Levels Of Individual Amino Acids Research Articles

Cryo-EM and Solid State NMR Together Provide a More Comprehensive Structural Investigation of Protein Fibrils.

The Tropomyosin 1 isoform I/C C-terminal domain (Tm1-LC) fibril structure is studied jointly with cryogenic electron microscopy (cryo-EM) and solid state nuclear magnetic resonance (NMR). This study demonstrates the complementary nature of these two structural biology techniques. Chemical shift assignments from solid state NMR are used to determine the secondary structure at the level of individual amino acids, which is faithfully seen in cryo-EM reconstructions. Additionally, solid state NMR demonstrates that the region not observed in the reconstructed cryo-EM density is primarily in a highly mobile random coil conformation rather than adopting multiple rigid conformations. Overall, this study illustrates the benefit of investigations combining cryo-EM and solid state NMR to investigate protein fibril structure.

Fetal growth delay caused by loss of non-canonical imprinting is resolved late in pregnancy and culminates in offspring overgrowth.

Germline epigenetic programming, including genomic imprinting, substantially influences offspring development. Polycomb Repressive Complex 2 (PRC2) plays an important role in Histone 3 Lysine 27 trimethylation (H3K27me3)-dependent imprinting, loss of which leads to growth and developmental changes in mouse offspring. In this study, we show that offspring from mouse oocytes lacking the PRC2 protein Embryonic Ectoderm Development (EED) were initially developmentally delayed, characterised by low blastocyst cell counts and substantial growth delay in mid-gestation embryos. This initial developmental delay was resolved as offspring underwent accelerated fetal development and growth in late gestation resulting in offspring that were similar stage and weight to controls at birth. The accelerated development and growth in offspring from Eed-null oocytes was associated with remodelling of the placenta, which involved an increase in fetal and maternal tissue size, conspicuous expansion of the glycogen-enriched cell population, and delayed parturition. Despite placental remodelling and accelerated offspring fetal growth and development, placental efficiency, and fetal blood glucose levels were low, and the fetal blood metabolome was unchanged. Moreover, while expression of the H3K27me3-imprinted gene and amino acid transporter Slc38a4 was increased, fetal blood levels of individual amino acids were similar to controls, indicating that placental amino acid transport was not enhanced. Genome-wide analyses identified extensive transcriptional dysregulation and DNA methylation changes in affected placentas, including a range of imprinted and non-imprinted genes. Together, while deletion of Eed in growing oocytes resulted in fetal growth and developmental delay and placental hyperplasia, our data indicate a remarkable capacity for offspring fetal growth to be normalised despite inefficient placental function and the loss of H3K27me3-dependent genomic imprinting.

Branched-chain amino acid levels are inversely associated with incident and prevalent chronic kidney disease in people with type 2 diabetes.

To investigate the association of plasma metabolites with incident and prevalent chronic kidney disease (CKD) in people with type 2 diabetes and establish whether this association is causal. The Hoorn Diabetes Care System cohort is a large prospective cohort consisting of individuals with type 2 diabetes from the northwest part of the Netherlands. In this cohort we assessed the association of baseline plasma levels of 172 metabolites with incident (Ntotal = 462/Ncase = 81) and prevalent (Ntotal = 1247/Ncase = 120) CKD using logistic regression. Additionally, replication in the UK Biobank, body mass index (BMI) mediation and causality of the association with Mendelian randomization was performed. Elevated levels of total and individual branched-chain amino acids (BCAAs)-valine, leucine and isoleucine-were associated with an increased risk of incident CKD, but with reduced odds of prevalent CKD, where BMI was identified as an effect modifier. The observed inverse effects were replicated in the UK Biobank. Mendelian randomization analysis did not provide evidence for a causal relationship between BCAAs and prevalent CKD. Our study shows the intricate relationship between plasma BCAA levels and CKD in individuals with type 2 diabetes. While an association exists, its manifestation varies based on disease status and BMI, with no definitive evidence supporting a causal link between BCAAs and prevalent CKD.

