Conventional Molecular Biology Techniques Research Articles

Using a DNA mini-barcode within the ITS region to identify toxic Amanita in mushroom poisoning cases

Mushroom poisoning contributes significantly to global foodborne diseases and related fatalities. Amanita mushrooms frequently cause such poisonings; however, identifying these toxic species is challenging due to the unavailability of fresh and intact samples. It is often necessary to analyze residues, vomitus, or stomach extracts to obtain DNA sequences for the identification of species responsible for causing food poisoning. This usually proves challenging to obtain usable DNA sequences that can be analyzed using conventional molecular biology techniques. Therefore, this study aimed to develop a DNA mini-barcoding method for the identification of Amanita species. Following the evaluation and optimization of universal primers for DNA mini-barcoding in Amanita mushrooms, we found that the internal transcribed spacer (ITS) gene sequence primer ITS-a was the most suitable DNA barcode primer for identifying Amanita species. Forty-three Amanita samples were subsequently amplified and sequenced. The sequences obtained were analyzed for intra- and inter-species genetic distances, and a phylogenetic tree was constructed. The findings indicated that the designed primers had strong universality among the Amanita samples and could accurately identify the target gene fragment with a length of 290 bp. Notably, the DNA mini-barcode accurately identified the 43 Amanita samples, demonstrating high consistency with the conventional DNA barcode. Furthermore, it effectively identified DNA from digested samples. In summary, this DNA mini-barcode is a promising tool for detecting accidental ingestion of toxic Amanita mushrooms. It may be used as an optimal barcode for species identification and traceability in events of Amanita-induced mushroom poisoning.Key points• Development of a DNA mini-barcoding method for Amanita species identification without fresh samples.• The ITS-a primer set was optimized for robust universality in Amanita samples.• The mini-barcode is suitable for screening toxic mushroom species in mushroom poisoning cases.Graphical

Primary Duck Hepatocyte Culture and Duck Hepatitis B Virus Infection Model.

Duck hepatitis B virus (DHBV) is an avian member of the hepatotropic DNA viruses, or hepadnaviridae. It shares with the human hepatitis B virus (HBV) a similar genomic organization and replication strategy via reverse transcription, but is simpler than HBV in lacking the X gene and in expressing just two coterminal envelope proteins: Large (L) and small (S). DHBV has been extensively used as a convenient and valuable animal model for study of thehepadnaviral life cycle, and for drug screening in vitro but also in vivo. Ducks and primary duck hepatocytes (PDHs) are inexpensive, easily accessible, and readily infected with DHBV. The high levels of genome replication and protein expression in duck liver and PDHs also facilitate monitoring of viral life cycle using conventional molecular biology techniques such as Southern blot for replicative DNA and covalently closed circular DNA (cccDNA), Northern blot for viral RNAs, and Western blot for viral proteins.

Single Cell Label-Free Probing of Chromatin Dynamics During B Lymphocyte Maturation.

Large-scale intracellular signaling during developmental growth or in response to environmental alterations are largely orchestrated by chromatin within the cell nuclei. Chemical and conformational modifications of the chromatin architecture are critical steps in the regulation of differential gene expression and ultimately cell fate determination. Therefore, establishing chemical properties of the nucleus could provide key markers for phenotypic characterization of cellular processes on a scale of individual cells. Raman microscopy is a sensitive technique that is capable of probing single cell chemical composition—and sub-cellular regions—in a label-free optical manner. As such, it has great potential in both clinical and basic research. However, perceived limitations of Raman spectroscopy such as low signal intensity and the difficulty in linking alterations in vibrational signals directly with ensuing biological effects have hampered advances in the field. Here we use immune B lymphocyte development as a model to assess chromatin and transcriptional changes using confocal Raman microscopy in combination with microfluidic devices and correlative transcriptomics, thereby linking changes in chemical and structural properties to biological outcomes. Live B lymphocytes were assessed before and after maturation. Multivariate analysis was applied to distinguish cellular components within each cell. The spectral differences between non-activated and activated B lymphocytes were then identified, and their correlation with known intracellular biological changes were assessed in comparison to conventional RNA-seq analysis. Our data shows that spectral analysis provides a powerful tool to study gene activation that can complement conventional molecular biology techniques and opens the way for mapping the dynamics in the biochemical makeup of individual cells.

