Perchlorate and nitrate remediation efficiency and microbial diversity in a containerized wetland bioreactor

We have developed a method to remove perchlorate (14-27 microg/L) and nitrate (48 mg/L) from contaminated groundwater using a wetland bioreactor. The bioreactor has operated continuously in a remote field location for more than 2 yr with a stable ecosystem of indigenous organisms. This study assesses the bioreactorfor long-term perchlorate and nitrate remediation by evaluating influent and effluent groundwater for oxidation-reduction conditions and nitrate and perchlorate concentrations. Total community DNA was extracted and purified from 10-g sediment samples retrieved from vertical coring of the bioreactor during winter. Analysis by denaturing gradient gel electrophoresis of short, 16S rDNA, polymerase-chainreaction products was used to identify dominant microorganisms. Bacteria genera identified were closely affiliated with bacteria widely distributed in soils, mud layers, and fresh water. Of the 17 dominant bands sequenced, most were gram negative and capable of aerobic or anaerobic respiration with nitrate as the terminal electron acceptor (Pseudomonas, Acinetobacter, Halomonas, and Nitrospira). Several identified genera (Rhizobium, Acinetobactor, and Xanthomonas) are capable of fixing atmospheric nitrogen into a combined form (ammonia) usable by host plants. Isolates were identified from the Proteobacteria class, known for the ability to reduce perchlorate. Initial bacterial assessments of sediments confirm the prevalence of facultative anaerobic bacteria capable of reducing perchlorate and nitrate in situ.     

High-affinity near-infrared fluorescent small-molecule contrast agents for in vivo imaging of prostate-specific membrane antigen

Surgical resection remains a definitive treatment for prostate cancer. Yet, prostate cancer surgery is performed without image guidance for tumor margin, extension beyond the capsule and lymph node positivity, and without verification of other occult metastases in the surgical field. Recently, several imaging systems have been described that exploit near-infrared (NIR) fluorescent light for sensitive, real-time detection of disease pathology intraoperatively. In this study, we describe a high-affinity (9 nM), single nucleophile-containing, small molecule specific for the active site of the enzyme PSMA. We demonstrate production of a tetra-sulfonated heptamethine indocyanine NIR fluorescent derivative of this molecule using a high-yield LC/MS purification strategy. Interestingly, NIR fluorophore conjugation improves affinity over 20-fold, and we provide mechanistic insight into this observation. We describe the preparative production of enzymatically active PSMA using a baculovirus expression system and an adenovirus that co-expresses PSMA and GFP. We demonstrate sensitive and specific in vitro imaging of endogenous and ectopically expressed PSMA in human cells and in vivo imaging of xenograft tumors. We also discuss chemical strategies for improving performance even further. Taken together, this study describes nearly complete preclinical development of an optically based small-molecule contrast agent for image-guided surgery.     

Seasonal temperature compensation in the horse mussel, Modiolus modiolus: metabolic enzymes, oxidative stress and heat shock proteins

Seasonal collections of the subtidal horse mussel, Modiolus modiolus, from a depth of 10 m were made at the Isles of Shoals, New Hampshire to assess changes in overall energetic demand, measured as respiration, the maximal activities of rate-limiting enzymes of intermediate metabolism, level of oxidative stress, and the expression of heat shock proteins (HSP). Weighted respiration rates of mussels from winter collections were significantly lower than summer rates but decreased by less than 20%. Specific activities of several rate-limiting enzymes were measured in mussels from the summer and winter collections at the temperature of collection and the reciprocal seasonal temperature (15 and 5 degrees C). Comparisons of these enzyme activities and the protein concentrations of hexokinase and citrate synthase show that a quantitative strategy is used to acclimatize to winter temperatures by these rate-limiting enzymes of intermediate metabolism. The activities and protein concentrations of the antioxidant enzyme, Cu/Zn superoxide dismutase (SOD) is seasonally indistinguishable while the concentration of HSP 70 was greater in winter than in summer samples. These results show that mussels seasonally compensate for decreases in temperature by increasing the concentration of rate-limiting metabolic enzymes while maintaining the same level of antioxidant protection in summer and winter consistent with high aerobic metabolism in both winter and summer. Lastly, the significantly greater concentrations of HSP70 in winter samples suggests that protein chaperone functions must be maintained while other seasonal adjustments to cold temperatures are occurring.     

Improving signal intensities for genes with low-expression on oligonucleotide microarrays

Background  

DNA microarrays using long oligonucleotide probes are widely used to evaluate gene expression in biological samples. These oligonucleotides are pre-synthesized and sequence-optimized to represent specific genes with minimal cross-hybridization to homologous genes. Probe length and concentration are critical factors for signal sensitivity, particularly when genes with various expression levels are being tested. We evaluated the effects of oligonucleotide probe length and concentration on signal intensity measurements of the expression levels of genes in a target sample.     

Microwave-assisted synthesis of novel thiazolocarbazoles and evaluation as potential anticancer agents. Part III

Novel 6-substituted thiazolocarbazole derivatives have been synthesized under microwave irradiation via the corresponding imino-1,2,3-dithiazoles. In vitro antitumor potential of these polyheterocyclic compounds was evaluated. Among all the tested thiazolocarbazoles, compound 10 is the most effective in inhibiting cell growth.     

Synthesis and cytotoxic activity of thiazolofluorenone derivatives

The synthesis and biological evaluation of some novel thiazolofluorenones, thiazolofluorenes and thiazoloanthraquinones, substituted with amino side-chains are described. These polyheterocyclic compounds have been synthesized via the corresponding imino-1,2,3-dithiazoles. Their cytotoxic activity and their eventual selective effect on a phase of the cell cycle were evaluated in vitro, using the murine lymphocytic L1210 leukaemia cell line.     

