Problems in Measuring Bacterial Diversity and a Possible Solution

The indices of species diversity used by plant and animal ecologists are not appropriate for bacterial diversity because of the inherent difficulty of defining a bacterial species. Arbitrary cutoff points to define a species or biotype lead to severe statistical problems. We suggest in this paper that a mean dissimilarity-based index without any attempt to define a species provides a statistically sound measurement of bacterial diversity.     

Parameterization and classification of the protein universe via geometric techniques

We present a scheme for the classification of 3487 non-redundant protein structures into 1207 non-hierarchical clusters by using recurring structural patterns of three to six amino acids as keys of classification. This results in several signature patterns, which seem to decide membership of a protein in a functional category. The patterns provide clues to the key residues involved in functional sites as well as in protein-protein interaction. The discovered patterns include a "glutamate double bridge" of superoxide dismutase, the functional interface of the serine protease and inhibitor, interface of homo/hetero dimers, and functional sites of several enzyme families. We use geometric invariants to decide superimposability of structural patterns. This allows the parameterization of patterns and discovery of recurring patterns via clustering. The geometric invariant-based approach eliminates the computationally explosive step of pair-wise comparison of structures. The results provide a vast resource for the biologists for experimental validation of the proposed functional sites, and for the design of synthetic enzymes, inhibitors and drugs.     

Oligophilic bacteria as tools to monitor aseptic pharmaceutical production units

The bacterial loads of air, surfaces, and personnel in clean rooms are routinely monitored using a set of standard media. Bacteria that can grow on these media are a tiny fraction of the total numbers in any environment. A substantial proportion of bacteria long thought to be unculturable were recently shown to be oligophilic. Oligophile counts in clean rooms in our studies exceeded the standard plate counts by up to 2 orders of magnitude. They responded to disinfection routines in ways similar to the responses of conventional bacteria. We suggest that oligophiles are better tools than conventional bacteria for environmental monitoring in aseptic pharmaceutical production units.     

The amino acid requirements of Corynebacterium diphtheriae PW 8 substrain CN 2000

AIMS: To determine the amino acid requirement and utilization pattern of Corynebacterium diphtheriae during growth and toxin production. METHODS AND RESULTS: Comparing across different batches of beef-based media, the growth and toxin yield were correlated significantly with nine of the amino acids. The amino acid utilization pattern during growth of C. diphtheriae further showed that only four of the nine amino acids, namely cystine, histidine, aspartate and methionine, were critical for growth of the vaccine strain. Further investigations using synthetic media with combinations of amino acid supplements demonstrated that among the four, cystine was the most growth limiting. CONCLUSIONS: Only certain amino acids are critical for growth and toxin production by C. diphtheriae, cystine being the single most important. SIGNIFICANCE AND IMAPCT OF THE STUDY: Owing to the potential threat from Bovine Spongiform Encephalopathy (BSE), a need is recognized by vaccine manufacturers to substitute beef-based production media. An understanding of the specific amino acid requirements would help to develop and optimize alternative production media.     

Inhibitors of Abeta production: solid-phase synthesis and SAR of alpha-hydroxycarbonyl derivatives

Inhibitors of amyloid-beta (Abeta) protein production have been widely pursued as a potential treatment for Alzheimer's disease. Following the identification of a 5 microM screening hit, SAR was initiated using solid-phase synthetic techniques. Two series of alpha-hydroxy esters and ketones which are sub-micromolar inhibitors of Abeta production were identified. The most potent alpha-hydroxyketone identified is approximately 30-fold more potent than the initial lead.     

Serum-Induced Differentiation of Glioblastoma Neurospheres Leads to Enhanced Migration/Invasion Capacity That Is Associated with Increased MMP9

Glioblastoma (GBM) is a highly infiltrative brain tumor in which cells with properties of stem cells, called glioblastoma stem cells (GSCs), have been identified. In general, the dominant view is that GSCs are responsible for the initiation, progression, invasion and recurrence of this tumor. In this study, we addressed the question whether the differentiation status of GBM cells is associated with their invasive capacity. For this, several primary GBM cell lines were used, cultured either as neurospheres known to enrich for GSCs or in medium supplemented with 10% FCS that promotes differentiation. The differentiation state of the cells was confirmed by determining the expression of stem cell and differentiation markers. The migration/invasion potential of these cells was tested using in vitro assays and intracranial mouse models. Interestingly, we found that serum-induced differentiation enhanced the invasive potential of GBM cells, which was associated with enhanced MMP9 expression. Chemical inhibition of MMP9 significantly reduced the invasive potential of differentiated cells in vitro. Furthermore, the serum-differentiated cells could revert back to an undifferentiated/stem cell state that were able to form neurospheres, although with a reduced efficiency as compared to non-differentiated counterparts. We propose a model in which activation of the differentiation program in GBM cells enhances their infiltrative potential and that depending on microenvironmental cues a significant portion of these cells are able to revert back to an undifferentiated state with enhanced tumorigenic potential. Thus, effective therapy should target both GSCs and differentiated offspring and targeting of differentiation-associated pathways may offer therapeutic opportunities to reduce invasive growth of GBM.     

Presence of two types of flowers with respect to nectar sugar in two gregariously flowering species

Many species of animal-pollinated flowers are known to vary widely in the nectar content of flowers. Some proportion of flowers in many species is apparently nectarless, and such flowers are believed to be ‘cheaters’. Cheating may explain a part of the variability in nectar content. If cheating exists as a qualitatively different strategy then we expect bimodality in the distribution of nectar content of flowers. It has been shown in a multispecies study that gregarious species have a higher proportion of cheater flowers. We studied the frequency distribution of total nectar sugar in two gregariously flowering species Lantana camara and Utricularia purpurascens, which differed in other floral and ecological characters. At the population level, both the species showed significant bimodality in the total sugar content of flowers. The obvious sources of heterogeneity in the data did not explain bimodality. In Lantana camara, bimodality was observed within flowers of some of the individual plants sampled. In Utricularia purpurascens the proportion of nectarless flowers was more in high-density patches, suggesting that the gregariousness hypothesis may work within a species as well. The results support the hypothesis of cheating as a distinct strategy since two distinct types of flowers were observed in both the species. The effect of density in Utricularia purpurascens also supports the gregariousness hypothesis.