Array-Based N-Glycan Profiling of Cells in Culture.

N-glycan imaging mass spectrometry (N-glycan IMS) enables the detection and characterization of N-glycans in thin histological tissue sections. N-glycan IMS is used to study N-glycan regulation and localization in tissue-specific regions, such as tumor and normal adjacent to tumor, or by cell type within a tissue. Once a specific tissue-localized N-glycan signature is found to be associated with by a disease state, it has been challenging to study modulation of the same N-glycan signature by conventional molecular biology techniques. Here we describe a protocol that adapts tissue N-glycan IMS analysis workflows to cells grown on glass slides in an array format. Cells are grown under normal conditions in a cell culture chamber, fixed to maintain normal morphology, and sprayed with a thin coating of PNGase F to release N-glycans for imaging mass spectrometry profiling.

Loss of NFAT2 expression results in the acceleration of clonal evolution in chronic lymphocytic leukemia.

Chronic lymphocytic leukemia (CLL) can be defined as a clonal expansion of B cells with stereotypic BCRs. Somatic hypermutation of the BCR heavy chains (IGVH) defines a subgroup of patients with a better prognosis. In up to 10% of CLL cases, a transformation to an aggressive B cell lymphoma (Richter's syndrome) with a dismal prognosis can be observed over time. NFAT proteins are transcription factors originally identified in T cells, which also play an important role in B cells. The TCL1 transgenic mouse is a well-accepted model of CLL. Upon B cell-specific deletion of NFAT2, TCL1 transgenic mice develop a disease resembling human Richter's syndrome. Whereas TCL1 Bcells exhibit tonic anergic BCR signaling characteristic of human CLL, loss of NFAT2 expression leads to readily activated BCRs indicating different BCR usage with altered downstream signaling. Here, we analyzed BCR usage in wild-type and TCL1 transgenic mice with and without NFAT2 deletion employing conventional molecular biology techniques and next-generation sequencing (NGS). We demonstrate that the loss of NFAT2 in CLL precipitates the selection of unmutated BCRs and the preferential usage of certain VDJ recombinations, which subsequently results in the accelerated development of oligoclonal disease.

