Molecular dynamics of synthetic leucine-serine ion channels in a phospholipid membrane

Molecular dynamics calculations were carried out on models of two synthetic leucine-serine ion channels: a tetrameric bundle with sequence (LSLLLSL)(3)NH(2) and a hexameric bundle with sequence (LSSLLSL)(3)NH(2). Each protein bundle is inserted in a palmitoyloleoylphosphatidylcholine bilayer membrane and solvated by simple point charge water molecules inside the pore and at both mouths. Both systems appear to be stable in the absence of an electric field during the 4 ns of molecular dynamics simulation. The water motion in the narrow pore of the four-helix bundle is highly restricted and may provide suitable conditions for proton transfer via a water wire mechanism. In the wider hexameric pore, the water diffuses much more slowly than in bulk but is still mobile. This, along with the dimensions of the pore, supports the observation that this peptide is selective for monovalent cations. Reasonable agreement of predicted conductances with experimentally determined values lends support to the validity of the simulations.     

Genetic engineering of Bacillus subtilis for the commercial production of riboflavin

Recombinant DNA engineering was combined with mutant selection and fermentation improvement to develop a strain of Bacillus subtilis that produces commercially attractive levels of riboflavin. The B. subtilis riboflavin production strain contains multiple copies of a modified B. subtilis riboflavin biosynthetic operon (rib operon) integrated at two different sites in the B. subtilis chromosome. The modified rib operons are expressed constitutively from strong phage promoters located at the 5′ end and in an internal region of the operon. The engineered strain also contains purine analog-resistant mutations designed to deregulate the purine pathway (GTP is the precursor for riboflavin), and a riboflavin analog-resistant mutation in ribC that deregulates the riboflavin biosynthetic pathway. Received 22 June 1998/ Accepted in revised form 6 November 1998     

A protease that increases during a period of enzymic and metabolic adjustment in Tetrahymena.

The specific activity of a neutral protease (assayed at pH 8, using azocasein as substrate) in Tetrahymena doubled or tripled within a few hours after the onset of shaking of statically grown, stationary phase cultures. The increase occurred during a period when several peroxisomal enzymes were decreasing. The increase was prevented by actinomycin D or cycloheximide, both of which also prevented the decrease in peroxisomal enzymes. Protease activity towards hemoglobin at pH 3.6 increases during this period, but to a lesser extent, while activity towards BANA (α-N-benzoyl-d,l-arginine 2-naphthylamide) was almost unchanged. The three protease activities have been partially purified by gel filtration and affinity chromatography, and are indistinguishable on this basis. Chromatography on DEAE-Sephadex yields three peaks having activity towards BANA but not towards hemoglobin and azocasein, and two peaks having activity towards all three substrates. The activities towards azocasein and hemoglobin are also indistinguishable on the basis of sensitivity to a variety of inhibitors, to temperature, and chromatography on CM Sephadex. The partially purified protease has an absolute sulfhydryl requirement when azocasein is used as substrate and is inhibited by leupeptin, chymostatin, TLCK, TPCK, and iodacetamide but not by pepstatin or PMSF. Activity towards BANA is much more susceptible to these inhibitors than is that towards azocasein. About half of the activity towards azocasein sediments with the large particle (40,000g-min) fraction. The distribution between two components of this fraction resembles that of a lysosomal marker. However, the activity did not follow the distribution of marker enzymes of any of the typical cell organelles when either subfraction was centrifuged through a sucrose density gradient, nor did it follow; the distribution pattern of the other two protease activities. Much of the activity, in fact, remained at the top of the gradient, even after repeated washings of the particulate fraction or fractionation in the presence of a membrane-stabilizing agent or a protease inhibitor. The protease or proteases appears to be in part responsible for the rapid loss of enzyme activity that is characteristic of Tetrahymena homogenates. The existence of a protease that can attack cellular enzymes at physiological pH suggests that extralysosomal breakdown of proteins can occur in a eukaryotic cell and may be of importance in the regulation of cellular enzyme levels.     

Relative stoichiometry in ribosomal proteins in HeLa cell nucleoli.

Total protein was released from isolated HeLa cell nucleoli by guanidine hydrochloride, purified by cesium chloride density gradient centrifugation, and analyzed by two-dimensional polyacrylamide gel electrophoresis. Conditions of electrophoresis restricted attention to proteins that are positively charged at pH 8.6. Most of the major nucleolar protein spots co-electrophoresed with ribosomal proteins; the majority of ribosomal proteins from both the large and small ribosomal subunits were represented. Several proteins found in association with polysomes but not on ribosomal subunits and several proteins unique to the nucleolus were also identified in these nucleolar protein patterns. In order to determine whether the ribosomal proteins found in the nucleolus represented sizable pools of ribosomal proteins, or merely ribosomal proteins contained in the preribosomal particles, [35S]methionine-labeled nucleoli were mixed with [3H]methionine-labeled polysomes. From analysis of isotopic ratios in individual protein spots it was possible to determine the stoidchiometry of individual ribosomal proteins in the nucleolus relative to their complement on cytoplasmic ribosomes. All but a few proteins exhibited relative nucleolar stoichiometry values of approximately one, indicating that there are not significant pools of most ribosomal proteins in isolated nucleoli.     

