A halotolerant and thermotolerant <Emphasis Type="Italic">Bacillus</Emphasis> sp. degrades hydrocarbons and produces tensio-active emulsifying agent

A Bacillus sp. strain DHT, isolated from oil-contaminated soil, grew and produced biosurfactant when cultured in variety of substrate at salinities of up to 100 g l⁻¹ and temperatures up to 45°C. It was capable of utilizing crude oil, fuels, various pure alkanes and PAHs as a sole carbon and energy source across a wide range of temperature and salinity. Over the range evaluated, the degradation of hydrocarbon and biosurfactant production was not influenced by salinity (0–10% wv⁻¹) and temperature (30–45°C). The biosurfactant produced by the organism emulsified a range of hydrocarbons with hexadecane as the best substrate and toluene as the poorest. From 16S rDNA analysis, strain DHT was related to Bacillus licheniformis.     

Mutation analysis of oxisterol-binding-protein gene in patients with age-related macular degeneration

Allelic variants of several genes are increasingly recognized as susceptibility factors in age-related macular degeneration (AMD). Because of its metabolic characteristics the macula is sensitive to oxidative damage, and supplementation with antioxidants has been shown to be effective in slowing the progression of disease in AMD patients. The oxisterol-binding-protein (OSBP2) gene is expressed mainly in the retinal pigmented epithelium underlying the macular region. Its product specifically binds and transports oxisterols, the cytotoxic effects of which may be involved in macular damage. The aim of this study was to search for allelic variants of OSBP2 gene, as well as to evaluate several risk factors in 24 patients with AMD; 17 with nonexudative (NE) and 7 with neovascular (NV) form. Total cholesterol was elevated in 66% of the patients, high-density lipoprotein (HDL) cholesterol was reduced in 12%; vitamin A or vitamin E deficiency was not observed. OSBP2 gene analysis was performed in AMD patients and in 110 control subjects by single-stranded conformational polymorphism (SSCP) analysis followed by direct sequencing. Six allelic variants were detected: 2 nonpolymorphic unique exonic variants in 2 AMD subjects and 4 polymorphic variants (2 exonic and 2 intronic). These data indicate a possible role of OSBP2 gene in the pathogenesis of oxidative damage to the macula induced by oxysterols in AMD patients.     

Tryptophan phosphorescence studies of the D-galactose/D-glucose-binding protein from Escherichia coli provide a molecular portrait with structural and dynamics features of the protein

The D-galactose/D-glucose-binding protein (GGBP) from E. coli serves as an initial component for both chemotaxis toward glucose and high-affinity active transport of the sugar. In this work, we have used phosphorescence spectroscopy to investigate the effects of glucose and calcium on the dynamics and stability of GGBP. We found that GGBP exhibits a phosphorescence spectrum composed of two energetically distinct 0,0-vibrational bands centered at 404.43 and 409.61 nm; the large energy separation between them indicates two classes of chromophores making distinct dipolar interactions with their surrounding. Interestingly, the high-energy spectral component (404.43 nm) is one of the bluest spectra reported to date in proteins. Considering the ground state dipole direction, low-energy configurations for the indole side chain in proteins leading to blue-shifted spectra can arise from negative charges in proximity to the imidazole-ring nitrogen and/or positive charges near C4-C5 of the benzene ring. Among the five tryptophan residues of GGBP, Trp-284, located at the N-terminal domain of the protein, and Trp-183, located in the protein hinge region, make strong attractive charge interactions with surrounding side chains. Regarding Trp-284, the indole ring nitrogen is in contact with the negative charge of the Asp-267, whereas Trp-183 is next to the Glu-149 residue. In the latter, the ground state energy is further lowered by the proximity of the Arg-158 to the negative end (near C6) of the indole dipole. Regarding the red spectral component (409.61 nm), it is more intense than the blue component, presumably because more residues contribute to it. lambda 0,0 is typical of environments that are weakly polar or characterized by charges positioned near 90 degrees from the ground state dipole direction (the case of W195 and W127). The binding of glucose modifies the phosphorescence lifetime values as well as the spectrum of GGBP, shifting the blue band 0.54 nm to the blue and the red band 1 nm to the red. Finally, the removal of the calcium from GGBP structure causes variations in lifetime values and spectral shifts similar to those induced by glucose binding to the native protein. Aided by a detailed inspection of the three-dimensional structure of GGBP, these results contribute to a better understanding of the structure/function relationship of this protein.     

