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Toward a Zero-Waste Biorefinery: Confocal Microscopy as a Tool for the Analysis of Lignocellulosic Biomass
No full textLignocellulosic biomass is essentially composed of three components, cellulose, hemicellulose and lignin, with a highly complicated physical structure. The complex network provides significant challenges for the effective analysis of the components in actual biomass while attempted isolation of the individual components usually leads to cross contamination and hence the need to detect the contaminating components. A new method has been developed for the semiquantitative analysis of three main components in important large volume types of lignocellulosic biomass (pubescens, softwood and wheat straw) using confocal microscopy in the absence of stains of other additives. Standard titration and thermogravimetric methods have been used to confirm the confocal microscopy results. This breakthrough opens the door to quick and easy method for measuring both the ratio of the three major components in biomass and the purity of the isolated components
CLADES: A classification-based machine learning method for species delimitation from population genetic data
No full textSpecies are considered to be the basic unit of ecological and evolutionary studies. As multilocus genomic data are increasingly available, there have been considerable interests in the use of DNA sequence data to delimit species. In this study, we show that machine learning can be used for species delimitation. Our method treats the species delimitation problem as a classification problem for identifying the category of a new observation on the basis of training data. Extensive simulation is first conducted over a broad range of evolutionary parameters for training purposes. Each pair of known populations is combined to form training samples with a label of same species or different species. We use support vector machine (SVM) to train a classifier using a set of summary statistics computed from training samples as features. The trained classifier can classify a test sample to two outcomes: same species or different species. Given multilocus genomic data of multiple related organisms or populations, our method (called CLADES) performs species delimitation by first classifying pairs of populations. CLADES then delimits species by maximizing the likelihood of species assignment for multiple populations. CLADES is evaluated through extensive simulation and also tested on real genetic data. We show that CLADES is both accurate and efficient for species delimitation when compared with existing methods. CLADES can be useful especially when existing methods have difficulty in delimitation, for example with short species divergence time and gene flow
Soil Nematode Trophic Groups in Four Different Plantations in Southern China: Implications for Restoration
No full textIntensive anthropogenic disturbances have caused forest ecosystem degradation and soil erosion. Exotic fast-growing species are selected as pioneer species for restoration in degraded hilly lands of southern China. To better understand the potentials of the soil nematode trophic group composition in carbon sequestration, we investigated nematode trophic groups in Acacia, Eucalyptus, and Schima (native species as control) monoculture plantations in southern China after 23 years of reforestation. Our results showed that although total soil nematode abundance was not affected, the Acacia plantation significantly altered nematode trophic group composition over native species. Bacterivore and microbivore