Showing papers in "BioTechniques in 2012"
TL;DR: For amplification of ancient DNA, it is found that some commonly used polymerases strongly bias against amplification of endogenous DNA in favor of GC-rich microbial contamination, in this case reducing the fraction of endogenous sequences to almost half.
Abstract: High-throughput sequencing technologies frequently necessitate the use of PCR for sequencing library amplification. PCR is a sometimes enigmatic process and is known to introduce biases. Here we perform a simple amplification-sequencing assay using 10 commercially available polymerase-buffer systems to amplify libraries prepared from both modern and ancient DNA. We compare the performance of the polymerases with respect to a previously uncharacterized template length bias, as well as GC-content bias, and find that simply avoiding certain polymerase can dramatically decrease the occurrence of both. For amplification of ancient DNA, we found that some commonly used polymerases strongly bias against amplification of endogenous DNA in favor of GC-rich microbial contamination, in our case reducing the fraction of endogenous sequences to almost half.
295 citations
TL;DR: Current BiFC technology is reviewed, focusing on the development and improvement of BiFC systems, the understanding of split sites in fluorescent proteins, and enhancements in the signal-to-noise ratio.
Abstract: Over the past decade, bimolecular fluorescence complementation (BiFC) has emerged as a key technique to visualize protein-protein interactions in a variety of model organisms. The BiFC assay is based on reconstitution of an intact fluorescent protein when two complementary non-fluorescent fragments are brought together by a pair of interacting proteins. While the originally reported BiFC method has enabled the study of many protein-protein interactions, increasing demands to visualize protein-protein interactions under various physiological conditions have not only prompted a series of recent BiFC technology improvements, but also stimulated interest in developing completely new approaches. Here we review current BiFC technology, focusing on the development and improvement of BiFC systems, the understanding of split sites in fluorescent proteins, and enhancements in the signal-to-noise ratio. In addition, we provide perspectives on possible future improvements of the technique.
240 citations
TL;DR: Standard LAMP primers are adapted to contain a quencher-fluorophore duplex region that upon strand separation results in a gain of fluorescent signal, allowing the real-time detection of 1-4 target sequences in a single LAMP reaction tube utilizing a standard real- time fluorimeter.
Abstract: Loop-mediated isothermal amplification (LAMP) is a rapid and reliable sequence-specific isothermal nucleic acid amplification technique. To date, all reported real-time detection methods for LAMP h...
234 citations
TL;DR: A novel enabling methodology to enable the isolation and study of osteocytes from skeletally mature young and old mice should prove useful in advancing the understanding of the roles mature osteocytes play in bone health and disease.
Abstract: The purpose of this work was to establish a methodology to enable the isolation and study of osteocytes from skeletally mature young (4-month-old) and old (22-month-old) mice. The location of osteocytes deep within bone is ideal for their function as mechanosensors. However, this location makes the observation and study of osteocytes in vivo technically difficult. Osteocytes were isolated from murine long bones through a process of extended collagenase digestions combined with EDTA-based decalcification. A tissue homogenizer was used to reduce the remaining bone fragments to a suspension of bone particles, which were placed in culture to yield an outgrowth of osteocyte-like cells. All of the cells obtained from this outgrowth that displayed an osteocyte-like morphology stained positive for the osteocyte marker E11/GP38. The osteocyte phenotype was further confirmed by a lack of staining for alkaline phosphatase and the absence of collagen1a1 expression. The outgrowth of osteocytes also expressed additional osteocyte-specific genes such as Sost and Mepe. This technique facilitates the isolation of osteocytes from skeletally mature bone. This novel enabling methodology should prove useful in advancing our understanding of the roles mature osteocytes play in bone health and disease.
180 citations
TL;DR: A novel recombination-based cloning strategy called 2in1 that enables co-expression of fusion proteins on a cell-by-cell basis from a single plasmid, and significantly increases the credibility of protein-protein interaction results allowing ratiometric comparison between different protein pairs.
