Comparative analysis and distribution of Omega-3 lcPUFA Biosynthesis genes in marine molluscs

Recent research has identified marine molluscs as an excellent source of omega-3 long-chain polyunsaturated fatty acids (lcPUFAs), based on their potential for endogenous synthesis of lcPUFAs. In this study we generated a representative list of fatty acyl desaturase (Fad) and elongation of very long-chain fatty acid (Elovl) genes from major orders of Phylum Mollusca, through the interrogation of transcriptome and genome sequences, and various publicly available databases. We have identified novel and uncharacterised Fad and Elovl sequences in the following species: Anadara trapezia, Nerita albicilla, Nerita melanotragus, Crassostrea gigas, Lottia gigantea, Aplysia californica, Loligo pealeii and Chlamys farreri. Based on alignments of translated protein sequences of Fad and Elovl genes, the haeme binding motif and histidine boxes of Fad proteins, and the histidine box and seventeen important amino acids in Elovl proteins, were highly conserved. Phylogenetic analysis of aligned reference sequences was used to reconstruct the evolutionary relationships for Fad and Elovl genes separately. Multiple, well resolved clades for both the Fad and Elovl sequences were observed, suggesting that repeated rounds of gene duplication best explain the distribution of Fad and Elovl proteins across the major orders of molluscs. For Elovl sequences, one clade contained the functionally characterised Elovl5 proteins, while another clade contained proteins hypothesised to have Elovl4 function. Additional well resolved clades consisted only of uncharacterised Elovl sequences. One clade from the Fad phylogeny contained only uncharacterised proteins, while the other clade contained functionally characterised delta-5 desaturase proteins. The discovery of an uncharacterised Fad clade is particularly interesting as these divergent proteins may have novel functions. Overall, this paper presents a number of novel Fad and Elovl genes suggesting that many mollusc groups possess most of the required enzymes for the synthesis of lcPUFAs.

Omega-Hydroxylation of acyclic monoterpene alcohols by rat lung microsomes

Rat lung microsomes were shown to �-hydroxylate acyclic monoterpene alcohols in the presence of NADPH and O2. NADH could neither support hydroxylation efficiently nor did it show synergistic effect. The hydroxylase activity was greater in microsomes prepared from β-naphthoflavone (BNF)-treated rats than from phenobarbital (PB)-treated or control microsomal preparations. Hydroxylation was specific to the C-8 position in geraniol and has a pH optimum of 7.8. The inhibition of the hydroxylase activity by SKF-525A, CO, N-ethylmaleimide, ellipticine, α-naphthoflavone, cyt. Image and p-CMB indicated the involvement of the cyt. P-450 system. However, NaN3 stimulated the hydroxylase activity to a significant level. Rat kidney microsomes were also capable of �-hydroxylating geraniol although the activity was lower than that observed with lungs.

Omega-hydroxylation of acyclic monoterpene alcohols by rat lung microsomes

Rat lung microsomes were shown to ω-hydroxylate acyclic monoterpene alcohols in the presence of NADPH and O2. NADH could neither support hydroxylation efficiently nor did it show synergistic effect. The hydroxylase activity was greater in microsomes prepared from β-naphthoflavone (BNF)-treated rats than from phenobarbital (PB)-treated or control microsomal preparations. Hydroxylation was specific to the C-8 position in geraniol and has a pH optimum of 7.8. The inhibition of the hydroxylase activity by SKF-525A, CO, N-ethylmaleimide, ellipticine, α-naphthoflavone, cyt. Image and p-CMB indicated the involvement of the cyt. P-450 system. However, NaN3 stimulated the hydroxylase activity to a significant level. Rat kidney microsomes were also capable of ω-hydroxylating geraniol although the activity was lower than that observed with lungs.

Stereochemistry of peptides and polypeptides containing omega amino acids

The omega amino acids have a larger degree of conformational variability than the alpha amino acids, leading to a greater diversity of backbone structures in peptides and polypeptides. The synthetic accessibility of chiral beta-amino acids and the recent observation of novel helical folds in oligomers of cyclic beta-amino acids has led to renewed interest in the stereochemistry of omega-amino acid containing peptides. This review focuses on the conformational characteristics of the polymethylene chain in omega-amino acid segments and surveys structural features in peptides established by X-ray diffraction. The literature on polymers of achiral omega-amino acids (nylon derivatives) and chiral, substituted derivatives derived from trifunctional alpha-amino acids, reveals that while sheet-like, intermolecular hydrogen bonded structures are formed by the former, folded helices appear favoured by the latter. omega-Amino acids promise to expand the repertoire of peptide folds.

