The “erythromycin-resistance” methylated sequence of Staphylococcus aureus ribosomal RNA

We have determined the sequence of an oligonucleotide from the large ribosomal subunit RNA of Staphylococcus aureus whose methylation renders the organism resistant to erythromycin and other antibiotics (the “MLS” phenotype). Analysis of RNase A digests of [³H]methyl-, ³²P-labeled RNA yielded the sequence GG · m₂⁶A · AAGACp, where m₂⁶A is an N⁶-dimethylated adenosine residue that in sensitive cells is unmethylated. Comparison with homologous sequences recently reported for Saccharomyces cerevesiae mitochondria indicates that an A to G mutation in this latter system mimics dimethylation in St. aureus with regard to functional consequences.     

An evolutionary interpretation of the “motivation to oviposit”

The ovipositional behavior of parasitoids and other insects is often described by phrases such as “motivation to oviposit” or “ovipositional drive”. This paper shows how an evolutionary (i.e. functional) interpretation can be given to such phrases. A detailed model for the parasitisation of Sycamore aphids by M. pseudoplatani is developed, using experiments by Collins and Dixon (1986). Two models are developed: i) one in which egg complement is the only state variable and ii) one in which egg complement and information concerning host densities are state variables. Comparisons of the behaviour of simulated parasitoids, using the decisions associated with the models, and the experiments suggest that both egg complement and information are important for the parasitoid's decision making. Accepting previously parasitized hosts may be optimal, and not simply an error in parasitoid perception. A number of other detailed predictions are made, such as the relative fitness of first and second eggs in superparasitized hosts and the nature of the memory of the parasitoid.     

“Action potentials” in NEUROSPORA CRASSA, a mycelial fungus

Occasional spontaneous “action potentiais” are found in mature hyphae of the fungus Neurospora crassa. They can arise either from low-level sinusoidal oscillations of the membrane potential or from a linear slow depolarization which accelerates into a rapid upstroke at a voltage 5–20 mV depolarized from the normal resting potential (near − 180 mV). The “action potentiais” are long-lasting, 1–2 min and at the peak reach a membrane potential near −40 mV. A 2− to 8−fold increase of membrane conductance accompanies the main depolarization, but a slight decrease of membrane conductance occurs during the slow depolarization. Two plausible mechanisms for the phenomenon are (a) periodic increases of membrane permeability to inorganic ions, particularly H⁺ or Cl^- and (b) periodic decreases in activity of the major electrogenic pump (H⁺) of the Neurospora membrane, coupled with a nonlinear (inverse sigmoid) current-voltage relationship.Identification of action potential-like disturbances in fungi means that such behavior has now been found in all major biologic taxa which have been probed with suitable electrodes. As yet there is no obvious function for the events in fungi.     

Evolution of Protein Targeting into “Complex” Plastids: The “Secretory Transport Hypothesis”

Abstract: In algae different types of plastids are known, which vary in pigment content and ultrastructure, providing an opportunity to study their evolutionary origin. One interesting feature is the number of envelope membranes surrounding the plastids. Red algae, green algae and glaucophytes have plastids with two membranes. They are thought to originate from a primary endocytobiosis event, a process in which a prokaryotic cyanobacterium was engulfed by a eukaryotic host cell and transformed into a plastid. Several other algal groups, like euglenophytes and heterokont algae (diatoms, brown algae, etc.), have plastids with three or four surrounding membranes, respectively, probably reflecting the evolution of these organisms by so‐called secondary endocytobiosis, which is the uptake of a eukaryotic alga by a eukaryotic host cell. A prerequisite for the successful establishment of primary or secondary endocytobiosis must be the development of suitable protein targeting machineries to allow the transport of nucleus‐encoded plastid proteins across the various plastid envelope membranes. Here, we discuss the possible evolution of such protein transport systems. We propose that the secretory system of the respective host cell might have been the essential tool to establish protein transport into primary as well as into secondary plastids.     

“The smallest grain in the balance”

Darwin viewed evolution as a continuous force perfectly sensitive to variation. The nearly‐neutral theory of evolution says something quite different. Both may be right.     

The Exceptional “Blind” Gut of Appendicularia sicula (Appendicularia, Tunicata)

In this work, we studied for the first time the histology and ultrastructure of the gut of Appendicularia sicula and demonstrated the absence of any trace of anus. Appendicularians are small holoplanktonic tunicates, characterised by very fast ingestion and quick food transfer along their gut. The high production of faecal pellets released in the aqueous environment, associated with a high filtration rate, highlights their important role in marine ecosystems. Due to the absence of an anus, in contrast with other appendicularians, A. sicula, one of the smallest species, accumulates undigested faecal material within its body, with consequent extreme enlargement of its rectum. The gut, the epithelium of which is generally extremely reduced, is formed of an oesophagus, a globular stomach, thin proximal and mid-intestine, and a huge rectum. The latter, when filled with faecal material, may occupy most of the volume of the trunk in fully grown specimens. Although profoundly altered, the gut of these animals does show several similarities to that of Fritillaria (a genus of the same family, Fritillariidae), with which it has in common many features such as specialised mitochondrial pump cells. In A. sicula, the structural simplifications of organs seem to reach their extreme condition in comparison to other appendicularians.     

