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Sample records for broad-range pcr cloning

  1. Broad-range PCR, cloning and sequencing of the full 16S rRNA gene for detection of bacterial DNA in synovial fluid samples of Tunisian patients with reactive and undifferentiated arthritis

    OpenAIRE

    Siala, Mariam; Gdoura, Radhouane; Fourati, Hela; Rihl, Markus; Jaulhac, Benoit; Younes, Mohamed; Sibilia, Jean; Baklouti, Sofien; Bargaoui, Naceur; Sellami, Slaheddine; Sghir, Abdelghani; Hammami, Adnane

    2009-01-01

    Introduction Broad-range rDNA PCR provides an alternative, cultivation-independent approach for identifying bacterial DNA in reactive and other form of arthritis. The aim of this study was to use broad-range rDNA PCR targeting the 16S rRNA gene in patients with reactive and other forms of arthritis and to screen for the presence of DNA from any given bacterial species in synovial fluid (SF) samples. Methods We examined the SF samples from a total of 27 patients consisting of patients with rea...

  2. Escherichia coli Vertebral Osteomyelitis Diagnosed According to Broad-range 16S rRNA Gene Polymerase Chain Reaction (PCR).

    Science.gov (United States)

    Shibata, Satoshi; Tanizaki, Ryutaro; Watanabe, Koji; Makabe, Kenta; Shoda, Naoki; Kutsuna, Satoshi; Nagamatsu, Maki; Oka, Shinichi; Ohmagari, Norio

    2015-01-01

    Identifying the causative agent of pyogenic osteomyelitis is often challenging, especially when antibiotics are administered before a biopsy. We herein present a case of osteomyelitis in the cervical vertebrae presenting with progressive paralytic symptoms, in which we successfully identified Escherichia coli from a biopsy specimen using broad-range 16S rRNA gene polymerase chain reaction (PCR) even though sensitive antibiotics had been used for more than 50 days before the biopsy. Broad-range 16S rRNA gene PCR is a useful diagnostic method, especially when prebiopsy antibiotics are unavoidably used for a clinically unstable state.

  3. Comparison between a Broad-Range Real-Time and a Broad-Range End-Point PCR Assays for the Detection of Bacterial 16S rRNA in Clinical Samples.

    Science.gov (United States)

    Meddeb, Mariam; Koebel, Christelle; Jaulhac, Benoît; Schramm, Frédéric

    2016-01-01

    Broad range PCR targeting the 16S rRNA gene is widely used to test clinical samples for the presence of bacterial DNA. End-point 16S PCR is both time-consuming and at high risk of cross-contamination. Prior to the replacement of the 16S end-point PCR assay routinely used in our clinical laboratory by a new 16S real-time PCR assay, we aimed to compare the performances of both techniques for the direct diagnosis of bacterial infections in clinical samples. In this prospective study, 129 clinical samples were included for direct comparison of both techniques. The sensitivity of 16S real-time PCR assay (76%) was significantly higher than that of end-point 16S PCR assay (41%) (pPCR assays did not differ significantly (p=0.43). The 16S real-time PCR assay yielded an etiological diagnosis in 19% of culture-negative samples. It constitutes a reliable and complementary diagnostic tool to the bacterial culture.

  4. Broad-range PCR as a supplement to culture for detection of bacterial pathogens in patients with a clinically diagnosed spinal infection

    DEFF Research Database (Denmark)

    Fuursted, K.; Arpi, M.; Lindblad, B.E.;

    2008-01-01

    We aimed to evaluate broad-range PCR and subsequent sequencing compared to conventional culture in the diagnosis of spinal infection. The method was a prospective study of all patients admitted to Aarhus University Hospital for surgery during a 12-months period with a clinically diagnosed infection...... of the spine. Samples from patients undergoing surgery for non-infectious causes (malignancy etc.) were included as control group. Specimens were submitted to conventional culture and molecular investigation with 16S rRNA gene amplification and sequence analysis. 38 patients were included in the study...... (clinically diagnosed spinal infections=18; non-infectious diseases=20). The specificity was excellent for both culture and PCR (95% and 100%, respectively). A true culture positive result was obtained in 50% of patients (9/18) and 61% was positive (11/18) by broad-range PCR. When combined, culture and PCR...

  5. Overlap extension PCR cloning.

    Science.gov (United States)

    Bryksin, Anton; Matsumura, Ichiro

    2013-01-01

    Rising demand for recombinant proteins has motivated the development of efficient and reliable cloning methods. Here we show how a beginner can clone virtually any DNA insert into a plasmid of choice without the use of restriction endonucleases or T4 DNA ligase. Chimeric primers encoding plasmid sequence at the 5' ends and insert sequence at the 3' ends are designed and synthesized. Phusion(®) DNA polymerase is utilized to amplify the desired insert by PCR. The double-stranded product is subsequently employed as a pair of mega-primers in a PCR-like reaction with circular plasmids. The original plasmids are then destroyed in restriction digests with Dpn I. The product of the overlap extension PCR is used to transform competent Escherichia coli cells. Phusion(®) DNA polymerase is used for both the amplification and fusion reactions, so both steps can be monitored and optimized in the same way. PMID:23996437

  6. Comparative Analysis of Two Broad-Range PCR Assays for Pathogen Detection in Positive-Blood-Culture Bottles: PCR–High-Resolution Melting Analysis versus PCR-Mass Spectrometry

    OpenAIRE

    Jeng, Kevin; Gaydos, Charlotte A; Blyn, Lawrence B.; Yang, Samuel; Won, Helen; Matthews, Heather; Toleno, Donna; Hsieh, Yu-Hsiang; Carroll, Karen C.; Hardick, Justin; Masek, Billy; Kecojevic, Alexander; Sampath, Rangarajan; Peterson, Stephen; Rothman, Richard E.

    2012-01-01

    Detection of pathogens in bloodstream infections is important for directing antimicrobial treatment, but current culture-based approaches can be problematic. Broad-range PCR assays which target conserved genomic motifs for postamplification amplicon analysis permit detection of sepsis-causing pathogens. Comparison of different broad-range assays is important for informing future implementation strategies. In this study, we compared positive-blood-culture bottles processed by PCR coupled to hi...

  7. Broad-Range PCR Coupled with Electrospray Ionization Time of Flight Mass Spectrometry for Detection of Bacteremia and Fungemia in Patients with Neutropenic Fever.

    Science.gov (United States)

    Desmet, S; Maertens, J; Bueselinck, K; Lagrou, K

    2016-10-01

    Infection is an important complication in patients with hematologic malignancies or solid tumors undergoing intensive cytotoxic chemotherapy. In only 20 to 30% of the febrile neutropenic episodes, an infectious agent is detected by conventional cultures. In this prospective study, the performance of broad-range PCR coupled with electrospray ionization time of flight mass spectrometry (PCR/ESI-MS) technology was compared to conventional blood cultures (BC) in a consecutive series of samples from high-risk hematology patients. In 74 patients, BC and a whole-blood sample for PCR/ESI-MS (Iridica BAC BSI; Abbott, Carlsbad, CA, USA) were collected at the start of each febrile neutropenic episode and, in case of persistent fever, also at day 5. During 100 different febrile episodes, 105 blood samples were collected and analyzed by PCR/ESI-MS. There was evidence of a bloodstream infection (BSI) in 36/105 cases (34%), based on 14 cases with both PCR/ESI-MS and BC positivity, 17 cases with BC positivity only, and 5 cases with PCR/ESI-MS positivity only. The sensitivity of PCR/ESI-MS was 45%, specificity was 93%, and the negative predictive value was 80% compared to blood culture. PCR/ESI-MS detected definite pathogens (Fusobacterium nucleatum and Streptococcus pneumoniae) missed by BC, whereas it missed both Gram-negative and Gram-positive organisms detected by BC. PCR/ESI-MS testing detected additional microorganisms but showed a low sensitivity (45%) compared to BC in neutropenic patients. Our results indicate a lower concordance between BC and PCR/ESI-MS in the neutropenic population than what has been previously reported in other patient groups with normal white blood cell distribution, and a lower sensitivity than other PCR-based methods.

  8. Evaluation of viral extraction methods on a broad range of Ready-To-Eat foods with conventional and real-time RT-PCR for Norovirus GII detection.

    Science.gov (United States)

    Baert, Leen; Uyttendaele, Mieke; Debevere, Johan

    2008-03-31

    Noroviruses (NoV) are a common cause of foodborne outbreaks. In spite of that, no standard viral detection method is available for food products. Therefore, three viral elution-concentration methods and one direct RNA isolation method were evaluated on a broad range of Ready-To-Eat (RTE) food products (mixed lettuce, fruit salad, raspberries and two RTE dishes) artificially seeded with a diluted stool sample contaminated with NoV genogroup II. These seeding experiments revealed two categories of RTE products, fruits and vegetables grouped together and RTE dishes (penne and tagliatelle salads) which are rich in proteins and fat formed another category. The RNA extracts were amplified and detected with two conventional RT-PCR systems (Booster and Semi-nested GII) and one real-time RT-PCR (Real-time GII) assay. A fast direct RNA isolation method detected 10(2) RT-PCRU on 10 g penne and tagliatelle salads with the conventional RT-PCR assays. However real-time RT-PCR was less sensitive for penne salad. A viral elution-concentration method, including a buffer solution for the elution step and one polyethylene glycol (PEG) precipitation step, was able to detect 10(2) RT-PCRU on 50 g frozen raspberries with conventional and real-time RT-PCR assays. Moreover the latter extraction method used no environmental hazardous chemical reagents and was easy to perform.

  9. Evaluation of a broad range real-time polymerase chain reaction (RT-PCR) assay for the diagnosis of septic synovitis in horses.

    Science.gov (United States)

    Elmas, Colette R; Koenig, Judith B; Bienzle, Dorothee; Cribb, Nicola C; Cernicchiaro, Natalia; Coté, Nathalie M; Weese, J Scott

    2013-07-01

    Septic synovitis is a potentially debilitating and life-threatening disorder in horses. We hypothesized that a universal bacterial real-time PCR (RT-PCR) assay would have improved sensitivity and decreased turn-around time for detection of bacteria in synovial fluid (SF) samples. Forty-eight SF samples were collected from 36 horses that presented to two referral institutions with suspected septic synovitis. Universal RT-PCR, bacterial culture and SF analysis were performed on all samples, and an interpretation on the sample being septic or not was derived by three board certified specialists from the history, clinical assessment and SF characteristics. RT-PCR results were compared to a composite standard comprised of positive culture and interpretation by all three specialists of samples as "septic". For 41 of 48 samples (85%), culture and RT-PCR results were concordant. Compared to the composite standard, 83% of samples were correctly classified by RT-PCR (turn-around time of approximately 4 hours). Relative sensitivity and specificity of RT-PCR were 87% and 72% respectively, and 56% and 86% for culture. Hence, universal RT-PCR was a rapid and highly sensitive test, which may accelerate diagnosis and improve outcome for horses with septic synovitis.

  10. Detection of a broad range of Leishmania species and determination of parasite load of infected mouse by real-time PCR targeting the arginine permease gene AAP3

    OpenAIRE

    Tellevik, Marit Gjerde; Müller, Karl Erik; Rebbestad, Karen; Nerland, Audun Helge

    2014-01-01

    Leishmaniasis is one of the world's most neglected infectious diseases, affecting around 12 million people and more than 350 million at risk of infection. The clinical picture varies from self-healing cutaneous lesions to severe visceral infections, but still no commercial vaccines for humans are available and the currently used drugs have unpleasant side effects. Here we report a real-time PCR assay targeting the arginine permease gene AAP3 that can be applied for all the nine different spec...

  11. Detection of a broad range of Leishmania species and determination of parasite load of infected mouse by real-time PCR targeting the arginine permease gene AAP3.

    Science.gov (United States)

    Tellevik, Marit Gjerde; Muller, Karl Erik; Løkken, Karen Rebbestad; Nerland, Audun Helge

    2014-09-01

    Leishmaniasis is one of the world's most neglected infectious diseases, affecting around 12 million people and more than 350 million at risk of infection. The clinical picture varies from self-healing cutaneous lesions to severe visceral infections, but still no commercial vaccines for humans are available and the currently used drugs have unpleasant side effects. Here we report a real-time PCR assay targeting the arginine permease gene AAP3 that can be applied for all the nine different species of the Leishmania genus tested; 4 Old World species and 5 New World species, from both L. (Leishmania) and L. (Viannia) subgenera. No cross-reaction was seen with Trypanosoma cruzi, Trypanosoma brucei, human or mouse genomic DNA. The assay has a high sensitivity, with a limit of detection of 10fg DNA for L. (L.) major and L. (L.) donovani, and 100fg DNA for L. (V.) braziliensis, and can be used for both qualitative and quantitative purposes. This AAP3-Assay, run in duplex with a host specific gene-assay, was also successfully used for quantification of parasite load of footpads from L. (L.) major-infected mice. It can therefore be a valuable tool in applications like monitoring effects of drugs, the selection of vaccine candidates and in screening patients, including asymptomatic carriers. PMID:24859532

  12. Development of a Broad-Range 23S rDNA Real-Time PCR Assay for the Detection and Quantification of Pathogenic Bacteria in Human Whole Blood and Plasma Specimens

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    Paolo Gaibani

    2013-01-01

    Full Text Available Molecular methods are important tools in the diagnosis of bloodstream bacterial infections, in particular in patients treated with antimicrobial therapy, due to their quick turn-around time. Here we describe a new broad-range real-time PCR targeting the 23S rDNA gene and capable to detect as low as 10 plasmid copies per reaction of targeted bacterial 23S rDNA gene. Two commercially available DNA extraction kits were evaluated to assess their efficiency for the extraction of plasma and whole blood samples spiked with different amount of either Staphylococcus aureus or Escherichia coli, in order to find the optimal extraction method to be used. Manual QIAmp extraction method with enzyme pre-treatment resulted the most sensitive for detection of bacterial load. Sensitivity of this novel assay ranged between 10 and 103 CFU per PCR reaction for E. coli and S. aureus in human whole blood samples depending on the extraction methods used. Analysis of plasma samples showed a 10- to 100-fold reduction of bacterial 23S rDNA in comparison to the corresponding whole blood specimens, thus indicating that whole blood is the preferential sample type to be used in this real-time PCR protocol. Our results thus show that the 23S rDNA gene represents an optimal target for bacteria quantification in human whole blood.

