茎环法RT-qPCR定量检测细胞抗猪瘟病毒siRNA的表达

RNAi(RNA interference)已成为特异抗病毒治疗研究的热点,但siRNA(small interfering RNA)的定量检测仍是评价RNAi抗病毒效果的瓶颈。为了检测抗CSFV特异siRNA分子(siN1和siN2)在细胞中的表达水平,设计并以交叉组合方法筛选了具有较高特异性和灵敏度的siRNA特异茎环引物(SLP-N1-6和SLP-N2-8),成功地建立了最优的siN1和siN2的茎环法RT-qPCR检测方法。该方法表现出良好的特异性和较高的灵敏度,能检测出102至108个拷贝的siRNA,至少可达7个数量级的检测范围,平行性好(Rsq=0.999),扩增效率高(Eff.=98.2%)。茎环法RT-qPCR能准确地定量检测抗CSFV的PK-15细胞克隆的siN1/siN2表达水平,可结合常规的检测病毒水平的间接免疫荧光和TCID50等技术定量评价RNAi抗CSFV的有效性,为未来抗猪瘟转基因猪的抗病毒效果评价提供了先进的检测技术。     

Evaluating online sampling probes for substrate concentration and protein production by a Design of Experiments screening approach

A polypropylene sampling probe and ceramic sampling probe were tested for the online measurement of substrate and protein concentrations in fed batch cultivations of a recombinant Pichia pastoris strain overexpressing the enzyme HRP. Although small substrate molecules could be determined precisely under process conditions, online and offline data for enzyme activity and protein content showed offsets for both sampling probes. An easy‐to‐do multivariate Design of Experiments (DoE) screening approach revealed the limitations for both sampling probes. Online and offline determined data for enzymatic activity were fitted to a suitable exponential equation. A direct correlation of these equations showed a linear relation between online and offline data for the polypropylene probe and a quadratic relation for the ceramic probe. Using the resulting formulas, observed offsets could be compensated for by mathematical transformation, which consequently could allow the use of online calculator tools to determine the enzymatic activity and the protein content in quasi real‐time. This study demonstrates the usefulness of a DoE approach to evaluate online sampling probes in a short time and introduces a strategy to obtain data with two different online sampling probes also for large target molecules despite observed offsets.     

A quick and simple FISH protocol with hybridization-sensitive fluorescent linear oligodeoxynucleotide probes

Fluorescence in situ hybridization (FISH) is a powerful tool used in karyotyping, cytogenotyping, cancer diagnosis, species specification, and gene-expression analysis. Although widely used, conventional FISH protocols are cumbersome and time consuming. We have now developed a FISH method using exciton-controlled hybridization-sensitive fluorescent oligodeoxynucleotide (ECHO) probes. ECHO-FISH uses a 25-min protocol from fixation to mounting that includes no stringency washing steps. We use ECHO-FISH to detect both specific DNA and RNA sequences with multicolor probes. ECHO-FISH is highly reproducible, stringent, and compatible with other fluorescent cellular labeling techniques. The resolution allows detection of intranuclear speckles of poly(A) RNA in HeLa cells and dissociated hippocampal primary cultures, and mRNAs in the distal dendrites of hippocampal neurons. We also demonstrate detection of telomeric and centromeric DNA on metaphase mouse chromosomes. The simplicity of the ECHO-FISH method will likely accelerate cytogenetic and gene-expression analysis with high resolution.     

Development of a new CARD-FISH protocol for quantification of Legionella pneumophila and its application in two hospital cooling towers

Aims: Open cooling towers are frequent sources of infections with Legionella pneumophila. The gold standard for the detection of Leg. pneumophila is based on cultivation lasting up to 10 days and detecting only culturable cells. Alternative fluorescence in situ hybridization (FISH) protocols have been proposed, but they result in faint fluorescence signals and lack specificity because of cross‐hybridization with other Legionella species. Our aim was thus to develop a new FISH protocol for rapid and specific detection of Leg. pneumophila in water samples. Methods and Results: A novel catalysed reporter deposition FISH (CARD‐FISH) protocol for the detection of Leg. pneumophila was developed, which significantly enhanced signal intensity as well as specificity of the probe through the use of a novel competitor probe. The developed protocol was compared with the culture method for monitoring the seasonal development of culturable and nonculturable Leg. pneumophila in two hospital cooling tower systems. Seasonal fluctuations of Leg. pneumophila concentrations detected via CARD‐FISH were related to the development of the total bacterial community in both cooling towers, with temperature and biocide as the main factors controlling this development. Conclusions: Our results clearly showed that the majority of the Leg. pneumophila cells were in a nonculturable state. Thus, detection of Leg. pneumophila with culture methods may underestimate the total numbers of Leg. pneumophila present. Significance and Impact of the Study: Rapid, sensitive and specific detection and quantification of Leg. pneumophila in water systems is prerequisite for reliable risk estimation. The new protocol significantly improves current methodology and can be used to monitor and screen for Leg. pneumophila concentrations in cooling towers or other water systems.     

