Marine Tubificidae (Oligochaeta) of Antarctica, with descriptions of three new species of Phallodrilinae

Five species of Tubificidae are recorded from Antarctic waters: Torodrilus lowryi Cook, 1970, Torodrilus sp. (subfamily Rhyacodrilinae), Marionidrilus antarcticus sp. n., M. weddellensis sp. n., and Thalassodrilus bicki sp. n. (subfamily Phallodrilinae); only T. lowryi was known from Antarctica before. The status of the two Southern Hemisphere genera Torodrilus Cook, 1970, and Marionidrilus Erséus, 1992, are discussed; although the taxonomic position of the two new species of Marionidrilus is somewhat uncertain. Thalassodrilus bicki , however, appears closely related to Northern Hemisphere taxa.     

The marine Tubificidae (Oligochaeta) of the barrier reef ecosystems at Carrie Bow Cay, Belize, and other parts of the Caribbean Sea, with descriptions of twenty-seven new species and revision of Heterodrilus, Thalassodrilides and Smithsonidrilus

Fifty-nine species of Tubifieidae are recorded from Belize on the Caribbean side of Central America. Twenty-five are new to science: Ainudrilus geminus sp.n., Heronidrilus gravidus sp.n., Heterodrilus flexuosus sp.n., H. ranus sp.n., H. modestus sp.n., Coralliodrilus rugosus sp.n., C. randyi sp.n., Phallodrilus compactus sp. n., P. singularis sp.n., P. vicinus sp.n., P. nasutus sp.n., P. bipartitus sp.n., Inanidrilus reginae sp.n., Olavius finitimus sp.n., O. vacuus sp.n., O. (Olavius) pravus sp.n., Bathydrilus vetustus sp.n., B. egenus sp.n., Thalassodrilides bruneti sp.n., Limnodriloides anxius sp.n., L. major sp.n., L. sacculus sp.n., L. adversus sp.n., Smithsonidrilus appositus sp.n., S. involutus sp.n. Phylogenetic analyses indicate that Heterodrilus Pierantoni, 1902, Thalassodrilides Brinkhurst & Baker, 1979, and Marcusaedrilus Righi & Kanner, 1979, are paraphyletic taxa as previously defined. They are therefore revised to include also apomorphic species earlier attributed to separate genera; in so doing, Marcusaedrilus becomes a junior synonym of Smithsonidrilus Brinkhurst, 1966. Smithsonidrilus pauper sp.n. (Peru), and S. multiglandularis sp.n. (Florida and Puerto Rico) are also described, and Limnodriloides claviger Erséus, 1982 is regarded as a synonym of L. pierantonii (Hrabě, 1971).     

Molecular characterization of a gene encoding N-myristoyl transferase (NMT) from Triticum aestivum (bread wheat).

Myristoyl-CoA:protein N-myristoyl transferase (NMT; EC 2.3.1.97) acylates the Gly residue abutting the N-terminal Met with a myristic acid following the removal of the Met residue in certain eukaryotic proteins, and in some cases myristoylation is essential to cell growth and survival. We report the cloning of a full-length cDNA encoding NMT from Triticum aestivum (TaNMT). The cDNA included a predicted open reading frame of 1317 nucleotides, which encoded a predicted protein of 438 amino acids containing all of the residues that are important for NMT activity. The TaNMT amino acid and nucleotide sequences were compared with NMTs from 14 other species encompassing a wide array of taxonomic groups. Among the experimentally validated NMTs, TaNMT was most similar to that of Arabidopsis thaliana. Southern blot analysis of wheat genomic DNA showed that TaNMT is encoded by a single copy gene, with one copy per haploid genome. We expressed TaNMT in Escherichia coli cells and determined that the recombinant protein possessed NMT activity, catalyzing the N-myristoylation of peptides from known or putatively myristoylated proteins from plants and animals without a strong preference for the plant peptides. TaNMT is the second experimentally validated plant NMT sequence and the first from a monocotyledonous species.     