MorphoBank: phylophenomics in the “cloud”

A highly interoperable informatics infrastructure rapidly emerged to handle genomic data used for phylogenetics and was instrumental in the growth of molecular systematics. Parallel growth in software and databases to address needs peculiar to phylophenomics has been relatively slow and fragmented. Systematists currently face the challenge that Earth may hold tens of millions of species (living and fossil) to be described and classified. Grappling with research on this scale has increasingly resulted in work by teams, many constructing large phenomic supermatrices. Until now, phylogeneticists have managed data in single‐user, file‐based desktop software wholly unsuitable for real‐time, team‐based collaborative work. Furthermore, phenomic data often differ from genomic data in readily lending themselves to media representation (e.g. 2D and 3D images, video, sound). Phenomic data are a growing component of phylogenetics, and thus teams require the ability to record homology hypotheses using media and to share and archive these data. Here we describe MorphoBank, a web application and database leveraging software as a service methodology compatible with “cloud” computing technology for the construction of matrices of phenomic data. In its tenth year, and fully available to the scientific community at‐large since inception, MorphoBank enables interactive collaboration not possible with desktop software, permitting self‐assembling teams to develop matrices, in real time, with linked media in a secure web environment. MorphoBank also provides any user with tools to build character and media ontologies (rule sets) within matrices, and to display these as directed acyclic graphs. These rule sets record the phylogenetic interrelatedness of characters (e.g. if X is absent, Y is inapplicable, or X–Z characters share a media view). MorphoBank has enabled an order of magnitude increase in phylophenomic data collection: a recent collaboration by more than 25 researchers has produced a database of > 4500 phenomic characters supported by > 10 000 media.
© The Willi Hennig Society 2011.     

From “Overweight” to “About Right”: Evidence of a Generational Shift in Body Weight Norms

In this article, we describe differences in the self‐perception of weight status in the United States between the two most recent National Health and Nutrition Examination Survey (NHANES) periods (1988–1994 and 1999–2004), and test the hypothesis that secular increases in adult mean BMI, adult obesity, and childhood obesity contributed to changes over time in weight perceptions. We find that the probability of self‐classifying as overweight is significantly lower on average in the more recent survey, for both women and men, controlling for objective weight status and other factors. Among women, the decline in the tendency to self‐classify as overweight is concentrated in the 17–35 age range, and is more pronounced among women with normal BMI than those with overweight BMI. Among men, the shift away from feeling overweight is roughly equal across age groups. Overweight men exhibit a sharper decline in feeling overweight than normal weight men. Despite the declines in feeling overweight between surveys, weight misperception did not increase significantly for men and decreased by a sizable margin among women. We interpret the findings as evidence of a generational shift in social norms related to body weight. As a result, people may be less likely to desire weight loss than previously, limiting the effectiveness of public health campaigns aimed at weight reduction. On the other hand, there may be health benefits associated with improved body image.     

An “omics” approach to bridge community ecology and island biogeography

Understanding the dynamics of communities in space and time requires reconciling ecological and evolutionary processes, including colonization, adaptation, speciation and extinction. In practice, this has been challenging because empirical data obtained by traditional methods and predictive models typically focus on particular processes driving local community assembly and biogeographical structure. In this issue of Molecular Ecology, by using phylogenomics, population genomics and phenomics approaches, Darwell et al. show that ant community assembly on islands is governed by predictable eco‐evolutionary trends of geographical range expansion, adaptive radiation and local population decline. The authors provide one of the most robust lines of evidence that the evolutionary progression of island communities may often be directional and repeatable, as predicted by the concept of taxon cycles.     

From “magic bullet” to “specially engineered shotgun loads”: the new genetics and the need for individualized pharmacotherapy

Steady progress in the identification of human pharmacogenetic variants and new discoveries of disease susceptibility genes makes the old notion of one disease/one drug untenable. Advances in the ability to rapidly identify these variants, when coupled with appropriate drug delivery systems, should revolutionize pharmacotherapy. BioEssays 20 :683–685, 1998.© 1998 John Wiley & Sons Inc.     

A critique of the “ultra‐high risk” and “transition” paradigm

The transdiagnostic expression of psychotic experiences in common mental disorder (anxiety/depression/substance use disorder) is associated with a poorer prognosis, and a small minority of people may indeed develop a clinical picture that meets criteria for schizophrenia. However, it appears neither useful nor valid to observe early states of multidimensional psychopathology in young people through the “schizo”‐prism, and apply misleadingly simple, unnecessary and inefficient binary concepts of “risk” and “transition”. A review of the “ultra‐high risk” (UHR) or “clinical high risk” (CHR) literature indicates that UHR/CHR samples are highly heterogeneous and represent individuals diagnosed with common mental disorder (anxiety/depression/substance use disorder) and a degree of psychotic experiences. Epidemiological research has shown that psychotic experiences are a (possibly non‐causal) marker of the severity of multidimensional psychopathology, driving poor outcome, yet notions of “risk” and “transition” in UHR/CHR research are restrictively defined on the basis of positive psychotic phenomena alone, ignoring how baseline differences in multidimensional psychopathology may differentially impact course and outcome. The concepts of “risk” and “transition” in UHR/CHR research are measured on the same dimensional scale, yet are used to produce artificial diagnostic shifts. In fact, “transition” in UHR/CHR research occurs mainly as a function of variable sample enrichment strategies rather than the UHR/CHR “criteria” themselves. Furthermore, transition rates in UHR/CHR research are inflated as they do not exclude false positives associated with the natural fluctuation of dimensional expression of psychosis. Biological associations with “transition” thus likely represent false positive findings, as was the initial claim of strong effects of omega‐3 polyunsatured fatty acids in UHR samples. A large body of UHR/CHR intervention research has focused on the questionable outcome of “transition”, which shows lack of correlation with functional outcome. It may be more productive to consider the full range of person‐specific psychopathology in all young individuals who seek help for mental health problems, instead of “policing” youngsters for the transdiagnostic dimension of psychosis. Instead of the relatively inefficient medical high‐risk approach, a public health perspective, focusing on improved access to a low‐stigma, high‐hope, small scale and youth‐specific environment with acceptable language and interventions may represent a more useful and efficient strategy.