Correlation between Biogenic Amines and Their Precursors in Stored Chicken Meat

Biogenic amines (BAs) are biologically active substances found in the cells of microorganisms, plants, and animals. These BAs serve many vital functions in the body. However, an excessive amount can be toxic, especially for individuals taking monoamine oxidase (MAO) and diamine oxidase (DAO) inhibitors. They primarily form in products rich in amino acids, the primary substrates for BA formation. The aim of this study was to determine the formation of BAs and their precursor amino acids in chicken breast and leg muscles stored under chilling conditions. Analyses of BA and AA determinations were conducted on days 1, 3, 5, 7, and 10 of muscle storage. There was a noted increase in BAs with the storage of both muscle types (p < 0.05). Distinct levels of BAs were detected (p < 0.05) in the muscles, except for putrescine (p > 0.05). Interactions emerged between the two factors for various Bas, including histamine (p = 0.001), tyramine (p < 0.001), BAI index (p < 0.001), tryptamine (p < 0.001), agmatine (p = 0.001), spermidine (p < 0.001), TOTAL BA-1 (p < 0.001), and TOTAL BA-2 (p = 0.016). There was no evident interaction between the type of meat and storage time concerning amino acid content (p > 0.05). Correlations in breast muscles were observed for biogenic amine–amino acid pairs such as putrescine–ornithine (r = −0.57) (p < 0.05), spermidine–ornithine (r = −0.73) (p < 0.05), and phenylethylamine–phenylethylalanine (r = −0.50) (p < 0.05). In leg muscles, significant correlations were found for histamine–histidine (r = −0.87) (p < 0.05), putrescine–ornithine (r = −0.96) (p < 0.05), and phenylethylamine–phenylethylalanine (r = −0.65) (p < 0.05). The results obtained can be used in the future to estimate the levels of BAs with knowledge of the levels of individual amino acids and inversely.

A biological sequence comparison algorithm using quantum computers

Genetic information is encoded as linear sequences of nucleotides, represented by letters ranging from thousands to billions. Differences between sequences are identified through comparative approaches like sequence analysis, where variations can occur at the individual nucleotide level or collectively due to various phenomena such as recombination or deletion. Detecting these sequence differences is vital for understanding biology and medicine, but the complexity and size of genomic data require substantial classical computing power. Inspired by human visual perception and pixel representation on quantum computers, we leverage these techniques to implement pairwise sequence analysis. Our method utilizes the Flexible Representation of Quantum Images (FRQI) framework, enabling comparisons at a fine granularity to single letters or amino acids within gene sequences. This novel approach enhances accuracy and resolution, surpassing traditional methods by capturing subtle genetic variations with precision. In summary, our approach offers algorithmic advantages, including reduced time complexity, improved space efficiency, and accurate sequence comparisons. The novelty lies in applying the FRQI algorithm to compare quantum images in genome sequencing, allowing for examination at the individual letter or amino acid level. This breakthrough holds promise for advancing biological data analysis and enables a more comprehensive understanding of genetic information.

Using NMR-detected hydrogen-deuterium exchange to quantify protein stability in cosolutes, under crowded conditions in vitro and in cells

We review the use of nuclear magnetic resonance (NMR) spectroscopy to assess the exchange of amide protons for deuterons (HDX) in efforts to understand how high concentration of cosolutes, especially macromolecules, affect the equilibrium thermodynamics of protein stability. HDX NMR is the only method that can routinely provide such data at the level of individual amino acids. We begin by discussing the properties of the protein systems required to yield equilibrium thermodynamic data and then review publications using osmolytes, sugars, denaturants, synthetic polymers, proteins, cytoplasm and in cells.

An alternative plant-based fermented milk with kefir culture using apricot (Prunus armeniaca L.) seed extract: Changes in texture, volatiles and bioactivity during storage

The aim of the study was to produce kefir from apricot seed extract (ASE) as an alternative functional dairy food for vegans and lactose-intolerant people, the elderly, people with cardiovascular disease and diabetes. Kefir was produced by using cow's milk (100%, as control) and 100% ASE, and cow's milk was mixed with 25%, 50% and 75% (v/v) with ASE for kefir production and the resultant kefir samples were stored at 4 °C for 21 days. In proportion to the level of ASE, more yellowish color, lower viscosity, firmness, consistency and TPA values were developed. Additionally, a higher syneresis was observed in kefir samples with increasing levels of ASE. Angiotensin-converting enzyme-inhibitory (ACE-i) and antioxidant activities increased with the increasing levels of ASE used in the kefir production. The levels of individual free amino acids significantly changed by use of ASE and some amino acids including Gln, Gly and Arg dramatically increased, while others decreased by increasing levels of the ASE. Relatively lower levels of γ-amino butyric acid (GABA) were observed in the samples when compared to the free amino acids, and its concentration decreased by increasing levels of the ASE. The counts for yeasts, lactobacilli and lactococci increased with addition of ASE. Qualitative and quantitative differences were seen in volatile composition of kefir with the addition of ASE and acceptable sensory scores were obtained for all samples during storage. Concentrations of carboxylic acids decreased with increasing levels of ASE in kefir formula; however, the levels of alcohols and aldehydes increased. In conclusion, ASE can be considered in the formulation of fermented milk products or used purely in the production of plant-based fermented non-dairy beverages.

