Exploring the Biological and Chemical Complexity of the Ligases

Using a novel method to map and cluster chemical reactions, we have re-examined the chemistry of the ligases [Enzyme Commission (EC) Class 6] and their associated protein families in detail. The type of bond formed by the ligase can be automatically extracted from the equation of the reaction, replicating the EC subclass division. However, this subclass division hides considerable complexities, especially for the C–N forming ligases, which fall into at least three distinct types. The lower levels of the EC classification for ligases are somewhat arbitrary in their definition and add little to understanding their chemistry or evolution. By comparing the multi-domain architecture of the enzymes and using sequence similarity networks, we examined the links between overall reaction and evolution of the ligases. These show that, whilst many enzymes that perform the same overall chemistry group together, both convergent (similar function, different ancestral lineage) and divergent (different function, common ancestor) evolution of function are observed. However, a common theme is that a single conserved domain (often the nucleoside triphosphate binding domain) is combined with ancillary domains that provide the variation in substrate binding and function.     

Vegetation cover change and driving factors in Fujian Province between 1975 and 2014北大核心CSCD

Aims Fujian Province has been one of the most severe soil erosion regions since Ming and Qing Dynasty in China. Recently, several ecological restoration projects have been implemented and they have significantly changed vegetation cover in this region. Methods We analyzed the four-decade vegetation cover change in Fujian Province using seven time-series data of Landsat Multispectral Scanner (MSS), Thematic Mapper (TM), and Operational Land Imager (OLI) between 1975 and 2014. We further explored the possible drivers on vegetation cover change by incorporating statistical data of plantation, cropland and urbanized area. Important findings Vegetation coverage in Fujian Province has increased from 69.0% to 77.8% between 1975 and 2014. However, a slight decrease was observed between 1995 and 2005. Spatially, forest was the primary vegetation type in the northwest, where croplands and human settlements were scattered along rivers or oceans. Shrubs and bare lands were also scattered across the northwest. In southwest, the areas of bare land, shrub land and cropland decreased, while areas of forest and human settlements expanded. The vegetation coverage and urbanized area increased at the cost of cropland and bare land.     

A straightforward protocol for the preparation of high performance microarray displaying synthetic MUC1 glycopeptides

Background

Human serum MUC1 peptide fragments bearing aberrant O-glycans are secreted from columnar epithelial cell surfaces and known as clinically important serum biomarkers for the epithelial carcinoma when a specific monoclonal antibody can probe disease-relevant epitopes. Despite the growing importance of MUC1 glycopeptides as biomarkers, the precise epitopes of most anti-MUC1 monoclonal antibodies remains unclear.

Methods

A novel protocol for the fabrication of versatile microarray displaying peptide/glycopeptide library was investigated for the construction of highly sensitive and accurate epitope mapping assay of various anti-MUC1 antibodies.

Results

Selective imine-coupling between aminooxy-functionalized methacrylic copolymer with phosphorylcholine unit and synthetic MUC1 glycopeptides-capped by a ketone linker at N-terminus provided a facile and seamless protocol for the preparation of glycopeptides microarray platform. It was demonstrated that anti-KL-6 monoclonal antibody shows an extremely specific and strong binding affinity toward MUC1 fragments carrying sialyl T antigen (Neu5Acα2,3Galβ1,3GalNAcα1→) at Pro-Asp-Thr-Arg motif when compared with other seven anti-MUC1 monoclonal antibodies such as VU-3D1, VU-12E1, VU-11E2, Ma552, VU-3C6, SM3, and DF3. The present microarray also uncovered the occurrence of IgG autoantibodies in healthy human sera that bind specifically with sialyl T antigen attached at five potential O-glycosylation sites of MUC1 tandem repeats.

Conclusion

We established a straightforward strategy toward the standardized microarray platform allowing highly sensitive and accurate epitope mapping analysis by reducing the background noise due to nonspecific protein adsorption.

General significance

The present approach would greatly accelerate the discovery research of new class autoantibodies as well as the development of therapeutic mAbs reacting specifically with disease-relevant epitopes.     

KIRA指标的拓展及其在中国植被与气候关系研究中的应用

根据Kira以月平均气温5℃为界的热量指数和干湿度指数概念,提出了以月平均气温10℃为界的生物热量指数,包括生物温暖指数(BWI)和生物寒冷指数(BCI),并修正其干湿度指数为生物干湿度指数(BK).利用中国689个标准气象台站的资料,分析我国主要植被类型分布与热量因子和干湿度因子的关系,得出两者之间较好的相关性,生物温暖指数、寒冷指数和干湿度指数的散点图较好地表现了中国各植被类型与气候指标的关系和格局.以10℃为界的生物温暖指数不仅对我国森林植被的地理分布和温度气候带的划分具有较好的指示作用,而且对西南部高山、亚高山地区的植被与气候关系指示性较强;生物寒冷指数则对亚热带和热带的指示性很好,能够较好区分亚热带南部及热带地区;由热量指数和降水量综合得出的生物干湿度指数,对中国西北部干旱、半干旱区以至全国的植被分布与水分、热量因子的关系分析有较好的应用价值.     

Oviposition site preferences of the threatened butterfly <Emphasis Type="Italic">Parnassius mnemosyne</Emphasis> – implications for conservation

Recent studies on the threatened clouded apollo butterfly, Parnassius mnemosyne, have identified suitable habitats on a large scale. More detailed knowledge on specific habitat requirements of ovipositing females is still needed. Some earlier observations suggest that females just drop their eggs without discrimination. This study suggests that females can be rather choosy in their oviposition site selection and that they actively search for oviposition sites with suitable vegetation structure. By identifying factors influencing female oviposition, such as distance to shrub, valuable knowledge is generated for restoration plans considered in the study area. This stresses the importance of proper management of extant habitats in order to prevent local extinctions of P. mnemosyne and it also highlights the need for data on specific oviposition requirements in butterfly conservation.     

