Duplication and expression analysis of multicopy miRNA gene family members in Arabidopsis and rice

To understand the expansion ofmulticopy microRNA （miRNA） families in plants, we localized the reported miRNA genes from Arabidopsis and rice to their chromosomes, respectively, and observed that 37% of 117 miRNA genes from Arabidopsis and 35% of 173 miRNA genes from rice were segmental duplications in the genome. In order to characterize whether the expression diversification has occurred among plant multicopy miRNA family members, we designed PCR primers targeting 48 predicted miRNA precursors from 10 families in Arabidopsis and rice. Results from RT-PCR data suggest that the transcribed precursors of members within the same miRNA family were present at different expression levels. In addition, although miRl60 and miR162 sequences were conserved in Arabidopsis and rice, we found that the expression patterns of these genes differed between the two species. These data suggested that expression diversification has occurred in multicopy miRNA families, increasing our understanding of the expression regulation of miRNAs in plants.

Long-term maintenance of stable copy number in the eukaryotic SMC family： origin of a vertebrate meiotic SMC1 and fate of recent segmental duplicates

Members of the Structural Maintenance of Chromosome (SMC) family have long been of interest to molecular and evolutionary biologists for their role in chromosome structural dynamics, particularly sister chro-matid cohesion, condensation, and DNA repair. SMC and related proteins are found in all major groups of living organisms and share a common structure of conserved N and C globular domains separated from the conserved hinge domain by long coiled-coil regions. In eukaryotes there are six paralogous proteins that form three het-erodimeric pairs, whereas in prokaryotes there is only one SMC protein that homodimerizes. From recently com-pleted genome sequences, we have identified SMC genes from 34 eukaryotes that have not been described in previous reports. Our phylogenetic analysis of these and previously identified SMC genes supports an origin for the vertebrate meiotic SMC1 in the most recent common ancestor since the divergence from invertebrate animals. Additionally, we have identified duplicate copies due to segmental duplications for some of the SMC paralogs in plants and yeast, mainly SMC2 and SMC6, and detected evidence that duplicates of other paralogs were lost, suggesting differential evolution for these genes. Our analysis indicates that the SMC paralogs have been stably maintained at very low copy numbers, even after segmental (genome-wide) duplications. It is possible that such low copy numbers might be selected during eukaryotic evolution, although other possibilities are not ruled out.

SU(3) spin-orbit coupled fermions in an optical lattice

We propose a scheme to realize the SU(3)spin-orbit coupled three-component fermions in an one-dimensional optical lattice.The topological properties of the single-particle Hamiltonian are studied by calculating the Berry phase,winding number and edge state.We also investigate the effects of the interaction on the ground-state topology of the system,and characterize the interaction-induced topological phase transitions,using a state-of-the-art density-matrix renormalization-group numerical method.Finally,we show the typical features of the emerging quantum phases,and map out the many-body phase diagram between the interaction and the Zeeman field.Our results establish a way for exploring novel quantum physics induced by the SOC with SU(N)symmetry.

Evolutionary divergence of subgenomes in common carp provides insights into speciation and allopolyploid success

Hybridization and polyploidization have made great contributions to speciation,heterosis,and agricultural production within plants,but there is still limited understanding and utilization in animals.Subgenome structure and expression reorganization and cooperation post hybridization and polyploidization are essential for speciation and allopolyploid success.However,the mechanisms have not yet been comprehensively assessed in animals.Here,we produced a high-fidelity reference genome sequence for common carp,a typical allotetraploid fish species cultured worldwide.This genome enabled in-depth analysis of the evolution of subgenome architecture and expression responses.Most genes were expressed with subgenome biases,with a trend of transition from the expression of subgenome A during the early stages to that of subgenome B during the late stages of embryonic development.While subgenome A evolved more rapidly,subgenome B contributed to a greater level of expression during development and under stressful conditions.Stable dominant patterns for homoeologous gene pairs both during development and under thermal stress suggest a potential fixed heterosis in the allotetraploid genome.Preferentially expressing either copy of a homoeologous gene at higher levels to confer development and response to stress indicates the dominant effect of heterosis.The plasticity of subgenomes and their shifting of dominant expression during early development,and in response to stressful conditions,provide novel insights into the molecular basis of the successful speciation,evolution,and heterosis of the allotetraploid common carp.

A high-strength self-healing nano-silica hydrogel with anisotropic differential conductivity

Soft nano electronic materials based on conductive hydrogels have attracted considerable attention due to their exceptional properties.Particle deposition and poor interface compatibility often diminish the mechanical strength and electron transport capabilities of the conductive hydrogel.Mechanical damage can severely impact the performance of the conductive hydrogel and can even damage electronic devices based on the conductive hydrogel.In the current study,a transparent nano-silica hydrogel is prepared by employing an extremely easy-to-operate method.This approach can preclude the deposition of particles via strong mechanical force.In addition,controlling the concentration of the reaction interface makes the hydrogel grow along the mechanical force in the direction with a special directional hole structure formed.The hydrogel is transparent,showing excellent self-healing properties—it can self-heal within 15 seconds.Remarkably,the hydrogel after self-healing maintains its performance.Moreover,it has excellent mechanical properties and can be stretched in length.Up to 1,200%of the original length,the tensile strength of the gel spline can reach 7 MPa.The viscosity of the hydrogel can reach 1.67×10^(8)(MPs).In addition,a large amount of Na+in this hydrogel endow it a conductivity of 389 ps/cm.The conductivity of this hydrogel is adjustable result from the special pore structure.Lastly,the difference between the horizontal and vertical conductivity of the same sample can reach 3-4 times,thus this hydrogel can be used in the field of nano conductive materials.

