Assessing the sensitivity of habitats to fishing: from seabed maps to sensitivity maps.

In the Welsh part of the Irish Sea, a method was developed for assessing the sensitivity of different seabed habitats to existing fishing activities, across a range of potential fishing intensities. The resistance of 31 habitats and their associated biological assemblage to damage by 14 categories of fishing activity were assessed along with the rate at which each habitat would recover following impact (resilience). Sensitivity was scored based on a combination of the resistance of a habitat to damage and its subsequent rate of recovery. The assessments were based, wherever possible, on scientific literature, with expert judgement used to extrapolate results to habitat and gear combinations not directly examined in the published literature. The resulting sensitivity matrices were then subject to further peer review at a series of workshops. Following consensus on the habitat sensitivity, these data were combined with the most resolved sea-floor habitat maps. These habitat sensitivity maps can help inform the development of site-specific management plans, as well as having a place in spatial planning and aiding managers in developing dialogue with other stakeholders. A case study of their application is provided.

The repeatability of vegetation classification and mapping.

The mapping of habitats as defined by plant communities is a common component of the planning and monitoring of conservation management. However, there are major concerns about the subjectivity and risk of observer bias in most commonly used plant community mapping protocols. This study provides the first test of the consistency of habitat maps based on the mapping units defined by the National Vegetation Classification (NVC), the most widely used classification of plant communities used for habitat mapping on conservation sites in the UK. Seven surveyors mapped the same upland site within five weeks in summer 2008 and the spatial correspondence of the resulting maps was assessed. The NVC is a hierarchical classification and pair-wise spatial agreement between maps decreased with lower levels of sub-classification. The average area of agreement between maps was 77.6% at the habitat level, 34.2% at the community level and 18.5% at the sub-community level. Spatial disparity in the location of mapped boundaries between vegetation types only made a small contribution to overall differences; the majority of variation between maps was due to discrepancies in classification, with vegetation types containing similar species composition most often confused. Factors relating to surveyor effort (cost, time taken and length of route) were not able to explain the substantial differences between maps. However, the methods used to assign areas to vegetation type did seem to have an effect, with surveyors who relied primarily on their own experience having the highest levels of mean agreement with other maps. The study raises serious concerns with current practice of using the NVC for site description and monitoring/surveillance. Since this is just a single case study, we recommend that further work is carried out with the aim of determining the degree and source of variation between surveyors and how consistency can be increased.

MolCom: a method to compare protein molecules based on 3-D structural and chemical similarity.

This paper describes an improved method for conducting global feature comparisons of protein molecules in three dimensions and for producing a new form of multiple structure alignment. Our automated MolCom method incorporates an octtree strategy to partition and examine molecular properties in three-dimensional space at multiple levels of analysis. The MolCom method's multiple alignment is in the form of an octtree which locates regions in three-dimensional space where correspondence between molecules is identified based on a dynamic set of molecular features. MolCom offers a practical solution to the inherent compromise between computational complexity and analytical detail. MolCom is currently the only method that can analyze and compare a series of defined physicochemical properties using multiple, simultaneous levels of resolution. It is also the only method that provides a consensus structure outlining precisely where the similarity exists in three-dimensional space. Using a modest-sized collection of structural properties, separate experiments were conducted to calibrate MolCom and to verify that the spatial analyses and resulting structure alignments accurately identified both similar and dissimilar structures. The accuracy of MolCom was found to be over 99% and the similarity scores correlated strongly with the z-scores of the Alignment by Incremental Combinatorial Extension of the Optimal Path method.

Preliminary results of combined therapy with topotecan and carboplatin in advanced non-small-cell lung cancer.

