Evaluation of the Method Based on Restriction Fragment Length Polymorphism Analysis as Simple Analysis Method of Lactic Acid Bacteria in Foods

Lactic acid bacteria have not only been used to produce various kinds of fermented food, but also used as probiotic products. As lactic acid bacterial group was consisted from diverse genera, a simple inspection method by which numbers and contained microorganisms could be automatically analyzed without any preliminary information was required to use them more effectively. In this manuscript, lactic acid bacterial groups in commercial products of kimuchi, komekouji-miso, and yoghurt were identified and enumerated by our newly developed method [1]-[3], to evaluate whether the method could be used as an inspection method of various food samples. In kimuchi, numerically dominant bacteria were Lactobacillus sakei, and L. casei (1.4 × 104 MPN g-1) and Leuconostoc spp. (l.4 × 104 MPN). In kouji-miso, numerically dominant bacteria was Bacillus spp. (3 × 103 MPN), which mainly included B. subtilis group and B. cereus group. Lactic acid bacteria such as Lactobacillus spp., or Lactococcus spp., included in the komekouji-miso, could be enumerated after 3 days incubation (1.24 × 104 MPN), but not detected after 7 days incubation. In yoghurt A and C, Lactococcus lactis was detected as numerically dominant lactic acid bacteria (3.0 × 105 MPN). In yoghurt B, Lactobacillus spp., or Lactococcus spp., was detected not only by a culturebased method but also by an unculture-based method, although there was a difference between the both estimated numbers. The present results suggested that the method might become useful as a simple inspection method of food microorganisms, because time and labor of the analysis could be reduced by using an unculture-based method and MCE-202 MultiNA. In this study, Bifidobacteriium spp. was not detected in B and C yoghurt, in spite of indicating their existence, and numbers of lactic acid bacteria were lower than the level of the daily product regulation, because 16S rDNA of Bifidobacteriium spp. might not be amplified by the used PCR condition. The PCR condition must be changed so as to amplify Bifidobacterium spp., before the method will be used as an inspection method for lactic acid bacteria.

The Use of Restriction Fragment Length Polymorphism and Fluorescence in Situ Hybridization to Investigate Microbiota of Piglets after Feeding Oregano

A total of 80 piglets (7.9 ± 1.0 kg) were used in a feeding experiment with dried oregano. The diets differed in their oregano content: 0 g, 2 g, 4 g and 8 g oregano/kg feed, corresponding to 0, 23.5, 46.9 and 93.9 mg carvacrol/kg DM. After the experimental period of 5 weeks, 20 piglets of both extreme feeding groups were slaughtered: 10 animals of the control group and 10 animals of the group that received 8 g oregano/kg. Ingesta samples of jejunum, caecum and colon were collected and analyzed by FISH and PCR RFLP to compare the diversity of microbiota. The results showed no significant changes in microbiota in response to oregano. The patterns of the PCR-RFLP showed a similarity of 61.8% - 91.8% in both feeding groups. In conclusion, an effect of oregano on the in- testinal microbiota could not be shown under the methods used.

Research on the Correlation Between rs2110385 Polymorphisms of the Visfatin Gene and Nonproliferative Diabetic Retinopathy

Objective:To investigate the association between rs2110385 polymorphisms of the visfatin gene and the risk of type 2 diabetic retinopathy(DR).Methods:172 Han subjects were selected from Xi’an Shaanxi Province;140 patients with type 2 diabetes mellitus(T2DM)and 32 normal controls(NC)were selected from our hospital.Patients with diabetes were divided into a non-DR group(T2DM)(n=69)and a nonproliferative diabetic retinopathy Group(DR)(n=71)after dilated fundus photography and fundus fluorescein angiography.rs2110385/AluⅠgenotypes were detected by standardized polymerase chain reaction-restriction fragment length polymorphism(PCR-RFLP),and the differences in the detection rates of different genotypes in the above populations were compared.Results:1)The visfatin level in the DR Group was significantly higher than that in the NC and T2DM groups(P<0.05).2)The frequency of GG genotype and G allele of rs2110385 in the DR Group were higher than those in the T2DM and NC groups(80.3,69.6,50.0,86.6,79,65.6,P<0.05).3)There were significant differences in allele frequency and genotype frequency distribution of rs2110385 between the DR Group and the NC group(P<0.01).Conclusion:Visfatin increased in the nonproliferative diabetic retinopathy group and could be a potential indicator for the clinical prediction of DR.The G allele of the rs2110385 polymorphic site may be related to the risk of DR.

