Isolation and characterization of a new CO-utilizing strain, Thermoanaerobacter thermohydrosulfuricus subsp. carboxydovorans, isolated from a geothermal spring in Turkey

A novel anaerobic, thermophilic, Gram-positive, spore-forming, and sugar-fermenting bacterium (strain TLO) was isolated from a geothermal spring in Ayaş, Turkey. The cells were straight to curved rods, 0.4–0.6 μm in diameter and 3.5–10 μm in length. Spores were terminal and round. The temperature range for growth was 40–80°C, with an optimum at 70°C. The pH optimum was between 6.3 and 6.8. Strain TLO has the capability to ferment a wide variety of mono-, di-, and polysaccharides and proteinaceous substrates, producing mainly lactate, next to acetate, ethanol, alanine, H₂, and CO₂. Remarkably, the bacterium was able to grow in an atmosphere of up to 25% of CO as sole electron donor. CO oxidation was coupled to H₂ and CO₂ formation. The G + C content of the genomic DNA was 35.1 mol%. Based on 16S rRNA gene sequence analysis and the DNA–DNA hybridization data, this bacterium is most closely related to Thermoanaerobacter thermohydrosulfuricus and Thermoanaerobacter siderophilus (99% similarity for both). However, strain TLO differs from Thermoanaerobacter thermohydrosulfuricus in important aspects, such as CO-utilization and lipid composition. These differences led us to propose that strain TLO represents a subspecies of Thermoanaerobacter thermohydrosulfuricus, and we therefore name it Thermoanaerobacter thermohydrosulfuricus subsp. carboxydovorans.     

Sponge-Cell Culture? A Molecular Identification Method for Sponge Cells

Dissociated sponge cells are easily confused with unicellular organisms. This has been an obstacle in the development of sponge-cell lines. We developed a molecular detection method to identify cells of the sponge Dysidea avara in dissociated cell cultures. The 18S ribosomal RNA gene from a Dysidea avara specimen was sequenced and compared to eukaryotic 18S rDNA sequences picked up from a proliferating cell culture that originated from a dissociated Dysidea avara specimen. Our method proved unambiguously that this was not a sponge-cell culture. Therefore, it provides a valuable tool for further research on sponge-cell cultures.     

Extending McNemar's test: estimation and inference when paired binary outcome data are misclassified

McNemar's test is popular for assessing the difference between proportions when two observations are taken on each experimental unit. It is useful under a variety of epidemiological study designs that produce correlated binary outcomes. In studies involving outcome ascertainment, cost or feasibility concerns often lead researchers to employ error-prone surrogate diagnostic tests. Assuming an available gold standard diagnostic method, we address point and confidence interval estimation of the true difference in proportions and the paired-data odds ratio by incorporating external or internal validation data. We distinguish two special cases, depending on whether it is reasonable to assume that the diagnostic test properties remain the same for both assessments (e.g., at baseline and at follow-up). Likelihood-based analysis yields closed-form estimates when validation data are external and requires numeric optimization when they are internal. The latter approach offers important advantages in terms of robustness and efficient odds ratio estimation. We consider internal validation study designs geared toward optimizing efficiency given a fixed cost allocated for measurements. Two motivating examples are presented, using gold standard and surrogate bivariate binary diagnoses of bacterial vaginosis (BV) on women participating in the HIV Epidemiology Research Study (HERS).     

