In situ detection of salicylic acid binding sites in plant tissues

The determination of hormone‐binding sites in plants is essential in understanding the mechanisms behind hormone function. Salicylic acid (SA) is an important plant hormone that regulates responses to biotic and abiotic stresses. In order to label SA‐binding sites in plant tissues, a quantum dots (QDs) probe functionalized with a SA moiety was successfully synthesized by coupling CdSe QDs capped with 3‐mercaptopropionic acid (MPA) to 4‐amino‐2‐hydroxybenzoic acid (PAS), using 1‐ethyl‐3‐(3‐dimethyllaminopropyl) carbodiimide (EDC) as the coupling agent. The probe was then characterized by dynamic light scattering and transmission electron microscopy, as well as UV/vis and fluorescence spectrophotometry. The results confirmed the successful conjugation of PAS to CdSe QDs and revealed that the conjugates maintained the properties of the original QDs, with small core diameters and adequate dispersal in solution. The PAS–CdSe QDs were used to detect SA‐binding sites in mung bean and Arabidopsis thaliana seedlings in vitro and in vivo. The PAS–CdSe QDs were effectively transported into plant tissues and specifically bound to SA receptors in vivo. In addition, the effects of the PAS–CdSe QDs on cytosolic Ca²⁺ levels in the tips of A. thaliana seedlings were investigated. Both SA and PAS–CdSe QDs had similar effects on the trend in cytosolic‐free Ca²⁺ concentrations, suggesting that the PAS–CdSe QDs maintained the bioactivity of SA. To summarize, PAS–CdSe QDs have high potential as a fluorescent probe for the in vitro/in vivo labeling and imaging of SA receptors in plants. Copyright © 2014 John Wiley & Sons, Ltd.     

Multiple gene detection by in situ RT-PCR in isolated plant cells and tissues

With the number of functional genomic approaches in plant biology increasing daily, the demand for rapid and reliable RNA localization techniques for gene characterization is being felt. We present herein a novel, liquid phase in situ RT-PCR (IS-RT-PCR) protocol using a combination of gene-specific fluorescent primers and spectral confocal microscopy to localize target RNA in epicotyl sections and xylogenic suspension cultures of Zinnia elegans. Potential sources of artefacts from fixation to gene detection were systematically eliminated using both fluorescent primers and nucleotides for 18S rRNA gene detection, resulting in a set of optimal parameters for IS-RT-PCR that may be readily adapted to any target gene. By judiciously choosing fluorescent primers with non-overlapping fluorochromes, we have shown that our technique is readily adapted to multiplex IS-RT-PCR, enabling the simultaneous localization of more than one gene within a complex tissue or heterogeneous cell population. A 6-carboxy-2',4,4',5',7,7'-hexachlorofluorescein (6-HEX)-labelled primer and a tetrachloro-6-carboxy-fluorescein (TET)-labelled primer were designed for two marker genes associated with programmed cell death in tracheary elements (TEs): an endonuclease (Zen1) and a cysteine protease (ZcP4), respectively. An additional Cyan5 (Cy5)-labelled primer was used to monitor 18SrRNA expression. As expected, the 18S signal was constitutively expressed throughout epicotyls sections and living cells in xylogenic in vitro cultures, whereas Zen1 and ZcP4 were co-localized in forming TEs both in planta and in vitro. Analogous to clustering analysis of gene expression using microarrays to elucidate common metabolic pathways and developmental processes, this novel technique is perfectly adapted to gaining a better understanding of gene function via the coordinated expression of genes in specific cell types of complex tissues and cell populations.     

Fibered confocal fluorescence microscopy for imaging apoptotic DNA fragmentation at the single-cell level in vivo

The major characteristic of cell death by apoptosis is the loss of nuclear DNA integrity by endonucleases, resulting in the formation of small DNA fragments. The application of confocal imaging to in vivo monitoring of dynamic cellular events, like apoptosis, within internal organs and tissues has been limited by the accessibility to these sites. Therefore, the aim of the present study was to test the feasibility of fibered confocal fluorescence microscopy (FCFM) to image in situ apoptotic DNA fragmentation in surgically exteriorized sheep corpus luteum in the living animal. Following intra-luteal administration of a fluorescent DNA-staining dye, YO-PRO-1, DNA cleavage within nuclei of apoptotic cells was serially imaged at the single-cell level by FCFM. This imaging technology is sufficiently simple and rapid to allow time series in situ detection and visualization of cells undergoing apoptosis in the intact animal. Combined with endoscope, this approach can be used for minimally invasive detection of fluorescent signals and visualization of cellular events within internal organs and tissues and thereby provides the opportunity to study biological processes in the natural physiological environment of the cell in living animals.     