abundance, trophic diversity, and microbivore-driven soil organic carbon storage were higher in Acacia mangium than Schima superba. In contrast, plant parasitic nematode abundance and fungivore/bacterivore ratio were lower in Acacia mangium than Schima superba. As a result, Acacia mangium as a fast-growing pioneer tree species could be widely planted to maintain soil biodiversity and store carbon in restoring degraded forests in southern China. Eucalyptus exserta plantation enlarged the soil nematode community, including bacterivores, fungivores, and herbivores, suggesting that there is almost no allelopathy when eliminating anthropogenic disturbance in this study. Reasonable management is crucial for providing timber products and improving the ecological function of Eucalyptus plantations. Our results also highlight the critical roles of soil water and nutrient availability in regulating soil nematode trophic group composition and carbon sequestration
Synthesis and inhibitory effect of 10-chlorocanthin-6-one on ovarian cancer HO8910PM cells
No full textTo synthesize and determine the antitumor activity of 10-chlorocanthin-6-one in ovarian cancer HO8910PM cells. Among the synthesized canthin-6-one analogs, 10-chlorocanthin-6-one was the most cytotoxic (IC50 = 4.9 mu M), as demonstrated by a dose-dependent cytotoxicity assay. Moreover, 10-chlorocanthin-6-one induced apoptosis through the activation of poly(ADP-ribose) polymerase and caspase-3 cleavage, upregulation of Bcl-2, and downregulation of Bim, x-linked inhibitor of apoptosis protein (XIAP), and survivin in HO8910PM cells. Furthermore, Bim RNA, upregulated in a concentration-dependent manner, and knockdown of Bim via short-hairpin RNAs attenuated the inhibitory effects of 10-chlorocanthin-6-one on HO8910PM cell growth. 10-Chlorocanthin-6-one inhibits cell proliferation and induces apoptosis in H08910PM cells. The underlying molecular mechanisms of 10-chlorocanthin-6-one include activation of the Bim-mediated mitochondrial apoptotic pathway via upregulation of Bim and downregulation of Bcl-2, XIAP, and survivin. These data suggest that Bim is a potential target of 10-chlorocanthin-6-one, further demonstrating its potential use in the prevention and treatment of ovarian cancer
Phylogeny and systematics of the brake fern genus Pteris (Pteridaceae) based on molecular (plastid and nuclear) and morphological evidence
No full textThe brake fern genus Pteris belongs to Pteridaceae subfamily Pteridoideae. It is one of the largest fern genera and has been estimated to contain 200-250 species distributed on all continents except Antarctica. Previous studies were either based on plastid data only or based on both plastid and nuclear data but the sampling was small. In addition, an infrageneric classification of Pteris based on morphological and molecular evidence has not been available yet. In the present study, based on molecular data of eight plastid markers and one nuclear marker (gapCp) of 256 accessions representing ca. 178 species of Pteris, we reconstruct a global phylogeny of Pteris. The 15 major Glades identified earlier are recovered here and we further identified a new major Glade. Our nuclear phylogeny recovered 11 of these 16 major clades, seven of which are strongly supported. The inclusion of Schizostege in Pteris is confirmed for the first time. Based on the newly reconstructed phylogeny and evidence from morphology, distribution and/or ecology, we classify Pteris into three subgenera: P. subg. Pteris, P. subg. Campteria, and P. subg. Platyzoma. The former two are further divided into three and 12 sections, respectively
