Analysis and prediction of major blood proteins based on their amino acid and dipeptide composition

A method has been developed for predicting blood proteins using the SVM based machine learning approach. In this prediction method a two-step strategy was deployed to predict blood proteins and their subclasses. We have developed models of blood proteins and achieved the maximum accuracies of 90.57% and 91.39% with Matthews correlation coefficient (MCC) of 0.89 and 0.90 using single amino acid and dipeptide composition respectively. Furthermore, the method is able to predict major subclasses of blood proteins; developed based on amino acid (AC) and dipeptide composition (DC) with a maximum accuracy 90.38%, 92.83%, 87.41%, 92.52% and 85.27%, 89.07%, 94.82%, 86.31 for albumin, globulin, fibrinogen, and regulatory proteins respectively. All modules were trained, tested, and evaluated using the five-fold cross-validation technique.

Interacting amino acid preferences of 3D pattern pairs at the binding sites of transient and obligate protein complexes

To assess the physico-chemical characteristics of protein-protein interactions, protein sequences and overall structural folds have been analyzed previously. To highlight this, discovery and examination of amino acid patterns at the binding sites defined by structural proximity in 3-dimensional (3D) space are essential. In this paper, we investigate the interacting preferences of 3D pattern pairs discovered separately in transient and obligate protein complexes. These 3D pattern pairs are not necessarily sequence-consecutive, but each residue in two groups of amino acids from two proteins in a complex is within certain °A threshold to most residues in the other group. We develop an algorithm called AA-pairs by which every pair of interacting proteins is represented as a bipartite graph, and it discovers all maximal quasi-bicliques from every bipartite graph to form our 3D pattern pairs. From 112 and 2533 highly conserved 3D pattern pairs discovered in the transient and obligate complexes respectively, we observe that Ala and Leu is the highest occuring amino acid in interacting 3D patterns of transient (20.91%) and obligate (33.82%) complexes respectively. From the study on the dipeptide composition on each side of interacting 3D pattern pairs, dipeptides Ala-Ala and Ala-Leu are popular in 3D patterns of both transient and obligate complexes. The interactions between amino acids with large hydrophobicity difference are present more in the transient than in the obligate complexes. On contrary, in obligate complexes, interactions between hydrophobic residues account for the top 5 most occuring amino acid pairings.

Organotin(IV) complexes derived from proteinogenic amino acid: Synthesis, structure and evaluation of larvicidal efficacy on Anopheles stephensi mosquito larvae

Five new organotin(IV) complexes of composition [Bz2SnL1]n (1), [Bz3SnL1HH2O] (2), [Me2SnL2H2O] (3), [Me2SnL3] (4) and [Bz3SnL3H]n (5) (where L1 = (2S)-2-([(E)-(4-hydroxypentan-2-ylidene)]amino)-4-methylpentanoate, L2 = (rac)-2-([(E)-1-(2-hydroxyphenyl)methylidene]amino)-4-methylpentanoate and L3 = (2S)- or (rac)-2-([(E)-1-(2-hydroxyphenyl)ethylidene]amino)-4-methylpentanoate) were synthesized and characterized using 1H NMR, 13C NMR, 119Sn NMR and infrared spectroscopic techniques. The crystal structure of 2 reveals a distorted trigonal-bipyramidal geometry around the tin atom where the oxygen atoms of the carboxylate ligand and a water ligand occupy the axial positions, while the three benzyl ligands are located at the equatorial positions. On the other hand, the analogous derivative of enantiopure L3H (5) consists of polymeric chains, in which the ligand-bridged tin atoms adopt the same trans-Bz3SnO2 trigonal-bipyramidal configuration and are now coordinated to a phenolic oxygen atom instead of H2O. In 2, the OH hydrogen of the ketoimine substituent has moved to the nearby nitrogen atom while in the salicylidene derivative 5, the OH is located almost midway between the phenolic oxygen atom and the nitrogen atom of the C=N group. For the dibenzyltin derivative 1, a polymeric chain structure is observed as a result of a long intermolecular SnO bond involving the exocyclic carbonyl oxygen atom from the tridentate ligand of a neighbouring tin-complex unit. The tin atom in this complex has distorted octahedral coordination geometry. In contrast, the racemic dimethyltin(IV) complexes 3 and 4 display discrete monomeric structures with a distorted octahedral- and trigonal-bipyramidal geometry, respectively. The structures show that the coordination mode of the Schiff base ligand depends primarily on the number of bulky benzyl ligands (R) at the tin atom, as indeed found in the structures of related complexes where R = phenyl. With three bulky R groups, the tridentate chelating O,N,O coordination mode is preferred, whereas with fewer or less bulky R ligands, only the carboxylate and hydroxy groups are involved, which leads to polymers. Larvicidal efficacies of two of the new tribenzyltin(IV) complexes (2 and 5) were assessed on the second larval instar of Anopheles stephensi mosquito larvae and compared with two triphenyltin(IV) analogues, [Ph3SnL1H]n and [Ph3SnL3H]n. The results demonstrate that the compounds containing Sn-Ph ligands are more effective than those with Sn-Bz ligands.

