Construction and Analysis of the Model of Energy Metabolism in E. coli

Genome-scale models of metabolism have only been analyzed with the constraint-based modelling philosophy and there have been several genome-scale gene-protein-reaction models. But research on the modelling for energy metabolism of organisms just began in recent years and research on metabolic weighted complex network are rare in literature. We have made three research based on the complete model of E. coli’s energy metabolism. We first constructed a metabolic weighted network using the rates of free energy consumption within metabolic reactions as the weights. We then analyzed some structural characters of the metabolic weighted network that we constructed. We found that the distribution of the weight values was uneven, that most of the weight values were zero while reactions with abstract large weight values were rare and that the relationship between w (weight values) and v (flux values) was not of linear correlation. At last, we have done some research on the equilibrium of free energy for the energy metabolism system of E. coli. We found that (free energy rate input from the environment) can meet the demand of (free energy rate dissipated by chemical process) and that chemical process plays a great role in the dissipation of free energy in cells. By these research and to a certain extend, we can understand more about the energy metabolism of E. coli.     

Development and application of photoautotrophic micropropagation plant system

Research has revealed that most chlorophyllous explants/plants in vitro have the ability to grow photoautotrophically (without sugar in the culture medium), and that the low or negative net photosynthetic rate of plants in vitro is not due to poor photosynthetic ability, but to the low CO₂ concentration in the air-tight culture vessel during the photoperiod. Moreover, numerous studies have been conducted on improving the in vitro environment and investigating its effects on growth and development of cultures/plantlets on nearly 50 species since the concept of photoautotrophic micropropagation was developed more than two decades ago. These studies indicate that the photoautotrophic growth in vitro of many plant species can be significantly promoted by increasing the CO₂ concentration and light intensity in the vessel, by decreasing the relative humidity in the vessel, and by using a fibrous or porous supporting material with high air porosity instead of gelling agents such as agar. This paper reviews the development and characteristics of photoautotrophic micropropagation systems and the effects of environmental conditions on the growth and development of the plantlets. The commercial applications and the perspective of photoautotrophic micropropagation systems are discussed.     

Designing Commensurate and Incommensurate Resonances for Enhanced Dipole Emission in Coupled Plasmonic Nanorods

Plasmonic nanorods and their clusters are the fundamental units in plasmonic nanoantenna engineering. A theory that can predict the resonance of single nanorod already exists but is in lack for a heterodimer. Here, we propose a model combining the effective circuit theory for the response of spherical nanoparticles together with standard transmission line theory for hemispherically capped nanorod antennas. The resonances of multiple orders are predictable by defining the reflection phase at the terminals of such antennas, in both symmetric and asymmetric coupled nanorods. The theoretical results compare favorably with full-wave finite element numerical calculations. By the analytical formula, it is easy to control the length of the antennas for regulating the cooperative resonant properties and consequently the radiation characteristics of a nearby electric dipole. Consequently, we obtain both commensurate and incommensurate resonance features in such nanorod-based heterodimer antennas, showing respectively cumulative and selective responses from the individual nanorods.     

Engineering the Saccharomyces cerevisiae β-Oxidation Pathway to Increase Medium Chain Fatty Acid Production as Potential Biofuel

Fatty acid-derived biofuels and biochemicals can be produced in microbes using β-oxidation pathway engineering. In this study, the β-oxidation pathway of Saccharomyces cerevisiae was engineered to accumulate a higher ratio of medium chain fatty acids (MCFAs) when cells were grown on fatty acid-rich feedstock. For this purpose, the haploid deletion strain Δpox1 was obtained, in which the sole acyl-CoA oxidase encoded by POX1 was deleted. Next, the POX2 gene from Yarrowia lipolytica, which encodes an acyl-CoA oxidase with a preference for long chain acyl-CoAs, was expressed in the Δpox1 strain. The resulting Δpox1 [pox2+] strain exhibited a growth defect because the β-oxidation pathway was blocked in peroxisomes. To unblock the β-oxidation pathway, the gene CROT, which encodes carnitine O-octanoyltransferase, was expressed in the Δpox1 [pox2+] strain to transport the accumulated medium chain acyl-coAs out of the peroxisomes. The obtained Δpox1 [pox2+, crot+] strain grew at a normal rate. The effect of these genetic modifications on fatty acid accumulation and profile was investigated when the strains were grown on oleic acids-containing medium. It was determined that the engineered strains Δpox1 [pox2+] and Δpox1 [pox2+, crot+] had increased fatty acid accumulation and an increased ratio of MCFAs. Compared to the wild-type (WT) strain, the total fatty acid production of the strains Δpox1 [pox2+] and Δpox1 [pox2+, crot+] were increased 29.5% and 15.6%, respectively. The intracellular level of MCFAs in Δpox1 [pox2+] and Δpox1 [pox2+, crot+] increased 2.26- and 1.87-fold compared to the WT strain, respectively. In addition, MCFAs in the culture medium increased 3.29-fold and 3.34-fold compared to the WT strain. These results suggested that fatty acids with an increased MCFAs ratio accumulate in the engineered strains with a modified β-oxidation pathway. Our approach exhibits great potential for transforming low value fatty acid-rich feedstock into high value fatty acid-derived products.     