Atlas of metabolism reveals palmitic acid results in mitochondrial dysfunction and cell apoptosis by inhibiting fatty acid β-oxidation in Sertoli cells.

In recent years, the impact of lipotoxicity on male fertility has received extensive attention, especially on Sertoli cells (SCs). In SCs, energy metabolism is important as disorders of energy metabolism result in infertility eventually. However, the underlying mechanism of lipotoxicity on energy metabolism in SCs remains unknown. Advances in high-throughput metabolomics and lipidomics measurement platforms provide powerful tools to gain insights into complex biological systems. Here, we aimed to explore the potential molecular mechanisms of palmitic acid (PA) regulating energy metabolism in SCs based on metabolomics and lipidomics. The results showed that glucose metabolism-related metabolites were not significantly changed, which suggested that PA treatment had little effect on glucose metabolism and may not influence the normal energy supply from SCs to germ cells. However, fatty acid β-oxidation was inhibited according to accumulation of medium- and long-chain acylcarnitines in cells. In addition, the pool of amino acids and the levels of most individual amino acids involved in the tricarboxylic acid (TCA) cycle were not changed after PA treatment in SCs. Moreover, PA treatment of SCs significantly altered the lipidome, including significant decreases in cardiolipin and glycolipids as well as remarkable increases in ceramide and lysophospholipids, which indicated that mitochondrial function was affected and apoptosis was triggered. The increased apoptosis rate of SCs was verified by elevated protein expression levels of Cleaved Caspase-3 and Bax as well as decreased Bcl-2 protein expression level. Together, these findings indicated that PA may result in mitochondrial dysfunction and increased apoptosis by inhibiting fatty acid β-oxidation of SCs.

The Effects of Purple Corn Pigment on Growth Performance, Blood Biochemical Indices, Meat Quality, Muscle Amino Acids, and Fatty Acids of Growing Chickens.

Simple SummaryAnthocyanin is a large type of polyphenol compound that is a strong natural antioxidant and widely exists in natural plant and food fields. Specifically, anthocyanins can relieve oxidative stress by scavenging oxygen free radicals to improve meat quality and extend the shelf life of meat products. Chicken meat contains high-quality protein and other substances important in the human diet and has become quite popular among consumers. Therefore, anthocyanin is a natural pigment that has been extremely valuable. We hypothesized that anthocyanin-rich purple corn pigment can improve growth performance, enhance antioxidant activity, and improve meat quality, muscle amino acid, and fatty acid profiles in chickens. The results of the current study indicate that the consumption of anthocyanin-rich purple corn pigment by growing chickens has the potential to increase growth performance, enhance antioxidant and immune capacities, heighten meat quality, and improve essential amino acids, umami amino acids, and unsaturated fatty acids in muscle.This study investigated the effects of dietary supplementation with different levels of purple corn pigment (PCP) on the growth performance, blood biochemical indices, meat quality, muscle amino acids, and fatty acids of growing chickens. A total of 288 (8 weeks of age) growing Chishui black-bone chickens (body weight, 940 ± 80 g; mean ± standard deviation) were randomly divided into 4 groups using a completely randomized design. The four diet groups were as follows: (1) control, basal diet; (2) treatment 1, treatment 2, and treatment 3, which were basal diet with 80, 160, and 240 mg/kg PCP, respectively. The results showed that compared with the control group, the feeding of anthocyanins significantly (p < 0.05) increased the average daily feed intake and average daily gain in chickens. Moreover, chickens receiving 80 mg/kg PCP significantly increased (p < 0.05) plasma total antioxidant capacity, superoxide dismutase, glutathione peroxidase, catalase, high-density lipoprotein cholesterol, and albumin concentrations relative to the control group. For meat quality, dietary supplementation with PCP significantly (p < 0.05) reduced the drip loss and water loss rate in breast muscle. Additionally, chickens receiving PCP tended to increase (p < 0.05) the levels of most individual amino acids, essential amino acids, and umami amino acids in the muscle. Specifically, the addition of 80 mg/kg PCP significantly improved (p < 0.05) total polyunsaturated fatty acids in chicken muscle. Accordingly, the consumption of anthocyanin-rich PCP by the growing chickens had the potential to increase the growth performance, enhance antioxidant and immune capacities, increase meat quality, and improve essential and umami amino acids as well as unsaturated fatty acids in the muscle.