Probing the energy landscape of protein folding/unfolding transition states

Previous molecular dynamics (MD) simulations of the thermal denaturation of chymotrypsin inhibitor 2 (CI2) have provided atomic-resolution models of the transition state ensemble that is well supported by experimental studies. Here, we use simulations to further investigate the energy landscape around the transition state region. Nine structures within approximately 35 ps and 3 A C(alpha) RMSD of the transition state ensemble identified in a previous 498 K thermal denaturation simulation were quenched under the quasi-native conditions of 335 K and neutral pH. All of the structures underwent hydrophobically driven collapse in response to the drop in temperature. Structures less denatured than the transition state became structurally more native-like, while structures that were more denatured than the transition state tended to show additional loss of native structure. The structures in the immediate region of the transition state fluctuated between becoming more and less native-like. All of the starting structures had the same native-like topology and were quite similar (within 3.5 A C(alpha) RMSD). That the structures all shared native-like topology, yet diverged into either more or less native-like structures depending on which side of the transition state they occupied on the unfolding trajectory, indicates that topology alone does not dictate protein folding. Instead, our results suggest that a detailed interplay of packing interactions and interactions with water determine whether a partially denatured protein will become more native-like under refolding conditions.     

Increasing temperature accelerates protein unfolding without changing the pathway of unfolding

We have traditionally relied on extremely elevated temperatures (498K, 225 degrees C) to investigate the unfolding process of proteins within the timescale available to molecular dynamics simulations with explicit solvent. However, recent advances in computer hardware have allowed us to extend our thermal denaturation studies to much lower temperatures. Here we describe the results of simulations of chymotrypsin inhibitor 2 at seven temperatures, ranging from 298K to 498K. The simulation lengths vary from 94ns to 20ns, for a total simulation time of 344ns, or 0.34 micros. At 298K, the protein is very stable over the full 50ns simulation. At 348K, corresponding to the experimentally observed melting temperature of CI2, the protein unfolds over the first 25ns, explores partially unfolded conformations for 20ns, and then refolds over the last 35ns. Above its melting temperature, complete thermal denaturation occurs in an activated process. Early unfolding is characterized by sliding or breathing motions in the protein core, leading to an unfolding transition state with a weakened core and some loss of secondary structure. After the unfolding transition, the core contacts are rapidly lost as the protein passes on to the fully denatured ensemble. While the overall character and order of events in the unfolding process are well conserved across temperatures, there are substantial differences in the timescales over which these events take place. We conclude that 498K simulations are suitable for elucidating the details of protein unfolding at a minimum of computational expense.     

Expression of cyclooxygenases 1 and 2 and prostaglandin E synthase in bovine endometrial tissue during the estrous cycle

In ruminants, endometrial prostaglandin F(2alpha) (PGF(2alpha)) is responsible for luteolysis and prostaglandin E(2) (PGE(2)) is thought to be involved in maternal recognition of pregnancy. In the present study, healthy uteri were collected from cows at the abattoir, and days of the estrous cycle were determined macroscopically. The uteri were classified into seven groups as Days 1-3, 4-6, 7-9, 10-12, 13-15, 16-18, and 19-21 of the estrous cycle. Endometrial scrapings were collected. The expression of cyclooxygenase (COX)-1 and COX-2 mRNAs and proteins and PGE synthase (PGES) mRNA was analyzed by Northern and Western blot. There was no expression of COX-1, either mRNA or protein, on any day of the estrous cycle. In contrast, COX-2 mRNA and protein were expressed at low and high levels on Days 1-12 and 13-21 of the estrous cycle, respectively. The level of expression of PGES was moderate, low, and high on Days 1-3, 4-12, and 13-21 of the estrous cycle, respectively. There were significant correlations between COX-2 mRNA and protein levels and between COX-2 and PGES mRNA levels. COX-1 mRNA and protein are not expressed on any day of the estrous cycle, whereas COX-2 mRNA and protein and PGES mRNA are differentially expressed and regulated in bovine endometrium during the estrous cycle. COX-2, rather than COX-1, is the primary isoenzyme involved in the endometrial production of prostaglandins, and the COX-2 and PGES pathway is responsible for the endometrial production of PGE(2) in the bovine endometrium during the estrous cycle.     

The Deoxyxylulose Phosphate Pathway for the Biosynthesis of Plastidic Isoprenoids: Early Days in Our Understanding of the Early Stages of Gibberellin Biosynthesis

The identification of a novel pathway for isopentenyl diphosphate synthesis by Rohmer, Arigoni and colleagues in the early 1990's has led to a reappraisal of terpenoid biosynthesis in many organisms. It is now apparent that in plants there are two biosynthetic routes to isopentenyl diphosphate-the classical mevalonate pathway in the cytosol and the deoxyxylulose phosphate pathway in plastids. Sesquiterpenoids and sterols are predominantly synthesized in the cytosol by the mevalonate pathway whereas monoterpenoids, diterpenoids, the phytol side-chain of chlorophyll, carotenoids, and the nonaprenyl side-chain of plastoquinone-9 are synthesized within plastids by the deoxyxylulose phosphate pathway. Our assumptions that the early stages of gibberellin biosynthesis are plastid-localized has led to several attempts to demonstrate that the deoxyxylulose phosphate pathway is the biosynthetic route to gibberellins. Although definitive evidence is still not available there is a growing body of evidence, mostly from transgenic plants and from the use of the inhibitor, fosmidomycin, that gibberellins are synthesized from deoxyxylulose phosphate-derived isopentenyl diphosphate. However, there is evidence that a small amount of cross-talk between the two pathways may occur, implying that the pathways are not totally autonomous. Implications for the regulation of the early stages of gibberellin biosynthesis are discussed.