Neutron diffraction studies towards deciphering the protonation state of catalytic residues in the bacterial KDN9P phosphatase

The enzyme 2-keto-3-deoxy-9-O-phosphonononic acid phosphatase (KDN9P phosphatase) functions in the pathway for the production of 2-keto-3-deoxy-D-glycero-D-galacto-nononic acid, a sialic acid that is important for the survival of commensal bacteria in the human intestine. The enzyme is a member of the haloalkanoate dehalogenase superfamily and represents a good model for the active-site protonation state of family members. Crystals of approximate dimensions 1.5 × 1.0 × 1.0 mm were obtained in space group P2(1)2(1)2, with unit-cell parameters a = 83.1, b = 108.9, c = 75.7 Å. A complete neutron data set was collected from a medium-sized H/D-exchanged crystal at BIODIFF at the Heinz Maier-Leibnitz Zentrum (MLZ), Garching, Germany in 18 d. Initial refinement to 2.3 Å resolution using only neutron data showed significant density for catalytically important residues.

Scena propylea (Druce) (Lepidoptera: Erebidae) an endemic species of Mexico

A revision of the bibliography, as well as an analysis on the data from the specimen labels of Scena propylea (Druce) (Erebidae: Arctiinae: Euchromiina) deposited in different scientific collections, was carried out and included information from 1894 to 2010. Its geographical distribution is restricted to the Trans-Mexican Volcanic Belt which determines this species as endemic. Data are provided on the biogeography, ecology and biology for this species. Its food plant is Thenardia floribunda (Apocynaceae) which is also endemic to Mexico. From this analysis, we propose the inclusion of both species in the document known as the Norma Oficial Mexicana 059 which encompasses the environmental protection of wild flora and fauna species native to Mexico and their risk categories, as well as the specifications for their inclusion, exclusion or change and a list of all species at risk.

A novel methane sensor based on porous SnO2 nanorods: room temperature to high temperature detection

We report for the first time a novel room temperature methane (CH(4)) sensor fabricated using porous tin oxide (SnO(2)) nanorods as the sensing material. The porous SnO(2) nanorods were synthesized by using multiwall carbon nanotubes (MWCNTs) as templates. Current versus time curves were obtained demonstrating the room temperature sensing capabilities of the sensor system when exposed to 0.25% CH(4) in air. The sensor also exhibited a wide temperature range for different concentrations of CH(4) (25-500 °C), making it useful in harsh environments as well.

Random amplified polymorphic DNA analysis in Hordeum species

Random amplified polymorphic DNA analysis was performed by applying a set of 13 arbitrary 10-mer primers to 19 Hordeum species and subspecies. High levels of variation in fragment pattern were observed both within and among species with most of the primers used. Genetic similarities between accessions and species were calculated from the fragment patterns. The resulting phenograms confirmed previous relationships among the Hordeum species.

Evolution of the magnetic properties of Co10Cu90 nanoparticles prepared by wet chemistry with thermal annealing

Nanoparticles of Co10Cu90 alloy have been prepared by sonochemical wet method. According to transmission electron microscopy, bimetallic particles with typical diameter of 50-100 nm consisting of nanocrystallites with average diameter of 15-20 nm were obtained. The samples were annealed at 300 degrees C and 450 degrees C. Zero field cooled and field cooled temperature dependences of magnetization in the temperature range of 5-400 K at 50 Oe, as well as magnetization hysteresis loops at 15, 100 and 305 K were measured by vibrating sample magnetometry. Presence of antiferromagnetic phase, most probably of the oxide Co3O4, was observed in as-prepared sample. The lowest coercivity was found for the CoCu sample annealed at-300 degrees C, whereas for as prepared sample and the one annealed at 450 degrees C it was significantly higher. The samples were additionally probed by continuous wave ferromagnetic resonance at room, temperature using a standard X-band electron spin resonance spectrometer. A good correspondence between evolution of the coercivity and the microwave resonance fields with annealing temperature was observed.