Changes in the amino acid profiles during embryonic development of the blacklip abalone (Haliotis Rubra)

Changes in the total amino acid (TAA) and the free amino acid (FAA) contents during embryonic development, through newly spawned eggs, to pre-settled larvae of blacklip abalone (Haliotis rubra) are described. The TAA (protein bound + free) and the FAA contents increased prior to hatching but decreased towards settlement, but the changes were not always significant between different stages of development. Threonine, arginine, lysine and leucine accounted for nearly 50 % of the total essential amino acids (TEAA) in all developmental stages. The mean FAA content of newly spawned eggs was 262.8 ± 28.2 pmol·ind^–1 and accounted for 11.5 ± 8.3 % of the TAA. Free essential amino acid (FEAA) content increased significantly as development progressed (P < 0.05), in which threonine, arginine and lysine accounted for over 63 % of this pool. In all developmental stages, the FAA pool was dominated by the non-essential amino acids taurine + proline which accounted for 79.5 % of the total. Generally, the FAA accounted for between 10 to 15 % of the TAA in the different developmental stages of blacklip abalone. All evidence appears to indicate that in blacklip abalone the energy requirements during early ontogeny are mostly met with from the lipid reserves, and that there is a tendency to conserve amino acids until pre-settlement.

Variation in the fatty acid composition of the blubber in Cape fur seals (Arctocephalus pusillus pusillus) and the implications for dietary interpretation

Analysis of the fatty acid (FA) composition of blubber is a valuable tool in interpreting the diet of marine mammals. This technique is based on the principle that particular FA present in prey can be incorporated largely untransformed into predator adipose tissue stores, thereby providing biochemical signatures with which to identify prey species. Several studies of phocid seals and cetaceans have documented vertical stratification in the FA composition of blubber such that inferences about diet may vary greatly depending on the layer of the blubber that is analysed. It is not known whether blubber in otariid seals (fur seals and sea lions) also displays vertical stratification in FA composition. Furthermore, it is not known whether the FA composition of blubber is uniform in these species. In the present study, the vertical and regional variation in FA composition of blubber was investigated in seven adult female Cape fur seals (Arctocephalus pusillus pusillus). The proportion of monounsaturated fatty acids (MUFA) was greater in the outer (43.6±1.3%) than inner portion (40.9±1.2%; t20=5.59, P<0.001) whereas the proportions were greater in the inner than outer portions for saturated fatty acids (23.6±0.5% and 21.9±0.6%, respectively, t20 = 5.31, P<0.001) and polyunsaturated fatty acids (PUFA, 35.5±0.7% and 34.5±0.7%, respectively, t20 = 3.81, P < 0.001). There was an inverse relationship between MUFA and PUFA in the blubber, independent of sampling location. In addition, with the exception of the inner portion from non-lactating females, blubber from the mammary area had the highest proportions of 18:1ω9c and total MUFA, followed by blubber from the rump and neck, suggesting that the deposition and mobilisation of blubber lipids may not be uniform around the body in otariid seals. These results support the need for blubber tissue to be sampled from the same site on animals, and to the full depth of the blubber layer, to minimise variation in FA profiles that could occur if different sites and depths were sampled. Such standardisation of sampling will further aid in interpreting diet in otariid seals using the FA Signature Analysis approach.