HRCA技术在转基因植物检测中的应用

超分支滚环扩增技术（Hyperbranched rolling cycle amplification, HRCA）在近几年中逐渐引起人们的注意,并越来越多的用于基础研究和实际检测中。在本文中我们对该技术在转基因植物检测中的应用情况作了较全面的探索;根据4种转基因植物中常用的外源基因或DNA片段设计了4条锁式探针（Padlock probe）,利用质粒pKK2328中的一段序列作为锁式探针中的共同连接部分,并根据该共同的连接部分序列设计一对通用的HRCA引物;利用同位素标记的锁式探针对HRCA反应中的连接一步的特异性研究表明,只有当锁式探针和相应的检测靶DNA同时存在于连接体系中时,锁式探针才能被有效地进行连接,从线性分子变为环型分子,在没有相应靶DNA存在时锁式探针仅以线性形式存在;连接时间的研究表明,如果所检测的靶DNA是质粒或较短的DNA片段时,较短的连接时间（5～10min）就可以取得理想的最终检测效果,如果检测的靶DNA是复杂的植物基因组DNA时,连接时间需要较大程度的延长（30～60min）才能取得理想的最终检测结果;HRCA的反应时间研究表明,较长的反应时间可以明显增加最终产物的量;对Bst DNA聚合酶大片段酶用量的研究表明,在其它条件不变的情况下酶的用量可以在较大的范围内变化（0.5u～4u）而不影响最终检测结果;在上述研究的基础上,对转基因烟草进行实际检测,取得了与预期一致的理想结果。为了提高检测效率,仿效复合式PCR（Multiplex PCR,MPCR）的原理采用复合式HRCA（Multiplex HRCA, MHRCA）方法对转基因烟草进行检测,并利用反向点杂交进行结果分析,取得同预期完全一致的结果。我们的研究表明HRCA方法完全可以用于转基因植物的检测,而且其使用比MPCR技术更方便,效率更高。     

Group-specific 16S rRNA targeted probes for the detection of type I and type II methanotrophs by fluorescence in situ hybridisation

The study of methane-oxidising bacteria (methanotrophs) is of special interest, because of their role in the natural reduction of methane emissions from many different sources. Therefore new probes were developed to detect specifically either type I (Methylococcaceae) or type II methanotrophs (Methylocystaceae). The probes have shown high specificity in fluorescence in situ hybridisations (FISH), as demonstrated by parallel hybridisation of target and reference strains as well as sequence data analysis. With these probes, methanotrophs were detected in soil and root samples from rice microcosms, demonstrating their applicability even in a complex environmental matrix.     

Respiration response imaging for real-time detection of microbial function at the single-cell level

The ability to detect specific functions of uncultured microbial cells in complex natural communities remains one of the most difficult tasks of environmental microbiology. Here we present respiration response imaging (RRI) as a novel fluorescence microscopy-based approach for the identification of microbial function, such as the ability to use C(1) substrates, at a single-cell level. We demonstrate that RRI could be used for the investigation of heterogeneity of a single microbial population or for functional profiling of microbial cells from complex environmental communities, such as freshwater lake sediment.     

MicroRNA定量检测方法的研究进展

MicroRNA是一类内源性的非编码小分子RNA, 通过下调蛋白编码基因的表达而对不同的细胞发育过程起到重要的调控作用。分析组织或细胞样本中microRNA的表达可为研究这类分子的生物学功能提供重要的信息。近年来, 研究者发展了许多方法检测不同的生理和病理学过程中microRNA的表达差异, 并发现microRNA的异常表达与癌症、神经紊乱和心脏疾病等的发生相关。文章系统地介绍了最新发展的microRNA定量检测方法, 详细阐述了基于探针杂交技术的Northern blotting法、微阵列芯片法、纳米金标记法、桥连同位素标记法, 以及基于扩增技术的定量PCR检测法、滚环扩增法、引物入侵法和新一代大规模高通量测序法等, 并对这些方法的优缺点进行了分析比较。     

Fast-in Situ hybridization and immunoenzymatic color pigment detection of mouse bone marrow micronucleus

The development of a whole mouse genomic DNA probe coupled to color pigment painting detection methodology can accurately verify mouse micronuclei induced by chemicals or drugs leading to a lower probability of potential artifacts. Using color pigment painting detection of probes in conjunction with Wright's Giemsa counterstain instead of the current fluorescence detection technology ensures low cost, high resolution permanent documentation of slides for a particular test compound. The permanent color pigment-detected micronuclei and adjoining counterstain allows slides to be stored for future analysis without enhancing the signal or adding antifading agents that are associated with fluorescence detection. Combining innovative technology such as fast-in situ hybridization of DNA probes with immunoenzymatic color pigment detection provides rapid verification of true micronuclei (DNA containing) within 2-3 hr.     