Consolidation of glycosyl hydrolase family 30: a dual domain 4/7 hydrolase family consisting of two structurally distinct groups

In this work glycosyl hydrolase (GH) family 30 (GH30) is analyzed and shown to consist of its currently classified member sequences as well as several homologous sequence groups currently assigned within family GH5. A large scale amino acid sequence alignment and a phylogenetic tree were generated and GH30 groups and subgroups were designated. A partial rearrangement in the GH30 defining side-associated β-domain contributes to the differentiation of two major groups that contain up to eight subgroups. For this CAZy family of Clan A enzymes the dual domain fold is conserved, suggesting that it may be a requirement for evolved function. This work redefines GH family 30 and serves as a guide for future efforts regarding enzymes classified within this family.

Differential rates of digestion of bacteria by freshwater and marine phagotrophic protozoa

Differential decreases over time of two bacterial species, Escherichia coli and Enterococcus faecalis, in a freshwater and a marine ecosystem were observed and explained by a differential rate of digestion of these bacteria by phagotrophic flagellates and ciliates. For this purpose, fluorescence-labeled bacteria (FLB) were used and prepared from the two species cited above. The number of FLB was observed for 5 days in fresh and marine waters in the presence or absence (0.2-mum-pore-size-filtered water) of natural microbiota. These experiments showed a longer persistence of Enterococcus faecalis FLB as opposed to Escherichia coli FLB in the presence of natural microbiota. Removal of FLB was due to protozoan grazing because no decrease of FLB number was observed in the absence of natural microbiota. In short-term (about 40 min) ingestion experiments, we found similar clearance rates of Escherichia coli and Enterococcus faecalis FLB by assemblages of flagellates from the freshwater and the marine ecosystem and by cultured assemblages of ciliates from the marine ecosystem. Clearance rates of Enterococcus faecalis FLB were greater than those of Escherichia coli FLB for assemblages of ciliates from the freshwater ecosystem. Comparison of rates of ingestion and digestion of FLB by protozoa showed that Escherichia coli FLB were digested and ingested at similar rates. However, Enterococcus faecalis FLB were digested slower than they were ingested. These results suggest that a longer persistence of Enterococcus faecalis as opposed to Escherichia coli can be explained by a differential digestion by flagellates and ciliates in aquatic ecosystems. Moreover, rates of ingestion and digestion were strongly correlated for both FLB types.

Control of magnetization reversal by combining shape and magnetocrystalline anisotropy in epitaxial Fe planar nanowires

This work presents an analysis of the in-plane magnetization reversal mechanisms of Fe nanowires, with widths from 100 nm to 1 microm, fabricated in epitaxial Au(001)/Fe(001)/MgO(001) thin films by means of focused ion and electron beam lithographies, with either positive or negative resist. The experimental results show that the switching mechanisms and hysteresis are almost exclusively functions of the dimensions of the wires and of the Fe intrinsic properties, with minor influence of the specific fabrication route employed upon optimization of nanostructure parameters in terms of crystallinity and morphology, and well defined and reproducible geometry. The reversal processes evolve from wall pinning at low angles between the applied field and the axis of the wires to basically uniform magnetization rotation at high angles. This behaviour can be described in terms of single spin configurations, thus ruling out the formation of multidomain structures even at high angles. The ability to achieve these high quality and well controlled nanowires allowed us to develop an analytical model, based on uniform magnetization configurations considering just the intrinsic Fe properties and the shape and dimensions of the wires. This simple approach provides a very good qualitative and quantitative agreement with the experimental results, thus evidencing the relatively small role of other extrinsic factors in the magnetization processes.

Spectroscopic signature of a ubiquitous metal binding site in the metallo-β-lactamase superfamily

The metallo-β-lactamase (MβL) superfamily is a functionally diverse group of metalloproteins sharing a distinctive αβ/αβ fold and a characteristic metal binding motif. A large number of open reading frames identified in genomic sequencing efforts have been annotated as members of this superfamily through sequence comparisons. However, structural and functional studies performed on purified proteins are normally needed to unequivocally include a newly discovered protein in the MβL superfamily. Here we report the spectroscopic characterization of recombinant YcbL, a gene product annotated as a member of the MβL superfamily whose function in vivo remains unknown. By taking advantage of the structural features characterizing the MβL superfamily metal binding motif, we performed spectroscopic studies on Zn(II)- and Co(II)-substituted YcbL to structurally interrogate the metal binding site. The dinuclear center in Co(II)-YcbL was shown to display characteristic electronic absorption features in the visible region, which were also observed in an engineered MβL aimed at mimicking this metal site. Thus, the spectroscopic features reported herein can be employed as a signature to readily identify and characterize the presence of these ubiquitous metal binding sites.

