Automated metabolite identification from biological fluid <Superscript>1</Superscript>H NMR spectra

Introduction

Metabolite identification in biological samples using Nuclear Magnetic Resonance (NMR) spectra is a challenging task due to the complexity of the biological matrices.

Objectives

This paper introduces a new, automated computational scheme for the identification of metabolites in 1D ¹H NMR spectra based on the Human Metabolome Database.

Methods

The methodological scheme comprises of the sequential application of preprocessing, data reduction, metabolite screening and combination selection.

Results

The proposed scheme has been tested on the 1D ¹H NMR spectra of: (a) an amino acid mixture, (b) a serum sample spiked with the amino acid mixture, (c) 20 blood serum, (d) 20 human amniotic fluid samples, (e) 160 serum samples from publicly available database. The methodological scheme was compared against widely used software tools, exhibiting good performance in terms of correct assignment of the metabolites.

Conclusions

This new robust scheme accomplishes to automatically identify peak resonances in ¹H-NMR spectra with high accuracy and less human intervention with a wide range of applications in metabolic profiling.

     

Functional Analysis of the Disulfide-Bonded Loop/Chain Reversal Region of Human Immunodeficiency Virus Type 1 gp41 Reveals a Critical Role in gp120-gp41 Association

Human immunodeficiency virus type 1 (HIV-1) entry into cells is mediated by the surface-exposed envelope protein (SU) gp120, which binds to cellular CD4 and chemokine receptors, triggering the membrane fusion activity of the transmembrane (TM) protein gp41. The core of gp41 comprises an N-terminal triple-stranded coiled coil and an antiparallel C-terminal helical segment which is packed against the exterior of the coiled coil and is thought to correspond to a fusion-activated conformation. The available gp41 crystal structures lack the conserved disulfide-bonded loop region which, in human T-lymphotropic virus type 1 (HTLV-1) and murine leukemia virus TM proteins, mediates a chain reversal, connecting the antiparallel N- and C-terminal regions. Mutations in the HTLV-1 TM protein gp21 disulfide-bonded loop/chain reversal region adversely affected fusion activity without abolishing SU-TM association (A. L. Maerz, R. J. Center, B. E. Kemp, B. Kobe, and P. Poumbourios, J. Virol. 74:6614-6621, 2000). We now report that in contrast to our findings with HTLV-1, conservative substitutions in the HIV-1 gp41 disulfide-bonded loop/chain reversal region abolished association with gp120. While the mutations affecting gp120-gp41 association also affected cell-cell fusion activity, HIV-1 glycoprotein maturation appeared normal. The mutant glycoproteins were processed, expressed at the cell surface, and efficiently immunoprecipitated by conformation-dependent monoclonal antibodies. The gp120 association site includes aromatic and hydrophobic residues on either side of the gp41 disulfide-bonded loop and a basic residue within the loop. The HIV-1 gp41 disulfide-bonded loop/chain reversal region is a critical gp120 contact site; therefore, it is also likely to play a central role in fusion activation by linking CD4 plus chemokine receptor-induced conformational changes in gp120 to gp41 fusogenicity. These gp120 contact residues are present in diverse primate lentiviruses, suggesting conservation of function.     

Effects of strength training with elastic band programme on fitness components in young female handball players: a randomized controlled trial

