Characterization of the Nit6803 nitrilase homolog from the cyanotroph Pseudomonas fluorescens NCIMB 11764

We report the purification and characterization of a nitrilase (E.C. 3.5.5.1) (Nit11764) essential for the assimilation of cyanide as the sole nitrogen source by the cyanotroph, Pseudomonas fluorescens NCIMB 11764. Nit11764, is a member of a family of homologous proteins (nitrile_sll0784) for which the genes typically reside in a conserved seven-gene cluster known as Nit1C. The physical properties and substrate specificity of Nit11764 resemble those of Nit6803, the current reference protein for the family, and the only true nitrilase that has been crystallized. The substrate binding pocket of the two enzymes places the substrate in direct proximity to the active site nucleophile (C160) and conserved catalytic triad (Glu44, Lys126). The two enzymes exhibit a similar substrate profile, however, for Nit11764, cinnamonitrile, was found to be an even better substrate than fumaronitrile the best substrate previously identified for Nit6803. A higher affinity for cinnamonitrile (Km 1.27 mM) compared to fumaronitrile (Km 8.57 mM) is consistent with docking studies predicting a more favorable interaction with hydrophobic residues lining the binding pocket. By comparison, 3,4-dimethoxycinnamonitrile was a poorer substrate the substituted methoxyl groups apparently hindering entry into the binding pocket. in situ ¹H NMR studies revealed that only one of the two nitrile substituents in the dinitrile, fumaronitrile, was attacked yielding trans-3-cyanoacrylate (plus ammonia) as a product. The essentiality of Nit11764 for cyanotrophy remains uncertain given that cyanide itself is a poor substrate and the catalytic efficiencies for even the best of nitrile substrates (~5 × 10³ M^?1 s^?1) is less than stellar.     

A reconsideration of Gallicolumba (Aves: Columbidae) relationships using fresh source material reveals pseudogenes,chimeras, and a novel phylogenetic hypothesis

Phylogenetic analyses of nuclear and mitochondrial DNA sequences were used to test a recent phylogenetic hypothesis for the avian genus Gallicolumba that relied heavily on preserved museum study skins for DNA samples. Our comparisons show that several published gene sequences represent pseudogenes or chimeras of multiple taxa, and these sequences had an adverse influence on phylogeny estimation. A new phylogenetic hypothesis strongly supports the monophyly of Philippine bleeding-hearts, the monophyly of Gallicolumba sensu stricto, and places Leucosarcia as part of an Australasian radiation rather than sister to Alopecoenas. These findings clarify Gallicolumba biogeography and also highlight the need for greater caution in the use of suboptimal source material in molecular systematic studies.     

Muscle Gene Expression Associated with Increased Marbling in Beef Cattle

The objective of this study was to identify specific bovine genes expressed within skeletal muscle that are associated with intramuscular fat deposition. Twenty-eight Angus-Simmental cross steers and heifers were harvested at the University of Illinois Meat Science Laboratory. Four pairs of animals were identified based on similar adjusted backfat thickness but differing amounts of intramuscular fat within each pair. RNA was extracted from muscle samples devoid of visible fat and microarray analysis was performed. Based on this analysis, 9 genes were selected and expression was subsequently confirmed by qPCR. Expression levels of MYH3, HOXD10, MXRA8, and CASQ2 were increased in animals with high marbling, whereas levels of NPNT, MRC1, DNER, and CYPB4 were decreased in high marbled animals. The remaining gene, ACTN2 was determined to be a false positive and was, therefore, excluded from further study. Despite the positive results of the preliminary study, associations between gene expression and intramuscular fat content did not extend to the larger population of cattle. A significant negative association existed between expression of MRC1 and marbling level (P = 0.04). Therefore, this study was unable to identify a particular skeletal muscle gene set whose expression correlated well with marbling levels in the larger population of beef cattle.     

Does interhemispheric communication relate to the bilateral function of muscles? A study of scapulothoracic muscles using transcranial magnetic stimulation

Interhemispheric connections have been demonstrated between the motor cortex controlling muscle pairs. However, these investigations have tended to concentrate upon hand muscles. We have extended these investigations to proximal muscles that control the scapula upon the trunk and help to move and stabilise the shoulder. Using a paired pulse transcranial magnetic stimulation protocol, the interhemispheric interactions between different shoulder girdle muscle pairs, serratus anterior, upper trapezius and lower trapezius were investigated. Test motor evoked potentials were conditioned using conditioning pulse intensities of 80% and 120% of active motor threshold at three different condition-test intervals, during three different tasks. Interhemispheric inhibition was observed in upper trapezius using a conditioning intensity of 120% and condition-test interval of 8 ms (17 ± 18%, p < 0.007). A trend towards inhibition was observed in lower trapezius and serratus anterior using a conditioning intensity of 120% and a condition-test interval of 8 ms (13 ± 22%; p < 0.07 and 10 ± 19% respectively; p < 0.07). No interhemispheric facilitation was evoked. The study demonstrates that a low level of interhemispheric inhibition rather than interhemispheric facilitation could be evoked between these muscle pairs.     

