Scanometric DNA array detection with nanoparticle probes

A method for analyzing combinatorial DNA arrays using oligonucleotide-modified gold nanoparticle probes and a conventional flatbed scanner is described here. Labeling oligonucleotide targets with nanoparticle rather than fluorophore probes substantially alters the melting profiles of the targets from an array substrate. This difference permits the discrimination of an oligonucleotide sequence from targets with single nucleotide mismatches with a selectivity that is over three times that observed for fluorophore-labeled targets. In addition, when coupled with a signal amplification method based on nanoparticle-promoted reduction of silver(I), the sensitivity of this scanometric array detection system exceeds that of the analogous fluorophore system by two orders of magnitude.     

磁性纳米颗粒负载质粒DNA的研究

【目的】研究磁性纳米颗粒(MNP)负载质粒DNA形成的纳米载体-基因复合物的生物物理学特性、负载形态与负载机理,为基于磁性纳米载体定向编辑技术的应用奠定基础。【方法】以MNP作为基因载体,与质粒DNA pRGEB32制备纳米载体-基因复合物MNP-pRGEB32,分析MNP负载、保护pRGEB32的能力,并对其粒度分布、Zeta电位、结合形态进行研究。【结果】MNP通过静电作用压缩、吸附、聚集pRGEB32,形成纳米载体-基因复合物。MNP能有效负载并保护pRGEB32。【结论】MNP可作为一种理想的基因转移载体。     

Atmospheric electrical detection of organized convection

Relatively simple atmospheric electrical instrumentation carried on a small aircraft constitutes a flexible and sensitive system for detecting organized convection. Data can be obtained close to the sea surface, and low-velocity flight enhances the spatial resolution. With a slow-flying airplane or powered glider, it may be possible to trace the circulation of individual convection cells and to investigate the trajectory of air which forms cumulus clouds, one of the major unsolved problems in tropical meteorology. Since space charge near the ocean surface was found on some days to be organized on a horizontal scale equivalent to the cumulus cloud scale, this suggests that some of the air which forms maritime cumulus clouds may come from within a few meters of the ocean and that atmospheric electrical instrumentation may have the potential for tracing air from the sea surface to the clouds. Although the atmospheric electrical instrumentation technique described here cannot be used for direct measurement of air velocity, it may be possible to develop model that can be used to calculate air velocities from electric field data. Even though with the technique described here it is not possible to make direct measurements of wind velocity, airborne electric field records can provide useful information about convection by delineating patterns in the wind field and structural features of thermals (rising bodies of relatively warm air) and by making possible the remote detection of thermals (29). Future plans include attempting to trace interfaces between adjacent roll vortices from the sea surface through the depth of the mixed layer (i) by flying the aircraft parallel to the wind so as to nullify the horizontal electric field (measured between wing-tip probes) while ascending and descending along the interface between adjacent roll vortices and (ii) by measuring vertical and horizontal potential gradient variations at different flight levels (30). The sensitivity of atmospheric electrical instrumentation to the top of the mixed layer and structure within it can be used to explore another important problem in boundary layer convection-why convective cloud cover and oceanic rainfall are greater at night than during the day(31). Workers in atmospheric electricity have long recognized that their domain is strongly controlled by turbulence in the lower atmosphere, and many have believed that the most effective use of atmospheric electrical techniques to assist meteorological research would be in studying exchange processes. Reiter [see (8)] effectively extended atmospheric electrical studies of boundary layer phenomena through a height range by mounting instruments on cable cars traveling between the valley floor and mountain tops in the Alps. The airborne measurements described here extend this approach. Relating the electrical structure of the atmosphere to its dynamic structure poses an interesting problem which may contribute to our understanding of the atmosphere.     