  13. The extraction of fungal genome DNA and the establishunent of a broad-range fungal PCR%真菌基因组DNA的提取和通用PCR检测方法的建立

    Institute of Scientific and Technical Information of China (English)

    曹国君; 赵缜; 彭奕冰; 季育华; 孙佳彬; 卫蓓文; 刘璐

    2011-01-01

    目的 改良真菌基因组DNA的提取方法,建立真菌通用聚合酶链反应(PCR),为目前临床真菌感染的早期诊断、预防和治疗提供有效工具.方法 参考前人报道的多种真菌基因组DNA的提取方法,作改良以确立本研究中所采纳的手段,并应用真菌核糖体DNA(rDNA)通用引物,以实验室保存的标准菌株及临床分离菌株来建立临床真菌感染检测用通用PCR.结果 白念珠菌和烟曲霉在75℃温度下分别作用60和80 min可以完全破灭活.经目前多种破壁方法的探讨,发现对于白念珠菌(单细胞真菌)选用酶消化法,破壁效率高达98.29%,而烟曲霉(多细胞真菌)则需要酶消化法与打击器振荡法联合应用,其破壁率也可达66.68%,进一步用酚氯仿法抽提其基因组DNA,能够获得相对纯度高且有一定得量.当选择真菌rDNAITS2区间的一对通用引物,通过PCR反应体系的优化,使得本研究中建立的通用PCR,对于白念珠菌和烟曲霉的检测下限分别为5个和9.7个,其PCR产物测序结果与数据库比对完全一致,同时选择临床分离的或实验室保存的其他真菌、细菌和病毒株进行验证,该方法仅针对真菌群,结合测序分析可以实现种属水平的鉴定.结论 改良真菌基因组DNA提取后所建立的针对真菌rDNA的通用PCR敏感且特异,适宜实验室操作.%Objective To improve a method for the extraction of fungal genome DNA, and establish a broad-range fungal polymerase chain reaction (PCR) ,in order to provide the reference for early diagnosis, prevention and treatment of fungal infection disease. Methods According to the former fungal genome DNA extraction methods, a method was formed and improved in this experiment. The fungal ribosome deoxyribonucleic acid ( rDNA) was applied as universal primer. A broad-range fungal PCR was established by testing the standard strains and the isolated clinical strains stored. Results Candida albicans and Aspergillus

  14. Analysis of bacterial DNA in synovial tissue of Tunisian patients with reactive and undifferentiated arthritis by broad-range PCR, cloning and sequencing

    OpenAIRE

    Siala, Mariam; Jaulhac, Benoit; Gdoura, Radhouane; Sibilia, Jean; Fourati, Hela; Younes, Mohamed; Baklouti, Sofien; Bargaoui, Naceur; Sellami, Slaheddine; Znazen, Abir; Barthel, Cathy; Collin, Elody; Hammami, Adnane; Sghir, Abdelghani

    2008-01-01

    Introduction Bacteria and/or their antigens have been implicated in the pathogenesis of reactive arthritis (ReA). Several studies have reported the presence of bacterial antigens and nucleic acids of bacteria other than those specified by diagnostic criteria for ReA in joint specimens from patients with ReA and various arthritides. The present study was conducted to detect any bacterial DNA and identify bacterial species that are present in the synovial tissue of Tunisian patients with reacti...

  15. Diagnostic Utility of Broad Range Bacterial 16S rRNA Gene PCR with Degradation of Human and Free Bacterial DNA in Bloodstream Infection Is More Sensitive Than an In-House Developed PCR without Degradation of Human and Free Bacterial DNA

    Directory of Open Access Journals (Sweden)

    Petra Rogina

    2014-01-01

    Full Text Available We compared a commercial broad range 16S rRNA gene PCR assay (SepsiTest to an in-house developed assay (IHP. We assessed whether CD64 index, a biomarker of bacterial infection, can be used to exclude patients with a low probability of systemic bacterial infection. From January to March 2010, 23 patients with suspected sepsis were enrolled. CD64 index, procalcitonin, and C-reactive protein were measured on admission. Broad range 16S rRNA gene PCR was performed from whole blood (SepsiTest or blood plasma (IHP and compared to blood culture results. Blood samples spiked with Staphylococcus aureus were used to assess sensitivity of the molecular assays in vitro. CD64 index was lower in patients where possible sepsis was excluded than in patients with microbiologically confirmed sepsis (P=0.004. SepsiTest identified more relevant pathogens than blood cultures (P=0.008; in three patients (13% results from blood culture and SepsiTest were congruent, whereas in four cases (17.4% relevant pathogens were detected by SepsiTest only. In vitro spiking experiments suggested equal sensitivity of SepsiTest and IHP. A diagnostic algorithm using CD64 index as a decision maker to perform SepsiTest shows improved detection of pathogens in patients with suspected blood stream infection and may enable earlier targeted antibiotic therapy.

  16. In vivo cloning of PCR products in E. coli.

    OpenAIRE

    Oliner, J D; Kinzler, K W; Vogelstein, B

    1993-01-01

    This report describes an efficient method to clone PCR products exploiting endogenous Escherichia coli enzymatic activities. PCR products are engineered to contain terminal sequences identical to sequences at the two ends of a linearized vector. PCR products and vector DNA are then simply co-transfected into E. coli strain JC8679, obviating the requirement for enzymatic treatment of the PCR product or in vitro ligation. The high rate of homologous recombination in this strain results in effic...

  17. Exponential megapriming PCR (EMP cloning--seamless DNA insertion into any target plasmid without sequence constraints.

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    Alexander Ulrich

    Full Text Available We present a fast, reliable and inexpensive restriction-free cloning method for seamless DNA insertion into any plasmid without sequence limitation. Exponential megapriming PCR (EMP cloning requires two consecutive PCR steps and can be carried out in one day. We show that EMP cloning has a higher efficiency than restriction-free (RF cloning, especially for long inserts above 2.5 kb. EMP further enables simultaneous cloning of multiple inserts.

  18. Changes of 5' Terminal Nucleotides of PCR Primers Causing Variable T-A Cloning Efficiency

    Institute of Scientific and Technical Information of China (English)

    Mei-Qin Liu; Xin Shen; Wei-Lun Yin; Cun-Fu Lu

    2007-01-01

    T-A cloning takes advantage of the unpaired adenosyl residue added to the 3' terminus of amplified DNAs by Taq and other thermostable DNA polymerase and uses a linearized plasmid vector with a protruding 3' thymidylate residue at each of its 3' termini to clone polymerase chain reaction (PCR)-derived DNA fragments. It is a simple,reliable, and efficient ligation-dependent cloning method for PCR products, but the drawback of variable cloning efficiency occurs during application. In the present work, the relationship between variable T-A cloning efficiency and the different 5' end nucleotide base of primers used in PCR amplification was studied. The results showed that different cloning efficiency was obtained with different primer pairs containing A, T, C and G at the 5' terminus respectively. The data shows that when the 5' end base of primer pair was adenosyl, more white colonies could be obtained in cloning the corresponding PCR product in comparison with other bases. And the least white colonies were formed when using the primer pair with 5' cytidylate end. The gluanylate end primers resulted in almost the same cloning efficiency in the white colonies amount as the thymidylate end primer did, and this efficiency was much lower than that of adenosyl end primers. This presumably is a consequence of variability in 3'dA addition to PCR products mediated by Taq polymerase. Our results offer instructions for primer design for researchers who choose T-A cloning to clone PCR products.

  19. Optimal Cloning of PCR Fragments by Homologous Recombination in Escherichia coli

    OpenAIRE

    Jacobus, Ana Paula; Gross, Jeferson

    2015-01-01

    PCR fragments and linear vectors containing overlapping ends are easily assembled into a propagative plasmid by homologous recombination in Escherichia coli. Although this gap-repair cloning approach is straightforward, its existence is virtually unknown to most molecular biologists. To popularize this method, we tested critical parameters influencing the efficiency of PCR fragments cloning into PCR-amplified vectors by homologous recombination in the widely used E. coli strain DH5α. We found...

  20. FastCloning: a highly simplified, purification-free, sequence- and ligation-independent PCR cloning method

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    Lu Jia

    2011-10-01

    Full Text Available Abstract Background Although a variety of methods and expensive kits are available, molecular cloning can be a time-consuming and frustrating process. Results Here we report a highly simplified, reliable, and efficient PCR-based cloning technique to insert any DNA fragment into a plasmid vector or into a gene (cDNA in a vector at any desired position. With this method, the vector and insert are PCR amplified separately, with only 18 cycles, using a high fidelity DNA polymerase. The amplified insert has the ends with ~16-base overlapping with the ends of the amplified vector. After DpnI digestion of the mixture of the amplified vector and insert to eliminate the DNA templates used in PCR reactions, the mixture is directly transformed into competent E. coli cells to obtain the desired clones. This technique has many advantages over other cloning methods. First, it does not need gel purification of the PCR product or linearized vector. Second, there is no need of any cloning kit or specialized enzyme for cloning. Furthermore, with reduced number of PCR cycles, it also decreases the chance of random mutations. In addition, this method is highly effective and reproducible. Finally, since this cloning method is also sequence independent, we demonstrated that it can be used for chimera construction, insertion, and multiple mutations spanning a stretch of DNA up to 120 bp. Conclusion Our FastCloning technique provides a very simple, effective, reliable, and versatile tool for molecular cloning, chimera construction, insertion of any DNA sequences of interest and also for multiple mutations in a short stretch of a cDNA.

  1. Quick and clean cloning: a ligation-independent cloning strategy for selective cloning of specific PCR products from non-specific mixes.

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    Frank Thieme

    Full Text Available We have developed an efficient strategy for cloning of PCR products that contain an unknown region flanked by a known sequence. As with ligation-independent cloning, the strategy is based on homology between sequences present in both the vector and the insert. However, in contrast to ligation-independent cloning, the cloning vector has homology with only one of the two primers used for amplification of the insert. The other side of the linearized cloning vector has homology with a sequence present in the insert, but nested and non-overlapping with the gene-specific primer used for amplification. Since only specific products contain this sequence, but none of the non-specific products, only specific products can be cloned. Cloning is performed using a one-step reaction that only requires incubation for 10 minutes at room temperature in the presence of T4 DNA polymerase to generate single-stranded extensions at the ends of the vector and insert. The reaction mix is then directly transformed into E. coli where the annealed vector-insert complex is repaired and ligated. We have tested this method, which we call quick and clean cloning (QC cloning, for cloning of the variable regions of immunoglobulins expressed in non-Hodgkin lymphoma tumor samples. This method can also be applied to identify the flanking sequence of DNA elements such as T-DNA or transposon insertions, or be used for cloning of any PCR product with high specificity.

  2. Optimal cloning of PCR fragments by homologous recombination in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Ana Paula Jacobus

    Full Text Available PCR fragments and linear vectors containing overlapping ends are easily assembled into a propagative plasmid by homologous recombination in Escherichia coli. Although this gap-repair cloning approach is straightforward, its existence is virtually unknown to most molecular biologists. To popularize this method, we tested critical parameters influencing the efficiency of PCR fragments cloning into PCR-amplified vectors by homologous recombination in the widely used E. coli strain DH5α. We found that the number of positive colonies after transformation increases with the length of overlap between the PCR fragment and linear vector. For most practical purposes, a 20 bp identity already ensures high-cloning yields. With an insert to vector ratio of 2:1, higher colony forming numbers are obtained when the amount of vector is in the range of 100 to 250 ng. An undesirable cloning background of empty vectors can be minimized during vector PCR amplification by applying a reduced amount of plasmid template or by using primers in which the 5' termini are separated by a large gap. DpnI digestion of the plasmid template after PCR is also effective to decrease the background of negative colonies. We tested these optimized cloning parameters during the assembly of five independent DNA constructs and obtained 94% positive clones out of 100 colonies probed. We further demonstrated the efficient and simultaneous cloning of two PCR fragments into a vector. These results support the idea that homologous recombination in E. coli might be one of the most effective methods for cloning one or two PCR fragments. For its simplicity and high efficiency, we believe that recombinational cloning in E. coli has a great potential to become a routine procedure in most molecular biology-oriented laboratories.

  3. Diagnosis of ventricular drainage-related bacterial meningitis by broad-range real-time polymerase chain reaction

    DEFF Research Database (Denmark)

    Deutch, Susanna; Dahlberg, Daniel; Hedegaard, Jesper;

    2007-01-01

    OBJECTIVE: To compare a broad-range real-time polymerase chain reaction (PCR) diagnostic strategy with culture to evaluate additional effects on the etiological diagnosis and the quantification of the bacterial load during the course of ventricular drainage-related bacterial meningitis (VR...

  4. Microvariation artifacts introduced by PCR and cloning of closely related 16S rRNA gene sequences

    NARCIS (Netherlands)

    Speksnijder, A.G.C.L.; Kowalchuk, G.A.; Jong, S. de; Kline, E.; Stephen, J.R.; Laanbroek, H.J.

    2001-01-01

    A defined template mixture of seven closely related 16S-rDNA clones was used in a PCR-cloning experiment to assess and track sources of artifactual sequence variation in 16S rDNA clone libraries. At least 14% of the recovered clones contained aberrations. Artifact sources were polymerase errors, a m

  5. Microvariation Artifacts Introduced by PCR and Cloning of Closely Related 16S rRNA Gene Sequences

    NARCIS (Netherlands)

    Speksnijder, A.G.C.L.; Kowalchuk, G.A.; Jong, de S.; Kline, E.; Stephen, J.R.; Laanbroek, H.J.

    2001-01-01

    A defined template mixture of seven closely related 16S-rDNA clones was used in a PCR-cloning experiment to assess and track sources of artifactual sequence variation in 16S rDNA clone libraries. At least 14% of the recovered clones contained aberrations. Artifact sources were polymerase errors, a m

  6. A new trilocus sequence-based multiplex-PCR to detect major Acinetobacter baumannii clones.

    Science.gov (United States)

    Martins, Natacha; Picão, Renata Cristina; Cerqueira-Alves, Morgana; Uehara, Aline; Barbosa, Lívia Carvalho; Riley, Lee W; Moreira, Beatriz Meurer

    2016-08-01

    A collection of 163 Acinetobacter baumannii isolates detected in a large Brazilian hospital, was potentially related with the dissemination of four clonal complexes (CC): 113/79, 103/15, 109/1 and 110/25, defined by University of Oxford/Institut Pasteur multilocus sequence typing (MLST) schemes. The urge of a simple multiplex-PCR scheme to specify these clones has motivated the present study. The established trilocus sequence-based typing (3LST, for ompA, csuE and blaOXA-51-like genes) multiplex-PCR rapidly identifies international clones I (CC109/1), II (CC118/2) and III (CC187/3). Thus, the system detects only one (CC109/1) out of four main CC in Brazil. We aimed to develop an alternative multiplex-PCR scheme to detect these clones, known to be present additionally in Africa, Asia, Europe, USA and South America. MLST, performed in the present study to complement typing our whole collection of isolates, confirmed that all isolates belonged to the same four CC detected previously. When typed by 3LST-based multiplex-PCR, only 12% of the 163 isolates were classified into groups. By comparative sequence analysis of ompA, csuE and blaOXA-51-like genes, a set of eight primers was designed for an alternative multiplex-PCR to distinguish the five CC 113/79, 103/15, 109/1, 110/25 and 118/2. Study isolates and one CC118/2 isolate were blind-tested with the new alternative PCR scheme; all were correctly clustered in groups of the corresponding CC. The new multiplex-PCR, with the advantage of fitting in a single reaction, detects five leading A. baumannii clones and could help preventing the spread in healthcare settings.