Genetic Mapping of Laminaria japonica and L. Iongissima Using Amplified Fragment Length Polymorphism Markers in a ＂Two-Way Pseudo- Testcross＂ Strategy

With a ＂two-way pseudo-testcross＂ mapping strategy, we applied the amplified fragment length polymorphism （AFLP） markers to construct two moderate density genetic linkage maps for Laminaria. The linkage maps were generated from the 60 progenies of the F1 cross family （Laminaria iongissima Aresch. × L. Japonica Miyabe） with twenty pairs of primer combinations. Of the 333 polymorphic loci scored in 60 progenies, 173 segregated in a 1：1 ratio, corresponding to DNA polymorphisms heterozygous in a single parent, and the other 58 loci existing in both parents followed a 3：1 Mendelian segregation ratio. Among the loci with 1：1 segregating ratios, 79 loci were ordered in 14 linkage groups （648.6 cM） of the paternal map, and 72 loci were ordered in 14 linkage groups （601.9 cM） of the maternal map. The average density of loci was approximately 1 per 8 cM. To Investigate the homologies between two parental maps, we used 58 loci segregated 3：1 for further analysis, and deduced one homologous linkage group. The linkage data developed in these maps will be useful for detecting loci-controlling commercially important traits for Laminaria.

Association of TNF-α-238G/A and 308 G/A Gene Polymorphisms with Pulmonary Tuberculosis among Patients with Coal Worker’s Pneumoconiosis

Objectives Tumor necrosis factor-α （TNF-α） may play an important role in host＇s immune response to mycobacterium tuberculosis （M. tuberculosis） infection. This study was to investigate the association of TNF-α gene polymorphism with pulmonary tuberculosis （TB） among patients with coal worker＇s pneumoconiosis （CWP）. Methods A case-control study was conducted in 113 patients with confirmed CWP complicated with pulmonary TB and 113 non-TB controls with CWP. They were matched in gender, age, job, and stage of pneumoconiosis. All participants were interviewed with questionnaires and their blood specimens were collected for genetic determination with informed consent. The TNF-α gene polymorphism was determined with polymerase chain reaction of restriction fragment length polymorphism （PCR-RFLP）. Frequency of genotypes was assessed for Hardy-Weinberg equilibrium by chi-square test or Fisher＇s exact probability. Factors influencing the association of individual susceptibility with pulmonary TB were evaluated with logistic regression analysis. Gene-environment interaction was evaluated by a multiplieative model with combined OR. All data were analyzed using SAS version 8.2 software. Results No significant difference in frequency of the TNF-α-308 genotype was found between CWP complicated with pulmonary TB and non-TB controls （2,2=5.44, P=-0.07）. But difference in frequency of the TNF-α-308 A allele was identified between them （2,2-5.14, P=0.02）. No significant difference in frequencies of the TNF-α-238 genotype and allele （P=0.23 and P=0.09, respectively） was found between cases and controls either, with combined （GG and AA） OR of 3.96 （95% confidence interval of 1.30-12.09） at the -308 locus of the TNF-α gene, as compared to combination of the TNF-α-238 GG and TNF-α-308 GG genotypes. Multivariate-adjusted odds ratio of the TNF-α-238 GG and TNF-α-308 GA genotypes was 1.98 （95% CI of 1.06-3.71） for risk for pulmonary TB in patients with CWP. There was a synergic interaction between the TNF-a-308 GG genotype and body mass index （OR=4.92）, as well as an interaction between the TNF-α-308 GG genotype and history of BCG immunization or history of TB exposure. And, the interaction of the TNF-α-238 GG genotype and history of BCG immunization or TB exposure with risk for pulmonary TB in them was also indicated. Conclusions TNF-α-308 A allele is associated with an elevated risk for pulmonary TB, whereas TNF-α-238 A allele was otherwise.

