Journal of Biological Methods (JBM)
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Concentrating white spot syndrome virus by alum for field detection using a monoclonal antibody based flow-through assay
No full textA simple and easy method of concentrating white spot syndrome virus by employing aluminium sulphate, alum as a flocculant was developed and evaluated for field detection. The concentrated virus was detected by a monoclonal antibody based flow-through assay, RapiDot and compared its performance with polymerase chain reaction. The semi-purified virus that was flocculated by 15 and 30 ppm alum in a 50 ml cylinder can be detected successfully by both RapiDot and I step PCR. In addition, alum could also flocculate the virus that is detectable by II step PCR and the concentration of virus was similar to the one observed in water from an infected pond. Furthermore, experimental infection studies validated the successful concentration of virus by alum flocculation followed by rapid detection of virus using monoclonal antibody based RapiDot. Overall, the results obtained in this study indicate that the white spot syndrome virus in water could be easily flocculated by alum for sensitive field detection by monoclonal antibody based RapiDot
A descriptive guide for absolute quantification of produced shRNA pseudotyped lentiviral particles by real-time PCR
No full textGene silencing techniques, including RNA interference methodologies, are widely used in reverse genetics to study the role of specific genes in biological processes. RNA interference has become easier to implement thanks to the RNAi Consortium (TRC), which has developed libraries of short hairpin RNA (shRNA) sequences in pseudotyped lentiviral particles capable of targeting most genes in the human and mouse genomes. However, a problem is the lack of a simple method to titrate the homemade lentiviral particle product, making it difficult to optimise and standardise shRNA experiments. Here we provide a guide describing a quick, non-laborious and reliable method for the titration of TRC pseudotyped lentiviral particles that is based on the detection and measurement of viral RNA using quantitative PCR. Our data demonstrate that purified linearised shRNA plasmids represent more suitable standards than circular or unpurified linearised plasmids. We also show that for precise absolute quantification, it is important to determine suitable plasmid and viral cDNA concentrations in order to find the linear range for quantification, as well as to reduce inhibition and primer dimer amplification. Finally, we show that the lentivirus concentration impacts the level of knockdown in transduced cells. Primers utilised in this non-functional titration can potentially be applied to functional titration of proviral DNA copies or transgene expression, overcoming problems arising from the absence of fluorescent reporter genes in TRC plasmids
Establishment of a Drosophila AD model
No full textAlzheimer’s Disease (AD) is the most common form of dementia that affects people’s health greatly. Though amyloid precursor protein (APP) has been implicated in the pathogenesis of AD, the exact role of APP and its underlying mechanism in AD progression have remained largely elusive. Drosophila melanogaster has been extensively used as a model organism to study a wide range of human diseases including AD. In this protocol, we expressed full length human APP in the Drosophila nervous system and examined its effect on locomotion and choice ability. We found that expression of APP produced locomotion defects in larvae as measured by plate crawling ability assay (PCA), and in adult flies as monitored by plate cycling ability assay (CLA). In addition, expression of APP results in male courtship choice (MCC) defect, since wild-type males court preferentially toward young virgin females over old ones, while APP-expressing males failed to show this preference. This protocol enables us to screen for novel AD candidate genes as well as therapeutic compounds to ameliorate the disease
Method for selective quantification of adipose-derived stromal/stem cells in tissue
No full textFat grafts are valuable for soft-tissue regeneration and augmentation. However, fat graft systems require further improvement for the prediction of graft retention. The concentration of adipose-derived stromal/stem cells (ASCs) is one of the most important factors that affect graft retention; however, current cell quantification techniques have not been applied to adipose tissue. Here we developed a method for the selective quantification of ASCs in tissue (SQAT). We identified a characteristic methylated site in the CD31 promoter after searching for specific markers of ASCs. This DNA methylation was not detected in any cell type other than ASCs in adipose tissue. Therefore, analyzing this methylation may be a suitable approach for quantifying ASCs in tissues because DNA is readily extracted from tissues. SQAT is based on quantifying this methylation by qPCR using methylation-sensitive HapII-treated DNA as the template. SQAT was validated based on the numbers of ASCs determined by CD31−/CD34+-based flow cytometry. The results obtained by both methods were perfectly correlated, thereby demonstrating that SQAT is a useful tool for quantifying ASCs. SQAT analysis using ASCs isolated from suctioned fat according to the standard protocol (i.e., collagenase treatment) showed that the yield of ASCs was 59% ± 21%, which suggests that the ASC isolation technique requires further improvement. Furthermore, SQAT is an excellent method for quantifying ASCs in arbitrary samples (particularly tissue), which could dramatically improve ASC isolation technologies and fat graft systems, thereby facilitating the prediction of graft retention
Serum proteins are extracted along with monolayer cells in plasticware and interfere with protein analysis
No full textWashing and lysing monolayer cells directly from cell culture plasticware is a commonly used method for protein extraction. We found that multiple protein bands were enriched in samples with low cell numbers from the 6-well plate cultures. These proteins contributed to the overestimation of cell proteins and led to the uneven protein loading in Western blotting analysis. In Coomassie blue stained SDS-PAGE gels, the main enriched protein band is about 69 kDa and it makes up 13.6% of total protein from 104 U251n cells. Analyzed by mass spectrometry, we identified two of the enriched proteins: bovine serum albumin and bovine serum transferrin. We further observed that serum proteins could be extracted from other cell culture plates, dishes and flasks even after washing the cells 3 times with PBS. A total of 2.3 mg of protein was collected from a single well of the 6-well plate. A trace amount of the protein band was still visible after washing the cells 5 times with PBS. Thus, serum proteins should be considered if extracting proteins from plasticware, especially for samples with low cell numbers.