Biotechnological approaches to overcome hybridization barriers and use of micropropagation tool for further improvement in Heliconia: a review

Plant Cell, Tissue and Organ Culture (PCTOC) - Heliconia, also known as ‘False-Bird-of-Paradise’, is a genus of flowering plants in the monotypic family of Heliconiaceae.The genus...     

Ethylene emission and abscission of immature ‘Montmorency’ sour cherry fruitlets vary with ethephon concentration,phenology stage and ambient temperatures following application

Plant Growth Regulation - Ethylene is an endogenous plant hormone associated with natural senescence and abscission of plant organs. Ethylene release from the degradation of 2-chloroethylphosphonic...     

Elementary Energy Transfer Pathways in Allochromatium vinosum Photosynthetic Membranes

Allochromatium vinosum (formerly Chromatium vinosum) purple bacteria are known to adapt their light-harvesting strategy during growth according to environmental factors such as temperature and average light intensity. Under low light illumination or low ambient temperature conditions, most of the LH2 complexes in the photosynthetic membranes form a B820 exciton with reduced spectral overlap with LH1. To elucidate the reason for this light and temperature adaptation of the LH2 electronic structure, we performed broadband femtosecond transient absorption spectroscopy as a function of excitation wavelength in A. vinosum membranes. A target analysis of the acquired data yielded individual rate constants for all relevant elementary energy transfer (ET) processes. We found that the ET dynamics in high-light-grown membranes was well described by a homogeneous model, with forward and backward rate constants independent of the pump wavelength. Thus, the overall B800→B850→B890→ Reaction Center ET cascade is well described by simple triexponential kinetics. In the low-light-grown membranes, we found that the elementary backward transfer rate constant from B890 to B820 was strongly reduced compared with the corresponding constant from B890 to B850 in high-light-grown samples. The ET dynamics of low-light-grown membranes was strongly dependent on the pump wavelength, clearly showing that the excitation memory is not lost throughout the exciton lifetime. The observed pump energy dependence of the forward and backward ET rate constants suggests exciton diffusion via B850→ B850 transfer steps, making the overall ET dynamics nonexponential. Our results show that disorder plays a crucial role in our understanding of low-light adaptation in A. vinosum.     

Formation and Repair of Mismatches Containing Ribonucleotides and Oxidized Bases at Repeated DNA Sequences

The cellular pool of ribonucleotide triphosphates (rNTPs) is higher than that of deoxyribonucleotide triphosphates. To ensure genome stability, DNA polymerases must discriminate against rNTPs and incorporated ribonucleotides must be removed by ribonucleotide excision repair (RER). We investigated DNA polymerase β (POL β) capacity to incorporate ribonucleotides into trinucleotide repeated DNA sequences and the efficiency of base excision repair (BER) and RER enzymes (OGG1, MUTYH, and RNase H2) when presented with an incorrect sugar and an oxidized base. POL β incorporated rAMP and rCMP opposite 7,8-dihydro-8-oxoguanine (8-oxodG) and extended both mispairs. In addition, POL β was able to insert and elongate an oxidized rGMP when paired with dA. We show that RNase H2 always preserves the capacity to remove a single ribonucleotide when paired to an oxidized base or to incise an oxidized ribonucleotide in a DNA duplex. In contrast, BER activity is affected by the presence of a ribonucleotide opposite an 8-oxodG. In particular, MUTYH activity on 8-oxodG:rA mispairs is fully inhibited, although its binding capacity is retained. This results in the reduction of RNase H2 incision capability of this substrate. Thus complex mispairs formed by an oxidized base and a ribonucleotide can compromise BER and RER in repeated sequences.     

