Evaluation of denoising algorithms for biological electron tomography

Tomograms of biological specimens derived using transmission electron microscopy can be intrinsically noisy due to the use of low electron doses, the presence of a "missing wedge" in most data collection schemes, and inaccuracies arising during 3D volume reconstruction. Before tomograms can be interpreted reliably, for example, by 3D segmentation, it is essential that the data be suitably denoised using procedures that can be individually optimized for specific data sets. Here, we implement a systematic procedure to compare various nonlinear denoising techniques on tomograms recorded at room temperature and at cryogenic temperatures, and establish quantitative criteria to select a denoising approach that is most relevant for a given tomogram. We demonstrate that using an appropriate denoising algorithm facilitates robust segmentation of tomograms of HIV-infected macrophages and Bdellovibrio bacteria obtained from specimens at room and cryogenic temperatures, respectively. We validate this strategy of automated segmentation of optimally denoised tomograms by comparing its performance with manual extraction of key features from the same tomograms.     

Differential expression of iutA and ibeA in the early stages of infection by extra-intestinal pathogenic E. coli

Extraintestinal pathogenic Escherichia coli strains are responsible for a number of infections in humans and animals. Several ExPEC virulence genes have already been described such as iutA involved in iron acquisition and ibeA required for invasion of eukaryotic cells. In this study we used the chicken model to study the expression of iutA and ibeA by two ExPEC strains during growth of bacteria in LB medium and during the infection. Expression of iutA and ibeA were shown to be higher in stationary phase than in exponential phase in vitro. During infection, iutA expression was increased at least 50-fold in the airsac and in the lung 3, 6 and 24h. p.i. compared to in vitro grown bacteria. Expression of ibeA was increased 2.5-9-fold in the airsac in the early stages of the infection only. This is the first report analyzing quantitatively the expression of ExPEC virulence genes during the course of the infection. The model described could be useful to study the expression of other ExPEC virulence genes.     

Variation in Chemical Composition and Antibacterial Activity of the Essential Oil of Wild Populations of Phlomis olivieri

Various species of the genus Phlomis have been reported to produce metabolites demonstrating significant pharmacological efficiency. In this study, the essential oils from twelve populations of Phlomis olivieri collected from natural habitats were investigated for their chemical components. The hydrodistillated essential oil analyzed by GC‐FID and GC/MS. Analyses revealed 27 compounds, constituting 90.52 – 98.51% of the essential oils. Results indicated that the major components of the essential oils from various populations of P. olivieri were germacrene D (26.54 – 56.41%), bicyclogermacrene (6.38 – 30.55%), β‐caryophyllene (5.32 – 24.52%) and α‐pinene (1.29 – 15.53%). Principal component analyses (PCA) was used to identify any geographical variations in essential oil composition. Notably, three groups of Iranian P. olivieri populations were determined according to the major compounds. Results of the in vitro antibacterial activity indicated that P. olivieri essential oils showed good inhibitory activities against bacteria, especially Bacillus subtilis. The results of this study gave new insights for cultivation and industrial uses of P. olivieri in Iran.     

Nesprin-3, a novel outer nuclear membrane protein, associates with the cytoskeletal linker protein plectin

Despite their importance in cell biology, the mechanisms that maintain the nucleus in its proper position in the cell are not well understood. This is primarily the result of an incomplete knowledge of the proteins in the outer nuclear membrane (ONM) that are able to associate with the different cytoskeletal systems. Two related ONM proteins, nuclear envelope spectrin repeat (nesprin)-1 and -2, are known to make direct connections with the actin cytoskeleton through their NH2-terminal actin-binding domain (ABD). We have now isolated a third member of the nesprin family that lacks an ABD and instead binds to the plakin family member plectin, which can associate with the intermediate filament (IF) system. Overexpression of nesprin-3 results in a dramatic recruitment of plectin to the nuclear perimeter, which is where these two molecules are colocalized with both keratin-6 and -14. Importantly, plectin binds to the integrin alpha6beta4 at the cell surface and to nesprin-3 at the ONM in keratinocytes, suggesting that there is a continuous connection between the nucleus and the extracellular matrix through the IF cytoskeleton.     

