Effects of freshwater release on oyster reef density, reproduction, and disease in a highly modified estuary.

Few estuaries remain unaffected by water management and altered freshwater deliveries. The Caloosahatchee River Estuary is a perfect case study for assessing the impact of altered hydrology on natural oyster reef (Crassostrea virginica) populations. The watershed has been highly modified and greatly enlarged by an artificial connection to Lake Okeechobee. Accordingly, to generate data to support water management recommendations, this study monitored various oyster biometrics over 15 years along the primary salinity gradient. Oyster reef densities were significantly affected by both prolonged high volume freshwater releases creating hyposaline conditions at upstream sites and by a lack of freshwater input creating hypersaline conditions at downstream sites. Low freshwater input led to an increase in disease caused by Perkinsus marinus and predation. Moderate (< 2000 cfs) and properly timed (winter/spring) freshets benefited oysters with increased gametogenesis, good larval mixing, and a reprieve from disease. If high volume freshets occurred in the late summer, extensive mortality occurred at the upstream site due to low salinity. These findings suggest freshwater releases in the late summer, when reproductive stress is at its peak and pelagic larvae are most vulnerable, should be limited to < 2000 cfs, but that longer freshets (1-3 weeks) in the winter and early spring (e.g., December-April) benefit oysters by reducing salinity and lessening disease intensity. Similar strategies can be employed in other managed systems, and patterns regarding the timing of high volume flows are applicable to all estuaries where the management of healthy oyster reefs is a priority.

High-resolution molecular identification of smalltooth sawfish prey.

The foundation of food web analysis is a solid understanding of predator-prey associations. Traditional dietary studies of fishes have been by stomach content analysis. However, these methods are not applicable to Critically Endangered species such as the smalltooth sawfish (Pristis pectinata). Previous research using the combination of stable isotope signatures from fin clips and 18S rRNA gene sequencing of fecal samples identified the smalltooth sawfish as piscivorous at low taxonomic resolution. Here, we present a high taxonomic resolution molecular technique for identification of prey using opportunistically acquired fecal samples. To assess potential biases, primer sets of two mitochondrial genes, 12S and 16S rRNA, were used alongside 18S rRNA, which targets a wider spectrum of taxa. In total, 19 fish taxa from 7 orders and 11 families native to the Gulf of Mexico were successfully identified. The sawfish prey comprised diverse taxa, indicating that this species is a generalist piscivore. These findings and the molecular approach used will aid recovery planning for the smalltooth sawfish and have the potential to reveal previously unknown predator-prey associations from a wide range of taxa, especially rare and hard to sample species.

Molecular cloning and expression of a 2-Cys peroxiredoxin gene in the crustacean Eurypanopeus depressus induced by acute hypo-osmotic stress.

Peroxiredoxins (Prxs) are a family of ubiquitous proteins that help minimize the harmful effects of oxidative stress by catalyzing the reduction of hydrogen peroxide (H2O2) and organic hydroperoxides to less harmful forms. A full-length cDNA corresponding to a 2-Cys Prx gene was isolated from the flatback mud crab Eurypanopeus depressus and designated as EdPrx-1 (GenBank accession no. EU684547). EdPrx-1 has a major open-reading frame of 594 bp and is capable of encoding a polypeptide of 198 amino acid residues. Like other 2-Cys Prxs, EdPrx-1 protein possesses two conserved cysteine residues that play an essential role for the antioxidant activity of the proteins. The EdPrx-1 protein, as deduced from the cDNA sequence, shows a high level (74-93%) of sequence similarity to the 2-Cys Prxs from other crustaceans as well as those from many arthropod species (73-76% similarity). It shares about 70% sequence similarity with homologs from mammalian species. EdPrx-1 gene is expressed at low level in the gill, hypodermis, and hepatopancreas tissues of the crab under non-stressed condition; however, its expression is elevated about three-fold in the gills under hypo-osmotic stress. This suggests a possible role in protecting against oxidative stress caused by the increased metabolic activities associated with hyperosmoregulation.