Discovery of potent nucleotide-mimicking competitive inhibitors of hepatitis C virus NS3 helicase

Among the enzymes involved in the life cycle of HCV, the non-structural protein NS3, with its double function of protease and NTPase/helicase, is essential for the virus replication. Exploiting our previous knowledge in the development of nucleotide-mimicking NS3 helicase (NS3h) inhibitors endowed with key structural and electronic features necessary for an optimal ligand-enzyme interaction, we developed the tetrahydroacridinyl derivative 3a as the most potent NS3h competitive inhibitor reported to date (HCV NS3h K(i)=20 nM).     

Mercury-resistant bacterial strains Pseudomonas and Psychrobacter spp. isolated from sediments of Orbetello Lagoon (Italy) and their possible use in bioremediation processes

This study was aimed to isolate Hg-resistant bacteria from contaminated sediments of the Orbetello Lagoon in Italy and to assess their possible use as biofilms in bioremediation processes. Enrichment cultures prepared from contaminated sediments in the presence of 0.05 mM of mercury and under aerobic conditions allowed the isolation of five heterotrophic bacterial strains. 16S rDNA gene sequencing assigned the isolated strains to the genera Pseudomonas and Psychrobacter. For the first time mercury-resistant bacterial strains belonging to the genus Psychrobacter were evidenced. Minimum inhibitory concentrations in the presence of HgCl₂ and of CH₃HgCl showed high levels of resistance. EC50 values for the isolated bacterial strains in the presence of HgCl₂ and of CH₃HgCl confirmed the adaptation to the metal. Hg-resistant strains ORHg1, ORHg4 and ORHg5 showed the capacity to volatilize inorganic and organic mercury to elemental mercury, and formed biofilms on pumice particles, and were shown to play a role in the removal of mercury from sediment leachates. This study reports isolation and characterization of new Hg-resistant bacterial strains and provides novel insight into their possible use in bioremediation processes of mercury polluted sediments.     

Relative burden of large CNVs on a range of neurodevelopmental phenotypes

While numerous studies have implicated copy number variants (CNVs) in a range of neurological phenotypes, the impact relative to disease severity has been difficult to ascertain due to small sample sizes, lack of phenotypic details, and heterogeneity in platforms used for discovery. Using a customized microarray enriched for genomic hotspots, we assayed for large CNVs among 1,227 individuals with various neurological deficits including dyslexia (376), sporadic autism (350), and intellectual disability (ID) (501), as well as 337 controls. We show that the frequency of large CNVs (>1 Mbp) is significantly greater for ID-associated phenotypes compared to autism (p = 9.58 × 10(-11), odds ratio = 4.59), dyslexia (p = 3.81 × 10(-18), odds ratio = 14.45), or controls (p = 2.75 × 10(-17), odds ratio = 13.71). There is a striking difference in the frequency of rare CNVs (>50 kbp) in autism (10%, p = 2.4 × 10(-6), odds ratio = 6) or ID (16%, p = 3.55 × 10(-12), odds ratio = 10) compared to dyslexia (2%) with essentially no difference in large CNV burden among dyslexia patients compared to controls. Rare CNVs were more likely to arise de novo (64%) in ID when compared to autism (40%) or dyslexia (0%). We observed a significantly increased large CNV burden in individuals with ID and multiple congenital anomalies (MCA) compared to ID alone (p = 0.001, odds ratio = 2.54). Our data suggest that large CNV burden positively correlates with the severity of childhood disability: ID with MCA being most severely affected and dyslexics being indistinguishable from controls. When autism without ID was considered separately, the increase in CNV burden was modest compared to controls (p = 0.07, odds ratio = 2.33).