Analysis of the Arabidopsis Floral Proteome:Detection of over 2000 Proteins and Evidence for Posttranslational Modifications

The proteome of the Arabidopsis flower has not been extensively studied previously. Here, we report a proteomic analysis of the wild type Arabidopsis flower. Using both two-dimensional electrophoresis/mass spectrometry （2-DGEIMS） and multi-dimensional protein identification technology （MudPIT） approaches, we identified 2 446 proteins. Although a single experiment or analysis uncovered only a subset of the proteins we identified, a combination of multiple experiments and analyses facilitated the detection of a greater number of proteins. When proteins are grouped according to RNA expression levels revealed by microarray experiments, we found that proteins encoded by genes with relatively high levels of expression were detected with greater frequencies. On the other hand, at the level of the individual gene/protein, there was not a good correlation between protein spot intensity and microarray values. We also obtained strong evidence for post-translational modification from 2-DGE and MudPIT data. We detected proteins that are annotated to function in protein synthesis, folding, modification, and degradation, as well as the presence of regulatory proteins such as transcription factors and protein kinases. Finally, sequence and evolutionary analysis of genes for active methyl group metabolisms suggests that these genes are highly conserved. Our results allow the formulation of hypotheses regarding post-translational regulation of proteins in the flower, providing new understanding about Arabidopsis flower development and physiology.

Phylogenomic Insights into Deep Phylogeny of Angiosperms Based on Broad Nuclear Gene Sampling

Angiosperms(flowering plants)are the most diverse and species-rich group of plants.The vast majority(99.95%)of angiosperms form a clade called Mesangiospermae,which is subdivided into five major groups:eudicots,monocots,magnoliids,Chloranthales,and Ceratophyllales.The relationships among these Mesangiospermae groups have been the subject of long debate.In this study,we assembled a phylogenomic dataset of 1594 genes from 151 angiosperm taxa,including representatives of all five lineages,to investigate the phylogeny of major angiosperm lineages under both coalescent-and concatenationbased methods.We dissected the phylogenetic signal and found that more than half of the genes lack phylogenetic information for the backbone of angiosperm phylogeny.We further removed the genes with weak phylogenetic signal and showed that eudicots,Ceratophyllales,and Chloranthales form a clade,with magnoliids and monocots being the next successive sister lineages.Similar frequencies of gene tree conflict are suggestive of incomplete lineage sorting along the backbone of the angiosperm phylogeny.Our analyses suggest that a fully bifurcating species tree may not be the best way to represent the early radiation of angiosperms.Meanwhile,we inferred that the crown-group angiosperms originated approximately between 255.1 and 222.2 million years ago,and Mesangiospermae diversified into the five extant groups in a short time span(27 million years)at the Early to Late Jurassic.

Genome-wide Analysis of Kelch Repeatcontaining F-box Family

The ubiquitin-dependent protein degradation pathway plays diverse roles in eukaryotes. Previous studies indicate that both F-box and Kelch motifs are common in a variety of organisms. F-box proteins are subunits of E3 ubiquitin ligase complexes called SCFs （SKP1, Cullinl, F-box protein, and Rbxl）; they have an N-terminal F-box motif that binds to SKP1 （S-phase kinase associated protein）, and often have C-terminal protein-protein interaction domains, which specify the protein substrates for degradation via the ubiquitin pathway. One of the most frequently found protein interaction domains in F-box proteins is the Kelch repeat domain. Although both the F-box and Kelch repeats are ancient motifs, Kelch repeats-containing F-box proteins （KFB） have only been reported for human and Arabidopsis previously. The recent sequencing of the rice genome and other plant genomes provides an opportunity to examine the possible evolution history of KFB. We carried out extensive BLAST searches to identify putative KFBs in selected organisms, and analyzed their relationships phylogenetically. We also carried out the analysis of both gene duplication and gene expression of the KFBs in rice and Arabidopsis. Our study indicates that the origin of KFBs occurs before the divergence of animals and plants, and plant KFBs underwent rapid gene duplications.

A facile approach towards self-reinforced antibacterial paper(SRAP)

A facile process to prepare self-reinforced antibacterial paper(SRAP)was developed by in situ synthesis of zinc oxide(ZnO)in partially dissolved cellulose.The SRAP was fabricated by impregnating filter paper in zinc chloride(ZnCl_(2))solution and then reacting with sodium hydroxide(NaOH).Filter paper was firstly impregnated with ZnCl_(2) solution of 65 wt%concentration for 5 seconds at 80℃,and then pressed at 3.85 kPa for 5 seconds to remove excess liquid.Subsequently,the paper was soaked in a 0.8 wt%NaOH solution for 1 hour,and then washed with deionized water,and dried finally to yield SRAP.Energy dispersive X-ray spectroscopy(EDS),X-ray photoelectron spectroscopy(XPS)and scanning electron microscope(SEM)were used to characterize the SRAP.The results revealed that the SRAP contained intact cellulose fibers as the skeleton,gelled cellulose as the matrix,and clusters of nano ZnO particles as the filler.The SRAP had a much higher density,tensile and burst strength,compared with the untreated cellulose paper,and the folding strength was enhanced by more than fifteen times.In addition,the SRAP had outstanding antibacterial properties due to the presence of nano ZnO particles.