Characterization of serogroup C meningococci isolated from 14 provinces of China during 1966—2005 using comparative genomic hybridization

Neisseria meningitidis is a major cause of bacterial meningitis and septicemia worldwide. In China, serogroup A strains were responsible for over 95% of the cases, while serogroup B strains were mainly the cause of localized outbreaks and sporadic cases. Before 2003, serogroup C strains were only re-covered from a few sporadic cases. However, a sudden increase in the number of cases due to sero-group C strains occurred during 2003—2005 in Anhui Province, China. Many cases were found in other provinces at the same time. Multilocus sequence typing (MLST) results indicated that the unique se-quence type 4821 clone meningococci, a new hyper-virulent lineage, was responsible for the serogroup C meningitis outbreaks. We have completed the project of sequencing the whole genome of the Chi-nese N. meningitidis serogroup C representative isolate 053442. We fabricated a whole-genome mi-croarray of N. meningitidis isolate 053442 and analyzed the genome composition differences among 81 serogroup C isolates which were isolated from 14 provinces of China during 1966—2005. The com-parative genomic hybridization (CGH) result shows that the genome compositions of nearly all sero-group C isolates are similar to that of 053442. The products of many absent open reading frames (ORFs) are conserved hypothetical proteins. The results will provide a valuable resource from which one can analyze the genome composition and genetic background of serogroup C meningococci in China.     

Characterization of serogroup C meningococci isolated from 14 provinces of China during 1966–2005 using comparative genomic hybridization

Neisseria meningitidis is a major cause of bacterial meningitis and septicemia worldwide. In China, serogroup A strains were responsible for over 95% of the cases, while serogroup C strains were only recovered from a few sporadic cases. However, a sudden increase in the number of cases due to serogroup C strains occurred during 2003–2005 in Anhui Province, China. Many cases were found in other provinces at the same time. Multilocus sequence typing (MLST) results indicated that the unique sequence type 4821 clone meningococci, a new hyper-virulent lineage, was responsible for the serogroup C meningitis outbreaks. We have completed the project of sequencing the whole genome of the Chinese N. meningitidis serogroup C representative isolate 053442. We fabricated a whole-genome microarray of N. meningitidis isolate 053442 and analyzed the genome composition differences among 81 serogroup C isolates which were isolated from 14 provinces of China during 1966–2005. The comparative genomic hybridization (CGH) result shows that the genome compositions of nearly all serogroup C isolates are similar to that of 053442. The products of many absent open reading frames (ORFs) are conserved hypothetical proteins. The results will provide a valuable resource from which one can analyze the genome composition and genetic background of serogroup C meningococci in China.     

Characterization of dominant lactic acid bacteria isolated from São Jorge cheese, using biochemical and ribotyping methods

Aims: To identify, using phenotypic and genotypic methods, the dominant lactic acid bacteria (LAB) present in São Jorge cheese – one of the 11 Portuguese cheeses currently bearing an Appéllation d’Origine Protegée status. Methods and Results: A total of 225 isolates from milk, curd and cheeses throughout ripening were identified to the genus level, 108 to the species level and ten to the strain level. Phenotypic methods indicated that lactobacilli, followed by enterococci, were the dominant bacteria. The most frequently isolated species were Lactobacillus paracasei, Lactobacillus rhamnosus, Enterococcus faecalis and Enterococcus faecium. Ribotyping differentiated three L. paracasei, two E. faecalis and one Lactobacillus plantarum types. Enterococcus spp. exhibited the highest esterase and β-galactosidase activities among all isolates. Conclusions: The dominant LAB in São Jorge cheese are L. paracasei, L. rhamnosus, E. faecalis and E. faecium. Enterococcus likely plays a leading role upon acidification and aroma development in said cheese. Significance and Impact of the Study:  Our results support that a combination of conventional biochemical methods with genotypic methods allows for a thorough characterization and identification of isolates. Despite the limited number of isolates subject to molecular subtyping, a few specific Enterococcus and Lactobacillus strains were found that are promising ones for development of a starter culture. Hence, L. paracasei and E. faecalis are good candidates for a tentative starter culture, designed for manufacturing of São Jorge cheese at large – which takes advantage of actual isolates, in attempts to eventually standardize the quality of said cheese variety.     

Purification of bacterial genomic DNA in less than 20 min using chelex-100 microwave: examples from strains of lactic acid bacteria isolated from soil samples

We established a Chelex 100-Microwave method for the purification of bacterial genomic DNA (gDNA) in less than 20 min with high yield and good quality, useful for multiple purposes. It combines Chelex 100, proteinase K, RNase A and heating in a microwave oven. The resulting gDNA was used directly to identify bacterial species of the Order Lactobacillales by means of PCR amplification of their 16S rDNA gene, isolated from sediments on the Yucatan Peninsula, Mexico. This method produced gDNA free of phenolic and protein residual contaminants from 100 of these isolated bacteria. 16S rDNA amplification and sequencing showed Pediococcus acidilactici to prevail in inland lagoons, and Pediococcus pentosaceus, Lactobacillus plantarum, Lactobacillus sp., and Lactobacillus fermentum to be most abundant in the soils of livestock farms. The combination of Chelex 100, enzymes and microwave heating used in the Chelex 100-Microwave method produced large amounts of highly pure gDNA from Gram-positive and Gram-negative bacteria, in less than 20 min.     

