Biochemical and nucleic acid hybridisation studies on Brevibacterium linens and related strains

Twenty coryneform bacteria identified as Brevibacterium linens or related strains from different private and public collections were studied biochemically in respect to the composition of the cell walls and in respect to the nucleic acid hybridisation. Investigation of the cell walls revealed an identical meso-diaminopimelic acid containing directly cross-linked peptidoglycan type which is not amidated. The characteristic polymers of the polysaccharide moiety of the cell walls were found to be teichoic acids which belong to the poly(glycerolphosphate) and the poly(ribitolphosphate) type. Furthermore a novel mannitol containing teichoic acid is present which is tentatively characterized as poly(mannitolphosphate). Arabinoglactan and ribose as distinctive sugar components together with galactose and glucose in the cell walls of B. linens could not be detected in any strain. The biochemical findings lend support to the view that B. linens and related strains form a distinctive group which is clearly distinguished from all other coryneform bacteria. This is supported by DNA-23S/16S ribosomal ribonucleic acid reassociation studies. Deoxyribonucleic acid-deoxyribonucleic acid homology studies show the incoherency of B. linens which obviously comprises two species.     

The isolation of protoplasts of the fission yeastSchizosaccharomyces byTrichoderma viride and snail enzymes

The formation of protoplasts of the fission yeastsSchizosaccharomyces pombe andSchizosaccharomyces versatilis after the combined application of snail enzymes andTrichoderma viride enzymes in an osmotic stabilizer (0.4m KC1, pH 5.5) was studied by light and electron microscopy. The effect of the enzymes used leads during 30 min to the formation of 100% protoplast population. Using electron microscopy no original walls or wall remnants were detected in the suspension of protoplasts. Protoplasts are viable and in liquid nutrient medium they regenerate cell walls and revert into normal cells. Such a protoplast population may be useful for biochemical study of protoplast metabolism by quantitative methods as well as for the chemical study of regenerating cell walls.     

Carbohydrate composition of the isolated cell walls of dermatophytes

In an attempt to evaluate taxonomic character of sugar composition of dermatophytes, the purified cell walls from 13 species are analyzed on neutral sugar composition by gas liquid chromatography. The results were principally compatible with those obtained by conventional morphological examination. Neutral sugar components of dermatophytes cell walls were mannose and glucose in the ratio of 1∶2.7 for Epidermophyton and 1∶1.4 for Microsporum. There were two types in Trichophyton, in which the ratios of mannose to glucose were 1∶1.6 and 1∶3.8. The cases of Trichophyton ferrugineum and Trichophyton mentagrophytes were exceptional. The ratio of the former was 1∶1.4, which implied the relation to Microsporum group, and the ratio of the latter was 1∶2.3, which was supposed to be the intermediate of two types of Trichophyton group. Albino type cell wall of Epidermophyton floccosum was more rich in glucose than pigmented type one.     

Regeneration of the cell wall of protoplasts of the fission yeastSchizosaccharomyces versatilis in liquid media and their reversion to cells

Regeneration of the cell wall and reversion of protoplasts with a completely regenerated cell wall to cells were studied by light and electron microscopy in protoplasts of the fission yeastsSchizosaccharomyces versatilis. On their surface the protoplasts regenerated a complete new wall even m liquid media The wall regeneration began with the formation of a thin irregular net of flat bundles of long microfibrils and the net was gradually filled with aggregates of short straight microfibrils and small piles of amorphous material. Osmotically resistant organisms with regenerated walls were detected after a 4–6 h cultivation Depending on the nutrient medium used 10–80 % of protoplasts with the regenerated wall were obtained that reverted subsequently to cells. The high percentage of the wall regeneration and reversion to cells was reached by combining cultivation in a poor medium with that in a rich medium Reversion to cells could only occur after the protoplasts had regenerated rigid cell walls These walled protoplasts underwent septation, and, by polar growth, produced cylindrical cells, further dividing by fission.     

