A conformation-induced fluorescence method for microRNA detection

MicroRNAs play important roles in a large variety of biological systems and processes through their regulation of target mRNA expression, and show promise as clinical biomarkers. However, their small size presents challenges for tagging or direct detection. Innovation in techniques to sense and quantify microRNAs may aid research into novel aspects of microRNA biology and contribute to the development of diagnostics. By introducing an additional stem loop into the fluorescent RNA Spinach and altering its 3′ and 5′ ends, we have generated a new RNA, Pandan, that functions as the basis for a microRNA sensor. Pandan contains two sequence-variable stem loops that encode complementary sequence for a target microRNA of interest. In its sensor form, it requires the binding of a target microRNA in order to reconstitute the RNA scaffold for fluorophore binding and fluorescence. Binding of the target microRNA resulted in large changes in fluorescence intensity. The median fold change in fluorescence observed for the sensors tested was ∼50-fold. Pandan RNA sensors exhibit good signal-to-noise ratios, and can detect their target microRNAs within complex RNA mixtures.     

A computational method for reliable gait event detection and abnormality detection for feedback in rehabilitation

In this paper, a gait event detection algorithm is presented that uses computer intelligence (fuzzy logic) to identify seven gait phases in walking gait. Two inertial measurement units and four force-sensitive resistors were used to obtain knee angle and foot pressure patterns, respectively. Fuzzy logic is used to address the complexity in distinguishing gait phases based on discrete events. A novel application of the seven-dimensional vector analysis method to estimate the amount of abnormalities detected was also investigated based on the two gait parameters. Experiments were carried out to validate the application of the two proposed algorithms to provide accurate feedback in rehabilitation. The algorithm responses were tested for two cases, normal and abnormal gait. The large amount of data required for reliable gait-phase detection necessitate the utilisation of computer methods to store and manage the data. Therefore, a database management system and an interactive graphical user interface were developed for the utilisation of the overall system in a clinical environment.     

A computational method for reliable gait event detection and abnormality detection for feedback in rehabilitation

In this paper, a gait event detection algorithm is presented that uses computer intelligence (fuzzy logic) to identify seven gait phases in walking gait. Two inertial measurement units and four force-sensitive resistors were used to obtain knee angle and foot pressure patterns, respectively. Fuzzy logic is used to address the complexity in distinguishing gait phases based on discrete events. A novel application of the seven-dimensional vector analysis method to estimate the amount of abnormalities detected was also investigated based on the two gait parameters. Experiments were carried out to validate the application of the two proposed algorithms to provide accurate feedback in rehabilitation. The algorithm responses were tested for two cases, normal and abnormal gait. The large amount of data required for reliable gait-phase detection necessitate the utilisation of computer methods to store and manage the data. Therefore, a database management system and an interactive graphical user interface were developed for the utilisation of the overall system in a clinical environment.     

基于斑块的红树林空间演变机理分析方法

现有红树林空间动态分析多是从整体的角度分析其面积的变化情况及其影响因素,着重于面积变化的定量分析和影响因素的定性分析,对其变化的发生途径缺乏深入分析,也不研究其斑块数量的变化动态。由于一定区域范围内的红树林由成百上千甚至更多空间上相互分离的斑块组成,各斑块边界和面积变化动态构成了区域红树林整体的空间分布变化动态,因此,只有深入摸清各个斑块的变化情况及其影响因素,才能对区域红树林整体变化情况作出全面、详细和准确的分析评估。提出了基于斑块的红树林空间演变机理分析方法,首先通过两期高空间分辨率遥感图像提取红树林空间分布信息,在GIS支持下采用叠置分析方法,根据前、后两期各个斑块的空间位置、形状和面积变化情况以及图像表征,逐一分析确定每个斑块变化的主要驱动因子(即变化原因,包括自然过程、围垦、养殖塘和盐田建设、工程建设和人工造林5种)和变化途径(即变化类型,包括稳定、扩张、萎缩、碎化、消失和新增6种),在此基础上构建斑块数量和面积变化的驱动因子-变化途径状态矩阵,通过总驱动量、总驱动率、净驱动量、净驱动率、趋势驱动率、总流量、总流率、净流量、净流率、趋势净流率和作用力等系列指标定量地评估红树林斑块数量和面积的变化动态。该方法不但能够定量地表达了各个驱动因子对红树林斑块数量和面积变化的影响程度,而且能够准确地阐明了红树林斑块数量和面积发生变化的途径,并且还能够准确地反映了每个驱动因子通过何种途径影响斑块数量和面积的变化,实现了红树林空间动态变化分析的定位化、定量化和精确化。     