Human impacts on Persoonia falcata. Perspectives on post-contact vegetation change in the Keep River region, Australia, from contemporary vegetation surveys

Persoonia falcata R. Br. and Buchanania obovata Engl. seeds are consistently preserved in abundance from archaeological sites across the Keep River region from 3500 b.p. up until the contact period. Although artefacts continued to be deposited after establishment of the pastoral industry, remains of these two plant species disappear in the upper levels of all excavated deposits. The contemporary vegetation in the vicinity of these sites appears to lack P. falcata, although B. obovata remains in abundance. These observations raise questions regarding (1) the impact of changing land-use and fire regimes, (2) the impact of Aboriginal land management on particular plant species and (3) the reorientation of Aboriginal site use across the region after settlement. These issues are explored in this paper using a comparative analysis of stand structure of the contemporary vegetation around previously excavated sites, as well as from published information on recent regional fire history. Results show improved recruitment of P. falcata (that is, seedlings are recruited into adult life stages) in the only site where Aboriginal people have re-introduced customary management. Both the timing of burning and significant unburnt periods appear important to the post-contact decline and also in the future success of populations of P. falcata in the region.     

谷子窄颖花突变体sins1的表型分析和突变基因定位

利用甲基磺酸乙酯(EMS,ethyl methyl sulfonate)诱变剂处理野生型Yugu1(豫谷1号),在后代中发现了一个可以稳定遗传的颖花明显变窄的突变体,将其命名为sins1。与Yugu1相比,突变体sins1的株高显著降低了3.89%,穗长和穗粗分别显著降低了17.42%和21.62%,旗叶叶长和叶宽分别显著降低了15.09%和25.78%,千粒重显著降低了40.96%,谷码数显著降低了25%,均达到显著水平(P0.05)。利用突变体sins1为母本、SSR41为父本构建F_2定位群体,F_2正常颖花与窄颖花植株数目的分离比例为3∶1,表明该突变性状由隐性单基因控制。利用F_2群体隐性单株,最终将突变基因定位在3号染色体上SSR标记3-2658与CAAS3031间约7.709 Mb的距离内,为下一步精细定位提供了基础,同时也为促进禾本科作物颖花的研究提供了方向。     

Genetics of seedling and adult plant resistance to net blotch (Pyrenophora teres f. teres) and spot blotch (Cochliobolus sativus) in barley

Net blotch (caused by Pyrenophora teres f. teres) and spot blotch (Cochliobolus sativus) are important foliar diseases of barley in the midwestern region of the USA. To determine the number and chromosomal location of Mendelian and quantitative trait loci (QTL) controlling resistance to these diseases, a doubled haploid population (Steptoe/Morex) was evaluated to the pathogens at the seedling stage in the greenhouse and at the adult plant stage in the field. Alleles at two or three unlinked loci were found to confer resistance to the net blotch pathogen at the seedling stage depending on how progeny exhibiting an intermediate infection response were classified. This result was corroborated in the quantitative analysis of the raw infection response data as 2 major QTL were identified on chromosomes 4 and 6M. A third QTL was also identified on chromosome 6P. Seven QTL were identified for net blotch resistance at the adult plant stage and mapped to chromosomes 1P, 2P, 3P, 3M, 4, 6P, and 7P. The 7 QTL collectively accounted for 67.6% of the phenotypic variance under a multiple QTL model. Resistance to the spot blotch pathogen was conferred by a single gene at the seedling stage. This gene was mapped to the distal region of chromosome 1P on the basis of both qualitative and quantitative data analyses. Two QTL were identified for spot blotch resistance at the adult plant stage: the largest QTL effect mapped to chromosome 5P and the other mapped to chromosome 1P near the seedling resistance locus. Together, the 2 QTL explained 70.1% of the phenotypic variance under a multiple QTL model. On the basis of the chromosomal locations of resistance alleles detected in this study, it should be feasible to combine high levels of resistance to both P. teres f. teres and C. sativus in barley cultivars.     

Production of monoclonal antibodies to the prion protein and their characterization

Antibodies to the prion protein (PrP), particularly, monoclonal antibodies, are necessary tools in the diagnostics and study of prion diseases and potential means of their immunotherapy. For the production of monoclonal antibodies, BALB/c mice were immunized by a recombinant bovine PrP. Three stable hybridomas producing antibodies of IgM class were prepared. The antibodies were bound to PrP in a solid-phase enzyme immunoassay and immunoblotting. The epitope mapping accomplished with the use of synthetic peptides showed that an epitope located in region 25–36 of PrP corresponds to one antibody, and epitopes located in region 222–229, to the other two. The antibodies to fragment 222–229 purified by affinity chromatography recognized with a high specificity conglomerates of a pathogenic prion in the brain tissue of cows suffering from spongiform encephalopathy. Thus, in nontransgenic mice, PrP-specific monoclonal antibodies were produced, useful in studies and diagnostics of prion diseases.     

Integration of CAPS markers into the RFLP map generated using recombinant inbred lines of Arabidopsis thaliana

Konieczny and Ausubel have described a technique whereby Arabidopsis thaliana loci can be rapidly mapped to one of the ten chromosome arms using a small number of F2 progeny from crosses between the ecotypes Landsberg erecta and Columbia. The technique involves the use of 18 co-dominant, cleaved amplified polymorphic sequence (CAPS) markers which are evenly distributed throughout the Arabidopsis genome. We have mapped these 18 markers using recombinant inbred (RI) lines generated in our laboratory. These data enable a better integration of loci mapped relative to the CAPS markers into the restriction fragment length polymorphism (RFLP) map generated using Arabidopsis RI lines.