The effectiveness of feeding of diets with valine when rearing broiler chickens

Providing the necessary level of complete protein and amino acids in diets is necessary for intensive growth, health and high productivity of poultry. Protein nutrition of poultry can be regulated at the level of individual amino acids with the help of their additives and also improve the amino acid profile of the diet. Valine is the fourth limiting amino acid in broiler diets. A research has been carried out in the AO “Yaroslavl Broiler” poultry farm to assess the effect of the input of synthetic valine to the main diet on the zootechnical indicators of broiler chickens and the profitability of production. During the entire growing period, the poultry received rations developed according to the feed program of AO “Yaroslavl Broiler”. The reduced baseline level of total crude protein by 0,5–1,5 % below the standard in the compound feed recipes was compensated by the addition of three limiting amino acids, in the control group (lysine, methionine, threonine) and four, in the experimental group (lysine, methionine, threonine and valine). It has been shown that the addition of valine to the diet in an amount of 0,04–0,10 % did not reduce its nutritional values. Together with the first three limiting amino acids, the addition of crystalline valine improved the amino acid profile of the diet. Valine levels in the experimental group were higher than in the control group and only slightly below the recommended values for broiler chickens of the cross Ross 308 with a final weight of 2,5–3,0 kg. In broiler chickens have been receiving diets with additional valine, the average daily gain in live weight was 62,12 g, the average live weight of a chick was 2,74 kg, the feed conversion was 1,63 and the total meat yield was 207 449 kg, which were better than in the control group. Also, less feed was consumed in the experimental group, and the productivity index was 392,3 and was higher than in the control group.

Equivalence of the transition heat capacities of proteins and DNA

It has been reported for many globular proteins that the native heat capacity at 25 °C, per gram, is the same. This has been interpreted to indicate that heat capacity is a fundamental property of native proteins that provides important information on molecular structure and stability. Heat capacities for both proteins and DNA has been suggested to be related to universal effects of hydration/solvation on native structures. Here we report on results from thermal denaturation analysis of two well-known proteins, human serum albumin and lysozyme, and a short DNA hairpin. The transition heat capacities at the Tm for the three molecules were quantitatively evaluated by differential scanning calorimetry. When normalized per gram rather than per mol the transition heat capacities were found to be precisely equivalent. This observation for the transition heat capacities of the proteins is consistent with previous reports. However, an identical transition heat capacity for DNA has not been reported and was unexpected. Further analysis of the collected data suggested a mass dependence of hydration effects on thermal denaturation that is preserved at the individual protein amino acid and DNA base levels. Equivalence of transition heat capacities suggests the possibility of a universal role of hydration effects on the thermal stability of both proteins and DNA.

Hepatitis B viral capsid disassembly and genome synthesis: from the atomic level to the whole cell

The disassembly of hepatitis B viral capsid, which leads to the release of its genetic material into the host cell nucleus, is a fundamental step in the infection cycle, speculated to occur at the nuclear pore complexes (NPCs) within the nuclear envelope. The capsid consists of identical protein monomers that dimerize and then arrange themselves into pentamers or hexamers on the capsid surface. By applying atomistic molecular dynamics simulation to an entire solvated HBV capsid, totaling ∼6 million atoms, and engineering a mechanical stress mimicking the impact of the nuclear pores, we monitor the capsid disassembly and analyze the process down to the level of individual amino acids in 20 independent simulation replicas.

Metabolome analysis revealed that soybean-Aspergillus oryzae interaction induced dynamic metabolic and daidzein prenylation changes.