Study of matrix metalloproteinases and their inhibitors in prostate cancer

BACKGROUND

Extracellular matrix metalloproteases (MMPs) have raised an extraordinary interest in cancer research because of their potential role in basal membrane and extracellular matrix degradation, consequently facilitating tumour invasion and metastases development.

METHODS

An immunohistochemical study was performed using tissue arrays and specific antibodies against MMPs 1, 2, 7, 9, 11, 13, 14, and their tissue inhibitors, TIMPs 1, 2 and 3. More than 2600 determinations on cancer specimens from 133 patients with clinically localised prostate carcinoma, 20 patients with prostatic intraepithelial neoplasia and 50 patients with benign prostate hyperplasia and controls, were performed.

RESULTS

When compared with benign pathologies, prostate carcinomas had higher expression of all MMPs and TIMPs. Dendogram shows a first-order division of tumours into two distinct MMPs/TIMPs molecular profiles, one of them with high MMPs/TIMs expression profile (n=70; 52.6%). Tumours with high expression of MMP-11 or -13, or cluster thereof, were significantly associated with higher probability of biochemical recurrence.

CONCLUSION

The expression of MMPs and TIMPs seems to have an important role in the molecular biology of prostate carcinomas, and their expression by tumours may be of clinical interest to used as indicators of tumour aggressiveness.

Influence of visfatin on histopathological changes of non-alcoholic fatty liver disease

BACKGROUND

Non-alcoholic fatty liver disease (NAFLD) is a common liver disease. The aim of the present study was to explore the relation of visfatin with underlying histopathological changes of NAFLD patients.

SUBJECTS

A population of 55 NAFLD patients was analyzed in a cross-sectional study. A liver biopsy was realized. Weight, basal glucose, insulin, insulin resistance (HOMA), total cholesterol, LDL cholesterol, HDL cholesterol, triglycerides, and visfatin levels were measured. A bioimpedance was performed.

RESULTS AND CONCLUSIONS

The mean age was 42.8 +/- 11.2 years, the mean BMI was 33.1 +/- 10.2 with 37 males (67.3%) and 18 females (32.7%). Probabilities to have; portal inflammation increased 1.11 (CI95%:1.03-1.50) with each increment of 1 ng/ml of visfatin concentration, high grade of steatosis increased 1.25 (CI 95%:1.06-1.61) with each unit of insulin concentrations, fibrosis increased 1.12 (CI 95%:1.02-1.43) with each unit of fat mass and lobulillar inflammation increased 13.4 (CI 95%:1.3-147) with each unit of HOMA-IR. Portal inflammation frequencies were different between groups (low visfatin group 13.07 < ng/ml: 37.5% versus high visfatin group 13.07 > ng/ml: 62.5%; P < 0.05). In conclusion, several histopathological changes in liver biopsies could be explained by insulin concentrations, HOMA-IR, and fat mass amount. Moreover, visfatin plasma concentrations could predict the presence of portal inflammation in NAFLD patients.

Role of specific microbial communities in the bioavailability of iron in Doñana National Park

The Doñana National Park contains highly complex microbial communities that play critical roles in the bioavailability and biogeochemical cycling of elements. In this study, we analyzed the formation of Fe-rich films on the surface of shallow waters at Doñana National Park as a model for future applications in bioremediation. Phytoplankton composition and abundance, physicochemical measurements, culture enrichments, and molecular detection of microorganisms were determined during this study. Natural samples were incubated in the laboratory and enrichments producing similar phenomena were obtained. Bacteria belonging to the genera Enterobacter were the major participants in surface Fe-film formation in laboratory enrichments. Film formation was dependent on wind exposure and only those sites protected from the direct influence of wind developed these films. A higher concentration of euglenophytes was found in the proximity of film-covered waters. Available iron (Fe2+) and total Fe concentrations were high (18.8 and 46.6 mg/L, respectively) underneath the surface film, and higher than in film-free waters and pore-sediment water. The concentration of phosphate and its availability were higher in the iron-rich film sediment, as 61% of total P was bound to iron oxy-hydroxides. Our results provide evidence of the link between P and Fe biogeochemical cycling in aquatic systems on sandy soils at the Doñana National Park. In addition, they provide significant insights into the bioavailability of these elements with potential interest in the role of microorganisms for metal sequestration in natural environments and utilization in bioremediation processes.

