RGB color coded images in scanning electron microscopy of biological surfaces.

We present here a methodological approach for the creation of color images in scanning electron microscopy by processing grayscale images taken simultaneously from at least three different detectors in a scanning electron microscope. The final color images are then produced by merging together those grayscale images in RGB color space. We show the images from non-conductive standard sample together with those obtained from real microbiological samples. The first one represents a microbial biofilm naturally grown on fiber glass filter. The other shows individual Bacillus subtilis cells from batch culture. All the image handling was done in open source image processing software ImageJ or GNU Image Manipulation Program (Gimp) or, alternatively, in proprietary AnalySis 3.2 Pro software processing suite.

Reverse endoventricular artificial obturator in tricuspid valve position. Experimental feasibility research study.

The concept of vena contracta space reduction in tricuspid valve position was tested in an animal model. Feasibility of specific artificial obturator body (REMOT) fixed to the right ventricular apex and interacting with tricuspid valve leaflets was evaluated in three different animal studies. Catheter-based technique was used in three series of experiment in 7 sheep. First acute study was designed for evaluation if the screwing mode of guide wire anchoring to the right ventricular apex is feasible for the whole REMOT body fixing. Longer study was aimed to evaluate stability of the REMOT body in desired position when fixing the screwing wire on its both ends (to the right ventricular apex and to the skin in the neck area). X-ray methods and various morphological methods were used. The third acute study was intended to the REMOT body deployment without any fixing wire. In all of 7 sheep the REMOT was successfully inserted into the right heart cavities and then fixed to the right ventricular apex area. When the REMOT was left in situ more than 6 months it was stable, induced adhesion to the tricuspid valve leaflet and was associated with a specific cell invasion. Releasing of the REMOT from the guiding tools was also successfully verified. Deployment of the obturator body in the aim to reduce the tricuspid valve orifice is feasible and well tolerated in the short and longer term animal model. Specific cell colonization including neovascularization of the obturator body was observed.

Lactobacillus rodentium sp. nov., from the digestive tract of wild rodents.

Three strains of regular, long, Gram-stain-positive bacterial rods were isolated using TPY, M.R.S. and Rogosa agar under anaerobic conditions from the digestive tract of wild mice (Mus musculus). All 16S rRNA gene sequences of these isolates were most similar to sequences of Lactobacillus gasseri ATCC 33323T and Lactobacillus johnsonii ATCC 33200T (97.3% and 97.2% sequence similarities, respectively). The novel strains shared 99.2-99.6% 16S rRNA gene sequence similarities. Type strains of L. gasseri and L. johnsonii were also most related to the newly isolated strains according to rpoA (83.9-84.0% similarities), pheS (84.6-87.8%), atpA (86.2-87.7%), hsp60 (89.4-90.4%) and tuf (92.7-93.6%) gene sequence similarities. Phylogenetic studies based on 16S rRNA, hsp60, rpoA, atpA and pheS gene sequences, other genotypic and many phenotypic characteristics (results of API 50 CHL, Rapid ID 32A and API ZYM biochemical tests; cellular fatty acid profiles; cellular polar lipid profiles; end products of glucose fermentation) showed that these bacterial strains represent a novel species within the genus Lactobacillus. The name Lactobacillus rodentium sp. nov. is proposed to accommodate this group of new isolates. The type strain is MYMRS/TLU1T (=DSM 24759T=CCM 7945T).

Vagococcus entomophilus sp. nov., from the digestive tract of a wasp (Vespula vulgaris).

Three unknown Gram-stain-positive, catalase-negative, facultatively anaerobic and coccus-shaped strains of bacteria were isolated from the digestive tracts of wasps (Vespula vulgaris). Analysis of 16S rRNA gene sequences revealed that these strains had identical sequences and showed that Vagococcus salmoninarum, with 96.2% sequence similarity, was the closest phylogenetic neighbour. Further analyses based on hsp60 and pheS gene sequences of representatives of the family Enteroccocaceae and genotypic and phenotypic characterization using (GTG)5-PCR fingerprintings, EcoRI ribotyping, DNA G+C content, whole-cell protein profiling, cellular fatty acid profiles analysis and extensive biotyping confirmed that the investigated strains were representatives of a novel bacterial species within the genus Vagoccocus for which the name Vagoccocus entomophilus sp. nov. is proposed. The type strain is VOSTP2(T) ( = DSM 24756(T) = CCM 7946(T)).

