Soil bacterial assemblage responses to wildfire in low elevation southern California habitats.

Understanding how wildfires and modification in plant assemblages interact to influence soil bacteria assemblages is a crucial step in understanding how these disturbances may influence ecosystem structure and function. Here, we resampled soil from three study sites previously surveyed in spring 2016 and 2017 and compared soil bacterial assemblages prior to and six months after (spring 2019) the 2018 Woolsey Fire in the Santa Monica Mountain National Recreation Area using Illumina sequencing of the 16S rRNA gene. All sites harbored both native California sage scrub and a non-native (grassland or forbland) habitat, allowing us to examine how fire influenced bacterial assemblages in common southern California habitats. Most results contrasted with our a-priori hypotheses: (1) richness and diversity increased following the fire, (2) heat/drought resistant and sensitive bacteria did not show consistent and differing patterns by increasing and decreasing, respectively, in relative abundance after the fire, and (3) bacterial assemblage structure was only minimally impacted by fire, with no differences being found between 2017 (pre-fire) and 2019 (post-fire) in three of the six habitats sampled. As sage scrub and non-native grasslands consistently harbored unique bacterial assemblages both before and following the fire, modifications in plant compositions will likely have legacy effects on these soils that persist even after a fire. Combined, our results demonstrate that bacterial assemblages in southern California habitats are minimally affected by fire. Because direct impacts of fire are limited, but indirect impacts, e.g., modifications in plant compositions, are significant, plant restoration efforts following a fire should strive to revegetate sage scrub areas to prevent legacy changes in bacterial composition.

Structural and Kinetic Characterization of Hyperthermophilic NADH-Dependent Persulfide Reductase from Archaeoglobus fulgidus.

NADH-dependent persulfide reductase (Npsr) has been proposed to facilitate dissimilatory sulfur respiration by reducing persulfide or sulfane sulfur-containing substrates to H2S. The presence of this gene in the sulfate and thiosulfate-reducing Archaeoglobus fulgidus DSM 4304 and other hyperthermophilic Archaeoglobales appears anomalous, as A. fulgidus is unable to respire S0 and grow in the presence of elemental sulfur. To assess the role of Npsr in the sulfur metabolism of A. fulgidus DSM 4304, the Npsr from A. fulgidus was characterized. AfNpsr is specific for persulfide and polysulfide as substrates in the oxidative half-reaction, exhibiting k cat/K m on the order of 104 M-1 s-1, which is similar to the kinetic parameters observed for hyperthermophilic CoA persulfide reductases. In contrast to the bacterial Npsr, AfNpsr exhibits low disulfide reductase activity with DTNB; however, similar to the bacterial enzymes, it does not show detectable activity with CoA-disulfide, oxidized glutathione, or cystine. The 3.1 Å X-ray structure of AfNpsr reveals access to the tightly bound catalytic CoA, and the active site Cys 42 is restricted by a flexible loop (residues 60-66) that is not seen in the bacterial homologs from Shewanella loihica PV-4 and Bacillus anthracis. Unlike the bacterial enzymes, AfNpsr exhibits NADH oxidase activity and also shows no detectable activity with NADPH. Models suggest steric and electrostatic repulsions of the NADPH 2'-phosphate account for the strong preference for NADH. The presence of Npsr in the nonsulfur-reducing A. fulgidus suggests that the enzyme may offer some protection against S0 or serve in another metabolic role that has yet to be identified.

Sulfur-dependent microbial lifestyles: deceptively flexible roles for biochemically versatile enzymes.

A wide group of microbes are able to "make a living" on Earth by basing their energetic metabolism on inorganic sulfur compounds. Because of their range of stable redox states, sulfur and inorganic sulfur compounds can be utilized as either oxidants or reductants in a diverse array of energy-conserving reactions. In this review the major enzymes and basic chemistry of sulfur-based respiration and chemolithotrophy are outlined. The reversibility and versatility of these enzymes, however, means that they can often be used in multiple ways, and several cases are discussed in which enzymes which are considered to be hallmarks of a particular respiratory or lithotrophic process have been found to be used in other, often opposing, metabolic processes. These results emphasize the importance of taking into account the geochemistry, biochemistry and microbiology of an organism and/or environment when trying to interpret the function of a particular sulfur-dependent redox enzyme.