A simple DNA stretching method for fluorescence imaging of single DNA molecules

Stretching or aligning DNA molecules onto a surface by means of molecular combing techniques is one of the critical steps in single DNA molecule analysis. However, many of the current studies have focused on λ-DNA, or other large DNA molecules. There are very few studies on stretching methodologies for DNA molecules generated via PCR (typically smaller than 20 kb). Here we describe a simple method of stretching DNA molecules up to 18 kb in size on a modified glass surface. The very low background fluorescence allows efficient detection of single fluorescent dye labels incorporated into the stretched DNA molecules.     

A rapid fluorescence polarization-based method for genotypic detection of drug resistance in Mycobacterium tuberculosis

Rapid detection of drug-resistant Mycobacterium tuberculosis is critical to the effective early treatment and prevention of the transmission of tuberculosis. However, conventional drug susceptibility tests for M. tuberculosis require up to several weeks. In the present study, the One Label Extension genotyping method was adapted for rapid detection of drug resistance-associated sequence variations in six genes of M. tuberculosis, viz. rpoB, rpsL, rrs, embB, katG, or inhA. The method utilizes polymerase chain reaction amplified fragments of the drug resistant genes as reaction templates, and proceeds with template-directed primer extension incorporating a fluorescence-labeled nucleotide, which is then measured by fluorescence polarization. A total of 121 M. tuberculosis isolates from clinical sputum specimens were examined by this genotyping method and verified by direct sequencing of polymerase chain reaction amplicons harboring previously reported mutational sites associated with M. tuberculosis drug resistance. Based on phenotyping results obtained from microbiology-based drug susceptibility tests, the sensitivity, specificity, and test efficiency estimated for One Label Extension assays were respectively 83.9 %, 95.5 %, and 92.4 % with ropB in rifampin resistance, 67.3 %, 97.1 %, and 84.3 % with rpsL and rrs in streptomycin resistance, 60.0 %, 96.0 %, and 91.4 % with embB in ethambutol resistance, 68.4 %, 94.9 %, and 86.3 % with inhA and katG in isoniazid resistance, and 74.1 %, 98.9 %, and 93.2 % in multiple drug resistance defined as resistance to at least both isoniazid and rifampin. In conclusion, examination of clinical sputum specimens by One Label Extension based genotyping provides a valid method for the rapid molecular detection of drug-resistant M. tuberculosis.     

Development of high-sensitivity near-infrared fluorescence imaging device for early cancer detection

We have developed a high-sensitivity near-infrared (NIR) optical imaging system for noninvasive cancer detection based on the molecular-labeled fluorescent contrast agents. Recent developments in molecular beacons offer a way to selectively tag various precancer and cancer signatures and provide high tumor-to-background contrast. Near-infrared imaging can deeply probe tissue up to a couple of centimeters; thus, it possesses the potential for noninvasive detection of breast or lymph node cancer. A phase cancellation (in- and antiphase) device is used to increase the sensitivity in detecting fluorescent photons and the accuracy of tumor localization. The optoelectronic system consists of the laser diode sources, fiber optics, interference filter (to select the fluorescent photons), and the high-sensitivity photon detector (photomultiplier tube). The source-detector pair scans the tissue surface in multiple directions, and the localization image can be obtained by angular back-projection reconstruction. Simulations and experimental data demonstrated the feasibility of detection and localization offluorescent object embedded inside the highly scattering media. Tumor-bearing mouse model with injection of fluorescent contrast agents is used to simulate the human breast tumor labeled with molecular beacons. The system can detect fluorescent contrast agents as small as one nanomole at the depth of three centimeters, with a three-millimeter localization error. This instrument has the potential for tumor diagnosis and imaging, and the accuracy of the localization suggests that this system could help guide the clinical fine-needle biopsy. Also, this portable device would be complementary to x-ray mammography and provide add-on information on early diagnosis and localization of breast tumor.     