Topotecan is a topoisomerase I inhibitor and an analogue of camptothecin with demonstrated activity in small-cell lung cancer. However, less is known about the potential role of topotecan in advanced non-small-cell lung cancer (NSCLC). Platinum-based combination therapy is currently recommended in NSCLC patients presenting with good performance status. Because topotecan demonstrates a novel mechanism of action, its investigation in platinum combinations is warranted. In phase I/II trials of topotecan given as part of a cisplatin-based regimen, significant antitumor activity has been observed, providing the rationale for conducting further studies aimed at assessing survival benefit. However, this combination exhibits sequence dependence, with increasing hematologic toxicity observed when cisplatin is administered on day 1 of a 5-day topotecan course. Cisplatin has been associated with dose-limiting nonhematologic toxicities. Carboplatin exhibits a different toxicity profile compared with cisplatin, which makes it an attractive agent to study in combination. A hypothesis can be made that carboplatin in combination with newer agents such as topotecan might compare favorably with classic cisplatin-based regimens, particularly with respect to efficacy:toxicity ratio. Therefore, a phase II study was initiated to determine the efficacy, toxicity, and safety of carboplatin-topotecan combination in advanced NSCLC. Preliminary results reported here show that topotecan with carboplatin is generally well tolerated with manageable hematologic toxicity. Indirect comparison with cisplatin-topotecan combination suggests a lower incidence of dose-limiting nonhematologic toxicity. Whether or not the carboplatin-topotecan regimen is able to offer tumor response and survival benefit comparable to those observed with cisplatin-based combinations remains to be established.

Roles for ligases in the RNA editing complex of Trypanosoma brucei: band IV is needed for U-deletion and RNA repair.

Trypanosome RNA editing utilizes a seven polypeptide complex that includes two RNA ligases, band IV and band V. We now find that band IV protein contributes to the structural stability of the editing complex, so its lethal genetic knock-out could reflect structural or catalytic requirements. To assess the catalytic role in editing, we generated cell lines which inducibly replaced band IV protein with an enzymatically inactive but structurally conserved version. This induction halts cell growth, showing that catalytic activity is essential. These induced cells have impaired in vivo editing, specifically of RNAs requiring uridylate (U) deletion; unligated RNAs cleaved at U-deletion sites accumulated. Additionally, mitochondrial extracts of cells with reduced band IV activity were deficient in catalyzing U-deletion, specifically at its ligation step, but were not deficient in U-insertion. Thus band IV ligase is needed to seal RNAs in U-deletion. U-insertion does not appear to require band IV, so it might use the other ligase of the editing complex. Furthermore, band IV ligase was also found to serve an RNA repair function, both in vitro and in vivo.

Topotecan given as a 21-day infusion in the treatment of advanced ovarian cancer.

A phase II programme was carried out in both Europe and North America to evaluate the activity of topotecan administered as a 21-day continuous intravenous infusion to patients with recurrent ovarian cancer. The European results are reported here. Patients who had failed first line therapy with a platinum-based regimen received topotecan 0.4 mg/m(2)/day, as a 21-day infusion every 28 days. Patients were only permitted one prior regimen. 35 patients were enrolled and evaluable for response. 3 patients (8.6%) had a partial response to treatment (95% CI 1.8%, 23.1%) with a median time to response of 8.1 weeks and a median duration of response of 17.6 weeks. Response was also evaluated by CA125 and was also found to be 8%. For all 35 patients, median time to progression was 16.1 weeks and median survival was 43.6 weeks. The principal toxicity was myelosuppression although grade 4 neutropenia occurred in only 8.8% of patients (2.1% of courses) and infectious complications were relatively infrequent. Non-haematological toxicity was generally mild and mainly consisted of gastrointestinal events, alopecia and fatigue. A prolonged infusion of topotecan was well tolerated with a low incidence of severe neutropenia. Responses were seen in both North American and European patients. Response rates varied between the 2 studies possibly due to differences in patient demographics.

Phase I pharmacologic study of oral topotecan and intravenous cisplatin: sequence-dependent hematologic side effects.