Influence of salinity on prevalence of the parasite Loxothylacus panopaei in the xanthid Panopeus obesus in SW Florida.

This study was conducted to examine the potential influence of salinity, a proxy for freshwater inflow, on the prevalence of the castrator parasite Loxothylacus panopaei on saltmarsh mud crabs Panopeus obesus on SW Florida oyster reefs. Spatial and seasonal patterns of the presence of potential host crabs and the prevalence of the parasite were assessed in the Caloosahatchee, Estero, and Faka Union estuaries. Lift nets (1 m2) containing 5 1 of oyster clusters were deployed on intertidal reefs at 3 sites along the salinity gradient of each estuary. Nets were deployed during 3 seasonally dry and 3 seasonally wet months for a period of 30 d. P. obesus densities tended to increase downstream in higher salinity waters, with crabs being absent from the upper station in the Caloosahatchee during both seasons and absent from the upper station of the Faka Union during wet months. Parasite prevalence was reduced upstream in each estuary during wet months compared to dry months, and for those estuaries that experienced higher relative levels of freshwater inflow. Furthermore, parasite prevalence was positively correlated with the mean salinity of capture of host crabs. Based on the distribution of P. obesus and the above patterns related to salinity, it appears that freshwater inflow and seasonal rains might regulate the prevalence of this parasite in SW Florida by creating spatiotemporal, low salinity refuges for its host.

Patient preferences versus physician perceptions of treatment decisions in cancer care.

PURPOSE: To examine patient preferences as well as physician perceptions of these preferences for decision making and communication in palliative care. PATIENTS AND METHODS: Medical decision-making preferences (DMPs) were prospectively studied in 78 assessable cancer patients after initial assessment at a palliative care outpatient clinic. DMPs were assessed with a questionnaire using five possible choices ranging from 1 (patient prefers to make the treatment decision) to 5 (patient prefers the physician to make the decision). In addition, the physician's perception of this preference was assessed. RESULTS: Full concordance between the physician and the patient was seen in 30 (38%) of 78 cases; when the five original categories were recombined to cover active, shared, and passive decision making, there was concordance in 35 (45%) of 78 cases. The kappa coefficient for agreement between physician and patient was poor at 0.14 (95% confidence limit, -0.01 to 0.30) for simple kappa and 0.17 (95% confidence interval [CI], 0.00 to 0.34) for weighted kappa (calculated on the three regrouped categories). Active, shared, and passive DMPs were chosen by 16 (20%) of 78, 49 (63%) of 78, and 13 (17%) of 78 patients, and by 23 (29%) of 78, 30 (39%) of 78, and 25 (32%) of 78 physicians, respectively. The majority of patients (49 [63%] of 78; 95% CI, 0.51 to 0.74) preferred a shared approach with physicians. Physicians predicted that patients preferred a less shared approach than they in fact did. Patient age or sex did not significantly alter DMP. CONCLUSION: An individual approach is needed and each patient should be assessed prospectively for DMP.

Novel translational model for breast cancer chemoprevention study: accrual to a presurgical intervention with tamoxifen and N-[4-hydroxyphenyl] retinamide.