Validation of a Next-Generation Sequencing Panel for AML Routine Diagnosis

Numerous recurrently mutated genes have been described in the last years for acute myeloid leukemia (AML). Nevertheless, only a few of them (NPM1, CEBPA, FLT3), and usually individually analyzed, have been systematically incorporated into clinical laboratories to stratify prognosis and guide risk-adapted therapy. So far, technology made impossible their simultaneous study, however, development of high throughput techniques as "next generation sequencing" (NGS) allows a parallel assay. Recently, our group designed a NGS panel (custom panel) interrogating the complete coding sequence of 87 genes potentially involved in AML. Interactome analysis revealed that 13 genes were highly implicated in AML pathogenesis. Although NGS has been broadly utilized in the investigational scope, its application to the routine diagnosis is still far from become a standard. The aim of this study is to validate the clinical applicability to routine laboratories of a hotspot NGS panel that includes these 13 genes and other potentially actionable targets.We included 62 "de novo" AML patients in which we tested the Ion Ampliseq AML community panel (Life Technologies) (IAAC panel) in the Ion PGM/Proton platforms. This panel includes hotspots of ASXL1 (exon 12), BRAF (V600E), CBL (exons 8-9), FLT3 (codons 676, 830-850), IDH1 (exon 4), IDH2 (exon 4), JAK 2 (exon 14), KIT (exons 8, 10, 11 and 17), KRAS (exons 2-4), NRAS (exons 2-4), PTPN11 (exons 3,7,8,13), RUNX1 (exons 3-8) y WT1 (exons 7 and 9), and the entire coding sequence of CEBPA, DNMT3A, GATA, TET2 and TP53. The design does not include the FLT3-ITD region. This panel requires only a total of 40 ng of DNA, far less than the custom panel (250 ng), which is very convenient in a clinical laboratory, where the input sample can be limited.The hotspot NGS panel detected 153 variants in 62 patients (2.47 mutations/patient). Mean read depth and uniformity were 1580 and 94.89%, respectively. The IAAC panel detected 25 NPM1 mutations, 20 TET2 and DNMT3A mutations, 14 in CEBPA, 12 in TP53, 11 in RUNX1, 8 in FLT3, 7 in IDH2, 6 in ASXL1, GATA2 and NRAS, 5 in PTPN11 and KRAS, 3 in WT1, 2 in CBL and 1 mutation in IDH1, KIT, and BRAF. Only 4 patients (6%) remained wild-type for these genes after the analysis with the IAAC panel.These samples had previously been analyzed by conventional molecular biology techniques (CMBT) for FLT3-D835, NPM1-T288, DNMT3A-R882 and CEBPA. The IAAC panel found 100% of these previously known mutations plus 5 extra mutations that were negative by CMBT. These mutations were reconfirmed by Sanger sequencing. Therefore, the IAAC panel detects more mutations than CMBT.To further assess the suitability of the hotspot panel, we selected a subset of 25 patients that had been also analyzed by the custom panel (Sure Desing Tool (Agilent) and an Illumina platform). This allowed us to analyze the complete coding sequence of the genes included in the IAAC panel and thus look for mutations outside the hotspots. A total of 53 variants were found with the custom panel. Fifty of these variants (95%) were also detected with the IAAC panel. The remaining 3 variants (5%) were located outside the hotspot regions. Additionally, the IAAC panel detected 13 variants in the overlapping regions that were not found with the custom panel. This could be explained because when focusing on recurrent regions of particular genes, it is possible to increase the mean read depth and therefore reach higher sensibility, which can be achieved with the IAAC panel but not with the custom panel.In conclusion, the Ion Ampliseq AML community panel detects mutations currently analyzed in most of clinical laboratories with validated prognostic relevance (NPM1 and CEBPA) in one assay, with low sample input requirement and with 100% sensibility compared with CMBT. In addition, this panel is able to find out alterations in these genes that are lost by CMBT. Moreover, other mutations with probable diagnostic or prognostic value and/or potential therapeutic targets are also studied and identified with high sensibility. Only a few changes are excluded of the covered regions. Therefore, IAAC panel is useful for routine diagnosis; however, detection of FLT3 internal tandem duplications is not possible, which limits its clinical utility. DisclosuresNo relevant conflicts of interest to declare.

Molecular imaging strategies for in vivo tracking of microRNAs: a comprehensive review.

MicroRNAs (miRNAs) are single-stranded non-coding RNAs of ~22 nucleotides, which can negatively regulate gene expression through induction of mRNA degradation and/or post-transcriptional gene silencing. MiRNAs are key factors in the regulation of many biological processes such as cell proliferation, differentiation, and death. Since miRNAs are known to be in close association with cancer development, non-invasive imaging of miRNA expression and/or activity is of critical importance, for which conventional molecular biology techniques are not suitable or applicable. Over the last several years, various molecular imaging techniques have been investigated for imaging of miRNAs. In this review article, we summarize the current state-of-the-art imaging of miRNAs, which are typically based on fluorescent proteins, bioluminescent enzymes, molecular beacons, and/or various nanoparticles. Non-invasive imaging of miRNA expression and/or biological activity is still at its infancy. Future research on more clinically relevant, non-toxic techniques is required to move the field of miRNA imaging into clinical applications. Non-invasive imaging of miRNA is an invaluable method that can not only significantly advance our understandings of a wide range of human diseases, but also lead to new and more effective treatment strategies for these diseases.

Extremely Reduced Levels of Heterozygosity in the Vertebrate Pathogen Encephalitozoon cuniculi

The genomes of microsporidia in the genus Encephalitozoon have been extensively studied for their minimalistic features, but they have seldom been used to investigate basic characteristics of the biology of these organisms, such as their ploidy or their mode of reproduction. In the present study, we aimed to tackle this issue by mapping Illumina sequence reads against the genomes of four strains of E. cuniculi. This approach, combined with more conventional molecular biology techniques, resulted in the identification of heterozygosity in all strains investigated, a typical signature of a diploid nuclear state. In sharp contrast with similar studies recently performed on a distant microsporidian lineage (Nematocida spp.), the level of heterozygosity that we identified across the E. cuniculi genomes was found to be extremely low. This reductive intraindividual genetic variation could result from the long-term propagation of these strains under laboratory conditions, but we propose that it could also reflect an intrinsic capacity of these vertebrate pathogens to self-reproduce.