Preparation,reversion, mutagenesis and intra-species fusion of protoplasts ofOudemansiella mucida

A technique was developed for preparation and reversion of protoplasts of the mucidin-producing fungusOudemansiella mucida. The protoplasts can be obtained in sufficient amounts from an exponentially growing young mycelium treated with snail digestive juice in the presence of an osmotic stabilizer. The resulting protoplasts readily regenerate their cell walls and, at a frequency of 10-20%, reverse into mycelium. InO. mucida, which does not form asexual spores, protoplasts are a suitable starting material for mutagenesis. Auxotrophic and higher-producing mutants were obtained in this way. Fusion of protoplasts of two compatible monokaryotic auxotrophic isolates, induced by polyethylene glycol, yielded nutritionally complemented dikaryotes forming clamp connections and producing mucidin.     

Paenibacillus yonginensis sp. nov., a potential plant growth promoting bacterium isolated from humus soil of Yongin forest

Strain DCY84^T, a Gram-stain positive, rod-shaped, aerobic, spore-forming bacterium, motile by means of peritrichous flagella, was isolated from humus soil from Yongin forest in Gyeonggi province, South Korea. Strain DCY84^T shared the highest sequence similarity with Paenibacillus barengoltzii KACC 15270^T (96.86 %), followed by Paenibacillus timonensis KACC 11491^T (96.49 %) and Paenibacillus phoenicis NBRC 106274^T (95.77 %). Strain DCY84^T was found to able to grow best in TSA at temperature 30 °C, at pH 8 and at 0.5 % NaCl. MK-7 menaquinone was identified as the isoprenoid quinone. The major polar lipids were identified as phosphatidylethanolamine, an unidentified aminophospholipid, two unidentified aminolipids and an unidentified polar lipid. The peptidoglycan was found to contain the amino acids meso-diaminopimelic acid, alanine and d-glutamic acid. The major fatty acids of strain DCY84^T were identified as branched chain anteiso-C_15:0, saturated C_16:0 and branched chain anteiso-C_17:0. The cell wall sugars of strain DCY84^T were found to comprise of ribose, galactose and xylose. The major polyamine was identified as spermidine. The DNA G+C content was determined to be 62.6 mol%. After 6 days of incubation, strain DCY84^T produced 52.96 ± 1.85 and 72.83 ± 2.86 µg/ml l-indole-3-acetic acid, using media without l-tryptophan and supplemented with l-tryptophan, respectively. Strain DCY84^T was also found to be able to solubilize phosphate and produce siderophores. On the basis of the phenotypic characteristics, genotypic analysis and chemotaxonomic characteristics, strain DCY84^T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus yonginensis sp. nov. is proposed. The type strain is DCY84^T (=KCTC 33428^T = JCM 19885^T).     

The prognostic value of osteopontin expression in non-small cell lung cancer: a meta-analysis

To investigate the association of Osteopontin (OPN) expression in tumor tissue with clinicopathological features of non-small cell lung carcinoma (NSCLC) patients. Publications assessing the clinicopathological characteristics and prognostic significance of OPN in expression NSCLC were identified up to March 2014. A meta-analysis of eligible studies was performed using standard statistical methods to clarify the association between OPN expression and these clinical parameters. A total of eleven studies met the inclusion criteria, and included 1536 cases of NSCLC tumor tissue and 340 cases of normal lung tissue. The OPN expression rate in NSCLC tissue was higher than normal tissue [Odds ratio (OR) 6.427; 95 % confidence interval (CI) 4.689–8.808; P = 0.000]. Simultaneously, we also found that OPN expression was positively associated with stage (OR 0.332; 95 % CI 0.250–0.440; P = 0.000), lymph node metastasis (OR 3.094; 95 % CI 2.295–4.172; P = 0.000), tumor size (tumor size <3 cm vs. ≥3 cm; OR 0.484; 95 % CI 0.303–0.773; P = 0.002) and pathology (OR 0.611; 95 % CI 0.466–0.800; P = 0.000). It was unrelated that OPN expression in NSCLC tissue with and degree of differentiation and other clinical features (P > 0.05). Experimental findings indicate that, OPN plays a crucial role in the development of NSCLC.     