A broader active site in Pyrococcus horikoshii CoA disulfide reductase accommodates larger substrates and reveals evidence of subunit asymmetry.

Within the family of pyridine nucleotide disulfide oxidoreductase (PNDOR), enzymes are a group of single-cysteine containing FAD-dependent reductases that utilize a tightly bound coenzyme A to assist in the NAD(P)H-dependent reduction of di-, per-, and polysulfide substrates in bacteria and archaea. For many of these homodimeric enzymes, it has proved difficult to determine the substrate specificity and metabolic function based on sequence and genome analysis alone. Coenzyme A-disulfide reductase (CoADR) isolated from Pyrococcus horikoshii (phCoADR) reduces Co-A per- and polysulfides, but, unlike other highly homologous members of this group, is a poor CoA disulfide reductase. The phCoADR structure has a narrower access channel for CoA substrates, which suggested that this restriction might be responsible for the enzyme's poor activity toward the bulky CoA disulfide substrate. To test this hypothesis, the substrate channel was widened by making four mutations along the channel wall (Y65A, Y66A, P67G, and H367G). The structure of the quadruple mutant shows a widened substrate channel, which is supported by a fourfold increase in kcat for the NAD(P)H-dependent reduction of CoA disulfide and enhanced activity toward the substrate at lower temperatures. Anaerobic titrations of the enzyme with NADH revealed a half-site reactivity not observed with the wild-type enzyme in which one subunit of the enzyme could be fully reduced to an EH4 state, while the other remained in an EH2 or EH2·NADH state. These results suggest that for these closely related enzymes, substrate channel morphology is an important determinant of substrate specificity, and homology modeling will be the preferred technique for predicting function among PNDORs.

A Randomized, Open-Label Phase 2 Study of the CXCR4 Inhibitor LY2510924 in Combination with Sunitinib Versus Sunitinib Alone in Patients with Metastatic Renal Cell Carcinoma (RCC).

PURPOSE: The chemokine (C-X-C Motif) receptor 4 (CXCR4) and its ligand, stromal-cell derived factor-1 (SDF-1), are frequently overexpressed in a variety of solid tumors, and are believed to play important roles in the regulation of organ-specific metastasis, tumor growth, invasion, and survival. In this randomized Phase 2 trial, we evaluated the safety and efficacy of LY2510924 (LY), a peptide antagonist of CXCR4, combined with sunitinib (SUN) in the first-line treatment of advanced renal cell carcinoma (RCC). PATIENTS AND METHODS: Eligible patients were randomized (2:1) to receive LY (20 mg SC daily) + SUN (50 mg PO daily for 4 weeks followed by 2 weeks off) or SUN alone. Response was assessed after two cycles; patients continued treatment until tumor progression or intolerable toxicity. The study was powered to detect a 47 % increase in median progression-free survival (PFS). RESULTS: One hundred eight patients were randomized and treated (LY + SUN, 72; SUN, 36); median duration of treatment of five cycles. Observed median PFS was 8.1 months with LY + SUN and 12.3 months with SUN; Bayesian time-to-event HR 1.23; 95 % credible interval: 0.74, 1.96. LY was well tolerated; the toxicity profile was typical of SUN. No efficacy differences were seen between treatments groups when subsets with high versus low levels of CXCR4 tumor expression were compared. CONCLUSIONS: The addition of LY to SUN in the first-line treatment of metastatic RCC was well tolerated, but did not improve the PFS or overall survival (OS) vs. SUN alone. CXCR4 remains an unproven therapeutic target for the treatment of RCC. GOV IDENTIFIER: NCT01391130.

Characterization of the mechanism of the NADH-dependent polysulfide reductase (Npsr) from Shewanella loihica PV-4: formation of a productive NADH-enzyme complex and its role in the general mechanism of NADH and FAD-dependent enzymes.