The Association between RASSF1 Gene Polymorphisms and Lung Cancer Susceptibility among People in Hubei Province of China

The relationship between Ala/Ser polymorphism in 133 codon of exon 3 region of the RASSF1 gene and genetic susceptibility of lung cancer in Hubei province Han population was investigated by a case-control study. Polymerase chain reaction-restriction fragment length polymorphism （PCR-RFLP） technique was adopted to analyze the polymorphism of codon 133 of exon 3 in the RASSF1 gene of 100 pathologically diagnosed lung cancer patients, and 100 healthy controls. The relationship between different genotypes and the susceptibility of lung cancer was analyzed. Among 200 blood samples from Han people in Hubei Province, including 100 from lung cancer patients and 100 from healthy controls, the frequencies of Ala/Ala, Ala/Ser, Ser/Ser genotype of the RASSF1 in lung cancer patients were 83%, 16%, 1%, and those in healthy controls was 93%, 7%, 0% respectively, with the difference being statistically significant between two groups （P〈0.05）. The individuals with Ala/Ser genotype had higher risk of suffering from lung cancer, with an OR of 2.341, and 95% CI of 1.009-6.393 respectively. It was concluded that RASSF1Ala133Ser was a susceptible genetic factor of lung cancer. Ala/Ser genotype increased the risk of lung cancer.

Mapping of a New Gene Wbph6(t) Resistant to the Whitebacked Planthopper, Sogatella furcifera, in Rice

A rice population consisting of 90 TN1/Guiyigu F3 lines was employed to analyze the linkage between DNA markers and a new gene Wbph6(t) conferring resistance to whitebacked planthopper, Sogatella furcifera By using the mapping approach of bulked extremes and recessive class, Wbph6(t) was mapped onto the short arm of chromosome 11 with a genetic distance of 21.2 cM to SSLP marker RM167.

Uptake of copper ion by activated sludge and its bacterial community variation analyzed by 16S rDNA

The effect and uptake of copper ion on SBR(sequence batch reactor) biological treatment system was studied. Special nutrient and powder activated carbon(PAC) additive were tested as uptake stimulation technique. Results showed that copper ion had higher effect on unacclimated activated sludge system than on acclimated one. The special nutrient adding could enhance the uptake of copper significantly, while PAC adding could improve the sludge settling and decrease the turbidity of effluent. The variation of bacterial community analyzed by 16S rDNA method showed the acclimation of copper could increase copper resistance species, and excess accumulation could cause some species diminish. It was confirmed that acclimation could improve the resistance and uptake ability of microorganism to heavy metal.

Molecular characterization of bacterial community in aerobic granular sludge stressed by pentachlorophenol

To characterize the effects of pentachlorophenol (PCP) on the performance and microbial community of aerobic granular sludge in sequencing batch reactor (SBR), the web-based terminal restriction fragment length polymorphism (T-RFLP) and real-time PCR (RT- PCR) techniques were used to explore the bacterial community structure. When PCP increased from 0 to 50 mg/L, the COD removal rate changed little, while the ammonia removal rate dropped from 100% to 64.9%. The results of molecular characterization showed t...

Bacterial diversity in activated sludge from a consecutively aerated submerged membrane bioreactor treating domestic wastewater

The bacterial diversity of activated sludge from submerged membrane bioreactor (SMBR) was investigated. A 16S rDNA clone library was generated, and 150 clones were screened using restriction fragment length polymorphism (RFLP). Of the screened clones, almost full-length 16S rDNA sequences of 64 clones were sequenced. Phylogenetic tree was constructed with a database containing clone sequences from this study and bacterial rDNA sequences from NCBI for identification purposes. The 90.6% of the clones were a?l...

Comparative Analysis of Genetic Diversity and Structure in Rice Using ILP and SSR Markers