Metal plasmon-coupled fluorescence imaging and label free coenzyme detection in cells

Flavin adenine dinucleotide (FAD) is a key metabolite in cellular energy conversion. Flavin can also bind with some enzymes in the metabolic pathway and the binding sites may be changed due to the disease progression. Thus, there is interest on studying its expression level, distribution, and redox state within the cells. FAD is naturally fluorescent, but it has a modest extinction coefficient and quantum yield. Hence the intrinsic emission from FAD is generally too weak to be isolated distinctly from the cellular backgrounds in fluorescence cell imaging. In this article, the metal nanostructures on the glass coverslips were used as substrates to measure FAD in cells. Particulate silver films were fabricated with an optical resonance near the absorption and the emission wavelengths of FAD which can lead to efficient coupling interactions. As a result, the emission intensity and quantum yield by FAD were greatly increased and the lifetime was dramatically shortened resulting in less interference from the longer lived cellular background. This feature may overcome the technical limits that hinder the direct observation of intrinsically fluorescent coenzymes in the cells by fluorescence microscopy. Fluorescence cell imaging on the metallic particle substrates may provide a non-invasive strategy for collecting the information of coenzymes in cells.     

A sensitive fluorescence quenching method for the detection of tartrazine with acriflavine in soft drinks

In this work, a simple, rapid, sensitive, selective spectrofluorimetric method was applied to detect tartrazine. The fluorescence of acriflavine could be efficiently quenched by tartrazine. The method manifested real time response as well as presented satisfied linear relationship to tartrazine. The linear response range of tartrazine (R² = 0.9995) was from 0.056 to 5 μmol L^?1. The detection limit (3σ/k) was 0.017 μmol L^?1, indicating that this method could be applied to detect traces of tartrazine. The accuracy and precision of the method was further assured by recovery studies via a standard addition method, with percentage recoveries in the range of 96.0% to 103.0%. Moreover, a quenching mechanism was investigated systematically by the linear plots at varying temperatures based on the Stern–Volmer equation, fluorescence lifetime and UV–visible absorption spectra, all of which proved to be static quenching. This sensitive, selective assay possessed a great application prospect for the food industry owing to its simplicity and rapidity for the detection of tartrazine.     

A novel fluorescence imaging technique combining deconvolution microscopy and spectral analysis for quantitative detection of opportunistic pathogens

A novel fluorescence imaging technique based on deconvolution microscopy and spectral analysis is presented here as an alternative to confocal laser scanning microscopy. It allowed rapid, specific and simultaneous identification of five major opportunistic pathogens, relevant for public health, in suspension and provided quantitative results.     

A novel fluorescence imaging technique combining deconvolution microscopy and spectral analysis for quantitative detection of opportunistic pathogens

A novel fluorescence imaging technique based on deconvolution microscopy and spectral analysis is presented here as an alternative to confocal laser scanning microscopy. It allowed rapid, specific and simultaneous identification of five major opportunistic pathogens, relevant for public health, in suspension and provided quantitative results.     

A method for transient expression in maize endosperm

The ability to screen the functionality of gene constructs in a transient system of appropriate tissues informs the researcher of the potential success of stable transformation. For this purpose, we developed a transient system to test the functionality of endosperm-preferred promoters in maize. Two endosperm-preferred promoters from rice (a globulin and a glutelin promoter) were employed. Ears of Zea mays L. were harvested at 17 d after pollination, surface sterilized and the endosperm excised. Using Agrobacterium tumefaciens co-cultivation and sonication, transient expression of the target genes was detected after 4 and 5 d. We demonstrate expression of CBH I and CHB II (both exo-cellulases) up to 1.7% TSP, under the rice globulin and glutelin promoters.     