Magnetoencephalography: detection of the brain's electrical activity with a superconducting magnetometer

Measurements of the brain's magnetic field, called magnetoencephalograms (MEG's), have been taken with a superconducting magnetometer in a heavily shielded room. This magnetometer has been adjusted to a much higher sensitivity than was previously attainable, and as a result MEG's can, for the first time, be taken directly, without noise averaging. MEG's are shown, simultaneously with the electroencephalogram (EEG), of the alpha rhythm of a normal subject and of the slow waves from an abnormal subject. The normal MEG shows the alpha rhythm, as does the EEG, when the subject's eyes are closed; however, this MEG also shows that higher detector sensitivity, by a factor of 3, would be necessary in order to clearly show the smaller brain events when the eyes are open. The abnormal MEG, including a measurenment of the direct-current component, suggests that the MEG may yield some information which is new and different from that provided by the EEG.     

何首乌种特异DNA探针的筛选

为筛选得到何首乌(Fallopia multiflora)种特异DNA探针,通过何首乌gDNA和其近缘植物毛脉蓼(F.multifora var.cillinerve)gDNA之间的的抑制消减杂交(Suppression subtraction hybridization,SSH)得到何首乌的差减片段,再将标记的差减片段和多物种gDNA阵列杂交筛选得到了4条何首乌DNA探针,探针通过反向斑点杂交检测,能很好地区分何首乌及其混伪品.获得的探针在中药鉴定基因芯片的制备及何首乌种质和生药鉴定方面具应用前景.     

Force microscopy with light-atom probes

The charge distribution in atoms with closed electron shells is spherically symmetric, whereas atoms with partially filled shells can form covalent bonds with pointed lobes of increased charge density. Covalent bonding in the bulk can also affect surface atoms, leading to four tiny humps spaced by less than 100 picometers in the charge density of adatoms on a (001) tungsten surface. We imaged these charge distributions by means of atomic force microscopy with the use of a light-atom probe (a graphite atom), which directly measured high-order force derivatives of its interaction with a tungsten tip. This process revealed features with a lateral distance of only 77 picometers.     

Nanoparticles with Raman spectroscopic fingerprints for DNA and RNA detection

Multiplexed detection of oligonucleotide targets has been performed with gold nanoparticle probes labeled with oligonucleotides and Raman-active dyes. The gold nanoparticles facilitate the formation of a silver coating that acts as a surface-enhanced Raman scattering promoter for the dye-labeled particles that have been captured by target molecules and an underlying chip in microarray format. The strategy provides the high-sensitivity and high-selectivity attributes of gray-scale scanometric detection but adds multiplexing and ratioing capabilities because a very large number of probes can be designed based on the concept of using a Raman tag as a narrow-band spectroscopic fingerprint. Six dissimilar DNA targets with six Raman-labeled nanoparticle probes were distinguished, as well as two RNA targets with single nucleotide polymorphisms. The current unoptimized detection limit of this method is 20 femtomolar.     

与磁性纳米粒结合的抗肿瘤方法

磁性纳米粒具有良好的磁靶向性、缓释性、粒径小等优点,文章综述了对磁性纳米粒进行表面修饰、外加磁场等方法,使药物在体内的循环时间延长,提高药物治疗效率,达到在肿瘤治疗中降低药物剂量和毒副作用的目的。     

Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray

A central challenge of genomics is to detect, simply and inexpensively, all differences in sequence among the genomes of individual members of a species. We devised a system to detect all single-nucleotide differences between genomes with the use of data from a single hybridization to a whole-genome DNA microarray. This allowed us to detect a variety of spontaneous single-base pair substitutions, insertions, and deletions, and most (>90%) of the approximately 30,000 known single-nucleotide polymorphisms between two Saccharomyces cerevisiae strains. We applied this approach to elucidate the genetic basis of phenotypic variants and to identify the small number of single-base pair changes accumulated during experimental evolution of yeast.     

用2个不同来源的DNA探针构建水稻RFLP连锁图谱(英文)

基于籼稻品种圭 6 30与粳稻品种台湾粳杂交产生的一个包含 111个株系的加倍单倍体 (DH)群体 ,构建了一个水稻 RFL P连锁图谱 .该图谱 (记为 DH图谱 )含有 175个 RFL P座位 ,全长 12 2 4 .6 c M,相邻标记间平均距离 7.0 c M.用于 RFL P分析的探针选自分别由日本水稻基因组计划 (RGP)和美国康耐尔大学 (CU)构建的 2个水稻图谱 .9个染色体区域发现明显的偏分离 ,但 DH图谱与 RGP和 CU图谱之间仍表现出较好的共线性 .因此 ,DH图谱可以作为那 2张图谱之间遗传信息相互沟通的桥梁 .本图谱还可用于对水稻中控制重要农艺性状的数量性状基因座的定位和分析     