Genetic diversity of 36 rice entries from the United States Department of Agriculture （USDA） rice collection was assessed using 103 ILP （intron length polymorphism） and 54 SSR （simple sequence repeats） markers. A total of 236 and 332 alleles were detected by the ILP and SSR markers, respectively. On average, the SSR markers produced higher polymorphism information content value and number of alleles than the ILP markers. Whereas the Nei＇s genetic distance measured using the SSR markers was much higher than that measured using the ILP markers. Manters test indicated that there was a statistically significant correlation （r=0.827, P〈0.001 ） between the two marker systems. UPGMA clustering based on the ILP and SSR markers resulted in consensus dendrograms. The cophenetic correlation coefficient （r=0.918, 0.878 and 0.924, P〈0.001 for the ILP, SSR and combined markers, respectively） showed a highly accurate dendrogram represented the genetic distance among these entries. The 36 entries were divided into four groups. Four African Oryza glaberrima accessions were clustered within a distinct group （I）, and the remaining entries were separated into three groups （11, III and IV）. All the entries could be also clustered into two main groups： One was composed of III and IV, considered as indica group, and the other was composed of I （O. glaberrima） and II （japonica-like）. Model-based cluster analysis revealed that the japonica-like group maintained very pure ancestry while the indica group shared mixed ancestry, especially for group III, which had seven admixtures sharing from 19.5% to 30.0% of ancestry with group IV （based on SSR markers）. It is suggested that ILP and SSR markers could be very useful for the genetic study and breeding in rice.

Comparison of Bacterioplankton Communities in Three Heavily Polluted Streams in China

Objective To compare the bacterioplankton communities in streams exposed to pollution of different types. Methods The bacterioplankton communities in three selected heavily polluted streams were investigated by using terminal‐restriction fragment length polymorphism （T‐RFLP） analysis in combination with 16S rRNA gene clone library analysis. Results Both T‐RFLP and 16S rRNA gene clone library revealed a great difference in bacterioplankton community composition in the different streams. Conclusion This work might provide some new insights into bioremediation of heavily polluted streams.

Development of Sequence Characterized Amplified Region (SCAR) Primers for the Detection of Resistance to Sporisorium reiliana in Maize

Head smut of maize （Zea mays L.）, which was caused by Sporisorium reiliana, occurred in most of the maize growing areas of the world. The purpose of this study was to develop SCAR markers for map-based cloning of resistance genes and MAS. Two sets of BC3 progenies, one （BC3Q） derived from the cross Qi319 （resistance）×Huangzao 4 （susceptible）, the other （BC3M） from Mol7 （resistance）× Huangzao 4 （susceptible）, were generated. Huangzao 4 was the recurrent parent in both progenies. A combination of BSA （bulked segregant analysis） with AFLP （amplified fragment length polymorphism） method was applied to map the genes involving the resistance to S. reiliana, and corresponding resistant and susceptible bulks and their parental lines were used for screening polymorphic AFLP primer pairs. One fragment of PI3M61-152 was converted into SCAR （sequence charactered amplified fragment） marker S130. The marker was mapped at chromosome bin 2.09, the interval of a major QTL region previously reported to contribute to S. reiliana resistance. Furthermore, S130 was highly and facilitate map-based cloni associated with resistance to S. reiliana, and could be useful for marker-assisted selection ng of resistance genes.

Diversity of symbiotic algae of the genus Symbiodinium in scleractinian corals of the Xisha Islands in the South China Sea

Symbiotic algae （Symbiodinium sp.） in scleractinian corals are important in understanding how coral reefs will respond to global climate change. The present paper reports on the diversity of Symbiodinium sp. in 48 scleractinian coral species from 25 genera and 10 families sampled from the Xisha Islands in the South China Sea, which were identified with the use of restriction fragment length polymorphism （RFLP） of the nuclear ribosomal DNA large subunit gene （rDNA）. The results showed that： （i） Symbiodinium Clade C was the dominant zooxanthellae in scleractinian corals in the Xisha Islands; （ii） Symbiodinium Clade D was found in the corals Montipora aequituberculata, Galaxea fascicularis, and Plerogyra sinuosa; and （iii） both Symbiodinium Clades C and D were found simultaneously in Montipora digitata, Psammocora contigua, and Galaxeafascicularis. A poor capacity for symbiosis polymorphism, as uncovered by RFLP, in the Xisha Islands indicates that the scleractinian corals have low adaptability to environmental changes. Further studies are needed to investigate zooxanthellae diversity using other molecular markers.