The NADH-dependent polysulfide reductase (Npsr) from Shewanella loihica PV-4 is a member of the single cysteine-containing subset of the family of disulfide reductases represented by glutathione reductase. We have determined the kinetics of the reductive half-reaction of the enzyme with NADH using stopped-flow spectroscopy and kinetic isotope effects, and these results indicate that the reductive and oxidative half-reactions are both partially rate-limiting for enzyme turnover. During reaction with NADH, the reduced nucleotide appears to bind rapidly in an unproductive conformation, followed by the formation of a productive E·NADH complex and subsequent electron transfer to FAD. F161 of Npsr fills the space in which the nicotinamide ring of NADH would be expected to bind. We have shown that while this residue is not absolutely required for catalysis, it does assist in the forward commitment to catalysis through its role in the reductive half reaction, where it appears to enhance hydride transfer in the productive E·NADH complex. While the fluorescence and absorbance spectra of the stable redox forms of the wild-type and F161A mutant enzymes are similar, intermediates formed during reduction and turnover have different characteristics and appear to indicate that the enzyme-NADH complex formed just prior to hydride transfer on the F161A enzyme has weaker FAD-NADH interactions than the wild-type enzyme, consistent with a "looser" enzyme-NADH complex. The 2.7Å crystal structure of the F161A mutant was determined, and shows that the nicotinamide ring of NADH would have the expected freedom of motion in the more open NADH binding cavity.

Pazopanib as second-line treatment after sunitinib or bevacizumab in patients with advanced renal cell carcinoma: a Sarah Cannon Oncology Research Consortium Phase II Trial.

BACKGROUND: This phase II trial examined the activity and toxicity of second-line treatment with pazopanib after failure of first-line single-agent treatment with sunitinib or bevacizumab in patients with advanced clear cell renal carcinoma. PATIENTS AND METHODS: Fifty-five patients with metastatic clear cell renal carcinoma who had previously received first-line treatment with sunitinib (39 patients) or bevacizumab (16 patients) were enrolled. Patients received pazopanib 800 mg orally daily and were evaluated for response after 8 weeks of treatment. Responses were measured using Response Evaluation Criteria in Solid Tumors (RECIST), version 1.0, and confirmed with repeated scans after 8 weeks. Patients with objective response or stable disease continued treatment until disease progression or unacceptable toxicity occurred. RESULTS: Fifteen of 55 patients (27%) had objective response to pazopanib. An additional 27 patients (49%) had stable disease, for a disease control rate of 76%. After a median follow-up of 16.7 months, the median progression-free survival for the entire group was 7.5 months (95% confidence interval, 5.4-9.4 months). Similar progression-free survival was observed regardless of whether previous treatment was with sunitinib or bevacizumab. The estimated overall survival rate for the entire group at 24 months was 43%. CONCLUSION: Pazopanib is an active agent for the treatment of advanced clear cell renal carcinoma, even after failure of sunitinib or bevacizumab. Treatment with pazopanib should be considered early in the sequence of therapy for patients with advanced renal cell carcinoma.

Structure and substrate specificity of the pyrococcal coenzyme A disulfide reductases/polysulfide reductases (CoADR/Psr): implications for S(0)-based respiration and a sulfur-dependent antioxidant system in Pyrococcus.