Discovery of Iliestheria (Crustacea: spinicaudatan) from the Lower Jurassic Sangonghe Formation in Junggar Basin,northwestern China

Iliestheria Li and Shen, 1995, was erected based on specimens of two co-occurring species from the Lower Jurassic Badaowan Formation in Nilka, Xinjiang Uygur Autonomous Region, northwestern China. Since then Iliestheria has not been reported in any other locality, partly because clam shrimp from the Lower Jurassic in western China have been reported with studies only based on the outline of the carapace, most of them as Euestheria or Palaeolimnadia components. Here we report a new species of Iliestheria from the Pliensbachian–Toarcian Sangonghe Formation, based on scanning electron microscopic characteristics of the carapace morphology. We also revise the diagnosis of the genus based on re-examination using SEM microscopy of the two species from the Badaowan Formation, to include spinicaudatans characterized by growth bands ornamented by radial lirae intercalated with 2–4 columns of puncta; radial lirae sporadically curved and branched to form fine reticulation on the growth bands in the anterior and upper parts of the carapace. This study indicates that the stratigraphic range of Iliestheria extends to late Early Jurassic.     

FHA2 is a plant-specific ISWI subunit responsible for stamen development and plant fertility

Imitation Switch (ISWI) chromatin remodelers are known to function in diverse multi‐subunit complexes in yeast and animals. However, the constitution and function of ISWI complexes in Arabidopsis thaliana remain unclear. In this study, we identified forkhead‐associated domain 2 (FHA2) as a plant‐specific subunit of an ISWI chromatin‐remodeling complex in Arabidopsis. By in vivo and in vitro analyses, we demonstrated that FHA2 directly binds to RLT1 and RLT2, two redundant subunits of the ISWI complex in Arabidopsis. The stamen filament is shorter in the fha2 and rlt1/2 mutants than in the wild type, whereas their pistil lengths are comparable. The shorter filament, which is due to reduced cell size, results in insufficient pollination and reduced fertility. The rlt1/2 mutant shows an early‐flowering phenotype, whereas the phenotype is not shared by the fha2 mutant. Consistent with the functional specificity of FHA2, our RNA‐seq analysis indicated that the fha2 mutant affects a subset of RLT1/2‐regulated genes that does not include genes involved in the regulation of flowering time. This study demonstrates that FHA2 functions as a previously uncharacterized subunit of the Arabidopsis ISWI complex and is exclusively involved in regulating stamen development and plant fertility.     

Cryptochrome‐mediated hypocotyl phototropism was regulated antagonistically by gibberellic acid and sucrose in Arabidopsis

Both phototropins(phot1 and phot2) and cryptochromes(cry1 and cry2) were proven as the Arabidopsis thaliana blue light receptors. Phototropins predominately function in photomovement, and cryptochromes play a role in photomorphogenesis. Although cryptochromes have been proposed to serve as positive modulators of phototropic responses, the underlying mechanism remains unknown. Here, we report that depleting sucrose from the medium or adding gibberellic acids(GAs) can partially restore the defects in phototropic curvature of the phot1 phot2 double mutants under high-intensity blue light; this restoration does not occur in phot1 phot2 cry1 cry2 quadruple mutants and nph3(nonphototropic hypocotyl 3) mutants which were impaired phototropic response in sucrose-containing medium. These results indicate that GAs and sucrose antagonistically regulate hypocotyl phototropism in a cryptochromes dependent manner, but it showed a crosstalk with phototropin signaling on NPH3.Furthermore, cryptochromes activation by blue light inhibit GAs synthesis, thus stabilizing DELLAs to block hypocotyl growth, which result in the higher GAs content in the shade side than the lit side of hypocotyl to support the asymmetric growth of hypocotyl. Through modulation of the abundance of DELLAs by sucrose depletion or added GAs, it revealed that cryptochromes have a function in mediating phototropic curvature.     

Experiencing winter for spring flowering: A molecular epigenetic perspective on vernalization

Many over-wintering plants, through vernalization, overcome a block to flowering and thus acquire competence to flower in the following spring after experiencing prolonged cold exposure or winter cold. The vernalization pathways in different angiosperm lineages appear to have convergently evolved to adapt to temperate climates. Molecular and epigenetic mechanisms for vernalization regulation have been well studied in the crucifer model plant Arabidopsis thaliana.Here, we review recent progresses on the vernalization pathway in Arabidopsis. In addition, we summarize current molecular and genetic understandings of vernalization regulation in temperate grasses including wheat and Brachypodium, two monocots from Pooideae, followed by a brief discussion on divergence of the vernalization pathways between Brassicaceae and Pooideae.