Leaf-cutting ants: an unexpected microenvironment holding human opportunistic black fungi

Fungus-growing ants of the genus Atta are known for their leaf-cutting habit, a lifestyle they have maintained since their 50-million-year-old co-evolution with a mutualistic fungus, cultivated as food. Recent studies have highlighted that, in addition to the mutualistic fungus, nests of ants harbor a great diversity of microbial communities. Such microorganisms include the dematiaceous fungi, which are characterized by their melanized cell walls. In order to contribute to the knowledge of fungal ecology, as well as opportunistic strains that may be dispersed by these social insects, we isolated and identified fungi carried by gynes of Atta capiguara and Atta laevigata, collected from colonies located in Fazenda Santana, Botucatu (São Paulo, Brazil). The isolation was carried out using the oil flotation technique, which is suitable for the growth of black fungi. Inoculated plates were incubated at 25 and 35 °C until black cultures were visible (20–45 days). Isolates were identified based on microscopic and molecular characteristics. Some isolated genera were: Cladophialophora, Cladosporium, Exophiala, Ochroconis, Phaeococcomyces, Phialophora and Penidiella. Hyaline species were also found. The results obtained from this work showed that leaf-cutting gynes may contribute to the dispersal of opportunistic dematiaceous fungi. It is suggested that more attention should be paid to this still unexplored subject.     

Genotyping and development of single-nucleotide polymorphism (SNP) markers associated with blast resistance genes in rice using GoldenGate assay

Development and large-scale genotyping of single-nucleotide polymorphism (SNP) is required to use identified sequence variation in the alleles of different genes to determine their functional relevance to the candidate gene(s). In the present study, Illumina GoldenGate assay was used to validate and genotype SNPs in a set of six major rice blast resistance genes, viz. Pi-ta, Piz(t), Pi54, Pi9, Pi5(1) and Pib, distributed over five chromosomes, to understand their functional relevance and study the population structure in rice. All the selected SNPs loci (96) of six blast (Magnaporthe oryzae) resistance genes were genotyped successfully in 92 rice lines with an overall genotype call rate of 92.0 % and minimum GenTrain cutoff score of ≥0.448. The highest genotyped SNPs were found in japonica type (97.1 %) rice lines, followed by indica (92.12 %), indica basmati (91.84 %) and minimum in case of wild species (82.0 %). Among the genotyped loci, the highest score (98.68 %) was observed in case of Piz(t), followed by Pi-ta, Pi5(1), Pib, Pi54 and Pi9. Polymorphism was obtained in 87.5 % SNPs loci producing 7,728 genotype calls. Minor allele frequency ranged from 0.01 to 0.49 and has good differentiating power for distinguishing different rice accessions. Population structure analysis revealed that a set of genotypes from four rice subpopulations had “admix” ancestry (>26 %) with more than one genetic background of indica, japonica and wild types. SNPs markers were validated in a set of 92 rice lines and converted into CAPS markers which can be used in blast resistance breeding programme.     

Total and cell wall phosphorus content inBacillus megaterium in phosphate-limited media

A comparative study of the amount of total and cell wall phosphorus inBacillus megaterium ATCC 33085, grown in media with or without phosphate limitation was carried out. The phosphorus levels were investigated during six successive subcultures. A progressive decrease in total phosphorus was found in cells cultivated in a phosphate-limited medium. A decline in the cell wall phosphorus level was observed starting only from the third subculture in phosphate-limited medium, and no phosphorus was detected in the walls of cells in the fifth subculture.     

Identification and immunocytochemical localization of α-galactosidase in resting and germinated date palm (Phoenix dactylifera L.) seeds