CellTrace™ Far Red & CellTracker™ Deep Red
No full textLong term monitoring of live cells in vitro or in vivo presents considerable challenges. Fluorescent tracers are used as one of the most common methods. However, fluorescent molecules usually are limited by cytotoxicity and/or lack of persistence within live cells over sufficient time periods. In this study, we evaluated our newly developed cell tracing/tracking reagents, CellTrac Far Red and CellTracker Deep Red, as novel red laser-excitable fluorescent dyes for flow cytometry and live cell imaging applications. These dyes cross the plasma membrane and covalently bind proteins inside cells, where the stable, well-retained fluorescent label offers a consistent, reliable fluorescent signal without affecting morphology or physiology and also exhibiting low cellular toxicity. CellTrace Far Red was demonstrated to be an excellent probe for cellular proliferation studies using flow cytometry, allowing measurement of up to eight generations of proliferating cells. CellTracker Deep Red was shown to be an excellent reagent for the study of cell movement, location and morphology by labeling and imaging live-cells with fluorescence microscopy. In addition, CellTracker Deep Red has excellent cell retention characteristics with bright fluorescence intensity even after 72 hours of cell staining, with signal retained after fixation, and can be multiplexed with other fluorescent dyes
CRISPR Explorer: A fast and intuitive tool for designing guide RNA for genome editing
No full textThe RNA-guided CRISPR-Cas9 (clustered, regularly interspaced, short palindromic repeat-CRISPR-associated 9) system has become a revolutionary technology for targeted genome engineering. The critical step of this technology requires the design of a highly specific and efficient guide RNA (gRNA) that will guide the Cas9 nuclease to the complementary DNA target sequence. CRISPR-Explorer is a new and user-friendly web server for selecting optimal CRISPR sites. It implements the latest scoring schemes of gRNA specificity and efficiency based on published empirical studies. The gRNA design results are generated instantly, thus removing wait times. The user can visualize the high-quality gRNAs with detailed design information through an interactive genome browser. Furthermore, the user can define and specify the parameters for gRNA selection in the Batch Design mode, which recognizes various input formats. CRISPR Explorer is freely accessible at: http://crisprexplorer.org
Development of a method for DNA extraction from oil palm leaves and the effects of pH and ionic strength on nucleic acid quantification
No full textOil palm (Elaeis guineensis Jacq.) has benefited little from molecular marker technologies although the long generation time and the unpredictable variations due to allogamy make it a high priority for improving breeding efficiency. Progress would require an efficient, low cost and high-throughput deoxyribonucleic acid (DNA) extraction method adapted for oil palm. A method for genomic DNA extraction from oil palm leaves that is simple and cost-effective was developed without the use of liquid nitrogen. A260/280 ratios between 1.987 and 2.078 were obtained. Furthermore, we could demonstrate that nucleic acid concentration and yield were inversely proportional to the pH and ionic strength of the solvent. The measured values varied significantly between 572 ng/µl and 496 ng/µl. DNA extracted with this method is stable and can be reproducibly amplified by PCR
Application of linker technique to trap transiently interacting protein complexes for structural studies
No full textProtein-protein interactions are key events controlling several biological processes. We have developed and employed a method to trap transiently interacting protein complexes for structural studies using Gly-rich linkers to fuse interacting partners, one of which is unstructured. Initial steps involve isothermal titration calorimetry to identify the minimum binding region of the unstructured protein in its interaction with its stable binding partner. This is followed by computational analysis to identify the approximate site of the interaction and to design an appropriate linker length. Subsequently, fused constructs are generated and characterized using size exclusion chromatography and dynamic light scattering experiments. The structure of the chimeric protein is then solved by crystallization, and validated both in vitro and in vivo by substituting key interacting residues of the full length, unlinked proteins with alanine. This protocol offers the opportunity to study crucial and currently unattainable transient protein interactions involved in various biological processe
Performance of pyrosequencing versus MALDI-TOF MS in bacteria identification in chronic lung disease
No full textRapid identification of the etiological agent in bacterial infection is necessary for correct diagnosis and appropriate therapy. In general, identification of pure cultures of bacteria using conventional phenotyping techniques requires 4-24 hours. Recently available new molecular technologies offer the potential of same day species identification once pure culture is available. Our aim was to evaluate the performance of rDNA V1 hypervariable region pyrosequencing, and the whole cell MALDI-TOF MS protein profiling in routine species identification. During the period from June 2012 to June 2014, 1.140 pure culture isolates were recovered from 402 samples from 126 patients suffering cystic fibrosis, chronic obstructive pulmonary disease or bronchiectasis. All the isolates were subjected to species identification by both techniques. Unfortunately, pyrosequencing was able to reach the species level in 43.2% of isolates only, whereas MALDI-TOF was clearly superior with 96.8% respectively. The overall sensitivity values also clearly underlined the superiority of MALDI-TOF MS with 96.8% compared to 85.1% achieved by pyrosequencing. Generally, MALDI-TOF MS turned out to be the best suitable technique in routine bacterial identification, whereas pyrosequencing could be recommended as the method of choice particularly in situations where MALDI-TOF MS fails to identify rare species