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Nevertheless, irradiated vaccines have not widely been used at an industrial level because of difficulties obtaining the necessary equipment. Recent successful clinical trials of irradiated vaccines against pathogens and tumors have led to a reevaluation of radiation technology as an alternative method to produce vaccines. Here, I will review the challenges associated with creating irradiated vaccines and introduce how radiation technology are applied to develop bacterial vaccines in our institute. Regulation of the AA synthesis and degradation is finely tuned by QS systems.

RhlR and LasR regulate the AA metabolism in a mutually antagonistic, and growth phase-dependent manner. QscR is also involved in this regulation by repressing both LasR and RhlR functions in a growth phase-dependent manner. In the presence of AA, AntR binds to two AntR-responsive elements AREs at the intergenic region between anta and antr, and bidirectionally activates both antabc and antr transcriptions.

As a result, the strength of transcriptional activation becomes dramatically asymmetric depending on the direction. In nature, there are many AA-producing bacteria as a tryptophan degradation product. So, microorganisms that exist in tryptophan-rich environments necessarily encounter exogenous AA as well as endogenously produced AA. Interestingly, AA deteriorates the biofilm structure of P. AA exerts this anti-biofilm effect by reducing the level of intracellular c-di-gmp and modulating the expression of Psl, Pel, and alginate, major extracellular polymeric substances EPSs of P.

AA also has a significant deteriorating effect on biofilms of other bacteria, such as Vibrio vulnificus, Bacillus subtilis, and Staphylococcus aureus. Since AA significantly enhanced swimming and swarming motility of P. These results suggest that AA may be a promising candidate for the development of anti-biofilm agent.

Pseudomonas aeruginosa usually coexists with other pathogens, such as Staphylococcus aureus. Virulence factor production by P. A mutant harboring a transposon insertion in the desb gene, encoding a desaturase, displayed significantly reduced the production of various exoproducts, including elastase, protease, pyocyanin, and rhamnolipids, as well as decreased motility, proving that DesB plays an important role in P. In addition, we found that the desb mutant exhibited reduced S.

The transcriptional profiles of the WT and desb mutant revealed that the expression of MvfR-controlled pqsa-e and phnab operons was significantly decreased, but the mexef-oprn operon was highly expressed. The results indicate that increase in MexEF-OprN efflux pump expression causes reduced intracellular levels of 4-hydroxyheptylquinoline HHQ , a ligand of MvfR, in desb mutant, leading to the decrease of MvfR binding to pqsa-e promoter and the reduction of 4-hydroxyalkylquinolines HAQs synthesis.

In conclusion, these results suggest that DesB contributes to virulence, and promotes the inhibition of S. Human airway is lined with mucus layer that contains a large amount of lysozyme, an enzyme that hydrolyzes bacterial cell walls, and thus can suppress bacterial growth on the airway surface. Of note, elevated lysozyme activity was observed in the bronchoalveolar lavage fluid BALF derived from CF patients, suggesting that the degree of P.

Consistent with this notion, P. In this work, we performed a forward genetic screening using a random transposon Tn insertion mutant library of PAO1, a prototype strain of P. Each of these mutants exhibited reduced virulence in an acute mouse airway infection model. Molecular mechanisms behind these sensitivities and potential implications of these findings with regards to the P. Pseudomonas aeruginosa is a bacterial pathogen that is prone to infect the respiratory tract of immunocompromised patients along with other microbial invaders.

The potential effects of these factors on the modulation of host inflammatory responses against competitive bacteria, such as Staphylococcus aureus, are unknown. Here, we report that human bradykinin receptors as important host defense responses against invading microbes are up-regulated by components secreted from P.

In addition to this, P. Upregulation of TLR2 influences the magnitude of proinflammatory responses to the secondary S. Moreover, P. Taken together, the results of this study demonstrate that P. Using k-mer abundance analysis, we first tried to detect diagnostic signatures from contamination-free Illumina reads that previously led to poor assemblies. Some sequencing reads with an extraordinary peak at low-frequency k-mer range, which could not be assembled normally despite conventional pretreatments including adapter sequence removal and quality trimming, were successfully assembled after filtration of reads with low abundance k-mer or subsampling of reads.

Second, simulated reads from pairs of bacterial chromosome sequences difference species or different strains were combined and assembled to investigate the effect of sequence differences and the ratios of mixed reads.