α-Galactosidases (EC 3.2.1.22) from resting and germinated date (Phoenix dactylifera L.) seeds were compared and localized using immunocytochemical methods. The enzyme was present in both the endosperm and embryo of resting seeds, in the endosperm undergoing digestion where the greatest specific activity was present, and in the haustorium of seedlings. The enzyme had a molecular mass of 140000 as determined by gel filtration and a pH optimum of 4.5. At least seven forms of the enzyme with isoelectric points ranging from 3.85 to 5.2 were detected in the haustorium whereas only four of these forms were present in the endosperm. The relative activity levels of the various forms also differed between the two tissues. On Western blots all enzyme forms were recognized by antibodies raised against mung-bean (Vigna radiata) α-galactosidase. Using immunogold techniques, label was shown to be present in the protein bodies of the resting embryo cells but to decrease in this organelle as the reserve protein was mobilized and to appear diffusely in the cytoplasm in subsequent stages. In resting endosperm cells, label occurred in the protein bodies and in a thin region of inner wall. In endosperm undergoing digestion, where different stages of protoplast and wall breakdown occurred, immunogold staining was localized in the flocculent contents of vacuoles which resulted from storageprotein breakdown, then dense staining occurred in the inner wall of cell cavities formed by the complete dissolution of the cytoplasm, and finally, staining was uniformly diffuse throughout the remaining endosperm wall adjacent to the haustorium surface. These observations indicate that the α-galactosidase present in cell walls of the date palm endosperm during mannan mobilization is not secreted by the haustorium but instead is probably a pregermination product stored mainly in the protein bodies of resting endosperm and is released to the wall following loss of membrane integrity.     

The level of genetic variability of cells in prolonged suspension culture of Arabidopsis thaliana

The level of heterogeneity and genetic variability of cells in a suspension of Arabidopsis thaliana cultured in vitro for more than seven years was studied. The considerable heterogeneity of the suspension in cell size was shown. As revealed by nuclear DNA cytophotometry, the suspension culture was mixoploid and the amount of DNA in the cells varied from 4 to 16 C. However, PCR with 6 RAPD- and 4 ISSR-primers and their intragroup combinations showed the lowest degree of variability of DNA markers. The genetic distances of clones obtained from a suspension culture of the parent plant were only 1.5%. Differences between the clones were identified with only one pair of 31 primer combinations tested, indicating low level of genetic heterogeneity of the suspension. The results showed that variations in the amount of DNA in the suspension culture cells are not accompanied by significant changes in the DNA sequence.     

Phenotypic and genotypic characteristics of Arcanobacterium haemolyticum isolated from clinical samples in a Danish hospital

Six Arcanobacterium haemolyticum strains isolated from six patients of two hospitals in Denmark were identified phenotypically, also including matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis, and by genotypic methods. The latter were performed by sequencing 16S rDNA and glyceraldehyde 3-phosphate dehydrogenase encoding gene gap and by amplification of an A. haemolyticum specific region of 16S–23S rDNA intergenic spacer region and 23S rDNA. The six A. haemolyticum strains were further investigated for the presence of seven potential virulence genes encoding arcanolysin, phospholipase D, hemolysin A, CAMP factor family protein, collagen binding protein, neuraminidase A and neuraminidase H which appeared to be present in two (seven virulence genes), two (six virulence genes) and two strains (four virulence genes), respectively. The phenotypic and genotypic properties described in the present study might help to reliably identify and further characterize A. haemolyticum isolated from human patients, a species which seems to be of increasing importance.     

Identification of proteolytic bacteria from the Arctic Chukchi Sea expedition cruise and characterization of cold-active proteases

Following collection of seawater samples during an Arctic Chukchi Sea expedition cruise of the Korean icebreaker Araon in 2012, a total of 15,696 bacteria were randomly isolated from Marine Broth 2216 agar plates. Of these, 2,526 (16%) showed proteolytic activity and were identified as mainly Alteromonas (31%), Staphylococcus (27%), and Pseudoalteromonas (14%). Among the proteolytic strains, seven were selected based on their significant ability to grow and produce a halo on skim milk plates at low temperatures (<5°C) owing to cold-active proteases. These strains were affiliated with the genus Pseudoalteromonas and were divided into three groups based on phylogenetic analysis of the 16S rRNA genes. Profiling cell membrane fatty acids confirmed the 16S rRNA-based differentiation and revealed the accordance between the two analyses. Seven genes for serine protease precursors were amplified from the corresponding strains, and based on sequence similarities, these genes were divided into three groups that were identical to those identified by the 16S rRNA phylogenetic analysis. Three protease genes from the representative strains of each group were composed of 2,127–2,130 bp, encoding 708–709 amino acids, and these genes yielded products with calculated molecular weights of approximately 72.3–72.8 kDa. Amino acid sequence analysis suggested that the precursors are members of the subtilase serine endo- and exo-peptidase clan and contain four domains (signal peptide, N-terminal prosequence, catalytic domain, and two pre-peptidase C-terminal domains). Upon expression in E. coli, each recombinant protease exhibited proteolytic activity on zymogram gels.     