The Zn2 Position in Metallo-β-Lactamases is Critical for Activity: A Study on Chimeric Metal Sites on a Conserved Protein Scaffold

Metallo-beta-lactamases (MbetaLs) are bacterial Zn(II)-dependent hydrolases that confer broad-spectrum resistance to beta-lactam antibiotics. These enzymes can be subdivided into three subclasses (B1, B2 and B3) that differ in their metal binding sites and their characteristic tertiary structure. To date there are no clinically useful pan-MbetaL inhibitors available, mainly due to the unawareness of key catalytic features common to all MbetaL brands. Here we have designed, expressed and characterized two double mutants of BcII, a di-Zn(II) B1-MbetaL from Bacillus cereus, namely BcII-R121H/C221D (BcII-HD) and BcII-R121H/C221S (BcII-HS). These mutants display modified environments at the so-called Zn2 site or DCH site, reproducing the metal coordination environments of structurally related metallohydrolases. Through a combination of structural and functional studies, we found that BcII-HD is an impaired beta-lactamase even as a di-Zn(II) enzyme, whereas BcII-HS exhibits the ability to exist as mono or di-Zn(II) species in solution, with different catalytic performances. We show that these effects result from an altered position of Zn2, which is incapable of providing a productive interaction with the substrate beta-lactam ring. These results indicate that the position of Zn2 is essential for a productive substrate binding and hydrolysis.

Immunological and structural characterization of an epitope from the Trypanosoma cruzi KMP-11 protein

The K1 peptide is an HLA-A*0201-restricted cytotoxic epitope derived from the Trypanosoma cruzi KMP-11 protein, this being the etiological agent of Chagas' disease. This work describes the K1 peptide's secondary structure and its recognition by sera from chagasic patients. Circular dichroism and NMR spectroscopy analysis revealed that the K1 peptide adopts an alpha-helical conformation. Fifty-six percent of individuals had anti-K1 and 86% anti-KMP-11 antibodies by ELISA in the chronic Chagas' group and 28 and 68% in the indeterminate Chagas' group, respectively. By contrast, no reactivity was observed in sera from healthy individuals and tuberculosis patients. Antibody response subclass specificity to the K1 peptide was IgG1 and IgG3. Taken together these results support the idea that the K1 peptide acts as a B-cell-inducer epitope during Chagas' disease.

Ecological genomics of marine Roseobacters

Bacterioplankton of the marine Roseobacter clade have genomes that reflect a dynamic environment and diverse interactions with marine plankton. Comparative genome sequence analysis of three cultured representatives suggests that cellular requirements for nitrogen are largely provided by regenerated ammonium and organic compounds (polyamines, allophanate, and urea), while typical sources of carbon include amino acids, glyoxylate, and aromatic metabolites. An unexpectedly large number of genes are predicted to encode proteins involved in the production, degradation, and efflux of toxins and metabolites. A mechanism likely involved in cell-to-cell DNA or protein transfer was also discovered: vir-related genes encoding a type IV secretion system typical of bacterial pathogens. These suggest a potential for interacting with neighboring cells and impacting the routing of organic matter into the microbial loop. Genes shared among the three roseobacters and also common in nine draft Roseobacter genomes include those for carbon monoxide oxidation, dimethylsulfoniopropionate demethylation, and aromatic compound degradation. Genes shared with other cultured marine bacteria include those for utilizing sodium gradients, transport and metabolism of sulfate, and osmoregulation.

