Data from: Positive selection drives adaptive diversification of the 4-coumarate: CoA ligase (4CL) gene in angiosperms

Lignin and flavonoids play a vital role in the adaption of plants to a terrestrial environment. 4-Coumarate: coenzyme A ligase (4CL) is a key enzyme of general phenylpropanoid metabolism which provides the precursors for both lignin and flavonoids biosynthesis. However, very little is known about how such essential enzymatic functions evolve and diversify. Here, we analyze 4CL sequence variation patterns in a phylogenetic framework to further identify the evolutionary forces that lead to functional divergence. The results reveal that lignin-biosynthetic 4CLs are under positive selection. The majority of the positively selected sites are located in the substrate-binding pocket and the catalytic center, indicating that nonsynonymous substitutions might contribute to the functional evolution of 4CLs for lignin biosynthesis. The evolution of 4CLs involved in flavonoid biosynthesis is constrained by purifying selection and maintains the ancestral role of the protein in response to biotic and abiotic factors. Overall, our results demonstrate that protein sequence evolution via positive selection is an important evolutionary force driving adaptive diversification in 4CL proteins in angiosperms. This diversification is associated with adaption to a terrestrial environment

Variations of Runoff and Sediment Load in the Middle and Lower Reaches of the Yangtze River, China (1950-2013)

<div><p>On the basis of monthly runoff series obtained in 1950–2013 and annual sediment load measured in 1956–-2013 at five key hydrological stations in the middle and lower reaches of the Yangtze River basin, this study used the Mann-Kendall methods to identify trend and abrupt changes of runoff and sediment load in relation to human activities. The results were as follows: (1) The annual and flood season runoffs showed significant decreasing trends at Yichang station, and showed slight downward trends at Hankou and Datong stations, while the abrupt changes of dry season runoff at Yichang, Hankou and Datong stations occurred in about 2007 and the change points were followed by significant increasing trends. The construction of the Three Gorges Dam, which began to operate in 2003, influenced the variations of runoff in the mainstream of Yangtze River, but the effect weakened with the distance along the downstream direction from TGD. (2) Since the 1990s, annual sediment loads at Yichang, Hankou, and Datong stations have been decreasing significantly, and after 2002, the annual sediment load at Yichang dropped below that of Hankou and Datong. The dams and deforestation/forestation contributed to the significant decreasing trend of the sediment load. In addition, the Three Gorges Dam aggravated the downward trend and caused the erosion of the riverbed and riverbanks in the middle and lower reaches. (3) The runoff and sediment load flowing from Dongting Lake into the mainstream of the Yangtze River showed significant decreasing trends at Chenglingji station after 1970s, and in contrast, slight increase in the sediment flow from Poyang Lake to the mainstream of the Yangtze River at Hukou station were detected over the post-TGD period (2003–2013). The result of the study will be an important foundation for watershed sustainable development of the Yangtze River under the human activities.</p></div

Sugar-rich sweet sorghum is distinctively affected by wall polymer features for biomass digestibility and ethanol fermentation in bagasse

Sweet sorghum has been regarded as a typical species for rich soluble-sugar and high lignocellulose residues, but their effects on biomass digestibility remain unclear. In this study, we examined total 63 representative sweet sorghum accessions that displayed a varied sugar level at stalk and diverse cell wall composition at bagasse. Correlative analysis showed that both soluble-sugar and dry-bagasse could not significantly affect lignocellulose saccharification under chemical pretreatments. Comparative analyses of five typical pairs of samples indicated that DP of crystalline cellulose and arabinose substitution degree of non-KOH-extractable hemicelluloses distinctively affected lignocellulose crystallinity for high biomass digestibility. By comparison, lignin could not alter lignocellulose crystallinity, but the KOH-extractable G-monomer predominately determined lignin negative impacts on biomass digestions, and the G-levels released from pretreatments significantly inhibited yeast fermentation. The results also suggested potential genetic approaches for enhancing soluble-sugar level and lignocellulose digestibility and reducing ethanol conversion inhibition in sweet sorghum. (C) 2014 Published by Elsevier Ltd

A display and analysis platform for gut microbiomes of minority people and phenotypic data in China

Abstract The minority people panmicrobial community database (MPPCD website: http://mppmcdb.cloudna.cn/ ) is the first microbe-disease association database of Chinese ethnic minorities. To research the relationships between intestinal microbes and diseases/health in the ethnic minorities, we collected the microbes of the Han people for comparison. Based on the data, such as age, among the different ethnic groups of the different regions of Sichuan Province, MPPCD not only provided the gut microbial composition but also presented the relative abundance value at the phylum, class, order, family and genus levels in different groups. In addition, differential analysis was performed in different microbes in the two different groups, which contributed to exploring the difference in intestinal microbe structures between the two groups. Meanwhile, a series of related factors, including age, sex, body mass index, ethnicity, physical condition, and living altitude, were included in the MPPCD, with special focus on living altitude. To date, this is the first intestinal microbe database to introduce altitude features. In conclusion, we hope that MPPCD will serve as a fundamental research support for the relationship between human gut microbes and host health and disease, especially in ethnic minorities

Poly(lactide-<i>co</i>-glycolide)/Fibrin Gel Construct as a 3D Model to Evaluate Gene Therapy of Cartilage in Vivo

Combination of gene therapy with tissue engineering can enhance the interplay between cells and matrix, leading to better restoration and regeneration of tissues and organs in vivo. In this study the PLGA/fibrin gel hybrids were employed to load lipofectamine/pDNA-TGF-β1 complexes and mesenchymal stem cells (MSCs) (experimental group), acting as a cartilage-mimetic tissue platform. The gene complexes distributed more evenly in the hybrid scaffolds, whereas they adhered onto the pore walls of the PLGA sponges. The filled fibrin gel rendered gene release in a slower manner, too. Moreover, the fibrin gel entrapped MSCs and contributed to a higher cell loading density in the hybrid constructs. In vivo assay showed that in the defects implanted with the experimental constructs both gene and protein expression levels of TGF-β1 were significantly higher than those of the fibrin-free group at weeks 1, 3, and 6 after surgery. The full articular cartilage defects repaired by the experimental group for 12 w were resurfaced by neo-tissues with a similar thickness, cell arrangement, and color to the normal neighboring cartilage and abundant glycosaminoglycans