Dissecting the Human Response to Staphylococcus aureus Systemic Infections

Staphylococcus aureus is a common human commensal and the leading cause of diverse infections. To identify distinctive parameters associated with infection and colonization, we compared the immune and inflammatory responses of patients with a diagnosis of invasive S. aureus disease to healthy donors. We analyzed the inflammatory responses founding a pattern of distinctive cytokines significantly higher in the patients with invasive disease. The measure of antibody levels revealed a wide antibody responsiveness from all subjects to most of the antigens, with significantly higher response for some antigens in the invasive patients compared to control. Moreover, functional antibodies against toxins distinctively associated with the invasive disease. Finally, we examined the genomic variability of isolates, showing no major differences in genetic distribution compared to a panel of representative strains. Overall, our study shows specific signatures of cytokines and functional antibodies in patients with different primary invasive diseases caused by S. aureus. These data provide insight into human responses towards invasive staphylococcal infections and are important for guiding the identification of novel preventive and therapeutic interventions against S. aureus.

Prevalence of protective haplotypes of the SLCO1B1 gene for statin transport in Mexican populations

Aim: To evaluate the genetic distribution of the rs4149056 and rs2306283 variants in the SLCO1B1 gene in Mexican Mestizo (admixed) and Native American groups. Materials & methods: We recruited 360 volunteers who were qPCR-genotyped with TaqMan probes. Results: Allele and genotype frequencies are reported. Among the expected rs4149056– rs2306283 haplotypes, T–A (42.35–58.47%) was the most prevalent which relates to the normal activity of the OATP1B1 transporter. This was followed by the T–G haplotype associated with further statin transport and cholesterol reduction (32.49–43.76%). Conclusion: Based on these SLCO1B1 gene variants, we confirmed that a minimum fraction of the Mexican study populations would be at risk from decreasing simvastatin transport and the development of statin-induced myopathy.

Genomic mating in outbred species: predicting cross usefulness with additive and total genetic covariance matrices

Diverse crops are both outbred and clonally propagated. Breeders typically use truncation selection of parents and invest significant time, land and money evaluating the progeny of crosses to find exceptional genotypes. We developed and tested genomic mate selection criteria suitable for organisms of arbitrary homozygosity level where the full-sibling progeny are of direct interest as future parents and/or cultivars. We extended cross variance and covariance variance prediction to include dominance effects and predicted the multivariate selection index genetic variance of crosses based on haplotypes of proposed parents, marker effects and recombination frequencies. We combined the predicted mean and variance into usefulness criteria for parent and variety development. We present an empirical study of cassava (Manihot esculenta), a staple tropical root crop. We assessed the potential to predict the multivariate genetic distribution (means, variances and trait covariances) of 462 cassava families in terms of additive and total value using cross-validation. Most variance (89%) and covariance (70%) prediction accuracy estimates were greater than zero. The usefulness of crosses were accurately predicted with good correspondence between the predicted and the actual mean performance of family members breeders selected for advancement as new parents and candidate varieties. We also used a directional dominance model to quantify significant inbreeding depression for most traits. We predicted 47,083 possible crosses of 306 parents and contrasted them to those previously tested to show how mate selection can reveal new potential within the germplasm. We enable breeders to consider the potential of crosses to produce future parents (progeny with top breeding values) and varieties (progeny with top own performance).

Functional gene assessment of bread wheat: breeding implications in Ningxia Province

Background The overall genetic distribution and divergence of cloned genes among bread wheat varieties that have occurred during the breeding process over the past few decades in Ningxia Province, China, are poorly understood. Here, we report the genetic diversities of 44 important genes related to grain yield, quality, adaptation and resistance in 121 Ningxia and 86 introduced wheat cultivars and advanced lines. Results The population structure indicated characteristics of genetic components of Ningxia wheat, including landraces of particular genetic resources, introduced varieties with rich genetic diversities and modern cultivars in different periods. Analysis of allele frequencies showed that the dwarfing alleles Rht-B1b at Rht-B1 and Rht-D1b at Rht-D1, 1BL/1RS translocation, Hap-1 at GW2-6B and Hap-H at Sus2-2B are very frequently present in modern Ningxia cultivars and in introduced varieties from other regions but absent in landraces. This indicates that the introduced wheat germplasm with numerous beneficial genes is vital for broadening the genetic diversity of Ningxia wheat varieties. Large population differentiation between modern cultivars and landraces has occurred in adaptation genes. Founder parents carry excellent allele combinations of important genes, with a higher number of favorable alleles than modern cultivars. Gene flow analysis showed that six founder parents have greatly contributed to breeding improvement in Ningxia Province, particularly Zhou 8425B, for yield-related genes. Conclusions Varieties introduced from other regions with rich genetic diversity and landraces with well-adapted genetic resources have been applied to improve modern cultivars. Founder parents, particularly Zhou 8425B, for yield-related genes have contributed greatly to wheat breeding improvement in Ningxia Province. These findings will greatly benefit bread wheat breeding in Ningxia Province as well as other areas with similar ecological environments.

