Characterization of highly informative cross-species microsatellite panels for the Australian dugong (Dugong dugon) and Florida manatee (Trichechus manatus latirostris) including five novel primers

The Australian dugong (Dugong dugon) and Florida manatee (Trichechus manatus latirostris) are threatened species of aquatic mammals in the order Sirenia. Sirenian conservation and management actions would benefit from a more complete understanding of genetic diversity and population structure. Generally, species-specific microsatellite markers are employed in conservation genetic studies; however, robust markers can be difficult and costly to isolate. To increase the number of available markers, dugong and manatee microsatellite primers were evaluated for cross-species amplification. Furthermore, one manatee and four dugong novel primers are reported. After polymerase chain reaction optimization, 23 (92%) manatee primers successfully amplified dugong DNA, of which 11 (48%) were polymorphic. Of the 32 dugong primers tested, 27 (84%) yielded product in the manatee, of which 17 (63%) were polymorphic. Dugong and manatee primers were compared and the most informative markers were selected to create robust and informative marker-panels for each species. These cross-species microsatellite marker-panels can be employed to assess other sirenian populations and can provide beneficial information for the protection and management of these unique mammals.     

Assessing the effects of primer specificity on eliminating numt coamplification in DNA barcoding: a case study from Orthoptera (Arthropoda: Insecta)

DNA barcoding is a diagnostic method of species identification based on sequencing a short mitochondrial DNA fragment of cytochrome oxidase I (COI), but its ability to correctly diagnose species is limited by the presence of nuclear mitochondrial pseudogenes (numts). Numts can be coamplified with the mitochondrial orthologue when using universal primers, which can lead to incorrect species identification and an overestimation of the number of species. Some researchers have proposed that using more specific primers may help eliminate numt coamplification, but the efficacy of this method has not been thoroughly tested. In this study, we investigate the taxonomic distribution of numts in 11 lineages within the insect order Orthoptera, by analysing cloned COI sequences and further test the effects of primer specificity on eliminating numt coamplification in four lineages. We find that numts are coamplified in all 11 taxa using universal (barcoding) primers, which suggests that numts may be widespread in other taxonomic groups as well. Increased primer specificity is only effective at reducing numt coamplification in some species tested, and only eliminates it in one species tested. Furthermore, we find that a number of numts do not have stop codons or indels, making it difficult to distinguish them from mitochondrial orthologues, thus putting the efficacy of barcoding quality control measures under question. Our findings suggest that numt coamplification is a serious problem for DNA barcoding and more quality control measures should be implemented to identify and eliminate numts prior to using mitochondrial barcodes for species diagnoses.     

An open issue: the inner mitochondrial membrane (IMM) as a free boundary problem

The inner mitochondrial membrane (IMM) is structured in cristae, which contributes to the best functioning of ions and adenylates exchange between the matrix and the intermembrane space. The central hypothesis of this paper is that the cristae structure favours a minimal mean free path of adenylates between translocation sites (translocase/ANT sites) and metabolic sites (ATPase sites). We propose a mathematical model and then give simulations. Based on simple hypotheses about cristae growth, they show that we can account for the major features of the IMM organization and functioning by minimizing the mean interdistance between ADP/ATP translocation and transformation sites.     

杜氏盐藻psaB基因cDNA克隆及系统进化分析

根据真核生物莱茵衣藻(Chlamydomonas reinhardtii)、Chlamydomonas moewusii及Chlorella vulgaris等光系统Ⅰ反应中心蛋白psaB基因的氨基酸高度保守序列,设计一对简并引物,利用TRIzol试剂提取杜氏盐藻(Dunaliella salina)细胞的总RNA,通过RT-PCR,得到的一段长为1.8kb左右的cDNA片段。PCR产物经T-A克隆并测序以及测序结果推导成氨基酸序列进行同源性比较,表明所克隆的1815bp序列为杜氏盐藻光系统Ⅰ反应中心psaB基因的cDNA片段,GenBank收录号为AY820754。根据已经得到的psaB的核苷酸序列推导成氨基酸序列与一些已知物种的psaB氨基酸序列相比较,同源性分别为Chlamydomonas reinhardtii 92%,Chlamydomonas moewusii 91%,Chlorella vulgaris 86%,Mesostigma viride 85%,Phy -scomitrella patenssubsp.Patens 85%,Nephroselmis olivacea 84%。此外,psaB密码子偏爱性分析表明:杜氏盐藻psaB基因第三位密码子A和T的组成分别为35.7%和39.17%,而G和C分别为7.27%和17.85%,即杜氏盐藻psaB基因密码子的组成大多为NNA和NNT。根据psaB基因的特征,作者对绿藻门的50个物种的psaB基因作了进化分析,结果表明:杜氏盐藻与Haematococcaceae中的大多数种类进化地位最为接近,这为更进一步弄清杜氏盐藻的遗传背景提供了理论依据。     

Mutations in the helix termination motif of mouse type I IRS keratin genes impair the assembly of keratin intermediate filament

Two classical mouse hair coat mutations, Rex (Re) and Rex wavy coat (Re(wc)), are linked to the type I inner root sheath (IRS) keratin genes of chromosome 11. An N-ethyl-N-nitrosourea-induced mutation, M100573, also maps close to the type I IRS keratin genes. In this study, we demonstrate that Re and M100573 mice bear mutations in the type I IRS gene Krt25; Re(wc) mice bear an additional mutation in the type I IRS gene Krt27. These three mutations are located in the helix termination motif of the 2B alpha-helical rod domain of a type I IRS keratin protein. Immunohistological analysis revealed abnormal foam-like immunoreactivity with an antibody raised to type II IRS keratin K71 in the IRS of Re/+ mice. These results suggest that the helix termination motif is essential for the proper assembly of types I and II IRS keratin protein complexes and the formation of keratin intermediate filaments.     