A New Threshold Voltage Model for Omega Gate Cylindrical Nanowire Transistor

In this work, for the first time, we present a physically based analytical threshold voltage model for omega gate silicon nanowire transistor. This model is developed for long channel cylindrical body structure. The potential distribution at each and every point of the of the wire is derived with a closed form solution of two dimensional Poisson's equation, which is then used to model the threshold voltage. Proposed model can be treated as a generalized model, which is valid for both surround gate and semi-surround gate cylindrical transistors. The accuracy of proposed model is verified for different device geometry against the results obtained from three dimensional numerical device simulators and close agreement is observed.

Hybrid peptide hairpins containing alpha- and omega-amino acids: Conformational analysis of decapeptides with unsubstituted beta-, gamma-, and delta-residues at positions 3 and 8

The effects of inserting unsubstituted omega-amino acids into the strand segments of model beta-hairpin peptides was investigated by using four synthetic decapeptides, Boc-Lcu-Val-Xxx-Val-D-Pro-Gly-Leu-Xxx-Val-Val- OMe: pepticle 1 (Xxx=Gly), pepticle 2 (Xxx=beta Gly=beta hGly=homoglycine, beta-glycine), pepticle 3 (Xxx=gamma Abu=gamma-aminobutyric acid), pepticle 4 (Xxx= delta Ava=delta-aminovaleric acid). H-1 NMR studies (500 MHz, methanol) reveal several critical cross-strand NOEs, providing evidence for P-hairpin conformations in peptides 2-4. In peptide 3, the NMR results support the formation of the nucleating turn, however, evidence for cross-strand registry is not detected. Single-crystal X-ray diffraction studies of peptide 3 reveal a beta-hairpin conformation for both molecules in the crystallographic asymmetric unit, stabilized by four cross-strand hydrogen bonds, with the gamma Abu residues accommodated within the strands. The D-Pro-Gly segment in both molecules (A,B) adopts a type II' beta-turn conformation. The circular dichroism spectrum for peptide 3 is characterized by a negative CD band at 229 rim, whereas for peptides 2 and 4, the negative band is centered at 225 nm, suggesting a correlation between the orientation of the amide units in the strand segments and the observed CD pattern.

Omega-3-rasvahappojen käyttö nivelrikkoisten koirien hoidossa

Nivelrikko on koirilla yleinen sairaus. Sen hoitoon yleisesti käytettävien tulehduskipulääkkeiden rinnalle etsitään hoitomuotoja tulehduskipulääkkeiden pitkäaikaiskäytöstä johtuvien haittavaikutusten takia. Tutkimuksemme tavoite oli selvittää omega-3-rasvahappojen käytön hyötyä nivelrikkoisten koirien hoidossa. Tutkimuksen alkuhetkellä tutkimusta vastaavasta aiheesta koirilla ei ollut tehty. Ihmisillä reumatoidin artriitin hoidossa omega-3-rasvahapoilla on todettu olevan positiivisia vaikutuksia, joten siihen viitaten myös nivelrikkoisilla koirilla saattaisi olla hyötyä omega-3-rasvahappojen käytöstä. Omega-3-rasvahapoilla on todettu olevan positiivisia vaikutuksia useisiin tulehduksellisiin sairauksiin. Tutkimushypoteesimme oli, että kalaöljyä syövän ryhmän kohtisuora maksimaalinen voima askelvoimalevyllä kasvaisi ja ryhmän arvioitu kivuliaisuus laskisi tutkimuksen aikana. Tutkimamme tuote oli omega-3-rasvahapporavintolisä (Doils® Nivelet, Nutraceuticoils, Belgia). Tutkimus oli satunnaistettu, kaksoissokkoutettu ja kontrolloitu kliininen tutkimus. Tutkimukseen haettiin koiria ilmoitusten perusteella. Alkukyselyn ja seulontakäynnin perusteella tutkimuksen aloitti 77 koiraa. Seulontakäynnillä koirille tehtiin kliininen yleistutkimus, ortopedinen tutkimus, suppea neurologinen tutkimus, röntgenkuvaus, askelvoimalevymittaus sekä verinäytteenotto. Koirat kävivät varsinaisen tutkimuksen aikana kahdella lähikäynnillä. Molemmilla kerroilla koirille suoritettiin röntgenkuvausta lukuun ottamatta samat toimenpiteet kuin seulontakäynnillä. Tutkimuksen aikana omistajat täyttivät kyselykaavakkeita yhteensä seitsemän kertaa. Tutkimuksessa arvioitiin nivelrikkoisten koirien kipua sekä omistajan että eläinlääkärin arvioiden avulla sekä askelvoimalevyn avulla. Arviointimenetelmistä saatuja tuloksia olivat omistajan täyttämästä kyselykaavakkeesta kipuindeksin kyselyn tulokset, liikkumisvaikeuksista kertova VAS, elämänlaadusta kertova VAS, varakipulääkkeiden käyttö, vertailevat kysymykset, omistajan arvio valmisteen tehosta ja koiran ryhmästä, eläinlääkärin arvio sekä askelvoimalevyltä saadut kaksi muuttujaa (kohtisuora maksimaalinen voima ja impulssi). Tutkimustuloksissa havaittiin omega-3-rasvahappojen käytössä nivelrikkoisten koirien hoidossa pieni hyöty. Kalaöljyryhmän ja lumeryhmän välillä ei havaittu tilastollisesti merkitsevää eroa. Ryhmien sisällä havaittiin muutamia tilastollisesti merkitseviä muutoksia. Kipuindeksin muutos paremmaksi kalaöljyryhmässä tutkimuksen aikana oli vahvasti tilastollisesti merkitsevä muutos (p=0,002). Myös askelvoimalevyn kohtisuoran maksimaalisen voiman parantuminen oli vahvasti tilastollisesti merkitsevä muutos kalaöljyä syöneessä ryhmässä(p=0,001). Myös lumeryhmässä oli kipuindeksissä ja askelvoimalevyn kohtisuorassa maksimaalisessa voimassa havaittavissa tilastollisesti merkitsevä trendi (p=0,07 & p=0,059), mutta p-arvot eivät yltäneet tilastolliseen merkitsevyyteen. Suuremmalla otoskoolla näissä muuttujissa olisi voitu havaita joko tilastollisesti merkitseviä eroja ryhmien välillä tai sitten olisimme voineet osoittaa molemmissa ryhmissä tapahtuneen positiivisia eli parantavia muutoksia. Tutkimuksessa ei havaittu sivuvaikutuksia kalaöljyryhmässä. Tutkimustulokset todistivat tutkimushypoteesimme heikosti todeksi. Omega-3-rasvahappoja voisi siis hyvin käyttää koirilla, joille ei sovi kipulääkkeet.