Feasibility of the AMLprofiler™ (Skyline array) in Patient Risk-Stratification in a Multicenter Trial. Comparison with the Standard Approach

AbstractAbstract 4813Accurate cytogenetic and molecular diagnosis of acute myeloid leukemia help to establish the prognosis and to select the best postconsolidation treatments. This genetic characterization is currently being performed by means cytogenetic techniques and molecular methods mainly based in PCR, capillary electrophoresis and Sanger sequencing. Recently, large and homogeneous series of AML patients have been analyzed by means expression arrays. These studies have helped to standardize the method and they are becoming an alternative to traditional methods in terms of simplicity and time. ObjectivesTo assess the usefulness of the AMLprofiler™ in genetic stratification of de novo AML enrolled in a cooperative Group. To investigate the applicability of the array diagnostic platform in multicenter trials. To compare the AMLprofiler™ with the standard approach. Patients and methodsTwenty one consecutive de novo AML cases enrolled in the Spanish CETLAM protocol were included in the study. Patients were recruited during 2012. Cytogenetic analysis was performed in each participating center and the results were sent to the HSCSP. Complete immunophenotype and molecular studies were performed centrally at the HSCSP. Purified DNA was employed to test FLT3-ITD and TKD mutations, NPM1, CEBPa and MLL. For each FLT3-ITD positive case, the allelic ratio was calculated. Given that FLT3 mutations are not detected by the AML-profiler™, this determination was common to both approaches. Purified RNA was used to assess the presence of the AML1-ETO and CBFb-MYH11 rearrangements and to test RNA integrity. We used the AMLprofiler™ assay which detects chromosomal aberrations (t(8;21), t(15;17), inv(16), mutations (CEBPA dm, NPM1 A/B/D) and genetic expresion of BAALC and EVI1. Only those cases fulfilling the quality required by the manufacturer were hybridized the AMLprofiler™array. Based on this requirement one case was ruled out. ResultsTwenty cases were analyzed with the AMLprofiler™ and with the conventional methods (21 intended/20 hybridized). There were 4 cases with FLT3-ITD. One case had a t(8;21) and it has been succesfully detected by both methods. There were 4 inv(16), in one case the RNA quality was not satisfactory and was not hybridized, in the remaining 3 cases the AMLprofiler detected the genetic lesion including one case with a cryptical translocation and in one case with a typical inv(16) but with a complex CBFb-MYH11 transcript. In 8 cases a NPM1 mutation was detected by molecular methods, in all NPM1 A, B or D, the AMLprofiler™ gave concordant results, one case with a non-ABD mutation was not detected. When considering technician times, AMLprofiler™ compared favorably with the conventional molecular biology techniques (mean times: 2958 min vs 3422 min). This figure does not take into consideration the cytogenetic workload performed in each participating center. ConclusionsThe AMLprofiler™ could be easily used to stratify de novo AML patients enrolled in multicenter trials. It provides accurate results and requiring less time than the currently employed methods in the CETLAM group. The AMLprofiler™ seems to be specially useful in the core binding-factor leukemias. The most important limitations are related to the need of an excellent RNA sample and the presence of rare NPM1 mutations. Disclosures:No relevant conflicts of interest to declare.

The Retinoblastoma Tumor Suppressor Regulates a Xenobiotic Detoxification Pathway

The retinoblastoma tumor suppressor (pRb) regulates cell cycle entry, progression and exit by controlling the activity of the E2F-family of transcription factors. During cell cycle exit pRb acts as a transcriptional repressor by associating with E2F proteins and thereby inhibiting their ability to stimulate the expression of genes required for S phase. Indeed, many tumors harbor mutations in the RB gene and the pRb-E2F pathway is compromised in nearly all types of cancers. In this report we show that both pRb and its interacting partners, the transcriptional factors E2F1-2-3, act as positive modulators of detoxification pathways important for metabolizing and clearing xenobiotics—such as toxins and drugs—from the body. Using a combination of conventional molecular biology techniques and microarray analysis of specific cell populations, we have analyzed the detoxification pathway in murine samples in the presence or absence of pRb and/or E2F1-2-3. In this report, we show that both pRb and E2F1-2-3 act as positive modulators of detoxification pathways in mice, challenging the conventional view of E2F1-2-3 as transcriptional repressors negatively regulated by pRb. These results suggest that mutations altering the pRb-E2F axis may have consequences beyond loss of cell cycle control by altering the ability of tissues to remove toxins and to properly metabolize anticancer drugs, and might help to understand the formation and progression rates of different types of cancer, as well as to better design appropriate therapies based on the particular genetic composition of the tumors.