Abstract: Gene expression and binary interaction techniques are vital tools that shape our understanding of protein complexes. An inherent flaw, however, with most current protein-protein interaction techniques is the variability in expression levels for fusion proteins when using several individual plasmids. Here, we describe a novel recombination-based cloning strategy called 2in1 that enables co-expression of fusion proteins on a cell-by-cell basis from a single plasmid. We demonstrate the utility of 2in1 through the development of a ratiometric bimolecular fluorescence complementation assay (rBiFC), in which both candidate genes are simultaneously cloned into a single vector backbone containing an internal fluorescent marker for expression control and ratiometric analysis. rBiFC significantly increases the credibility of protein-protein interaction results allowing ratiometric comparison between different protein pairs. In addition to its use in rBiFC, 2in1 can be introduced easily into other vector systems that rely on multiple gene expression and prove feasible in future synthetic biological approaches.
166 citations
TL;DR: This work presents a novel "small-intelligent" strategy to construct mutagenesis libraries that have a minimal gene library size without inherent amino acid biases, stop codons, or rare codons of Escherichia coli by coupling well-designed combinatorial degenerate primers with suitable PCR-basedmutagenesis methods.
Abstract: Site-saturation mutagenesis is a powerful tool for protein optimization due to its efficiency and simplicity. A degenerate codon NNN or NNS (K) is often used to encode the 20 standard amino acids, but this will produce redundant codons and cause uneven distribution of amino acids in the constructed library. Here we present a novel "small-intelligent" strategy to construct mutagenesis libraries that have a minimal gene library size without inherent amino acid biases, stop codons, or rare codons of Escherichia coli by coupling well-designed combinatorial degenerate primers with suitable PCR-based mutagenesis methods. The designed primer mixture contains exactly one codon per amino acid and thus allows the construction of small-intelligent mutagenesis libraries with one gene per protein. In addition, the software tool DC-Analyzer was developed to assist in primer design according to the user-defined randomization scheme for library construction. This small-intelligent strategy was successfully applied to the randomization of halohydrin dehalogenases with one or two randomized sites. With the help of DC-Analyzer, the strategy was proven to be as simple as NNS randomization and could serve as a general tool to efficiently randomize target genes at positions of interest.
145 citations
TL;DR: This is the first successful prokaryote-based CFPS reaction to be carried out with extract prepared by sonication or bead vortex mixing, and it is reported that high-yielding E. coli-based extract was prepared using equipment requiring a reduced capital investment and common to biotechnology laboratories.
Abstract: Escherichia coli-based cell extract is a vital component of inexpensive and high-yielding cell-free protein synthesis reactions However, effective preparation of E coli cell extract is limited to high-pressure (French press-style or impinge-style) or bead mill homogenizers, which all require a significant capital investment Here we report the viability of E coli cell extract prepared using equipment that is both common to biotechnology laboratories and able to process small volume samples Specifically, we assessed the low-capital-cost lysis techniques of: (i) sonication, (ii) bead vortex mixing, (iii) freeze-thaw cycling, and (iv) lysozyme incubation to prepare E coli cell extract for cell-free protein synthesis (CFPS) We also used simple shake flask fermentations with a commercially available E coli strain In addition, RNA polymerase was overexpressed in the E coli cells prior to lysis, thus eliminating the need to add independently purified RNA polymerase to the CFPS reaction As a result, high-yielding E coli-based extract was prepared using equipment requiring a reduced capital investment and common to biotechnology laboratories To our knowledge, this is the first successful prokaryote-based CFPS reaction to be carried out with extract prepared by sonication or bead vortex mixing
103 citations
TL;DR: This study is the first to report a successful genetic transformation of diatom by electroporation in an economical and efficient manner and provides a tightly regulated inducible gene expression system for diatom.
Abstract: Diatoms are important primary producers in the marine ecosystem. Currently it is difficult to genetically transform diatoms due to the technical limitations of existing methods. The promoter/terminator of the nitrate reductase gene of the model diatom Phaeodactylum tricornutum was cloned and used to drive chloramphenicol acetyltransferase (CAT) reporter gene expression. The construct was transferred by electroporation into P. tricornutum grown in medium lacking silicon. CAT expression was induced in transformed diatoms in the presence of nitrate, enabling growth in selective medium, and was repressed when ammonium was the only nitrogen source. Expression of CAT transcript and protein were demonstrated by RT-PCR and Western blot analysis, respectively. Our study is the first to report a successful genetic transformation of diatom by electroporation in an economical and efficient manner and provides a tightly regulated inducible gene expression system for diatom.