FAD and NAD(P)H-dependent coenzyme A disulfide reductases/polysulfide reductases (CoADR/Psr) have been proposed to be important for the reduction of sulfur and disulfides in the sulfur-reducing anaerobic hyperthermophiles Pyrococcus horikoshii and Pyrococcus furiosus; however, the form(s) of sulfur that the enzyme actually reduces are not clear. Here we determined the structure for the FAD- and coenzyme A-containing holoenzyme from P. horikoshii to 2.7 Å resolution and characterized its substrate specificity. The enzyme is relatively promiscuous and reduces a range of disulfide, persulfide, and polysulfide compounds. These results indicate that the likely in vivo substrates are NAD(P)H and di-, poly-, and persulfide derivatives of coenzyme A, although polysulfide itself is also efficiently reduced. The role of the enzyme in the reduction of elemental sulfur (S(8)) in situ is not, however, ruled out by these results, and the possible roles of this substrate are discussed. During aerobic persulfide reduction, rapid recycling of the persulfide substrate was observed, which is proposed to occur via sulfide oxidation by O(2) and/or H(2)O(2). As expected, this reaction disappears under anaerobic conditions and may explain observations by others that CoADR is not essential for S(0) respiration in Pyrococcus or Thermococcus but appears to participate in oxidative defense in the presence of S(0). When compared to the homologous Npsr enzyme from Shewanella loihica PV-4 and homologous enzymes known to reduce CoA disulfide, the phCoADR structure shows a relatively restricted substrate channel leading into the sulfur-reducing side of the FAD isoalloxazine ring, suggesting how this enzyme class may select for specific disulfide substrates.

Electron transfer reactivity of type zero Pseudomonas aeruginosa azurin.

Type zero copper is a hard-ligand analogue of the classical type 1 or blue site in copper proteins that function as electron transfer (ET) agents in photosynthesis and other biological processes. The EPR spectroscopic features of type zero Cu(II) are very similar to those of blue copper, although lacking the deep blue color, due to the absence of thiolate ligation. We have measured the rates of intramolecular ET from the pulse radiolytically generated C3-C26 disulfide radical anion to the Cu(II) in both type zero C112D/M121L and type 2 C112D Pseudomonas aeruginosa azurins in pH 7.0 aqueous solutions between 8 and 45 °C. We also have obtained rate/temperature (10-30 °C) profiles for ET reactions between these mutants and the wild-type azurin. Analysis of the rates and activation parameters for both intramolecular and intermolecular ET reactions indicates that the type zero copper reorganization energy falls in a range (0.9-1.1 eV) slightly above that for type 1 (0.7-0.8 eV), but substantially smaller than that for type 2 (>2 eV), consistent with XAS and EXAFS data that reveal minimal type zero site reorientation during redox cycling.

Characterization of an NADH-dependent persulfide reductase from Shewanella loihica PV-4: implications for the mechanism of sulfur respiration via FAD-dependent enzymes.

The NADH-dependent persulfide reductase (Npsr), a recently discovered member of the PNDOR family of flavoproteins that contains both the canonical flavoprotein reductase domain and a rhodanese domain, is proposed to be involved in the dissimilatory reduction of S(0) for Shewanella loihica PV-4. We have previously shown that polysulfide is a substrate for this enzyme, and a recently determined structure of a closely related enzyme (CoADR-Rhod from Bacillus anthracis) suggested the importance of a bound coenzyme A in the mechanism. The work described here shows that the in vivo oxidizing substrates of Npsr are the persulfides of small thiols such as CoA and glutathione. C43S, C531S, and C43,531S mutants were created to determine the role of the flavoprotein domain cysteine (C43) and the rhodanese domain cysteine (C531) in the mechanism. The absolute requirement for C43 in persulfide or DTNB reductase activity shows that this residue is involved in S-S bond breakage. C531 contributes to, but is not required for, catalysis of DTNB reduction, while it is absolutely required for reduction of any persulfide substrates. Titrations of the enzyme with NADH, dithionite, titanium(III), or TCEP demonstrate the presence of a mixed-disulfide between C43 and a tightly bound CoA, and structures of the C43 and C43,531S mutants confirm that this coenzyme A remains tightly bound to the enzyme in the absence of a C43-CoA S-S bond. The structure of Npsr suggests a likely site for binding and reaction with the persulfide substrate on the rhodanese domain. On the basis of kinetic, titration, and structural data, a mechanism for the reduction of persulfides by Npsr is proposed.

Cancer in nonagenarians: profile, treatments and outcomes.