PURPOSE: In in vitro studies, synergism and sequence-dependent effects were reported for the combination of topotecan and cisplatin. Recently, an oral formulation of topotecan became available. This phase I study was performed to assess the feasibility of the combination of oral topotecan and cisplatin, the pharmacokinetic interaction, and sequence-dependent effects. PATIENTS AND METHODS: Topotecan was administered orally (PO) daily for 5 days in escalating doses and cisplatin was given intravenously (IV) at a fixed dose of 75 mg/m(2) either before topotecan administration on day 1 (sequence CT) or after topotecan administration on day 5 (sequence TC) once every 3 weeks. Patients were treated in a randomized cross-over design. RESULTS: Forty-nine patients were entered onto the study; one patient was not eligible. Sequence CT induced significantly more severe myelosuppression than did sequence TC, and the maximum-tolerated dosage of topotecan in sequence CT was 1.25 mg/m(2)/d x 5. In sequence TC, the maximum-tolerated dosage of topotecan was 2.0 mg/m(2)/d x 5. Dose-limiting toxicity consisted of myelosuppression and diarrhea. Pharmacokinetics of topotecan and cisplatin were linear over the dose range studied; no sequence-dependent effects were observed. In addition, topotecan did not influence the protein binding of cisplatin or the platinum-DNA adduct formation in peripheral leukocytes in either sequence. CONCLUSION: The recommended dosages for phase II studies involving patients like the patients in our study are topotecan 1.25 mg/m(2)/d PO x 5 preceded by cisplatin 75 mg/m(2) IV day 1 once every 3 weeks, and topotecan 2.0 mg/m(2)/d PO followed by cisplatin 75 mg/m(2) IV day 5. No pharmacokinetic interaction could be discerned in our study. The antitumor efficacy of both schedules should be evaluated in a randomized phase II study.

Phase II study of oral topotecan in advanced non-small cell lung cancer.

This study was designed to assess the activity of oral topotecan (TPT) in patients with advanced non-small cell lung cancer previously untreated with chemotherapy. Eligible patients had inoperable stage III or stage IV non-small cell lung cancer and were chemotherapy-naive. Other inclusion criteria were Eastern Cooperative Oncology Group performance status 0, 1, or 2, adequate bone marrow, and renal and hepatic function. Of 30 patients, 29 were assessable for response. Oral TPT was administered for 5 days every 21 days for up to six cycles unless disease progression or unacceptable toxicity occurred. Patients received a dose of 2.3 mg/m2/day for the first cycle. Dose modification for subsequent cycles was based on tolerability. Patients completed symptom questionnaires every 3 weeks. Pharmacokinetics were evaluated in all patients during cycle 1. Three patients had radiological responses with a reduction in tumor size of 30-40%. No patients achieved complete or partial responses to treatment. Thirteen patients had a stable disease (43.3%), and the median survival was 39.9 weeks with a 1-year survival of 33.3%. At the time of analysis, 27 patients had died. Median time to progression was 12.3 weeks. Treatment was well tolerated. A total of 125 cycles of treatment were completed. Twelve patients (40%) experienced grade III/IV neutropenia. Five patients (16.6%) had grade III/IV anemia. There were two episodes of grade III/IV thrombocytopenia. The main nonhematological toxicities consisted of grade III nausea (13%) and grade III vomiting (13%). The most frequently reported disease-related symptoms at baseline were dyspnea, cough, and fatigue. There was a subsequent improvement in patient scores of dyspnea in 17% of patients, 31% showed improvement in cough, and 32% showed improvement in fatigue. The mean area under the curve of TPT following 2.3 mg/m2 p.o. was 51.6 ng.h/ml (%SD, 25%). The area under the curve of TPT on day 1 of the first cycle was correlated with the percentage fall in leukocytes. Although oral TPT at the applied dose and schedule showed modest activity as a single agent, almost one-half of the patients had a stable disease, and median time to progression was 12.3 weeks. The overall median survival was a promising 39.9 weeks, and useful palliation of symptoms was seen.

Correlated atomic force and transmission electron microscopy of nanotubular structures in pulmonary surfactant.