A method for repetitive artifact suppression in multichannel EEG recordings

An artifact suppression method based on the assumption of linear independence of EEG and artifact signals is described. This assumption allows the use of principal component analysis for their separation. The method makes it possible to eliminate electrooculogram (EOG) signals from multichannel EEG recordings regardless of the use of special EOG channels in the recording, as well as to eliminate any other repetitive artifacts, including pulse and electrocardiogram artifacts, ones related to mechanical instability of the reference electrode, etc.     

A rapid detection method for apoptosis and necrosis measurement using the Cellometer imaging cytometry

Apoptosis and necrosis play an important role in various aspects of preclinical pharmaceutical drug discovery and validation. The ability to quickly determine the cytotoxic effect of chemical compounds on cancer cells allows researchers to efficiently identify potential drug candidates for further development in the pharmaceutical discovery pipeline. Recently, a new imaging cytometry system has been developed by Nexcelom Bioscience LLC (Lawrence, MA, USA) for fluorescence-based cell population analysis. Currently, fluorescence-based cell death assays have not been demonstrated by the Cellometer system, which can potentially provide a quick, simple, and inexpensive alternative method for smaller biomedical research laboratories. In this study, we demonstrate for the first time the use of Cellometer imaging cytometry for necrosis/apoptosis detection by studying the dose–response effect of heat and drug-induced cell death in Jurkat cells labeled with annexin V-FITC (apoptotic) and propidium iodide (necrotic). The experimental results were evaluated to validate the imaging cytometric capabilities of the Cellometer system as compared to the conventional flow cytometry. Similar cell population results were obtained from the two methods. The ability of Cellometer to rapidly and cost-effectively perform fluorescent cell-based assays has the potential of improving research efficiency, especially where a flow or laser scanning cytometer is not available or in situations where a rapid analysis of data is desired.     

Intraoperative detection of IDH-mutant glioma using fluorescence lifetime imaging

Identifying isocitrate dehydrogenase (IDH)-mutation and glioma subtype during surgery instead of days later can aid in modifying tumor resection strategies for better survival outcomes. We report intraoperative identification of IDH-mutant glioma (N = 12 patients) with a clinically compatible fluorescence lifetime imaging (FLIm) device (excitation: 355 nm; emission spectral bands: 390/40 nm, 470/28 nm, 542/50 nm). The fluorescence-derived parameters were analyzed to study the optical contrast between IDH-mutant tumors and surrounding brain tissue. IDH-mutant oligodendrogliomas exhibited shorter lifetimes (3.3 ± 0.1 ns) than IDH-mutant astrocytomas (4.1 ± 0.1 ns). Both IDH-mutant glioma subtypes had shorter lifetimes than white matter (4.6 ± 0.4 ns) but had comparable lifetimes to cortex. Lifetimes also increased with malignancy grade within IDH-mutant oligodendrogliomas (grade 2: 2.96 ± 0.08 ns, grade 3: 3.4 ± 0.3 ns) but not within IDH-mutant astrocytomas. The current results support the feasibility of FLIm as a surgical adjuvant for identifying IDH-mutant glioma tissue.     

