Dinucleotide microsatellite DNA loci from the ant Myrmica scabrinodis

We describe the isolation and characterization of five dinucleotide microsatellite loci in the ant Myrmica scabrinodis, which were obtained using a magnetic bead hybridization selection protocol. The PCR primers were tested on nine to 11 individuals. The number of alleles ranged from two to 13, and the observed heterozygosity from 0.200 to 0.778.     

Characterization of RNA primers synthesized by the human breast cancer cell DNA synthesome

We previously reported on the purification and characterization of a functional multi‐protein DNA replication complex (the DNA synthesome) from human cells and tissues. The synthesome is fully competent to carry‐out all phases of the DNA replication process in vitro. In this study, DNA primase, a component of the synthesome, is examined to determine its activity and processivity in the in vitro synthesis and extension of RNA primers. Our results show that primase activity in the P4 fraction of the synthesome is 30‐fold higher than that of crude cell extracts. The synthesome synthesizes RNA primers that are 7–10 ribonucleotides long and DNA primers that are 20–40 deoxyribonucleotides long using a poly(dT) template of exogenous single‐stranded DNA. The synthesome‐catalyzed RNA primers can be elongated by E. coli DNA polymerase I to form the complementary DNA strands on the poly(dT) template. In addition, the synthesome also supports the synthesis of native RNA primers in vitro using an endogenous supercoiled double‐stranded DNA template. Gel analysis demonstrates that native RNA primers are oligoribonucleotides of 10–20 nt in length and the primers are covalently link to DNA to form RNA‐primed nascent DNA of 100–200 nt. Our study reveals that the synthesome model is capable of priming and continuing DNA replication. The ability of the synthesome to synthesize and extend RNA primers in vitro elucidates the organizational and functional properties of the synthesome as a potentially useful replication apparatus to study the function of primase and the interaction of primase with other replication proteins. J. Cell. Biochem. 106: 798–811, 2009. © 2009 Wiley‐Liss, Inc.     

Microsatellite markers for the whelk Buccinum undatum

Five microsatellite loci are described for the commercially exploited marine gastropod, Buccinum undatum. Levels of polymorphism were variable with three to 19 alleles per locus and expected heterozygosities of 0.26–0.94 in 60 individuals of the population from which the loci were isolated. Homozygote excess at two of the loci might be attributable to null alleles, and these loci should not be used in, for example, parentage analysis. Nevertheless, because null allele frequencies can be estimated and their effects partitioned, all are useful markers for studies of population differentiation.     

Primers for the amplification of sequence‐characterized loci in Cryphonectria cubensis populations

We describe the development of DNA markers for the fungal pathogen of Eucalyptus, Cryphonectria cubensis. These markers originated from cloned intershort sequence repeat polymerase chain reactions, which enrich for medium to highly repetitive DNA sequences. In total, 10 markers were isolated, eight of which were polymorphic, and these can subsequently be applied to study populations of C. cubensis.     

Genome‐enabled development of DNA markers for ecology,evolution and conservation

Molecular markers have become a fundamental piece of modern biology’s toolkit. In the last decade, new genomic resources from model organisms and advances in DNA sequencing technology have altered the way that these tools are developed, alleviating the marker limitation that researchers previously faced and opening new areas of research for studies of non‐model organisms. This availability of markers is directly responsible for advances in several areas of research, including fine‐scaled estimation of population structure and demography, the inference of species phylogenies, and the examination of detailed selective pressures in non‐model organisms. This review summarizes methods for the development of large numbers of DNA markers in non‐model organisms, the challenges encountered when utilizing different methods, and new research applications resulting from these advances.     

气候和土地利用变化影响下生态屏障带水土流失趋势研究

受气候和地形等诸多因素影响，我国"两屏三带"国家生态屏障带中的川滇-黄土高原区域和南方丘陵带水土流失十分严重，自然灾害频发。但是，针对川滇-黄土高原区域和南方丘陵带水土流失时空格局变化，特别是未来气候变化和土地利用变化影响下水土流失变化趋势的研究很少。因此，本研究以川滇-黄土高原区域和南方丘陵带为研究对象，利用修正土壤流失方程（RUSLE）定量分析了该区在2000-2015年水土流失的时空变化规律及其影响因素，并预测了在RCP2.6和RCP4.5的未来气候情景下及土地利用变化条件下水土流失的变化趋势。研究结果表明：（1）黄土高原地区在植被恢复的积极作用下，水土流失显著缓解；（2）川滇地区的西南部因植被盖度的增长和降雨的减少水土流失显著缓解，但四川省境内人口密集区农田面积增加以及降水增加造成水土流失大幅度加剧；（3）南方丘陵带受降水增加影响导致了部分区域的水土流失恶化；（4）在未来气候变化情景下，由于大部分地区降雨将减少使土壤侵蚀趋于缓解，但四川、黄土高原和南方丘陵带大部分地区仍然面临未来农田面积增加带来的水土侵蚀压力。考虑到未来气候变化情景下降雨减少的趋势，建议在黄土高原地区提高草地在土地利用类型中的占比，在减少耗水量的同时维持地表盖度，缓解水土侵蚀；此外，各区域仍需控制农田面积，而且需通过加强坡耕地上保水保土耕作措施降低农田区域的土壤侵蚀压力。     