Characterization of symbiotic and endophytic bacteria isolated from root nodules of herbaceous legumes grown in Qinghai–Tibet plateau and in other zones of China

Qinghai-Tibet plateau is the highest place in the world and the environment in that plateau is hard for animals and plants, with low temperature, low concentration of oxygen and high solar radiation. In this study, 61 root nodule isolates from Vicia, Oxytropis, Medicago, Melilotus and Onobrychis species grown in Qinghai-Tibet plateau and in loess plateau were comparatively characterized. Based upon the results of numerical taxonomy, ARDRA, AFLP, DNA-DNA hybridization and 16S rDNA sequencing, the isolates were classified as Rhizobium leguminosarum, Sinorhizobium meliloti, Sinorhizobium fredii, Mesorhizobium sp., Phyllobacterium sp., Stenotrophomonas sp. and two non-symbiotic groups related to Agrobacterium and Enterobacteriaceae. The strains isolated from Qinghai-Tibet plateau and from the loess plateau were mixed in these species or groups. Oxytropis spp. and Medicago archiducis-nicolai grown in Qinghai-Tibet plateau were recorded as new hosts for R. leguminosarum, as well as Oxytropis glabra and Medicago lupulina for S. fredii. In addition, strains resistant to high alkaline (pH 11) and high concentration of NaCl (3-5%, w/v) were found in each of the rhizobial species. This was the first systematic study of rhizobia isolated from Qinghai-Tibet plateau.     

Anti-phase oscillation of Asian monsoons during the Younger Dryas period: Evidence from peat cellulose δC of Hani, Northeast China

Significant changes in the global atmospheric and oceanic circulation system occurred during the Younger Dryas cold period. Several researchers have demonstrated a weakening of intensity of the Indian Ocean Summer Monsoon during that period. However, the exact characteristics of the East Asian Summer Monsoon still remain vague. Here we present a late-glacial precipitation proxy record of the East Asian Summer Monsoon, based on the peat cellulose δ¹³C found in Hani, Northeast China. Both the peat cellulose record and a pollen record from Lake Sihailongwan sediment indicate an abrupt increase in precipitation in the region during the Younger Dryas period. These results support the occurrence of wet conditions in the north and of dry conditions in the south of the Chinese Mainland during that period. By examining the activity of the East Asian Summer Monsoon on an interannual timescale, we propose a theory for the anomalous precipitation distribution that we attribute to the occurrence of an El Niño-like phenomenon in the Equatorial Pacific Ocean during the Younger Dryas. In this case, the intensity of the Western Pacific subtropical high may strengthen, and its position over the western Pacific Ocean may move northward. This could cause an enhancement of the East Asian Summer Monsoon and migration of a monsoonal rainbelt towards the northern region of the Chinese mainland, resulting in a precipitation distribution of wet conditions in the north and dry conditions in the south. Therefore, this anomalous rainfall distribution should be considered to indicate the strengthening of the East Asian Summer Monsoon, in anti-phase with the Indian Ocean Summer monsoon that weakened during the same period. This agrees with the previously revealed anti-phase variations of the two monsoons during the ice-rafted debris cold events of the North Atlantic Ocean. It appears that, in relation to the abrupt temperature drop in the Northern Hemisphere on centennial to millennial time scales, anti-phase variations of the two Asian summer monsoons occurred.     

Cloning and Characterization of AKR4C14, a Rice Aldo–Keto Reductase, from Thai Jasmine Rice

Aldo–keto reductase (AKR) is an enzyme superfamily whose members are involved in the metabolism of aldehydes/ketones. The AKR4 subfamily C (AKR4C) is a group of aldo–keto reductases that are found in plants. Some AKR4C(s) in dicot plants are capable of metabolizing reactive aldehydes whereas, such activities have not been reported for AKR4C(s) from monocot species. In this study, we have screened Indica rice genome for genes with significant homology to dicot AKR4C(s) and identified a cluster of putative AKR4C(s) located on the Indica rice chromosome I. The genes including OsI_04426, OsI_04428 and OsI_04429 were successfully cloned and sequenced by qRT-PCR from leaves of Thai Jasmine rice (KDML105). OsI_04428, later named AKR4C14, was chosen for further studies because it shares highest homology to the dicot AKR4C(s). The bacterially expressed recombinant protein of AKR4C14 was successfully produced as a MBP fusion protein and his-tagged protein. The recombinant AKR4C14 were capable of metabolizing sugars and reactive aldehydes i.e. methylglyoxal, a toxic by-product of the glycolysis pathway, glutaraldehyde, and trans-2-hexenal, a natural reactive 2-alkenal. AKR4C14 was highly expressed in green tissues, i.e. leaf sheets and stems, whereas flowers and roots had a significantly lower level of expression. These findings indicated that monocot AKR4C(s) can metabolize reactive aldehydes like the dicot AKR4C(s) and possibly play a role in detoxification mechanism of reactive aldehydes.     