植被覆盖度对夏季降温效应的影响——以内蒙古为例

随着全球变暖的加剧,区域热环境问题日益凸显,植被的降温作用逐渐得到广泛关注。目前已有的研究多从样地尺度分析不同类型植被的降温效应。而区域尺度的研究多从定性的角度揭示地表温度与植被覆盖的关系,对评估植被的实际降温效应具有一定的局限性。以内蒙古为研究区,以MODIS地表温度数据为基础,采用近邻分析法,将森林、灌丛和草地的MODIS地表温度与相邻5km范围内的低覆盖地表作为对照,分析植被的降温效应以及植被覆盖度对降温效应的影响。从2015年7月地表温度平均值的结果来看,降温度数在蒙东、蒙中和蒙甘区均呈现森林>灌丛>草地。森林的降温范围在0.67-1.03℃,灌丛为0.60-0.95℃,草地为0.47-0.86℃。植被降温度数与植被覆盖度的回归拟合为对数分布,均呈显著正相关（P<0.01）。且在不同的植被覆盖度范围内植被降温效应具有显著差异,植被覆盖度水平较低时（<40%）,植被覆盖度的增加能更显著地降低地表温度。从整体来看,植被覆盖度每增加10%,森林降温0.12-0.39℃;灌丛降温0.1-0.2℃;草地降温0.049-0.075℃。综上,内蒙古作为全球气候变化最为敏感的区域之一,研究植被的夏季降温效应能够为内蒙古的气候调节服务评估提供重要的理论支撑及案例参考。     

Focus: Personalized Medicine: Simultaneously Detection of 50 Mutations at 20 Sites in the BRAF and RAS Genes by Multiplexed Single-Nucleotide Primer Extension Assay Using Fine-Needle Aspirates of Thyroid Nodules

Fine-needle aspiration (FNA) is commonly used for primary evaluation of thyroid nodules. Twenty to 30 percent of thyroid nodules remain indeterminate after FNA evaluation. Studies show the BRAF p.V600E to be highly specific for papillary thyroid carcinoma (PTC), while RAS mutations carry up to 88 percent positive predictive value for malignancy. We developed a two-tube multiplexed PCR assay followed by single-nucleotide primer extension assay for simultaneous detection of 50 mutations in the BRAF (p.V600E, p.K601E/Q) and RAS genes (KRAS and NRAS codons 12, 13, 19, 61 and HRAS 61) using FNA smears of thyroid nodules. Forty-two FNAs and 27 paired formalin-fixed, paraffin-embedded (FFPE) tissues were tested. All BRAF p.V600E-positive FNA smears (five) carried a final diagnosis of PTC on resection. RAS mutations were found in benign as well as malignant lesions. Ninety-two percent concordance was observed between FNA and FFPE tissues. In conclusion, our assay is sensitive and reliable for simultaneous detection of multiple BRAF/RAS mutations in FNA smears of thyroid nodules.     

不同营养模式下内蒙古沙漠小型盐湖卤虫种群特征与环境负载力

通过对桑根达莱淖尔卤虫的养殖实验与卵囊解剖,研究了内蒙古沙漠小型盐湖投饵、施肥与自然状态3种营养模式下卤虫的生境、种群动态、生殖特征,分析了环境对卤虫资源的负载力。结果表明:1在起始种群相同的情况下,不同营养模式对种群结构与密度有显著影响;2不同营养模式对个体生长速度影响存在差异,投饵对加快个体生长速度效果最明显,但在性成熟速度方面不同营养模式没有出现统计学显著差异;3不同营养模式对卤虫的怀卵量、卵生/卵胎生比例有显著影响;与空白组相比,投饵组平均怀卵量提高了35.52%—72.71%,施肥组提高了11.34%—26.15%;4卤虫资源的环境负载力为0.3—0.4 kg/m3,加以补充肥料,可提高到0.45 kg/m3,在投喂饲料的情况下可以达到0.5 kg/m3;5卤虫蛋白可开发量按环境负载力的1/3估计,对照组、施肥组和投饵组的相应年开发量分别为2.61—2.98 kg/m3、4.5—5.4 kg/m3和7.51—8.67 kg/m3,滞育卵产量分别为0.73、1.10 g/m3和1.17 g/m3。     

Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis

The polymerase chain reaction is fundamental to molecular biology and is the most important practical molecular technique for the research laboratory. We have developed and tested efficient tools for PCR primer and probe design, which also predict oligonucleotide properties based on experimental studies of PCR efficiency. The tools provide comprehensive facilities for designing primers for most PCR applications and their combinations, including standard, multiplex, long-distance, inverse, real-time, unique, group-specific, bisulphite modification assays, Overlap-Extension PCR Multi-Fragment Assembly, as well as a programme to design oligonucleotide sets for long sequence assembly by ligase chain reaction. The in silico PCR primer or probe search includes comprehensive analyses of individual primers and primer pairs. It calculates the melting temperature for standard and degenerate oligonucleotides including LNA and other modifications, provides analyses for a set of primers with prediction of oligonucleotide properties, dimer and G-quadruplex detection, linguistic complexity, and provides a dilution and resuspension calculator.