Gene–gene interactions of fatty acid synthase (FASN) using multifactor-dimensionality reduction method in Korean cattle

We examined the gene–gene interactions of five exonic single nucleotide polymorphisms (SNPs) in the gene encoding fatty acid synthase using 513 Korean cattle and using the model free and the non-parametrical multifactor dimensionality reduction method for the analysis. The five SNPs of g.12870 T>C, g.13126 T>C, g.15532 C>A, g.16907 T>C and g.17924 G>A associated with a variety of fatty acid compositions and marbling score were used in this study. The two-factor interaction between g.13126 T>C and g.15532 C>A had the highest training-balanced among the five-factor models and a testing-balanced accuracy at 70.18 % on C18:1 with a cross-validation consistency of 10 out of 10. Also, the two-factor interaction between g.13126 T>C and g.15532 C>A had the highest testing-balanced accuracy at 68.59 % with a 10 out of 10 cross-validation consistency, than any other models on MUFA. In MS, a single SNP g.15532 C>A had the best accuracy at 58.85 % and the two-factor interaction model g.12870 T>C and g.15532 C>A had the highest testing-balanced accuracy at 64.00 %. The three-factor interaction model g.12870 T>C, g.13126 T>C and g.15532 C>A was recorded as having a high testing-balanced accuracy of 63.24 %, but it was lower than the two-factor interaction model. We used likelihood ratio tests for interaction, and Chi square tests to validate our results, with all tests showing statistical significance. We also compared this with mean scores between the high-risk trait group and low-risk trait group. The genotypes of TTCA, TTAA and TCAA at g.15532 and g.13126 on C18:1, genotypes TTCC, TTCA, TTAA, TCAA CCAA at g.15532 and g.13126 on MUFA and genotypes CCCC, TCCA, CCCA, TTAA, TCAA and CCAA at g.15532 and g.12870 on MS were recommended for the genetic improvement of beef quality.     

Arabidopsis Fused kinase TWO-IN-ONE dominantly inhibits male meiotic cytokinesis

Arabidopsis Fused kinase TWO-IN-ONE (TIO) controls phragmoplast expansion through its interaction with the Kinesin-12 subfamily proteins that anchor the plus ends of interdigitating microtubules in the phragmoplast midzone. Previous analyses of loss-of-function mutants and RNA interference lines revealed that TIO positively controls both somatic and gametophytic cell cytokinesis; however, knowledge of the full spectrum of TIO functions during plant development remains incomplete. To characterize TIO functions further, we expressed TIO and a range of TIO variants under control of the TIO promoter in wild-type Arabidopsis plants. We discovered that TIO-overexpressing transgenic lines produce enlarged pollen grains, arising from incomplete cytokinesis during male meiosis, and show sporophytic abnormalities indicative of polyploidy. These phenotypes arose independently in TIO variants in which either gametophytic function or the ability of TIO to interact with Kinesin-12 subfamily proteins was abolished. Interaction assays in yeast showed TIO to bind to the AtNACK2/TETRASPORE, and plants doubly homozygous for kinesin-12a and kinesin-12b knockout mutations to produce enlarged pollen grains. Our results show TIO to dominantly inhibit male meiotic cytokinesis in a dosage-dependent manner that may involve direct binding to a component of the canonical NACK-PQR cytokinesis signaling pathway.     

A robust,simple, high‐throughput technique for time‐resolved plant volatile analysis in field experiments

Plant volatiles (PVs) mediate interactions between plants and arthropods, microbes and other plants, and are involved in responses to abiotic stress. PV emissions are therefore influenced by many environmental factors, including herbivore damage, microbial invasion, and cues from neighboring plants, and also light regime, temperature, humidity and nutrient availability. Thus, an understanding of the physiological and ecological functions of PVs must be based on measurements reflecting PV emissions under natural conditions. However, PVs are usually sampled in the artificial environments of laboratories or climate chambers. Sampling of PVs in natural environments is difficult, being limited by the need to transport, maintain and provide power to instruments, or use expensive sorbent devices in replicate. Ideally, PVs should be measured in natural settings with high replication, spatio‐temporal resolution and sensitivity, and modest costs. Polydimethylsiloxane (PDMS), a sorbent commonly used for PV sampling, is available as silicone tubing for as little as 0.60 € m^?1 (versus 100–550 € each for standard PDMS sorbent devices). Small pieces of silicone tubing (STs) of various lengths from millimeters to centimeters may be added to any experimental setting and used for headspace sampling, with little manipulation of the organism or headspace. STs have sufficiently fast absorption kinetics and large capacity to sample plant headspaces over a timescale of minutes to hours, and thus can produce biologically meaningful ‘snapshots’ of PV blends. When combined with thermal desorption coupled to GC–MS (a 40‐year‐old widely available technology), use of STs yields reproducible, sensitive, spatio‐temporally resolved quantitative data from headspace samples taken in natural environments.     