Surrogate end point biomarkers for risk assessment and efficacy of potential chemopreventive agents are needed to improve the efficiency and reduce the cost of chemoprevention trials. It is imperative to develop the best clinical breast model for translational surrogate end point biomarker studies, especially with respect to accrual feasibility. We have initiated a prospective study to develop biomarkers for tamoxifen and N-[4-hydroxyphenyl] retinamide by administering either a placebo or both drugs for 2-4 weeks to women with ductal carcinoma in situ or early invasive cancers in the interval between the initial diagnostic core biopsy and definitive surgery. The principle end point is pretreatment versus posttreatment tumor levels of Ki-67; a number of other exploratory markers will also be examined. The planned target sample size is 100 patients. Between February 1997 and February 2000, 4514 women who had either an abnormal mammogram or a diagnosed breast cancer were screened for the study. Of these 4514 screened patients, 52 (1%) were registered on the study. Major factors of nonparticipation in the remaining 4462 women were as follows: (a) no evidence of malignancy (2081 patients; 46%); (b) ineligible per protocol criteria (575 patients; 13%); (c) preoperative chemotherapy/tamoxifen (520 patients; 11%); (d) surgery scheduling conflict (360 patients; 8%); (e) outside needle biopsy (221 patients; 5%); (f) no residual disease after excisional biopsy (345 patients; 8%); and (g) second opinion only (123 patients; 3%). Other nonparticipation factors included fine needle aspiration only, refusal, tumor size > 2 cm, and estrogen replacement therapy (35 patients each; 2% each). The protocol was amended in midstudy to allow outside needle biopsy, tumor > 2 cm, and estrogen replacement therapy. Accrual to biomarker (nontherapeutic) protocols with delay in definitive cancer surgery is challenging but feasible. Although some accrual problems remain, we have nonetheless succeeded in recruiting 50% of our target sample size in a 3-year period.

The correlation of axillary ultrasonography with histologic breast cancer downstaging after induction chemotherapy.

BACKGROUND: The goal of this study was to examine the role of ultrasonography in detecting axillary lymph node metastases in stage II breast cancer patients after induction chemotherapy (IC). METHODS: Of 172 consecutive patients with T1-3, N0-1, M0 breast cancer registered in a prospective IC trial, a subset of 130 evaluable patients were chosen, with (1) both physical and ultrasonographic examinations of the axilla before and after IC; (2) exactly four cycles of IC; (3) no presurgical radiation therapy; and (4) an axillary lymph node dissection. RESULTS: Before IC, 32 patients (25%) were negative for axillary involvement by both physical and ultrasonographic examinations. After IC, this number increased to 64 (49%). Of these, 31 (48%) were positive by pathology examination. In most cases, however, the residual tumor was minimal. CONCLUSIONS: Stage II breast cancer patients who were or became node negative by both ultrasonographic and physical examinations after IC had a 48% incidence of nodal metastases. Because the residual tumor was minimal, irradiation may be sufficient for adequate local control of the axilla.

A new crystal form of penicillin acylase from Escherichia coli.

A new crystal form of penicillin acylase (penicillin amidohydrolase, E.C. 3.5.1.11) from Escherichia coli W (ATCC 11105) is reported. The crystals were grown using a combination of hanging-drop and streak-seeding methods. The crystals are in the monoclinic space group P2(1) with cell dimensions a = 51.52, b = 131.95, c = 64.43 A, beta = 106.12 degrees. There is one heterodimer in the asymmetric unit (V(m) = 2.45 A(3) Da(-1)) and the solvent content is 49%. Preliminary data have been collected to d(min) = 2.7 A using a MAR Research image plate and a rotating-anode X-ray source. Subsequent experiments show diffraction beyond 1.3 A at a synchrotron radiation source.

Structure determination and refinement of the Humicola insolens endoglucanase V at 1.5 A resolution.

The structure of the catalytic core of the endoglucanase V (EGV) from Humicola insolens has been determined by the method of multiple isomorphous replacement at 1.5 A resolution. The final model, refined with X-PLOR and PROLSQ, has a crystallographic R factor of 0.163 (R(free) = 0.240) with deviations from stereochemical target values of 0.012 A and 0.037 degrees for bonds and angles, respectively. The model was further refined with SHELXL, including anisotropic modelling of the protein-atom temperature factors, to give a final model with an R factor of 0.105 and an R(free) of 0.154. The initial isomorphous replacement electron-density map was poor and uninterpretable but was improved by the use of synchrotron data collected at a wavelength chosen so as to optimize the f" contribution of the anomalous scattering from the heavy atoms. The structure of H. insolens EGV consists of a six-stranded beta-barrel domain, similar to that found in a family of plant defence proteins, linked by a number of disulfide-bonded loop regions. A long open groove runs across the surface of the enzyme either side of which lie the catalytic aspartate residues. The 9 A separation of the catalytic carboxylate groups is consistent with the observation that EGV catalyzes the hydrolysis of the cellulose, beta(1-->4) links with inversion of configuration at the anomeric C1 atom. This structure is the first representative from the glycosyl hydrolase family 45.