89 citations
TL;DR: A systematic method to perform high-throughput genotyping analysis of the Combined DNA Index System (CODIS) STR loci using short-read (150 bp) massively parallel sequencing technology is presented.
Abstract: DNA-based methods for human identification principally rely upon genotyping of short tandem repeat (STR) loci. Electrophoretic-based techniques for variable-length classification of STRs are universally utilized, but are limited in that they have relatively low throughput and do not yield nucleotide sequence information. High-throughput sequencing technology may provide a more powerful instrument for human identification, but is not currently validated for forensic casework. Here, we present a systematic method to perform high-throughput genotyping analysis of the Combined DNA Index System (CODIS) STR loci using short-read (150 bp) massively parallel sequencing technology. Open source reference alignment tools were optimized to evaluate PCR-amplified STR loci using a custom designed STR genome reference. Evaluation of this approach demonstrated that the 13 CODIS STR loci and amelogenin (AMEL) locus could be accurately called from individual and mixture samples. Sensitivity analysis showed that as few as 18,500 reads, aligned to an in silico referenced genome, were required to genotype an individual (>99% confidence) for the CODIS loci. The power of this technology was further demonstrated by identification of variant alleles containing single nucleotide polymorphisms (SNPs) and the development of quantitative measurements (reads) for resolving mixed samples.
87 citations
TL;DR: An approach for focused gallium-ion beam scanning electron microscopy with energy filtered detection of backscattered electrons to create near isometric voxels for high-resolution whole cell visualization allowed us to create three-dimensional volumes of high-pressure frozen, freeze-substituted Saccharomyces cerevisiae yeast cells with pixel resolutions down to 3 nm/pixel in x, y, and z.
Abstract: We developed an approach for focused gallium-ion beam scanning electron microscopy with energy filtered detection of backscattered electrons to create near isometric voxels for high-resolution whole cell visualization. Specifically, this method allowed us to create three-dimensional volumes of high-pressure frozen, freeze-substituted Saccharomyces cerevisiae yeast cells with pixel resolutions down to 3 nm/pixel in x, y, and z, supported by both empirical data and Monte Carlo simulations. As a result, we were able to segment and quantify data sets of numerous targeted subcellular structures/organelles at high-resolution, including the volume, volume percentage, and surface area of the endoplasmic reticulum, cell wall, vacuoles, and mitochondria from an entire cell. Sites of mitochondrial and endoplasmic reticulum interconnectivity were readily identified in rendered data sets. The ability to visualize, segment, and quantify entire eukaryotic cells at high-resolution (potentially sub-5 nanometers isotropic voxels) will provide new perspectives and insights of the inner workings of cells.
76 citations
TL;DR: The 10-fold increase in cell yield enables cell-specific transcriptome analysis by protocols such as nanoCAGE and RNA seq, and enables cell of pure populations of neurons from mature postnatal mouse brain to be isolated using fluorescence activated cell sorting.
Abstract: Efficient isolation of specific, intact, living neurons from the adult brain is problematic due to the complex nature of the extracellular matrix consolidating the neuronal network. Here, we present significant improvements to the protocol for isolation of pure populations of neurons from mature postnatal mouse brain using fluorescence activated cell sorting (FACS). The 10-fold increase in cell yield enables cell-specific transcriptome analysis by protocols such as nanoCAGE and RNA seq.
TL;DR: It is found that miR-221 levels are prognostic in breast cancer illustrating the high-throughput method and confirming that miRNAs can be valuable biomarkers in cancer.
Abstract: MicroRNAs (miRNAs) have emerged as key regulators in the pathogenesis of cancers where they can act as either oncogenes or tumor suppressors. Most miRNA measurement methods require total RNA extracts which lack critical spatial information and present challenges for standardization. We have developed and validated a method for the quantitative analysis of miRNA expression by in situ hybridization (ISH) allowing for the direct assessment of tumor epithelial expression of miRNAs. This co-localization based approach (called qISH) utilizes DAPI and cytokeratin immunofluorescence to establish subcellular compartments in the tumor epithelia, then multiplexed with the miRNA ISH, allows for quantitative measurement of miRNA expression within these compartments. We use this approach to assess miR-21, miR-92a, miR-34a, and miR-221 expression in 473 breast cancer specimens on tissue microarrays. We found that miR-221 levels are prognostic in breast cancer illustrating the high-throughput method and confirming that miRNAs can be valuable biomarkers in cancer. Furthermore, in applying this method we found that the inverse relationship between miRNAs and proposed target proteins is difficult to discern in large population cohorts. Our method demonstrates an approach for large cohort, tissue microarray-based assessment of miRNA expression.