布鲁氏菌病荧光偏振抗体检测方法的建立

【目的】布鲁氏菌病(Brucellosis)简称布病,是由布鲁氏菌引起的以感染家畜为主的人畜共患传染病,造成严重的公共卫生问题。目前全世界范围内消除该病的主要方法是扑杀与免疫相结合,所以建立快速准确的诊断方法对防治和清除布病非常必要。本文建立布鲁氏菌病荧光偏振(FPA)抗体检测方法,为布鲁氏菌病(布病)的快速高效诊断提供技术手段。【方法】提纯猪种布鲁氏菌S2株脂多糖O链(OPS),经异硫氰酸荧光素(FITC)标记后作为诊断抗原。通过对样品稀释液、抗原稀释度、反应时间等条件的优化,初步建立了布鲁氏菌荧光偏振诊断方法。用该方法对148份布病阳性血清(其中牛血清70份,羊血清78份)和155份布病阴性血清(其中牛血清82份,羊血清73份)进行检测,确定其敏感性和特异性。按确定的技术参数,制备3批布鲁氏菌FPA抗体检测试剂盒,使用质控阴、阳性血清分别评价试剂盒的批内和批间重复性。用400份临床样本比较本研究开发试剂盒与商品化进口FPA试剂盒的符合率。【结果】使用0.5%蔗糖磷酸缓冲液作为血清样品稀释液;标记抗原的使用浓度为90μg/m L;最佳反应时间为3-5 min。本检测方法的判定标准为:δm P值20时为阴性,δm P值≥20时为阳性。按上述条件建立的FPA检测148份布病阳性血清和155份布病阴性血清,结果敏感性为98.6%,特异性为98.7%。对400份临床样本的比对检测显示,研究建立的FPA方法与进口商品化试剂盒的总符合率为94.0%。【结论】研究建立的布鲁氏菌PFA抗体检测方法具有良好的特异性和敏感性,可作为一种重要的布病诊断快速诊断方法。     

A sensitive fluorescence method for detection of E. Coli using rhodamine 6G dyeing

Negatively charged bacteria combined with positively charged alkaline dye rhodamine 6G (Rh6G) in NaH₂PO₄–Na₂HPO₄ buffer solution pH 7.4, by electrostatic interaction. The dyed bacteria exhibited a strong fluorescence peak at 552 nm and fluorescence intensity was directly linear to Escherichia coli (E. coli), Bacillus subtilis (B. subtilis) and Staphylococcus aureus (S. aureus) concentrations in the range of 7.06 × 10⁴ to 3.53 × 10⁷, 4.95 × 10⁵ to 2.475 × 10⁸ and 32.5 to 16250 colony forming unit/mL (cfu/mL) respectively, with detection limits of 3.2 × 10⁴ cfu/mL E. coli, 2.3 × 10⁵ cfu/mL B. subtilis and 16 cfu/mL S. aureus, respectively. Samples were cultured for 12 h, after which the linear detection range for E. coli was 2 to 88 cfu/mL. This simple, rapid and sensitive method was used for the analysis of water and drinking samples. Copyright © 2015 John Wiley & Sons, Ltd.     

New method for HPLC separation and fluorescence detection of malonaldehyde in normal human plasma

A new method for the detection of free and total malonaldehyde (MDA) in human plasma samples based on the derivatization of MDA with 9-fluorenylmethoxycarbonyl hydrazine (FMOC-hydrazine) in an acidic medium was developed. Derivatization was achieved after 4 h at 50 degrees C. The derivatized samples were analyzed by HPLC using a reversed-phase C18 column with fluorescence detection (Ex=270 nm, Em=310 nm). The benefit of this direct injection of deproteinized plasma is to avoid the use of an internal standard. The detection limit was 0.1 pmol (4.0 nmol/L). The recovery of MDA spiked in different human plasma samples was 95.3% (n=25; R.S.D. 5.1%) for the hydrolysation procedure. The total and free MDA in plasma of 15 healthy male volunteers are 426+/-29.8 nmol/L and 153+/-9.6 nmol/L, respectively.     

Near-infrared fluorescence detection permits accurate imaging of loading controls for Western blot analysis

Housekeeping proteins are typically chosen as internal loading controls for Western blot analysis because of their high, relatively constant expression. It was previously reported that antibodies against beta-actin did not reliably identify differences in sample loading, and extended antibody incubations caused a failure to discriminate differences in target protein levels. Here, beta-actin and GAPDH were evaluated as loading controls using near-infrared fluorescence. A load-dependent response in signal intensity was observed over a 250-fold range of sample concentrations, with R(2) values as high as 0.9939. Longer antibody incubations continued to detect differences in protein level and load-dependent responses became more linear.