Several isoflavonoids are well known for their ability to act as soybean phytoalexins. However, the overall effects of the soybean–Aspergillus oryzae interaction on metabolism remain largely unknown. The aim of this study is to reveal an overview of nutritive and metabolic changes in germinated and A. oryzae-elicited soybeans. The levels of individual nutrients were measured using the ustulation, ashing, Kjeldahl, and Folch methods. The levels of individual amino acids were measured using high-performance liquid chromatography. Low-molecular-weight compounds were measured through metabolome analysis using liquid chromatography-mass spectrometry. Although the levels of individual nutrients and amino acids were strongly influenced by the germination process, the elicitation process had little effect on the change in the contents of individual nutrients and amino acids. However, after analyzing approximately 700 metabolites using metabolome analysis, we found that the levels of many of the metabolites were strongly influenced by soybean–A. oryzae interactions. In particular, the data indicate that steroid, terpenoid, phenylpropanoid, flavonoid, and fatty acid metabolism were influenced by the elicitation process. Furthermore, we demonstrated that not the germination process but the elicitation process induced daidzein prenylation, suggesting that the soybean–A. oryzae interactions produce various phytoalexins that are valuable for health promotion and/or disease prevention.

Characterizing ligand-induced conformational changes in clinically relevant galectin-1 by HN/H2O (D2O) exchange

Glycans of cellular glycoconjugates serve as biochemical signals for a multitude of (patho)physiological processes via binding to their receptors (e.g. lectins). In the case of human adhesion/growth-regulatory galectin-1 (Gal-1), small angle neutron scattering and fluorescence correlation spectroscopy have revealed a significant decrease of its gyration radius and increase of its diffusion coefficient upon binding lactose, posing the pertinent question on the nature and region(s) involved in the underlying structural alterations. Requiring neither a neutron source nor labeling, diffusion measurements by 1H NMR spectroscopy are shown here to be sufficiently sensitive to detect this ligand-induced change. In order to figure out which region(s) of Gal-1 is (are) affected at the level of peptides, we first explored the use of H/D exchange mass spectrometry (HDX MS). Hereby, we found a reduction in proton exchange kinetics beyond the lactose-binding site. The measurement of fast HN/H2O exchange by phase-modulated NMR clean chemical exchange (CLEANEX) NMR on 15N-labeled Gal-1 then increased the spatial resolution to the level of individual amino acids. The mapped regions with increased protection from HN/H2O (D2O) exchange that include the reduction of solvent exposure around the interface can underlie the protein's compaction. These structural changes have potential to modulate this galectin's role in lattice formation on the cell surface and its interaction(s) with protein(s) at the F-face.

Mapping low-affinity/high-specificity peptide–protein interactions using ligand-footprinting mass spectrometry

Short linear peptide motifs that are intracellular ligands of folded proteins are a modular, incompletely understood molecular interaction language in signaling systems. Such motifs, which frequently occur in intrinsically disordered protein regions, often bind partner proteins with modest affinity and are difficult to study with conventional structural biology methods. We developed LiF-MS (ligand-footprinting mass spectrometry), a method to map peptide binding sites on folded protein domains that allows consideration of their dynamic disorder, and used it to analyze a set of D-motif peptide-mitogen-activated protein kinase (MAPK) associations to validate the approach and define unknown binding structures. LiF-MS peptide ligands carry a short-lived, indiscriminately reactive cleavable crosslinker that marks contacts close to ligand binding sites with high specificity. Each marked amino acid provides an independent constraint for a set of directed peptide-protein docking simulations, which are analyzed by agglomerative hierarchical clustering. We found that LiF-MS provides accurate ab initio identification of ligand binding surfaces and a view of potential binding ensembles of a set of D-motif peptide-MAPK associations. Our analysis provides an MKK4-JNK1 structural model, which has thus far been crystallographically unattainable, a potential alternate binding mode for part of the NFAT4-JNK interaction, and evidence of bidirectional association of MKK4 peptide with ERK2. Overall, we find that LiF-MS is an effective noncrystallographic way to understand how short linear motifs associate with specific sites on folded protein domains at the level of individual amino acids.