Pulmonary surfactant stabilizes the lung by reducing surface tension at the air-water interface of the alveoli. Surfactant is present in the lung in a number of morphological forms, including tubular myelin (TM). TM is composed of unusual 40 x 40 nm square elongated proteolipid tubes. Atomic force microscopy (AFM) was performed on polymer-embedded Lowicryl and London Resin-White (LR-White) unstained thin sections. AFM was used in imaging regions of the sections where TM was detected by transmission electron microscopy (EM) of corresponding stained sections. Tapping- and contact-mode AFM imaging of the unstained sections containing TM indicated a highly heterogeneous surface topography with height variations ranging from 10 to 100 nm. In tapping-mode AFM, tubular myelin was seen as hemispherical protrusions of 30-70 nm in diameter, with vertical dimensions of 5-8 nm. In contact-mode AFM and with phase imaging using a sharper (>10 nm nominal radius) probe, square open-ended tubes which resembled typical electron micrographs of such regions were observed. The cross-hatch structures observed inside the tubes using EM were not observed using AFM, although certain multilobe structures and topographic heterogeneity were detected inside some tubes. Other regions of multilamellar bodies and some regions where such bilayer lamella appear to fuse with the tubes were found in association with TM using AFM. EM of acetone-delipidated tubes in LR-White revealed rectangular tubular cores containing cross-hatched structures, presumably protein skeletons. AFM surface topography of these regions showed hollow depressions at positions at which the protein was anticipated instead of the protrusions seen in the lipid-containing sections. Gold-labeled antibody to surfactant protein A was found associated somewhat randomly within the regions containing the protein skeletons. The topography of the gold particles was observed as sharp peaks in contact-mode AFM. This study suggests a method for unambiguous detection of three-dimensional nanotubes present in low abundance in a biological macromolecular complex. Only limited detection of proteins and lipids in surfaces of embedded tubular myelin was possible. EM and AFM imaging of such unusual biological structures may suggest unique lipid-protein associations and arrangements in three dimensions.

Effects of eyelid scrubbing on the lid margin.

PURPOSE: To compare the effects of eyelid scrubbing with an eyelid cleansing solution (ECS) to eyelid scrubbing with ECS and the addition of antibacterial or anti-inflammatory pharmaceuticals on the clinical appearance, microbial status, tissue histology, and the inflammatory cell profile of the normal eyelid margin. METHODS: Eyelid scrubbing was performed twice daily using ECS; ECS with the antibacterial sulfacetamide (ECS+); and ECS with sulfacetamide and prednisolone acetate (ECS++) over a 21 day period on three groups of 16 rabbits with clinically normal eyelids. RESULTS: Significant hyperemia of the margin occurred in all three groups over the 3 week period; however, the degree of hyperemia was less with ECS+ (P<0.05) and ECS++ (P<0.05). Chemosis, tearing, mucus discharge, and the microbial status were not significantly different than controls. There were no marked histologic differences in the tissues, except for increased red blood cell packing in the small vessels near the lid margins in scrubbed eyelids, consistent with hyperemia. The inflammatory cell profile showed minimal changes that were not statistically significant in any of the three groups, except that >50% of mast cells showed evidence of degranulation. CONCLUSIONS: Use of ECS with an antibiotic, or an antibiotic and steroid solution, resulted in less inflammation than scrubbing with ECS alone.

Filaments of surfactant protein A specifically interact with corrugated surfaces of phospholipid membranes.

Pulmonary surfactant, a mixture of lipids and surfactant proteins (SPs), plays an important role in respiration and gas exchange. SP-A, the major SP, exists as an octadecamer that can self-associate to form elongated protein filaments in vitro. We have studied here the association of purified bovine SP-A with lipid vesicle bilayers in vitro with negative staining with uranyl acetate and transmission electron microscopy. Native bovine surfactant was also examined by transmission electron microscopy of thinly sectioned embedded material. Lipid vesicles made from dipalmitoylphosphatidylcholine and egg phosphatidylcholine (1:1 wt/wt) generally showed a smooth surface morphology, but some large vesicles showed a corrugated one. On the smooth-surfaced vesicles, SP-As primarily interacted in the form of separate octadecamers or as multidirectional protein networks. On the surfaces of the striated vesicles, SP-As primarily formed regularly spaced unidirectional filaments. The mean spacing between adjacent striations and between adjacent filaments was 49 nm. The striated surfaces were not essential for the formation of filaments but appeared to stabilize them. In native surfactant preparations, SP-A was detected in the dense layers. This latter arrangement of the lipid bilayer-associated SP-As supported the potential relevance of the in vitro structures to the in vivo situation.

Formation of membrane lattice structures and their specific interactions with surfactant protein A.

Biological membranes exist in many forms, one of which is known as tubular myelin (TM). This pulmonary surfactant membranous structure contains elongated tubes that form square lattices. To understand the interaction of surfactant protein (SP) A and various lipids commonly found in TM, we undertook a series of transmission-electron-microscopic studies using purified SP-A and lipid vesicles made in vitro and also native surfactant from bovine lung. Specimens from in vitro experiments were negatively stained with 2% uranyl acetate, whereas fixed native surfactant was delipidated, embedded, and sectioned. We found that dipalmitoylphosphatidylcholine-egg phosphatidylcholine (1:1 wt/wt) bilayers formed corrugations, folds, and predominantly 47-nm-square latticelike structures. SP-A specifically interacted with these lipid bilayers and folds. We visualized other proteolipid structures that could act as intermediates for reorganizing lipids and SP-As. Such a reorganization could lead to the localization of SP-A in the lattice corners and could explain, in part, the formation of TM-like structures in vivo.

