there is a direct relationship between the quantity of liver confiscated for fasciolosis and the serological response of slaughtered animals. A significant relationship between highly infected livers and positive serological titres was noted. However, two groups of results were conflicting: the presence of macroscopically healthy, undamaged livers with a positive serology (8.3% of 120 cattle), or the existence of highly damaged livers with a negative serology (13.0% of 31 cattle). These results indicate that partial removal of the liver in the case of fasciolosis is unreliable, so this method does not represent a good tool to establish epidemiological data on this disease.