High-level production of gamma-linolenic acid in Brassica juncea using a delta6 desaturase from Pythium irregulare

gamma-Linolenic acid (GLA), a nutritionally important fatty acid in mammals, is synthesized by a delta6 desaturase. Here, we report identification of PiD6, a new cDNA from the oleaginous fungus, Pythium irregulare, encoding a 459-amino acid protein that shares sequence similarity to carboxyl-directed desaturases from various species. Expression of PiD6 in yeast (Saccharomyces cerevisiae) revealed that it converts exogenously supplied linoleic acid into GLA, indicating that it encodes a delta6 fatty acid desaturase. Expression of the desaturase in Brassica juncea under the control of the Brassica napus napin promoter resulted in production of three delta6 unsaturated fatty acids (18:2-6, 9; 18:3-6, 9, 12; and 18:4-6, 9, 12, 15) in seeds. Among them, GLA (18:3-6, 9, 12) is the most abundant and accounts for up to 40% of the total seed fatty acids. Lipid class and positional analysis indicated that GLA is almost exclusively incorporated into triacylglycerol (98.5%) with only trace amounts found in the other lipids. Within triacylglycerols, GLA is more abundant at the sn-2 position.     

Subtype selective antagonism of substantia nigra pars compacta Group I metabotropic glutamate receptors protects the nigrostriatal system against 6-hydroxydopamine toxicity in vivo

Evidence suggests that increased glutamatergic input to the substantia nigra pars compacta as a result of hyperactivity of subthalalmic nucleus output pathways may contribute to the progressive degeneration of nigral dopaminergic neurones in Parkinson's disease (PD), a debilitating neurodegenerative disorder which affects approximately 1% of people aged over 65. Substantial electrophysiological evidence suggests that the excitation of nigral dopaminergic neurones is regulated by the activation of Group I metabotropic glutamate receptors (mGluR), comprising mGluR1 and mGluR5 subtypes. As activation of these receptors by endogenous glutamate may promote multiple cascades leading to excitotoxic neuronal death, it may be hypothesised that functional antagonism of Group I mGluR should be neuroprotective and could form the basis of a novel neuroprotective treatment for PD. To investigate this hypothesis, the neuroprotective potential of the selective competitive mGlu1 antagonist (+)-2-methyl-4-carboxyphenylglycine ((S)-(+)-alpha-amino-4-carboxy-2-methlybenzeneacetic acid; LY367385) and the selective allosteric mGlu5 antagonist 2-methyl-6-(phenylethynyl)-pyridine (MPEP) was tested in a rodent 6-hydroxydopamine (6-OHDA) model of PD in vivo. Both acute and subchronic intranigral administration of either LY367385 or MPEP resulted in significant neuroprotection of nigral tyrosine hydroxylase immunoreactive cell bodies, which correlated closely with prevention of striatal monoamine depletion following 6-OHDA lesioning. This neuroprotective action of LY367385 and MPEP displayed a clear concentration-dependent effect, suggesting a receptor-mediated mechanism of action. LY367385 produced robust neuroprotection at all concentrations tested (40, 200 and 1000 nmol in 4 microL), whilst MPEP displayed a bell-shaped neuroprotective profile with significant neuroprotection at low concentrations (2 and 10 nmol in 4 microL) but not at higher concentrations (50 nmol). Importantly, subchronic intranigral administration of MPEP and LY367385 appeared to slow the degeneration of remaining nigral dopaminergic neurones and prevented further striatal dopamine depletion in animals with established 6-OHDA induced nigrostriatal lesions, suggesting that these compounds may significantly influence disease progression in this model.     

Detection of Ophthalmic Acid in Serum from Acetaminophen-Induced Acute Liver Failure Patients Is More Frequent in Non-Survivors

Background/Aim

Acetaminophen (APAP) hepatotoxicity is related to the formation of N-acetyl-p-benzoquinone imine (NAPQI), which is detoxified through conjugation with reduced glutathione (GSH). Ophthalmic acid (OA) is an analogue of GSH in which cysteine is replaced with 2-aminobutyrate. Metabolomics studies of mice with APAP-induced acute liver failure (APAP-ALF) identified OA as a marker of oxidative stress and hepatic GSH consumption. The aim of the current study was to determine whether OA is detectable in APAP-ALF human patients either early (day 2) or late (day 4) and whether OA levels were associated with in-hospital survival in the absence of liver transplant.