Novel ACTG1 mutation causing autosomal dominant non-syndromic hearing impairment in a Chinese family

γ -actin （ACTG1） gene is a cytoplasmic nonmuscle actin gene, which encodes a major cytoskeletal protein in the sensory hair cells of the cochlea. Mutations in ACTG1 were found to cause autosomal dominant, progressive, sensorineural hearing loss linked to the DFNA 20/26 locus on chromosome 17q25.3 in European and American families, respectively. In this study, a novel missense mutation （c.364A〉G; p.I122V） co-segregated with the affected individuals in the family and did not exist in the unaffected family members and 150 unrelated normal controls. The alteration of residue Ile122 was predicted to damage its interaction with actin-binding proteins, which may cause disruption of hair cell organization and function. These findings strongly suggested that the I122V mutation in ACTG1 caused autosomal dominant non-syndromic hearing impairment in a Chinese family and expanded the spectrum of ACTG1 mutations causing hearing loss.

Isolation and characterization of the AGAMOUS homologous gene NTAG in Chinese narcissus (Narcissus tazetta var. chinensis Roem)

Amaryllidaceae, a monocot plant family, consists of many important ornamental bulb flower species. Chinese narcissus （Narcissus tazetta var. chinensis Roem）, its flowers developed at high temperatures and bloomed at lower temperatures during the Chinese Spring Festival, is a traditional Chinese flower with high economic and ornamental value. To study its flower development, a full length cDNA containing MADS box domain from narcissus was isolated by a reverse transcription polymerase chain reaction （RT-PCR） with degenerate oligo-nucleotide primers derived from a conserved MADS- and K-box domain sequence. The 5＇ and the 3＇ regions of the gene were amplified using the PCR protocol for the rapid amplification of cDNA ends （RACE）. The 690 bp open reading frame encodes 230 amino acid residues. A comparison of the deduced amino acid sequence of NTAG with the sequence of other MADS box proteins showed 91.3% amino acid identities with HAG （Hyacinthus orientalis）. Sequence analysis and alignment showed significant similarity with other AG homologues. RNA blot analysis indicated that the narcissus NTAG gene was expressed only in reproductive organs, especially in stamens and carpels. These results indicated that the NTAG gene was an AG homologue and that the AG genes appeared to be structurally and functionally conserved between dicots and monocots.

Genetic Relationships among Prunus mume var. pendula Using AFLP Markers

Genetic relationships among Prunus mume var. pendula were studied by using AFLP markers. 18 accessions representing 14 cultivars of Prunus mume var. pendula were selected from the germplasm collection at the Research Center of China Mei Flower. Seven Mse I-EcoR I AFLP primer combinations revealed 450 legible bands, and 269 of which were polymorphic markers. A similarity matrix was prepared using the simple matching coefficient of similarity and Neis (72) distance coefficient. A UPGMA dendrogram demonstrated the genetic relationships of the cultivars. The information given by AFLP markers was basically consistent with the morphological classification and the evolutionary history of the morphotypes, and roughly supported the new revised classification system for Chinese Mei Cultivars. But there were still several exceptions: 1) the Guhong Chuizhi inserted between the Tiaoxue Chuizhi and the Danfen Chuizhi; 2) the Wufu Chuizhi kept off the Pink Pendant Form, and the Moshan Chuizhi was removed from Viridiflora Pendant Form; 3) the Danbi Chuizhi and the Shuangbi Chuizhi of Viridiflora Pendant Form got together well but fell within the Pink Pendant Form.

Is type Ⅰ alpha 2 collagen gene responsible for intracranial aneurysm in Northeast China?

In this study, we investigated whether a single nucleotide polymorphism （rs42524 G 〉 C） in the type I alpha 2 collagen gene was associated with sporadic ruptured intracranial aneurysm or its clinical characteristics in patients from Northeast China. Genotyping of the rs42524 G 〉 C polymorphism was carried out using a polymerase chain reaction-restriction fragment length polymorphism assay. The data showed that the frequency of the rs42524 GC ＋ CC genotype was significantly higher than the GG genotype among intracranial aneurysm patients whose Hunt and Hess grading scale was 〉 3. In addition, the rs42524 G 〉 C genotype was found to have a statistically significant association with intracranial aneurysm risk. These findings indicate that the type I alpha 2 collagen gene gene may be involved in a predisposition to intracranial aneurysm in the Northeast Chinese population. Crucially, the rs42524 C allele may be an important risk factor for increased severity of the condition in patients with ruptured intracranial aneurysms.