This study examined the effect of a 10-week programme of strength training with elastic band (STEB) on fitness components in young female handball players. Twenty-six young female handball players (aged 15.8 ± 0.2 years) from the same club participated in this study. They were randomly assigned between experimental (EG; n = 13) and control (CG; n = 13) groups. The EG performed the STEB, replacing some handball-specific drills in the regular handball training. The CG followed the regular handball training (i.e., mainly technical-tactical drills, small sided and simulated games, and injury prevention drills). Two-way analyses of variance were used to assess: handgrip; back extensor strength; medicine ball throw; 30 m sprint times; Modified Illinois change-of-direction (Illinois-MT); four jump tests: squat jump (SJ), countermovement jump (CMJ), countermovement jump with arm swing (CMJA) and five-jump test (5JT); static (Stork test) and dynamic balance (Y Balance Test); and repeated sprint T-test (RSTT). Results revealed significant gains in handgrip - right (p < 0.001, d = 1.75: large), handgrip - left (p < 0.001, d = 2.52: large), back extensor (p < 0.001, d = 2.01: large), and medicine ball throw (p = 0.002, d = 0.95: large) with EG compared to the CG. The EG also demonstrated greater improvement in sprint performance over 20 m (Δ = 10.6%, p = 0.001, d = 1.07: large) and 30 m (Δ = 7.2%, p < 0.0001, d = 1.56: large) compared to the CG. The EG showed better Illinois-MT (Δ = 5.6%, p = 0.034, d = 0.62: medium) compared to the CG. Further, EG posted significant improvements in the SJ (Δ = 17.3%, p = 0.048, d = 0.58: medium), CMJ (Δ = 17.7%, p = 0.017 d = 0.71: medium), and CMJA (Δ = 16.3%, p = 0.019, d = 0.69: medium) compared to the CG. Similarly, the EG exhibited significant improvement in RSTT best time [p = 0.025, d = 0.66 (medium)], RSTT mean time [p = 0.019, d = 0.69 (medium)] and RSTT total time [p = 0.019, d = 0.69 (medium)] compared to the CG. In conclusion, the 10-week STEB improved the physical abilities in young female handball players.     

Oral cavity gate of an entry into the Communication Network

For ages naso-oro-pharyngreal cavity was considered as gate of entry toliving organism for air and food. In recent years, however, the thoughtshave changed considerably. Several lines of evidence indicate that the oralcavity with adjacent cavities plays a pivotal role for the recognition ofsignals coming from the surrounding world. These signals in form of food,germs, poisonous substances are initially analyzed in oral cavity andmessages are distributed by a variety of communication pathways intopertinent parts of the body. All these diverse functions are performed byanatomical structures present in the naso-oro-pharyngreal cavity. Thefollowing article describes some of the functions discovered recently.     

Prediction of the coupling specificity of GPCRs to four families of G-proteins using hidden Markov models and artificial neural networks

MOTIVATION: G-protein coupled receptors are a major class of eukaryotic cell-surface receptors. A very important aspect of their function is the specific interaction (coupling) with members of four G-protein families. A single GPCR may interact with members of more than one G-protein families (promiscuous coupling). To date all published methods that predict the coupling specificity of GPCRs are restricted to three main coupling groups G(i/o), G(q/11) and G(s), not including G(12/13)-coupled or other promiscuous receptors. RESULTS: We present a method that combines hidden Markov models and a feed-forward artificial neural network to overcome these limitations, while producing the most accurate predictions currently available. Using an up-to-date curated dataset, our method yields a 94% correct classification rate in a 5-fold cross-validation test. The method predicts also promiscuous coupling preferences, including coupling to G(12/13), whereas unlike other methods avoids overpredictions (false positives) when non-GPCR sequences are encountered. AVAILABILITY: A webserver for academic users is available at http://bioinformatics.biol.uoa.gr/PRED-COUPLE2     

A method for the prediction of GPCRs coupling specificity to G-proteins using refined profile Hidden Markov Models

Background  

G- Protein coupled receptors (GPCRs) comprise the largest group of eukaryotic cell surface receptors with great pharmacological interest. A broad range of native ligands interact and activate GPCRs, leading to signal transduction within cells. Most of these responses are mediated through the interaction of GPCRs with heterotrimeric GTP-binding proteins (G-proteins). Due to the information explosion in biological sequence databases, the development of software algorithms that could predict properties of GPCRs is important. Experimental data reported in the literature suggest that heterotrimeric G-proteins interact with parts of the activated receptor at the transmembrane helix-intracellular loop interface. Utilizing this information and membrane topology information, we have developed an intensive exploratory approach to generate a refined library of statistical models (Hidden Markov Models) that predict the coupling preference of GPCRs to heterotrimeric G-proteins. The method predicts the coupling preferences of GPCRs to G_s, G_i/o and G_q/11, but not G_12/13 subfamilies.     