Modification of glyceraldehyde-3-phosphate dehydrogenase,EC 1.2.1.12, isolated from rainbow trout during acclimation at 5 or 15°C—II. Biochemical characterization of G3PDH muscle isolates

• 1.1. G3PDH was isolated from the lateral muscle of rainbow trout (Salmo gairdneri) acclimated at 5°C (cold) and 15°C (warm).
• 2.2. No differences were found in muscle concentration, molecular weights, isoelectric focusing patterns, amino acid compositions or peptide maps between cold and warm isolates.
• 3.3. Cold and warm G3PDH contained mannose in variable concentration but no other prosthetic groups.

     

Sphaerotylos C. J. Chen—A Remarkable New Genus of Urticaceae from China,with Notes on Stigmas of the Family

A new subtribe of the family Urticaceae, Sphaerotylinae C. J. Chen, a new genus, Sphaerotylos C. J. Chen and its type species S. medogensis C. J. Chen from south-eastern Xizang (Tibet) in China are described and illustrated. The subtribe is regarded as a primitive group in the tribe Boehmerieae. The ring-shaped stigma and the ball-like connective are the first discovery in the family Urticaceae. The types of the stigma of the family, their taxonomic significance and their evolution are also discussed in the present paper.     

Genetic diversity in horses inferred from distribution of hemotypes—I. Analysis of similarity among 14 populations of 10 breeds using generalized Mahalanobis distance (D2)

• 1.1. Ninety-one pairwise comparisons of 14 populations yielded highly significant T² values for inter-breed differences while four subpopulations of Thoroughbred horses were nearly identical.
• 2.2. Generalized Mahalanobis distance was carried out by comparing simultaneously all 14 populations with respect to 26 variables (phenotypes) contributing most to the discriminant function.
• 3.3. The number of variables could be reduced to 12 phenotypes in final comparisons.
• 4.4. In general the calculated distances agreed with known relationships between horse breeds.
• 5.5. However the obtained distances are thought to be biased due to the nature of selected phenotypes which do not always correspond to “breed-markers”.

     

Modification of glyceraldehyde-3-phosphate dehydrogenase,EC 1.2.1.12, isolated from rainbow trout during acclimation at 5 or 15°C—I. Changes in the activity of individual muscle isolates as evidence for variable adaptive responses

• 1.1. The mean K_m and V_max values for G3PDH isolated from the lateral muscle of cold-adapted (5°C) rainbow trout, Salmo gairdneri, were twice those of enzyme from warm-adapted (15°C) trout when assayed at 7°C but not at any other temperature.
• 2.2. The entropy of activation of warm enzyme was about 3 times that of cold enzyme. However, enthalpy or free energy of activation among acclimation groups differed less or not at all.
• 3.3. Individual G3PDH isolates within either adaptation group differed in kinetic characteristics.

     

Modelling the dynamics of organic carbon in fertilization and tillage experiments in the North China Plain using the Rothamsted Carbon Model—initialization and calculation of C inputs

Modelling of the carbon dynamics in arable soils is complex and the accuracy of the predictions is unknown before the model is applied to each specific site. Objectives were (i) to test the accuracy of predictions of the carbon dynamics using the Rothamsted Carbon (RothC) Model in a field trial in Quzhou, North China Plain, using different methods for initialization and estimation of carbon input into the soil and (ii) to test the applicability of the RothC model for plots with either conventional tillage (CT) or no-tillage (NT) systems. A field trial was conducted with applications of differing amounts of N (0, 112 or 187 kg N ha^?1 year^?1), P (0, 75 or 150 kg P₂O₅ ha^?1 year^?1) and wheat straw (0, 2.25 or 4.5 t DM ha^?1 year^?1) in differing combinations with either CT or NT for 18 years. CT and NT affected stocks of soil organic carbon (SOC) similarly. Carbon inputs from crops were either estimated from published regression functions that relate C inputs to crop yield including rhizodeposition (models 1 and 2) or published root:aboveground biomass ratios (model 3). Model 1, which was not calibrated to the site conditions, was successful in predicting the carbon dynamics in seven out of nine treatments (model efficiencies EF ranged from 0.28 to 0.87), whereas for two treatments, EF (?0.35 and?2.3) indicated an unsuccessful prediction. The prediction of the C dynamics in NT experiments using model 1 was generally successful, but this may have been due to the fact that NT did not have a specific effect on SOC stocks for this trial. Model 2, which was the same as model 1 except for an optimization of the stock of inert organic matter using one treatment, predicted SOC stocks in the remaining eight treatments overall better than model 1. Model 3 was less successful than models 1 and 2 in all treatments (?19 ≤ EF ≤ 0.56). The results indicate that the RothC model may successfully predict C dynamics—for the site studied even without prior calibration as in model 1—, but care should be taken in choosing an appropriate approach for estimating C inputs into the soil.