Random drift versus selection in academic vocabulary: an evolutionary analysis of published keywords

The evolution of vocabulary in academic publishing is characterized via keyword frequencies recorded in the ISI Web of Science citations database. In four distinct case-studies, evolutionary analysis of keyword frequency change through time is compared to a model of random copying used as the null hypothesis, such that selection may be identified against it. The case studies from the physical sciences indicate greater selection in keyword choice than in the social sciences. Similar evolutionary analyses can be applied to a wide range of phenomena; wherever the popularity of multiple items through time has been recorded, as with web searches, or sales of popular music and books, for example.     

Analysis of 17,576 potentially functional SNPs in three case-control studies of myocardial infarction

Myocardial infarction (MI) is a common complex disease with a genetic component. While several single nucleotide polymorphisms (SNPs) have been reported to be associated with risk of MI, they do not fully explain the observed genetic component of MI. We have been investigating the association between MI and SNPs that are located in genes and have the potential to affect gene function or expression. We have previously published studies that tested about 12,000 SNPs for association with risk of MI, early-onset MI, or coronary stenosis. In the current study we tested 17,576 SNPs that could affect gene function or expression. In order to use genotyping resources efficiently, we staged the testing of these SNPs in three case-control studies of MI. In the first study (762 cases, 857 controls) we tested 17,576 SNPs and found 1,949 SNPs that were associated with MI (P<0.05). We tested these 1,949 SNPs in a second study (579 cases and 1159 controls) and found that 24 SNPs were associated with MI (1-sided P<0.05) and had the same risk alleles in the first and second study. Finally, we tested these 24 SNPs in a third study (475 cases and 619 controls) and found that 5 SNPs in 4 genes (ENO1, FXN (2 SNPs), HLA-DPB2, and LPA) were associated with MI in the third study (1-sided P<0.05), and had the same risk alleles in all three studies. The false discovery rate for this group of 5 SNPs was 0.23. Thus, we have identified 5 SNPs that merit further examination for their potential association with MI. One of these SNPs (in LPA), has been previously shown to be associated with risk of cardiovascular disease in other studies.     

Identification and characterization of small molecule inhibitors of Plasmodium falciparum dihydroorotate dehydrogenase

Plasmodium falciparum causes the most deadly form of malaria and accounts for over one million deaths annually. The malaria parasite is unable to salvage pyrimidines and relies on de novo biosynthesis for survival. Dihydroorotate dehydrogenase (DHOD), a mitochondrially localized flavoenzyme, catalyzes the rate-limiting step of this pathway and is therefore an attractive antimalarial chemotherapeutic target. Using a target-based high throughput screen, we have identified a series of potent, species-specific inhibitors of P. falciparum DHOD (pfDHOD) that are also efficacious against three cultured strains (3D7, HB3, and Dd2) of P. falciparum. The primary antimalarial mechanism of action of these compounds was confirmed to be inhibition of pfDHOD through a secondary assay with transgenic malaria parasites, and the structural basis for enzyme inhibition was explored through in silico structure-based docking and site-directed mutagenesis. Compound-mediated cytotoxicity was not observed with human dermal fibroblasts or renal epithelial cells. These data validate pfDHOD as an antimalarial drug target and provide chemical scaffolds with which to begin medicinal chemistry efforts.     

Novel role of the muskelin-RanBP9 complex as a nucleocytoplasmic mediator of cell morphology regulation

The evolutionarily conserved kelch-repeat protein muskelin was identified as an intracellular mediator of cell spreading. We discovered that its morphological activity is controlled by association with RanBP9/RanBPM, a protein involved in transmembrane signaling and a conserved intracellular protein complex. By subcellular fractionation, endogenous muskelin is present in both the nucleus and the cytosol. Muskelin subcellular localization is coregulated by its C terminus, which provides a cytoplasmic restraint and also controls the interaction of muskelin with RanBP9, and its atypical lissencephaly-1 homology motif, which has a nuclear localization activity which is regulated by the status of the C terminus. Transient or stable short interfering RNA–based knockdown of muskelin resulted in protrusive cell morphologies with enlarged cell perimeters. Morphology was specifically restored by complementary DNAs encoding forms of muskelin with full activity of the C terminus for cytoplasmic localization and RanBP9 binding. Knockdown of RanBP9 resulted in equivalent morphological alterations. These novel findings identify a role for muskelin–RanBP9 complex in pathways that integrate cell morphology regulation and nucleocytoplasmic communication.     

Prediction of fluid forces acting on a hand model in unsteady flow conditions

The aim of this study was to develop a method to predict fluid forces acting on the human hand in unsteady flow swimming conditions. A mechanical system consisting of a pulley and chain mechanism and load cell was constructed to rotate a hand model in fluid flows. To measure the angular displacement of the hand model a potentiometer was attached to the axis of the rotation. The hand model was then fixed at various angles about the longitudinal axis of the hand model and rotated at different flow velocities in a swimming flume for 258 different trials to approximate a swimmer's stroke in unsteady flow conditions. Pressures were taken from 12 transducers embedded in the hand model at a sampling frequency of 200Hz. The resultant fluid force acting on the hand model was then determined on the basis of the kinetic and kinematic data taken from the mechanical system at the frequency of 200Hz. A stepwise regression analysis was applied to acquire higher order polynomial equations that predict the fluid force acting on the accelerating hand model from the 12 pressure values. The root mean square (RMS) difference between the resultant fluid force measured and that predicted from the single best-fit polynomial equation across all trials was 5N. The method developed in the present study accurately predicted the fluid forces acting on the hand model.     

