Reversible unfolding of the severe acute respiratory syndrome coronavirus main protease in guanidinium chloride

Chemical denaturant sensitivity of the dimeric main protease from severe acute respiratory syndrome (SARS) coronavirus to guanidinium chloride was examined in terms of fluorescence spectroscopy, circular dichroism, analytical ultracentrifuge, and enzyme activity change. The dimeric enzyme dissociated at guanidinium chloride concentration of <0.4 M, at which the enzymatic activity loss showed close correlation with the subunit dissociation. Further increase in guanidinium chloride induced a reversible biphasic unfolding of the enzyme. The unfolding of the C-terminal domain-truncated enzyme, on the other hand, followed a monophasic unfolding curve. Different mutants of the full-length protease (W31 and W207/W218), with tryptophanyl residue(s) mutated to phenylalanine at the C-terminal or N-terminal domain, respectively, were constructed. Unfolding curves of these mutants were monophasic but corresponded to the first and second phases of the protease, respectively. The unfolding intermediate of the protease thus represented a folded C-terminal domain but an unfolded N-terminal domain, which is enzymatically inactive due to loss of regulatory properties. The various enzyme forms were characterized in terms of hydrophobicity and size-and-shape distributions. We provide direct evidence for the functional role of C-terminal domain in stabilization of the catalytic N-terminal domain of SARS coronavirus main protease.     

Sequence Heterogeneity of the Ten rRNA Operons in Clostridium perfringens

We have cloned and sequenced rRNA operons of Clostridium perfringens strain 13 and analyzed the sequence structure in view of the phylogenesis. The organism had ten copies of rRNA operons all of that comprised of 16S, 23S and 5S rDNAs except for one operon. The operons clustered around the origin of replication, ranging within one-third of the whole genome sequence as it is arranged in a circle. Seven operons were transcribed in clockwise direction, and the remaining three were transcribed in counter clockwise direction assuming that the gyrA was transcribed in clockwise direction. Two of the counter clockwise operons contained tRNA^Ile genes between the 16S and 23S rDNAs, and the other had a tRNA^Ile genes between the 16S and 23S rDNAs and a tRNA^Asn gene in the place of the 5S rDNA. Microheterogeneity was found within the rRNA structural genes and spacer regions. The length of each 16S, 23S and 5S rDNA were almost identical among the ten operons, however, the intergenic spacer region of 16S-23S and 23S-5S were variable in the length depending on loci of the rRNA operons on the chromosome. Nucleotide sequences of the helix 19, helix 19a, helix 20 and helix 21 of 23S rDNA were divergent and the diversity appeared to be correlated with the loci of the rRNA operons on the chromosome.     

Next generation organoids for biomedical research and applications

Organoids are in vitro cultures of miniature fetal or adult organ-like structures. Their potentials for use in tissue and organ replacement, disease modeling, toxicology studies, and drug discovery are tremendous. Currently, major challenges facing human organoid technology include (i) improving the range of cellular heterogeneity for a particular organoid system, (ii) mimicking the native micro- and matrix-environment encountered by cells within organoids, and (iii) developing robust protocols for the in vitro maturation of organoids that remain mostly fetal-like in cultures. To tackle these challenges, we advocate the principle of reverse engineering that replicates the inner workings of in vivo systems with the goal of achieving functionality and maturation of the resulting organoid structures with the input of minimal intrinsic (cellular) and environmental (matrix and niche) constituents. Here, we present an overview of organoid technology development in several systems that employ cell materials derived from fetal and adult tissues and pluripotent stem cell cultures. We focus on key studies that exploit the self-organizing property of embryonic progenitors and the role of designer matrices and cell-free scaffolds in assisting organoid formation. We further explore the relationship between adult stem cells, niche factors, and other current developments that aim to enhance robust organoid maturation. From these works, we propose a standardized pipeline for the development of future protocols that would help generate more physiologically relevant human organoids for various biomedical applications.     

藻类批量培养中的比增长率最大值

批量培养谷皮菱形藻、莱茵衣藻、粉核小球藻、斜生栅藻、羊角月牙藻和铜绿微囊藻等六种藻类,在对数生长期,逐日计数而确定比增长率最大值（μｍａｒ）,发现（μｍａｒ）值出现的时间在各种藻类中不同。同时讨论了每种藻类的（μｍａｒ）与营养物质、光强、温度和起始浓度之间的关系。铜绿微囊藻的（μｍａｒ）在一定的总磷（ＴＰ）浓度范围内随ＴＰ浓度呈上升趋势。根据获得增大率最大值的条件,对它们在浮游植物群落中的生态位作     

三蕊草属Sinochasea Keng系统位置的研究

叶片表皮、叶片横切面、花粉和淀粉粒的微观特征,对青藏高原的特有类群三蕊草属Sinochasea Keng的系统位置进行了探讨。结果表明,三蕊草S.trigyna Keng在上述微观性状上与毛蕊草Duthiea brachypodia(P.Candargy) Keng et Keng f.差距最小,与冠毛草Stephanachne pappophorea(Hack.)Keng差距次之,与宝兴野青茅Deyeuxia moupinensis(Franch.) Pilger和拂子茅Calamagrostis epigeios(L.) Roth差距最大;三蕊草属的系统位置应处于毛蕊草所隶的燕麦族Aveneae中;在系统演化上,燕麦族是最原始的类群,它可能直接或间接地派生了针茅族Stipeae和剪股颖族Agrostideae。     

When should we expect early bursts of trait evolution in comparative data? Predictions from an evolutionary food web model

Conceptual models of adaptive radiation predict that competitive interactions among species will result in an early burst of speciation and trait evolution followed by a slowdown in diversification rates. Empirical studies often show early accumulation of lineages in phylogenetic trees, but usually fail to detect early bursts of phenotypic evolution. We use an evolutionary simulation model to assemble food webs through adaptive radiation, and examine patterns in the resulting phylogenetic trees and species' traits (body size and trophic position). We find that when foraging trade-offs result in food webs where all species occupy integer trophic levels, lineage diversity and trait disparity are concentrated early in the tree, consistent with the early burst model. In contrast, in food webs in which many omnivorous species feed at multiple trophic levels, high levels of turnover of species' identities and traits tend to eliminate the early burst signal. These results suggest testable predictions about how the niche structure of ecological communities may be reflected by macroevolutionary patterns.     