Hydrothermal pretreatment on the anaerobic digestion of washed vinegar residue
No full textThe aim of this work was to study the acetate separation from fresh vinegar residue (FVR) to avoid inhibition of methanogenesis and hydrothermal treatment on washed vinegar residue (WVR) to enhance methane production. The optimal liquid-solid ratio was 10: 1 mL/g for the washing of FVR. The methane yields of the FVR, WVR, and washed leachate (WL) were 273 L/kg VS, 199 L/kg VS, and 306.9 L/kg COD, respectively. The optimal hydrothermal temperature was 160 degrees C for WVR, with maximum methane yield of 258.38 L/kg VS. Hydrothermal pretreatment destroyed the structure of lignocellulose and improved the hydrolysis of hemicellulose. Compared with thermophilic digestion of FVR, thermophilic digestion of 160 degrees C treated FVR, and thermophilic digestion of WVR with mesophilic digestion of WL, the thermophilic digestion of 160 degrees C treated WVR with mesophilic digestion of WL obtained the maximum total methane yield of 102.5 L/kg FVR. (C) 2017 Elsevier Ltd. All rights reserved
Dataset of muCT scan of the holotype specimen of Batrachuperus londongensis Liu and Tian, 1978, an endemic hynobiid (Amphibia, Urodela) from Mount Emei, Sichuan Province, China
No full text小鲵科蝾螈类是有尾两栖类的一个原始类群,对了解蝾螈类的早期演化具有重要意义.由于该科化石稀少、对现存属种骨骼形态研究不足、基于分子数据的分支分析结果不一致以及缺少利用形态特征构建分支演化树的原因,该科在起源、某些特征演化和内部谱系关系存在诸多分歧.龙洞山溪鲵生活于中国四川峨眉山龙洞河,是现存小鲵类中唯一具有兼性童体型的蝾螈.该属种自发现至今已有40年,然而未有对其骨骼系统的详细研究.本文利用中国科学院成都生物研究所高精度CT扫描成像系统(Quantum GX microCT Imaging System)对龙洞山溪鲵的正模标本(CIB 14380)进行了分段扫描,所得分辨率在67.1~144 mum之间.扫描结果揭示出童体型的多个特殊形态特征,如舌器骨化程度较高、腕骨和跗骨完全骨化.这是 muCT扫描技术在中国现存小鲵类形态研究中的首次应用.本数据集包括正模标本的 muCT扫描原始数据、扫描参数、头骨和全身骨骼的三维重建图和视频、头部的3D pdf和可用于3D打印的stl文件.扫描所获取的骨骼结构在任意截面上轮廓清晰可辨,读者可利用常用三维软件,如VG Studio读取并使用该数据.以上文件的共享为相关科研人员提供了可供参照对比的原始数据,对小鲵科我国特有属种的形态学研究具有一定价值
Discovery of Odorrana yizhangensis in Tianping Mountains, Hunan Province of China with Intraspecific Genetic Divergence of the Species
No full text2012年和2013年在湖南省桑植县天平山采集到6号臭蛙类标本,经形态比较和分子系统学分析,鉴定为宜章臭蛙(Odorrana yizhangensis),表明天平山为该物种的新分布点。这些标本与宜章臭蛙的主要鉴别特征相符:体型较小;体背面棕色斑大而密,形状不规则;腹面褐色,其上斑纹稀少;股后部色浅,深色斑明显。雄性头体长(52.45 2.54)mm(48.96 ~ 54.92 mm,n = 3),雌性头体长(73.11 1.43)mm(71.26 ~ 74.74 mm,n = 3),均比模式标本群体的头体长略大。基于线粒体16S rRNA基因片段(502 bp)的系统关系分析结果表明,分析的天平山臭蛙标本与宜章臭蛙已知种群聚为一支系,天平山种群与宜章臭蛙已知种群间的遗传距离为0.002 0 ~ 0.008 1,远小于宜章臭蛙与其近缘种龙胜臭蛙(O. lungshengensis)之间的遗传距离(0.035 2 ~ 0.043 9);这表明采自天平山的臭蛙样本属于宜章臭蛙。本文为宜章臭蛙物种的地理分布与系统学提供了新的信息
Influence of ecological restoration on soil biological fertility in desertified grassland
No full text生物学肥力是土壤肥力的重要构成部分,能够指示生态恢复措施下沙化草地的土壤质量变化。以围栏禁牧草本模式(enclosure plus grass,EG)、围栏禁牧灌草间作模式(enclosure intercropping shrub-grass,ESG)和围栏禁牧沙障+灌草间作模式(enclosure plus sand-barrier and shrub-grass,ESSG)3种恢复地为研究对象,以未恢复的沙化草地(desertification grassland without restoration,CK)为对照,采用调查采样法、综合评价法研究生态恢复措施及年限对沙化草地土壤微生物数量、微生物生物量及酶活性的影响。结果表明,3种恢复模式提高了沙化草地土壤中各项生物学肥力指标,ESSG模式下土壤质量的恢复效果最优,生物学肥力指数(biological fertility index,BFI)分别显著高出EG和ESG模式41.5%和43.1%(P<0.05)。EG和ESG模式下,土壤各项生物学肥力指标随恢复年限的增加而增加,≤5、7~9和≥15 a恢复地的BFI值均显著高于未恢复地(0年)(P<0.05),且≥15 a的恢复地又显著高于≤5和7~9 a恢复地(P<0.05)。因此,在本研究的时间范围内,时间越长生态措施下土壤质量的恢复效果越好,但其最佳恢复期有待进一步研究确定
Distribution changes and refugia of three spruce taxa since the last interglacial
No full text基于物种现代分布信息和19个环境变量数据,利用最大熵模型(MaxEnt)模拟丽江云杉、紫果云杉和青杄在末次间冰期、末次盛冰期、全新世中期和现代的适生分布区,用云杉孢粉数据进行结果验证,探讨物种分布动态与气候变化的关系,推测其生物避难所.受试者工作特征曲线下方面积(AUC)以及孢粉数据验证结果显示,模拟结果较准确.结果表明:等温性、最暖季均温和最暖季均温分别是影响丽江云杉、紫果云杉和青杄分布的首要环境因子,相对于降水,温度对其分布的影响更重要; 3种云杉的喜寒习性和分布地的深切峡谷地貌特征导致其在末次盛冰期扩张;青杄和紫果云杉在末次间冰期可能存在生物避难所,分别位于湖北神农架地区和四川二郎山及其邻近区.本研究较为准确地模拟了3种云杉属植物末次间冰期以来几个重要地质历史时期的适生分布,推测了青杄和紫果云杉的生物避难所,为深入分析云杉属植物现代分布格局的形成、预测其在气候变化背景下的变化趋势以及3种云杉林的可持续管理和保护提供了科学依据