Alloscardovia macacae sp. nov., isolated from the milk of a macaque (Macaca mulatta), emended description of the genus Alloscardovia and proposal of Alloscardovia criceti comb. nov.

A novel bacterial strain, designated M8(T), was isolated from milk of a female macaque bred in captivity. The strain was Gram-stain-positive, anaerobic, irregular coccoid-rod-shaped without catalase activity. Analysis of 16S rRNA gene sequence similarity revealed that the isolate was most closely related to Alloscardovia omnicolens CCUG 31649(T) (96.4%) and Metascardovia criceti OMB105(T) (96.6%). Sequences of hsp60, fusA, and xfp genes also confirmed that the strain was most closely related to the type strains of A. omnicolens and M. criceti. The isolate produced fructose-6-phosphate phosphoketolase which is in agreement with classification within the family Bifidobacteriaceae. The major fatty acids were C18 : 1ω9c (35.8%), C16 : 1 (6.2 %) and C14 : 0 (5.7 %). Polar lipid analysis revealed five different glycolipids, two unidentified phospholipids and diphosphatidylglycerol. The peptidoglycan was of the type A4α l-Lys-d-Asp with the presence of d(l)-alanine, d-glutamine, d-asparagine and l-lysine. The DNA G+C content of strain M8(T) was 50.1 mol%. On the basis of genetic, phylogenetic and phenotypic data, strain M8(T) represents a novel species of the genus Alloscardovia for which the name Alloscardovia macacae sp. nov. is proposed. The type strain is M8(T) ( = DSM 24762(T) = CCM 7944(T)). In addition, our results also revealed that Alloscardovia omnicolens DSM 21503(T) and Metascardovia criceti DSM 17774(T) do not belong to different genera within the family Bifidobacteriaceae. We therefore propose to reclassify Metascardovia criceti as Alloscardovia criceti comb. nov. An emended description of the genus Alloscardovia is also provided.

The use of glass beads cultivation system to study the global effect of the ppk gene inactivation in Streptomyces lividans.

The glass beads cultivation system developed in our laboratory for physiological studies of filamentous microorganisms supports differentiation and allows complete recovery of bacterial colonies and their natural products from cultivation plates. Here, we used this system to study the global effect of ppk gene disruption in Streptomyces lividans. The ppk encoding the enzyme polyphosphate kinase (P) catalyses the reversible polymerisation of gamma phosphate of ATP to polyphosphates. The resulting are phosphate and energy stock polymers. Because P activity impacts the overall energetic state of the cell, it is also connected to secondary metabolite (e.g. antibiotic) biosynthesis. We analysed the global effects of the disruption of this gene including its influence on the production of pigmented antibiotics, on morphological differentiation, on the levels of ATP and on the whole cytoplasmic protein expression pattern of S. lividans. We observed that the S. lividans ppk mutant produced antibiotics earlier and in greater amount than the wild-type (wt) strain. On the other hand, we did not observe any obvious effect on colony morphological development. In agreement with the function of Ppk, we detected much lower levels of ATP in ppk- mutant than in the wt strain. Proteomic analysis revealed that the genes that were influenced by ppk inactivation included enzymes involved in carbon or nitrogen metabolism, phosphate transport and components of the cell translational machinery. We showed that the synthesis of translation elongation factor Tu is during sporulation much higher in ppk- mutant than in wild-type strain.

Bombiscardovia coagulans gen. nov., sp. nov., a new member of the family Bifidobacteriaceae isolated from the digestive tract of bumblebees.