An increasing number of nonagenarians are treated for cancer. However, very few data are available to guide treatment choices in this often frail population. The charts of all patients registered at Moffitt Cancer Center between 1993 and 2006 who were aged 90 or older at the time of treatment/evaluation were reviewed, and those treated for an active cancer (n=177) were included in the analysis. For 23.5% of patients, the index cancer was a second malignancy. Initial treatments were: surgery 41%, chemotherapy 9%, radiation therapy 15%, concomitant chemo-radiation therapy 2%, hormonal therapy 12%, targeted therapy 8%, photodynamic therapy 1%, observation/supportive care 3%, hospice 9%. The median survival was 1.69 years [95% CI=1.34, 2.17, range 0.1-6.21]. For early stage cancer it was 2.02 years [95% CI=1.56, 2.87], and for advanced stage cancer, 1.06 years [95% CI=0.58, 1.63] (p=0.02 by log-rank). Treatment related mortality was low (1.1%). In conclusion, our nonagenarians underwent a broad range of treatments with low treatment related mortality. Advanced cancer still limits the survival of nonagenarians. Second cancers are frequent in older cancer survivors.

Single agent vinflunine in the salvage treatment of patients with castration-resistant prostate cancer: a phase II trial of the Sarah Cannon research consortium.

Patients with metastatic prostate cancer resistant to hormones and docetaxel were treated with vinflunine (320 mg/m(2) every 21 days), a new vinca alkaloid with improved preclinical activity. Only 1 of 36 patients (3%) had partial response; the median progression-free survival (PFS) was 2.1 months. Treatment was well tolerated, with myelosuppression as the only frequent toxicity. Vinflunine has a low level of activity in the treatment of refractory metastatic prostate cancer, and should not be further developed for this indication.

WITHDRAWN: Cancer in nonagenarians: Profile, treatments and outcomes.

This article has been withdrawn with the permission of the authors, it has been published in volume1, issue 1 of the Journal of Geriatric Oncology (www.geriatriconcology.net). The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.

Shewanella and Photobacterium spp. in oysters and seawater from the Delaware Bay.

Shewanella algae, S. putrefaciens, and Photobacterium damselae subsp. damselae are indigenous marine bacteria and human pathogens causing cellulitis, necrotizing fasciitis, abscesses, septicemia, and death. Infections are rare and are most often associated with the immunocompromised host. A study was performed on the microbiological flora of oysters and seawater from commercial oyster harvesting sites in the Delaware Bay, New Jersey. From 276 water and shellfish samples tested, 1,421 bacterial isolates were picked for biochemical identification and 170 (12.0%) of the isolates were presumptively identified as S. putrefaciens, 26 (1.8%) were presumptively identified as P. damselae subsp. damselae, and 665 (46.8%) could not be identified using the API 20E identification database. Sequencing of the 16S rRNA genes of 22 S. putrefaciens-like isolates identified them as S. abalonesis, S. algae, S. baltica, S. hafniensis, S. marisflavi, S. putrefaciens, Listonella anguillarum, and P. damselae. Beta-hemolysis was produced by some S. algae and P. damselae isolates, while isolates of S. baltica and L. anguillarum, species perceived as nonpathogenic, also exhibited beta-hemolysis and growth at 37 degrees C. To our knowledge, this is the first time these beta-hemolytic strains were reported from shellfish or seawater from the Delaware Bay. Pathogenic Shewanella and Photobacterium species could pose a health threat through the ingestion of contaminated seafood, by cuts or abrasions acquired in the marine environment, or by swimming and other recreational activities.

Borrelia burgdorferi bb0728 encodes a coenzyme A disulphide reductase whose function suggests a role in intracellular redox and the oxidative stress response.

