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21.
《Fly》2013,7(3):138-144
Sample homogenization is an essential step for genomic DNA extraction, with multiple downstream applications in Molecular Biology. Genotyping hundreds or thousands of samples requires an automation of this homogenization step, and high throughput homogenizer equipment currently costs 7000 euros or more. We present an apparatus for homogenization of individual Drosophila adult flies in 96-well micro-titer dishes, which was built from a small portable paint-shaker (F5 portable paint-shaker, Ushake). Single flies are disrupted in each well that contains extraction buffer and a 4-mm metal ball. Our apparatus can hold up to five 96-well micro-titer plates. Construction of the homogenizer apparatus takes about 3–4 days, and all equipment can be obtained from a home improvement store. The total material cost is approximately 700 euros including the paint-shaker. We tested the performance of our apparatus using the ZR-96 Quick-gDNA? kit (Zymo Research) homogenization buffer and achieved nearly complete tissue homogenization after 15 minutes of shaking. PCR tests did not detect any cross contamination between samples of neighboring wells. We obtained on average 138 ng of genomic DNA per fly, and DNA quality was adequate for standard PCR applications. In principle, our tissue homogenizer can be used for isolation of DNA suitable for library production and high throughput genotyping by Multiplexed Shotgun Genotyping (MSG), as well as RNA isolation from single flies. The sample adapter can also hold and shake other items, such as centrifuge tubes (15–50 mL) or small bottles. 相似文献
22.
Shifa Xiong Yunxiao Zhao Yicun Chen Ming Gao Liwen Wu Yangdong Wang 《Ecology and evolution》2020,10(16):8949-8958
Analysis of genetic diversity and population structure among Quercus fabri populations is essential for the conservation and utilization of Q. fabri resources. Here, the genetic diversity and structure of 158 individuals from 13 natural populations of Quercus fabri in China were analyzed using genotyping‐by‐sequencing (GBS). A total of 459,564 high‐quality single nucleotide polymorphisms (SNPs) were obtained after filtration for subsequent analysis. Genetic structure analysis revealed that these individuals can be clustered into two groups and the structure can be explained mainly by the geographic barrier, showed gene introgression from coastal to inland areas and high mountains could significantly hinder the mutual introgression of genes. Genetic diversity analysis indicated that the individual differences within groups are greater than the differences between the two groups. These results will help us better understand the genetic backgrounds of Q. fabri. 相似文献
23.
Lorenzo Fattorini Sara Franceschi Piermaria Corona 《Biometrical journal. Biometrische Zeitschrift》2020,62(7):1810-1825
The estimation of individual values (marks) in a finite population of units (e.g., trees) scattered onto a survey region is considered under 3P sampling. For each unit, the mark is estimated by means of an inverse distance weighting interpolator. Conditions ensuring the design-based consistency of maps are considered under 3P sampling. A computationally simple mean squared error estimator is adopted. Because 3P sampling involves the prediction of marks for each unit in the population, prediction errors rather than marks can be interpolated. Then, marks are estimated by the predictions plus the interpolated errors. If predictions are good, prediction errors are more smoothed than raw marks so that the procedure is likely to better meet consistency requirements. The purpose of this paper is to provide theoretical and empirical evidence on the effectiveness of the interpolation based on prediction errors to prove that the proposed strategy is a tool of general validity for mapping forest stands. 相似文献
24.
Song Y McFarland DC Velleman SG 《Comparative biochemistry and physiology. Part A, Molecular & integrative physiology》2012,161(1):44-52
Syndecan-4 core protein is composed of extracellular, transmembrane, and cytoplasmic domains. The cytoplasmic domain functions in transmitting signals into the cell through the protein kinase C alpha (PKCα) pathway. The glycosaminoglycan (GAG) and N-linked glycosylated (N-glycosylated) chains attached to the extracellular domain influence cell proliferation. The current study investigated the function of syndecan-4 cytoplasmic domain in combination with GAG and N-glycosylated chains in turkey muscle cell proliferation, differentiation, fibroblast growth factor 2 (FGF2) responsiveness, and PKCα membrane localization. Syndecan-4 or syndecan-4 without the cytoplasmic domain and with or without the GAG and N-glycosylated chains were transfected or co-transfected with a small interfering RNA targeting syndecan-4 cytoplasmic domain into turkey muscle satellite cells. The overexpression of syndecan-4 mutants increased cell proliferation but did not change differentiation. Syndecan-4 mutants had increased cellular responsiveness to FGF2 during proliferation. Syndecan-4 increased PKCα cell membrane localization, whereas the syndecan-4 mutants decreased PKCα cell membrane localization compared to syndecan-4. However, compared to the cells without transfection, syndecan-4 mutants increased cell membrane localization of PKCα. These data indicated that the syndecan‐4 cytoplasmic domain and the GAG and N-glycosylated chains are critical in syndecan-4 regulating satellite cell proliferation, responsiveness to FGF2, and PKCα cell membrane localization. 相似文献
25.
Geometric morphometric studies are increasingly becoming common in systematics and palaeontology. The samples in such studies
are often small, due to the paucity of material available for analysis. However, very few studies have tried to assess the
impact of sampling error on analytical results. Here, this issue is addressed empirically using repeated randomized selection
experiments to build progressively smaller samples from an original dataset of ∼400 vervet monkey (Cercopithecus aethiops) skulls. Size and shape parameters (including mean size and shape, size and shape variances, angles of allometric trajectories)
that are commonly used in geometric morphometric studies, are estimated first in the original sample and then in the random
subsamples. Estimates are then compared to give an indication of what is the minimum desirable sample size for each parameter.
