Identification of Genome-Wide Variations among Three Elite Restorer Lines for Hybrid-Rice

Rice restorer lines play an important role in three-line hybrid rice production. Previous research based on molecular tagging has suggested that the restorer lines used widely today have narrow genetic backgrounds. However, patterns of genetic variation at a genome-wide scale in these restorer lines remain largely unknown. The present study performed re-sequencing and genome-wide variation analysis of three important representative restorer lines, namely, IR24, MH63, and SH527, using the Solexa sequencing technology. With the genomic sequence of the Indica cultivar 9311 as the reference, the following genetic features were identified: 267,383 single-nucleotide polymorphisms (SNPs), 52,847 insertion/deletion polymorphisms (InDels), and 3,286 structural variations (SVs) in the genome of IR24; 288,764 SNPs, 59,658 InDels, and 3,226 SVs in MH63; and 259,862 SNPs, 55,500 InDels, and 3,127 SVs in SH527. Variations between samples were also determined by comparative analysis of authentic collections of SNPs, InDels, and SVs, and were functionally annotated. Furthermore, variations in several important genes were also surveyed by alignment analysis in these lines. Our results suggest that genetic variations among these lines, although far lower than those reported in the landrace population, are greater than expected, indicating a complicated genetic basis for the phenotypic diversity of the restorer lines. Identification of genome-wide variation and pattern analysis among the restorer lines will facilitate future genetic studies and the molecular improvement of hybrid rice

Recombinant Diploid Saccharomyces cerevisiae Strain Development for Rapid Glucose and Xylose Co-Fermentation

Cost-effective production of cellulosic ethanol requires robust microorganisms for rapid co-fermentation of glucose and xylose. This study aims to develop a recombinant diploid xylose-fermenting Saccharomyces cerevisiae strain for efficient conversion of lignocellulosic biomass sugars to ethanol. Episomal plasmids harboring codon-optimized Piromyces sp. E2 xylose isomerase (PirXylA) and Orpinomyces sp. ukk1 xylose (OrpXylA) genes were constructed and transformed into S. cerevisiae. The strain harboring plasmids with tandem PirXylA was favorable for xylose utilization when xylose was used as the sole carbon source, while the strain harboring plasmids with tandem OrpXylA was beneficial for glucose and xylose cofermentation. PirXylA and OrpXylA genes were also individually integrated into the genome of yeast strains in multiple copies. Such integration was beneficial for xylose alcoholic fermentation. The respiration-deficient strain carrying episomal or integrated OrpXylA genes exhibited the best performance for glucose and xylose co-fermentation. This was partly attributed to the high expression levels and activities of xylose isomerase. Mating a respiration-efficient strain carrying the integrated PirXylA gene with a respiration-deficient strain harboring integrated OrpXylA generated a diploid recombinant xylose-fermenting yeast strain STXQ with enhanced cell growth and xylose fermentation. Co-fermentation of 162 g L−1 glucose and 95 g L−1 xylose generated 120.6 g L−1 ethanol in 23 h, with sugar conversion higher than 99%, ethanol yield of 0.47 g g−1, and ethanol productivity of 5.26 g L−1·h−1

Recombinant xylose-fermenting yeast construction for the co-production of ethanol and cis,cis-muconic acid from lignocellulosic biomass

New exogenous cis,cis-muconic acid biosynthetic pathway genes were expressed in Saccharomyces cerevisiae. The xylose isomerase gene from Bacteroides valgutus and pentose phosphate pathway genes from S. cerevisiae were overexpressed in the yeast strain. The strain was further modified by the overexpression of gene Aro1 (with a stop codon of AroE) and a feedback-resistant Aro4opt mutant gene from S. cerevisiae. Under oxygen-limited conditions, it produced 65 mg/L cis,cis-muconic acid from xylose. Co-fermentation of 88 g/L glucose and 50 g/L xylose generated 54 g/L ethanol and 248 mg/L cis,cis-muconic acid. Under aerobic conditions, muconic acid titer reached 424 mg/L. With the supplement of 1 g/L catechol, 1286 mg/L muconic acid was produced. Fermentation of an oil palm empty fruit bunch hydrolysate resulted in 31.3 g/L ethanol and 53.4 mg/L muconic acid. This is the first report on the production of muconic acid from lignocellulosic biomass hydrolysate using a recombinant xylose-fermenting yeast.</p

Enhanced ethanol production from industrial lignocellulose hydrolysates by a hydrolysate-cofermenting Saccharomyces cerevisiae strain