Identifying N60D mutation in omega subunit of Escherichia coli RNA polymerase by bottom-up proteomic approach

Escherichia coli RNA polymerase is a multi-subunit enzyme containing alpha(2)beta beta'omega sigma, which transcribes DNA template to intermediate RNA product in a sequence specific manner. Although most of the subunits are essential for its function, the smallest subunit omega (average molecular mass similar to 10,105 Da) can be deleted without affecting bacterial growth. Creating a mutant of the omega subunit can aid in improving the understanding of its role. Sequencing of rpoZ gene that codes for omega subunit from a mutant variant suggested a substitution mutation at position 60 of the protein: asparagine (N) -> aspartic acid (D). This mutation was verified at the protein level by following a typical mass spectrometry (MS) based bottom-up proteomic approach. Characterization of in-gel trypsin digested samples by reverse phase liquid chromatography (LC) coupled to electrospray ionization (ESI)-tandem mass spectrometry (MS/MS) enabled in ascertaining this mutation. Electron transfer dissociation (ETD) of triply charged (M + 3H)(3+)] tryptic peptides (residues 53-67]), EIEEGLINNQILDVR from wild-type and EIEEGLIDNQILDVR from mutant, facilitated in unambiguously determining the site of mutation at residue 60.

Conformational properties of hybrid peptides containing alpha and omega-amino acids

This review briefly surveys the conformational properties of guest omega-amino acid residues when incorporated into host alpha-peptide sequences. The results presented focus primarily on the use of beta- and gamma-residues in alphaomega sequences. The insertion of additional methylene groups into peptide backbones enhances the range of accessible conformations, introducing additional torsional variables. A nomenclature system, which permits ready comparisons between alpha-peptides and hybrid sequences, is defined. Crystal structure determination of hybrid peptides, which adopt helical and beta-hairpin conformations permits the characterization of backbone conformational parameters for beta- and gamma-residues inserted into regular alpha-polypeptide structures. Substituted beta- and gamma-residues are more limited in the range of accessible conformation than their unsubstituted counterparts. The achiral beta,beta-disubstituted gamma-amino acid, gabapentin, is an example of a stereochemically constrained residue in which the torsion angles about the C-beta-C-gamma (theta(1)) and C-alpha-C-beta (theta(2)) bonds are restricted to the gauche conformation. Hybrid sequences permit the design of novel hydrogen bonded rings in peptide structures.