BAC Modification through Serial or Simultaneous Use of CRE/Lox Technology

Bacterial Artificial Chromosomes (BACs) are vital tools in mouse genomic analyses because of their ability to propagate large inserts. The size of these constructs, however, prevents the use of conventional molecular biology techniques for modification and manipulation. Techniques such as recombineering and Cre/Lox methodologies have thus become heavily relied upon for such purposes. In this work, we investigate the applicability of Lox variant sites for serial and/or simultaneous manipulations of BACs. We show that Lox spacer mutants are very specific, and inverted repeat variants reduce Lox reaction rates through reducing the affinity of Cre for the site, while retaining some functionality. Employing these methods, we produced serial modifications encompassing four independent changes which generated a mouse HoxB BAC with fluorescent reporter proteins inserted into four adjacent Hox genes. We also generated specific, simultaneous deletions using combinations of spacer variants and inverted repeat variants. These techniques will facilitate BAC manipulations and open a new repertoire of methods for BAC and genome manipulation.

Cell Signaling

Cell Signaling

Seamless cloning and domain swapping of synthetic and complex DNA

The use of synthetic DNA can avoid problems that are sometimes encountered with conventional molecular biology techniques using DNA with high GC content, strong secondary structures, or repeat sequences. However, very complex DNA may still resist PCR and synthesis of DNA from oligonucleotides. In the method described here, separately synthesized DNA segments were seamlessly joined independently of the presence of restriction sites in the target DNA. This method allowed the reconstruction of complex DNA by concatenation of easily synthesized segments and permitted repeated swapping of segments, from a few nucleotides to large fragments of complex DNA for phenotypic analysis.

Nucleic Acid Beacons for Long-Term Real-Time Intracellular Monitoring

Real time intracellular monitoring of biological molecules inside living cells is important in many biomedical studies and reveals valuable information unobtainable by conventional molecular biology techniques. A variety of methods and molecular probes have been developed, but long term (from a few hours to days) intracellular monitoring with high sensitivity and selectivity is impossible and has not been accomplished. We have used locked nucleic acids (LNA) to engineer novel molecular beacons (MBs) for long-term intracellular monitoring. The LNA-MBs were made of a mixed LNA and DNA bases to have extremely high biostability. The new beacons were tested with MDA-MB-231 cancer cells and used effectively to monitor mRNA expression levels in real-time for 5-24 h. After 24 h inside living cells, the LNA-MBs were still functional, demonstrating a greatly enhanced stability enabling the measurement of intracellular gene expression over an extended period of time.

Quantitative Protein Network Monitoring in Response to DNA Damage

Conventional molecular biology techniques have identified a large number of cell signaling pathways; however, the importance of these pathways often varies, depending on factors such as treatment type, dose, time after treatment, and cell type. Here, we describe a technique using "reverse-phase" protein lysate microarrays (RPAs) to acquire multiple dimensions of information on protein dynamics in response to DNA damage. Whole-cell lysates from three cellular stress treatments (IR, UV, and ADR) were collected at four doses per treatment, and each, in turn, at 10 time points, resulting in a single-slide RPA consisting of 10,240 features, including replicates. The dynamic molecular profile of 18 unique protein species was compared to phenotypic fate by FACS analysis for corresponding stress conditions. Our initial quantitative results in this new platform confirmed that (1) there is clear stress dose-response effect in p53 protein and (2) a comparison of the rates of increase of p21 and Cyclin D3/p53-Ser15 in response to DNA damage may be associated with the pattern of DNA content. This method, offering a quantitative time-course monitoring of protein expression levels, can provide an experimental reference for developing mathematical models of cell signaling dynamics. Although the present study focuses on the DNA damage-repair pathway, the technique is generally useful to the study of protein signaling.