TL;DR: An efficient and reliable procedure for the capture of affinity-tagged proteins and associated complexes from human cell lines is reported, and isolations of triple-FLAG and GFP- Tagged fusion proteins involved in RNA metabolism are presented.
Abstract: An efficient and reliable procedure for the capture of affinity-tagged proteins and associated complexes from human cell lines is reported. Through multiple optimizations, high yield and low background affinity-purifications are achieved from modest quantities of human cells expressing endogenous-level tagged proteins. Isolations of triple-FLAG and GFP-tagged fusion proteins involved in RNA metabolism are presented.
TL;DR: A sequencing method on the Pacific Biosciences RS sequencer for small DNA molecules that avoids the need for a standard library preparation is developed, offering a significant advantage over current protocols which typically require 400-500 ng of sheared DNA for the library preparation.
Abstract: We have developed a sequencing method on the Pacific Biosciences RS sequencer (the PacBio) for small DNA molecules that avoids the need for a standard library preparation. To date this approach has been applied toward sequencing single-stranded and double-stranded viral genomes, bacterial plasmids, plasmid vector models for DNA-modification analysis, and linear DNA fragments covering an entire bacterial genome. Using direct sequencing it is possible to generate sequence data from as little as 1 ng of DNA, offering a significant advantage over current protocols which typically require 400–500 ng of sheared DNA for the library preparation.
TL;DR: In vivo and in vitro BiFC assays using the newly identified pair of Venus fragments will serve as a useful tool for measuring protein- protein interactions with high specificity and low background fluorescence and could be applied to the screening of inhibitors that block protein-protein interactions.
Abstract: The bimolecular fluorescence complementation (BiFC) assay is a method for visualizing protein-protein interactions in living cells. To visualize the cofilin-actin interaction in living cells, a series of combinations of the N- and C-terminal fragments of Venus fused upstream or downstream of cofilin and actin were screened systematically. A new pair of split Venus fragments, Venus (1-210) fused upstream of cofilin and Venus (210-238) fused downstream of actin, was the most effective combination for visualizing the specific interaction between cofilin and actin in living cells. This pair of Venus fragments was also effective for detecting the active Ras-dependent interaction between H-Ras and Raf1 and the Ca(2+)-dependent interaction between calmodulin and its target M13 peptide. In vitro BiFC assays using the pair of purified BiFC probes provided the means to detect the specific interactions between cofilin and actin and between H-Ras and Raf1. In vivo and in vitro BiFC assays using the newly identified pair of Venus fragments will serve as a useful tool for measuring protein-protein interactions with high specificity and low background fluorescence and could be applied to the screening of inhibitors that block protein-protein interactions.
TL;DR: A simple modification to the FTSS workflow is described that improves the limit of detection of cell-line gDNA mixtures from50%-20% to 5% for G>A transitions and from 50%-5% to5% forG>C and G>T transversions.
Abstract: Fluorescent dye terminator Sanger sequencing (FTSS), with detection by automated capillary electrophoresis (CE), has long been regarded as the gold standard for variant detection. However, software analysis and base-calling algorithms used to detect mutations were largely optimized for resequencing applications in which different alleles were expected as heterozygous mixtures of 50%. Increasingly, the requirements for variant detection are an analytic sensitivity for minor alleles of A transitions and from 50%-5% to 5% for G>C and G>T transversions. In addition, we use two different sample types to compare the limit of detection of sequence variants in codons 12 and 13 of the KRAS gene between Sanger sequencing and other methodologies including shifted termination assay (STA) detection, single-base extension (SBE), pyrosequencing (PS), high- resolution melt (HRM), and real-time PCR (qPCR).
TL;DR: A novel microscale hydroxyapatite chromatography (HAC) normalization method to remove eukaryotic and prokaryotic high abundant rRNA species, thereby increasing sequence coverage depth and transcript diversity across non-rRNA populations.
