Biodegradation of chemically modified flax fibers in soil and in vitro with selected bacteria

The extent and rate of degradation of flax (Linum usitatissimum) fibers, both in the native state and after surface chemical modification (acetylation or poly(ethylene glycol), PEG, grafting), was investigated under laboratory conditions in two different biodegrading environments. Degradation of the fibers under aerobic conditions by the action of the microorganisms present in soil is assessed with the ASTM 5988-96 method by monitoring carbon dioxide evolution. In vitro biodegradation experiments were carried out by exposing the fibers to a pure culture of Cellvibrio fibrovorans bacteria and measuring the mass loss as a function of time. Despite the complexity of the system, the results of degradation in soil were satisfactorily reproducible, although the absolute rates were found to change in different experiments using the same soil. The degradation rate of acetylated fibers in soil nearly equals that of unmodified fibers, whereas in the pure culture, acetylated fibers biodegrade slower than native fibers. The opposite happens with the PEG-grafted fibers, which degrade slower than unmodified flax in soil and at a comparable rate upon in vitro exposure to the bacterial culture. The different biodegradation kinetics observed in the two biodegrading environments were attributed to differences of biocenoses, abiotic factors, and biodegradation assessing methods. Nevertheless, the final extent of biodegradation was the same for modified and unmodified fibers both in soil and in the pure culture, showing that the surface chemical modifications applied do not significantly affect biodegradability of the flax fibers.     

Some protein tyrosine phosphatases target in part to lipid rafts and interact with caveolin-1

A profile-based search of the SWISS-PROT database reveals that most protein tyrosine phosphatases (PTPs) contain at least one caveolin-1-binding motif. To ascertain if the presence of caveolin-binding motif(s) in PTPs corresponds to their actual localization in caveolin-1-enriched membrane fractions, we performed subcellular fractionating experiments. We found that all tested PTPs (PTP1B, PTP1C, SHPTP2, PTEN, and LAR) are actually localized in caveolin-enriched membrane fractions, despite their distribution in other subcellular sites, too. More than 1/2 of LAR and about 1/4 of SHPTP2 and PTP-1C are localized in caveolin-enriched membrane fractions whereas, in these fractions, PTP-1B and PTEN are poorly concentrated. Co-immunoprecipitation experiments with antibodies specific for each tested PTP demonstrated that all five phosphatases form molecular complexes with caveolin-1 in vivo. Collectively, our findings propose that particular PTPs could perform some of their cellular actions or are regulated by recruitment into caveolin-enriched membrane fractions.     

Time-Lapse Imaging of Conformational Changes in Supercoiled DNA by Scanning Force Microscopy

Most of the scanning force microscopy (SFM) images of supercoiled DNA on untreated mica thus far reported have not shown tight plectonemic structure seen by electron microscopy, but instead less coiled molecules and sometimes a partly "condensed" state with intimate chain-chain interactions. By observing time-lapse images of conformational changes of DNA induced by decreasing ionic strength of imaging buffer in solution SFM, we could show that the process of water rinsing, an indispensable step for preparation of dried samples, may be responsible for some of the conformational anomalies in the images previously reported. We have studied several protocols to observe supercoiled DNA molecules by SFM and discuss the merits and the demerits. Images obtained following uranyl acetate treatment may be ideal for the detection of DNA damage, as the supercoiled and nicked forms are easily distinguishable.     

Monitoring equilibria and kinetics of protein folding/unfolding reactions by capillary zone electrophoresis

A method is described here for studying conformational transitions of proteins due to denaturing agents: capillary zone electrophoresis (CZE) in acidic, isoelectric buffers. The sample is run in 50 mM isoelectric glutamic acid (pH = pI = 3.2) added with 1 mM oligoamine (tetraethylene pentamine) for quenching protein interaction to the capillary wall (final pH = 3.3). Muscle acylphosphatase (AcP), in this buffer, exhibited a free solution mobility of 2.63 x 10(-4) cm(2) V(-1) s(-1). By studying the unfolding kinetics, as a function of time of incubation in 7 M urea, it was possible to measure the rate constant of the unfolding reaction, estimated to be 0.00030+/-0.00006 s(-1). The same measurements, when repeated via spectroscopic monitoring of intrinsic fluorescence, gave a value of 0.00034+/-0.00002 s(-1), thus in excellent agreement with CZE data. By equilibrium unfolding CZE studies, it was possible to construct the typical sigmoidal transition of unfolding vs urea molarity: the midpoint of this transition, at which the folded and unfolded states should be equally populated, was estimated to be at 4.56 M urea. Similar experiments by fluorometric analysis gave a value of 4.60 M urea as midpoint of the unfolding curve.     

Use of Formalin-Fixed Paraffin-Embedded Samples for Gene Expression Studies in Breast Cancer Patients

To obtain gene expression profiles from samples collected in clinical trials, we conducted a pilot study to assess feasibility and estimate sample attrition rates when profiling formalin-fixed, paraffin-embedded specimens. Ten matched fresh-frozen and fixed breast cancer samples were profiled using the Illumina HT-12 and Ref-8 chips, respectively. The profiles obtained with Ref 8, were neither technically nor biologically reliable since they failed to yield the expected separation between estrogen receptor positive and negative samples. With the use of Affymetrix HG-U133 2.0 Plus chips on fixed samples and a quantitative polymerase chain reaction -based sample pre-assessment step, results were satisfactory in terms of biological reliability, despite the low number of present calls (M = 21%±5). Compared with the Illumina DASL WG platform, Affymetrix data showed a wider interquartile range (1.32 vs 0.57, P<2.2 E-16,) and larger fold changes. The Affymetrix chips were used to run a pilot study on 60 fixed breast cancers. By including in the workflow the sample pre-assessment steps, 96% of the samples predicted to give good results (44/46), were in fact rated as satisfactory from the point of view of technical and biological meaningfulness. Our gene expression profiles showed strong agreement with immunohistochemistry data, were able to reproduce breast cancer molecular subtypes, and allowed the validation of an estrogen receptor status classifier derived in frozen samples. The approach is therefore suitable to profile formalin-fixed paraffin-embedded samples collected in clinical trials, provided that quality controls are run both before (sample pre-assessment) and after hybridization on the array.     