Effects of dietary oil source on growth and fillet fatty Acid composition of Murray cod, Maccullochella peelii peelii

The Murray cod, an Australian native freshwater fish, supports a relatively small but increasing aquaculture industry in Australia. Presently, there are no dedicated commercial diets available for Murray cod; instead, nutritionally sub-standard feeds formulated for other species are commonly used. The aim of the present investigation was to assess the suitability of two plant based lipid sources, canola oil (CO) and linseed oil (LO), as alternatives to fish oil for juvenile Murray cod. Five iso-nitrogenous, iso-calorific, iso-lipidic semi-purified experimental diets were formulated with 17% lipid originating from 100% cod liver oil (FO), 100% canola oil, 100% linseed oil and 1 : 1 blends of canola and cod liver oil (CFO) and 1 : 1 blends of linseed and cod liver oil (LFO). Each of the diets was fed to apparent satiation twice daily to triplicate groups of 50 Murray cod with initial mean weights of 6.45 ± 1.59 g for 84 days at 22 °C. Final mean weight, specific growth rate and daily feed consumption were significantly higher for the FO and LFO treatments compared to the LO treatment. Feed conversion and protein efficiency ratios were not significantly different amongst treatments. Experimental diets containing vegetable oil and vegetable oil blend(s) had significantly higher concentrations of n-6 fatty acids, predominantly in the form of linoleic acid (LA), while n-3 fatty acids were present in significantly higher concentrations in LO and LFO treatments. The fatty acid composition of Murray cod fillet was reflective of the dietary lipid source. Fillet of fish fed the FO was highest in EPA (20:5n-3), ArA (20:4n-6) and DHA (22:6n-3). Fish fed the CO diet had high concentrations of oleic acid (OlA) (192.2 ± 10.5 mg g lipid− 1), while the fillet of Murray cod fed the LO diet was high in α-linolenic acid (LnA) (107.1 ± 6.7 mg g lipid− 1). The present study suggests that fish oil can be replaced by up to 100% with canola oil and by up to 50% with linseed oil in Murray cod diets with no significant effect on growth.

Modification of tissue fatty acid composition in Murray cod (Maccullochella peelii peelii, Mitchell) resulting from a shift from vegetable oil diets to a fish oil diet.

The dynamics of fatty acid composition modifications were examined in tissues of Murray cod fed diets containing fish oil (FO), canola oil (CO) and linseed oil (LO) for a 25-week period and subsequently transferred to a FO (finishing/wash-out) diet for a further 16 weeks. At the commencement of the wash-out period, following 25 weeks of vegetable oil substitution diets, the fatty acid compositions of Murray cod fillets were reflective of the respective diets. After transfer to the FO diet, differences decreased in quantity and in numerousness, resulting in a revert to the FO fatty acid composition. Changes in percentages of the fatty acids and total accumulation in the fillet could be described by exponential equations and demonstrated that major modifications occurred in the first days of the finishing period. A dilution model was tested to predict fatty acid composition. In spite of a general reliability of the model (Y=0.9234X+0.4260, R²=0.957, P<0.001, where X is the predicted percentage of fatty acid; Y the observed percentage of fatty acid), in some instances the regression comparing observed and predicted values was markedly different from the line of equity, indicating that the rate of change was higher than predicted (i.e. Y=0.4205X+1.191, R²=0.974, P<0.001, where X is the predicted percentage of α-linolenic acid; Y the observed percentage of α-linolenic acid). Ultimately, using the coefficient of distance (D), it was shown that the fatty acid composition of fish previously fed the vegetable oil diets returned to the average variability of the fillet fatty acid composition of Murray cod after 70 or 97 days (LO and CO respectively).