Solution structure of Am2766: A highly hydrophobic d-conotoxin from Conus amadis that inhibits inactivation of brain voltage gated sodium channels

The three-dimensional (3D) NMR solution structure (MeOH) of the highly hydrophobic δ-conotoxin δ-Am2766 from the molluscivorous snail Conus amadis has been determined. Fifteen converged structures were obtained on the basis of 262 distance constraints, 25 torsion-angle constraints, and ten constraints based on disulfide linkages and H-bonds. The root-mean-square deviations (rmsd) about the averaged coordinates of the backbone (N, Cα, C) and (all) heavy atoms were 0.62±0.20 and 1.12±0.23 Å, respectively. The structures determined are of good stereochemical quality, as evidenced by the high percentage (100%) of backbone dihedral angles that occupy favorable and additionally allowed regions of the Ramachandran map. The structure of δ-Am2766 consists of a triple-stranded antiparallel β-sheet, and of four turns. The three disulfides form the classical ‘inhibitory cysteine knot’ motif. So far, only one tertiary structure of a δ-conotoxin has been reported; thus, the tertiary structure of δ-Am2766 is the second such example.Another Conus peptide, Am2735 from C. amadis, has also been purified and sequenced. Am2735 shares 96% sequence identity with δ-Am2766. Unlike δ-Am2766, Am2735 does not inhibit the fast inactivation of Na+ currents in rat brain Nav1.2 Na+ channels at concentrations up to 200 nM.

On the possibility of an alpha-sq omega-type dynamo in a thin layer inside the sun

If the solar dynamo operates in a thin layer of 10,000-km thickness at the interface between the convection zone and the radiative core, using the facts that the dynamo should have a period of 22 years and a half-wavelength of 40 deg in the theta-direction, it is possible to impose restrictions on the values which various dynamo parameters are allowed to have. It is pointed out that the dynamo should be of alpha-sq omega nature, and kinematical calculations are presented for free dynamo waves and for dynamos in thin rectangular slabs with appropriate boundary conditions. An alpha-sq omega dynamo is expected to produce a significant poloidal field which does not leak to the solar surface. It is found that the turbulent diffusity eta and alpha-coefficient are restricted to values within about a factor of 10, the median values being eta of about 10 to the 10th sq cm/sec and alpha of about 10 cm/sec. On the basis of mixing length theory, it is pointed out that such values imply a reasonable turbulent velocity of the order 30 m/s, but rather small turbulent length scales like 300 km.

Modelling multiple disulphide loop containing polypeptides by random conformation generation. The test cases of α-conotoxin GI and edothelin I

A general procedure for arriving at 3-D models of disulphiderich olypeptide systems based on the covalent cross-link constraints has been developed. The procedure, which has been coded as a computer program, RANMOD, assigns a large number of random, permitted backbone conformations to the polypeptide and identifies stereochemically acceptable structures as plausible models based on strainless disulphide bridge modelling. Disulphide bond modelling is performed using the procedure MODIP developed earlier, in connection with the choice of suitable sites where disulphide bonds could be engineered in proteins (Sowdhamini,R., Srinivasan,N., Shoichet,B., Santi,D.V., Ramakrishnan,C. and Balaram,P. (1989) Protein Engng, 3, 95-103). The method RANMOD has been tested on small disulphide loops and the structures compared against preferred backbone conformations derived from an analysis of putative disulphide subdatabase and model calculations. RANMOD has been applied to disulphiderich peptides and found to give rise to several stereochemically acceptable structures. The results obtained on the modelling of two test cases, a-conotoxin GI and endothelin I, are presented. Available NMR data suggest that such small systems exhibit conformational heterogeneity in solution. Hence, this approach for obtaining several distinct models is particularly attractive for the study of conformational excursions.

Glasslike elastic properties in the omega-beta alloys

We have measured the internal friction and speed of sound in several polycrystalline alloys, using compound torsional oscillators at frequencies between 60 kHz and 100 kHz and temperatures between 50 mK and 100 K. By combining these data with existing elastic and thermal data on similar alloys, we find that those alloys which can undergo diffusionsless phase transitions, such as Ti:Nb, Ti:V, or Zr:Nb in certain ranges of composition have glasslike excitations, since they have elastic properties which agree in magnitude and temperature dependence with those of amorphous solids. By contrast, crystalline continuous solution alloys, such as Nb:Ta, or alloys with diffusive phase transitions, such as high-pressure quenched Al94Si6, have the same elastic properties as are known for crystals.

On the athermal nature of the beta to omega transformation

One characteristic feature of the athermal beta -> omega transformation is the short time scale of the transformation. So far, no clear understanding of this issue exists. Here we construct a model that includes contributions from a Landau sixth-order free energy density, kinetic energy due to displacement, and the Rayleigh dissipation function to account for the dissipation arising from the rapid movement of the parent product interface during rapid nucleation. We also include the contribution from omega-like fluctuations to local stress. The model shows that the transformation is complete on a time scale comparable to the velocity of sound. The estimated nucleation rate is several orders higher than that for diffusion-controlled transformations. The model predicts that the athermal omega phase is limited to a certain range of alloying composition. The estimated nucleation rate and the size of ``isothermal'' particles beyond 17% Nb are also consistent with experimental results. The model provides an explanation for the reprecipitation process of the omega particles in the ``cleared'' channels formed during deformation of omega-forming alloys. The model also predicts that acoustic emission should be detectable during the formation of the athermal phase. (C) 2011 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.