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This observation led us to the idea that poor assemblies of some yeasts genomes might be due to heterozygous diploid status that were yet unknown for the sequencing subjects. Using Illumina reads from diverse source encompassing laboratory yeast strains to natural isolates genera Kluyveromyces, Issatchenkia, Candida and Cryptococcus , we are testing this hypothesis by combination of different values of k-mer and bubble size during de novo assembly and by measurement of SNP frequencies after re-mapping of reads on the assemblies.

Secreted virulence factors interact with commensal flora and host cells and enable Salmonella to survive and thrive in hostile environments. Outer membrane vesicles OMVs released from many Gram-negative bacteria function as a delivery vehicle for complex molecules, including virulence factors. In order to understand the roles of OMV in virulence regulation of Salmonella, a proteomic analysis was conducted on OMVs harvested under two different conditions mimicking the infection environments.

Comparative proteomic profiling between two conditions identified 14 proteins that were associated with the OMV fraction isolated only under the acidic minimal medium conditions, which reproduced the nutrient-deficient intracellular milieu. The absence of these 14 proteins each influenced Salmonella survival inside host cells either increased or decreased , proposing these OMV-associated proteins as new virulence factors in Salmonella. Another valuable finding is that OMV was able to deliver some virulence effectors that have been known to be secreted via Salmonella pathogenicity island SPI -1 or -2 type three secretion systems T3SSs.

OMVs possessing SPI-1 effectors on the surface increased the amount of F-actin contents in the host cell membrane, when added to the culture of epithelial cells, whereas OMVs lacking SPI-1 effectors did not influence the level of F-actin in host cells. Proteomic profiling provides a deeper insight into how Salmonella exploits OMV to interact with the environments. While agar has been utilized as a gel medium for pure culture technique, its resistance to microbial degradation hampered the utilization of red algal biomass.

The metabolic fate of agar is not fully understood. Like other polymer degradation, the metabolic pathway of agar has a typical pattern dividing into distinct steps.

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So as to use agar as raw materials, we collected representative genes involved in the agarolytic pathway. Based on a computational genomics approach, we predicted the core gene set for microbial agarolytic pathway. Using known functional agarases and hydrolases as a probe, we surveyed 2, microbial genomes in the public database and selected 12 potential agarolytic genomes. RNAseq analysis of three agarolytic microorganisms, Saccharophagus degradans, Marinimicrobium agarolyticum and Vibrio sp.

EJY3 corroborated the core gene set. The predicted core genes provide a minmal gene set for design and construction of a synthetic agarolytic system. However, microbial production of butanol is challenging primarily due to butanol toxicity and low titer of butanol production. Here, we analyzed and compared transcriptome of wild-type E. Gene association network of E. The mutated genes showed correlated relationship between the gene expression change and degree of network connection. The analyses identified potential gene candidates that can be engineered to increase butanol tolerance in E.

It has long been regarded that one fungal species make symbiotic relationship with one microalgal species in a thallus.


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However, the specific relationship between the mycobiont and the photobiont has been challenged by recent studies. One species of mycobiont can make symbiotic partnerships with various photobiont species when they grow at geographically distant locations. Several different algal genotypes can be present in a single lichen thallus.

In addition, the results of the algal community composition in lichens from King George Island, Antarctica indicated that each lichen thallus contained diverse algal species and the composition of algal community was mostly related to the mycobiont species. In this study, the genetic diversity and composition of symbiotic microalgae populations in the widespread geographical distribution of the seven lichen genera, Cetraria, Cladonia, Ocheloechia, Psoroma, Stereocaulon, Usnea, and Umbilicaria, were investigated based on eukaryotic LSU rrna gene.

To understand the effect of geography and climate on microalgal diversity, samples were collected from bi-polar and sub-polar regions. The results revealed that each lichen thallus contained diverse microalgal OTUs as the previous studies. However, each mycobiont genus showed preference on specific lineage of microalgal species as a major photobiont partner, which is composed of phylogenetically related OTUs.

Although some microalgal OTUs were detected from several regions including Southern and Northern hemisphere regardless of climate, most microalgal OTUs were recovered only from specific geographical region and climatic zone. Considering these results, we conclude that the composition of microalgal community in lichens are affected by mycobiont speceis, geography, and climate.

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As demonstrated by the world-wide distribution of lichens in various kinds of habitats from the tropics to the Polar regions, lichen symbiosis seems to be a highly successful adaptation to a diverse range of environmental conditions. To get insight in the genetic features linked to the symbiosis in both fungi and algae, whole-genome sequences of five lichen-forming fungal isolates and two algal isolates were determined.