One hundred and eighty-seven fructose-6-phosphate phosphoketolase positive strains were isolated from the digestive tract of three different bumblebee species. Analyses of the partial 16S rRNA gene sequences of the representative strains showed only 92.8% and 92.5% similarity to Bifidobacterium coryneforme YIT 4092(T) and Bifidobacterium indicum JCM 1302(T), 92.2% similarity to Alloscardovia omnicolens CCUG 18650 and slightly reduced similarity of 91% to other members of the family Bifidobacteriaceae. On the other hand, analyses of the partial heat-shock protein 60 (hsp60) gene sequence revealed that the proposed type strain BLAPIII-AGV(T) was affiliated only to the 60 kDa chaperonin sequence of uncultured bacteria from human vagina (79-80%) and the hsp60 gene sequence of A. omnicolens CCUG 31649(T) (75.5%). The peptidoglycan type was A4α with an l-Lys-d-Asp interpeptide bridge. The polar lipids contained diphosphatidylglycerol, an unknown phospholipid, six glycolipids and two phosphoglycolipids. The major fatty acids were C(18:1), C(20:0) and C(18:0). These and other analyses indicated that the isolates represented a new genus within the family Bifidobacteriaceae. This observation was further substantiated by determination of the DNA G+C contents (46.1-47.1 mol%). Affinity of the strains to some scardovial genera (Aeriscardovia, Alloscardovia and Metascardovia) was also confirmed by their ability to grow under aerobic conditions. Besides the above mentioned differences, Bombiscardovia coagulans was found to differ from all scardovial genera in the ability to grow at temperatures as low as 5°C, which was another major phenotypically different characteristic of this new member of the family Bifidobacteriaceae. Hence, on the basis of phylogenetic analyses using partial 16S rRNA and hsp60 gene sequence data, and the temperature related phenotypic difference, we propose a novel taxa, B. coagulans gen. nov., sp. nov. (type strain=BLAPIII-AGV(T)=DSM 22924(T)=ATCC BAA-1568(T)).

Comparative study of the life cycle dependent post-translation modifications of protein synthesis elongation factor Tu present in the membrane proteome of streptomycetes and mycobacteria.

We present the results of analysis of membrane phosphoproteomes from individual morphological stages of Streptomyces coelicolor that reflect developmentally dependent heterogeneity and phosphorylation of intrinsic and externally added purified Strepomyces aureofaciens EF-Tu. Fast growing nonpathogenic Mycobacterium smegmatis was used as a non-differentiating actinomycetes comparative model. Streptomycetes membrane fraction was found to contain protein kinase(s) catalyzing phosphorylation of both its own and an externally added EF-Tu, whereas Mycobacterium membrane fraction contains protein kinase phosphorylating only its own EF-Tu.

Effect of protein kinase inhibitors on protein phosphorylation and germination of aerial spores from Streptomyces coelicolor.

In vitro phosphorylation reaction using extracts prepared from cells in the exponential phase of growth and aerial spores of Streptomyces coelicolor displayed the presence of multiply phosphorylated proteins. Effect of protein kinase inhibitors (PKIs) (geldanamycin, wortmannin, apigenin, genistein, roscovitine, methyl 2,5-dihydroxycinnamate, rapamycin, staurosporine) was determined on protein phosphorylation and on germination of spores. The in vitro experiments showed differences in phosphoprotein pattern due to the presence of PKIs. Cultivation of aerial spores with PKIs led to a significant delay in germ tube emergence and filament formation. However, none of the tested PKIs completely blocked the germination process. These results indicate that protein kinases of spores form complex networks sharing common modulating site that plays an important role in proper timing of early developmental events.

Post-translational modification(s) and cell distribution of Streptomyces aureofaciens translation elongation factor Tu overproduced in Escherichia coli.

We cloned EF-Tu from Streptomyces aureofaciens on a pET plasmid and overproduced it using the T7 RNA polymerase system in Escherichia coli. Streptomyces EF-Tu represented more than 40% of the total cell protein and was stored mostly in inclusion bodies formed apically at both ends of E. coli cells. Analysis of the inclusion bodies by transmission and scanning electron microscopy did not reveal any internal or surface ultrastructures. We developed the method for purification of S. aureofaciens EF-Tu from isolated inclusion bodies based on the ability of the protein to aggregate spontaneously. EF-Tu present in inclusion bodies was not active in GDP binding. Purified protein showed a similar charge heterogeneity as EF-Tu isolated from the mycelium of S. aureofaciens and all of the isoforms reacted with EF-Tu antibodies. All isoforms also reacted with monoclonal antibodies against O-phosphoserine and O-phosphothreonine.

Preparation of nanoparticles by electrocoagulation from soluble exopolysaccharide produced by Claviceps viridis.