Population momentum and the demand on land and water resources

Future world population growth is fuelled by two components: the demographic momentum, which is built into the age composition of current populations, and changes in reproductive behaviour and mortality of generations yet to come. This paper investigates, by major world regions and countries, what we know about population growth, what can be projected with reasonable certainty, and what is pure speculation. The exposition sets a frame for analysing demographic driving forces that are expected to increase human demand and pressures on land and water resources. These have been contrasted with current resource assessments of regional availability and use of land, in particular with estimates of remaining land with cultivation potential. In establishing a balance between availabilty of land resources and projected needs, the paper distinguishes regions with limited land and water resources and high population pressure from areas with abundant resources and low or moderate demographic demand. Overall, it is estimated that two-thirds of the remaining balance of land with rainfed cultivation potential is currently covered by various forest ecosystems and wetlands. The respective percentages by region vary between 23% in Southern Africa to 89% in South-Eastern Asia. For Latin America and Asia the estimated share of the balance of land with cultivation potential under forest and wetland ecosystems is about 70%, in Africa this is about 60%. If these were to be preserved, the remaining balance of land with some potential for rainfed crop cultivation would amount to some 550 million hectares. The regions which will experience the largest difficulties in meeting future demand for land resources and water, or alternatively have to cope with much increased dependency on external supplies, include foremost Western Asia, South-Central Asia, and Northern Africa. A large stress on resources is to be expected also in many countries of Eastern, Western and Southern Africa <br>     

High temporal and inter‐individual variation detected in the human ileal microbiota

The diversity and temporal stability of the predominant bacteria in the human ileum was studied with the use of ileal effluent samples of seven individuals with Brooke ileostomies. The total number of bacteria within the ileal effluent was in the range of 10⁷–10⁸ bacteria per gram (wet weight). The diversity of the bacteria in the ileal effluent showed marked differences compared with that in faecal samples from age‐matched healthy adults. The ileal effluent had a higher relative abundance of species within the orders Lactobacillales and Clostridiales, mainly Streptococcus bovis‐related species, and the Veillonella group, and a lower proportion of species related to Ruminococcus gnavus, R. obeum and Bacteroides plebeius. In addition, inter‐individual differences were found, indicative of a highly personal ileal microbiota profile. Furthermore, temporal profiles showed large fluctuations per individual over a period of 9–28 days (average similarity over a period of 9 days was as low as 44%), and differences between morning and afternoon profiles were observed. Parallel cloning and sequencing efforts revealed several phylotypes that were not identified in previous studies (12 out of 65 phylotypes showed less than 97% sequence similarity with previously reported sequences). Achaea were found to be below detection limit by quantitative PCR. Overall, the results indicate that the microbiota of the human ileum is relatively unstable, less complex and consisting of different dominating phylotypes when compared with the colonic microbiota.     

Septum formation is regulated by the RHO4‐specific exchange factors BUD3 and RGF3 and by the landmark protein BUD4 in Neurospora crassa

Rho GTPases have multiple, yet poorly defined functions during cytokinesis. By screening a Neurospora crassa knock‐out collection for Rho guanine nucleotide exchange factor (GEF) mutants that phenocopy rho‐4 defects (i.e. lack of septa, slow growth, abnormal branching and cytoplasmic leakage), we identified two strains defective in homologues of Bud3p and Rgf3 of budding and fission yeast respectively. The function of these proteins as RHO4‐specific GEFs was determined by in vitro assays. In vivo microscopy suggested that the two GEFs and their target GTPase act as two independent modules during the selection of the septation site and the actual septation process. Furthermore, we determined that the N. crassa homologue of the anillinrelated protein BUD4 is required for septum initiation and that its deficiency leads to typical rho4 defects. Localization of BUD4 as a cortical ring prior to septation initiation was independent of functional BUD3 or RGF3. These data position BUD4 upstream of both RHO4 functions in the septation process and make BUD4 a prime candidate for a cortical marker protein involved in the selection of future septation sites. The persistence of both BUD proteins and of RHO4 at the septal pore suggests additional functions of these proteins at mature septa.     

A one-step efficient and specific non-radioactive non-fluorescent method for in situ hybridization of banded chromosomes

A non-radioactive method for in situ hybridization of cosmid probes to metaphase chromosomes is described. Two procedures are involved: (i) hybridization with a cosmid probe labelled by nick translation in the presence of digoxigenin dUTP. The signal is visualized by an alkaline phosphatase conjugated antibody. (ii) FPG banding of the chromosomes. The steps involved in these two procedures are combined in an order which allows simultaneous observation of the banding pattern and the hybridization signal. The metaphases can thus be analysed after a single photographic step. This technique is considerably simpler than the method used previously.