  7. PCR Cloning of Partial "nbs" Sequences from Grape ("Vitis aestivalis" Michx)

    Science.gov (United States)

    Chang, Ming-Mei; DiGennaro, Peter; Macula, Anthony

    2009-01-01

    Plants defend themselves against pathogens via the expressions of disease resistance (R) genes. Many plant R gene products contain the characteristic nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains. There are highly conserved motifs within the NBS domain which could be targeted for polymerase chain reaction (PCR) cloning of R…

  8. Construction of chimeric antibodies: cloning of immunoglobulin genes including their promoter regions by PCR.

    Science.gov (United States)

    Mocikat, R; Kütemeier, G; Harloff, C

    1992-03-01

    In the production of recombinant antibodies, it is necessary to have an immunoglobulin gene promoter for driving the expression of the antibody genes. Here we describe a simple PCR method that allows cloning of the immunoglobulin genes together with their own promoters despite the fact that the sequence of the upstream part of the gene is unknown.

  9. Rapid and Robust PCR-Based All-Recombinant Cloning Methodology.

    Science.gov (United States)

    Dubey, Abhishek Anil; Singh, Manika Indrajit; Jain, Vikas

    2016-01-01

    We report here a PCR-based cloning methodology that requires no post-PCR modifications such as restriction digestion and phosphorylation of the amplified DNA. The advantage of the present method is that it yields only recombinant clones thus eliminating the need for screening. Two DNA amplification reactions by PCR are performed wherein the first reaction amplifies the gene of interest from a source template, and the second reaction fuses it with the designed expression vector fragments. These vector fragments carry the essential elements that are required for the fusion product selection. The entire process can be completed in less than 8 hours. Furthermore, ligation of the amplified DNA by a DNA ligase is not required before transformation, although the procedure yields more number of colonies upon transformation if ligation is carried out. As a proof-of-concept, we show the cloning and expression of GFP, adh, and rho genes. Using GFP production as an example, we further demonstrate that the E. coli T7 express strain can directly be used in our methodology for the protein expression immediately after PCR. The expressed protein is without or with 6xHistidine tag at either terminus, depending upon the chosen vector fragments. We believe that our method will find tremendous use in molecular and structural biology. PMID:27007922

  10. A Lactobacillus plantarum esterase active on a broad range of phenolic esters.

    Science.gov (United States)

    Esteban-Torres, María; Landete, José María; Reverón, Inés; Santamaría, Laura; de las Rivas, Blanca; Muñoz, Rosario

    2015-05-01

    Lactobacillus plantarum is the lactic acid bacterial species most frequently found in the fermentation of food products of plant origin on which phenolic compounds are abundant. L. plantarum strains showed great flexibility in their ability to adapt to different environments and growth substrates. Of 28 L. plantarum strains analyzed, only cultures from 7 strains were able to hydrolyze hydroxycinnamic esters, such as methyl ferulate or methyl caffeate. As revealed by PCR, only these seven strains possessed the est_1092 gene. When the est_1092 gene was introduced into L. plantarum WCFS1 or L. lactis MG1363, their cultures acquired the ability to degrade hydroxycinnamic esters. These results support the suggestion that Est_1092 is the enzyme responsible for the degradation of hydroxycinnamic esters on the L. plantarum strains analyzed. The Est_1092 protein was recombinantly produced and biochemically characterized. Surprisingly, Est_1092 was able to hydrolyze not only hydroxycinnamic esters, since all the phenolic esters assayed were hydrolyzed. Quantitative PCR experiments revealed that the expression of est_1092 was induced in the presence of methyl ferulate, an hydroxycinnamic ester, but was inhibited on methyl gallate, an hydroxybenzoic ester. As Est_1092 is an enzyme active on a broad range of phenolic esters, simultaneously possessing feruloyl esterase and tannase activities, its presence on some L. plantarum strains provides them with additional advantages to survive and grow on plant environments.

  11. Detection of Mycobacterium tuberculosis in extrapulmonary biopsy samples using PCR targeting IS6110, rpoB and nested-rpoB PCR Cloning

    Directory of Open Access Journals (Sweden)

    Hossein eMeghdadi

    2015-07-01

    Full Text Available Present study was aimed to examine the diagnostic utility of PCR and nested PCR techniques for the detection of Mycobacterium tuberculosis (MTB DNA in samples from patients with extra pulmonary tuberculosis (EPTB. In total 80 formalin-fixed, paraffin-embedded (FFPE samples comprising 70 samples with definite diagnosis of EPTB and 10 samples from known non- EPTB on the basis of histopathology examination, were included in the study.PCR amplification targeting IS6110, rpoB gene and nested PCR targeting the rpoB gene were performed on the extracted DNAs from 80 FFPE samples. The strong positive samples were directly sequenced. For negative samples and those with weak band in nested-rpoB PCR, TA cloning was performed by cloning the products into the plasmid vector with subsequent sequencing. The 95% confidence intervals for the estimates of sensitivity and specificity were calculated for each method.Fourteen (20%, 34 (48.6% and 60 (85.7% of the 70 positive samples confirmed by histopathology, were positive by rpoB-PCR, IS6110- PCR and nested-rpoB PCR, respectively. By performing TA cloning on samples that yielded weak (no.=8 or negative results (no.=10 in the PCR methods, we were able to improve their quality for later sequencing. All samples with weak band and 7 out of 10 negative samples, showed strong positive results after cloning. So nested-rpoB PCR cloning revealed positivity in 67 out of 70 confirmed samples (95.7%. The sensitivity of these combination methods was calculated as 95.7% in comparison with histopathology examination. The confidence intervals for sensitivity of the PCR methods were calculated as 11.39-31.27% for rpoB-PCR, 36.44-60.83% for IS6110- PCR, 75.29-92.93% for nested-rpoB PCR and 87.98-99.11% for nested-rpoB PCR cloning. The 10 true EPTB negative samples by histopathology, were negative by all tested methods including cloning and were used to calculate the specificity of the applied methods. The confidence intervals for

  12. Characterization of a circulating PRRSV strain by means of random PCR cloning and full genome sequencing

    Directory of Open Access Journals (Sweden)

    Nauwynck Hans J

    2011-04-01

    Full Text Available Abstract PRRS is a pig disease of major economic importance that causes respiratory and reproductive problems in pigs. Over the last years it has become clear that PRRSV heterogeneity is increasing. Consequently, this has a potential impact on diagnosis and strategies to counter this disease. The use of sequence-independent PCR techniques for the detection and characterization of PRRSV could be useful to bypass problems associated with the heterogeneity of this virus. A random PCR cloning approach was tested for the characterization of PRRSV strain 07V063 of unknown genetic background that circulated on a Belgian farm. By using this approach, 7305 bp of sequence data were obtained, distributed randomly across the genome. Using RT-PCR with strain-specific primers, the full length sequence (15014 nt was obtained. Phylogenetic relationships using ORF5 and ORF1a (NSP2 sequences showed that 07V063 was classified in type 1 subtype 1 and that 07V063 was genetically different from prototype Lelystad Virus (LV. 07V063 showed 87-93% aa identity with LV ORFs coding for structural proteins. Most variation (compared to LV was noticed in Nsp2 (81% identity with a deletion of 28 aa. This deletion was different from other known deletions in this ORF. In conclusion, it is shown that this random PCR cloning approach can be used for the characterization of new PRRSV strains of unknown genetic background.

  13. Sources of blood meals of sylvatic Triatoma guasayana near Zurima, Bolivia, assayed with qPCR and 12S cloning.

    Directory of Open Access Journals (Sweden)

    David E Lucero

    2014-12-01

    Full Text Available In this study we compared the utility of two molecular biology techniques, cloning of the mitochondrial 12S ribosomal RNA gene and hydrolysis probe-based qPCR, to identify blood meal sources of sylvatic Chagas disease insect vectors collected with live-bait mouse traps (also known as Noireau traps. Fourteen T. guasayana were collected from six georeferenced trap locations in the Andean highlands of the department of Chuquisaca, Bolivia.We detected four blood meals sources with the cloning assay: seven samples were positive for human (Homo sapiens, five for chicken (Gallus gallus and unicolored blackbird (Agelasticus cyanopus, and one for opossum (Monodelphis domestica. Using the qPCR assay we detected chicken (13 vectors, and human (14 vectors blood meals as well as an additional blood meal source, Canis sp. (4 vectors.We show that cloning of 12S PCR products, which avoids bias associated with developing primers based on a priori knowledge, detected blood meal sources not previously considered and that species-specific qPCR is more sensitive. All samples identified as positive for a specific blood meal source by the cloning assay were also positive by qPCR. However, not all samples positive by qPCR were positive by cloning. We show the power of combining the cloning assay with the highly sensitive hydrolysis probe-based qPCR assay provides a more complete picture of blood meal sources for insect disease vectors.

  14. Overlap extension PCR cloning: a simple and reliable way to create recombinant plasmids.

    Science.gov (United States)

    Bryksin, Anton V; Matsumura, Ichiro

    2010-06-01

    Here we describe a straightforward, efficient, and reliable way to clone an insert of choice into a plasmid of choice without restriction endonucleases or T4 DNA ligase. Chimeric primers containing plasmid sequence at the 5' ends and insert sequence at the 3' ends were used to PCR-amplify insertion sequences of various sizes, namely the genes for GFP (gfp), beta-d-glucuronidase (gusA), and beta-galactosidase (lacZ), as well as the entire luxABCDE operon. These inserts were employed as mega-primers in a second PCR with a circular plasmid template. The original plasmid templates were then destroyed in restriction digests with DpnI, and the overlap extension PCR products were used to transform competent Escherichia coli cells. Phusion DNA polymerase was used for the amplification and fusion reactions, so both reactions were easy to monitor and optimize. PMID:20569222

  15. Overlap extension PCR cloning: a simple and reliable way to create recombinant plasmids

    OpenAIRE

    Bryksin, Anton V.; Matsumura, Ichiro

    2010-01-01

    Here we describe a straightforward, efficient, and reliable way to clone an insert of choice into a plasmid of choice without restriction endonucleases or T4 DNA ligase. Chimeric primers containing plasmid sequence at the 5′ ends and insert sequence at the 3′ ends were used to PCR-amplify insertion sequences of various sizes, namely the genes for GFP (gfp), β-D-glucuronidase (gusA), and β-galactosidase (lacZ), as well as the entire luxABCDE operon. These inserts were employed as mega-primers ...

  16. Fusion primer and nested integrated PCR (FPNI-PCR: a new high-efficiency strategy for rapid chromosome walking or flanking sequence cloning

    Directory of Open Access Journals (Sweden)

    Wang Zhen

    2011-11-01

    Full Text Available Abstract Background The advent of genomics-based technologies has revolutionized many fields of biological enquiry. However, chromosome walking or flanking sequence cloning is still a necessary and important procedure to determining gene structure. Such methods are used to identify T-DNA insertion sites and so are especially relevant for organisms where large T-DNA insertion libraries have been created, such as rice and Arabidopsis. The currently available methods for flanking sequence cloning, including the popular TAIL-PCR technique, are relatively laborious and slow. Results Here, we report a simple and effective fusion primer and nested integrated PCR method (FPNI-PCR for the identification and cloning of unknown genomic regions flanked known sequences. In brief, a set of universal primers was designed that consisted of various 15-16 base arbitrary degenerate oligonucleotides. These arbitrary degenerate primers were fused to the 3' end of an adaptor oligonucleotide which provided a known sequence without degenerate nucleotides, thereby forming the fusion primers (FPs. These fusion primers are employed in the first step of an integrated nested PCR strategy which defines the overall FPNI-PCR protocol. In order to demonstrate the efficacy of this novel strategy, we have successfully used it to isolate multiple genomic sequences namely, 21 orthologs of genes in various species of Rosaceace, 4 MYB genes of Rosa rugosa, 3 promoters of transcription factors of Petunia hybrida, and 4 flanking sequences of T-DNA insertion sites in transgenic tobacco lines and 6 specific genes from sequenced genome of rice and Arabidopsis. Conclusions The successful amplification of target products through FPNI-PCR verified that this novel strategy is an effective, low cost and simple procedure. Furthermore, FPNI-PCR represents a more sensitive, rapid and accurate technique than the established TAIL-PCR and hiTAIL-PCR procedures.

  17. MEGAWHOP cloning: a method of creating random mutagenesis libraries via megaprimer PCR of whole plasmids.

    Science.gov (United States)

    Miyazaki, Kentaro

    2011-01-01

    MEGAWHOP allows for the cloning of DNA fragments into a vector and is used for conventional restriction digestion/ligation-based procedures. In MEGAWHOP, the DNA fragment to be cloned is used as a set of complementary primers that replace a homologous region in a template vector through whole-plasmid PCR. After synthesis of a nicked circular plasmid, the mixture is treated with DpnI, a dam-methylated DNA-specific restriction enzyme, to digest the template plasmid. The DpnI-treated mixture is then introduced into competent Escherichia coli cells to yield plasmids carrying replaced insert fragments. Plasmids produced by the MEGAWHOP method are virtually free of contamination by species without any inserts or with multiple inserts, and also the parent. Because the fragment is usually long enough to not interfere with hybridization to the template, various types of fragments can be used with mutations at any site (either known or unknown, random, or specific). By using fragments having homologous sequences at the ends (e.g., adaptor sequence), MEGAWHOP can also be used to recombine nonhomologous sequences mediated by the adaptors, allowing rapid creation of novel constructs and chimeric genes. PMID:21601687

  18. Cloning a Full-length cDNA Encoding UDP-glucose Pyrophosphorylase from Amorpha fruticosa by PCR-based Methods

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    A method based on degenerate Oligo-primed polymerase chain reaction (PCR) and random amplification of cDNA end (RACE) PCR for cloning a full-length cDNA is described. An Amorpha fruticosa cDNA clone encoding UDP-glucose pyrophosphorylase (UGP), a key enzyme producing UDP-glucose in the synthesis of sucrose and cell ulose, is cloned by using this method. We design 5' RACE primers based on UGP A1 fragment, which obtains from degenerate PCR. Inverse PCR and nested PCR enable cloning of the remainder 5' and 3' end fragments of the gene. The deduced amino acid sequence exhibits significant homology with the other UGP genes cloned. This method is more simple and inexpensive than screening cDNA library, and can be easily adapted to clone other genes.