An amphipathic polypeptide derived from poly‐γ‐glutamic acid for the stabilization of membrane proteins

Difficulties in the extraction of membrane proteins from cell membrane and their solubilization in native conformations have hindered their structural and biochemical analysis. To overcome these difficulties, an amphipathic polypeptide was synthesized by the conjugation of octyl and glucosyl groups to the carboxyl groups of poly‐γ‐glutamic acid (PGA). This polymer, called amphipathic PGA (APG), self‐assembles as mono‐disperse oligomers consisted of 4–5 monomers. APG shows significantly low value of critical micelle concentration and stabilization activity toward membrane proteins. Most of the sodium dodecyl sulfate (SDS)‐solubilized membrane proteins from Escherichia coli remain soluble state in the presence of APG even after the removal of SDS. In addition, APG stabilizes purified 7 transmembrane proteins such as bacteriorhodopsin and human endothelin receptor Type A (ET_A) in their active conformations. Furthermore, ET_A in complex with APG is readily inserted into liposomes without disrupting the integrity of liposomes. These properties of APG can be applied to overcome the difficulties in the stabilization and reconstitution of membrane proteins.     

The genomic architecture of the PROS1 gene underlying large tandem duplication mutation that causes thrombophilia from hereditary protein S deficiency

Hereditary protein S deficiency from a mutation in the PROS1 gene causes a genetic predisposition to develop venous thromboembolic disorders in humans. Recently, the acknowledgment of the clinical significance of large copy number mutations in protein S deficiency has increased. In this study, the authors investigated the genomic architecture of PROS1 in order to understand the microscopic sequence environment leading to large intragenic copy number mutations in the gene. The study subjects were 3 unrelated male patients with hereditary protein S deficiency from a tandem duplication mutation involving exons 5–10 of PROS1. Breakpoint analyses revealed 10-bp microhomology sequences in the intervening sequence (IVS)-4 and IVS-10 at the duplication junction without additional sequence changes, suggesting a single replication-based event as the potential molecular mechanism of rearrangement and founder effect in the mutant alleles. Further analyses on nucleotide sequences flanking the microhomology sequence revealed the presence of a repeat element (LTR-ERV1) and quadruplex-forming G-rich sequences in IVS-4. The results from genotyping multi-allelic short tandem repeats supported founder effect in the identical mutations in the 3 unrelated patients. In conclusion, we identified unique genomic architectures in the intervening sequences of PROS1 that underlie a large intragenic tandem duplication mutation leading to inherited thrombophilia.     

Metabolomics investigation of flavonoid synthesis in soybean leaves depending on the growth stage

Soybean (Glycine max L.) leaves have unique nutraceutical and pharmacological benefits, and have been widely used as a source of healthy and functional food stuffs in Korea. In this study, we investigated the phytochemical metabolomic changes of soybean leaves depending on growth stages (maturation period) assessed based on UPLC–QTOF–MS analysis. Principal component analysis was carried out to trace the metabolite profiles of the phytochemicals from the vegetable stage (1D) through the seven reproductive stages (R1–R7). On the loading plot, significant changes in the contents of metabolites were found during the growth, and eight flavonoid kaempferol glycosides (2, 3, 6, 8, and 10), daidzein (14), genistein (17), and coumestrol (19) were evaluated as growth markers among the 19 isolated metabolites. The kaempferol glycosides were increasingly synthesized from the 1D to the R6 stage but decreased rapidly at stages R7–R8. The extensively synthesized daidzein and genistein were shown during seed growth in the pod (R5–R6), while coumestrol was increased significantly at stages R7–R8 (maturity period). The synthetic pathway of the flavonoids could be elucidated based on the concentration of the individual metabolites. These results demonstrate that the metabolite production changed depending on the growth stage; a possible pathway could be deduced using metabolomic analysis to provide information regarding physiological characterization and optimal harvesting time for crops.     

A New High Power LiNi0.81Co0.1Al0.09O2 Cathode Material for Lithium‐Ion Batteries

Among the various Ni‐based layered oxide systems in the form of LiNi_1‐y‐zCo_yAl_zO₂ (NCA), the compostions between y = 0.1–0.15, z = 0.05 are the most successful and commercialized cathodes used in electric vehicles (EVs) and hybrid electric vehicles (HEVs). However, tremendous research effort has been dedicted to searching for better composition in NCA systems to overcome the limitations of these cathodes, particularly those that arise when they are used use at high discharge/charge rates (>5C) and in high temperature (60 °C) environments. In addition, improving the thermal stability at 4.5 V is also very important in terms of the total amount of heat generated and the onset temperature. Here, a new NCA composition in the form of LiNi_0.81Co_0.1Al_0.09O₂ (y = 0.1, z = 0.09) is reported for the first time. Compared to the LiNi_0.85Co_0.1Al_0.05O₂ cathode, LiNi_0.81Co_0.1Al_0.09O₂ exhibits an excellent rate capability of 155 mAh g^?1 at 10 C with a cut‐off voltage range between 3 and 4.5 V, corresponding to 562 Wh kg^?1 at 24 °C. It additionally provides significantly improved thermal stability and electrochemical performance at the high temperature of 60 °C, with a discharge capacity of 122 mAh g^?1 after 200 cycles with capacity retention of 59%.