The cellular responses of Borrelia burgdorferiTo reactive oxygen species (ROS) encountered during the different stages of its infective cycle are poorly understood. Few enzymes responsible for protecting proteins, DNA/RNA and lipids from damage by ROS have been identified and characterized. Data presented here suggest that bb0728 encodes an enzyme involved in this process. Biochemical analyses on purified recombinant BB0728 indicated that it functioned as a coenzyme A disulphide reductase (CoADR) (specific activity approximately 26 units per mg of protein). This enzyme was specific for coenzyme A (CoA) disulphide, required NADH and had no significant activity against other disulphides, such as oxidized glutathione or thioredoxin. The high intracellular concentration of reduced CoA (CoASH) in B. burgdorferi cells ( approximately 1 mM) and absence of glutathione suggest that CoA is the major low-molecular-weight thiol in this spirochete. Interestingly, CoASH was able to reduce H(2)O(2) and be regenerated by CoADR suggesting one role for the system may be to protect B. burgdorferi from ROS. Further, mobility-shift assays and transcriptional fusion data indicated that bb0728 was positively regulated by the Borrelia oxidative stress response regulator, BosR. Taken together, these data suggest a role for BB0728 in intracellular redox and the oxidative stress response in B. burgdorferi.

Adjuvant chemotherapy for non-small cell lung cancer.

Studies of adjuvant chemotherapy for non-small cell lung cancer (NSCLC) did not provide a consistent disease-free survival or overall survival benefit in the 1980s and early 1990s. However, recently reported studies have changed the practice of NSCLC treatment, for which adjuvant chemotherapy is now considered the standard of care. This review outlines the issues that may have limited the detection of beneficial effects of adjuvant chemotherapy in early trials and provides detailed analysis of the results of recently published trials of adjuvant chemotherapy for NSCLC.

Determination of coenzyme A levels in Pyrococcus furiosus and other Archaea: implications for a general role for coenzyme A in thermophiles.

Physiologically significant levels of intracellular coenzyme A were identified in Pyrococcus furiosus, Thermococcus litoralis, and Sulfolobus solfataricus, suggesting a role for CoA as an important low molecular mass thiol in the thermophilic Archaea. In P. furiosus, cells grown in the presence of sulfur showed significantly higher levels of oxidized CoA compared with those grown in the absence of S(0). T. litoralis showed strikingly similar CoA levels, although with low disulfide levels in both the presence and absence of S(0). S. solfataricus showed similarly high levels of CoA thiol, with correspondingly low levels of the CoA disulfide. These results are consistent with the identification of a coenzyme A disulfide reductase (CoADR) in P. furiosus and horikoshii as well as the presence of CoADR homologues in the genomes of S. solfataricus and T. kodakaraensis.

Discovery and characterization of a Coenzyme A disulfide reductase from Pyrococcus horikoshii. Implications for this disulfide metabolism of anaerobic hyperthermophiles.

We have cloned NADH oxidase homologues from Pyrococcus horikoshii and P. furiosus, and purified the recombinant form of the P. horikoshii enzyme to homogeneity from Escherichia coli. Both enzymes (previously referred to as NOX2) have been shown to act as a coenzyme A disulfide reductases (CoADR: CoA-S-S-CoA + NAD(P)H + H+-->2CoA-SH + NAD(P)+). The P. horikoshii enzyme shows a kcat app of 7.2 s(-1) with NADPH at 75 degrees C. While the enzyme shows a preference for NADPH, it is able to use both NADPH and NADH efficiently, with both giving roughly equal kcats, while the Km for NADPH is roughly eightfold lower than that for NADH. The enzyme is specific for the CoA disulfide, and does not show significant reductase activity with other disulfides, including dephospho-CoA. Anaerobic reductive titration of the enzyme with NAD(P)H proceeds in two stages, with an apparent initial reduction of a nonflavin redox center with the first reduction resulting in what appears to be an EH2 form of the enzyme. Addition of a second of NADPH results in the formation of an apparent FAD-NAD(P)H complex. The behavior of this enzyme is quite different from the mesophilic staphylococcal version of the enzyme. This is only the second enzyme with this activity discovered, and the first from a strict anaerobe, an Archaea, or hyperthermophilic source. P. furiosus cells were assayed for small molecular mass thiols and found to contain 0.64 micromol CoA.g dry weight(-1) (corresponding to 210 microM CoA in the cell) consistent with CoA acting as a pool of disulfide reducing equivalents.