The Solution NMR Structure of 2′-O-Methyl CGCGCG RNA Duplex

Abstract

Complete assignments of nonexchangeable protons in ¹H NMR spectra of 2′-O-methyl-CGCGCG complemented by its analysis of ¹³C and ³¹P NMR spectra revealed A-RNA double helical structure in low salt solution.     

Regulation of Auxin Homeostasis and Gradients in Arabidopsis Roots through the Formation of the Indole-3-Acetic Acid Catabolite 2-Oxindole-3-Acetic Acid

The native auxin, indole-3-acetic acid (IAA), is a major regulator of plant growth and development. Its nonuniform distribution between cells and tissues underlies the spatiotemporal coordination of many developmental events and responses to environmental stimuli. The regulation of auxin gradients and the formation of auxin maxima/minima most likely involve the regulation of both metabolic and transport processes. In this article, we have demonstrated that 2-oxindole-3-acetic acid (oxIAA) is a major primary IAA catabolite formed in Arabidopsis thaliana root tissues. OxIAA had little biological activity and was formed rapidly and irreversibly in response to increases in auxin levels. We further showed that there is cell type–specific regulation of oxIAA levels in the Arabidopsis root apex. We propose that oxIAA is an important element in the regulation of output from auxin gradients and, therefore, in the regulation of auxin homeostasis and response mechanisms.     

Hrabalicrinus zitti gen. et sp. nov., and other Upper Jurassic crinoids (Echinodermata,Crinoidea) from the Brno area (Czech Republic)

Jurassic (Oxfordian) crinoids from the Brno area (Czech Republic) are described in details for the first time. A rich crinoid assemblage consisting of cups, isolated cup elements, brachial plates, columnals, pluricolumnals, and cirrals is assigned to isocrinids Isocrinus amblyscalaris (Thurmann), Balanocrinus subteres (Münster), B. pentagonalis (Goldfuss), Isocrinida indet., comatulid Hrabalicrinus zitti gen. et sp. nov., cyrtocrinids Lonchocrinus sp., Cyrtocrinus cf. nutans (Goldfuss), Pilocrinus moussoni (Desor), Tetracrinus moniliformis Münster, Cyrtocrinida indet., and millericrinids (Millericrinida indet.). Crinoids already mentioned from the Jurassic strata of the Czech Republic are subsequently revised. Apart from the isolated remains of Isocrinida, Millericrinida, and Thiolliericrinida, the presence of any other taxon reported from this area should be treated with extreme caution. A rare example of non-regenerative columnal healing (the so-called callus) in I. amblyscalaris is also described. Based on sedimentology and microfacies, the Jurassic limestones were deposited in various palaeoenvironments of upper carbonate platform and shelf lagoon (0 to > 50 m palaeodepth).     

Anticonvulsant Effectiveness and Neurotoxicity Profile of 4-butyl-5-[(4-chloro-2-methylphenoxy)methyl]-2,4-dihydro-3H-1,2,4-triazole-3-thione (TPL-16) in Mice

Neurochemical Research - Protective (antiseizure) effects of 4-butyl-5-[(4-chloro-2-methylphenoxy)-methyl]-2,4-dihydro-3H-1,2,4-triazole-3-thione (TPL-16) and acute neurotoxic effects were...     

Hinge-loop mutation can be used to control 3D domain swapping and amyloidogenesis of human cystatin C

Cystatins are natural inhibitors of cysteine proteases, enzymes that are widely distributed in animals, plants, and microorganisms. Human cystatin C (hCC) has been also recognized as an aggregating protein directly involved in the formation of pathological amyloid fibrils, and these amyloidogenic properties greatly increase in a naturally occurring L68Q hCC variant. For a long time only dimeric structure of wild-type hCC has been known. The dimer is created through 3D domain swapping process, in which two parts of the cystatin structure become separated from each other and next exchanged between two molecules. Important role in the domain swapping plays the L1 loop, which connects the exchanging segments and, upon dimerization, transforms from a β-turn into a part of a long β-strand. In the very recently published first monomeric structure of human cystatin C (hCC-stab1), dimerization was abrogated due to clasping of the β-strands from the swapping domains by an engineered disulfide bridge. We have designed and constructed another mutated cystatin C with the smallest possible structural intervention, that is a single-point mutation replacing hydrophobic V57 from the L1 loop by polar asparagine, known as a stabilizer of a β-turn motif. V57N hCC mutant occurred to be stable in its monomeric form and crystallized as a monomer, revealing typical cystatin fold with a five-stranded antiparallel β-sheet wrapped around an α-helix. Here we report a 2.04 Å resolution crystal structure of V57N hCC and discuss the architecture of the protein in comparison to chicken cystatin, hCC-stab1 and dimeric hCC.     