Structures of oligosaccharide-bound forms of the endoglucanase V from Humicola insolens at 1.9 A resolution.

Cellulose, a polymer of beta-1,4-linked glucose residues, is the major polysaccharide component of plant cell walls and the most abundant biopolymer. The underlying mechanisms of the enzymatic degradation of cellulose are of increasing commercial and ecological significance. Endoglucanase V, from the cellulolytic soil hyphomycete Humicola insolens, is an endocellulase, the catalytic core of which consists of 210 amino acids and is known to hydrolyze the beta-1,4 links with inversion of configuration at the anomeric carbon. The major products of cellulose hydrolysis are cellobiose and cellotriose. The crystal structures of the endoglucanase V (EGV) from H. insolens, in native, product (cellobiose), inactive mutant (D10N), and oligosaccharide-bound [(D10N)-cellohexaose] forms, have been determined at resolutions of 1.9 A or better. EGV consists of a six-stranded beta-barrel domain with long interconnecting loops. A 40 A groove exists along the surface of the enzyme, and this contains the catalytic residues, Asp 10 and Asp 121. The two catalytic aspartates sit to either side of the substrate binding groove in an ideal conformation for facilitating cleavage by inversion, their carboxyl groups being separated by approximately 8.5 A. The complex between substrate and inactive mutant reveals excellent density for an oligosaccharide in six of the enzyme's seven substrate binding subsites. No sugar moiety, however, is seen bound to the -1 subsite at the point of cleavage. The geometry of the cleavage site suggests that the enzyme would favor the binding of sugars with an elongated glycosidic bond, as found in the transition state, as opposed to the binding of substrate. The oligosaccharide complexes reveal solvent water suitably placed for participation in a single displacement reaction as first suggested by Koshland in 1953 [Koshland, D. E. (1953) Biol. Rev. 28, 416-436]. A large conformational change takes place upon substrate binding. This "lid flipping" has the effect of increasing the hydrophobic environment of the catalytic proton donor, enclosing the active site at the point of cleavage, and bringing a third aspartate (Asp 114) in close proximity to the substrate. Site-directed mutagenesis of the catalytic residues has been used to confirm their significance in catalysis.

The crystal structure of a cyanogenic beta-glucosidase from white clover, a family 1 glycosyl hydrolase.

BACKGROUND: beta-glucosidases occur in a variety of organisms and catalyze the hydrolysis of aryl and alkyl-beta-D-glucosides as well as glucosides with only a carbohydrate moiety (such as cellobiose). The cyanogenic beta-glucosidase from white clover (subsequently referred to as CBG) is responsible for the cleavage of cyanoglucosides. Both CBG and the cyanoglucosides occur within the plant cell wall where they are found in separate compartments and only come into contact when the leaf tissue experiences mechanical damage. This results in the eventual production of hydrogen cyanide which acts as a deterrent to grazing animals. beta-glucosidases have been assigned to particular glycosyl hydrolase families on the basis of sequence similarity; this classification has placed CBG in family 1 (there are a total of over 40 families) for which a three-dimensional structure has so far not been determined. This is the first report of the three-dimensional structure of a glycosyl hydrolase from family 1. RESULTS: The crystal structure of CBG has been determined using multiple isomorphous replacement. The final model has been refined at 2.15 A resolution to an R factor of 18.9%. The overall fold of the molecule is a (beta/alpha)8 [or (alpha/beta)8] barrel (in common with a number of glycosyl hydrolases) with all residues located in a single domain. CONCLUSIONS: Sequence comparisons between beta-glucosidases of the same family show that residues Glu183 and Glu397 are highly conserved. Both residues are positioned at the end of a pocket located at the C terminus of the barrel and have been assigned the respective roles of proton donor and nucleophile on the basis of inhibitor-binding and mutagenesis experiments. These roles are consistent with the environments of the two residues. The pocket itself is typical of a sugar-binding site as it contains a number of charged, aromatic and polar groups. In support of this role, we present crystallographic data on a possible product complex between CBG and glucose, resulting from co-crystallization of the native enzyme with its natural substrate, linamarin.