The last 10 amino acid residues beyond the hydrophobic motif are critical for the catalytic competence and function of protein kinase Cá*

The segment C-terminal to the hydrophobic motif at the V5 domain of protein kinase C (PKC) is the least conserved both in length and in amino acid identity among all PKC isozymes. By generating serial truncation mutants followed by biochemical and functional analyses, we show here that the very C terminus of PKCα is critical in conferring the full catalytic competence to the kinase and for transducing signals in cells. Deletion of one C-terminal amino acid residue caused the loss of ~60% of the catalytic activity of the mutant PKCα, whereas deletion of 10 C-terminal amino acid residues abrogated the catalytic activity of PKCα in immune complex kinase assays. The PKCα C-terminal truncation mutants were found to lose their ability to activate mitogen-activated protein kinase, to rescue apoptosis induced by the inhibition of endogenous PKC in COS cells, and to augment melatonin-stimulated neurite outgrowth. Furthermore, molecular dynamics simulations revealed that the deletion of 1 or 10 C-terminal residues results in the deformation of the V5 domain and the ATP-binding pocket, respectively. Finally, PKCα immunoprecipitated using an antibody against its C terminus had only marginal catalytic activity compared with that of the PKCα immunoprecipitated by an antibody against its N terminus. Therefore, the very C-terminal tail of PKCα is a novel determinant of the catalytic activity of PKC and a promising target for selective modulation of PKCα function. Molecules that bind preferentially to the very C terminus of distinct PKC isozymes and suppress their catalytic activity may constitute a new class of selective inhibitors of PKC.

Growth performance, feed efficiency and fatty acid composition of juvenile Murray cod, Maccullochella peelii peelii, fed graded levels of canola and linseed oil

n two independent experiments, the effects of dietary inclusion of canola and linseed oil were evaluated in juvenile Murray cod (Maccullochella peelii peelii, Mitchell) over a 112-day period. In each experiment, fish received one of five semi-purified diets in which the dietary fish oil was replaced with canola oil (Experiment A) or linseed oil (Experiment B) in graded increments of 25% (0–100%). Murray cod receiving the graded canola and linseed oil diets ranged in final weight from 112.7 ± 7.6 to 73.8 ± 9.9 g and 93.9 ± 3.6 to 74.6 ± 2.2 g, respectively, and exhibited a negative trend in growth as the inclusion level increased. The fatty acid composition of the fillet and liver were modified extensively to reflect the fatty acid composition of the respective diets. Levels of oleic acid (18:1 n-9) and linoleic acid (18:2 n-6) increased with each level of canola oil inclusion while levels of α-linolenic acid (18:3 n-3) increased with each level of linseed oil inclusion. The concentration of n-3 highly unsaturated fatty acids in the fillet and liver decreased as the amount of vegetable oil in the diets increased. It is shown that the replacement of fish oil with vegetable oils in low fish meal diets for Murray cod is possible to a limited extent. Moreover, this study reaffirms the suggestion for the need to conduct ingredient substitution studies for longer periods and where possible to base the conclusions on regression analysis in addition to anova.

Plasma phospholipid fatty acid composition as a biomarker of habitual dietary fat intake in an ethnically diverse cohort

Background and aim
As an evaluation of fatty acid intake measurement, our aim was to examine associations between diet and plasma phospholipid (PL) fatty acids, and whether these were modified by age, sex, country of birth, fasting status, use of cholesterol-lowering medication, body size, chronic disease and other lifestyle factors.