Total fertilization failure and idiopathic subfertility

Background  

To gain more insight in whether failure of intrauterine insemination (IUI) treatment in patients with idiopathic subfertility could be related to diminished fertilization, the aim of this study is to compare the fertilization of an initial IVF procedure after six cycles of IUI and the fertilization of an initial IVF procedure without preceding IUI cycles in couples with idiopathic subfertility.     

Uncertainty in ensemble forecasting of species distribution

Species distribution modelling has been widely applied in order to assess the potential impacts of climate change on biodiversity. Many methodological decisions, taken during the modelling process and forecasts, may, however, lead to a large variability in the assessment of future impacts. Using measures of species range change and turnover, the potential impacts of climate change on French stream fish species and assemblages were evaluated. Our main focus was to quantify the uncertainty in the projections of these impacts arising from four sources of uncertainty: initial datasets (Data), statistical methods [species distribution models (SDM)], general circulation models (GCM), and gas emission scenarios (GES). Several modalities of the aforementioned uncertainty sources were combined in an ensemble forecasting framework resulting in 8400 different projections. The variance explained by each source was then extracted from this whole ensemble of projections. Overall, SDM contributed to the largest variation in projections, followed by GCM, whose contribution increased over time equalling almost the proportion of variance explained by SDM in 2080. Data and GES had little influence on the variability in projections. Future projections of range change were more consistent for species with a large geographical extent (i.e., distribution along latitudinal or stream gradients) or with restricted environmental requirements (i.e., small thermal or elevation ranges). Variability in projections of turnover was spatially structured at the scale of France, indicating that certain particular geographical areas should be considered with care when projecting the potential impacts of climate change. The results of this study, therefore, emphasized that particular attention should be paid to the use of predictions ensembles resulting from the application of several statistical methods and climate models. Moreover, forecasted impacts of climate change should always be provided with an assessment of their uncertainty, so that management and conservation decisions can be taken in the full knowledge of their reliability.     

Bladder cancer stem cells

Stem cells are undifferentiated cells that renew themselves while simultaneously producing differentiated tissue- or organspecific cells through asymmetric cell division. The appreciation of the importance of stem cells in normal tissue biology has prompted the idea that cancers may also develop from a progenitor pool (the "cancer stem cell (CSC) hypothesis"), and this idea is gaining increasing acceptance among scientists. CSCs are sub-populations of cancer cells responsible for tumor initiation, differentiation, recurrence, metastasis, and drug resistance. First identified in the hematopoietic system, CSCs have also been discovered in solid tumors of the breast, colon, pancreas, and brain. Recently, the tissue-specific stem cells of the normal urothelium have been proposed to reside in the basal layer, and investigators have isolated phenotypically similar populations of cells from urothelial cancer cell lines and primary tumors. Herein, we review the CSC hypothesis and apply it to explain the development of the two different types of bladder cancer: noninvasive ("superficial") carcinoma and invasive carcinoma. We also examine potential approaches to identify CSCs in bladder cancer as well as therapeutic applications of these findings. While exciting, the verification of the existence of CSCs in bladder cancer raises several new questions. Herein, we identify and answer some of these questions to help readers better understand bladder cancer development and identify reasonable therapeutic strategy for targeting stem cells.     

Analysis of short RNAs in the malaria parasite and its red blood cell host

RNA interference (RNAi) is an RNA degradation process that involves short, double-stranded RNAs (dsRNA) as sequence specificity factors. The natural function of the RNAi machinery is to generate endogenous short double-stranded RNAs to regulate gene expression. It has been shown that treatment of Plasmodium falciparum, the etiologic agent of malaria, with dsRNA induces degradation of the corresponding microRNA (miRNA), yet typical RNAi-associated genes have not been identifiable in the parasite genome. To clarify this discrepancy we set out to clone short RNAs from P. falciparum-infected red blood cells and from purified parasites. We did not find any short RNA that was not a rRNA or tRNA fragment. Indeed, only known human miRNAs were isolated in parasite preparations indicating that very few if any short RNAs exist in P. falciparum. This suggests a different mechanism than classical RNAi in observations of dsRNA-mediated degradation. Of the human miRNAs identified, the human miRNA mir-451 accumulates at a very high level in both infected and healthy red blood cells. Interestingly, mir-451 was not detectable in a series of immortalised cell lines representing progenitor stages of all major blood lineages, suggesting that mir-451 may play a role in the differentiation of erythroid cells.