Penicillin acylase has a single-amino-acid catalytic centre.

Penicillin acylase (penicillin amidohydrolase, EC 3.5.1.11) is widely distributed among microorganisms, including bacteria, yeast and filamentous fungi. It is used on an industrial scale for the production of 6-aminopenicillanic acid, the starting material for the synthesis of semi-synthetic penicillins. Its in vivo role remains unclear, however, and the observation that expression of the Escherichia coli enzyme in vivo is regulated by both temperature and phenylacetic acid has prompted speculation that the enzyme could be involved in the assimilation of aromatic compounds as carbon sources in the organism's free-living mode. The mature E. coli enzyme is a periplasmic 80K heterodimer of A and B chains (209 and 566 amino acids, respectively) synthesized as a single cytoplasmic precursor containing a 26-amino-acid signal sequence to direct export to the cytoplasm and a 54-amino-acid spacer between the A and B chains which may influence the final folding of the chains. The N-terminal serine of the B chain reacts with phenylmethylsulphonyl fluoride, which is consistent with a catalytic role for the serine hydroxyl group. Modifying this serine to a cysteine inactivates the enzyme, whereas threonine, arginine or glycine substitution prevents in vivo processing of the enzyme, indicating that this must be an important recognition site for cleavage. Here we report the crystal structure of penicillin acylase at 1.9 A resolution. Our analysis shows that the environment of the catalytically active N-terminal serine of the B chain contains no adjacent histidine equivalent to that found in the serine proteases. The nearest base to the hydroxyl of this serine is its own alpha-amino group, which may act by a new mechanism to endow the enzyme with its catalytic properties.

Poly(ethylene) glycol monomethyl ethers - an alternative to poly(ethylene) glycols in protein crystallization.

Poly(ethylene) glycol monomethyl ethers (Peg-mmes) are a series of methyl substituted poly(ethylene) glycols that have been used with some success in the crystallization of a number of hydrophobic proteins. Crystallization of a lipase from Humicola lanuginosa complexed with the C12 substrate analogue from Peg-mme 5000, an endoglucanase 1 and a 59 kDa fragment of human topoisomerase IIalpha crystallized from Peg-mme are described. The use of Peg-mme for improving the quality of crystals previously grown from normal poly(ethylene) glycol 8000 is also described. We suggest that these modified Peg-mmes should be regularly used in screening for crystallization.

Crystallization and preliminary X-ray analysis of Candida albicans phosphomannose isomerase.

Crystals of recombinant phosphomannose isomerase from Candida albicans have been obtained in a form suitable for X-ray diffraction analysis. The enzyme plays a key role in the biosynthesis of the mannan component of the fungal cell wall. It crystallizes in monoclinic space group C2, with cell dimensions a = 124.9 A, b = 52.9 A, c = 85.9 A and beta = 127.4 degrees. The crystals diffract to Bragg spacings beyond 1.7 A, native data have been collected to 2.4 A and a search for heavy-metal derivatives is in progress. The asymmetric unit contains one molecule of the enzyme (M(r) approximately 49,000) with a Vm of 2.3 A3/Da.

Crystallization and preliminary X-ray analysis of nonglycosylated tissue inhibitor of metalloproteinases-1, N30QN78Q TIMP-1.

