Biodegradation of organophosphorus insecticides by two organophosphorus hydrolase genes (opdA and opdE) from isolated Leuconostoc mesenteroides WCP307 of kimchi origin

This study is aimed to reveal the molecular incidence of organophosphorus insecticides degradation during the fermentation of Korean food yeulmu-mulkimchi. To this end, two opdA and opdE which consist of 930 and 894 bp that encode 309 and 297 amino acids, respectively, were cloned from the Leuconostoc mesenteroides WCP307 strain that was isolated from chlorpyrifos (CP) impregnated kimchi. The Escherichia coli that harbored the opdA and opdE genes depleted a CP concentration of 72% and 83%, respectively, in an M9 medium after 6 days. The OpdA and OpdE enzymes molecular weights were estimated to be approximately 35 and 33 kDa and showed optimal activities at 30 °C with a pH of 7.0 and 6.0, respectively. However, the mutated OpdA (Ser128 → Ala128) and OpdE (Ser129 → Ala129) enzymes had no activities on OP insecticides and ρ-nitrophenyl butyrate substrates. In addition, the OpdA and OpdE enzymes showed profound catalytic activities against cadusafos, comnaphos, diazinon, dyfonate, ethoprophos, fenamiphos, methylparathion, and parathion insecticides. Therefore, it is assumed that OpdA and OpdE enzymes detoxified the pesticides contaminated kimchi composition like Chinese cabbages during fermentation. Furthermore, the OpdA and OpdE enzymes augmented the diversity of new LAB-opd enzymes group in nature.     

Domestication of the Emblematic White Cheese-Making Fungus Penicillium camemberti and Its Diversification into Two Varieties

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Genetic associations of common deletion polymorphisms in families with Avellino corneal dystrophy

Although the locations of many common deletion variants in the human genome are unknown, such deletions may be causative in rare disorders. Deletions can be mapped through the identification of Mendelian inconsistencies in pedigrees. Data for a total of 341,577 SNPs from an ACD family cohort (n = 551) and 341,039 SNPs from a Korean-Vietnamese family cohort (n = 554) were collected for a genome-wide association study using Illumina 370K-Duo Beadchips^®. In the present study, a Mendelian inconsistency analysis of genotype data identified 1029 deletion variants in Korean and Korean-Vietnam family cohorts of 404 trios comprising 1105 individuals. Small-deletion copy number variations adjacent to 10 deletion variants were then validated by the real-time quantitative polymerase chain reaction. The expected copy numbers of each deletion variant were directly matched to its genotype cluster image. Deletion variants were also in strong linkage disequilibrium with nearby SNPs. To determine the overall contribution of the 1029 deletion variants, we analyzed case-control trio associations with the risk for Avellino corneal dystrophy. One SNP marker (rs885945) neighboring the gene encoding major histocompatibility complex class I F (HLA-F) was significantly associated with the risk of Avellino corneal dystrophy (P = 0.0003). rs885945 showed high LD with SNPs within the HLA-F gene. Therefore, HLA-F may be a potential candidate gene for Avellino corneal dystrophy.     

The combined role of glaciation and hybridization in shaping the distribution of genetic variation in a Patagonian southern beech

Aim The distribution of the genetic variation in long‐lived species is a combination of both, historical and current processes. In Nothofagus nervosa (Phil.) Dim. et Mil., the possible existence of multiple glacial refugia, the unidirectional gene flow along fragmented areas and the natural hybridization with the related species Nothofagus obliqua (Mirb.) Oerst. highlights as the most important factors responsible for modelling its genetic structure. The present study aims to find out the relative importance of these evolutionary processes in determining the distribution pattern of the genetic variation in N. nervosa. Location The study was carried out in north‐western Patagonia, Argentina. Twenty populations covering the entire distribution range of N. nervosa in Argentina were analysed. For comparison purposes, three populations from Chile were also included. Methods Genetic variation was detected using isozyme gene markers; diversity and differentiation parameters were calculated. A cluster analysis was performed and the correlation between genetic and geographical distances was tested. Results Levels of genetic variation were relatively high given the small distribution range of the species in Argentina. Genetic and geographical distances were not correlated and a longitudinal trend in the genetic variation was evident. Hotspots of diversity with rare and private alleles were observed among western populations, while hybrid seeds were found almost exclusively among eastern populations. Main conclusions The higher level of diversity observed in western populations could be related with the location of glacial refugia. Furthermore, it should also reflect low levels of gene flow given the eastward unidirectional winds. On the contrary, ancient and current interspecific hybridization processes would mainly cause the particular genetic constitution of the eastern populations. Evidence is presented supporting that glaciations and hybridization were the main factors shaping the distribution of the genetic variation in N. nervosa.     

