Small colony variants: a pathogenic form of bacteria that facilitates persistent and recurrent infections

Small colony variants constitute a slow-growing subpopulation of bacteria with distinctive phenotypic and pathogenic traits. Phenotypically, small colony variants have a slow growth rate, atypical colony morphology and unusual biochemical characteristics, making them a challenge for clinical microbiologists to identify. Clinically, small colony variants are better able to persist in mammalian cells and are less susceptible to antibiotics than their wild-type counterparts, and can cause latent or recurrent infections on emergence from the protective environment of the host cell. This Review covers the phenotypic, genetic and clinical picture associated with small colony variants, with an emphasis on staphylococci, for which the greatest amount of information is available.     

Microphytobenthos of Arctic Kongsfjorden (Svalbard, Norway): biomass and potential primary production along the shore line

During summer 2007, Arctic microphytobenthic potential primary production was measured at several stations around the coastline of Kongsfjorden (Svalbard, Norway) at ≤5 m water depth and at two stations at five different water depths (5, 10, 15, 20, 30 m). Oxygen planar optode sensor spots were used ex situ to determine oxygen exchange in the overlying water of intact sediment cores under controlled light (ca. 100 μmol photons m⁻² s⁻¹) and temperature (2–4°C) conditions. Patches of microalgae (mainly diatoms) covering sandy sediments at water depths down to 30 m showed high biomass of up to 317 mg chl a m⁻². In spite of increasing water depth, no significant trend in “photoautotrophic active biomass” (chl a, ratio living/dead cells, cell sizes) and, thus, in primary production was measured at both stations. All sites from ≤5 to 30 m water depth exhibited variable rates of net production from −19 to +40 mg O₂ m⁻² h⁻¹ (−168 to +360 mg C m⁻² day⁻¹) and gross production of about 2–62 mg O₂ m⁻² h⁻¹ (17–554 mg C m⁻² day⁻¹), which is comparable to other polar as well as temperate regions. No relation between photoautotrophic biomass and gross/net production values was found. Microphytobenthos demonstrated significant rates of primary production that is comparable to pelagic production of Kongsfjorden and, hence, emphasised the importance as C source for the zoobenthos.     

The Interplay of Proton,Electron, and Metabolite Supply for Photosynthetic H2 Production in Chlamydomonas reinhardtii

To obtain a detailed picture of sulfur deprivation-induced H₂ production in microalgae, metabolome analyses were performed during key time points of the anaerobic H₂ production process of Chlamydomonas reinhardtii. Analyses were performed using gas chromatography coupled to mass spectrometry (GC/MS), two-dimensional gas chromatography combined with time-of-flight mass spectrometry (GCxGC-TOFMS), lipid and starch analysis, and enzymatic determination of fermentative products. The studies were designed to provide a detailed metabolite profile of the solar Bio-H₂ production process. This work reports on the differential analysis of metabolic profiles of the high H₂-producing strain Stm6Glc4 and the wild-type cc406 (WT) before and during the H₂ production phase. Using GCxGC-TOFMS analysis the number of detected peaks increased from 128 peaks, previously detected by GC/MS techniques, to ∼1168. More detailed analysis of the anaerobic H₂ production phase revealed remarkable differences between wild-type and mutant cells in a number of metabolic pathways. Under these physiological conditions the WT produced up to 2.6 times more fatty acids, 2.2 times more neutral lipids, and up to 4 times more fermentation products compared with Stm6Glc4. Based on these results, specific metabolic pathways involving the synthesis of fatty acids, neutral lipids, and fermentation products during anaerobiosis in C. reinhardtii have been identified as potential targets for metabolic engineering to further enhance substrate supply for the hydrogenase(s) in the chloroplast.     