Biodegradation kinetics of 2,4-D by bacterial strains isolated from soil

The aim of the study was to characterize the 2,4-dichlorophenoxyacetic acid (2,4-D) degradative potential of three bacterial strains identified by MIDI-FAME profiling as Burkholderia cepacia (DS-1), Pseudomonas sp. (DS-2) and Sphingomonas paucimobilis (DS-3) isolated from soil with herbicide treatment history. All strains were capable of using herbicide as the only source of carbon and energy when grown in mineral salt medium (MSM) containing 2,4-D (50 mg/l). Over a 10 day incubation period, 69%, 73% and 54% of the initial dose of 2,4-D were degraded by strains DS-1, DS-2 and DS-3, respectively. Analysis of 2,4-dichlorophenol (2,4-DCP) concentration, the main metabolite of 2,4-D degradation, revealed that strains DS-1 and DS-2 may also have the potential to metabolize this compound. The percentage of 2,4-DCP removal was 67% and 77% in relation to maximum values of 9.5 and 9.2 mg/l determined after 4 and 2 days for MSM+DS-1 and MSM+DS-2, respectively. The degradation kinetics of 2,4-D (50 mg/kg) in sterile soil (SS) showed different potential of tested strains to degrade 2,4-D. The times within which the initial 2,4-D concentration was reduced by 50% (DT₅₀) were 6.3, 5.0 and 9.4 days for SS+DS-1, SS+DS-2 and SS+DS-3, respectively.     

From genotype to phenotype in bovine functional genomics

In past 5 years, the promise that came with genome sequencing has revolutionized the functional genomics research field at unprecedented manner. It would soon know what all known genes do, particularly genes involved in genetic improvement of animal health and increase food animal production. With the availability of full bovine genomic sequence, yet we still have a lot of daunting tasks on 'genotype-to-phenotype problem' particularly about the phenotypic variations and trying to predict what genes are likely to be involved, and improved integrated interactive database. This article outlined and discussed about the current status of bovine functional genomics, recent development in bovine genome databases particularly in annotation of bovine genome, bovine quantitative trait loci database and its potential impact to unveil the from genotype-to-phenotype problem.     

Subcellular localization of UDP-GlcNAc, UDP-Gal and SLC35B4 transporters

The mechanisms of transport and distribution of nucleotide sugars in the cell remain unclear. In an attempt to further characterize nucleotide sugar transporters (NSTs), we determined the subcellular localization of overexpressed epitope-tagged canine UDP-GlcNAc transporter, human UDP-Gal transporter splice variants (UGT1 and UGT2), and human SLC35B4 transporter splice variants (longer and shorter version) by indirect immunofluorescence using an experimental model of MDCK wild-type and MDCK-RCA(r) mutant cells. Our studies confirmed that the UDP-GlcNAc transporter was localized to the Golgi apparatus only and its localization was independent of the presence of endogenous UDP-Gal transporter. After overexpression of UGT1, the protein colocalized with the Golgi marker only. When UGT2 was overexpressed, the protein colocalized with the endoplasmic reticulum (ER) marker only. When UGT1 and UGT2 were overexpressed in parallel, UGT1 colocalized with the ER and Golgi markers and UGT2 with the ER marker only. This suggests that localization of the UDP-Gal transporter may depend on the presence of the partner splice variant. Our data suggest that proteins involved in nucleotide sugar transport may form heterodimeric complexes in the membrane, exhibiting different localization which depends on interacting protein partners. In contrast to previously published data, both splice variants of the SLC35B4 transporter were localized to the ER, independently of the presence of endogenous UDP-Gal transporter.     

Inhibition by purine nucleotides of the release of reactive oxygen species from muscle mitochondria: indication for a function of uncoupling proteins as superoxide anion transporters

Release of reactive oxygen species (ROS), measured as the sum of hydrogen peroxide (H₂O₂) and superoxide anion radical (), from respiring rat heart and skeletal muscle mitochondria was significantly decreased by millimolar concentrations of GTP or GDP. Attempts to differentiate between the two forms of ROS showed that the release of rather than that of H₂O₂ was affected. Meanwhile, intramitochondrial ROS accumulation, measured by inactivation of aconitase, increased. These results suggest that guanine nucleotides inhibit the release of from mitochondria. As these nucleotides are known inhibitors of uncoupling proteins (UCPs), it is proposed that UCPs may function as carriers of , thus enabling its removal from the matrix compartment.