Hybridization and speciation

Hybridization has many and varied impacts on the process of speciation. Hybridization may slow or reverse differentiation by allowing gene flow and recombination. It may accelerate speciation via adaptive introgression or cause near‐instantaneous speciation by allopolyploidization. It may have multiple effects at different stages and in different spatial contexts within a single speciation event. We offer a perspective on the context and evolutionary significance of hybridization during speciation, highlighting issues of current interest and debate. In secondary contact zones, it is uncertain if barriers to gene flow will be strengthened or broken down due to recombination and gene flow. Theory and empirical evidence suggest the latter is more likely, except within and around strongly selected genomic regions. Hybridization may contribute to speciation through the formation of new hybrid taxa, whereas introgression of a few loci may promote adaptive divergence and so facilitate speciation. Gene regulatory networks, epigenetic effects and the evolution of selfish genetic material in the genome suggest that the Dobzhansky–Muller model of hybrid incompatibilities requires a broader interpretation. Finally, although the incidence of reinforcement remains uncertain, this and other interactions in areas of sympatry may have knock‐on effects on speciation both within and outside regions of hybridization.     

Association of the lipoprotein receptor-related protein 2 gene with gout and non-additive interaction with alcohol consumption

Introduction

The T allele of a single nucleotide polymorphism (SNP: rs2544390) in lipoprotein receptor-related protein 2 (LRP2) is associated with higher serum urate and risk of gout in Japanese individuals. SNP rs2544390 also interacts with alcohol consumption in determining hyperuricemia in this population. We investigated the association of rs2544390 with gout, and interaction with all types of alcohol consumption in European and New Zealand (NZ) Māori and Pacific subjects, and a Māori study cohort from the East Coast region of NZ’s North Island.

Methods

Rs2544390 was genotyped by Taqman®. From NZ a total of 1205 controls and 1431 gout cases clinically ascertained were used. Publicly available genotype and serum urate data were utilized from the Atherosclerosis Risk in Communities (ARIC) study and the Framingham Heart Study (FHS). Alcohol consumption data were obtained by consumption frequency questions in all study cohorts. Multivariate adjusted logistic regression was done using STATA.

Results

The T allele of rs2544390 was associated with increased risk of gout in the combined Māori and Pacific Island cohort (OR = 1.20, P = 0.009), and associated with gout in the European subjects, but with a protective effect (OR = 0.79, P_Unadjusted = 0.02). Alcohol consumption was positively associated with risk of gout in Māori and Pacific subjects (0.2% increased risk/g/week, P = 0.004). There was a non-additive interaction between any alcohol intake and the risk of gout in the combined Māori and Pacific cohorts (P_Interaction = 0.001), where any alcohol intake was associated with a 4.18-fold increased risk in the CC genotype group (P = 6.6x10^-5), compared with a 1.14-fold increased risk in the CT/TT genotype group (P = 0.40). These effects were not observed in European subjects.

Conclusions

Association of the T-allele with gout risk in the Māori and Pacific subjects was consistent with this allele increasing serum urate in Japanese individuals. The non-additive interaction in the Māori and Pacific subjects showed that alcohol consumption over-rides any protective effect conferred by the CC genotype. Further exploration of the mechanism underlying this interaction should generate new understanding of the biological role of alcohol in gout, in addition to strengthening the evidence base for reduction of alcohol consumption in the management of gout.     

Synthesis of 4-Amino-8-(2, 2-Difluoro-2-Deoxy-β-D-Ribo Furanosyl Amino)Pyrimido [5, 4-D]Pyrimidine (dFARPP). Stability and Cellular Cytotoxicity

Abstract

The synthesis of β-dFARPP was accomplished by Mitsunobu coupling of 6-cyanopurine with 2-deoxy-2, 2-difluororibose followed by purine ring-expansion under the action of methanolic ammonia. The title compound inhibited the growth of proliferating human leukemic CCRF-CEM cells at 6.1μg/ml but had no effect on plaque formation by a variety of DNA and RNA viruses.     

The X-ray Crystal and Molecular Structure of 5-Amino-1-(2,3:5,6-Di-O-isopropylidene-α-D-mannofuranosyl) Imidazole-4-carboxamide

Abstract

5-Amino-1-(2,3:5,6-di-O-isopropylidene-α-D-mannofuranosyl) imidazole-4-carboxamide (ADIMIC) crystallizes with six molecules in a hexagonal unit cell of space group P6_3.. The imidazole ring is closely planar, the furanose ring pucker is O1′ endo-C4′ exo, and the dioxolane rings are puckered C6′ endo-O6′ exo and C7′ endo-O3′ exo. In addition to an intramolecular hydrogen bond from the 5-amino hydrogen to the 4-carboxamide oxygen, a circuit of intermolecular hydrogen bonds links nearly coplanar imidazole rings.     

Hydrolytic Reactions of 3′-Deoxy-3′-thioinosylyl-(3′→ >5′)-uridine; An RNA Dinucleotide Containing a 3′-S-Phosphorothiolate Linkage

Abstract

The course of hydrolysis of 3′-deoxy-3′-thioinosylyl-(3′ → 5′)-uridine (IspU) has been followed by HPLC over a wide pH-range. Two reactions of the internucleosidic thiophosphate linkage compete: (i) cleavage yielding thioinosine monophosphates and uridine, and (ii) isomerization to the 2′,5′-isomer of IspU. Under very acidic conditions, even acid-catalyzed depurination of the inosine moiety is observed. The stability of the thiophosphate linkage and the mechanisms of its rupture are discussed.