  19. Activation of toll-like receptors and dendritic cells by a broad range of bacterial molecules

    NARCIS (Netherlands)

    Boele, L.C.L.; Bajramovic, J.J.; Vries, A.M.M.B.C. de; Voskamp-Visser, I.A.I.; Kaman, W.E.; Kleij, D. van der

    2009-01-01

    Activation of pattern recognition receptors such as Toll-like receptors (TLRs) by pathogens leads to activation and maturation of dendritic cells (DC), which orchestrate the development of the adaptive immune response. To create an overview of the effects of a broad range of pathogenic bacteria, the

  20. Clones identification of Sequoia sempervirens (D.Don) Endl.in Chile by using PCR-RAPDs technique

    Institute of Scientific and Technical Information of China (English)

    Manuel TORAL IBA(N)EZ; Margarita CARU; Miguel A.HERRERA; Luis GONZALEZ; Luis M.MARTIN; Jorge MIRANDA; Rafael M.NAVARRO-CERRILLO

    2009-01-01

    A protocol of polymerase chain reaction-random amplified polymorphic DNAs (PCR-RAPDs) was established to analyse the gene diversity and genotype identification for clones of Sequoia sempervirens (D.Don) Endl.in Chile.Ten (out of 34) clones from introduction trial located in Voipir-Viilarrica,Chile,were studied.The PCR-RAPDs technique and a modified hexadecyltrimethylammonium bromide (CTAB) protocol were used for genomic DNA extraction.The PCR tests were carried out employing 10-mer random primers.The amplification products were detected by electrophoresis in agarose gels.Forty nine polymorphic bands were obtained with the selected primers (BG04,BF07,BF 12,BF13,and BF 14) and were ordered according to their molecular size.The genetic similarity between samples was calculated by the Jaccard index and a dendrogram was constructed using a cluster analysis of unweighted pair group method using arithmetic averages (UPGMA).Of the primers tested,5 (out of 60) RAPD primers were selected for their reproducibility and high polymorphism.A total of 49 polymorphic RAPD bands were detected out of 252 bands.The genetic similarity analysis demonstrates an extensive genetic variability between the tested clones and the dendrogram depicts the genetic relationships among the clones,suggesting a geographic relationship.The results indicate that the RAPD markers permitted the identification of the assayed clones,although they are derived from the same geographic origin.

  1. Changes in the Composition of Drinking Water Bacterial Clone Libraries Introduced by Using Two Different 16S rRNA Gene PCR Primers

    Science.gov (United States)

    Sequence analysis of 16S rRNA gene clone libraries is a popular tool used to describe the composition of natural microbial communities. Commonly, clone libraries are developed by direct cloning of 16S rRNA gene PCR products. Different primers are often employed in the initial amp...

  2. Broad range pH sensor based on sol-gel

    Institute of Scientific and Technical Information of China (English)

    Bai Xiao-peng

    2014-01-01

    A broad-range fibre optic pH sensor based on evanescent wave absorption is presented in this paper. This sensor is prepared by immobilizing a mixture of three pH sensitive indicators (dyes):cresol red, bromophenol blue and chlorophenol red onto the unclad fibre surface using a sol–gel cladding technology. Triton is introduced into the sol–gel cladding to improve the cladding quality. Smooth and strong sol–gel cladding with entrapped indicators and triton has been fabricated and observed using a scanning electron microscope (SEM), an energy dispersive X-ray detector (EDX) and an atomic force microscopy (AFM). The pH sensor based the cladding has shown a linear, reversible and repeatable response over a broad range of pH values between 4.5 and 13.0.

  3. Harnessing prions as test agents for the development of broad-range disinfectants

    OpenAIRE

    Wagenführ, Katja; Beekes, Michael

    2012-01-01

    The development of disinfectants with broad-range efficacy against bacteria, viruses, fungi, protozoa and prions constitutes an ongoing challenge. Prions, the causative agents of transmissible spongiform encephalopathies (TSEs) such as Creutzfeldt-Jakob disease (CJD) or its variant (vCJD) rank among the pathogens with the highest resistance to disinfection. Pilot studies have shown that different procedures devised for prion disinfection were also highly effective against microbial pathogens....

  4. Cloning of Thymidine Kinase Gene of Duck Plague Virus Using Degenerate PCR

    Institute of Scientific and Technical Information of China (English)

    HAN Xian-jie; WANG Jun-wei

    2005-01-01

    The DNA of duck plague virus (DPV) thymidine kinase (TK) gene was cloned and sequenced from a vaccine virus in the study. Degenerate oligonucleotide primers for the consensus site of herpesvirus UL24, TK, and glycoprotein H(gH) gene were used in the polymerase chain reaction (PCR) to amplify DNA product with 3 741-base-pairs (bp) in size. DNA sequence analysis revealed a 1 077-base-pairs (bp) open reading frame (ORF) encoding a 358 amino acid polypeptide homologous to herpesvirus TK proteins. The predicted TK protein shared 31.2, 41.3, 35.7, 37.4, and 28.4% identity with herpes simplex virus typel, equine herpesvirus type 4, Marek's disease virus 2, herpesvirus turkey, and infectious laryngotracheitis virus, respectively. Comparison of the amino acid sequences of other herpesvirus TK proteins showed that these proteins were not conserved on the whole, otherwise the portion of the TK proteins corresponding to the nucleotide binding domain and the nucleoside binding site were highly conserved among herpesvirus. Comparison with the amino acid sequences of the conserved nucleotide and nucleoside binding domains of other eleven herpesvirus TK proteins to the predicted DPV peptide confirmed its identity as the DPV TK protein.

  5. Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning.

    Science.gov (United States)

    Qiu, X; Wu, L; Huang, H; McDonel, P E; Palumbo, A V; Tiedje, J M; Zhou, J

    2001-02-01

    To evaluate PCR-generated artifacts (i.e., chimeras, mutations, and heteroduplexes) with the 16S ribosomal DNA (rDNA)-based cloning approach, a model community of four species was constructed from alpha, beta, and gamma subdivisions of the division Proteobacteria as well as gram-positive bacterium, all of which could be distinguished by HhaI restriction digestion patterns. The overall PCR artifacts were significantly different among the three Taq DNA polymerases examined: 20% for Z-Taq, with the highest processitivity; 15% for LA-Taq, with the highest fidelity and intermediate processitivity; and 7% for the conventionally used DNA polymerase, AmpliTaq. In contrast to the theoretical prediction, the frequency of chimeras for both Z-Taq (8.7%) and LA-Taq (6.2%) was higher than that for AmpliTaq (2.5%). The frequencies of chimeras and of heteroduplexes for Z-Taq were almost three times higher than those of AmpliTaq. The total PCR artifacts increased as PCR cycles and template concentrations increased and decreased as elongation time increased. Generally the frequency of chimeras was lower than that of mutations but higher than that of heteroduplexes. The total PCR artifacts as well as the frequency of heteroduplexes increased as the species diversity increased. PCR artifacts were significantly reduced by using AmpliTaq and fewer PCR cycles (fewer than 20 cycles), and the heteroduplexes could be effectively removed from PCR products prior to cloning by polyacrylamide gel purification or T7 endonuclease I digestion. Based upon these results, an optimal approach is proposed to minimize PCR artifacts in 16S rDNA-based microbial community studies.

  6. Restriction-ligation-free (RLF) cloning: a high-throughput cloning method by in vivo homologous recombination of PCR products.

    Science.gov (United States)

    Wang, Y; Liu, Y; Chen, J; Tang, M J; Zhang, S L; Wei, L N; Li, C H; Wei, D B

    2015-01-01

    In this study, we optimized a restriction-ligation-free (RLF) method to save time and cost of constructing multiple plasmids with the same gene insert, and examined the efficacy of RLF on high-throughput multi-plasmid cloning. This method utilizes the precise DNA repair and recombination systems within Escherichia coli, which allows to bypass the in vitro restriction and ligation enzyme reactions commonly included in routine cloning procedures. A homologous arm is linked to the 5'-end of the forward primer used to amplify both the target gene and vector. A different homologous arm is linked to the 5'-end of the reverse primer. Therefore, genes can be cloned into the vectors by homologous recombination after co-transformation of the amplified target gene and the linearized vector, which bear the same homologous arm on either end. More than twenty-four different plasmids were generated by this method, which uses two simple polymerase chain reaction steps. This method is highly efficient in cloning any gene of interest into any vector at any site without sequence constraints, as no restriction and ligation reactions are required. PMID:26505379

  7. NGS tools for traceability in candies as high processed food products: Ion Torrent PGM versus conventional PCR-cloning.

    Science.gov (United States)

    Muñoz-Colmenero, Marta; Martínez, Jose Luis; Roca, Agustín; Garcia-Vazquez, Eva

    2017-01-01

    The Next Generation Sequencing methodologies are considered the next step within DNA-based methods and their applicability in different fields is being evaluated. Here, we tested the usefulness of the Ion Torrent Personal Genome Machine (PGM) in food traceability analyzing candies as a model of high processed foods, and compared the results with those obtained by PCR-cloning-sequencing (PCR-CS). The majority of samples exhibited consistency between methodologies, yielding more information and species per product from the PGM platform than PCR-CS. Significantly higher AT-content in sequences of the same species was also obtained from PGM. This together with some taxonomical discrepancies between methodologies suggest that the PGM platform is still pre-mature for its use in food traceability of complex highly processed products. It could be a good option for analysis of less complex food, saving time and cost per sample.

  8. NGS tools for traceability in candies as high processed food products: Ion Torrent PGM versus conventional PCR-cloning.

    Science.gov (United States)

    Muñoz-Colmenero, Marta; Martínez, Jose Luis; Roca, Agustín; Garcia-Vazquez, Eva

    2017-01-01

    The Next Generation Sequencing methodologies are considered the next step within DNA-based methods and their applicability in different fields is being evaluated. Here, we tested the usefulness of the Ion Torrent Personal Genome Machine (PGM) in food traceability analyzing candies as a model of high processed foods, and compared the results with those obtained by PCR-cloning-sequencing (PCR-CS). The majority of samples exhibited consistency between methodologies, yielding more information and species per product from the PGM platform than PCR-CS. Significantly higher AT-content in sequences of the same species was also obtained from PGM. This together with some taxonomical discrepancies between methodologies suggest that the PGM platform is still pre-mature for its use in food traceability of complex highly processed products. It could be a good option for analysis of less complex food, saving time and cost per sample. PMID:27507519

  9. Nanoporous Anodic Alumina 3D FDTD Modelling for a Broad Range of Inter-pore Distances.

    Science.gov (United States)

    Bertó-Roselló, Francesc; Xifré-Pérez, Elisabet; Ferré-Borrull, Josep; Pallarès, Josep; Marsal, Lluis F

    2016-12-01

    The capability of the finite difference time domain (FDTD) method for the numerical modelling of the optical properties of nanoporous anodic alumina (NAA) in a broad range of inter-pore distances is evaluated. FDTD permits taking into account in the same numerical framework all the structural features of NAA, such as the texturization of the interfaces or the incorporation of electrolyte anions in the aluminium oxide host. The evaluation is carried out by comparing reflectance measurements from two samples with two very different inter-pore distances with the simulation results. Results show that considering the texturization is crucial to obtain good agreement with the measurements. On the other hand, including the anionic layer in the model leads to a second-order contribution to the reflectance spectrum. PMID:27518230

  10. Nanoporous Anodic Alumina 3D FDTD Modelling for a Broad Range of Inter-pore Distances

    Science.gov (United States)

    Bertó-Roselló, Francesc; Xifré-Pérez, Elisabet; Ferré-Borrull, Josep; Pallarès, Josep; Marsal, Lluis F.

    2016-08-01

    The capability of the finite difference time domain (FDTD) method for the numerical modelling of the optical properties of nanoporous anodic alumina (NAA) in a broad range of inter-pore distances is evaluated. FDTD permits taking into account in the same numerical framework all the structural features of NAA, such as the texturization of the interfaces or the incorporation of electrolyte anions in the aluminium oxide host. The evaluation is carried out by comparing reflectance measurements from two samples with two very different inter-pore distances with the simulation results. Results show that considering the texturization is crucial to obtain good agreement with the measurements. On the other hand, including the anionic layer in the model leads to a second-order contribution to the reflectance spectrum.

  11. Peracetic Acid Treatment Generates Potent Inactivated Oral Vaccines from a Broad Range of Culturable Bacterial Species.

    Science.gov (United States)

    Moor, Kathrin; Wotzka, Sandra Y; Toska, Albulena; Diard, Médéric; Hapfelmeier, Siegfried; Slack, Emma

    2016-01-01

    Our mucosal surfaces are the main sites of non-vector-borne pathogen entry, as well as the main interface with our commensal microbiota. We are still only beginning to understand how mucosal adaptive immunity interacts with commensal and pathogenic microbes to influence factors such as infectivity, phenotypic diversity, and within-host evolution. This is in part due to difficulties in generating specific mucosal adaptive immune responses without disrupting the mucosal microbial ecosystem itself. Here, we present a very simple tool to generate inactivated mucosal vaccines from a broad range of culturable bacteria. Oral gavage of 10(10) peracetic acid-inactivated bacteria induces high-titer-specific intestinal IgA in the absence of any measurable inflammation or species invasion. As a proof of principle, we demonstrate that this technique is sufficient to provide fully protective immunity in the murine model of invasive non-typhoidal Salmonellosis, even in the face of severe innate immune deficiency. PMID:26904024

  12. Construction and use of lambda PL promoter vectors for direct cloning and high level expression of PCR amplified DNA coding sequences.

    OpenAIRE

    Cheng, X.; Patterson, T A

    1992-01-01

    A set of plasmid vectors which allow single-step cloning and expression of PCR-amplified DNA coding sequences has been constructed. The vectors contain the phage lambda PL promoter, a synthetic translation initiation region (TIR), and convenient cloning sites. The cloning sites provide all or part of an AUG translation initiation codon and facilitate the precise fusion of target DNA sequences to vector transcriptional and translational signals. The vectors were constructed with synthetic TIRs...