Multicolor super-resolution imaging with photo-switchable fluorescent probes

Recent advances in far-field optical nanoscopy have enabled fluorescence imaging with a spatial resolution of 20 to 50 nanometers. Multicolor super-resolution imaging, however, remains a challenging task. Here, we introduce a family of photo-switchable fluorescent probes and demonstrate multicolor stochastic optical reconstruction microscopy (STORM). Each probe consists of a photo-switchable "reporter" fluorophore that can be cycled between fluorescent and dark states, and an "activator" that facilitates photo-activation of the reporter. Combinatorial pairing of reporters and activators allows the creation of probes with many distinct colors. Iterative, color-specific activation of sparse subsets of these probes allows their localization with nanometer accuracy, enabling the construction of a super-resolution STORM image. Using this approach, we demonstrate multicolor imaging of DNA model samples and mammalian cells with 20- to 30-nanometer resolution. This technique will facilitate direct visualization of molecular interactions at the nanometer scale.     

Electrostatic self-assembly of binary nanoparticle crystals with a diamond-like lattice

Self-assembly of charged, equally sized metal nanoparticles of two types (gold and silver) leads to the formation of large, sphalerite (diamond-like) crystals, in which each nanoparticle has four oppositely charged neighbors. Formation of these non-close-packed structures is a consequence of electrostatic effects specific to the nanoscale, where the thickness of the screening layer is commensurate with the dimensions of the assembling objects. Because of electrostatic stabilization of larger crystallizing particles by smaller ones, better-quality crystals can be obtained from more polydisperse nanoparticle solutions.     

基于电阻层析成像技术和ResNet的萝卜根系表型无损检测方法研究

【目的】针对现有根系表型检测方法存在价格昂贵、需要专人操作以及无法对根系表型进行原位无损检测等问题，提出一种基于电阻层析成像技术(Electrical resistance tomography,ERT)和深度残差神经网络(Deep residual network,ResNet)的萝卜根系表型无损检测方法。【方法】首先，利用COMSOL软件对萝卜-琼脂场域不同情况的ERT正问题进行仿真分析，并获得大量边界电压数据；然后，基于ResNet对萝卜-琼脂场域的内部电导率分布与边界电压之间的非线性映射关系建立模型，对萝卜-琼脂场域进行图像重建；最后，基于ERT研制一套萝卜根系表型检测装置，并进行试验验证。【结果】基于ERT和ResNet的萝卜根系表型检测方法能够实现萝卜根系表型的可持续无损检测，试验装置操作简单、成本低，图像重建相对误差小于5%。【结论】基于ERT的萝卜根系表型检测方法可以实现对萝卜根系表型的无损检测；结合ResNet算法，成像精度较高。该方法可有效应用于萝卜根系表型的检测。     

DNA amplification for direct detection of HIV-1 in DNA of peripheral blood mononuclear cells

By means of a selective DNA amplification technique called polymerase chain reaction, proviral sequences of the human immunodeficiency virus (HIV-1) were identified directly in DNA isolated from peripheral blood mononuclear cells (PBMCs) of persons seropositive but not in DNA isolated from PBMCs of persons seronegative for the virus. Primer pairs from multiple regions of the HIV-1 genome were used to achieve maximum sensitivity of provirus detection. HIV-1 sequences were detected in 100% of DNA specimens from seropositive, homosexual men from whom the virus was isolated by coculture, but in none of the DNA specimens from a control group of seronegative, virus culture-negative persons. However, HIV-1 sequences were detected in 64% of DNA specimens from seropositive, virus culture-negative homosexual men. This method of DNA amplification made it possible to obtain results within 3 days, whereas virus isolation takes up to 3 to 4 weeks. The method may therefore be used to complement or replace virus isolation as a routine means of determining HIV-1 infection.     