Abstract: Second-generation sequencing (SGS) has become the preferred method for RNA transcriptome profiling of organisms and single cells. However, SGS analysis of transcriptome diversity (including protein-coding transcripts and regulatory non-coding RNAs) is inefficient unless the sample of interest is first depleted of nucleic acids derived from ribosomal RNA (rRNA), which typically account for up to 95% of total intracellular RNA content. Here we describe a novel microscale hydroxyapatite chromatography (HAC) normalization method to remove eukaryotic and prokaryotic high abundant rRNA species, thereby increasing sequence coverage depth and transcript diversity across non-rRNA populations. RNA-seq analysis of Escherichia coli K-12 and human intracellular total RNA showed that HAC-based normalization enriched for all non-ribosomal RNA species regardless of RNA transcript abundance or length when compared with untreated controls. Microcolumn HAC normalization generated rRNA-depleted cDNA libraries comparable to the well-established duplex specific nuclease (DSN) normalization and Ribo-Zero rRNA-depletion methods, thus establishing microscale HAC as an effective, cost saving, and non-destructive alternative normalization technique.
TL;DR: An ensemble of mammalian protein expression vectors with CMV promoters of differing strengths are described that can combine high-transfection efficiencies with tunable protein expression levels to optimize the rescue of cellular phenotypes induced by siRNA transfection.
Abstract: Transient transfection of small interfering RNA (siRNA) provides a powerful approach for studying cellular protein functions, particularly when the target protein can be re-expressed from an exogenous siRNA-resistant construct in order to rescue the knockdown phenotype, confirm siRNA target specificity, and support mutational analyses. Rescue experiments often fail, however, when siRNA-resistant constructs are expressed at suboptimal levels. Here, we describe an ensemble of mammalian protein expression vectors with CMV promoters of differing strengths. Using CHMP2A rescue of HIV-1 budding, we show that these vectors can combine high-transfection efficiencies with tunable protein expression levels to optimize the rescue of cellular phenotypes induced by siRNA transfection.
TL;DR: This method allows the researcher to explore a large number of denaturants, at either constant or variable temperatures, within the same assay, providing estimates of denaturation kinetics that have been previously inaccessible.
Abstract: Protein stability can be monitored by many different techniques. However, these protocols are often lengthy, consume large amounts of protein, and require expensive and specialized instruments. Her...
TL;DR: It is demonstrated that it is possible to use an isolated chicken embryonic intestinal epithelium to create an organoid culture and prostaglandin E2 is as effective as R-spondin 1 and Noggin in promoting sustained growth and survival of epithelial spheroids.
Abstract: Investigating intestinal physiology in vitro remains challenging due to the lack of an effective primary enterocyte culture system. Recently developed protocols for growing organoids containing crypts and villus from adult mouse intestinal epithelium in Matrigel present an attractive alternative to the classical techniques. However, these approaches require the use of sophisticated and expensive serum-free medium supplemented with epithelial growth factor (EGF), Wnt agonist (R-spondin 1), and bone morphogenetic protein inhibitor (Noggin) in high concentrations. Here we demonstrate that is possible to use an isolated chicken embryonic intestinal epithelium to create such an organoid culture. Structures formed in Matrigel matrix in the first two days following isolation survive and enlarge during ensuing weeks. They have the appearance of empty spheres and comprise cells expressing cytokeratin (an epithelial cell marker), villin (a marker of enterocytes), and Sox-9 (a transcription factor characteristic of progenitors and stem cells of intestinal crypts). With chicken embryonic tissue as a source of organoids, prostaglandin E2 is as effective as R-spondin 1 and Noggin in promoting sustained growth and survival of epithelial spheroids.
TL;DR: It is shown that single-stranded DNA (ssDNA) is proportional to total non-red blood cell content and is a suitable RPMA normalization parameter and simple modifications to RPMA processing allow flexibility in using ssDNA-or protein-based normalization molecules.
