Avoiding ethics pitfalls in publishing: a perspective from COPE.

The mission of the Committee on Publication Ethics (COPE) is to promote integrity in research publication. COPE was started in 1997 with a small group of editors and now has a membership of more than 10 000. Throughout its history, COPE has provided a forum for discussion about ethical issues related to all aspects of scholarly publishing and developed resources to assist those who write, review, and edit scholarly work. This concise review provides examples of ethical issues related to authoring, reviewing, and editing scholarly manuscripts from the perspective of COPE.

Isolation, characterization, and regulation of the Candida albicans ERG27 gene encoding the sterol 3-keto reductase.

The Candida albicans ERG27 gene which encodes the 3-keto reductase enzyme required for sterol C-4 demethylation was isolated and found to encode a 349 amino acid protein that is 60% identical at the amino acid level to the Saccharomyces cerevisiae Erg27p. A C. albicans erg27 null was created in a strain containing an integrated ERG27 rescue cassette under the control of the pMAL2 inducible promoter. The C. albicans erg27 strain was able to grow only in the presence of maltose indicating that the ERG27 gene is essential. The C. albicans erg27 null showed complete loss of both 3-keto reductase and oxidosqualene cyclase (Erg7p) activities compromising all sterol synthesis. These results suggest that Erg27p inhibitors might be effective antifungals. To explore ERG27 regulation, an erg11 null strain was generated. C. albicans erg6 and erg24 mutants were also employed along with the inhibitors, itraconazole and zaragozic acid A, to characterize ERG27 expression using Northern analysis. Expression was increased two- to fourfold in erg11, erg6 and erg24 backgrounds. However, itraconazole which targets Erg11p (lanosterol demethylase) increased ERG27 expression 10-fold and zaragozic acid A which targets the Erg9p (squalene synthase) increased ERG27 expression fivefold. The azole and erg11 results support other observations that azoles may affect non-sterol targets.

Ergosterol gene expression in wild-type and ergosterol-deficient mutants of Candida albicans.

The ergosterol pathway is the major target of the azole antifungals. We have developed a panel of five viable ergosterol biosynthetic mutants (erg2, erg3, erg6, erg11 and erg24) and have performed Northern analyses to study transcriptional regulation using probes to four ergosterol biosynthetic genes (ERG2, ERG7, ERG11 and ERG25), as well as probes to two additional genes encoding ergosterol cytochrome coenzymes (CYB5 and NCP1). ERG11, which encodes the sterol 14-demethylase, the direct target of the azole antifungals, was the most up-regulated gene followed by ERG7 and ERG25. Transcription of the four ergosterol genes was most up-regulated in erg24 and erg6 mutant backgrounds, deficient in C-14 reductase and the C-24 sterol transmethylase, respectively. Unexpectedly, we also found that the two cytochrome genes, CYB5 encoding cytochrome b5 and NCP1 encoding the cytochrome P450 reductase, were not regulated markedly different from wild-type in the erg2, erg3, erg6, erg11 and erg24 strains of Candida albicans.

Disruption of the Candida albicans CYB5 gene results in increased azole sensitivity.

Sterol synthesis in fungi is an aerobic process requiring molecular oxygen and, for several cytochrome-mediated reactions, aerobically synthesized heme. Cytochrome b(5) is required for sterol C5-6 desaturation and the encoding gene, CYB5, is nonessential in Saccharomyces cerevisiae. Cyb5p and Ncp1p (cytochrome P-450 reductase) appear to have overlapping functions in this organism, with disruptions of each alone being viable. The cytochrome P-450 reductase phenotype has also been shown to demonstrate increased sensitivity to azole antifungals. Based on this phenotype, the CYB5 gene in the human pathogen Candida albicans was investigated to determine whether the cyb5 genotype was viable and would also demonstrate azole sensitivity. Sequential disruption of the CYB5 alleles by direct transformation resulted in viability, presumably conferred by the presence of a third copy of the CYB5 gene. Subsequent disruption procedures with a pMAL2-CYB5 rescue cassette and a CYB5-URA3 blaster cassette resulted in viable cyb5 strains with no third copy. The C. albicans CYB5 gene is concluded to be nonessential. Thus, the essentiality of this gene and whether we observed two or three alleles was dependent upon the gene disruption protocol. The C. albicans cyb5 strains produced a sterol profile containing low ergosterol levels and sterol intermediates similar to that reported for the S. cerevisiae cyb5. The C. albicans cyb5 shows increased sensitivity to azoles and terbinafine, an inhibitor of squalene epoxidase, and, unexpectedly, increased resistance to morpholines, which inhibit the ERG2 and ERG24 gene products. These results indicate that an inhibitor of Cyb5p would not be lethal but would make the cell significantly more sensitive to azole treatment.

