A cautionary tale of virus and disease

The recent identification of the gammaretrovirus XMRV and a second gammaretrovirus of a different subtype in chronic fatigue syndrome has aroused much interest, not least among sufferers. However, it remains highly controversial whether the detection of these viruses represents true infection or laboratory artifacts.     

Inhibitors of superoxide dismutases: A cautionary tale

An extensive search resulted in the identification of pamoic acid as an inhibitor of superoxide dismutases. Pamoic acid appeared to rapidly and reversibly inhibit all types of superoxide dismutases and did so in both the cytochrome c reduction and in the dianisidine photooxidation assays, used to measure this activity. It could nevertheless be shown that pamoic acid did not at all inhibit superoxide dismutase but rather diminished the sensitivity of the assays. The mechanism proposed to account for this effect involved oxidation of pamoate, by O₂^?, to yield a pamoate radical which can then reduce cytochrome c or oxidize pyrogallol. Pamoate thus competes with superoxide dismutase for the available O₂^?, without affecting the observable effects of that O₂^? upon cytochrome c or upon pyrogallol. It consequently makes these assays less responsive to superoxide dismutase, while appearing to be without effect in the absence of superoxide dismutase. Several of the predicted consequences of this proposal were affirmed. Other workers, interested in finding inhibitors for superoxide dismutases, are hereby forwarned of this subtle snare.     

Intra- and interobserver error in craniometry: A cautionary tale

This study investigates intra- and interobserver measurement error in craniometry. Data consists of 72 craniometric measurements taken on a series of 28 Sadlermuit Eskimo crania. Utermohle measured the series twice; Zegura measured it once. Statistical procedures used to demonstrate measurement imprecision include the mean difference, the method error statistic, two-way anova without replication, the t-test for paired comparisons, Fisher's distribution-free sign test, and the t-test for independent samples. The results indicate less intraobserver repeatability than expected as well as an alarming lack of interobserver reproducibility for many of these craniometric measurements. We hope these results will serve as a caution against the widespread belief that craniometric measurements are always produced with a high degree of precision by experienced craniometrists. In addition, these results suggest that investigators employing craniometric measurements to study population affinities, functional morphology, forensics, fossil primates, and human microevolution might profit from conducting a measurement error analysis as an important baseline for the interpretation of the biological significance of their results.     

Laboratory-dependent bacterial ecology: a cautionary tale

Although laboratory dependence is an acknowledged problem in microbiology, it is seldom intensively studied or discussed. We demonstrate that laboratory dependence is real and quantifiable even in the popular model Escherichia coli. Here laboratory effects alter the equilibrium composition of a simple community composed of two strains of E. coli. Our data rule out changes in the bacterial strains, chemical batches, and human handling but implicate differences in growth medium, especially the water component.     

HLA and AIDS: a cautionary tale

The human major histocompatibility complex HLA has been implicated repeatedly as a regulator of the outcome of HIV exposure and infection. A new study of long-term survivors who naturally depress HIV-1 replication and avoid the signs of AIDS for years after infection suggests that homozygosity for a group of HLA-B locus alleles termed Bw4 confers resistance, ostensibly by regulating natural killer cell-ligand interactions. However, close inspection of the accumulated evidence raises some questions and urges validation of the potential Bw4 effects in additional studies.     

Naming taxa from cladograms: a cautionary tale

The recent publication of a new hypothesis of cladistic relationships among American frogs referred to the genus Rana, accompanied by a new taxonomy and a new nomenclature of this group [Hillis D.M., Wilcox, T.P., 2005. Phylogeny of the New World true frogs (Rana). Molecular Phylogenetics and Evolution 34, 299-314], draws attention to the problems posed by the use of a "double nomenclature", following both the rules of the International Code of Zoological Nomenclature (designated here as "onomatophore-based nomenclature") and the rules of the draft Phylocode (designated here as "definition-based nomenclature"). These two nomenclatural systems, which rely upon widely different theoretical bases, are incompatible, and the latter cannot be viewed as a "modification" of the former. Accordingly, scientific names (nomina) following both systems should be clearly distinguished in scientific publications. Onomatophore-based nomina should continue to be written as they have been for about 250 years, whereas definition-based nomina should be written in a specific way, e.g., Lithobates. The combined use of both nomenclatural systems for the same taxonomy in the same paper requires good knowledge and careful respect of the rules of the Code regarding availability, allocation and validity of nomina. As shown by this example, not doing so may result in various problems, in particular in publishing nomina nuda or in using nomenclatural ranks invalid under the current Code. Attention is drawn to the fact that new nomina published without diagnostic characters are not available under the Code, and that the latter currently forbids the use of more than two ranks (subgenus and "aggregate of species") between the ranks genus and species.     

FURIN and placental syncytialisation: a cautionary tale

FURIN is a pro-protein convertase previously shown to be important for placental syncytialisation (Zhou et al. [1]), a process of cell fusion whereby placental cytotrophoblast cells fuse to form a multinucleated syncytium. This finding has been broadly accepted however, we have evidence suggesting the contrary. Spontaneously syncytialising term primary human trophoblast cells and BeWo choriocarcinoma cells were treated with either FURIN siRNA or negative control siRNA or the protease inhibitor, DEC-RVKR-CMK, or vehicle. Cells were then left to either spontaneously syncytialise (primary trophoblasts) or were induced to syncytialise with forskolin (BeWo). Effects on syncytialisation were measured by determining human chorionic gonadotrophin secretion and E-cadherin protein levels. We showed that FURIN is not important for syncytialisation in either cell type. However, in primary trophoblasts another protease also inhibited by DEC-RVKR-CMK, may be involved. Our results directly contrast with those published by Zhou et al. Zhou et al. however, used first trimester villous explants to study syncytialisation, and we used term primary trophoblasts. Therefore, we suggest that FURIN may be involved in syncytialisation of first trimester trophoblasts, but not term trophoblasts. What is more concerning is that our results using BeWo cells do not agree with their results, even though for the most part, we used the same experimental design. It is unclear why these experiments yielded different results, however we wanted to draw attention to simple differences in measuring syncytialisation or flaws in method reporting (including omission of cell line source and passage numbers, siRNA concentration and protein molecular weights) and choice of immunoblot loading controls, that could impact on experimental outcomes. Our study shows that careful reporting of methods by authors and thorough scrutiny by referees are vital. Furthermore, a universal benchmark for measuring syncytialisation is required so that various studies of syncytialisation can be validated.Subject terms: Proteases, Differentiation     

Dangerous weapons: a cautionary tale of CRISPR defence

The Cas/CRISPR system of prokaryotes is a recently recognized defence system that protects cells from invasion by foreign nucleic acids, such as plasmids or bacteriophages. Using the archaeon Sulfolobus, Gudbergsdottir et al. have demonstrated that when foreign DNA is both a target of the CRISPR system and also carries a gene that is essential for cell growth, surviving cells display mutations in the CRISPR system that eliminate the target directed spacer. This simulates natural scenarios where the invading DNA cannot be readily destroyed, such as a temperate bacteriophage that manages to evade CRISPR attack and integrate into the genome, so becoming ‘self’. CRISPR deletions ranged from precise removal of a single spacer up to elimination of an entire CRISPR array but the mechanism involved is not understood. Another surprising feature was that from one to two base mutations in the same target protospacer did not affect recognition by the Sulfolobus CRISPR system, something unexpected from studies in bacteria where spacer and target protospacer must match exactly. This study shows that even though the CRISPR system is a powerful weapon it can also be a dangerous one for the cell that carries it.