Electrocoagulation is an evolving technology that has been effectively applied for wastewater treatment but its applications in biotechnology and nanotechnology are very limited. This method was applied for the preparation of nanoparticles from soluble exopolysaccharide (EPS) produced by Claviceps viridis in a submerged batch culture. A cathode/anode pair electrode (Al or Fe) system was used for determination of the separation rates of electrocoagulation and the yields of EPS nanoparticles production. The separation rates of 0.170 +/- 0.003 mg EPS/sec (Fe electrodes) and 0.250 +/- 0.003 mg EPS/sec (Al electrodes) were calculated for voltage gradient 1 V/1 cm of electrodes distance and were constant during experiments. The specific yield of EPS nanoparticles production based on the consumed electric power was dependent on the material of the electrodes and its value was determined as 0.71 +/- 0.01 mg EPS/W for Fe electrodes and 0.91 +/- 0.01 mg EPS/W for Al electrodes, respectively.

Polishing and coating carbon fiber-reinforced carbon composites with a carbon-titanium layer enhances adhesion and growth of osteoblast-like MG63 cells and vascular smooth muscle cells in vitro.

Carbon fiber-reinforced carbon composites (CFRC) are considered to be promising materials for orthopedic and dental surgery. Their mechanical properties can be tailored to be similar to those of bone, and their chemical composition (close to pure carbon) promises that they will be tolerated well by the surrounding tissue. In this study, CFRC composites were fabricated from phenolic resin and unidirectionally oriented Torayca carbon fibers by carbonization (1000 degrees C) and graphitization (2500 degrees C). The material then was cut with a diamond saw into sheets of 8 x 10 x 3 mm, and the upper surface was polished by colloidal SiO2 and/or covered with a carbon-titanium (C:Ti) layer (3.3 microm) using the plasma-enhanced physical vapor deposition method. Three different kinds of modified samples were prepared: polished only, covered only, and polished + covered. Untreated samples served as a control. The surface roughness of these samples, measured by a Talysurf profilometer, decreased significantly after polishing but usually did not decrease after coating with a C:Ti layer. On all three modified surfaces, human osteoblast-like cells of the MG63 line and rat vascular smooth muscle cells (both cultured in a Dulbecco's minimum essential medium with 10% fetal bovine serum) adhered at higher numbers (by 21-87% on day 1 after seeding) and exhibited a shorter population doubling time (by 13-40%). On day 4 after seeding, these cells attained higher population densities (by 61-378%), volume (by 18-37%), and protein content (by 16-120%). These results were more pronounced in VSMC than in MG63 cells and in both groups of C:Ti-covered samples than in the polished only samples. The release of carbon particles from the CFRC composites was significantly decreased--by 8 times in the polished only, 24 times in the covered only, and 42 times in the polished + covered samples. These results show that both polishing and carbon-titanium covering significantly improve the biocompatibility of CFRC composites in vitro, especially when these two modifications are combined.

Stress-response sigma factor sigma(H) is essential for morphological differentiation of Streptomyces coelicolor A3(2).

We previously cloned the sigH gene encoding a stress-response sigma factor sigma(H) in Streptomyces coelicolor A3(2), located in an operon with the gene encoding proposed anti-sigma factor UshX. To clarify the in vivo function of sigma(H), a stable null mutant of sigH was prepared by homologous recombination. This mutation appeared to have no obvious effect on vegetative growth, but dramatically affected morphological differentiation. Microscopy showed that the sigH mutant produced undifferentiated hyphae with rare spore chains, giving the colony a pale gray color compared to the dark gray wild-type spores. The sigH mutation partially affected growth under conditions of high osmolarity. Expression of the sigH operon was investigated in the S. coelicolor sigH mutant. Out of four promoters directing expression of the sigH operon, the sigH-P2 promoter--the only promoter preferentially induced by salt-stress conditions--was inactive in the sigH mutant. The results indicated that the sigH-P2 promoter is dependent (directly or indirectly) upon sigma(H) and that the operon is autocatalytically activated. We propose that in S. coelicolor sigma(H) has a dual role, regulating the osmotic response and morphological differentiation.

Isolation and characterization of dcw cluster from Streptomyces collinus producing kirromycin.

A 4.5-kb BamHI fragment of chromosomal DNA of Streptomyces collinus containing gene ftsZ was cloned and sequenced. Upstream of ftsZ are localized genes ftsQ, murG, and ftsW, and downstream is yfiH. Gene ftsA is not adjacent to ftsZ or other genes of the cloned fragment. Protein FtsZ was isolated and characterized with respect to its binding to GTP and GTPase activity. The binding of GTP to FtsZ was Ca(2+) or Mg(2+) dependent with an optimum at 10 mM. The rate of GTP hydrolysis by FtsZ was stimulated by KCl. The presence of Ca(2+) (3-5 mM) resulted in a significant increase of GTPase activity. Higher concentrations of Ca(2+) than 5 mM had an inhibitory effect on GTPase activity. These results indicate that divalent ions (Ca(2+) or Mg(2+)) can be involved in regulation of GTP binding and hydrolysis of FtsZ. The maximum level of FtsZ was detected in aerial mycelium when spiral loops and sporulation septa were formed. FtsZ is degraded after finishing sporulation septa.