  13. Cloning

    Science.gov (United States)

    ... copies of whole animals Therapeutic cloning, which creates embryonic stem cells. Researchers hope to use these cells to grow healthy tissue to replace injured or diseased tissues in the human body. NIH: National Human Genome Research Institute

  14. Stable encoding of sounds over a broad range of statistical parameters in the auditory cortex.

    Science.gov (United States)

    Blackwell, Jennifer M; Taillefumier, Thibaud O; Natan, Ryan G; Carruthers, Isaac M; Magnasco, Marcelo O; Geffen, Maria N

    2016-03-01

    Natural auditory scenes possess highly structured statistical regularities, which are dictated by the physics of sound production in nature, such as scale-invariance. We recently identified that natural water sounds exhibit a particular type of scale invariance, in which the temporal modulation within spectral bands scales with the centre frequency of the band. Here, we tested how neurons in the mammalian primary auditory cortex encode sounds that exhibit this property, but differ in their statistical parameters. The stimuli varied in spectro-temporal density and cyclo-temporal statistics over several orders of magnitude, corresponding to a range of water-like percepts, from pattering of rain to a slow stream. We recorded neuronal activity in the primary auditory cortex of awake rats presented with these stimuli. The responses of the majority of individual neurons were selective for a subset of stimuli with specific statistics. However, as a neuronal population, the responses were remarkably stable over large changes in stimulus statistics, exhibiting a similar range in firing rate, response strength, variability and information rate, and only minor variation in receptive field parameters. This pattern of neuronal responses suggests a potentially general principle for cortical encoding of complex acoustic scenes: while individual cortical neurons exhibit selectivity for specific statistical features, a neuronal population preserves a constant response structure across a broad range of statistical parameters. PMID:26663571

  15. Personal glucose meters for detection and quantification of a broad range of analytes

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Yi; Xiang, Yu

    2015-02-03

    A general methodology for the development of highly sensitive and selective sensors that can achieve portable, low-cost and quantitative detection of a broad range of targets using only a personal glucose meter (PGM) is disclosed. The method uses recognition molecules that are specific for a target agent, enzymes that can convert an enzyme substrate into glucose, and PGM. Also provided are sensors, which can include a solid support to which is attached a recognition molecule that permits detection of a target agent, wherein the recognition molecule specifically binds to the target agent in the presence of the target agent but not significantly to other agents as well as an enzyme that can catalyze the conversion of a substance into glucose, wherein the enzyme is attached directly or indirectly to the recognition molecule, and wherein in the presence of the target agent the enzyme can convert the substance into glucose. The disclosed sensors can be part of a lateral flow device. Methods of using such sensors for detecting target agents are also provided.

  16. Oxidative Stress and Mitochondrial Dysfunction across Broad-Ranging Pathologies: Toward Mitochondria-Targeted Clinical Strategies

    Directory of Open Access Journals (Sweden)

    Giovanni Pagano

    2014-01-01

    Full Text Available Beyond the disorders recognized as mitochondrial diseases, abnormalities in function and/or ultrastructure of mitochondria have been reported in several unrelated pathologies. These encompass ageing, malformations, and a number of genetic or acquired diseases, as diabetes and cardiologic, haematologic, organ-specific (e.g., eye or liver, neurologic and psychiatric, autoimmune, and dermatologic disorders. The mechanistic grounds for mitochondrial dysfunction (MDF along with the occurrence of oxidative stress (OS have been investigated within the pathogenesis of individual disorders or in groups of interrelated disorders. We attempt to review broad-ranging pathologies that involve mitochondrial-specific deficiencies or rely on cytosol-derived prooxidant states or on autoimmune-induced mitochondrial damage. The established knowledge in these subjects warrants studies aimed at elucidating several open questions that are highlighted in the present review. The relevance of OS and MDF in different pathologies may establish the grounds for chemoprevention trials aimed at compensating OS/MDF by means of antioxidants and mitochondrial nutrients.

  17. Universal scaling law for the condensation energy across a broad range of superconductor classes

    Science.gov (United States)

    Kim, J. S.; Tam, G. N.; Stewart, G. R.

    2015-12-01

    One of the goals in understanding any new class of superconductors is to search for commonalities with other known superconductors. The present work investigates the superconducting condensation energy, U , in the iron based superconductors (IBSs), and compares their U with a broad range of other distinct classes of superconductor, including conventional BCS elements and compounds and the unconventional heavy fermion, S r2Ru O4 ,L i0.1ZrNCl ,κ -(BEDT-TTF)2Cu (NCS )2 , and optimally doped cuprate superconductors. Surprisingly, both the magnitude and Tc dependence (U ∝Tc3.4 ±0.2 ) of U are—contrary to the previously observed behavior of the specific heat discontinuity at Tc, Δ C —quite similar in the IBS and BCS materials for Tc>1.4 K. In contrast, the heavy fermion superconductors' U vs Tc are strongly (up to a factor of 100) enhanced above the IBS/BCS while the cuprate superconductors' U are strongly (factor of 8) reduced. However, scaling of U with the specific heat γ (or Δ C ) brings all the superconductors investigated onto one universal dependence upon Tc. This apparent universal scaling U / γ ∝Tc2 for all superconductor classes investigated, both weak and strong coupled and both conventional and unconventional, links together extremely disparate behaviors over almost seven orders of magnitude for U and almost three orders of magnitude for Tc. Since U has not yet been explicitly calculated beyond the weak coupling limit, the present results can help direct theoretical efforts into the medium and strong coupling regimes.

  18. Cloning of a Resistance Gene Analog from Wheat and Development of a Codominant PCR Marker for Pm21

    Institute of Scientific and Technical Information of China (English)

    Ya-Ping Chen; Hua-Zhong Wang; Ai-Zhong Cao; Chun-Mei Wang; Pei-Du Chen

    2006-01-01

    To investigate the mechanism of resistance to wheat (Triticum aestivum L.) powdery mildew, suppression subtractive hybridization was conducted between an isogenic resistant line carrying Pm21 and its recurrent parent Yangmai 5 to isolate the resistance relative genes. A cDNA fragment specifically expressed in the resistant line was obtained and its full length was cloned by in silico cloning and RT-PCR. This gene encoded a deduced protein of 219 amino acids with a leucine-rich repeat (LRR) motif, often found in plant resistance genes, and was designated as Ta-LRR2. Ta-LRR2 had an increased expression level in the resistant line after inoculation with Erysiphe graminis DC. f. sp. tritici Marchal. PCR analysis with different cytogenetic stocks suggested that Ta-LRR2 was specifically associated with chromosome arms 6VS and 6AS. Linkage analysis further showed that Ta-LRR2 could be used as a resistance gene analog polymorphism marker of Pm21 for marker-assisted selection in germplasm enhancement and breeding practice.Moreover, how to isolate Pm21 based on the information obtained for Ta-LRR2 is discussed.

  19. Construction of infectious cDNA clone derived from a classical swine fever virus field isolate in BAC vector using in vitro overlap extension PCR and recombination.

    Science.gov (United States)

    Kamboj, Aman; Saini, Mohini; Rajan, Lekshmi S; Patel, Chhabi Lal; Chaturvedi, V K; Gupta, Praveen K

    2015-12-15

    To develop reverse genetics system of RNA viruses, cloning of full-length viral genome is required which is often challenging due to many steps involved. In this study, we report cloning of full-length cDNA from an Indian field isolate (CSFV/IVRI/VB-131) of classical swine fever virus (CSFV) using in vitro overlap extension PCR and recombination which drastically reduced the number of cloning steps. The genome of CSFV was amplified in six overlapping cDNA fragments, linked by overlap extension PCR and cloned in a bacterial artificial chromosome (BAC) vector using in vitro recombination method to generate full-length cDNA clone. The full-length CSFV cDNA clone was found stable in E. coli Stellar and DH10B cells. The full-length RNA was transcribed in vitro using T7 RNA polymerase and transfected in PK15 cells using Neon-tip electroporator to rescue infectious CSFV. The progeny CSFV was propagated in PK15 cells and found indistinguishable from the parent virus. The expression of CSFV proteins were detected in cytoplasm of PK15 cells infected with progeny CSFV at 72 h post-infection. We concluded that the in vitro overlap extension PCR and recombination method is useful to construct stable full-length cDNA clone of RNA virus in BAC vector. PMID:26478540

  20. A PCR-based method for manipulation of the vaccinia virus genome that eliminates the need for cloning.

    Science.gov (United States)

    Turner, P C; Moyer, R W

    1992-11-01

    A general method is described for altering specific genes of vaccinia virus (VV). We demonstrate and evaluate the procedure by gene inactivation, using a dominant selectable marker in conjunction with recombinant polymerase chain reaction (PCR). Primers based on the sequence of the target gene enable amplification of flanking arms and their subsequent attachment to the gpt cassette that confers resistance to mycophenolic acid. Linear PCR constructs are transfected into cells infected with wild-type vaccinia virus. Mutant viruses with gpt inserted into the target gene by homologous recombination are then selected by growth in the presence of MPA. This technique was applied to the vaccinia virus thymidine kinase gene and compared to the traditional method of constructing gpt-containing plasmids by cloning. The PCR scheme was found to be highly efficient and could theoretically be used to insert any foreign DNA element into any nonessential target gene for which partial or complete sequence information is available. The procedure can potentially be used for a wide variety of genetic modifications, including the insertion of foreign genes, with poxviruses and other DNA viruses. Genomes of microorganisms, such as bacteria and yeast that can be transformed with linear DNA, are also candidates for manipulation by this methodology.

  1. Bridging PCR and partially overlapping primers for novel allergen gene cloning and expression insert decoration

    Institute of Scientific and Technical Information of China (English)

    Ai-Lin Tao; Shao-Heng He

    2004-01-01

    AIM: To obtain the entire gene open reading frame (ORF)and to construct the expression vectors for recombinant allergen production.METHODS: Gene fragments corresponding to the gene specific region and the cDNA ends of pollen allergens of short ragweed (Rg, Ambrosia artemisiifolia L.) were obtained by pan-degenerate primer-based PCR and rapid amplification of the cDNA ends (RACE), and the products were mixed to serve as the bridging PCR (BPCR) template. The full-length gene was then obtained. Partially overlapping primer-based PCR (POP-PCR) method was developed to overcome the other problem, i.e., the non-specific amplification of the ORF with routine long primers for expression insert decoration.Northern blot was conducted to confirm pollen sources of the gene. The full-length coding region was evaluated for its gene function by homologue search in GenBank database and Western blotting of the recombinant protein Amb a 8 (D106) expressed in Escherichia colipET-44 system.RESULTS: The full-length cDNA sequence of Amb a 8(D106)was obtained by using the above procedure and deduced to encode a 131 amino acid polypeptide. Multiple sequence alignment exhibited the gene D106sharing a homology as high as 54-89% and 79-89% to profilin from pollen and food sources, respectively. The expression vector of the allergen gene D106was successfully constructed by employing the combined method of BPCR and POP-PCR. Recombinant allergen rAmb a 8(D106) was then successfully generated.The allergenicity was hallmarked by immunoblotting with the allergic serum samples and its RNA source was confirmed by Northern blot.CONCLUSION: The combined procedure of POP-PCR and BPCR is a powerful method for full-length allergen gene retrieval and expression insert decoration, which would be useful for recombinant allergen production and subsequent diagnosis and immunotherapy of pollen and food allergy.

  2. An improved PCR strategy for fast screening of specific and random integrations in rAAV-mediated gene targeted cell clones

    Directory of Open Access Journals (Sweden)

    Sørensen Charlotte B

    2011-07-01

    Full Text Available Abstract Background Gene targeting by homologous recombination using recombinant adeno-associated virus (rAAV is becoming a useful tool for basic research and therapeutic applications due to the remarkably high targeting frequency of rAAV virus vectors. However, the screening for the pure gene-targeted and random-integration-free primary cell clones is difficult since the cells have a limited proliferation capacity and often cannot be grown to produce sufficient DNA for non-PCR based analysis. This hampers the applications of this technology. Findings In this study, we have developed an improved PCR screening method, which can be used for fast screening of clones with unwanted random integration (RI of the rAAV genome. This improved screening method includes four PCRs: a PCR for the selection gene (e.g. Neo-PCR, a PCR for targeted gene knockout (e.g. BRCA1-KO-PCR, and two generalized PCRs for random integration of the rAAV genome (5'-AAV-RI-PCR, and 3'-AAV-RI-PCR. We have shown that this screening method greatly facilitates the procedure of screening for BRCA1 (BReast CAncer susceptibility gene 1 targeted cell clones, eliminating cell clones with both BRCA1 knockout and random integration of the rAAV genome. Conclusions This screening method has facilitated the screening of correct gene-targeted cells. As the AAV-RI-PCRs are generalized PCRs, this method can also be applied for screening of rAAV-mediated targeting of other genes.

  3. Automated Broad-Range Molecular Detection of Bacteria in Clinical Samples.

    Science.gov (United States)

    Budding, Andries E; Hoogewerf, Martine; Vandenbroucke-Grauls, Christina M J E; Savelkoul, Paul H M

    2016-04-01

    Molecular detection methods, such as quantitative PCR (qPCR), have found their way into clinical microbiology laboratories for the detection of an array of pathogens. Most routinely used methods, however, are directed at specific species. Thus, anything that is not explicitly searched for will be missed. This greatly limits the flexibility and universal application of these techniques. We investigated the application of a rapid universal bacterial molecular identification method, IS-pro, to routine patient samples received in a clinical microbiology laboratory. IS-pro is a eubacterial technique based on the detection and categorization of 16S-23S rRNA gene interspace regions with lengths that are specific for each microbial species. As this is an open technique, clinicians do not need to decide in advance what to look for. We compared routine culture to IS-pro using 66 samples sent in for routine bacterial diagnostic testing. The samples were obtained from patients with infections in normally sterile sites (without a resident microbiota). The results were identical in 20 (30%) samples, IS-pro detected more bacterial species than culture in 31 (47%) samples, and five of the 10 culture-negative samples were positive with IS-pro. The case histories of the five patients from whom these culture-negative/IS-pro-positive samples were obtained suggest that the IS-pro findings are highly clinically relevant. Our findings indicate that an open molecular approach, such as IS-pro, may have a high added value for clinical practice. PMID:26763956

  4. FTO gene associated fatness in relation to body fat distribution and metabolic traits throughout a broad range of fatness

    DEFF Research Database (Denmark)

    Kring, Sofia I I; Holst, Claus; Zimmermann, Esther;

    2008-01-01

    A common single nucleotide polymorphism (SNP) of FTO (rs9939609, T/A) is associated with total body fatness. We investigated the association of this SNP with abdominal and peripheral fatness and obesity-related metabolic traits in middle-aged men through a broad range of fatness present already...

  5. Multiplex PCR for Simultaneous Detection of Bacteria of the Genus Listeria, Listeria monocytogenes, and Major Serotypes and Epidemic Clones of L. monocytogenes▿

    OpenAIRE

    Chen, Yi; Knabel, Stephen J.

    2007-01-01

    A multiplex PCR assay which combines detection of bacteria of the genus Listeria, Listeria monocytogenes serotypes 1/2a and 4b, and epidemic clones I, II, and III of L. monocytogenes was developed. The assay provides a rapid, reliable, and inexpensive method for screening and subgrouping this important food-borne pathogen.