A nonglycosylated (N30QN78Q) form of the human tissue inhibitor of metalloproteinases, TIMP-1, has been prepared and crystallized in a form suitable for X-ray diffraction analysis. Small single crystals have been grown using sodium tartrate as a precipitant. The crystals are in space group P2(1), with cell dimensions a = 35.28, b = 53.95, c = 48.56, and beta = 96.0 degrees. There is a single molecule of TIMP-1 in the asymmetric unit. The crystals diffract to at least 2.3 A resolution. Complete data have been collected to 2.9 A and a search for heavy-metal derivatives is in progress.

Structure and function of endoglucanase V.

Cellulose is the major polysaccharide component of plant cell walls and is the most abundant organic compound on the planet. A number of bacterial and fungal organisms can use cellulose as a food source, possessing cellulases (cellobiohydrolases and endoglucanases) that can catalyse the hydrolysis of the beta-(1,4) glycosidic bonds. They can be classified into seven distinct families. The three-dimensional structures of members of two of these families are known. Here we report the structure of a third cellulase, endoglucanase V, whose sequence is not represented in any of the above families. The enzyme is structurally distinct from the previously determined cellulases but is similar to a recently characterized plant defence protein. The active site region resembles that of lysozyme, despite the lack of structural similarity between these two enzymes.

Crystallization and preliminary X-ray analysis of a truncated tissue metalloproteinase inhibitor delta 128-194 TIMP-2.

Crystals of an active truncated form of a human tissue metallproteinase inhibitor (delta 128-194 TIMP-2), a protein implicated in a number of diseases of the connective tissues, have been grown in a form suitable for study by X-ray diffraction analysis. Crystals grow using polyethylene glycol 600 as a precipitant and are in space group P2(1)2(1)2, with cell dimensions a = 75.28 A, b = 100.77 A, c = 31.45 A. The asymmetric unit appears to contain two molecules of delta TIMP-2 with a Vm value of 2.3 A3/dalton. The crystals diffract to Bragg-spacings beyond 2.5 A. Native data to 3.2 A have been collected and a search for heavy-metal derivatives is in progress.

Crystallization and preliminary crystallographic analysis of the cyanogenic beta-glucosidase from the white clover Trifolium repens L.

The cyanogenic beta-glucosidase from Trifolium repens (white clover) has been crystallized, in a form suitable for X-ray analysis, from ammonium sulphate solutions. The crystals, which diffract to 3.0 A, are tetragonal, space group P4(3)2(1)2 or its enantiomorph P4(1)2(1)2. The cell dimensions are a = b = 69.92 A, c = 248.38 A.

Crystallization and preliminary X-ray analysis of a fungal endoglucanase I.

An endoglucanase I (EG1) from a fungal source (Humicola insolens) has been crystallized in a number of forms suitable for X-ray diffraction analysis. Four crystal forms have been grown from various precipitants using vapour phase diffusion methods in hanging drops. Three of these crystal forms diffract to beyond 2.5 A resolution. Two forms, obtained from ammonium sulphate at pH 5.4, or 8.0, grow as tetragonal bipyramids in space group P4(1)22 or P4(3)22, with approximate cell dimensions a = b = 102 A, c = 282 A. The other crystal forms were grown from polyethylene glycol 8000 at pH 8.0. One grows as monoclinic plates, space group P2(1), with cell dimensions a = 66.9 A, b = 75.2 A, c = 86.9 A and beta = 102.9 degrees and the other as long hexagonal rods in space group P6(1)22 or P6(5)22, with cell dimensions a = b = 119 A, c = 83 A.

Expression, purification and crystallization of penicillin G acylase from Escherichia coli ATCC 11105.

The penicillin acylase gene (pac) from Escherichia coli ATCC 11105 was cloned into pUC 9 and the resulting vector (pUPA-9), when transformed into E. coli strain 5K, allowed the constitutive overproduction of mature penicillin acylase when grown at 28 degrees C. The enzyme was purified from the periplasmic fraction of E. coli pUPA-9 by hydrophobic interaction chromatography and anion exchange. Crystals of penicillin acylase were grown in batch using polyethylene glycol 8000 as a precipitant. The crystals (space group P1) diffracted to beyond 2.3 A.