扩增片段长度多态性在蔷薇基因组DNA检测中的应用

采用单酶切和双酶切AFLP技术分别对5种不同蔷薇品种基因组DNA的遗传多态性进行了检测,比较了2种方法的多态性比率。单酶切采用10条人工设计的与接头序列相识别的AFLP选择性引物,用PstⅠ酶切,共获得108个AFLP标记,片段大小在100~2000 bp,得到33个多态位点,多态性位点百分率为30.56%;双酶切采用25对双酶切AFLP引物,在50~600 bp扩增出清晰条带658条,得到182个多态位点,占总扩增带的27.6%。对多态性片段进行统计,计算出不同品种间的相似系数和遗传距离。结果表明:硕苞蔷薇同其它4种蔷薇的遗传距离偏远,且其它四种蔷薇的遗传距离均较近,这与蔷薇品种来源和培育史相符。该研究表明两种AFLP标记均可用于蔷薇品种基因组DNA的遗传多态性的检测,准确评价尚待和其它品种对比研究后确定。     

Heterogeneity of murine leukemia virus in vitro DNA; detection of viral DNA in mammalian cells

Kinetic analysis of the reassociation of DNA synthesized in vitro by a murine leukemia virus DNA polymerase revealed two classes of double-stranded product representative of 25 and 100 percent of viral genetic information. The DNA product representing the smaller portion of the viral genome comprised 85 percent of the double-stranded DNA generated in vitro and was extensively duplicated in the genomes of both normal cells and cells containing RNA tumor virus.     

Optical detection of DNA conformational polymorphism on single-walled carbon nanotubes

The transition of DNA secondary structure from an analogous B to Z conformation modulates the dielectric environment of the single-walled carbon nanotube (SWNT) around which it is adsorbed. The SWNT band-gap fluorescence undergoes a red shift when an encapsulating 30-nucleotide oligomer is exposed to counter ions that screen the charged backbone. The transition is thermodynamically identical for DNA on and off the nanotube, except that the propagation length of the former is shorter by five-sixths. The magnitude of the energy shift is described by using an effective medium model and the DNA geometry on the nanotube sidewall. We demonstrate the detection of the B-Z change in whole blood, tissue, and from within living mammalian cells.     

减蛋综合征贵州分离毒全基因组探针的制备及检测

为准确检测鸡群中减蛋综合征病毒感染情况,从减蛋综合征病毒（ＥＤＳ）贵州分离毒株ＨＳ－１中提纯病毒ＤＮＡ后,用地高辛标记制备了全基因组探针。在Ｄｏｔ－ｂｌｏｔ中该探针不与正常鸭胚尿囊液核酸提取物及马立克氏病病毒（ＭＤＶ）ＤＮＡ发生反应,只与３株ＥＤＳ病毒（国际标准毒ＡＶ－１２７、贵州分离毒ＨＳ－１、南京分离毒（ＧＣ２）ＤＮＡ呈阳性反应,具有较高的特异性;可检测出３０ｐｇ的同源ＤＮＡ,具有较强的灵敏度     

Facile detection of mitochondrial DNA mutations in tumors and bodily fluids

Examination of human bladder, head and neck, and lung primary tumors revealed a high frequency of mitochondrial DNA (mtDNA) mutations. The majority of these somatic mutations were homoplasmic in nature, indicating that the mutant mtDNA became dominant in tumor cells. The mutated mtDNA was readily detectable in paired bodily fluids from each type of cancer and was 19 to 220 times as abundant as mutated nuclear p53 DNA. By virtue of their clonal nature and high copy number, mitochondrial mutations may provide a powerful molecular marker for noninvasive detection of cancer.     

Yeast RNA polymerase II genes: isolation with antibody probes

Genes encoding yeast RNA polymerase II subunits were cloned. Efficient isolation of these genes was accomplished by probing a phage lambda gt11 recombinant DNA expression library with polyvalent antibodies directed against purified yeast RNA polymerase II. The identity of genes that specify the largest RNA polymerase II subunits, the 220,000- and 150,000-dalton polypeptides, was confirmed by competitive radioimmune assay. Both of these genes exist in single copy in the yeast Saccharomyces cerevisiae.