Alteration of Lithium Pharmacology through Manipulation of Phosphoadenosine Phosphate Metabolism

Bisphosphate 3'-nucleotidase (BPNT1 in mammals and Met22/Hal2 in yeast) is one of five members of a family of signaling phosphatases united through a common tertiary structure and inhibition by subtherapeutic doses of the antibipolar drug lithium. Here we report a role for 3'-nucleotidase and its substrate, 3'-phosphoadenosine 5'-phosphate (PAP), in mediating the cellular effects of lithium. Lithium-induced inhibition of growth in yeast cells may be overcome by dose-dependent heterologous expression of human BPNT1. Disruption of the yeast 3'-nucleotidase gene or treatment of cells with lithium results in a >80-fold accumulation of PAP and leads to potent growth inhibition. These data indicate that the accumulation of a 3'-nucleotidase substrate, such as PAP, mediates the toxicity of lithium. To further probe this model we examined the growth inhibitory effects of lithium under conditions in which PAP biosynthetic machinery was concomitantly down-regulated. Disruption of met3 or met14 genes (ATP sulfurylase or phosphosulfate kinase), transcriptional down-regulation of MET3 through methionine addition, or administration of chlorate, a widely used cell-permeable sulfurylase inhibitor, function to reduce lithium-induced intracellular PAP accumulation and lithium toxicity; all of these effects were reversed by heterologous expression of human sulfurylase and kinase. Collectively, our data support a role for 3'-nucleotidase activity and PAP metabolism in aspects of lithium's mechanism of action and provide a platform for development of novel pharmacological modulators aimed at improving therapies for the treatment of bipolar disorder.

Gene microarray analysis of human brain arteriovenous malformations.

Human brain arteriovenous malformations (BAVMs) display abnormal expression of various angiogenesis-related genes and their products. We examined gene expression patterns in BAVMs by the gene microarray technique. We analyzed BAVM and control brain samples obtained by temporal lobectomy for medically intractable seizure by Affymetrix Human Gene Set U95Av2 (Affymetrix, Inc., Santa Clara, CA). The gene microarray data were compared with new and previously published data that used conventional molecular biology techniques. We analyzed six BAVM and five control brain samples. From 12,625 gene probes assayed, 1781 gene probes showed differential expression between BAVMs and controls. BAVM samples had a gene expression pattern that was distinct from those of control brain samples. Increased messenger ribonucleic acid expression of vascular endothelial growth factor A was accompanied by increased expression of its protein product. A majority of the gene data was in agreement with previously published data. The gene microarray data generated a new testable hypothesis regarding integrin, and we found increased expression of integrin alphavbeta3 protein in BAVMs. The gene expression pattern of BAVMs was distinct from those of control brain samples. We verified the gene microarray data by demonstrating that increased gene expression levels for angiogenesis-related molecules were accompanied by increased levels of their protein product expression. The gene microarray technique may be a useful tool to study multiple pathways simultaneously in BAVM specimens.

MRNA in situ hybridization to in vitro cultured cells.

AbstractIn basic and applied biomedical research there is a considerable interest in having reliable RNA in situ hybridization techniques, since these allow the detection of RNA expression in a morphological context at the individual cell level. Conventional molecular biology techniques for RNA analysis such as Northern hybridizations, RNase protection assays, and reverse transcription polymerase chain reactions (RT-PCR) demand the homogenization of the tissue or cell sample. In these cases the possibility of relating (changes in) RNA expression to histo-and cytomorphological information is lost to a very large extent.KeywordsReverse Transcription Polymerase Chain ReactionNorthern HybridizationRNase Protection AssayImmunocytochemical DetectionIndividual Cell LevelThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Utility of the polymerase chain reaction in detection of gene expression in drug-resistant human tumors.

Recently, an enzymatic amplification method, the polymerase chain reaction (PCR), was modified to amplify a sequence of a drug resistance gene. The PCR assay can confirm data achieved by conventional molecular biology techniques, while requiring less time and fewer patient cells. It can be quantitated for gene expression. The data generated make it possible to analyze m-RNA expression in tumor samples without being limited to detecting only gene amplification in response to cancer chemotherapy. The PCR assay can be an effective device in the early detection of resistance to chemotherapy.