Preparation of dehydro-l-(+)-ascorbic acid dimer by oxidation of ascorbic acid with arsenic acid/iodine and formation of complexes between arsenious acid and ascorbic acid

Ascorbic acid in the presence of a catalytic amount of iodine reduces arsenic acid in methanol giving the arsenious acid bound to the 2-methyl hemi-ketal of dehydroascorbic acid, 5, in 1:1 and in a more stable 2:1 5/As(III) molar ratio. Removal of the As(III) and treating the 2-methyl hemi-ketal of dehydroascorbic acid with refluxing acetonitrile affords the pure, crystalline dehydroascorbic acid dimer in good yields. Ascorbic acid also binds to As(III) of H(3)AsO(3) in a 1:1 and 2:1 ascorbic acid/As(III) molar ratio. The 1:1 complex is not stable and by expulsion of H(3)AsO(3) is transformed to the more stable 2:1 complex. The data do not permit distinguishing the 2:1 complexes between [AsL(2)(H(2)O)](-)H(+) or AsL(LH)(H(2)O) where L is the bis deprotonated and LH is the mono deprotonated 2-methyl hemi-ketal of dehydroascorbic acid or ascorbic acid. The 2:1 ascorbic acid/As(III) complex is oxidized by dioxygen, in a solvent-dependent manner, to dehydroascorbic acid implying dioxygen activation by the bound As(III). With thiophenol the same complex gives quantitatively triphenyl trithioarsenite, As(SPh)(3).     

Y chromosome haplogroups of elite Ethiopian endurance runners

Favourable genetic endowment has been proposed as part of the explanation for the success of East African endurance athletes, but no evidence has yet been presented. The Y chromosome haplogroup distribution of elite Ethiopian athletes (n=62) was compared with that of the general Ethiopian population (n=95) and a control group from Arsi (a region producing a disproportionate number of athletes; n=85). Athletes belonged to three groups: marathon runners (M; n=23), 5–km to 10–km runners (5–10K; n=21) and other track and field athletes (TF; n=18). DNA was extracted from buccal swabs and haplogroups were assigned after the typing of binary markers in multiplexed minisequencing reactions. Frequency differences between groups were assessed by using contingency exact tests and showed that Y chromosome haplogroups are not distributed amongst elite Ethiopian endurance runners in the same proportions as in the general population, with statistically significant (P<0.05) differences being found in four of the individual haplogroups. The geographical origins and languages of the athletes and controls suggest that these differences are less likely to be a reflection of population structure and that Y chromosome haplogroups may play a significant role in determining Ethiopian endurance running success.     

The conserved glycine-rich segment linking the N-terminal fusion peptide to the coiled coil of human T-cell leukemia virus type 1 transmembrane glycoprotein gp21 is a determinant of membrane fusion function

Retroviral transmembrane proteins (TMs) contain an N-terminal fusion peptide that initiates virus-cell membrane fusion. The fusion peptide is linked to the coiled-coil core through a conserved sequence that is often rich in glycines. We investigated the functional role of the glycine-rich segment, Met-326 to Ser-337, of the human T-cell leukemia virus type 1 (HTLV-1) TM, gp21, by alanine and proline scanning mutagenesis. Alanine substitution for the hydrophobic residue Ile-334 caused an approximately 90% reduction in cell-cell fusion activity without detectable effects on the lipid-mixing and pore formation phases of fusion. Alanine substitutions at other positions had smaller effects (Gly-329, Val-330, and Gly-332) or no effect on fusion function. Proline substitution for glycine residues inhibited cell-cell fusion function with position-dependent effects on the three phases of fusion. Retroviral glycoprotein fusion function thus appears to require flexibility within the glycine-rich segment and hydrophobic contacts mediated by this segment.     

Using HHsearch to tackle proteins of unknown function: A pilot study with PH domains

Advances in membrane cell biology are hampered by the relatively high proportion of proteins with no known function. Such proteins are largely or entirely devoid of structurally significant domain annotations. Structural bioinformaticians have developed profile‐profile tools such as HHsearch (online version called HHpred), which can detect remote homologies that are missed by tools used to annotate databases. Here we have applied HHsearch to study a single structural fold in a single model organism as proof of principle. In the entire clan of protein domains sharing the pleckstrin homology domain fold in yeast, systematic application of HHsearch accurately identified known PH‐like domains. It also predicted 16 new domains in 13 yeast proteins many of which are implicated in intracellular traffic. One of these was Vps13p, where we confirmed the functional importance of the predicted PH‐like domain. Even though such predictions require considerable work to be corroborated, they are useful first steps. HHsearch should be applied more widely, particularly across entire proteomes of model organisms, to significantly improve database annotations.