Candida albicans sterol C-14 reductase, encoded by the ERG24 gene, as a potential antifungal target site.

The incidence of fungal infections has increased dramatically, which has necessitated additional and prolonged use of the available antifungal agents. Increased resistance to the commonly used antifungal agents, primarily the azoles, has been reported, thus necessitating the discovery and development of compounds that would be effective against the major human fungal pathogens. The sterol biosynthetic pathway has proved to be a fertile area for antifungal development, and steps which might provide good targets for novel antifungal development remain. The sterol C-14 reductase, encoded by the ERG24 gene, could be an effective target for drug development since the morpholine antifungals, inhibitors of Erg24p, have been successful in agricultural applications. The ERG24 gene of Candida albicans has been isolated by complementation of a Saccharomyces cerevisiae erg24 mutant. Both copies of the C. albicans ERG24 gene have been disrupted by using short homologous regions of the ERG24 gene flanking a selectable marker. Unlike S. cerevisiae, the C. albicans ERG24 gene was not required for growth, but erg24 mutants showed several altered phenotypes. They were demonstrated to be slowly growing, with doubling times at least twice that of the wild type. They were also shown to be significantly more sensitive to an allylamine antifungal and to selected cellular inhibitors including cycloheximide, cerulenin, fluphenazine, and brefeldin A. The erg24 mutants were also slightly resistant to the azoles. Most importantly, erg24 mutants were shown to be significantly less pathogenic in a mouse model system and failed to produce germ tubes upon incubation in human serum. On the basis of these characteristics, inhibitors of Erg24p would be effective against C. albicans.

The Candida albicans ERG26 gene encoding the C-3 sterol dehydrogenase (C-4 decarboxylase) is essential for growth.

The Candida albicans ERG26 gene encoding the C-3 sterol dehydrogenase (C-4 decarboxylase) was cloned by complementing a Saccharomyces cerevisiae erg26 mutant with a C. albicans genomic library. Sequence analysis showed a 70% identity between the C. albicans and S. cerevisiae ERG26 genes at the amino acid level. Sequential disruption of both copies of the ERG26 gene in the presence of an integrated rescue cassette containing a third copy of the ERG26 gene under the control of the inducible pMAL2 promoter, resulted in cells capable of growing only in the presence of the inducer. The results establish that the ERG26 gene is essential for growth and that inhibitors of the Erg26p may represent a new and highly effective class of antifungal agents.

Ethnomethodologic analysis of accounts of feeding demented residents in long-term care.

PURPOSE: To describe the self-organizing activities and the unspoken knowledge that nursing assistants employ in performing the work of feeding as a routine part of their activities. In U.S. long-term care facilities, activities related to medical and nursing care are frequently based on the ability of nursing assistants to successfully accomplish the work of feeding. Nurses are not always aware of the difficulties involved in feeding nor the means by which food is offered and intake calculated. DESIGN: Qualitative phenomenologic. METHODS: Observations were conducted during 12 weekday mealtimes, October and November 1994. Data were collected using participant observation of mealtimes in the congregate dining room of one licensed long-term care facility. Data were analyzed using the framework of ethnomethodology to indicate the methods nursing assistants used to make sense of their interactions with demented residents. FINDINGS: Nursing assistants used several common behaviors: grouping the "difficult feeders" together; "marking the borders" by maintaining a tidy tray; and "loading the spoon" to maximize the amount of food given at one time. Estimations of the quantity of intake varied according to ideas about the nutritional content of various foods. CONCLUSIONS: Unsuccessful feeding interactions have implications for the quality of life for the demented. When inadequate intake leads to significant weight loss, medical and nursing interventions should be implemented.

The public and private problem of euthanasia. A comparison of The Netherlands and the United States.