Temperature and light requirements for growth of two diatom species (Bacillariophyceae) isolated from an Arctic macroalga

In the present study, two abundant epiphytic diatom taxa were isolated from the assimilation hairs of the brown macroalga Chordaria flagelliformis collected in the Arctic Kongsfjorden (Spitsbergen, Norway), established as unialgal cultures and their growth rates determined under controlled photon fluence rate and temperature conditions. Using morphological (light and scanning electron microscopy) and SSU rRNA gene data both isolates (ROS D99 and ROS D125) were identified as members of a Fragilaria–Synedropsis clade. The molecular data of ROS D99 and ROS D125 were not identical to any other published sequence. While ROS D99 has been identified as Fragilaria barbararum mainly due to the SEM characteristics, ROS D125 could not be definitely identified although morphological data speak for Fragilaria striatula. Both diatom species showed similar growth rates at all temperatures and photon fluence rates tested. They grew well between 0 and 15°C with optimum temperatures of 12–14°C, but did not survive 20°C. Therefore, compared to Antarctic diatoms both taxa from Kongsfjorden can be characterised as eurythermal organisms. Increasing photon fluence rates between 2 and 15 μmol m⁻² s⁻¹ were accompanied with an almost twofold increase in growth rates, but photon fluence rates >15 μmol m⁻² s⁻¹ did not further enhance growth pointing to low light requirements. From these data optimum, minimum and maximum photon fluence rates and temperatures for growth can be assessed indicating that both diatoms are well acclimated to the fluctuating environmental conditions in the Arctic habitat.     

The role of the integral membrane nucleoporins Ndc1p and Pom152p in nuclear pore complex assembly and function

The nuclear pore complex (NPC) is a large channel that spans the two lipid bilayers of the nuclear envelope and mediates transport events between the cytoplasm and the nucleus. Only a few NPC components are transmembrane proteins, and the role of these proteins in NPC function and assembly remains poorly understood. We investigate the function of the three integral membrane nucleoporins, which are Ndc1p, Pom152p, and Pom34p, in NPC assembly and transport in Saccharomyces cerevisiae. We find that Ndc1p is important for the correct localization of nuclear transport cargoes and of components of the NPC. However, the role of Ndc1p in NPC assembly is partially redundant with Pom152p, as cells lacking both of these proteins show enhanced NPC disruption. Electron microscopy studies reveal that the absence of Ndc1p and Pom152p results in aberrant pores that have enlarged diameters and lack proteinaceous material, leading to an increased diffusion between the cytoplasm and the nucleus.     

Integrating structured biological data by Kernel Maximum Mean Discrepancy

MOTIVATION: Many problems in data integration in bioinformatics can be posed as one common question: Are two sets of observations generated by the same distribution? We propose a kernel-based statistical test for this problem, based on the fact that two distributions are different if and only if there exists at least one function having different expectation on the two distributions. Consequently we use the maximum discrepancy between function means as the basis of a test statistic. The Maximum Mean Discrepancy (MMD) can take advantage of the kernel trick, which allows us to apply it not only to vectors, but strings, sequences, graphs, and other common structured data types arising in molecular biology. RESULTS: We study the practical feasibility of an MMD-based test on three central data integration tasks: Testing cross-platform comparability of microarray data, cancer diagnosis, and data-content based schema matching for two different protein function classification schemas. In all of these experiments, including high-dimensional ones, MMD is very accurate in finding samples that were generated from the same distribution, and outperforms its best competitors. Conclusions: We have defined a novel statistical test of whether two samples are from the same distribution, compatible with both multivariate and structured data, that is fast, easy to implement, and works well, as confirmed by our experiments. AVAILABILITY: http://www.dbs.ifi.lmu.de/~borgward/MMD.     

Identification of linear plasmid pAM1 in the flavonoid degrading strain Actinoplanes missouriensis(T) (DSM 43046)

By pulsed-field gel electrophoresis, a linear DNA element of about 100 kb was identified in Actinoplanes missouriensis(T) DSM 43046, which grows on the flavonoids hesperidin, rutin and quercetin, and which contains a CO forming quercetinase. Among six Actinoplanes species and strains tested, including A. globisporus(T) DSM 43857, A. philippinensis(T) DSM 43019, A. brasiliensis(T) DSM 43805, A. auranticolor(T) DSM 43031, and A. utahensis(T) DSM 43147, only the A. missouriensis strain exhibited such a genetic element. The linear plasmid, named pAM1, has proteins covalently attached to its 5'-ends like other linear replicons of actinomycetes. Attempts to cure pAM1 failed, however a mutant with reduced plasmid content was obtained, which showed reduced ability to degrade the flavonoid rutinosides rutin and hesperidin. Plasmid pAM1 is the first extrachromosomal genetic element identified in an Actinoplanes species and may be useful to develop genetic tools for biotechnologically important Actinoplanes strains.