The formin FMNL3 assembles plasma membrane protrusions that participate in cell–cell adhesion

FMNL3 is a vertebrate-specific formin protein previously shown to play a role in angiogenesis and cell migration. Here we define the cellular localization of endogenous FMNL3, the dynamics of GFP-tagged FMNL3 during cell migration, and the effects of FMNL3 suppression in mammalian culture cells. The majority of FMNL3 localizes in a punctate pattern, with >95% of these puncta being indistinguishable from the plasma membrane by fluorescence microscopy. A small number of dynamic cytoplasmic FMNL3 patches also exist, which enrich near cell–cell contact sites and fuse with the plasma membrane at these sites. These cytoplasmic puncta appear to be part of larger membranes of endocytic origin. On the plasma membrane, FMNL3 enriches particularly in filopodia and membrane ruffles and at nascent cell–cell adhesions. FMNL3-containing filopodia occur both at the cell–substratum interface and at cell–cell contacts, with the latter being 10-fold more stable. FMNL3 suppression by siRNA has two major effects: decrease in filopodia and compromised cell–cell adhesion in cells migrating as a sheet. Overall our results suggest that FMNL3 functions in assembly of actin-based protrusions that are specialized for cell–cell adhesion.     

Identity cards for patients infected with HIV?

Dr A C Srivastava has written to us to describe a case that raises the suggestion that people infected with the human immuno-deficiency virus (HIV) should carry identity cards. We asked two physicians, a general practitioner working with patients with the acquired immune deficiency syndrome (AIDS), and a general practitioner with a special interest in medical ethics to respond to the broad issues raised by Dr Srivastava''s letter.     

Hepatitis C Virus Phylogenetic Clustering Is Associated with the Social-Injecting Network in a Cohort of People Who Inject Drugs

It is hypothesized that social networks facilitate transmission of the hepatitis C virus (HCV). We tested for association between HCV phylogeny and reported injecting relationships using longitudinal data from a social network design study. People who inject drugs were recruited from street drug markets in Melbourne, Australia. Interviews and blood tests took place three monthly (during 2005–2008), with participants asked to nominate up to five injecting partners at each interview. The HCV core region of individual isolates was then sequenced and phylogenetic trees were constructed. Genetic clusters were identified using bootstrapping (cut-off: 70%). An adjusted Jaccard similarity coefficient was used to measure the association between the reported injecting relationships and relationships defined by clustering in the phylogenetic analysis (statistical significance assessed using the quadratic assignment procedure). 402 participants consented to participate; 244 HCV infections were observed in 238 individuals. 26 genetic clusters were identified, with 2–7 infections per cluster. Newly acquired infection (AOR = 2.03, 95% CI: 1.04–3.96, p = 0.037, and HCV genotype 3 (vs. genotype 1, AOR = 2.72, 95% CI: 1.48–4.99) were independent predictors of being in a cluster. 54% of participants whose infections were part of a cluster in the phylogenetic analysis reported injecting with at least one other participant in that cluster during the study. Overall, 16% of participants who were infected at study entry and 40% of participants with newly acquired infections had molecular evidence of related infections with at least one injecting partner. Likely transmission clusters identified in phylogenetic analysis correlated with reported injecting relationships (adjusted Jaccard coefficient: 0.300; p<0.001). This is the first study to show that HCV phylogeny is associated with the injecting network, highlighting the importance of the injecting network in HCV transmission.     

Lanthanum as an intracellular stain for electron microscopy

Summary Results obtained after the normal aldehyde fixation of duodenal enterocytes for electron microscopy have been compared with results obtained when 0.1% Malachite Green or 10mm lanthanum chloride had been added during aldehyde fixation. Sections were examined without further staining, and after counterstaining with lead citrate and uranyl acetate. In unstained sections, lanthanum-treated material showed improved contrast when compared to results from the other two methods. Also, after counterstaining, areas showing excellent contrast were much more frequent and more readily detected in the lanthanum-treated material. In the microvilli of enterocytes fixed in the presence of lanthanum, the plasmalemma-glycocalyx was defined more clearly and the results were more pleasing subjectively. When Malachite Green was present in the fixative, good contrast was observed more frequently than in routinely fixed tissues, but less often than in those treated with lanthanum. It is suggested that the addition of lanthanum chloride or Malachite Green to the fixative may prove useful in many ultrastructural studies.     

Contributions of Speed and Accuracy to Translational Selection in Bacteria

Among bacteria, we have previously shown that species that are capable of rapid growth have stronger selection on codon usage than slow growing species, and possess higher numbers of rRNA and tRNA genes. This suggests that fast-growers are adapted for fast protein synthesis. There is also considerable evidence that codon usage is influenced by accuracy of translation, and some authors have argued that accuracy is more important than speed. Here we compare the strength of the two effects by studying the codon usages in high and low expression genes and on conserved and variable sites within high expression genes. We introduce a simple statistical method that can be used to assess the significance and the strength of the two types of bias in the same sets of sequences. We compare our statistical measure of codon bias to the common used codon adaptation index, and show that the new measure is preferable for three reasons for the purposes of this analysis. Across a large sample of bacterial genomes, both effects from speed and accuracy are clearly visible, although the speed effect appears to be much stronger than the accuracy effect and is found to be significant in a larger proportion of genomes. It is also difficult to explain the correlation of codon bias in the high expression genes with growth rates and numbers of copies of tRNA and rRNA genes on the basis of selection for accuracy. Hence we conclude that selection for translational speed is a dominant effect in driving codon usage bias in fast-growing bacteria, with selection for accuracy playing a small supplementary role.