Euthanasia is an emerging public problem. The recent "medicalization" of the dying process in industrialized nations has engendered a fear of a painful and undignified death and the loss of control over one's final days. For people who live in societies with advanced medical resources and technology, euthanasia seems the only sure way to have "a good death." This article examines the public and private faces of euthanasia and provides another moral lens through which to view the issue. The article includes an interview with the son of a 78-year-old man who had active euthanasia performed by a family physician in the Netherlands.

A yeast sterol auxotroph (erg25) is rescued by addition of azole antifungals and reduced levels of heme.

Genetic disruption of the Saccharomyces cerevisiae C-4 sterol methyl oxidase ERG25 gene leads to sterol auxotrophy. We have characterized a suppression system that requires two mutations to restore viability to this disrupted strain. One suppressor mutation is erg11, which is blocked in 14alpha-demethylation of lanosterol and is itself an auxotroph. The second suppressor mutation required is either slu1 or slu2 (suppressor of lanosterol utilization). These mutations are leaky versions of HEM2 and HEM4, respectively; addition of exogenous hemin reverses the suppressing effects of slu1 and slu2. Suppression of erg25 by erg11 slu1 (or erg11 slu2) results in a slow-growing strain in which lanosterol, the first sterol in the pathway, accumulates. This result indicates that endogenously synthesized lanosterol can substitute for ergosterol and support growth. In the triple mutants, all but 1 (ERG6) of the 13 subsequent reactions of the ergosterol pathway are inactive. Azole antibiotics (clotrimazole, ketoconazole, and itraconazole) widely used to combat fungal infections are known to do so by inhibiting the ERG11 gene product, the 14alpha-demethylase. In this investigation, we demonstrate that treatment of the sterol auxotrophs erg25 slu1 or erg25 slu2 with azole antibiotics paradoxically restores viability to these strains in the absence of sterol supplementation via the suppression system we have described.

Cloning and characterization of the Saccharomyces cerevisiae C-22 sterol desaturase gene, encoding a second cytochrome P-450 involved in ergosterol biosynthesis.

The ERG5 gene from Saccharomyces cerevisiae was cloned by complementation of an erg5-1 mutation using a negative selection protocol involving screening for nystatin-sensitive transformants. ERG5 is the putative gene encoding the C-22 sterol desaturase required in ergosterol biosynthesis. The functional gene was localized to a 2.15-kb SacI-EcoRI DNA fragment containing an open reading frame of 538 amino acids (aa). ERG5 contains a 10-aa motif consistent with its role as a cytochrome P-450 (CyP450) enzyme and is similar to a number of mammalian CyP450 enzymes. Gene disruption demonstrates that ERG5 is not essential for cell viability.

Cloning and characterization of ERG25, the Saccharomyces cerevisiae gene encoding C-4 sterol methyl oxidase.

We have cloned the Saccharomyces cerevisiae C-4 sterol methyl oxidase ERG25 gene. The sterol methyl oxidase performs the first of three enzymic steps required to remove the two C-4 methyl groups leading to cholesterol (animal), ergosterol (fungal), and stigmasterol (plant) biosynthesis. An ergosterol auxotroph, erg25, which fails to demethylate and concomitantly accumulates 4,4-dimethylzy-mosterol, was isolated after mutagenesis. A complementing clone consisting of a 1.35-kb Dra I fragment encoded a 309-amino acid polypeptide (calculated molecular mass, 36.48 kDa). The amino acid sequence shows a C-terminal endoplasmic reticulum retrieval signal KKXX and three histidine-rich clusters found in eukaryotic membrane desaturases and in a bacterial alkane hydroxylase and xylene monooxygenase. The sterol profile of an ERG25 disruptant was consistent with the erg25 allele obtained by mutagenesis.

130 kb of DNA sequence reveals two new genes and a regional duplication distal to the human iduronate-2-sulfate sulfatase locus.

Deficiency of IDs activity results in Hunter Syndrome (mucopolysaccharidosis type II), a fatal X-linked recessive disorder. We report characterization of 28 cosmids around the IDS locus in Xq28. Four overlapping cosmids have been sequenced in their entirety generating a 130-kb contig. These studies show the fine structure of the IDS gene and identify an IDS pseudogene-like structure located 20 kb distal to the active gene. Two novel genes have also been identified in this sequence, and one of these genes is also locally duplicated. Both homologs are expressed, and a number of alternative transcript products have been characterized. The presence of a highly conserved pseudogene-like structure within a larger duplicated region close to the IDS gene has significant implications for the study of mutations at this locus.