Amino acid signature predictive of incident prediabetes: A case-control study nested within the longitudinal pathobiology of prediabetes in a biracial cohort

ObjectiveCirculating branched-chain amino acids (BCAAs, isoleucine, leucine, valine) and aromatic amino acids (AAAs, tyrosine and phenylalanine) predicted type 2 diabetes mellitus (T2DM) risk in a Caucasian population. Here, we assessed amino acid levels in relation to incident prediabetes among initially normoglycemic African Americans (AA) and European Americans (EA). Research design and methodsUsing a nested case-control design, we studied 70 adults (35 AA, 35 EA) who developed prediabetes (progressors) and 70 matched participants who maintained normoglycemia (nonprogressors) during 5.5 years of follow-up in the Pathobiology of Prediabetes in a Biracial Cohort study. Assessments included plasma amino acid levels, insulin sensitivity, and beta-cell function. ResultsThe total level of all 18 amino acid assayed was significantly associated with lean mass (r = 0.36, P < 0.0001), waist circumference (r = 0.27, P = 0.001), fasting plasma glucose (r = 0.24, P = 0.005), HOMA-IR (r = 0.22, P = 0.01) and HDL cholesterol (r = −0.18, P = 0.03). Individual amino acid levels were significantly associated with insulin sensitivity and insulin secretion. Compared with nonprogressors, progressors had higher baseline levels of asparagine and aspartic acid (P <0.0001), glutamine/glutamic acid (P = 0.005) and phenylalanine (P = 0.02), and lower histidine (P = 0.02) levels. In fully-adjusted logistic regression models, aspartic acid/asparagine (OR 2.72 [95% CI 1.91–3.87]) and histidine (OR 0.90 [95% CI 0.85–0.96]) were the only amino acids that significantly predicted incident prediabetes. ConclusionsBaseline plasma aspartic acid and asparagine levels predicted progression to prediabetes, whereas histidine levels were protective of prediabetes risk. Thus, the amino acid signature associated with prediabetes in a diverse population may be distinct from that previously linked to T2DM in Caucasians.

Neurotransmitter and amino acid levels in Nigerian children with autism spectrum disorders

Autism Spectrum Disorder (ASD), often referred to as Autism, is a clinically heterogeneous neurodevelopmental disorder with core-defining features of impaired socialization, impaired verbal and nonverbal communication, and restricted and repetitive patterns of behaviour. The disorder is presently diagnosed behaviourally, however the search for possible biomarkers that could aid earlier diagnosis have been on the increase. The present study aims to investigate plasma amino acid levels as a potential biomarker in ASD screening. Plasma levels of 20 amino acids (AA) (including neurotransmitters-GABA and glutamate) of autistic individuals and typical age and sex matched control, were determined using reversed-phase high performance liquid chromatography (RPHPLC). All statistical analyses (independent t-test, spearman correlation, cohen’s d effect size) were done using IBM SPSS version 20. A total of 31 plasma samples (18 Autism cases and 13 agesex matched controls) were analyzed with mean ages 8.44±4.87 for cases and 8.15±4.88 for controls. No significant intergroup difference was observed in the individual amino acid levels with the exception of glutamate (t = 5.472, df = 2.324, p = 0.000063), glutamine (t = 8.342, df = 14.780, p = 0.000001) , GABA (t = 6.601, df = 24.593, p = 0.000001), tryptophan (t = 3.568, df = 16.472, p = 0.002) and cysteine (t = 4.000, df = 13.762, p = 0.001).The amino acid profile and the glutamate - GABA levels can serve as biochemical markers for ASD, and can thus be utilized as screening for earlier diagnosis of the disorder. Keywords: Autism Spectrum Disorder (ASD), Biomarkers, Neurotransmitters, GABA, Glutamate, Diagnosis

PIRSitePredict for protein functional site prediction using position-specific rules.

Methods focused on predicting ‘global’ annotations for proteins (such as molecular function, biological process and presence of domains or membership in a family) have reached a relatively mature stage. Methods to provide fine-grained ‘local’ annotation of functional sites (at the level of individual amino acid) are now coming to the forefront, especially in light of the rapid accumulation of genetic variant data. We have developed a computational method and workflow that predicts functional sites within proteins using position-specific conditional template annotation rules (namely PIR Site Rules or PIRSRs for short). Such rules are curated through review of known protein structural and other experimental data by structural biologists and are used to generate high-quality annotations for the UniProt Knowledgebase (UniProtKB) unreviewed section. To share the PIRSR functional site prediction method with the broader scientific community, we have streamlined our workflow and developed a stand-alone Java software package named PIRSitePredict. We demonstrate the use of PIRSitePredict for functional annotation of de novo assembled genome/transcriptome by annotating uncharacterized proteins from Trinity RNA-seq assembly of embryonic transcriptomes of the following three cartilaginous fishes: Leucoraja erinacea (Little Skate), Scyliorhinus canicula (Small-spotted Catshark) and Callorhinchus milii (Elephant Shark). On average about 1200 lines of annotations were predicted for each species.