A look-ahead Monte Carlo simulation method for improving parental selection in trait introgression

Multiple trait introgression is the process by which multiple desirable traits are converted from a donor to a recipient cultivar through backcrossing and selfing. The goal of this procedure is to recover all the attributes of the recipient cultivar, with the addition of the specified desirable traits. A crucial step in this process is the selection of parents to form new crosses. In this study, we propose a new selection approach that estimates the genetic distribution of the progeny of backcrosses after multiple generations using information of recombination events. Our objective is to select the most promising individuals for further backcrossing or selfing. To demonstrate the effectiveness of the proposed method, a case study has been conducted using maize data where our method is compared with state-of-the-art approaches. Simulation results suggest that the proposed method, look-ahead Monte Carlo, achieves higher probability of success than existing approaches. Our proposed selection method can assist breeders to efficiently design trait introgression projects.

Functional Gene Assessment of Wheat: Breeding Implication in Ningxia Province

Background: The overall genetic distribution and divergences for cloned genes among wheat varieties that occurred during the breeding process of the past few decades in Ningxia province of China are poorly understood. Here we report the genetic diversities of 44 important genes underpinning grain yield, quality, adaptation and resistance in 121 Ningxia and 86 introduced wheat cultivars and advanced lines.Results: Population structure indicated characteristics of genetic components of Ningxia wheats including landraces of particular genetic resources, introduced varieties with rich genetic diversities and modern cultivars in different times. Analysis of allele frequencies showed that dwarfing alleles Rht-B1b at Rht-B1 and Rht-D1b at Rht-D1 , 1BL/1RS translocation, Hap-1 at GW2-6B and Hap-H at Sus2-2B are present very frequently in Ningxia modern cultivars and introduced varieties from other regions, but absent in landraces, indicating that the introduced wheat germplasm with numerous beneficial genes are vital for broadening genetic diversities of Ningxia wheat varieties. Large population differentiation occurred at adaptation genes between modern cultivars and well-adapted landraces. Founder parents have excellent allele combinations of important genes with a higher number of favorable alleles compared with modern cultivars. The gene flows manifested that six founder parents greatly contributed to breeding improvement in Ningxia province, in particular Zhou 8425B for yield related genes.Conclusions: These results will greatly benefit for wheat breeding in Ningxia province and other areas with similar ecological environments.

A Look-ahead Monte Carlo Simulation Method for Improving Parental Selection in Trait Introgression

ABSTRACTMultiple trait introgression is the process by which multiple desirable traits are converted from a donor to a recipient cultivar through backcrossing and selfing. The goal of this procedure is to recover all the attributes of the recipient cultivar, with the addition of the specified desirable traits. A crucial step in this process is the selection of parents to form new crosses. In this study, we propose a new selection approach that estimates the genetic distribution of the progeny of backcrosses after multiple generations using information of recombination events. To demonstrate the effectiveness of the proposed method, a case study has been conducted using maize data where our method is compared with state-of-the-art approaches. Simulation results suggest that the proposed method, look-ahead Monte Carlo, achieves higher probability of success than existing approaches.

MONITORING ESSENTIAL SOIL NUTRIENT BASE ON INTERNET OF THINGS ON DIPTEROCARPUS LITTORALIS PLANT

Dipterocarpus littoralis known locally as pelahlar, is a producer of endemic commercial wood in Nusakambangan. Pelahlar habitat that is isolated in one island and a narrow genetic distribution causes the risk of extinction of this species is increasing. The effort to conserve rare flora can be done by monitoring and observation the balance of essential nutrients at the site of growth. So we need a system that is able to monitor the balance of essential nutrients and pH in the soil to support the growth of rare flora based on the Internet of Things (IoT). This system consists of a sensor station and a central gate station that is connected based on a star network. scheduling of sending data from the sensor station to the gate station is determined from the results of competition between sensor stations based on the backoff of each sensor station. through this scheme an increase in throughput and collision values is based on the number of sensor stations. From our proposed scheme, it is found that the more sensor stations that compete, the smaller the value of the throughput of the system.