Abstract: Reverse phase protein microarrays (RPMA) are designed for quantitative, multiplexed analysis of proteins, and their posttranslational modified forms, from a limited amount of sample. To correct for sample to sample variability due to the number of cells in each lysate and the presence of extracellular proteins or red blood cells, a normalization method is required that is independent of these potentially confounding parameters. We adopted a gene microarray algorithm for use with RPMA to optimize the proteomic data normalization process and developed a systematic approach to RPMA processing and analysis, tailored to the study set. Our approach capitalizes on the gene microarray algorithms geNorm and NormFinder to identify the normalization parameter with the lowest variability across a proteomic sample set. Seven analytes (ssDNA, glyceraldehyde 3-phosphate dehydrogenase, α/β-tubulin, mitochondrial ribosomal protein L11, ribosomal protein L13a, β-actin, and total protein) were compared across sample sets including cell lines, tissues subjected to laser capture microdissection, and blood-contaminated tissues. We examined normalization parameters to correct for red blood cell content. We show that single-stranded DNA (ssDNA) is proportional to total non-red blood cell content and is a suitable RPMA normalization parameter. Simple modifications to RPMA processing allow flexibility in using ssDNA-or protein-based normalization molecules.
TL;DR: A genome improvement pipeline is developed after decreasing a loading bias against larger PCR products in the PacBio process that is not only cost-effective but also can close gaps greater than 2.5 kb in a single round of reactions, and sequence through high GC regions as well as difficult secondary structures such as small hairpin loops.
Abstract: Advances in sequencing technologies have dramatically reduced costs in producing high-quality draft genomes. However, there are still many contigs and possible misassembled regions in those draft genomes. Improving the quality of these genomes requires an efficient and economical means to close gaps and resequence some regions. Sequencing pooled gap region PCR products with Pacific Biosciences (PacBio) provides a significantly less expensive means for this need. We have developed a genome improvement pipeline with this strategy after decreasing a loading bias against larger PCR products in the PacBio process. Compared with Sanger technology, this approach is not only cost-effective but also can close gaps greater than 2.5 kb in a single round of reactions, and sequence through high GC regions as well as difficult secondary structures such as small hairpin loops.
TL;DR: Coupling egg white coatings with commercially available transfection reagents leads to high transfections efficiency with suspension cell lines including canine mastocytoma C2 and the human myeloid cell line HL-60.
Abstract: Transfection of suspension cells has proven to be very difficult using conventional methods. Here, we present a simple and time-saving new transfection protocol wherein cell culture plates coated with chicken egg white are seeded with suspension cells prior to transfection. Our results demonstrate that coupling egg white coatings with commercially available transfection reagents leads to high transfection efficiency with suspension cell lines including canine mastocytoma C2 and the human myeloid cell line HL-60. This new approach, which should prove applicable to a wide range of cell lines, solves a crucial problem for researchers working with suspension cells.
TL;DR: A eukaryotic cell-free system based on Spodoptera frugiperda cells was developed for the convenient synthesis of Fab antibody fragments and other disulfide bridge containing proteins, compatible with PCR-generated linear templates enabling automated generation of antibody fragments in a high-throughput manner.
Abstract: A eukaryotic cell-free system based on Spodoptera frugiperda cells was developed for the convenient synthesis of Fab antibody fragments and other disulfide bridge containing proteins. The system uses (i) a cell lysate that is mildly prepared under slightly reduced conditions, thus maintaining the activity of vesicles derived from the endoplasmic reticulum, (ii) signal peptide dependent translocation into these vesicles, and (iii) a redox potential based on reduced and oxidized glutathione. Monomeric heavy and light immunoglobulin chains are almost completely converted to highly active dimeric Fab joined by intermolecular disulfide bridges without supplementation of chaperones or protein disulfide isomerase. The applicability of the system is demonstrated by the synthesis of anti-lysozyme and anti-CD4 Fab antibody fragments yielding approximately 10 µg Fab per milliliter reaction mixture. The lack of endotoxins in this system is a prerequisite that synthesized Fab can be applied directly using whole synthesis reactions in cell-based assays that are sensitive to this substance class. Moreover, the system is compatible with PCR-generated linear templates enabling automated generation of antibody fragments in a high-throughput manner, and facilitating its application for screening and validation purposes.
TL;DR: A method for growing fibroblasts from human skin explants that increases the number of cells obtained by up to two orders of magnitude, thus increasing the amount of material available for research and diagnostic purposes and potentially for cell-based therapies.