Kytococcus sedentarius (formerly Micrococcus sedentarius) and Dermacoccus nishinomiyaensis (formerly Micrococcus nishinomiyaensis) produce monensins, typical Streptomyces cinnamonensis metabolites.

The environmental isolate Kytococcus sedentarius TR-2 was found to be a new producer of the oligoketide antibiotics monensin A and B. Electron microscopic studies demonstrated that the TR-2 strain had coccoid cells and DNA analysis revealed no close relationship to Streptomyces cinnamonensis, a typical monensin producer. Production of monensins was also proven with six culture collection K. sedentarius strains and three Dermacoccus nishinomiyaensis strains. The secondary metabolism of micrococci demonstrates a high degree of instability. Biosynthesis of monensins by micrococci endorses a phylogenetic relationship to Streptomyces spp.

The Streptomyces aureofaciens homologue of the whiB gene is essential for sporulation; its expression correlates with the developmental stage.

In previous experiments, a Streptomyces aureofaciens gene highly similar to the sporulation-specific whiB gene of Streptomyces coelicolor was identified. By integrative transformation, via double cross-over, a stable null mutant of the whiB-homologous gene of S. aureofaciens was obtained. The disruption blocked differentiation at a stage between the formation of aerial mycelium and the development of mature spores, producing white aerial hyphae without septation. Expression of the whiB gene was investigated during differentiation by S1 nuclease mapping, using RNA prepared from S. aureofaciens in various developmental stages. Two putative promoters were identified upstream of the whiB coding region. The stronger promoter, whiB-P2, was induced at the beginning of aerial mycelium formation, and the weaker promoter, whiB-P1, was expressed fairly constantly during differentiation. No differences in the expression of the whiB promoters were detected in an rpoZ-disrupted S. aureofaciens strain. The promoter bearing DNA fragment was inserted into the promoter-probe vector pARC1 to produce an expression pattern consistent with the results of direct RNA analysis.

Lesion of leukocytes, erythrocytes, and mesothelial cells by the coelomic fluid of Eisenia foetida earthworms.

Coelomic fluid of Eisenia foetida earthworms is known to exert strong proteolytic, hemolytic, bacteriostatic, and cytolytic properties. Ultrastructural observations revealed that coelomic fluid causes multiple ruptures and defects in the erythrocyte membrane as well as in the membrane of murine peritoneal leukocytes. Incubation of peritoneal cells in coelomic fluid resulted in a disorganization of the macrophage surface microvilli, changes in the organization of cytoplasmic organelles and disruption and degranulation of mast cells. Severe mesothelial damage was observed after intraperitoneal administration of the coelomic fluid.

Degradation of wood by the basidiomycete Coriolopsis occidentalis.

Chemical and microscopic features of wood decay by the basidiomycete Coriolopsis occidentalis are described. The fungus was grown on blocks of poplar, oak, and fir wood and caused significant mass, lignin, and saccharide losses in all kinds of wood. Poplar wood was particularly strongly affected. Twelve weeks after inoculation dry mass, lignin, and saccharide contents were reduced by about 50%. The blocks became covered with mycelia and electron microscopy showed that secondary cell walls were degraded from the lumina and middle lamellae dissolved during later stages of incubation. The results indicate that the fungus belongs to simultaneous white-rotters.

Instability of the production of avermectins, sporulation, and pigmentation in Streptomyces avermitilis.

Production of avermectins, sporulation ability, and colony pigmentation were followed in Streptomyces avermitilis C-18/6 cultures during serial transfer (for eight subcultures) in four different liquid media. These phenotypes were found to be unstable and independent of each other. A procedure was established whereby depressed avermectin production could be reversed but the degree of reversion was dependent on the history of the isolate, i.e., the type of medium used. The presence of isoleucine as the sole N source caused an immediate loss of avermectin production and this could not be reversed.