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For the five sequenced fungal genomes, average size and the number of predicted genes were Mb and 97,, respectively, and two sequenced algal genomes, average size and the number of predicted genes were Mb and 8,, respectively. We explored genomic features including genes encoding small secreted proteins SSPs , polyketide synthesis genes, carbohydrate active enzyme-related genes, cytochrome P genes, and transcription factor genes.

In addition, genome and proteome conservation analysis revealed that the lichen-forming fungal genomes share the majority of genetic materials in common, when compared in a pairwise manner. To gain a better understanding of the molecular determinants of symbiosis, we performed RNA-seq and analyzed gene expression during resynthesis between fungus and alga. We reveal that a number of genes encoding SSPs are involved in symbiosis during the resynthesis.

The availability of both fungal and algal genomes will provide an opportunity to decipher an understanding of the processes by which symbionts interact between both organisms. Our study will enhance our understanding of the adaptive evolution of the lichen-forming fungi with the algae to their ecological niches.

The family is evolutionary old, but its age is uncertain, as its group has been dated as either or Ma old. The family has four major branches recognized by all recent phylogenetic studies. One is tropical, the remaining three are cosmopolitan. However, austral Gondwanaland distributions dominate in two of them and Northern Hemisphere distributions in the last one.

These contrasting distributions all indicate a long evolutionary history. We have very recently expanded the tropical branch significantly by describing the new tropical genus Gibbosporina with 12 new species, tentatively dated as 75 Ma old. What came as an additional surprise, was that Xanthosporoma, another genus described as new to science by us, in , came out as a much older, but inaccurately defined link between the tropical branch and the two mainly austral branches.

More samples and more genes are now being analyzed to further study this topic. The genus Xanthopsoroma is very small with only two known species, but is very distinct in several characters, and related to Psorophorus, another new genus from our paper. Pannariaceae representatives were certainly present in the old Gondwanaland forests when the southern continents were much closer to each other than today, and when southern beech forest dominated in Antarctica.

After the opening of the Drake Strait and the cooling of Antarctica, representatives of some genera adapted to a cold, tree-less, terricolous habitat, in particular species of Psoroma.

They have some representatives on tree trunks in austral forests, however, no less than 7 species are accepted today from Antarctica. We will describe a new one P. Here it developed into the species P. Much more recently it had Pannaria is another key genus. We are now developing a phylogeny, still partly hypothetical, of 9 expected major clades, with six different world distribution patterns. Most austral clades have three symbiotic partners, are still very insufficiently known with regard to chemistry, and details in spore morphology and sexual organs.

Eight new species have been described by our group so far, the number will probably be tripled. One of the clades has as a polar distribution, with one bipolar species and some subantarctic species partly revised recently. We believe that this is a heterogeneous group, representing at least three undescribed genera, some small with an apparently long and isolated evolutionary history in southernmost South America and New Zealand, respectively.

However, their classification based on two genes has not been stable so far. Our present project aims to improve the classification considerably, involving five genes, many more sequences, and to elucidate the evolutionary history of the Pannariaceae lichen family on a global scale. Clade formations will probably reflect the old separation of Gondwanaland from Laurasia, the split-up of Gondwanaland, Tertiary cooling which formed a cold Antarctica, and later dramatic Quaternary glaciations. It has also shown local endemism developing in isolated austral islands, contrasting wide distributions in isolated islands within tropical cyclone belts.

Lichenological studies in this area dates back to when Hue for the first time reported the occurrence of L. From then until , Korean lichens were studied mostly by Japanese lichenologists.

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But it was in s, that Korean lichenologists started studying lichens by themselves and the first publication of Korean lichenologists came in the year However, Korean lichenology came into limelight in the year , when Park made her first international publication on macro-lichens of South Korea. After Park s contribution, several other workers K. Moon, J. Hur developed a keen interest in Korean lichens and started working on them.

The first checklist of Korean lichens came in the year , mentioning the occurrence of genera and species. This number pretends to be too few for Korea, in comparison to some European countries, like Greece etc. This point is further clarified by National wide survey supported by Korean National Arboretum during the last 10 years. Recent progress of Korean lichen biodiversity and database preparation is discussed in this presentation.

To reduce the size of the vector, the minimal replicon of pkw was determined. The pkw plasmid contains a putative origin of replication ori , a potential ribosomal binding site RBS , and the repa gene encoding a plasmid replication protein. These constructed vectors were electroporated into W. Subsequent segregational plasmid stability testing of pkucm1 and pkucm2 showed that the vector pkucm1 is highly stable up to generations but pkucm2 was completely lost after 60 generations, suggesting that the putative ori may be important for plasmid stability in the host strain.