Methods and results
Cross-sectional analysis of plasma PL fatty acid composition and dietary fatty acid intake over 12 months from a 121-item food frequency questionnaire (FFQ) in 4439 men and women aged 40–69 years, born in Australia, Greece or Italy. Crude correlation coefficients ranged from 0.18 to 0.40; and corrected correlation coefficients from 0.38 to 0.78 for total monounsaturated, polyunsaturated, n-6, n-3 fatty acids, oleic acid, linoleic acid, EPA and DHA. Weaker associations were observed for other fatty acids. The associations did not vary significantly by fasting status, use of lipid lowering medication or alcohol intake, but for some fatty acids did vary by sex, age, body mass index, country of birth, smoking and previous heart attack or diabetes.

Conclusions
The FFQ provides useful information on intakes of mono- and polyunsaturated fatty acids. Correlations did not differ by fasting status, or use of lipid-lowering medication.

Dietary conjugated linoleic acid differentially alters fatty acid composition and increases conjugated linoleic acid content in porcine adipose tissue

Conjugated linoleic acids (CLA) have been shown to decrease body fat content in pigs. It is possible that feeding pigs diets rich in CLA may increase carcass lipid CLA to levels that could provide health benefits when included as a part of a healthy diet. Therefore, the aim of the present study was to determine whether dietary CLA supplementation has any effect on the fatty acid composition of subcutaneous and intramuscular adipose tissue in pigs. Thirty-five female cross bred (Large White X Landrace) pigs (initial weight 57·2 kg and initial P2 back fat 11·5 mm) were used in the present study. Pigs were housed individually and randomly allocated to one of six dietary treatments (0·00, 1·25, 2·50, 5·00, 7·50 and 10·00 g CLA55 (55 g CLA isomers/100 g total fatty acids; Natural Lipids Ltd, Hovdebygda, Norway)/kg)
and fed their respective diets for 8 weeks. Twelve CLA isomers in the diet and in pig tissue lipids were separated by Agþ-HPLC. CLA was incorporated at fivefold higher levels in subcutaneous fat as compared with intramuscular fat and in a dose-dependant manner. Overall, the transfer efficiency of CLA was maximized at 5·00 g CLA55/kg. However, there was clear selectivity in the uptake or incorporation of cis,trans-9,11 isomer over the trans,cis-10,12 isomer. In general, CLA supplementation produced significant changes in skeletal muscle and adipose tissue fatty acid composition, indicating that dietary CLA had a potent affect on lipid transport and metabolism in vivo. Significant increases in myristic, palmitic and palmitoleic acids and a reduction in arachidonic acid were observed, suggesting an alteration in
activity of Δ5-, Δ6- and Δ9-desaturases in pig adipose tissue. In conclusion, feeding pigs diets supplemented with CLA increases carcass lipid CLA, but also results in changes in the fatty acid profile in pig fat that could potentially outweigh the benefits of CLA.

The last five amino acid residues at the C-terminus of PRK1 /KKN is essential for full lipid responsiveness

PRK1/PKN is a member of the protein kinase C (PKC) superfamily of serine/threonine protein kinases. Despite its important role as a RhoA effector, limited information is available regarding how this kinase is regulated. We show here that the last seven amino acid residues at the C-terminus is dispensable for the catalytic activity of PRK1 but is critical for the in vivo stability of this kinase. Surprisingly, the intact hydrophobic motif in PRK1 is dispensable for 3-phosphoinositide-dependent kinase-1 (PDK-1) binding and phosphorylation of the activation loop, as the PRK1-Δ940 mutant lacking the last two residues of the hydrophobic motif and the last 5 residues at the C-terminus interacts with PDK-1 in vivo and has a similar specific activity as the wild-type protein. We also found that the last four amino acid residues at the C-terminus of PRK1 is critical for the full lipid responsiveness as the PRK1-Δ942 deletion mutant is no longer activated by arachidonic acid. Our data suggest that the very C-terminus in PRK1 is critically involved in the control of the catalytic activity and activation by lipids. Since this very C-terminal segment is the least conserved among members of the PKC superfamily, it would be a promising target for isozyme-specific pharmaceutical interventions.