Potentiality of the cox1 gene in the taxonomic resolution of soil fungi

We explored the potential of the cox1 gene in the species resolution of soil fungi and compared it with the nuclear internal transcribed spacer (ITS) and small subunit (SSU)-rDNA. Conserved primers allowing the amplification of the fungal cox1 gene were designed, and a total of 47 isolates of Zygomycota and Ascomycota were investigated. The analysis revealed a lack of introns in >90% of the isolates. Comparison of the species of each of the six studied genera showed high interspecific sequence polymorphisms. Indeed, the average of nucleotide variations (4.2–11%) according to the genus, due mainly to the nucleotide substitutions, led to the taxonomic resolution of all the species studied regarding both ITS and SSU-rDNA, in which <88% were discriminated. The phylogenetic analysis performed after alignment of the cox1 gene across distant fungal species was in accordance with the well-known taxonomic position of the species studied and no overlap was observed between intra- and interspecific variations. These results clearly demonstrated that the cox1 sequences could provide good molecular markers for the determination of the species composition of environmental samples and constitute an important advance to study soil fungal biodiversity.     

Genetic organization and biogenesis of adhesive fimbriae of Escherichia coli

The genetic organization of the determinants of type 1, K88ab, K99 fimbriae and P(pap)pili of Escherichia coli is presented. The functions of the various gene products are described and a model for the process of fimbriae biogenesis is presented and discussed.     

Maize pyruvate decarboxylase mRNA is induced anaerobically

A cDNA was identified using an oligonucleotide designed by comparing the sequences of bacterial and yeast pyruvate decarboxylase. The sequence of the cDNA identified by the oligonucleotide contained an open reading frame that encoded a protein of 65 kDa that was similar in sequence to bacterial and yeast pyruvate decarboxylase. This protein was selectively precipitated by an antiserum specific for maize PDC. Northern-blot analysis shows that PDC mRNA is anaerobically induced. Southern-blot analysis of maize genomic DNA indicated that the maize PDC gene has a single or low copy number.     

Application of partial restriction procedure in both shotgun and non-random strategies for nucleotide sequencing

Partial digestion of a target DNA fragment with 4-bp-recognition restriction enzymes followed by a forced ligation to an M13 vector was employed for the construction of a subfragment library. The library can be used for either shotgun or non-random nucleotide sequencing. Application of the partial digests generated with the 4-bp recognition restriction enzymes instead of DNase I in the improved non-random strategy for nucleotide sequencing (Li and Wu, 1987) made the procedure as easy as that of the random strategy. The library can also be used in shotgun nucleotide sequencing directly, and few self-ligated subfragments were found. The usefulness of this procedure was demonstrated by the sequencing of a goat 6.5-kb EcoRI fragment, which is located 5' to the globin gene.     

Fine‐scale Population Genetic Structure of Two Dioecious Indian Keystone Species,Ficus hispida and Ficus exasperata (Moraceae)

Although Ficus (Moraceae) is a keystone plant genus in the tropics, providing resources to many frugivorous vertebrates, its population genetic structure, which is an important determinant of its long‐term survival, has rarely been investigated. We examined the population genetic structure of two dioecious fig species (Ficus hispida and Ficus exasperata) in the Indian Western Ghats using co‐dominant nuclear microsatellite markers. We found high levels of microsatellite genetic diversity in both species. The regression slopes between genetic relationship coefficients (f_ij) and spatial distances were significantly negative in both species indicating that, on average, individuals in close spatial proximity were more likely to be related than individuals further apart. Mean parent–offspring distance (σ) calculated using these slopes was about 200 m in both species. This should be contrasted with the very long pollen dispersal distances documented for monoecious Ficus species. Nevertheless, overall population genetic diversity remained large suggesting immigrant gene flow. Further studies will be required to analyze broader scale patterns.