Analysis of hepatitis C virus hypervariable region 1 sequence from cryoglobulinemic patients and associated controls

Chronic hepatitis C virus (HCV) infection is frequently associated with extrahepatic manifestations, including nonmalignant and malignant B-cell lymphoproliferative disorders. It has been reported that specific changes or recurring motifs in the amino acid sequence of the HCV hypervariable region 1 (HVR1) may be associated with cryoglobulinemia. We searched for specific insertions/deletions and/or amino acid motifs within HVR1 in samples from 80 symptomatic and asymptomatic patients with and 33 patients without detectable cryoglobulins, all with chronic HCV infection. At variance with the results of a previous study which reported a high frequency of insertions at position 385 of HVR1 from cryoglobulinemic patients, we found a 6.2% prevalence of insertions in samples from patients with and a 9.1% prevalence in those without cryoglobulinemia. Moreover, statistical and bioinformatics approaches including Fisher's exact test, k-means clustering, Tree determinant-residue identification, correlation of mutations, principal component analysis, and phylogenetic analysis failed to show statistically significant differences between sequences from cryoglobulin-negative and -positive patients. Our findings suggest that cryoglobulinemia may arise by virtue of as-yet-unidentified host- rather than virus-specific factors. Specific changes in HCV envelope sequence distribution are unlikely to be directly involved in the establishment of pathological B-cell monoclonal proliferation.     

Water quality and diversity of the Recent ostracod fauna in lowland springs from Lombardy (northern Italy)

Sedimentary records provide important information for understanding changes in the history of eutrophication in Lake Taihu. In addition, the catchment nutrient model SWAT provides a powerful tool to examine eutrophic changes in a long-term context. Since it is difficult to evaluate impacts of natural eutrophic development and anthropogenic changes in catchment discharge and land use, simulation of past changes provides a mirror on processes and dynamics. Boundaries in the simulations are set to a pre-industrial time to evaluate natural-agricultural nutrient changes in Taihu Basin a 100 years ago. Total nitrogen (TN) and total phosphorus (TP) in the main channel flowing into the lake are simulated in four sub-basins for 200 model years. Results show that modeling can capture basic features of basin nutrient development, where mean TN concentration (0.12 mg l⁻¹) can be compared in broad scale to mean TN concentration (0.17 mg kg⁻¹) from Lake Taihu sedimentary cores dating back about 100 years. Spatial nutrient simulations suggest that the two major nutrient sources are from the southwestern sub-basin (48% TN and 68% TP of the basin total) and the northwestern sub-basin (18% TN and 17% TP). There are differences of +7.3 × 10⁴ kg TN and +2.0 × 10⁵ kg TP between total input and output values, simulating mean annual amounts of nutrient deposited into the lake. TN and TP concentration differences between input and output sub-basins become smaller in the second 100 years than the first 100 years, suggesting a 100 year period to reach a balance of net nutrients. Catchment nutrient modeling provides a basis to evaluate how nutrient production and balance responded to environmental changes over 200 years in Taihu Basin.     

Insertion of a magnesium(II)-octacarboranyl(hexylsulfanyl) porphyrazine into liposomes: a physico-chemical study

The synthesis, characterization and liposome insertion of a novel magnesium(II) carboranyl-porphyrazine, i.e. [2,3,7,8,12,13,17,18-octakis-(1,2-dicarba-closo-dodecaboranyl)-hexylthio-5,10,15,20-porphyrazine]magnesium(II) complex, MgHECSPz, are described. MgHECSPz was designed to improve the potentiality in multiple approach anticancer therapy. Liposomal formulations with different surface charge were prepared as delivering agents. The obtained loaded vectors were characterized by DLS, SAXS, SANS and zeta potential measurements in order to define the overall properties and structural details of loaded liposomes.     

Lysine 58-cleaved beta2-microglobulin is not detectable by 2D electrophoresis in ex vivo amyloid fibrils of two patients affected by dialysis-related amyloidosis

The lysine 58 cleaved and truncated variant of beta(2)-microglobulin (DeltaK58-beta2m) is conformationally unstable and present in the circulation of a large percentage of patients on chronic hemodialysis, suggesting that it could play a role in the beta2-microglobulin (beta2m) amyloid fibrillogenesis associated with dialysis-related amyloidosis (DRA). However, it has yet to be detected in the amyloid deposits of such patients. Here, we extracted amyloid fibrils, without denaturation or additional purification, from different amyloidotic tissues of two unrelated individuals suffering from DRA, and characterized them by high-sensitivity bidimensional gel electrophoresis (2D-PAGE), immunoblotting, MALDI time-of-flight mass spectrometry, and protein sequencing. To confirm whether or not this species could be identified by our proteomic approaches, we mapped its location in 2D-PAGE, in mixtures of pure DeltaK58-beta2m, and extracts of amyloid fibrils from patients, to a discrete region of the gel distinct from other isoforms of beta2m. Using this approach, the two known principal isoforms found in beta2m amyloid were identified, namely, the full-length protein and the truncated species lacking six N-terminal amino acid residues (DeltaN6-beta2m). In contrast, we found no evidence for the presence of DeltaK58-beta2m.