Methods

Serum samples from 130 APAP-ALF patients (82 survivors, 48 non-survivors) were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and correlated with clinical data from the United States Acute Liver Failure Study Group (US ALFSG) Registry (2004–2011).

Results

Survivors had significantly lower admission bilirubin (4.2 vs. 5.7 mg/dl) and lactate levels (3.3 vs. 6.5 μmol/l, p<0.05 for all). During the first 7 days of the study, survivors were less likely to require mechanical ventilation (55% vs. 88%), vasopressor support (9.8% vs. 67%) or renal replacement therapy (26% vs. 63%, p< 0.001 for all). Non-survivors were more likely to have detectable OA levels early (31% vs. 15%, p = 0.034) and late (27% vs. 11%, p = 0.02). However there were no significant differences in mean OA levels between non-survivors and survivors (early 0.48 vs. 0.36, late 0.43 vs. 0.37, P > 0.5 for all).

Conclusion

OA was detectable more frequently in APAP-ALF non-survivors but mean OA levels were not associated with survival. The routine clinical administration of N-acetyl cysteine could replenish GSH levels and prevent OA production.     

The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads

Flax (Linum usitatissimum) is an ancient crop that is widely cultivated as a source of fiber, oil and medicinally relevant compounds. To accelerate crop improvement, we performed whole‐genome shotgun sequencing of the nuclear genome of flax. Seven paired‐end libraries ranging in size from 300 bp to 10 kb were sequenced using an Illumina genome analyzer. A de novo assembly, comprised exclusively of deep‐coverage (approximately 94× raw, approximately 69× filtered) short‐sequence reads (44–100 bp), produced a set of scaffolds with N₅₀ = 694 kb, including contigs with N₅₀ = 20.1 kb. The contig assembly contained 302 Mb of non‐redundant sequence representing an estimated 81% genome coverage. Up to 96% of published flax ESTs aligned to the whole‐genome shotgun scaffolds. However, comparisons with independently sequenced BACs and fosmids showed some mis‐assembly of regions at the genome scale. A total of 43 384 protein‐coding genes were predicted in the whole‐genome shotgun assembly, and up to 93% of published flax ESTs, and 86% of A. thaliana genes aligned to these predicted genes, indicating excellent coverage and accuracy at the gene level. Analysis of the synonymous substitution rates (K_s) observed within duplicate gene pairs was consistent with a recent (5–9 MYA) whole‐genome duplication in flax. Within the predicted proteome, we observed enrichment of many conserved domains (Pfam‐A) that may contribute to the unique properties of this crop, including agglutinin proteins. Together these results show that de novo assembly, based solely on whole‐genome shotgun short‐sequence reads, is an efficient means of obtaining nearly complete genome sequence information for some plant species.     

Investigations of combinations of mutations in the jellyfish green fluorescent protein (GFP) that afford brighter fluorescence, and use of a version (VisGreen) in plant, bacterial, and animal cells

Among the GFPs used for imaging green fluorescence, the Emerald version has been considered the best GFP to use but there is no formal report on its construction or the relevance of the amino acid (aa) substitutions in it relative to the commonly used GFPs. Here, we have shown that a version of Emerald makes Escherichia coli host cells visibly green even under dim room light conditions. Exploiting this feature, we have determined for the first time whether the changes in the structure of Emerald protein brought about by the aa substitutions are all indeed essential for brightness. F64L and S72A accompanying the classical S65T substitution on the chromophore-bearing helix are essential. Two amino acid changes, one on the surface (N149K) of the beta barrel that encases the helix and the other (I167T) near the chromophore enhance the visible green colour individually and additively when present together. The other two substitutions, M153T (on the surface) and H231L (on the surface), do not contribute to the visible green phenotype, even though in earlier studies M153T has been reported to enhance GFP fluorescence. The GFP version with F64L-S65T-S72A-N149K-I167T is referred to as VisGreen. We found VisGreen and Emerald to be indistinguishable in their quantum yield, molar extinction coefficient, folding efficiency, or photosensitivity. VisGreen rendered bacterial, plant, and animal cells highly fluorescent. Interestingly, N149K in the above combination was not essential to render bacterial cells highly fluorescent.