  6. Cloning of ribosomal ITS PCR products creates frequent, non-random chimeric sequences – a test involving heterozygotes between Gymnopus dichrous taxa I and II

    Directory of Open Access Journals (Sweden)

    Karen W. Hughes

    2015-06-01

    Full Text Available Gymnopus dichrous exists in the southern Appalachians (USA as two distinct entities with essentially identical nuclear ribosomal ITS1 sequences but differing ITS2 and LSU sequences (for convenience, called G. dichrous I and II. F1 ITS heterozygotes between the two are routinely collected from nature. Cloning of ITS PCR products from F1 heterozygotes produced sequences of both parental haplotypes but also numerous chimeric sequences (21.9%. The location of template switching was non-random leading to recovery of the same chimera several times and the chimeric region varied from 45bp to 300bp. By comparison, single-basidiospore isolates from heterozygote F1 fruitbodies showed no recombinant haplotypes within the ITS + LSU span and clones derived from P1 homozygotes were identical to the P1 parent. Thus, chimeric sequences are likely an artifact of the PCR-cloning process and not a consequence of natural recombination events found in nature, nor are they due to hidden existing variation within the ribosomal repeat. Chimeras and PCR-induced mutations are common in cloned PCR products and may result in incorrect sequence information in public databases.

  7. A simple, flexible and efficient PCR-fusion/Gateway cloning procedure for gene fusion, site-directed mutagenesis, short sequence insertion and domain deletions and swaps

    Directory of Open Access Journals (Sweden)

    Etchells J Peter

    2009-10-01

    Full Text Available Abstract Background The progress and completion of various plant genome sequencing projects has paved the way for diverse functional genomic studies that involve cloning, modification and subsequent expression of target genes. This requires flexible and efficient procedures for generating binary vectors containing: gene fusions, variants from site-directed mutagenesis, addition of protein tags together with domain swaps and deletions. Furthermore, efficient cloning procedures, ideally high throughput, are essential for pyramiding of multiple gene constructs. Results Here, we present a simple, flexible and efficient PCR-fusion/Gateway cloning procedure for construction of binary vectors for a range of gene fusions or variants with single or multiple nucleotide substitutions, short sequence insertions, domain deletions and swaps. Results from selected applications of the procedure which include ORF fusion, introduction of Cys>Ser mutations, insertion of StrepII tag sequence and domain swaps for Arabidopsis secondary cell wall AtCesA genes are demonstrated. Conclusion The PCR-fusion/Gateway cloning procedure described provides an elegant, simple and efficient solution for a wide range of diverse and complicated cloning tasks. Through streamlined cloning of sets of gene fusions and modification variants into binary vectors for systematic functional studies of gene families, our method allows for efficient utilization of the growing sequence and expression data.

  8. PrecisePrimer: an easy-to-use web server for designing PCR primers for DNA library cloning and DNA shuffling.

    Science.gov (United States)

    Pauthenier, Cyrille; Faulon, Jean-Loup

    2014-07-01

    PrecisePrimer is a web-based primer design software made to assist experimentalists in any repetitive primer design task such as preparing, cloning and shuffling DNA libraries. Unlike other popular primer design tools, it is conceived to generate primer libraries with popular PCR polymerase buffers proposed as pre-set options. PrecisePrimer is also meant to design primers in batches, such as for DNA libraries creation of DNA shuffling experiments and to have the simplest interface possible. It integrates the most up-to-date melting temperature algorithms validated with experimental data, and cross validated with other computational tools. We generated a library of primers for the extraction and cloning of 61 genes from yeast DNA genomic extract using default parameters. All primer pairs efficiently amplified their target without any optimization of the PCR conditions. PMID:24829457

  9. Selection strategy and the design of hybrid oligonucleotide primers for RACE-PCR: cloning a family of toxin-like sequences from Agelena orientalis

    Directory of Open Access Journals (Sweden)

    Lipkin Alexey

    2007-05-01

    Full Text Available Abstract Background the use of specific but partially degenerate primers for nucleic acid hybridisations and PCRs amplification of known or unknown gene families was first reported well over a decade ago and the technique has been used widely since then. Results here we report a novel and successful selection strategy for the design of hybrid partially degenerate primers for use with RT-PCR and RACE-PCR for the identification of unknown gene families. The technique (named PaBaLiS has proven very effective as it allowed us to identify and clone a large group of mRNAs encoding neurotoxin-like polypeptide pools from the venom of Agelena orientalis species of spider. Our approach differs radically from the generally accepted CODEHOP principle first reported in 1998. Most importantly, our method has proven very efficient by performing better than an independently generated high throughput EST cloning programme. Our method yielded nearly 130 non-identical sequences from Agelena orientalis, whilst the EST cloning technique yielded only 48 non-identical sequences from 2100 clones obtained from the same Agelena material. In addition to the primer design approach reported here, which is almost universally applicable to any PCR cloning application, our results also indicate that venom of Agelena orientalis spider contains a much larger family of related toxin-like sequences than previously thought. Conclusion with upwards of 100,000 species of spider thought to exist, and a propensity for producing diverse peptide pools, many more peptides of pharmacological importance await discovery. We envisage that some of these peptides and their recombinant derivatives will provide a new range of tools for neuroscience research and could also facilitate the development of a new generation of analgesic drugs and insecticides.

  10. Facile implementation of integrated tempering sampling method to enhance the sampling over a broad range of temperatures

    CERN Document Server

    Zhao, Peng; Gao, Yi Qin; Lu, Zhong-Yuan

    2013-01-01

    Integrated tempering sampling (ITS) method is an approach to enhance the sampling over a broad range of energies and temperatures in computer simulations. In this paper, a new version of integrated tempering sampling method is proposed. In the new approach presented here, we obtain parameters such as the set of temperatures and the corresponding weighting factors from canonical average of potential energies. These parameters can be easily obtained without estimating partition functions. We apply this new approach to study the Lennard-Jones fluid, the ALA-PRO peptide and the single polymer chain systems to validate and benchmark the method.

  11. Comparative quantitative analysis of BCR-ABL transcripts with the T315I mutant clone by polymerase chain reaction (PCR)-Invader method.

    Science.gov (United States)

    Tadokoro, Kenichi; Ishikawa, Maho; Suzuki, Makoto; Saito, Tomoyoshi; Suzuki, Yoshie; Yamaguchi, Toshikazu; Yagasaki, Fumiharu

    2011-09-01

    Drug resistance is a serious complication in the treatment of chronic myeloid leukemia (CML). The most common and best-characterized mechanism of secondary imatinib resistance in CML is the development of kinase domain mutations in the BCR-ABL gene. Second-generation tyrosine kinase inhibitors, such as dasatinib or nilotinib, overcome most of these mutations, but they are not effective against the T315I mutant. To determine whether these mutations contribute to clinical resistance, it is necessary to monitor the ratio of the mutant and wild-type forms. Here, we developed a polymerase chain reaction (PCR)-Invader assay for comparative quantitative analysis (qPI assay) of BCR-ABL transcripts with the T315I mutant clone. T315I ratios were calculated for the wild-type and mutant fold-over-zero (FOZ) values. In examination with 2 kinds of plasmids containing wild-type or T315I mutant PCR amplicons, mutant FOZ values were detected down to 1% of the total. The results of 12 serial samples from 2 patients (case A: Philadelphia-positive acute lymphoblastic leukemia and case B: CML) with the T315I mutant clone were compared with those of direct sequencing or 2 kinds of allele-specific oligonucleotide (ASO)-PCR. All samples showed the T315I mutation by qPI assay and ASO-PCR, and 10 samples showed it by direct sequencing. Significant correlation (correlation coefficient; r2 = 0.951) was noted between the qPI assay and quantitative ASO-PCR to analyze T315I mutant ratios. Thus, the qPI assay is a useful method for evaluating the T315I mutant clone in BCR-ABL transcripts.

  12. 仅采用 PCR 进行分子克隆的方法探索%An efficient method of molecular cloning only by polymerase chain reaction

    Institute of Scientific and Technical Information of China (English)

    薛奋勤; 许晴; 魏华; 李华; 薛冰

    2014-01-01

    Objective Due to the high cost in both time and money in gene cloning, a simple molecular cloning method based on polymerase chain reaction(PCR) is presented. Methods The vector and insert are amplified by PCR separately. After DpnI digestion of the mixture of the amplified vector and insert to eliminate the DNA templates used in PCR reactions, the mixture is directly transformed into competent E. coli DH5 cells to obtain the desired clones. Results Here we report a highly simplified,reliable and efficient PCR-based cloning technique to subclone total α-synuclein gene(cDNA) from vector pET into vector pGEX-4T-1, and place total nAChRβ2 gene from vector pCDNA3. 1 into vector pGEMHE. Conclusion This technique has many advantages over other cloning methods. First, we can insert any interested DNA sequences into a vector anywhere by primer designation, and it does not need to consider the restriction of multiple cloning site. Second, there is no need for any specialized enzyme digestion, gel purification of PCR product and linearized vector and enzyme ligation.%目的:针对目前各种费时且易失败的克隆方法和价格昂贵的试剂盒等问题,对一种仅采用聚合酶链反应(polymerase chain reaction,PCR)分子克隆方法进行了探索。方法利用高保真的 DNA 聚合酶具有3'-核酸外切酶活性的特点,采用 PCR 把载体和插入片段扩增出来,二者的扩增产物先加限制性内切酶 DpnI 后再按一定比例混合来消化甲基化的 DNA 模板,最后把DpnI 消化产物直接转化到感受态细胞来得到克隆基因。结果是一种简单、高效、可靠、且仅采用 PCR 的分子克隆方法,并利用此方法成功地把构建在载体 pET 上的α-突触核蛋白全长基因和构建在 pCDNA3.1上的乙酰胆碱受体亚基的全长基因分别重新构建在载体 pGEX-4T-1和 pGEMHE 上。结论在 PCR 扩增时能够通过引物设计来确定克隆位点,所以该方法可以把任何 DNA片段插入到

  13. Soil clone library analyses to evaluate specificity and selectivity of PCR primers targeting fungal 18S rDNA for denaturing-gradient gel electrophoresis (DGGE).

    Science.gov (United States)

    Takada Hoshino, Yuko; Morimoto, Sho

    2010-01-01

    We evaluated the fungal specificity and detection bias of four fungal 18S rRNA gene (18S rDNA) primer sets for denaturing-gradient gel electrophoresis (DGGE). We constructed and compared clone libraries amplified from upland and paddy field soils with each primer set (1, NS1/GCFung; 2, FF390/FR1-GC; 3, NS1/FR1-GC; and 4, NS1/EF3 for the first PCR and NS1/FR1-GC for the second PCR). Primer set 4 (for nested PCR) showed the highest specificity for fungi but biased specific sequences. Sets 1, 2, and 3 (for single PCR) amplified non-fungal eukaryotic sequences (from 7 to 16% for upland soil and from 20 to 31% for paddy field soil) and produced libraries with similar distributions of fungal 18S rDNA sequences at both the phylum and the class level. Set 2 tended to amplify more diverse fungal sequences, maintaining higher specificity for fungi. In addition, clone analyses revealed differences among primer sets in the frequency of chimeras. In upland field soil, the libraries amplified with primer sets 3 and 4, which targeted long fragments, contained many chimeric 18S rDNA sequences (18% and 48%, respectively), while the libraries obtained with sets 1 and 2, which targeted short fragments, contained fewer chimeras (5% and 10%, respectively).

  14. Development and Validation of Broad-Range Qualitative and Clade-Specific Quantitative Molecular Probes for Assessing Mercury Methylation in the Environment.

    Science.gov (United States)

    Christensen, Geoff A; Wymore, Ann M; King, Andrew J; Podar, Mircea; Hurt, Richard A; Santillan, Eugenio U; Soren, Ally; Brandt, Craig C; Brown, Steven D; Palumbo, Anthony V; Wall, Judy D; Gilmour, Cynthia C; Elias, Dwayne A

    2016-10-01

    Two genes, hgcA and hgcB, are essential for microbial mercury (Hg) methylation. Detection and estimation of their abundance, in conjunction with Hg concentration, bioavailability, and biogeochemistry, are critical in determining potential hot spots of methylmercury (MeHg) generation in at-risk environments. We developed broad-range degenerate PCR primers spanning known hgcAB genes to determine the presence of both genes in diverse environments. These primers were tested against an extensive set of pure cultures with published genomes, including 13 Deltaproteobacteria, nine Firmicutes, and nine methanogenic Archaea genomes. A distinct PCR product at the expected size was confirmed for all hgcAB(+) strains tested via Sanger sequencing. Additionally, we developed clade-specific degenerate quantitative PCR (qPCR) primers that targeted hgcA for each of the three dominant Hg-methylating clades. The clade-specific qPCR primers amplified hgcA from 64%, 88%, and 86% of tested pure cultures of Deltaproteobacteria, Firmicutes, and Archaea, respectively, and were highly specific for each clade. Amplification efficiencies and detection limits were quantified for each organism. Primer sensitivity varied among species based on sequence conservation. Finally, to begin to evaluate the utility of our primer sets in nature, we tested hgcA and hgcAB recovery from pure cultures spiked into sand and soil. These novel quantitative molecular tools designed in this study will allow for more accurate identification and quantification of the individual Hg-methylating groups of microorganisms in the environment. The resulting data will be essential in developing accurate and robust predictive models of Hg methylation potential, ideally integrating the geochemistry of Hg methylation to the microbiology and genetics of hgcAB IMPORTANCE: The neurotoxin methylmercury (MeHg) poses a serious risk to human health. MeHg production in nature is associated with anaerobic microorganisms. The recent

  15. Artificial neural network model to predict slag viscosity over a broad range of temperatures and slag compositions

    Energy Technology Data Exchange (ETDEWEB)

    Duchesne, Marc A. [Chemical and Biological Engineering Department, University of Ottawa, 161 Louis Pasteur, Ottawa, Ont. (Canada); CanmetENERGY, 1 Haanel Drive, Ottawa, Ontario (Canada); Macchi, Arturo [Chemical and Biological Engineering Department, University of Ottawa, 161 Louis Pasteur, Ottawa, Ont. (Canada); Lu, Dennis Y.; Hughes, Robin W.; McCalden, David; Anthony, Edward J. [CanmetENERGY, 1 Haanel Drive, Ottawa, Ontario (Canada)

    2010-08-15

    Threshold slag viscosity heuristics are often used for the initial assessment of coal gasification projects. Slag viscosity predictions are also required for advanced combustion and gasification models. Due to unsatisfactory performance of theoretical equations, an artificial neural network model was developed to predict slag viscosity over a broad range of temperatures and slag compositions. This model outperforms other slag viscosity models, resulting in an average error factor of 5.05 which is lower than the best obtained with other available models. Genesee coal ash viscosity predictions were made to investigate the effect of adding Canadian limestone and dolomite. The results indicate that magnesium in the fluxing agent provides a greater viscosity reduction than calcium for the threshold slag tapping temperature range. (author)

  16. Cloning of the koi herpesvirus (KHV gene encoding thymidine kinase and its use for a highly sensitive PCR based diagnosis

    Directory of Open Access Journals (Sweden)

    Gilad Oren

    2005-03-01

    Full Text Available Abstract Background Outbreaks with mass mortality among common carp Cyprinus carpio carpio and koi Cyprinus carpio koi have occurred worldwide since 1998. The herpes-like virus isolated from diseased fish is different from Herpesvirus cyprini and channel catfish virus and was accordingly designated koi herpesvirus (KHV. Diagnosis of KHV infection based on viral isolation and current PCR assays has a limited sensitivity and therefore new tools for the diagnosis of KHV infections are necessary. Results A robust and sensitive PCR assay based on a defined gene sequence of KHV was developed to improve the diagnosis of KHV infection. From a KHV genomic library, a hypothetical thymidine kinase gene (TK was identified, subcloned and expressed as a recombinant protein. Preliminary characterization of the recombinant TK showed that it has a kinase activity using dTTP but not dCTP as a substrate. A PCR assay based on primers selected from the defined DNA sequence of the TK gene was developed and resulted in a 409 bp amplified fragment. The TK based PCR assay did not amplify the DNAs of other fish herpesviruses such as Herpesvirus cyprini (CHV and the channel catfish virus (CCV. The TK based PCR assay was specific for the detection of KHV and was able to detect as little as 10 fentograms of KHV DNA corresponding to 30 virions. The TK based PCR was compared to previously described PCR assays and to viral culture in diseased fish and was shown to be the most sensitive method of diagnosis of KHV infection. Conclusion The TK based PCR assay developed in this work was shown to be specific for the detection of KHV. The TK based PCR assay was more sensitive for the detection of KHV than previously described PCR assays; it was as sensitive as virus isolation which is the golden standard method for KHV diagnosis and was able to detect as little as 10 fentograms of KHV DNA corresponding to 30 virions.