The PHB1/2 phosphocomplex is required for mitochondrial homeostasis and survival of human T cells

Many immune pathologies are the result of aberrant regulation of T lymphocytes. A functional proteomics approach utilizing two-dimensional gel electrophoresis coupled with mass spectrometry was employed to identify differentially expressed proteins in response to T cell activation. Two members of the prohibitin family of proteins, Phb1 and Phb2, were determined to be up-regulated 4-5-fold upon activation of primary human T cells. Furthermore, their expression was dependent upon CD3 and CD28 signaling pathways that synergistically led to the up-regulation (13-15-fold) of Phb1 and Phb2 mRNA levels as early as 48 h after activation. Additionally, orthophosphate labeling coupled with phosphoamino acid analysis identified Phb1 to be serine and Phb2 serine and tyrosine phosphorylated. Tyrosine phosphorylation of Phb2 was mapped to Tyr248 using mass spectrometry and confirmed by mutagenesis and phosphospecific antibodies. In contrast to previous reports of Phb1 and Phb2 being nuclear localized, subcellular fractionation, immunofluorescent, and electron microscopy revealed both proteins to localize to the mitochondrial inner membrane of human T cells. Accordingly, small interfering RNA-mediated knockdown of Phbs in Kit225 cells resulted in disruption of mitochondrial membrane potential. Additionally, Phb1 and Phb2 protein levels were up-regulated 2.5-fold during cytokine deprivation-mediated apoptosis of Kit225 cells, suggesting this complex plays a protective role in human T cells. Taken together, Phb1 and Phb2 are novel phosphoproteins up-regulated during T cell activation that function to maintain mitochondrial integrity and thus represent previously unrecognized therapeutic targets for regulating T cell activation, differentiation, viability, and function.     

The emergence of automated high-frequency flow cytometry: revealing temporal and spatial phytoplankton variability

Phytoplankton observation is the product of a number of trade-offsrelated to sampling processes, required level of diversity andsize spectrum analysis capabilities of the techniques involved.Instruments combining the morphological and high-frequency analysisfor phytoplankton cells are now available. This paper presentsan application of the automated high-resolution flow cytometerCytosub as a tool for analysing phytoplanktonic cells in theirnatural environment. High resolution data from a temporal studyin the Bay of Marseille (analysis every 30 min over 1 month)and a spatial study in the Southern Indian Ocean (analysis every5 min at 10 knots over 5 days) are presented to illustrate thecapabilities and limitations of the instrument. Automated high-frequencyflow cytometry revealed the spatial and temporal variabilityof phytoplankton in the size range 1–50 µm thatcould not be resolved otherwise. Due to some limitations (instrumentalmemory, volume analysed per sample), recorded counts could bestatistically too low. By combining high-frequency consecutivesamples, it is possible to decrease the counting error, followingPoisson’s law, and to retain the main features of phytoplanktonvariability. With this technique, the analysis of phytoplanktonvariability combines adequate sampling frequency and effectivemonitoring of community changes.     

Predominance of a bacteriocin-producing Lactobacillus salivarius component of a five-strain probiotic in the porcine ileum and effects on host immune phenotype

Relative predominance of each of five probiotic strains was investigated in the ileum of weaned pigs, compared with that in feces, when administered in combination at c. 5 x 10(9) CFU day(-1) for 28 days. Probiotic was excreted at 10(6)-10(9) CFU g(-1) feces, while ileal survival ranged from 10(2) to 10(6) CFU g(-1) digesta. In contrast to the feces, where Lactobacillus murinus DPC6002 predominated, the bacteriocin-producing Lactobacillus salivarus DPC6005 dominated over coadministered strains both in the ileum digesta and in mucosa. Probiotic administration did not alter counts of culturable fecal Lactobacillus or Enterobacteriaceae but higher ileal Enterobacteriaceae were observed in the ileal digesta of probiotic-fed pigs (P<0.05). We observed decreased CD25 induction on T cells and monocytes (P<0.01) and decreased CTLA-4 induction (P<0.05) by the mitogen phytohemagglutinin on CD4 T cells from the probiotic group. Probiotic treatment also increased the proportion of CD4+ CD8+ T cells within the peripheral T-cell population and increased ileal IL-8 mRNA expression (P<0.05). In conclusion, superior ileal survival of L. salivarius compared with the other coadministered probiotics may be due to a competitive advantage conferred by its bacteriocin. The findings also suggest that the five-strain combination may function as a probiotic, at least in part, via immunomodulation.     

Prevalence of Cryptosporidium genotypes in pre and post-weaned pigs in Australia

A total of 289 pig faecal samples were collected from pre-weaned and post-weaned piglets and sows from 1 indoor and 3 outdoor piggeries located in the south-west region of Western Australia and screened at the 18S rRNA locus for the presence of Cryptosporidium. An overall prevalence of 22.1% (64/289) was identified. Cryptosporidium was more prevalent in post-weaned animals (p < 0.05); 32.7% (51/156) versus 10.6% (13/123) for pre-weaned animals. Sequence analysis identified Cryptosporidium suis in all pre-weaned isolates genotyped (7/13). In post-weaned pigs that were genotyped (n = 38), the non-zoonotic Cryptosporidium species, pig genotype II was identified in 32 samples and C. suis in 6 samples. The zoonotic species Cryptosporidium parvum was not detected, suggesting that domestic pigs do not pose a significant public health risk. Pig genotype II was significantly (p < 0.05) associated with ‘normal’ stools, indicating an asymptomatic nature in the porcine host.