miRNA与其靶mRNA的相互作用：绑定位点的质量与数量特征的整合计算分析

miRNAs通过完全或不完全的碱基互补绑定到信使RNA(mRNA)上,通过抑制翻译或者直接导致mRNA降解的方式来调节靶基因的表达．为了研究miRNAs在转录水平上面的调控作用,两种人类基因组中组织特异的miRNAs(miR-1和miR-124)被转染到HeLa细胞中,微阵列(microarray)分析转染前后细胞中各基因mRNA表达水平变化情况的结果表明：动物基因组中靶基因与miRNAs不完全的碱基互补也会导致mRNA的直接降解．通过分析实验得到的mRNA表达水平变化数据,发现这相同miRNA的不同靶基因mRNA表达水平的下调倍数有着明显的差别,推测这些靶基因mRNA序列本身存在某些影响其受调节程度的因素．为此,提取和分析这些靶基因mRNA的序列特征,通过对这些序列特征与mRNA表达水平下调数据进行统计相关分析,最终发现,miRNA靶基因受调节的程度与以下几个因素相关联：mRNA序列中miRNA靶位点的个数,靶位点与miRNA序列碱基互补的程度,以及绑定后形成二级结构的稳定程度(即最低自由能的大小)．在此基础上,初步建立起一个多因子作用下的miRNA 靶基因mRNA表达水平下调程度模型,分析表明：该模型在一定程度上可以反映了部分序列特征对于miRNA靶基因mRNA表达水平下调程度的影响．     

Variations in the dorso-ventral organization of leaf structure and Kranz anatomy coordinate the control of photosynthesis and associated signalling at the whole leaf level in monocotyledonous species

Photosynthesis and associated signalling are influenced by the dorso-ventral properties of leaves. The degree of adaxial/abaxial symmetry in stomatal numbers, photosynthetic regulation with respect to light orientation and the total section areas of the bundle sheath (BS) cells and the surrounding mesophyll (M) cells on the adaxial and abaxial sides of the vascular bundles were compared in two C₄[ Zea mays (maize) and Paspalum dilatatum ] and one C₃[ Triticum turgidum (Durum wheat)] monocotyledonous species. The C₃ leaves had a higher degree of dorso-ventral symmetry than the C₄ leaves. Photosynthetic regulation was the same on each side of the wheat leaves, as were stomatal numbers and the section area of the BS relative to that of the M cells (BS/M section area ratio). In contrast, photosynthetic regulation in maize and P. dilatatum leaves showed a marked surface-specific response to light orientation. Compared to the adaxial sides of the C₄ monocotyledonous leaves, the abaxial surfaces had more stomata and the BS/M section area ratio was significantly higher. Differences in dorso-ventral structure, particularly in Kranz anatomy, serve not only to maximize photosynthetic capacity with respect light orientation in C₄ monocotyledonous leaves but also allow adaxial and abaxial-specific signalling from the respective M cells.     

用染色体原位杂交技术定位RFLP探针Fr.3-42于16p13

限制性片段长度多态性(RFLP)探针Fr.3-42(第九届人类基因定位国际会议编号D1(?)S21)为一长1.9kb的人类单拷贝EcoRI/HindⅢ片段,本实验采用染色体原位杂交方法,将该探针定位于16号染色体短臂末端(p13)。在另一研究中已证实Fr.3-42与人α-珠蛋白基因紧密连锁。     

rRNA based identification and detection systems for rhizobia and other bacteria

Ribosomal ribonucleic acids are excellent marker molecules for the elucidation of bacterial phylogeny; they also provide useful target sites for identification and detection with nucleic acid probes. Based on the currently available 16S rRNA sequence data, bacteria of the rhizobial phenotype (plant nodulation, nitrogen fixation) are members of three moderately related phylogenetic sub-groups of the -subclass of the Proteobacteria: i.e. the rhizobia group, the bradyrhizobia group, and the azorhizobia group. All rhizobia, azo-, brady-, meso- and sinorhizobia are closely related to and in some cases phylogenetically intermixed with, non-symbiotic and/or non-nitrogen-fixing bacteria. Especially in the case of Bradyrhizobium japonicum strains, the 16S rRNA sequence data indicate substantial heterogeneity. Specific probe design and evaluation are discussed. A multiprobe concept for resolving specificity problems with group specific probes is presented. In situ identification with group specific probes of rhizobia in cultures as well as rhizobia and cyanobacteria within plant material is shown.     

PEP car☐ykinase containing species in the Brachiaria group of the subfamily panicoideae

In the Gramineae, a survey of species among the Brachiaria group of the subfamily Panicoideae, tribe Paniceae revealed that they are PEP car?ykinase containing species. This group includes the genera Brachiaria, Eriochloa and Urochloa. With the exception of the genus Panicum, these are the only genera within the Panicoideae found to contain PEP car?ykinase species. It is suggested that the PEP car?ykinase species of the genus Panicum, P. fasciculatum, P. maximum, P. molle and P. texanum, might be best placed in the Brachiaria group.