Phase I and pharmacologic study of the combination of paclitaxel, cisplatin, and topotecan administered intravenously every 21 days as first-line therapy in patients with advanced ovarian cancer.

PURPOSE: To evaluate the feasibility of administering topotecan in combination with paclitaxel and cisplatin without and with granulocyte colony-stimulating factor (G-CSF) support as first-line chemotherapy in women with incompletely resected stage III and stage IV ovarian carcinoma. PATIENTS AND METHODS: Starting doses were paclitaxel 110 mg/m2 administered over 24 hours (day 1), followed by cisplatin 50 mg/m2 over 3 hours (day 2) and topotecan 0.3 mg/m2/d over 30 minutes for 5 consecutive days (days 2 to 6). Treatment was repeated every 3 weeks. After encountering dose-limiting toxicities (DLTs) without G-CSF support, the maximum-tolerated dose was defined as 5 microg/kg of G-CSF subcutaneously starting on day 6. RESULTS: Twenty-one patients received a total of 116 courses at four different dose levels. The DLT was neutropenia. At the first dose level, all six patients experienced grade 4 myelosuppression. G-CSF support permitted further dose escalation of cisplatin and topotecan. Nonhematologic toxicities, primarily fatigue, nausea/vomiting, and neurosensory neuropathy, were observed but were generally mild. Of 15 patients assessable for response, nine had a complete response, four achieved a partial response, and two had stable disease. CONCLUSION: Neutropenia was the DLT of this combination of paclitaxel, cisplatin, and topotecan. The recommended phase II dose is paclitaxel 110 mg/m2 (day 1), followed by cisplatin 75 mg/m2 (day 2) and topotecan 0.3 mg/m2/d (days 2 to 6) with G-CSF support repeated every 3 weeks.

Epidermal and dermal phospholipids of the human eyelid: a 31P nuclear magnetic resonance spectroscopy study.

The phospholipids of the skin are difficult to quantify because they represent only a small fraction of the skin tissue. In this study, 31P nuclear magnetic resonance, which permits precise profiling of these phospholipids, was used to compare the phospholipids of upper eyelid epidermal and dermal lipid extracts (n = 13 profiles). Phospholipid profiles included alkylacylphosphatidylcholine (AAPC), dihydrosphingomyelin (DHSM), diphosphatidylglycerol (cardiolipin), ethanolamine plasmalogen (EPLAS), lysophosphatidylcholine, phosphatidic acid, phosphatidylcholine (PC), phosphatidylethanolamine, phosphatidylinositol, phosphatidylserine, sphingomyelin, and uncharacterized phospholipids (U1 and U2, particularly enriched in the epidermis). The computed phospholipid metabolic index (n = 86 indexes) findings can be summarized as follows: a lower content of the en-ol and ether phospholipids in the epidermis relative to the dermis, internal compensation among the component phospholipids so as to maintain the choline functional group ratio, and a greater concentration of hydroxyl-containing functional groups in the epidermis. A membrane index (fmem) value of -0.37 for the epidermis deviated considerably from the value of -0.06 characteristic of living membranes and the dermis. The production of the reduced phosphatides, EPLAS and AAPC, indicates the use of alternative pathways between the two tissues. Relative to the dermis, increased PC in the epidermis coupled with decreased DHSM, EPLAS, and AAPC are factors enabling the epidermis of eyelid tissue to be an effective water barrier.

Values in action.

St. John Health System, Detroit, is committed to the values of wisdom, compassion, service to the neighbor, stewardship and servant leadership. When a patient walks through any one of the six St. John Hospitals, they see these words displayed many times. But what do they mean to the employees? Patients? The community? According to Anthony R. Tersigni, EdD, St. John president and CEO, "The values remind us of who we are and what our responsibilities are to the communities we serve."