Mean size, standard deviation of size and variance of shape are found to be fairly accurate even in relatively small samples.
In contrast, mean shapes and angles between static allometric trajectories are strongly affected by sampling error. If confirmed
in other groups, our findings may have substantial implications for studies of morphological variation in present and fossil
species. By performing rarefaction analyses like those presented in our study, morphometricians can be easily provided with
important clues on how a simple but crucial factor like sample size can alter results of their studies. 相似文献
26.
Christophe Sola Ingrid Filliol Eric Legrand Igor Mokrousov Nalin Rastogi 《Journal of molecular evolution》2001,53(6):680-689
This paper deals with phylogenetic relationships among a set of 90 clinical strains representative of the worldwide diversity
of the Mycobacterium tuberculosis complex (Kremer et al. 1999) using eight independent genetic markers: IS6110, IS1081, the direct repeat (DR) locus, and five variable number of tandem DNA repeat loci (VNTR). In a preliminary experiment, phylogenetic
trees based on single markers were constructed that led to the detection of some similarities between the VNTR-based and the
spoligotyping-based phylogenetic trees. In the second step, a more global phenetic approach based on pairwise comparison of
strains within each typing system was used, followed by calculations of mean genetic distances based on all the eight loci
and the use of the neighbor-joining algorithm for tree reconstruction. This analysis confirmed our preliminary observations
and suggested the existence of at least two new phylogeographical clades of M. tuberculosis, one defined as the ``East African–Indian family' (EA-I), which may find its origin on the African or Asian continents, and
the other as the ``Latin American and Mediterranean' (LA-M) family. The existence of these two families was also validated
by an independent phylogenetic analysis of spoligotyping on a larger set of shared types (n= 252) and further corroborated by VNTR and katG–gyrA results. The potential origin of these families of bacilli is discussed based on cattle domestication and human migration
history. In conclusion, the information contained in insertion sequence and repetitive DNAs may serve as a model for the phylogenetic
reconstruction of the M. tuberculosis complex. 相似文献
27.
一种快速、无损大豆种子DNA提取方法的建立和应用 总被引:1,自引:0,他引:1
基因分型是进行植物基因功能的遗传分析和分子标记辅助育种的重要环节。该研究以大豆(Glycine max)成熟种子为材料, 建立了通过钻孔采集样品、快速提取DNA进行基因型鉴定的方法。用此方法, 一个熟练的工作人员可以在1个小时内完成120个样品的采集和DNA提取; 同时种子钻孔取样后, 不会对大豆种子的萌发造成影响。利用该方法获得的DNA可满足PCR扩增的要求。实验重复性好, 成功率在98%以上。这种快速且无损的大豆种子基因型鉴定方法可以用于鉴定杂交种子、品种纯度以及遗传分析等研究工作。 相似文献
28.
Urban environments are warmer, have higher levels of atmospheric CO2 and have altered patterns of disturbance and precipitation than nearby rural areas. These differences can be important for plant growth and are likely to create distinct selective environments. We planted a common garden experiment with seeds collected from natural populations of the native annual plant Lepidium virginicum, growing in five urban and nearby rural areas in the northern United States to determine whether and how urban populations differ from those from surrounding rural areas. When grown in a common environment, plants grown from seeds collected from urban areas bolted sooner, grew larger, had fewer leaves, had an extended time between bolting and flowering, and produced more seeds than plants grown from seeds collected from rural areas. Interestingly, the rural populations exhibited larger phenotypic differences from one another than urban populations. Surprisingly, genomic data revealed that the majority of individuals in each of the urban populations were more closely related to individuals from other urban populations than they were to geographically proximate rural areas – the one exception being urban and rural populations from New York which were nearly identical. Taken together, our results suggest that selection in urban environments favors different traits than selection in rural environments and that these differences can drive adaptation and shape population structure. 相似文献
29.
Eggerding FA 《Molecular biotechnology》2000,14(3):223-233
A mutation detection strategy based on multiplex PCR followed by multiplex allele-specific oligonucleotide probe ligation
was developed to detect single nucleotide substitutions in ras oncogenes, a common genetic abnormality in many human cancers. Mutation-specific probes are synthesized for each possible
single-base, nonsilent mutation in codons 12, 13, and 61 of H-, K-, and N-ras oncogenes. Mutations are identified by competitive oligonucleotide probe ligation to detect normal and /or mutant genotypes
in one reaction. Three probes (one common and two allelic probes) are needed for analysis of each mutation. Probes hybridized
to target ras oncogene DNA are joined by a thermostable ligase if there are no mismatches at their junctions; temperature cycling results
in a linear increase in product. Common probes are labeled with fluorochromes, and allelic probes each have different lengths.
Ligation products are analyzed by denaturing polyacrylamide gel electrophoresis on a fluorescent DNA sequencer. We have applied
this technology to identify ras mutations in pancreatic cancers and lung cancers and in patients with myelodysplastic syndromes and leukemias. 相似文献
30.
本文对更一般的结构模型给出了参数的一种常用的仪器变量估计近似分布方差的一种算法.并且给出了未知真值x服从指数分布的例子.此算法对生物科学中统计规律的探讨有一定的应用价值. 相似文献