In-Vitro Activity of Doxycycline and β-Lactam Combinations Against Different Strains of <Emphasis Type="Italic">Burkholderia pseudomallei</Emphasis>

Although doxycycline is active against Burkholderia pseudomallei and has been used in the eradication stage of melioidosis therapy, it is not regularly used during the initial intensive phase. In order to assess its potential use in intensive phase therapy, we investigated in vitro pharmacodynamic activity of doxycycline and β-lactams alone and in combination against four Malaysian strains of B. pseudomallei. Using a checkerboard assay, the combinations of doxycycline and imipenem, doxycycline and ceftazidime, and doxycycline and amoxicillin–clavulanate tested against four strains showed indifferent effects with summation fractional inhibitory concentration values ranging from 0.62 to 2.12. Time-kill experiments also indicated that the combinations of doxycycline/β-lactam antibiotics against four tested strains did not fulfil synergy criteria, in which all combinations showed indifferent effects with ? 1.36 to 1.26-log CFU/mL compared to the most active monotherapy regimen in each combination. No re-growth of bacteria was detected after the early killing in doxycycline/β-lactam combination regimens compared to β-lactam monotherapy regimens, in which 9 out of 10 were associated with re-growth of bacteria. As no synergistic activity was observed, this in vitro study showed that doxycycline offers no additional benefit to be used in combination with β-lactams in the intensive phase of therapy.     

Analysis of Metabolic Capabilities Using Singular Value Decomposition of Extreme Pathway Matrices

It is now possible to construct genome-scale metabolic networks for particular microorganisms. Extreme pathway analysis is a useful method for analyzing the phenotypic capabilities of these networks. Many extreme pathways are needed to fully describe the functional capabilities of genome-scale metabolic networks, and therefore, a need exists to develop methods to study these large sets of extreme pathways. Singular value decomposition (SVD) of matrices of extreme pathways was used to develop a conceptual framework for the interpretation of large sets of extreme pathways and the steady-state flux solution space they define. The key results of this study were: 1), convex steady-state solution cones describing the potential functions of biochemical networks can be studied using the modes generated by SVD; 2), Helicobacter pylori has a more rigid metabolic network (i.e., a lower dimensional solution space and a more dominant first singular value) than Haemophilus influenzae for the production of amino acids; and 3), SVD allows for direct comparison of different solution cones resulting from the production of different amino acids. SVD was used to identify key network branch points that may identify key control points for regulation. Therefore, SVD of matrices of extreme pathways has proved to be a useful method for analyzing the steady-state solution space of genome-scale metabolic networks.     

Genotypic and phenotypic spectrum in tricho-rhino-phalangeal syndrome types I and III

Tricho-rhino-phalangeal syndrome (TRPS) is characterized by craniofacial and skeletal abnormalities. Three subtypes have been described: TRPS I, caused by mutations in the TRPS1 gene on chromosome 8; TRPS II, a microdeletion syndrome affecting the TRPS1 and EXT1 genes; and TRPS III, a form with severe brachydactyly, due to short metacarpals, and severe short stature, but without exostoses. To investigate whether TRPS III is caused by TRPS1 mutations and to establish a genotype-phenotype correlation in TRPS, we performed extensive mutation analysis and evaluated the height and degree of brachydactyly in patients with TRPS I or TRPS III. We found 35 different mutations in 44 of 51 unrelated patients. The detection rate (86%) indicates that TRPS1 is the major locus for TRPS I and TRPS III. We did not find any mutation in the parents of sporadic patients or in apparently healthy relatives of familial patients, indicating complete penetrance of TRPS1 mutations. Evaluation of skeletal abnormalities of patients with TRPS1 mutations revealed a wide clinical spectrum. The phenotype was variable in unrelated, age- and sex-matched patients with identical mutations, as well as in families. Four of the five missense mutations alter the GATA DNA-binding zinc finger, and six of the seven unrelated patients with these mutations may be classified as having TRPS III. Our data indicate that TRPS III is at the severe end of the TRPS spectrum and that it is most often caused by a specific class of mutations in the TRPS1 gene.