Multiple high-throughput analyses monitor the response of E. coli to perturbations

Analysis of cellular components at multiple levels of biological information can provide valuable functional insights. We performed multiple high-throughput measurements to study the response of Escherichia coli cells to genetic and environmental perturbations. Analysis of metabolic enzyme gene disruptants revealed unexpectedly small changes in messenger RNA and proteins for most disruptants. Overall, metabolite levels were also stable, reflecting the rerouting of fluxes in the metabolic network. In contrast, E. coli actively regulated enzyme levels to maintain a stable metabolic state in response to changes in growth rate. E. coli thus seems to use complementary strategies that result in a metabolic network robust against perturbations.     

Differentially methylated CpG sites related to fertility in Japanese Black bull spermatozoa: epigenetic biomarker candidates to predict sire conception rate

For semen suppliers, predicting the low fertility of service bull candidates before artificial insemination would help prevent economic loss; however, predicting bull fertility through in vitro assessment of semen is yet to be established. In the present study, we focused on the methylated CpG sites of sperm nuclear DNA and examined methylation levels to screen new biomarkers for predicting bull fertility. In frozen-thawed semen samples collected from Japanese Black bulls, for which the sire conception rate (SCR) was recorded, the methylation level of each CpG site was analyzed using human methylation microarray. According to regression analysis, 143 CpG sites related to SCR were significantly differentially methylated. Whole genome bisulfite sequence data were obtained from three semen samples and the differentially methylated regions (DMRs) that included the target CpG sites selected by human methylation microarray were confirmed. Using combined bisulfite restriction analysis, fertility-related methylation changes were detected in 10 DMRs. With the exception of one DMR, the methylation levels of these DMRs were significantly different between groups with high fertility (> 50%) and low fertility (< 40%). From multiple regression analysis of methylation levels and SCR, three DMRs were selected that could effectively predict bull fertility. We suggest that these fertility-related differences in spermatozoal methylation levels could be new epigenetic biomarkers for predicting bull fertility.     

Soil organic matter status of Chernozem soil in North Kazakhstan: effects of summer fallow

In North Kazakhstan there is concern about the degradation of Chernozem soil and agricultural sustainability by the inclusion and frequency of summer fallows in crop rotations in terms of their influence on the changes of soil organic matter (SOM) quality and quantity. We examined five fallow-wheat (Triticum aestivum L.) cropping systems with different frequencies of the fallow phase in Chernozem soil of North Kazakhstan; continuous wheat (CW), 6-y rotation (6R), 4-y rotation (4R), 2-y rotation (2R) and continuous fallow (CF). Soil samples were collected from the two phases of each rotation, pre- and post-fallow, and analyzed for potentially mineralizable C (PMC) and N (PMN), ‘light fraction’ organic matter (LF-OM), C (LF-C) and N (LF-N). Potentially mineralizable C was inversely proportional to the frequency of fallow and was highest in CW. Mineral N (min-N) and PMN were more responsive to rotation phase than other indices of SOM. Mineral N was higher in the post-fallow phase while PMN was higher in the pre-fallow phase. Light fraction organic matter was negatively correlated to the frequency of fallow and was higher in the pre-fallow than in the post-fallow phase in a rotation. The results suggested that the yearly input of plant residue in a less frequently fallowed system built up more PMC, whereas PMN was closely correlated to recent inputs of substrate added with plant residues. We conclude that a frequent fallow system may deplete SOM via accelerated mineralization. Also that LF-OM, PMC and PMN are more sensitive to detect subtle changes in SOM quality than total SOM. Our results may provide prediction of SOM response to fallow frequency in wheat-based rotation systems in Chernozem soils of semi-arid regions.     

Transmission of bacterial wilt resistance by First Division Restitution (FDR) 2n pollen via 4x×2x crosses in potatoes

Summary Resistance to bacterial wilt (Pseudomonas solanacearum) found in tuber-bearing Solanum species was transferred into a diploid potato breeding population. Simultaneous selections were made for agronomic characters, production of first division restitution (FDR) 2n pollen, and resistance. Diploid resistant genotypes were identified via inoculation with a virulent isolate (CIP-204) of race 3 of Pseudomonas solanacearum. These resistant diploid genotypes were crossed to susceptible tetraploid potatoes. An investigation was made to assess whether resistant diploid genotypes transmit resistance to bacterial wilt, which is a quantitatively inherited trait, to tetraploid potatoes via FDR 2n pollen. Tetraploid seedlings from 4x×2x crosses were inoculated with the same isolate CIP-204, and the percentage of surviving seedlings was scored. Some 4x×2x families from resistant diploid genotypes demonstrated a high level of survival rate. The transmission of bacterial wilt resistance was achieved by the use of FDR 2n pollen. It was speculated that a female x male interaction effect on the survival rate of the evaluated progeny may exist. Selecting proper 4x and 2x parents would be important for obtaining a higher frequency of transmission of resistance to bacterial wilt in the progeny.     

The phenotypic characteristics and relational database for Vietnamese native pig populations

Although there are a number of Vietnamese native pig (VnP) populations, some are on the verge of extinction, and therefore adequate management and conservation are necessary. In this study, we conducted a field survey of VnP populations and analyzed interrelationships among their characteristics. We also established a relational database for management of field data on these populations. For data collection, we conducted interviews with farmers and visual inspection of 32 VnP populations in 22 provinces of Vietnam, as well as taking photographs of individual animals. Data on the characteristics of VnP populations were subjected to multiple correspondence analysis (MCA). For establishment of the database, normalization and table partitioning were performed to eliminate redundancy and ensure consistency of the collected data items. Passport data, characteristics data, and image data were collected from a total of 1,918 VnPs and entered as a normalized table. Upon MCA, most of the populations were not separated from each other, but the Mong Cai, O Lam, and Chu Prong populations were separated from the other populations. Thus, we have constructed a relational database from comprehensive information on the characteristics of VnP populations.