Phylogeny and evolutionary history of glycogen synthase kinase 3/SHAGGY-like kinase genes in land plants

Background: GSK3 (glycogen synthase kinase 3) genes encode signal transduction proteins with roles in a variety of biological processes in eukaryotes. In contrast to the low copy numbers observed in animals, GSK3 genes have expanded into a multi-gene family in land plants (embryophytes), and have also evolved functions in diverse plant specific processes, including floral development in angiosperms. However, despite previous efforts, the phylogeny of land plant GSK3 genes is currently unclear. Here, we analyze genes from a representative sample of phylogenetically pivotal taxa, including basal angiosperms, gymnosperms, and monilophytes, to reconstruct the evolutionary history and functional diversification of the GSK3 gene family in land plants. Results: Maximum Likelihood phylogenetic analyses resolve a gene tree with four major gene duplication events that coincide with the emergence of novel land plant clades. The single GSK3 gene inherited from the ancestor of land plants was first duplicated along the ancestral branch to extant vascular plants, and three subsequent duplications produced three GSK3 loci in the ancestor of euphyllophytes, four in the ancestor of seed plants, and at least five in the ancestor of angiosperms. A single gene in the Amborella trichopoda genome may be the sole survivor of a sixth GSK3 locus that originated in the ancestor of extant angiosperms. Homologs of two Arabidopsis GSK3 genes with genetically confirmed roles in floral development, AtSK11 and AtSK12, exhibit floral preferential expression in several basal angiosperms, suggesting evolutionary conservation of their floral functions. Members of other gene lineages appear to have independently evolved roles in plant reproductive tissues in individual taxa. Conclusions: Our phylogenetic analyses provide the most detailed reconstruction of GSK3 gene evolution in land plants to date and offer new insights into the origins, relationships, and functions of family members. Notably, the diversity of this “green” branch of the gene family has increased in concert with the increasing morphological and physiological complexity of land plant life forms. Expression data for seed plants indicate that the functions of GSK3 genes have also diversified during evolutionary time

Empirical Comparisons of Different Statistical Models To Identify and Validate Kernel Row Number-Associated Variants from Structured Multi-parent Mapping Populations of Maize

Advances in next generation sequencing technologies and statistical approaches enable genomewide dissection of phenotypic traits via genome-wide association studies (GWAS). Although multiple statistical approaches for conducting GWAS are available, the power and cross-validation rates of many approaches have been mostly tested using simulated data. Empirical comparisons of single variant (SV) and multi-variant (MV) GWAS approaches have not been conducted to test if a single approach or a combination of SV and MV is effective, through identification and cross-validation of trait-associated loci. In this study, kernel row number (KRN) data were collected from a set of 6,230 entries derived from the Nested Association Mapping (NAM) population and related populations. Three different types of GWAS analyses were performed: 1) single-variant (SV), 2) stepwise regression (STR) and 3) a Bayesian-based multi-variant (BMV) model. Using SV, STR, and BMV models, 257, 300, and 442 KRN-associated variants (KAVs) were identified in the initial GWAS analyses. Of these, 231 KAVs were subjected to genetic validation using three unrelated populations that were not included in the initial GWAS. Genetic validation results suggest that the three GWAS approaches are complementary. Interestingly, KAVs in low recombination regions were more likely to exhibit associations in independent populations than KAVs in recombinationally active regions, probably as a consequence of linkage disequilibrium. The KAVs identified in this study have the potential to enhance our understanding of the genetic basis of ear development

Hubungan Kandidiasis Intertriginosa dan Diabetes Melitus Tipe 2 di Poliklinik Kulit dan Kelamin RSUD Dokter Soedarso Pontianak pada Tahun 2012