Abstract: Here we describe a method for growing fibroblasts from human skin explants that increases the number of cells obtained by up to two orders of magnitude, thus increasing the amount of material available for research and diagnostic purposes and potentially for cell-based therapies. Explants can be transferred sequentially up to 80 times, if required, at which point the explants appear to be completely depleted of fibroblasts. Utilizing skin samples obtained from 16 donors, aged 18-66 years old, the first 20 transfers produced cultures with lifespan and growth characteristics that were all very similar to each other, but the cultures derived from later transfers had a decreasing replicative capacity. Final cumulative population doublings did not correlate with donor age, but correlated positively with the telomere length at early passage. We also demonstrated that explants can be transduced directly by lentiviral infection, and that cryopreserved tissue can be explanted successfully using this procedure.
TL;DR: PrfectBLAST allows researchers to do nucleotide or amino acid sequence similarity searches against public (or user-customized) databases that are locally stored and does not require any dependencies or installation and can be used from a portable flash drive.
Abstract: prfectBLAST is a multiplatform graphical user interface (GUI) for the stand-alone BLAST+ suite of applications. It allows researchers to do nucleotide or amino acid sequence similarity searches against public (or user-customized) databases that are locally stored. It does not require any dependencies or installation and can be used from a portable flash drive. prfectBLAST is implemented in Java version 6 (SUN) and runs on all platforms that support Java and for which National Center for Biotechnology Information has made available stand-alone BLAST executables, including MS Windows, Mac OS X, and Linux. It is free and open source software, made available under the GNU General Public License version 3 (GPLv3) and can be downloaded at www.cicy.mx/sitios/jramirez or http://code.google.com/p/prfectblast/.
TL;DR: The phosphorothioate-based DNA recombination method (PTRec) is developed, an enzyme-free method that can be used for domain- and exon-shuffling or recombination of DNA fragments in general and is technically simple, fast, and reliable.
Abstract: Rational guided generation of protein chimeras has developed into an attractive approach in protein engineering for tailoring catalytic and biophysical properties of enzymes. Combinatorial recombin...
TL;DR: Fusing a peptide with a previously characterized 12-amino acid polystyrene binding sequence (PS-tag) improves overall peptide solubility and enzyme-linked immunosorbent assay (ELISA) results using the peptide as a capture agent.
Abstract: Peptide reagents can serve as alternatives or replacements to antibodies in sensing or diagnostic applications. The passive adsorption of peptides onto polystyrene surfaces can limit the target binding capability, especially for short, positively charged, or hydrophobic sequences. In this report, we show that fusing a peptide with a previously characterized 12-amino acid polystyrene binding sequence (PS-tag) improves overall peptide solubility and enzyme-linked immunosorbent assay (ELISA) results using the peptide as a capture agent. Specific improvements for protective antigen (PA; Bacillus anthracis) protein binding peptides selected from bacterial surface display were compared with native or biotinylated peptides. The PS-tag was added to either peptide terminus, using a (Gly)(4) spacer, and comparable binding affinities were obtained. Fusion with the PS-tag did not have any negative impact on peptide secondary structure as measured by circular dichroism. The addition of the PS-tag provides a convenient method to utilize peptide reagents from peptide display libraries as capture agents in an ELISA format without the need for a biotin tag or concerns about passive adsorption of critical residues for target capture.
TL;DR: The coupled assay was also used to determine the activity of partially purified DNA polymerases, revealing its potential use to monitor purification of phosphate- or pyrophosphate-releasing enzymes.
Abstract: A coupled enzyme assay able to monitor the kinetics of reactions catalyzed by phosphate- or pyrophosphate-releasing enzymes is presented here. The assay is based on the concerted action of inorganic pyrophosphatase (PPase), purine nucleoside phosphorylase (PNPase), and xanthine oxidase (XOD). In the presence of phosphate, PNPase catalyzes the phosphorolysis of inosine, generating hypoxanthine, which is oxidized to uric acid by XOD. The uric acid accordingly formed can be spectrophotometrically monitored at 293 nm, taking advantage of a molar extinction coefficient which is independent of pH between 6 and 9. The coupled assay was tested using DNA polymerases as a model system. The activity of Klenow enzyme was quantitatively determined, and it was found in agreement with the corresponding activity determined by traditional methods. Moreover, the continuous coupled assay was used to determine Km and Vmax of Klenow enzyme, yielding values in good agreement with previous observations. Finally, the coupled assay was also used to determine the activity of partially purified DNA polymerases, revealing its potential use to monitor purification of phosphate- or pyrophosphate-releasing enzymes.