Incidence of thyroid diseases in Zhejiang Province,China, after 15 years of salt iodization

Thyroid diseases(TD) can be induced by either deficient or excessive iodine intake. Universal Salt Iodization(USI) program has been implemented in China since 1995, to prevent iodine deficiency disorders (IDD). To evaluate the current conditions of TD and the role of USI, a multi-stage stratified random sampling scheme was used to perform a cross-sectional survey on the incidence of TD among participants in 6600 households in Zhejiang Province, a coastal area in China. Iodine nutrition status of the population was assessed by dietary iodine intake recall and urinary iodine concentration (UIC) of the participants, and TD were diagnosed by thyroid ultrasonography for 15122 participants and for 5873 participants by serum criteria for thyroid function(fT3, fT4, TSH, TRAb, TgAb, TPOAb; see Introduction for abbreviations). The median UIC of the surveyed population was 163 μg iodine/L. From the participants 23.2% had UIC < 100 μg/L which is moderately iodine-deficient according to WHO classification. Diffuse goiter was present in 2.3% of the population and thyroid nodule in 20.9%. The incidence of hyperthyroidism, subclinical hyperthyroidism, hypothyroidism, subclinical hypothyroidism, Graves’ disease and chronic lymphocytic thyroiditis was 0.5%, 0.6%, 0.6%, 7.8%, 0.2% and 0.3%, respectively. The proportion of several TD for participants with non-iodized salt intake was higher than that for participants with iodized salt intake.     

New mitochondrial primers for metabarcoding of insects,designed and evaluated using in silico methods

Insect metabarcoding has been mainly based on PCR amplification of short fragments within the “barcoding region” of the gene cytochrome oxidase I (COI). However, because of the variability of this gene, it has been difficult to design good universal PCR primers. Most primers used today are associated with gaps in the taxonomic coverage or amplification biases that make the results less reliable and impede the detection of species that are present in the sample. We identify new primers for insect metabarcoding using computational approaches (ecoprimers and degeprime ) applied to the most comprehensive reference databases of mitochondrial genomes of Hexapoda assembled to date. New primers are evaluated in silico against previously published primers in terms of taxonomic coverage and resolution of the corresponding amplicons. For the latter criterion, we propose a new index, exclusive taxonomic resolution, which is a more biologically meaningful measure than the standard index used today. Our results show that the best markers are found in the ribosomal RNA genes (12S and 16S); they resolve about 90% of the genetically distinct species in the reference database. Some markers in protein‐coding genes provide similar performance but only at much higher levels of primer degeneracy. Combining two of the best individual markers improves the effective taxonomic resolution with up to 10%. The resolution is strongly dependent on insect taxon: COI primers detect 40% of Hymenoptera, while 12S primers detect 12% of Collembola. Our results indicate that amplicon‐based metabarcoding of insect samples can be improved by choosing other primers than those commonly used today.     

地黄SCoT分子标记体系的建立和指纹图谱的构建

该研究采用L_(25)(5~6)正交设计和单因素两种方法,对影响地黄SCoT-PCR反应的5个因素(模板DNA浓度,引物浓度,ddH_2O和Mix的用量以及退火温度)进行了优化。结果表明:优化后的反应体系总体积为25μL,含有8μL ddH_2O,1μL模板DNA(80 ng·μL~(-1)),1μL引物(8μmol·L~(-1))和15μL Mix,退火温度为45℃。运用30份地黄种质材料,对优化的SCoT-PCR正交体系进行多次重复验证,获得了多态性丰富、条带清晰的扩增图谱,证明该反应体系稳定可靠。利用该体系对32条SCoT引物进行两次筛选,得到14个扩增产物清晰、重复性好且多态性条带相对较高的引物。利用SCoT_4等5条引物构建了上述地黄2个种共30份种质的SCoT指纹图谱。利用这5个SCoT引物指纹图谱可将7个地黄常用栽培品种区分开。这表明SCoT分子标记体系适用于地黄主要品种亲缘关系及遗传多样性的研究,所构建的指纹图谱也为地黄常见的7个栽培品种的区分提供参考依据。     

基于PIPE现象的质粒克隆位点序列设计与功能评价

分子克隆是现代生物学研究的核心技术之一,是基因工程、蛋白质工程中的重要手段。为提高分子克隆实验的操作效率,本研究设计并合成基于聚合酶引物不完全延伸（polymerase incomplete primer extension,PIPE）现象的质粒克隆位点序列。并以此为基础统一相关引物的设计方案,避免传统酶切--连接法中需针对不同载体MCS序列设计不同引物的缺点。该方案利用13 bp定长接头序列,在同一体系中使用2对引物、2种线性化模板同时扩增载体和插入片段,通过20个循环,在1次PCR过程中即合成可供转化使用的带缺口质粒产物。在NEB Q5酶系统中,利用此法将3种荧光素酶序列插入pET-15b及pET-21b(+)载体,均获得成功。且利用商品化感受态细胞（转化效率 > 5×108 cfu/μg）转化后所获得转化子数量均在300个以上,其中含插入片段的阳性克隆比例可达85%以上。基于本方案的设计及作用原理,可将其应用于10 kb以内载体和插入片段的快速重组。且具有通用性强、耗时少、阳性克隆得率高和成本低等优点,是传统DNA重组方法的有益补充,可作为各实验室的常规分子克隆手段之一。