  17. Characterization of passive film formed on AISI 316L stainless steel after magnetoelectropolishing in a broad range of polarization parameters

    Energy Technology Data Exchange (ETDEWEB)

    Rokosz, Krzysztof; Hryniewicz, Tadeusz [Politechnika Koszalinska, Division of Surface Electrochemistry, Raclawicka 15-17, PL 75-620 Koszalin (Poland); Raaen, Steiner [NTNU Trondheim, Institute of Physics, Trondheim (Norway)

    2012-09-15

    The aim of the paper is to present the changes in the surface film composition on AISI 316L stainless steel (SS) after electropolishing (EP) and magnetoelectropolishing (MEP) in a broad range of the process conditions. The X-ray photoelectron spectroscopy surface analyses were performed to reveal the effect of MEP. The EP process has been performed under natural convection (in a stagnant electrolyte), much above the polarization plateau. A series of experiments were carried out on AISI 316L SS samples in accordance with the five-level composite rotary statistical plan with the variables being the magnetic field intensity B (mT), and the anodic current density i (A dm{sup -2}). XP high resolution spectra have been obtained on AISI 316L SS surface concerning Fe 2p, Cr 2p, O 1s, S 2p, P 2p, and C 1s, respectively. The Cr:Fe ratio regarding both metallic M and compound X was also studied and calculated. At the end, the summary results of Cr/Fe = f(B, i) in relation to the corrosion potential, have been compared. The conclusions, concerning the selection of MEP process conditions, regarding the optimum Cr/Fe ratio and corrosion behavior, have been formulated. It was found the Cr:Fe ratio well correlates with the pitting corrosion potential. MEP process can modify not only the rate of dissolution to a determined extent, but also control the corrosion behavior and Cr:Fe ratio results. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  18. Rapid molecular characterization of Acinetobacter baumannii clones with rep-PCR and evaluation of carbapenemase genes by new multiplex PCR in Hospital District of Helsinki and Uusimaa.

    Directory of Open Access Journals (Sweden)

    Tanja Pasanen

    Full Text Available Multidrug-resistant Acinetobacter baumannii (MDRAB is an increasing problem worldwide. Prevalence of carbapenem resistance in Acinetobacter spp. due to acquired carbapenemase genes is not known in Finland. The purpose of this study was to examine prevalence and clonal spread of multiresistant A. baumannii group species, and their carbapenemase genes. A total of 55 Acinetobacter isolates were evaluated with repetitive PCR (DiversiLab to analyse clonality of isolates, in conjunction with antimicrobial susceptibility profile for ampicillin/sulbactam, colistin, imipenem, meropenem, rifampicin and tigecycline. In addition, a new real-time PCR assay, detecting most clinically important carbapenemase genes just in two multiplex reactions, was developed. The assay detects genes for KPC, VIM, IMP, GES-1/-10, OXA-48, NDM, GIM-1, SPM-1, IMI/NMC-A, SME, CMY-10, SFC-1, SIM-1, OXA-23-like, OXA-24/40-like, OXA-58 and ISAbaI-OXA-51-like junction, and allows confident detection of isolates harbouring acquired carbapenemase genes. There was a time-dependent, clonal spread of multiresistant A. baumannii strongly correlating with carbapenamase gene profile, at least in this geographically restricted study material. The new carbapenemase screening assay was able to detect all the genes correctly suggesting it might be suitable for epidemiologic screening purposes in clinical laboratories.

  19. Cloned plasmid DNA fragments as calibrators for controlling GMOs: different real-time duplex quantitative PCR methods.

    Science.gov (United States)

    Taverniers, Isabel; Van Bockstaele, Erik; De Loose, Marc

    2004-03-01

    Analytical real-time PCR technology is a powerful tool for implementation of the GMO labeling regulations enforced in the EU. The quality of analytical measurement data obtained by quantitative real-time PCR depends on the correct use of calibrator and reference materials (RMs). For GMO methods of analysis, the choice of appropriate RMs is currently under debate. So far, genomic DNA solutions from certified reference materials (CRMs) are most often used as calibrators for GMO quantification by means of real-time PCR. However, due to some intrinsic features of these CRMs, errors may be expected in the estimations of DNA sequence quantities. In this paper, two new real-time PCR methods are presented for Roundup Ready soybean, in which two types of plasmid DNA fragments are used as calibrators. Single-target plasmids (STPs) diluted in a background of genomic DNA were used in the first method. Multiple-target plasmids (MTPs) containing both sequences in one molecule were used as calibrators for the second method. Both methods simultaneously detect a promoter 35S sequence as GMO-specific target and a lectin gene sequence as endogenous reference target in a duplex PCR. For the estimation of relative GMO percentages both "delta C(T)" and "standard curve" approaches are tested. Delta C(T) methods are based on direct comparison of measured C(T) values of both the GMO-specific target and the endogenous target. Standard curve methods measure absolute amounts of target copies or haploid genome equivalents. A duplex delta C(T) method with STP calibrators performed at least as well as a similar method with genomic DNA calibrators from commercial CRMs. Besides this, high quality results were obtained with a standard curve method using MTP calibrators. This paper demonstrates that plasmid DNA molecules containing either one or multiple target sequences form perfect alternative calibrators for GMO quantification and are especially suitable for duplex PCR reactions.

  20. Broad-range detection of arboviruses belonging to Simbu serogroup lineage 1 and specific detection of Akabane, Aino and Peaton viruses by newly developed multiple TaqMan assays.

    Science.gov (United States)

    Shirafuji, Hiroaki; Yazaki, Ryu; Shuto, Yozo; Yanase, Tohru; Kato, Tomoko; Ishikura, Youji; Sakaguchi, Zenjiro; Suzuki, Moemi; Yamakawa, Makoto

    2015-12-01

    TaqMan assays were developed for the broad-range detection of arboviruses belonging to Simbu serogroup lineage 1 in the genus Orthobunyavirus and also for the specific detection of three viruses in the lineage, Akabane, Aino and Peaton viruses (AKAV, AINOV and PEAV, respectively). A primer and probe set was designed for the broad-range detection of Simbu serogroup lineage 1 (Pan-Simbu1 set) mainly targeting AKAV, AINOV, PEAV, Sathuperi and Shamonda viruses (SATV and SHAV), and the forward and reverse primers of the Pan-Simbu1 set were also used for the specific detection of AKAV with another probe (AKAV-specific set). In addition, two more primer and probe sets were designed for AINOV- and PEAV-specific detection, respectively (AINOV- and PEAV-specific sets). All of the four primer and probe sets successfully detected targeted viruses, and thus broad-range and specific detection of all the targeted viruses can be achieved by using two multiplex assays and a single assay in a dual (two-color) assay format when another primer and probe set for a bovine β-actin control is also used. The assays had an analytical sensitivity of 10 copies/tube for AKAV, at least 100 copies/tube for AINOV, 100 copies/tube for PEAV, one copy/tube for SATV and at least 10 copies/tube for SHAV, respectively. Diagnostic sensitivity of the assays was tested with field-collected bovine samples, and the results suggested that the sensitivity was higher than that of a conventional RT-PCR. These data indicate that the newly developed TaqMan assays will be useful tools for the diagnosis and screening of field-collected samples for infections of AKAV and several other arboviruses belonging to the Simbu serogroup lineage 1.

  1. Optimizing Taq polymerase concentration for improved signal-to-noise in the broad range detection of low abundance bacteria.

    Directory of Open Access Journals (Sweden)

    Rudolph Spangler

    Full Text Available BACKGROUND: PCR in principle can detect a single target molecule in a reaction mixture. Contaminating bacterial DNA in reagents creates a practical limit on the use of PCR to detect dilute bacterial DNA in environmental or public health samples. The most pernicious source of contamination is microbial DNA in DNA polymerase preparations. Importantly, all commercial Taq polymerase preparations inevitably contain contaminating microbial DNA. Removal of DNA from an enzyme preparation is problematical. METHODOLOGY/PRINCIPAL FINDINGS: This report demonstrates that the background of contaminating DNA detected by quantitative PCR with broad host range primers can be decreased greater than 10-fold through the simple expedient of Taq enzyme dilution, without altering detection of target microbes in samples. The general method is: For any thermostable polymerase used for high-sensitivity detection, do a dilution series of the polymerase crossed with a dilution series of DNA or bacteria that work well with the test primers. For further work use the concentration of polymerase that gave the least signal in its negative control (H(2O while also not changing the threshold cycle for dilutions of spiked DNA or bacteria compared to higher concentrations of Taq polymerase. CONCLUSIONS/SIGNIFICANCE: It is clear from the studies shown in this report that a straightforward procedure of optimizing the Taq polymerase concentration achieved "treatment-free" attenuation of interference by contaminating bacterial DNA in Taq polymerase preparations. This procedure should facilitate detection and quantification with broad host range primers of a small number of bona fide bacteria (as few as one in a sample.

  2. Short description of an alternative simplified method for screening recombinant clones within the "AdEasy-System" by Duplex-PCR

    Directory of Open Access Journals (Sweden)

    Kienle Peter

    2005-01-01

    Full Text Available Abstract Background Recombinant adenoviral vectors are highly efficient for in vitro and in vivo gene delivery. They can easily be produced in large numbers, transduce a wide variety of cell types and generate high levels of transgene expression. The AdEasy system is a widely used system for generating recombinant adenoviral vectors, which are created with a minimum of enzymatic manipulations and by employing homologous recombination in E. coli. In this paper we describe an alternative simplified method for screening recombinant DNA within the AdEasy system. This Duplex-PCR-method is independent of the transgene or insert and can be used for the complete AdEasy system. It is characterized by a simple standard protocol and the results can be obtained within a few hours. The PCR is run with two different primer sets. The primers KanaFor and KanaRev hybridizise with the Kanamycin resistence gene and AdFor and AdRev detect the adenoviral backbone. In case of recombinant clones, two diagnostic fragments with a size of 384 bp and 768 bp are generated. Results The practicability of this method was verified with three different transgenes: Cytosin Deaminase (AdCD, p53 (Adp53 and Granulocyte Macrophage Colony Stimulating Factor (AdGM-CSF. Recombinant clones are indicated by two diagnostic fragments and are then suitable for further processing. Conclusion In summary, the presented protocol allows fast detection of recombinants with an easy technique by minimizing the amount of necessary steps for generating a recombinant adenovirus. This method is time sparing and cost-effective.

  3. Establishment of Sequence-Tagged Sites on 15q11-q13 by Alu-Vector PCR Cloning of Yac-Generated Fragments

    Directory of Open Access Journals (Sweden)

    W. S. Kim

    1996-01-01

    Full Text Available Angelman syndrome (AS is caused by the loss of function of undefined gene(s on human chromosome 15. The majority of subjects have deletions involving maternally-derived chromosome 15q II-q 13, and the shortest region of deletion overlap (SRO has been localized to the region between D15S10 and D15S113. In this study, yeast artificial chromosomes (YACs, 6G-D4, 9H-D2 and 37D-F9, mapping within the AS SRO, were isolated from the ICI Y AC library. Alu-vector PCR products were amplified from the YACs and from YACs A229A2 and A33FI 0 which had been obtained from the St. Louis Y AC library. The PCR products were cloned and sequenced, and three new sequence-tagged sites were generated within the AS SRO, facilitating the characterization of gene(s involved in the Angelman syndrome.

  4. A methodology for model-based greenhouse design: Part 1, a greenhouse climate model for a broad range of designs and climates

    NARCIS (Netherlands)

    Vanthoor, B.H.E.; Stanghellini, C.; Henten, van E.J.; Visser, de P.H.B.

    2011-01-01

    With the aim of developing a model-based method to design greenhouses for a broad range of climatic and economic conditions, a greenhouse climate model has been developed and validated. This model describes the effects of the outdoor climate and greenhouse design on the indoor greenhouse climate. Fo

  5. Construction of a self-luminescent cyanobacterial bioreporter that detects a broad range of bioavailable heavy metals in aquatic environments.