Background. Intertriginous candidiasis is a type of cutaneous candidiasiswhich is located at the axila, inguinal, intergluteal, inframammary,interdigitalis, glands penis, and umbilicus. One of the risk factors ofintertriginous candidiasis patient is people with diabetes mellitus (DM).The increase of glucose concentration makes more susceptible frominfection. Objective. Define the association between intertriginouscandidiasis and DM type 2. Method. This research was a case controlstudy which took place in Dermatovenereology Outpatient Clinic RSUD dr.Soedarso from June until November 2013. The minimum sample for thisresearch was 126 people and divided into two groups. The case groupconsisted of 63 people and the control group consisted of 63 people. Thesubjects were selected by using consecutive sampling and analyzed bychi-square test. Result. There was an association between intertriginouscandidiasis with DM type 2 (p= 0,01). Odds Ratio (OR) value of thisresearch was 2,621 (IK 95% : 1,246 5,516). Conclusion. Intertriginouscandidiasis is associated with DM type 2 and people with DM type 2 havea possibility of 2,621 times higher risk of acquiring intertriginouscandidiasis than people without diabetes mellitus

A Targeted Enrichment Strategy for Massively Parallel Sequencing of Angiosperm Plastid Genomes

Premise of the study: We explored a targeted enrichment strategy to facilitate rapid and low-cost next-generation sequencing (NGS) of numerous complete plastid genomes from across the phylogenetic breadth of angiosperms

Influence of Weak Interlayer on the Mechanical Performance of the Bolted Rock Mass with a Single Free Surface in Deep Mining

The existence of the weak interlayer in the roadway surrounding rock mass presents a huge threat to the stability of the underground structure and the safety of mining engineering. By the characteristics of strong adaptability, superior anchoring effect and high efficiency of construction, rock bolt has been widely applied in mine reinforcement. However, the influence of the weak interlayer on the compressive performance of the bolted rock mass is still poorly understood due to the challenges in constructing an efficient experimental platform and complex testing processes. Here, we used the self-developed test system to investigate the influence of the thickness, uniaxial compressive strength, and dip angle of the weak interlayer on the compressive behavior of the bolted rock mass with a single free surface. The results show that the weak interlayer has a great weakening effect on the peak strength and elastic modulus of the specimens due to its low mechanical properties, as well as influencing the crack distribution and failure mode of the samples. As the strength of the weak interlayer is lower than 1.27 MPa, the thickness exceeds 20 mm, and the dip angle exceeds 15°, the synergistic bearing effect will be significantly reduced and affect the mechanical performance of the specimens. The evolution of the bolt force and bending moment are greatly impacted by the deformation process which could be divided into distinct stages of destruction, thereby providing an excellent detection method for judging the stability of the surrounding rock of the mine. The discovery of this research promote a better understanding of the impact of the weak interlayer on mining engineering and guide the mine reinforcement in the future

Empirical Comparisons of Different Statistical Models To Identify and Validate Kernel Row Number-Associated Variants from Structured Multi-parent Mapping Populations of Maize

Advances in next generation sequencing technologies and statistical approaches enable genomewide dissection of phenotypic traits via genome-wide association studies (GWAS). Although multiple statistical approaches for conducting GWAS are available, the power and cross-validation rates of many approaches have been mostly tested using simulated data. Empirical comparisons of single variant (SV) and multi-variant (MV) GWAS approaches have not been conducted to test if a single approach or a combination of SV and MV is effective, through identification and cross-validation of trait-associated loci. In this study, kernel row number (KRN) data were collected from a set of 6,230 entries derived from the Nested Association Mapping (NAM) population and related populations. Three different types of GWAS analyses were performed: 1) single-variant (SV), 2) stepwise regression (STR) and 3) a Bayesian-based multi-variant (BMV) model. Using SV, STR, and BMV models, 257, 300, and 442 KRN-associated variants (KAVs) were identified in the initial GWAS analyses. Of these, 231 KAVs were subjected to genetic validation using three unrelated populations that were not included in the initial GWAS. Genetic validation results suggest that the three GWAS approaches are complementary. Interestingly, KAVs in low recombination regions were more likely to exhibit associations in independent populations than KAVs in recombinationally active regions, probably as a consequence of linkage disequilibrium. The KAVs identified in this study have the potential to enhance our understanding of the genetic basis of ear development

Land Plant GSK3 matrix

MAFFT translation alignment of 445 plant genes encoding homologs of GSK3