ABSTRACT
A indentation-based device to measure tissue mechanical property was designed and built using over-the-counter and 3D-printed parts. The device costs less than 100 USD and is capable of measuring samples of various geometry because of its modular design. The device is light-weight, thus portable, for measurements that can be performed at different sites. It was demonstrated that the measurement results obtained using our device are comparable to previous observations. The elastic shear modulus of the human skin was in the range of 2 kPa to 8 kPa, and skin tissues in old mice were stiffer than young mice. Mechanical properties of the skin tissues belonging to the same test subject varied depending on the location of the measurement. In conclusion, because our device is economic, modular, portable, and robust, it is suitable to serve as a standard measurement platform for studying tissue mechanics.
Subject(s)
Elastic Modulus , Elasticity , Mechanical Phenomena , Skin Physiological Phenomena , Viscosity , Animals , Equipment Design , Female , Humans , Longitudinal Studies , Male , Mice , Models, Theoretical , Stress, MechanicalABSTRACT
KEY MESSAGE: The evolutionary origin of the phytochrome genes in soybean was analyzed. The expression profiles of PHYA paralogs were characterized. The heterologous expression of GmPHYA1 in Arabidopsis resulted in longer hypocotyls. The phytochromes (PHY) are a small family of red/far-red light photoreceptors which regulate a number of important developmental responses in plants. So far, the members of the PHY gene family in soybean (Glycine max) remain unclear and an understanding of each member's physiological functions is limited. Our present in silico analysis revealed that the soybean genome harbors four PHYA, two PHYB and two PHYE, totally four pairs of eight PHY loci. The phylogenetic analysis suggested that the four PHY paralogous pairs originated from the latest round of genome duplication (~13 million years ago) and the four copies of PHYA were remnants of the two rounds of genome duplication (~58 and ~13 million years ago). A possible evolutionary history of PHYA homologs in the three legume species (soybean, Medicago truncatula, and Lotus japonicus) was proposed and the fate of duplicate soybean PHYA genes following polyploidization was discussed. The expression profiles of a soybean PHYA paralogous pair (GmPHYA1 and GmPHYA2) showed that the transcript abundance was highest in the aerial organs of young plants. The physiological role of GmPHYA1 was explored by observing the de-etiolation phenotype of transgenic Arabidopsis plants constitutively expressing GmPHYA1. The GmPHYA1 protein interfered with the function of endogenous PHYA with respect to de-etiolation in a dominant negative manner when exogenously expressed in Arabidopsis. The elucidation of the PHY gene family members in soybean provide us with a general description and understanding of the photoreceptor gene family in this important crop plant.
Subject(s)
Arabidopsis/genetics , Genes, Dominant/genetics , Genes, Plant/genetics , Glycine max/genetics , Multigene Family , Phytochrome A/genetics , Transgenes/genetics , Arabidopsis/radiation effects , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Chromosomes, Plant/genetics , Cotyledon/genetics , Cotyledon/growth & development , Cotyledon/radiation effects , Gene Expression Profiling , Gene Expression Regulation, Plant/radiation effects , Hypocotyl/genetics , Hypocotyl/growth & development , Hypocotyl/radiation effects , Light , Phylogeny , Phytochrome A/metabolism , Plants, Genetically Modified , RNA, Messenger/genetics , RNA, Messenger/metabolism , Sequence Homology, Nucleic Acid , Glycine max/radiation effectsABSTRACT
The MADS family is an ancient and best-studied transcription factor and plays fundamental roles in almost every developmental process in plants. In the plant evolutionary history, the whole genome duplication (WGD) events are important not only to the plant species evolution, but to expansion of members of the gene families. Soybean as a model legume crop has experience three rounds of WGD events. Members of some MIKC(C) subfamilies, such as SOC, AGL6, SQUA, SVP, AGL17 and DEF/GLO, were expanded after soybean three rounds of WGD events. And some MIKC(C) subfamilies, MIKC* and type I MADS families had experienced faster birth-and-death evolution and their traces before the Glycine WGD event were not found. Transposed duplication played important roles in tandem arrangements among the members of different subfamilies. According to the expression profiles of type I and MIKC paralog pair genes, the fates of MIKC paralog gene pairs were subfunctionalization, and the fates of type I MADS paralog gene pairs were nonfunctionalization. 137 out of 163 MADS genes were close to 186 loci within 2 Mb genomic regions associated with seed-relative QTLs, among which 115 genes expressed during the seed development. Although MIKC(C) genes kept the important and conserved functions of the flower development, most MIKC(C) genes showed potentially essential roles in the seed development as well as the type I MADS.
Subject(s)
Glycine max/growth & development , Glycine max/genetics , MADS Domain Proteins/genetics , Plant Proteins/genetics , Seeds/growth & development , Seeds/genetics , Gene Expression Regulation, Plant , Genome, Plant , Quantitative Trait LociABSTRACT
Most of traditional reference genes chosen for real-time quantitative PCR normalization were assumed to be ubiquitously and constitutively expressed in vegetative tissues. However, seeds show distinct transcriptomes compared with the vegetative tissues. Therefore, there is a need for re-validation of reference genes in samples of seed development and germination, especially for soybean seeds. In this study, we aimed at identifying reference genes suitable for the quantification of gene expression level in soybean seeds. In order to identify the best reference genes for soybean seeds, 18 putative reference genes were tested with various methods in different seed samples. We combined the outputs of both geNorm and NormFinder to assess the expression stability of these genes. The reference genes identified as optimums for seed development were TUA5 and UKN2, whereas for seed germination they were novel reference genes Glyma05g37470 and Glyma08g28550. Furthermore, for total seed samples it was necessary to combine four genes of Glyma05g37470, Glyma08g28550, Glyma18g04130 and UKN2 [corrected] for normalization. Key message We identified several reference genes that stably expressed in soybean seed developmental and germinating processes.
Subject(s)
Gene Expression Regulation, Plant , Genes, Plant , Germination , Glycine max/genetics , Real-Time Polymerase Chain Reaction/standards , Seeds/growth & development , DNA, Complementary/genetics , Genomic Instability , Oligonucleotide Array Sequence Analysis/methods , RNA, Plant/genetics , Real-Time Polymerase Chain Reaction/methods , Reference Standards , Reverse Transcriptase Polymerase Chain Reaction/methods , Seeds/genetics , Glycine max/growth & development , Time Factors , TranscriptomeABSTRACT
The 4554 ORFs of Agrobacterium tumefaciens C58 Cereon were used for the prediction of signal peptides by the network tools, such as SignalP3.0, LipoP1.0, TMHMM2.0 and TargetP1.01. Total 203 signal peptides with conserved amino residues are found, among them, 158 are secretary types, 9 are RR-motif types, 28 are SignalPase II types and 8 are bacteriocin-pheromone types. However, only two signal peptides from the secreted proteins, AGR-C-1878p and AGR-C-1880p have the same amino sequences, showing the signal peptides of the strain are highly variable.