The metallo-beta-lactamase GOB is a mono-Zn(II) enzyme with a novel active site

Metallo-beta-lactamases (MbetaLs) are zinc-dependent enzymes able to hydrolyze and inactivate most beta-lactam antibiotics. The large diversity of active site structures and metal content among MbetaLs from different sources has limited the design of a pan-MbetaL inhibitor. Here we report the biochemical and biophysical characterization of a novel MbetaL, GOB-18, from a clinical isolate of a Gram-negative opportunistic pathogen, Elizabethkingia meningoseptica. Different spectroscopic techniques, three-dimensional modeling, and mutagenesis experiments, reveal that the Zn(II) ion is bound to Asp120, His121, His263, and a solvent molecule, i.e. in the canonical Zn2 site of dinuclear MbetaLs. Contrasting all other related MbetaLs, GOB-18 is fully active against a broad range of beta-lactam substrates using a single Zn(II) ion in this site. These data further enlarge the structural diversity of MbetaLs.

On the effect of nanocrystallization and disorder on the magnetic properties of Cu-rich, FeMnCu alloys

We report on the temperature dependencies of the Mössbauer spectra and the AC magnetic susceptibility measured in Cu-rich, FeMnCu samples prepared by mechanically alloying, using, on the one side, Cu and prealloyed FeMn powders and, on the other, pure element Cu, Mn, and Fe powders. From the correlation of the Mössbauer and susceptibility data we conclude about the basic characteristics of the phase distributions present in the different studied samples. Those distributions are a consequence of both the nanostructure induced upon milling and of the different signs of the Mn/Cu (negative) and Fe/Cu (positive) enthalpies of mixing. The proposed phase distributions are significantly different in the samples prepared from different precursors and this fact is analyzed in terms of the disproportion of the precursor FeMn alloy and in those of the favoured Mn/Cu interdiffusion and the hindered Fe/Cu one.

Novel chemolithotrophic, thermophilic, anaerobic bacteria Thermolithobacter ferrireducens gen. nov., sp. nov. and Thermolithobacter carboxydivorans sp. nov

Three thermophilic strains of chemolithoautotrophic Fe(III)-reducers were isolated from mixed sediment and water samples (JW/KA-1 and JW/KA-2(T): Calcite Spring, Yellowstone N.P., WY, USA; JW/JH-Fiji-2: Savusavu, Vanu Levu, Fiji). All were Gram stain positive rods (approximately 0.5 x 1.8 microm). Cells occurred singly or in V-shaped pairs, and they formed long chains in complex media. All utilized H(2) to reduce amorphous iron (III) oxide/hydroxide to magnetite at temperatures from 50 to 75 degrees C (opt. approximately 73 degrees C). Growth occurred within the pH(60C) range of 6.5-8.5 (opt. pH(60C) 7.1-7.3). Magnetite production by resting cells occurred at pH(60C) 5.5-10.3 (opt. 7.3). The iron (III) reduction rate was 1.3 mumol Fe(II) produced x h(-1) x ml(-1) in a culture with 3 x 10(7) cells, one of the highest rates reported. In the presence or absence of H(2), JW/KA-2(T) did not utilize CO. The G + C content of the genomic DNA of the type strain is 52.7 +/- 0.3 mol%. Strains JW/KA-1 and JW/KA-2(T) each contain two different 16S rRNA gene sequences. The 16S rRNA gene sequences from JW/KA-1, JW/KA-2(T), or JW/JH-Fiji-2 possessed >99% similarity to each other but also 99% similarity to the 16S rRNA gene sequence from the anaerobic, thermophilic, hydrogenogenic CO-oxidizing bacterium 'Carboxydothermus restrictus' R1. DNA-DNA hybridization between strain JW/KA-2(T) and strain R1(T) yielded 35% similarity. Physiological characteristics and the 16S rRNA gene sequence analysis indicated that the strains represent two novel species and are placed into the novel genus Thermolithobacter within the phylum 'Firmicutes'. In addition, the levels of 16S rRNA gene sequence similarity between the lineage containing the Thermolithobacter and well-established members of the three existing classes of the 'Firmicutes' is less than 85%. Therefore, Thermolithobacter is proposed to constitute the first genus within a novel class of the 'Firmicutes', Thermolithobacteria. The Fe(III)-reducing Thermolithobacter ferrireducens gen. nov., sp. nov. is designated as the type species with strain JW/KA-2(T) (ATCC 700985(T), DSM 13639(T)) as its type strain. Strain R1(T) is the type strain for the hydrogenogenic, CO-oxidizing Thermolithobacter carboxydivorans sp. nov. (DSM 7242(T), VKM 2359(T)).