Plastid number and plastid structural changes associated with tobacco mesophyll protoplast culture and plant regeneration

Mesophyll protoplasts were isolated from Nicotiana tabacum L. cv. Xanthi, and cell-colony formation induced in liquid culture. The plastid changes associated with the morphogenetic sequence from mesophyll protoplast to whole plant were examined. Minor ultrastructural changes in the plastids were evident after 1 d of culture, but by 8 d (four-to-eight-cell stage) the plastids were small, there was much less thylakoid membrane appression, and many prominent plastoglobuli were also present. Plastid-division figures were evident at this point of time and it was common to find plastids clustered around the nucleus. A typical proplastid was the dominant plastid type in the cultured cells from about 11 d until about five weeks when large amyloplasts and pregranal plastids were observed. Normally structured chloroplasts were present in the regenerated plant. There was no plastid division until the four-cell stage, with plastid numbers per cell approximately halving at each cell division, then stabilising around 12 per cell during cell-colony development, a number typical of meristematic cells. Though nucleoids were always present, their numbers in the plastids were reduced by the eight-cell stage.     

Chitinase in bean leaves: induction by ethylene,purification, properties,and possible function

Ethylene induced an endochitinase in primary leaves of Phaseolus vulgaris L. The enzyme formed chitobiose and higher chitin oligosaccharides from insoluble, colloidal or regenerated chitin. Less than 5% of the total chitinolytic activity was detected in an exochitinase assay proposed by Abeles et al. (1970, Plant Physiol. 47, 129–134) for ethylene-induced chitinase. In ethylene-treated plants, chitinase activity started to increase after a lag of 6 h and was induced 30 fold within 24 h. Exogenously supplied ethylene at 1 nl ml^?1 was sufficient for half-maximal induction, and enhancement of the endogenous ethylene formation also enhanced chitinase activity. Cycloheximide prevented the induction. Among various hydrolases tested, only chitinase and, to a lesser extent, β-1,3-glucanase were induced by ethylene. Induction of chitinase by ethylene occurred in many different plant species. Ethylene-induced chitinase was purified by affinity chromatography on a column of regenerated chitin. Its apparent molecular weight obtained by sodium dodecyl sulfate-gel electrophoresis was 30,000; the molecular weight determined from filtration through Sephadex G-75 was 22,000. The purified enzyme attacked chitin in isolated cell walls of Fusarium solani. It also acted as a lysozyme when incubated with Micrococcus lysodeikticus. It is concluded that ethylene-induced chitinase functions as a defense enzyme against fungal and bacterial invaders.     

Phloem unloading in aerial roots of Monstera deliciosa

Plants of Monstera deliciosa Liebm. pruned to exemplars with one leaf and one aerial root were labeled with 7.4 MBq ¹⁴CO₂ over the leaf blade. Microautoradiographs of soluble and insoluble radioactivity were prepared from three different regions of the aerial root. In addition, histochemical localization of ATPase was carried out on similar aerial roots. Vigorously growing aerial roots grew as fast as 26 mm d^-1, and zones of differentiation extended more than 10 cm from the root tip. In the region 2–3 cm from the root tip, in which only protoelements of the vascular tissue were differentiated, ¹⁴C-label was restricted to the protophloem. The activity of ATPase was recognized in many different cellular organelles of the meristematic phloem parenchyma. In the region 5–6 cm from the root tip, in which the first metaelements differentiated, all parenchyma cells of the central cylinder and many cortical cells showed ¹⁴C-label, in addition to the densely labeled protophloem. Differentiating vessels were heavily labeled at sites where secondary walls were formed. In this region of the root, ATPase activity was concentrated on the plasmalemma and cortical cytoplasma of the sieve tubes, and on the tonoplast of the phloem parenchyma cells. In contrast, the strands of internal metaphloem with giant sieve tubes, which are scattered among the metaxylem, were neither labeled nor did they show ATPase activity. In the zone 19–20 cm from the root tip, regions of cell differentiation in the sclerenchymatic mantle of the inner cortex, the late-formed metaxylem vessels and some strands of the internal metaphloem could be identified by dense ¹⁴C-label. Low ATPase activity was found in the plasmalemma of practically all living cells. In this nearly mature region, a strong peroxidase activity was observed in the radial walls of the endodermis. The results indicate that phloem unloading was strongest at sites of root differentiation, where ATPase activity was concentrated in the plasmalemma of sieve tubes and the tonoplast of phloem parenchyma.     