大兴安岭森林草原过渡带白桦及主要草本植物生态位关系的研究

以白桦、日阴菅及其它主要草本植物的个体数量为指标,分析了各植物种群在土壤有机质,速效P和pH值3个资源维上的生态位宽度和生态位重叠及其在不同海拔条件下的变化规律。日阴菅生态位宽度随海拔升高而增大,其余植物种类在有机质资源维上的生态位宽度,大都是以中等海拔（800m)的样带最宽,而在速效P资源维上,又以中等海拔的样带为最窄,由于高海拔及相应低气温在某种程度上限制了植物种群在土壤有机质和速效P的利用,主要植物种对之间在这两个资源维上的生态位重叠以高海拔（950m)样带为最小,在土壤pH值资源维上,溪荪与其它主要植物种间的生态位重叠皆以低海拔（650m)样带为最小,可能是其特殊的环境组合迫使溪荪发生了生态位移动,大多数种对在土壤有机质,速效P和pH值3个资源维上都以海拔800m的样带生态位重叠最大。     

水稻上部叶片叶绿素含量的高光谱估算模型

叶片叶绿素 (Chl) 状况是评价植株光合效率和营养胁迫的重要指标,实时无损监测Chl状况对作物生长诊断及氮素管理具有重要意义.以不同生态点、不同年份、不同施氮水平、不同类型水稻品种的4个田间试验为基础,于主要生育期同步测定了水稻主茎顶部4张叶片的高光谱反射率及Chl含量,并计算了350～2500 nm范围内任意两波段组合而成的比值(SR[λ1,λ2])和归一化(ND[λ1,λ2])光谱指数以及已报道的对Chl敏感的光谱指数,进一步系统分析了叶片Chl含量与上述光谱指数之间的定量关系.结果表明,红边波段的比值和归一化光谱指数可以较好地预测水稻上部4叶的Chl含量(R~2>0.9),但对于不同Chl指标其最佳组合波段有所差异.估算叶绿素a (Chla)、叶绿素总量(Chla+b)和叶绿素b (Chlb)的最佳比值光谱指数分别为SR(724,709)、SR(728,709)和SR(749,745),方程拟合决定系数R~2分别是0.947、0.946、0.905;最佳归一化光谱指数分别为ND(780,709)、ND(780,712)和ND(749,745),R~2分别是0.944、0.943、0.905.引入445 nm波段反射率对上述光谱指数进行修正,可以降低叶片表面反射差异的影响,提高模型的应用范围.利用不同年份独立的试验资料对所建模型进行了检验,结果表明,修正型比值光谱指数 mSR(724,709)、mSR(728,709) 和 mSR(749,745),以及修正型归一化光谱指数mND(780,709)、mND(780,712) 和 mND(749,745) 预测 Chla、Chla+b 和 Chlb 的效果更好,其测试的RMSE分别为 0.169、0.192、0.052、0.159、0.176、0.052,RE分别为8.18%、7.74%、13.01%、8.26%、7.59%、12.96%,均较修正前降低,说明修正后的光谱指数普适性更好.     

秦岭南坡两个大熊猫活动密集区的生境特征及大熊猫对生境的选择

对秦岭佛坪和长青2个保护区的大熊猫活动密集区的系列生境因子(包括海拔、坡度、坡向、水系密度、生境类型、竹子种类)进行了研究,并分析了其与大熊猫痕迹点的关系。结果表明：佛坪和长青保护区的生境特征既有相似性又有差异性,故2个保护区的大熊猫对生境的选择也呈相似性和差异性;在长青和佛坪保护区各存在1个大熊猫活动密集区,其具有明显的宏观生境特征;大熊猫活动密集区的生境资源可获得性和大熊猫对生境因子的适应选择对应关系明显;秦岭南坡大熊猫选择的生境特征主要是：海拔1 200～2 600 m,坡度20°～40°,水系密度为2～3条·km^-2,针阔叶混交林,巴山木竹和秦岭箭竹的分布区。     

Using food network unfolding to evaluate food–web complexity in terms of biodiversity: theory and applications

Food–web complexity often hinders disentangling functionally relevant aspects of food–web structure and its relationships to biodiversity. Here, we present a theoretical framework to evaluate food–web complexity in terms of biodiversity. Food network unfolding is a theoretical method to transform a complex food web into a linear food chain based on ecosystem processes. Based on this method, we can define three biodiversity indices, horizontal diversity (D_H), vertical diversity (D_V) and range diversity (D_R), which are associated with the species diversity within each trophic level, diversity of trophic levels, and diversity in resource use, respectively. These indices are related to Shannon's diversity index (H′), where H′ = D_H + D_V ? D_R. Application of the framework to three riverine macroinvertebrate communities revealed that D indices, calculated from biomass and stable isotope features, captured well the anthropogenic, seasonal, or other within‐site changes in food–web structures that could not be captured with H′ alone.