Raman spectroscopy as a method to replace off-line pH during mammalian cell culture processes

Raman spectroscopy is a robust, well-established tool utilized for measuring important cell culture process variables for example, feed, metabolites, and biomass in real-time. This study further expands the functionality of in-line Raman spectroscopy coupled with partial least squares (PLS) regression modelling to develop a pH measurement tool. Cell line specific models were developed to enhance the robustness for processes with different pH setpoints, deadbands, and cellular metabolism. The modelling strategy further improved robustness by reducing the temporal complexity of pH shifts by splitting data sets into two time zones reflective of major changes in pH. In addition, models were developed to assess if lactate and partial pressure of carbon dioxide (pCO₂) could be used in a PLS model for pH. Splitting the data sets into early and late for the process resulted in errors of 0.035 pH and 0.034 pH for the two respective Raman cell lines models which was within acceptance criteria. The lactate and pCO₂ PLS model with values provided by Raman models had a further 0.001 pH error reduction. This study illustrates the potential to eliminate off-line samples to correct for in-line measurements of pH and further illustrates the capabilities of Raman to measure additional process variables.     

Hydrophobic core of molten-globule state of bovine carbonic anhydrase B

The interaction which stabilizes the intermediate state of the protein folding and/or unfolding is important for understanding the structure formation mechanism of proteins. The partitioning of a hydrophobic fluorescence probe, pyrene, into the core of a ‘molten globule’ structure of bovine carbonic anhydrase B was measured, revealing a partition coefficient of about 10⁴. The result leads to the conclusion that the compact structure of the molten-globule state is formed by the hydrophobic interaction, as detergent micelles are formed by the same interaction.     

Isolation of (S)-2,3-dichloro-1-propanol assimilating bacterium,its characterization,and its use in preparation of (R)-2,3-dichloro-1-propanol and (S)-epichlorohydrin

Summary Linear alkylbenzene sulfonate (LAS) is a widely used anionic surfactant. Although approximately 1 million metric tons of LAS are produced annually, relatively little is known about the bacteria or the genetic factors that control LAS degradation in the environment. The objectives of this research were to: i) compare bacterial populations in wastewater and pristine pond systems; ii) determine the frequency of plasmids in bacteria from these sites; and iii) compare the frequency of DNA sequences coding for aromatic catabolism in isolates from these two sites. Plate counts indicated that exposure to wastewater resulted in higher levels of both heterotrophic bacteria and bacteria capable of growing on LAS containing medium (LAS/YEPG). In addition to higher numbers, a higher proportion of heterotrophs from the wastewater system were capable of growth on LAS/YEPG medium. Thus, the high levels of LAS in the wastewater system apparently selected fro organisms that were able to tolerate and/or degrade, it. Mineralization of¹⁴C-ring labelled LAS in any habitat related to the presence of organisms that grew on LAS/YEPG. Although may of these isolates could carry out primary degradation, no isolate, could mineralize¹⁴C-ring LAS in pure culture. A higher incidence of plasmids was found in bacteria from the wastewater pond and among bacteria that grew on LAS containing medium. However, the presence of plasmid, DNA did not necessarily confer the ability to degrade LAS nor was the ability to degrade LAS dependent on the presence of a plasmid. The incidence of selected genotypes for aromatic catabolism was similar among isolates on LAS/YEPG at both sites, suggesting that LAS ring degradation may be present in other populations or encoded by alternative sequences. In conclusion, LAS mineralization is mediated by a consortium and the evidence that initial attack of LAS is plasmid mediated is inconclusive.     

Oligonucleotide fingerprinting and RAPD analysis of Achillea species: Characterization and long-term monitoring of micropropagated clones

Two different DNA fingerprinting techniques were applied to a set of Achillea samples (Asteraceae), comprising ten taxa of the medicinally important A. millefolium group and six related species. Field-grown as well as in vitro-micropropagated plants were individually screened for abundance and polymorphism of target sequences recognized by oligonucleotide fingerprinting with 13 different microsatellite-complementary probes. While most probes revealed a high level of intra- and interspecific variability, fingerprints proved to be somatically stable in vegetatively propagated plant material. Analysis of the same samples by polymerase chain reaction with arbitrary 10-mer primers yielded less polymorphic patterns. Because of its higher discriminatory ability, oligonucleotide fingerprinting offers itself as the method of choice for the identification and discrimination of A. asplenifolia and A. roseoalba clones, as well as for monitoring their stability during micropropagation.Abbreviations BPA N-benzyl-9-[2-tetrahydropyranyl]-adenine - PCR polymerase chain reaction - RAPD random amplified polymorphic DNA - RFLP restriction fragment length polymorphism - TAE buffer 40 mM Tris acetate, 20 mM sodium acetate, 1 mM EDTA, pH 7.8 Part of the Ph.D. Thesis     

A fast‐responsive fluorescent probe for sulfite and its bioimaging

A turn‐on fluorescent probe Coumarin‐SO2 based on a nucleophilic addition reaction was developed for the rapid detection of SO₃^2– in aqueous media. The probe Coumarin‐SO2 displays excellent water solubility, fast response, highly sensitivity and highly selectivity over other biological related species. More importantly, living cell imaging experiments indicate the feasibility of using the probe for the detection of SO₃^2– in biological systems. Copyright © 2015 John Wiley & Sons, Ltd.