Effects of Icotinib on Advanced Non-Small Cell Lung Cancer with Different EGFR Phenotypes

Icotinib is the first oral epidermal growth factor receptor (EGFR) tyrosine kinase receptor inhibitor, which has been proven to exert significant inhibitory effects on non-small cell lung cancer in vitro. Clinical evidence has showed that the efficacy of Icotinib on retreating advanced non-small cell lung cancer is comparable to Gefitinib. However, different phenotypes of EGFR can affect the therapeutic outcomes of EGFR tyrosine kinase receptor inhibitor. Therefore, our study focused on efficacy and safety of Icotinib in patients with advanced non-small cell lung cancer of different EGPR phenotypes. Clinical data of patients with advanced non-small cell lung cancer who received Icotinib treatment from August, 2011 to May, 2013 were retrospectively analyzed. Kaplan–Meier analysis was used for survival analysis and comparison. 18 wild-type EGFR and 51 mutant type were found in a total of 69 patients. Objective response rate of patients with mutant type EGFR was 54.9 % and disease control rate was 86.3 %. Objective response rate of wild-type patients was 11.1 % (P = 0.0013 vs mutant type), disease control rate was 50.0 % (P = 0.0017). Median progression-free survival (PFS) of mutant type and wild-type patients were 9.7 and 2.6 months, respectively (P < 0.001). Median PFS of exon 19 mutated mutant patients was 11.3 months, mean PFS of exon 21 L858R mutated mutant patients was 8.7 months (P = 0.3145). Median overall survival (OS) of EGFR mutated patients had not reached. OS time of 13 wild-type patients was 12.9 months (P < 0.001). The common adverse reactions of Icotinib included rash, diarrhea, itching skin with occurrence rates of 24.6 % (17/69), 13.0 % (9/69), and 11.6 % (8/69), respectively. Most adverse reactions were grade I–II. Icotinib has great efficacy in EGFR mutated patients, making it an optimal regimen to treat EGFR mutated patients. Furthermore, most of adverse reactions associated with Icotinib treatment were tolerable.     

Flocculation of cell walls of brewer's yeast and effects of metal ions,protein-denaturants and enzyme treatments

Effects of metal ions, protein-denaturants and enzyme treatments on flocculation of cell walls of Beer Yeast IFO 2018 were investigated. Cell walls from flocculent cells grown in a complete medium were able to form flocs as were whole cells, but cell walls from non-flocculent cells, such as “Mg²⁺-deficient” cells, “early-phase” cells and “low-pH” cells, were not. The cell walls dispersed in distilled water reflocculated in solutions containing Ca²⁺ or other metal ions. Of the alkali metal ions tested, only Na⁺ inhibited flocculation of flocculent cell walls at a concentration more than 0.1 M. Ca²⁺ or Sn⁴⁺ was absolutely required for flocculation of cell walls in the physiological saline (NaCl, 150 mM), but the effect of Sn⁴⁺ seems rather non-specific, because it promoted flocculation of non-flocculent cell walls as well. Sr²⁺ and Ba²⁺ were antagonistic to Ca²⁺ and inhibited flocculation. Flocculation of cell walls was also depressed by high concentrations of protein-denaturants, e.g. urea and guanidine·HCl. Treatment with proteolytic enzymes deprived cell walls of floc-forming ability. Effect of metal ions, protein-denaturants and treatment with enzymes on the flocculation of intact cells was investigated as control. Since flocculating properties of cell walls were very similar to those of intact cells, flocculation must be an inherent property of cell walls.