Zmiana zawartości składników odżywczych, cholesterolu i błonnika w dietach eliminujących produkty pochodzenia zwierzęcego. Część I – makroskładniki

ABSTRAKTWstęp: Wykluczenie produktów pochodzenia zwierzęcego z codziennego jadłospisu związane jest z wieloma aspektami, m.in. ekonomicznymi, społecznymi, psychologicznymi i zdrowotnymi.Materiały i metody: Zgodnie z zasadami racjonalnego żywienia ułożono 25 jadłospisów o kaloryczności ±2000 kcal. Każdy z jadłospisów zmodyfikowano, tworząc 5 rodzajów diet eliminujących produkty pochodzenia zwierzęcego: dietę semiwegetariańską, laktoowowegetariańską, wegańską, dietę eliminującą mięso i nabiał oraz dietę wykluczającą tylko produkty mleczne. Otrzymane średnie zawartości składników odżywczych w dietach przeanalizowano przy użyciu programu Statistica 12.0.Wyniki: W analizowanych dietach podaż wielonienasyconych kwasów tłuszczowych wzrastała wraz z eliminacją mięsa i nabiału, a długołańcuchowych wielonienasyconych kwasów tłuszczowych wraz ze spożyciem ryb, mięsa i jaj. Udział białka roślinnego, węglowodanów i błonnika wzrastał istotnie w diecie wegańskiej, eliminującej nabiał oraz wykluczającej nabiał i mięso. Zaobserwowano także istotne zmiany w średniej zawartości poszczególnych aminokwasów. Zawartość histydyny spadała istotnie wraz z eliminacją mięsa w diecie. Nadto eliminacja mięsa i ryb wiązała się z istotnym obniżeniem zawartości waliny, treoniny, fenyloalaniny, metioniny, lizyny oraz izoleucyny. Dodatkowo w diecie wegańskiej odnotowano obniżenie zawartości aminokwasów endogennych – alaniny i cystyny.Wnioski: Niezależnie od rodzaju stosowanej diety eliminującej produkty pochodzenia zwierzęcego należy zadbać o jej odpowiednie zbilansowanie, aby zapobiec powstawaniu groźnych dla funkcjonowania organizmu niedoborów. Biorąc pod uwagę spożycie składników odżywczych, szczególnie w diecie wegańskiej, należy uwzględnić suplementację kwasami eikozapentaenowym i dokozaheksaenowym. Natomiast niskie spożycie tryptofanu wraz z ograniczeniem produktów mięsnych oraz pochodzenia zwierzęcego może być przeciwwskazaniem stosowania takich diet u sportowców, a także w stanach zaburzenia wytwarzania serotoniny, melatoniny i rodopsyny, obniżonej odporności, zaburzeniach poziomu neuroprzekaźników prowadzących do stanów lękowych i depresyjnych.

Mould starter selection for extended solid-state fermentation of quinoa

Solid-state fermentation of plant materials with food grade moulds is considered a method of obtaining bioactive food products and additives. However, the use of quinoa seeds as a substrate in such a process has not been thoroughly studied to date. In this paper, extended fermentation with Rhizopus oligosporus, Aspergillus oryzae and Neurospora intermedia (tempe, koji and oncom moulds, respectively) was performed in order to enhance the antioxidant potential of coloured quinoa (as measured by the total soluble phenols, ABTS˙+ and ˙OH scavenging activities, and the reducing power).The most efficient of the examined strains was Rhizopus, which caused an average improvement in the aforementioned qualities of 220% (black seeds) and 129% (red seeds), as compared to pre-cooked seeds. Four-day fermentation with Rhizopus resulted in a drastically enhanced amount of vanillin in the free phenolic fraction (130-fold in black quinoa seeds). However, the overall level of free and bound phenolics (as measured by the HPLC-DAD-ESI-TOF-MS method) in the material decreased. Both total peptides and individual free amino acid levels were significantly increased, which corresponded with the high antioxidant potential of the material. The fermented quinoa was also significantly enriched with total dietary fibre with dominant insoluble fraction.