Industrial production of lignocellulosic ethanol requires a microorganism utilizing both hexose and pentose, and tolerating inhibitors. In this study, a hydrolysate-cofermenting Saccharomyces cerevisiae strain was obtained through one step in vivo DNA assembly of pentose-metabolizing pathway genes, followed by consecutive adaptive evolution in pentose media containing acetic acid, and direct screening in biomass hydrolysate media. The strain was able to coferment glucose and xylose in synthetic media with the respective maximal specific rates of glucose and xylose consumption, and ethanol production of 3.47, 0.38 and 1.62 g/g DW/h, with an ethanol titre of 41.07 g/L and yield of 0.42 g/g. Industrial wheat straw hydrolysate fermentation resulted in maximal specific rates of glucose and xylose consumption, and ethanol production of 2.61, 0.54 and 1.38 g/g DW/h, respectively, with an ethanol titre of 54.11 g/L and yield of 0.44 g/g. These are among the best for wheat straw hydrolysate fermentation through separate hydrolysis and cofermentation.</p

Theoretical study of low-energy electron scattering with GeH

We present a comprehensive study of electron collisions with germylene (GeH2 using the UK molecular R-matrix codes for electron energies ranging from 0.01 to 10 eV. The calculations are performed within the static-exchange, static-exchange-polarization, and 17-state close-coupling approximations. The elastic integral, differential, momentum transfer cross sections and the excitation cross sections from the ground state to the six low-lying electron excited states are presented. We found three Feshbach resonances and one Core-excited resonance. These resonances reveal the probability of anion formation by an electron attachment process and further decay to neutral and negative ion fragments. The electronic and rotational excitation cross sections for e-GeH2 scattering are reported for the first time. The cross-section dataset obtained from the present calculations are expected to be sufficiently accurate and comprehensive for most current modeling applications involving neutral GeH2

Comparative review of multifunctionality and ecosystem services in sustainable agriculture

Two scientific communities with broad interest in sustainable agriculture independently focus on multifunctional agriculture or ecosystem services. These communities have limited interaction and exchange, and each group faces research challenges according to independently operating paradigms. This paper presents a comparative review of published research in multifunctional agriculture and ecosystem services. The motivation for this work is to improve communication, integrate experimental approaches, and propose areas of consensus and dialog for the two communities. This extensive analysis of publication trends, ideologies, and approaches enables formulation of four main conclusions. First, the two communities are closely related through their use of the term "function." However, multifunctional agriculture considers functions as agricultural activity outputs and prefers farm-centred approaches, whereas ecosystem services considers ecosystem functions in the provision of services and prefers service-centred approaches. Second, research approaches to common questions in these two communities share some similarities, and there would be great value in integrating these approaches. Third, the two communities have potential for dialog regarding the bundle of ecosystem services and the spectrum of multifunctional agriculture, or regarding land sharing and land sparing. Fourth, we propose an integrated conceptual framework that distinguishes six groups of ecosystem services and disservices in the agricultural landscape, and combines the concepts of multifunctional agriculture and ecosystem services. This integrated framework improves applications of multifunctional agriculture and ecosystem services for operational use. Future research should examine if the framework can be readily adapted for modelling specific problems in agricultural management

The Context-Dependent Effect of Urban Form on Air Pollution: A Panel Data Analysis

There have been debates and a lack of understanding about the complex effects of urban-scale urban form on air pollution. Based on the remotely sensed data of 150 cities in the Beijing-Tianjin-Hebei agglomeration in China from 2000 to 2015, we studied the effects of urban form on fine particulate matter (PM2.5) and nitrogen dioxide (NO2) concentrations from multiple perspectives. The panel models show that the elastic coefficients of aggregation index and fractal dimension are the highest among all factors for the whole region. Population density, aggregation index, and fractal dimension have stronger influences on air pollution in small cities, while area size demonstrates the opposite effect. Population density has a stronger impact on medium/high-elevation cities, while night light intensity (NLI), fractal dimension, and area size show the opposite effect. Low road network density can enlarge the influence magnitude of NLI and population density. The results of the linear regression model with multiplicative interactions provide evidence of interactions between population density and NLI or aggregation index. The slope of the line that captures the relationship between NLI on PM2.5 is positive at low levels of population density, flat at medium levels of population density, and negative at high levels of population density. The study results also show that when increasing the population density, the air pollution in a city with low economic and low morphological aggregation degrees will be impacted more greatly

Seasonal and Diurnal Variations in the Relationships between Urban Form and the Urban Heat Island Effect

At the city scale, the diurnal and seasonal variations in the relationship between urban form and the urban heat island effect remains poorly understood. To address this deficiency, we conducted an empirical study based on data from 150 cities in the Jing-Jin-Ji region of China from 2000 to 2015. The results derived from multiple regression models show that the effects of urban geometric complexity, elongation, and vegetation on urban heat island effect differ among different seasons and between day and night. The impacts of urban geometric factors and population density in summer, particularly those during the daytime, are significantly larger than those in winter. The influence of urban area and night light intensity is greater in winter than in summer and is greater during the day than at night. The effect of NDVI is greater in summer during the daytime. Urban vegetation is the factor with the greatest relative contribution during the daytime, and urban size is the dominant factor at night. Urban geometry is the secondary dominant factor in summer, although its contribution in winter is small. The relative contribution of urban geometry shows an upward trend at a decadal time scale, while that of vegetation decreases correspondingly. The results provide a valuable reference for top-level sustainable urban planning