Effects of dietary lipid type on muscle fatty acid composition, carcass leanness, and meat toughness in lambs.

Isonitrogenous amounts of two protein sources differing in rumen degradation rate and in lipid composition were fed to sheep with or without a rapidly fermentable cereal grain. The effects on intake, carcass leanness, and muscle fatty acid (FA) composition were examined. Thirty-eight crossbred wether lambs (9 mo, 35 to 48 kg) were allocated by stratified randomization to six treatment groups: 1) basal diet of alfalfa hay:oat hay (20:80) ad libitum = basal; 2) basal + lupin (358 g DM/d) = lupin; 3) basal + fish meal (168 g DM/d) = fish meal; 4) basal + barley (358 g DM/d) = barley; 5) basal + barley + lupin (179 + 179 g DM/d) = barley/lupin; or 6) basal + barley + fish meal (179 + 84 g DM/d) = barley/ fish meal. Lambs were fed individually. Dietary treatments were imposed for 8 wk, and the supplements were offered at 2-d intervals. Daily feed intake and weekly BW of lambs were recorded. At the end of the feeding period lambs were slaughtered after an overnight fast. Hot carcass weight (HCW) and fat depth (GR; total fat and muscle tissue depth at 12th rib, 110 mm from midline) were recorded. At 24 h postmortem samples of longissimus thoracis (LT) and longissimus lumborum (LL) muscles were taken from chilled (4 deg C) carcasses for the assessment of FA composition and meat tenderness, respectively. Lambs fed lupin or fish meal with or without barley had heavier slaughter weights (P < 0.004) and HCW (P < 0.001) than lambs fed basal or barley when initial BW was included as a covariate. The lupin diet also resulted in heavier carcasses (P < 0.05) than the fish meal or barley/fish meal diets. With GR as an indicator, fish meal and barley/ fish meal diets produced leaner carcasses (P < 0.01) than lupin and barley/lupin lambs. Long-chain n-3 FA content [20:5n-3 (P < 0.001), 22:5n-3 (P < 0.003), and 22:6n-3 (P < 0.001)] in the LT muscle were substantially higher with the fish meal and barley/fish meal diets, whereas muscle total n-6 FA was increased (P < 0.003) by lupin and barley/lupin compared with all other diets. Thus, increased muscle long-chain n-3 FA content occurred without an increase in fatness measured as GR, whereas increased muscle n-6 FA content was associated with an increase in carcass fatness. Under these circumstances, a reduction in carcass fatness had no effect on meat tenderness measured as Warner-Bratzler shear force.

Fatty acid composition of habitual omnivore and vegetarian diets

High-fat diets are implicated in the onset of cardiovascular disease (CVD), cancer, and obesity. Large intakes of saturated and trans FA, together with low levels of PUFA, particularly long-chain (LC) omega-3 (n−3) PUFA, appear to have the greatest impact on the development of CVD. A high n−6∶n−3 PUFA ratio is also considered a marker of elevated risk of CVD, though little accurate data on dietary intake is available. A new Australian food  composition database that reports FA in foods to two decimal places was used to assess intakes of FA in four habitual dietary groups. Analysis using the database found correlations between the dietary intakes of LC n−3 PUFA and the plasma phospholipid LC n−3 PUFA concentrations of omnivore and vegetarian subjects. High meat-eaters (HME), who consumed large  amounts of food generally, had significantly higher LC n−3 PUFA intakes (0.29 g/d) than moderate meat-eaters (MME) (0.14 g/d), whose intakes in turn were significantly higher than those of ovolacto-vegetarians or vegans (both 0.01 g/d). The saturated FA intake of MME subjects (typical of adult male Australians) was not different from ovolacto-vegetarian intakes, whereas n−6∶n−3 intake ratios in vegetarians were significantly higher than in omnivores. Thus, accurate dietary and plasma FA analyses suggest that regular moderate consumption of meat and fish maintains a plasma FA profile possibly more conducive to good health.