    Science.gov (United States)

    Martín-Betancor, Keila; Rodea-Palomares, Ismael; Muñoz-Martín, M A; Leganés, Francisco; Fernández-Piñas, Francisca

    2015-01-01

    A self-luminescent bioreporter strain of the unicellular cyanobacterium Synechococcus sp. PCC 7942 was constructed by fusing the promoter region of the smt locus (encoding the transcriptional repressor SmtB and the metallothionein SmtA) to luxCDABE from Photorhabdus luminescens; the sensor smtB gene controlling the expression of smtA was cloned in the same vector. The bioreporter performance was tested with a range of heavy metals and was shown to respond linearly to divalent Zn, Cd, Cu, Co, Hg, and monovalent Ag. Chemical modeling was used to link bioreporter response with metal speciation and bioavailability. Limits of Detection (LODs), Maximum Permissive Concentrations (MPCs) and dynamic ranges for each metal were calculated in terms of free ion concentrations. The ranges of detection varied from 11 to 72 pM for Hg(2+) (the ion to which the bioreporter was most sensitive) to 1.54-5.35 μM for Cd(2+) with an order of decreasing sensitivity as follows: Hg(2+) > Cu(2+) > Ag(+) > Co(2+) ≥ Zn(2+) > Cd(2+). However, the maximum induction factor reached 75-fold in the case of Zn(2+) and 56-fold in the case of Cd(2+), implying that Zn(2+) is the preferred metal in vivo for the SmtB sensor, followed by Cd(2+), Ag(+) and Cu(2+) (around 45-50-fold induction), Hg(2+) (30-fold) and finally Co(2+) (20-fold). The bioreporter performance was tested in real environmental samples with different water matrix complexity artificially contaminated with increasing concentrations of Zn, Cd, Ag, and Cu, confirming its validity as a sensor of free heavy metal cations bioavailability in aquatic environments. PMID:25806029

  6. Construction of a self- luminescent cyanobacterial bioreporter that detects a broad range of bioavailable heavy metals in aquatic environments

    Directory of Open Access Journals (Sweden)

    Keila eMartin-Betancor

    2015-03-01

    Full Text Available A self-luminescent bioreporter strain of the unicellular cyanobacterium Synechococcus sp. PCC 7942 was constructed by fusing the promoter region of the smt locus (encoding the transcriptional repressor SmtB and the metallothionein SmtA to luxCDABE from Photorhabdus luminescens; the sensor smtB gene controlling the expression of smtA was cloned in the same vector. The bioreporter performance was tested with a range of heavy metals and was shown to respond linearly to divalent Zn, Cd, Cu, Co, Hg and monovalent Ag. Chemical modelling was used to link bioreporter response with metal speciation and bioavailability. Limits of Detection (LODs, Maximum Permissive Concentrations (MPCs and dynamic ranges for each metal were calculated in terms of free ion concentrations. The ranges of detection varied from 11 to 72 pM for Hg2+ (the ion to which the bioreporter was most sensitive to 1.54-5.35 µM for Cd2+ with an order of decreasing sensitivity as follows: Hg2+ >> Cu2+ >> Ag+ > Co2+ ≥ Zn2+ > Cd2+. However, the maximum induction factor reached 75-fold in the case of Zn2+ and 56-fold in the case of Cd2+, implying that Zn2+ is the preferred metal in vivo for the SmtB sensor, followed by Cd2+, Ag+ and Cu2+ (around 45-50-fold induction, Hg2+ (30-fold and finally Co2+ (20-fold. The bioreporter performance was tested in real environmental samples with different water matrix complexity artificially contaminated with increasing concentrations of Zn, Cd, Ag and Cu, confirming its validity as a sensor of free heavy metal cations bioavailability in aquatic environments.

  7. Can job redesign interventions influence a broad range of employee outcomes by changing multiple job characteristics? A quasi-experimental study.

    Science.gov (United States)

    Holman, David; Axtell, Carolyn

    2016-07-01

    Many job redesign interventions are based on a multiple mediator-multiple outcome model in which the job redesign intervention indirectly influences a broad range of employee outcomes by changing multiple job characteristics. As this model remains untested, the aim of this study is to test a multiple mediator-multiple outcome model of job redesign. Multilevel analysis of data from a quasi-experimental job redesign intervention in a call center confirmed the hypothesized model and showed that the job redesign intervention affected a broad range of employee outcomes (i.e., employee well-being, psychological contract fulfillment, and supervisor-rated job performance) through changes in 2 job characteristics (i.e., job control and feedback). The results provide further evidence for the efficacy and mechanisms of job redesign interventions. (PsycINFO Database Record PMID:26641482

  8. A review of Spinosyns, a derivative of biological acting substances as a class of insecticides with a broad range of action against many insect pests

    OpenAIRE

    Bacci, L.; D. Lupi; Savoldelli, S.; B. Rossaro

    2016-01-01

    Spinosyns are a class of insecticides with a broad range of action against many insect pests belonging to different orders, noxious to a wide variety of agricultural crops; spinosyns were also used against insects of sanitary interest. Spinosyns are derivative of biological active substances produced by soil Actinomycete Saccharopolyspora spinosa; being of biological origin, they are considered to have a low environmental impact and they are not much aggressive against nontarget species. They...

  9. Can job redesign interventions influence a broad range of employee outcomes by changing multiple job characteristics? A quasi-experimental study

    OpenAIRE

    Holman, David

    2015-01-01

    Many job redesign interventions are based on a ‘multiple mediator/multiple outcome’ model in which the job redesign intervention indirectly influences a broad range of employee outcomes by changing multiple job characteristics. As this model remains untested, the aim of this study is to test a ‘multiple mediator/multiple outcome’ model of job redesign. Multilevel analysis of data from a quasi-experimental job redesign intervention in a call centre confirmed the hypothesized model an...

  10. Thermodynamical features of Verlinde's approach for a non-commutative Schwarzschild-anti-deSitter black hole in a broad range of scales

    OpenAIRE

    Mehdipour, S. Hamid

    2014-01-01

    We try to study the thermodynamical features of a non-commutative inspired Schwarzschild-anti-deSitter black hole in the context of entropic gravity model, particularly for the model that is employed in a broad range of scales, from the short distances to the large distances. At small length scales, the Newtonian force is failed because one finds a linear relation between the entropic force and the distance. In addition, there are some deviations from the standard Newtonian gravity at large l...

  11. Nitrogen-rich functional groups carbon nanoparticles based fluorescent pH sensor with broad-range responding for environmental and live cells applications.

    Science.gov (United States)

    Shi, Bingfang; Su, Yubin; Zhang, Liangliang; Liu, Rongjun; Huang, Mengjiao; Zhao, Shulin

    2016-08-15

    A nitrogen-rich functional groups carbon nanoparticles (N-CNs) based fluorescent pH sensor with a broad-range responding was prepared by one-pot hydrothermal treatment of melamine and triethanolamine. The as-prepared N-CNs exhibited excellent photoluminesence properties with an absolute quantum yield (QY) of 11.0%. Furthermore, the N-CNs possessed a broad-range pH response. The linear pH response range was 3.0 to 12.0, which is much wider than that of previously reported fluorescent pH sensors. The possible mechanism for the pH-sensitive response of the N-CNs was ascribed to photoinduced electron transfer (PET). Cell toxicity experiment showed that the as-prepared N-CNs exhibited low cytotoxicity and excellent biocompatibility with the cell viabilities of more than 87%. The proposed N-CNs-based pH sensor was used for pH monitoring of environmental water samples, and pH fluorescence imaging of live T24 cells. The N-CNs is promising as a convenient and general fluorescent pH sensor for environmental monitoring and bioimaging applications. PMID:27085956

  12. Reverse-transcription PCR (RT-PCR).

    Science.gov (United States)

    Bachman, Julia

    2013-01-01

    RT-PCR is commonly used to test for genetic diseases and to characterize gene expression in various tissue types, cell types, and over developmental time courses. This serves as a form of expression profiling, but typically as a candidate approach. RT-PCR is also commonly used to clone cDNAs for further use with other molecular biology techniques (e.g., see Oligo(dT)-primed RT-PCR isolation of polyadenylated RNA degradation intermediates and Circularized RT-PCR (cRT-PCR): analysis of RNA 5' ends, 3' ends, and poly(A) tails).

  13. New methods as alternative or corrective measures for the pitfalls and artifacts of reverse transcription and polymerase chain reactions (RT-PCR) in cloning chimeric or antisense-accompanied RNA.

    Science.gov (United States)

    Yuan, Chengfu; Liu, Yongming; Yang, Min; Liao, D Joshua

    2013-06-01

    We established new methods for cloning cDNA ends that start with reverse transcription (RT) and soon proceed with the synthesis of the second cDNA strand, avoiding manipulations of fragile RNA. Our 3'-end cloning method does not involve poly-dT primers and polymerase chain reactions (PCR), is low in efficiency but high in fidelity and can clone those RNAs without a poly-A tail. We also established a cDNA protection assay to supersede RNA protection assay. The protected cDNA can be amplified, cloned and sequenced, enhancing sensitivity and fidelity. We report that RT product using gene-specific primer (GSP) cannot be gene- or strand-specific because RNA sample contains endogenous random primers (ERP). The gene-specificity may be improved by adding a linker sequence at the 5'-end of the GSP to prime RT and using the linker as a primer in the ensuing PCR. The strand-specificity may be improved by using strand-specific DNA oligos in our protection assay. The CDK4 mRNA and TSPAN31 mRNA are transcribed from the opposite DNA strands and overlap at their 3' ends. Using this relationship as a model, we found that the overlapped sequence might serve as a primer with its antisense as the template to create a wrong-template extension in RT or PCR. We infer that two unrelated RNAs or cDNAs overlapping at the 5'- or 3'-end might create a spurious chimera in this way, and many chimeras with a homologous sequence may be such artifacts. The ERP and overlapping antisense together set complex pitfalls, which one should be aware of.

  14. Quest for a broad-range vaccine against Neisseria meningitidis serogroup B: implications of genetic variations of the surface-exposed proteins.

    Science.gov (United States)

    de Filippis, Ivano

    2009-09-01

    Despite the development of new vaccine formulations using new biotechnology resources to combat emerging and re-emerging diseases, serogroup B meningococcal disease is still a worldwide burden, accounting for many deaths and disabilities every year. The successful approach of coupling a polysaccharide (PS) with a carrier protein in order to increase long-lasting immunity could not be exploited against Neisseria meningitidis B because of the limitations of using the capsular PS of serogroup B meningococci. Tailor-made vaccines based on exposed proteins were shown to be a promising approach to overcome these flaws. However, the continuous adaptation of surface meningococcal structures to the external environment has led to genetic shifts of potential vaccine-target epitopes, hampering the quest for a broad-range vaccine that could be used against all serogroups, especially against serogroup B.

  15. A cross-sectional study on trans-fatty acids and risk markers of CHD among middle-aged men representing a broad range of BMI

    DEFF Research Database (Denmark)

    Nielsen, Birgit M.; Nielsen, Marie M.; Jakobsen, Marianne U.;

    2011-01-01

    Intake of trans-fatty acids (TFA), especially industrially produced TFA (I-TFA), has been associated with the risk of CHD through influence on serum lipid levels. Other causal pathways remain less investigated. In the present cross-sectional study of middle-aged men representing a broad range...... of interest (waist circumference, sagittal abdominal diameter, percentage of truncal fat, C-reactive protein, IL-6, blood lipids, blood pressure, HbA1c and insulin sensitivity index) were obtained through clinical examination. The associations were assessed by linear regression analysis. The median intake...... of total TFA among the 393 men was 1·3 g/d, covering a daily I-TFA intake of 0·4 g (10–90th percentile 0·0–1·0) and R-TFA intake of 0·9 g (10–90th percentile 0·4–1·8). Intake of these amounts of TFA showed no significant associations with abdominal fatness, inflammatory markers, blood lipids, blood...

  16. Antimicrobial properties of zeolite-X and zeolite-A ion-exchanged with silver, copper, and zinc against a broad range of microorganisms.

    Science.gov (United States)

    Demirci, Selami; Ustaoğlu, Zeynep; Yılmazer, Gonca Altın; Sahin, Fikrettin; Baç, Nurcan

    2014-02-01

    Zeolites are nanoporous alumina silicates composed of silicon, aluminum, and oxygen in a framework with cations, water within pores. Their cation contents can be exchanged with monovalent or divalent ions. In the present study, the antimicrobial (antibacterial, anticandidal, and antifungal) properties of zeolite type X and A, with different Al/Si ratio, ion exchanged with Ag(+), Zn(2+), and Cu(2+) ions were investigated individually. The study presents the synthesis and manufacture of four different zeolite types characterized by scanning electron microscopy and X-ray diffraction. The ion loading capacity of the zeolites was examined and compared with the antimicrobial characteristics against a broad range of microorganisms including bacteria, yeast, and mold. It was observed that Ag(+) ion-loaded zeolites exhibited more antibacterial activity with respect to other metal ion-embedded zeolite samples. The results clearly support that various synthetic zeolites can be ion exchanged with Ag(+), Zn(2+), and Cu(2+) ions to acquire antimicrobial properties or ion-releasing characteristics to provide prolonged or stronger activity. The current study suggested that zeolite formulations could be combined with various materials used in manufacturing medical devices, surfaces, textiles, or household items where antimicrobial properties are required.

  17. RT-PCR Screening for ETV6-RUNX1-positive Clones in Cord Blood From Newborns in the Danish National Birth Cohort

    DEFF Research Database (Denmark)

    Olsen, Marianne; Hjalgrim, Henrik; Melbye, Mads;

    2012-01-01

    BACKGROUND:: Several large biobanks comprising umbilical cord blood samples have been established allowing efforts to characterize the prevalence and risk factors for preleukemic cell clones in healthy newborns. This study explores the feasibility of demonstrating translocation ETV6-RUNX1 transcr...... history of childhood acute lymphoblastic leukemia. Finally, the estimated frequency of translocation ETV6-RUNX1-positive cells was below 10....

  18. 单核细胞增生性李斯特菌iap基因克隆和PCR条件优化%Cloning of iap gene of Listeria monocytogenes with PCR optimization

    Institute of Scientific and Technical Information of China (English)

    贾芙蓉; 罗雁非; 方玲; 郑岚; 刘伟林; 潘洪涛; 何成彦

    2010-01-01

    目的 构建单核细胞增生性李斯特菌Listeria monocytogenes 54002-4株p60蛋白iap基因原核克隆载体.方法 利用自行设计的引物通过梯度PCR优化扩增条件,扩增出单核细胞增生性李斯特菌54002-4株的iap基因.在iap基因的5'端和3'端分别引入BamH Ⅰ和Xho Ⅰ 2个酶切位点,琼脂糖凝胶电泳分析、回收PCR产物,并将回收纯化的PCR产物与pMD 18-T载体进行连接.将该重组质粒转化人大肠杆菌JM109感受态细胞,经1 mmol/L IPTG诱导4~6 h后,观察转化效果.结果 培养无色菌落细菌,提取质粒,经PCR鉴定和核苷酸序列测定后确定获得阳性重组质粒pMD18-T-Iap.结论 通过梯度PCR摸索出最佳反应条件,建立PCR优化条件和方法,经转化获得iap基因克隆载体.%Objective To construct a prokaryotic cloning vector of invasion- associated protein (iap) gene p60 of Listeria monocytogenes. Methods Under gradient PCR amplification conditions, Listeria monocytogenes 54002-4 strain iap gene was amplified with our in-house primers. BamH Ⅰ and Xho Ⅰ sites were induced to 5' and 3' terminals of iap gene, respectively. PCR products were then analyzed and collected by agarose gel electrophoresis. Purified PCR product was connected with the vector pMD18-T. The recombinant plasmid was transformed into Escherichia coli JM109 competent cells, with transformation effect observed after 1mmol/L IPTG induction for 4-6 h. Results Colorless bacterial colony was cultured and verified to produce positive recombinant plasmid pMD18-T-Iap by PCR and nucleotide sequencing. Conclusions PCR optimization conditions and methods are established through gradient PCR. Iap gene cloning vector is obtained after transformation.

  19. Inactivation of pathogenic viruses by plant-derived tannins: strong effects of extracts from persimmon (Diospyros kaki on a broad range of viruses.

    Directory of Open Access Journals (Sweden)

    Kyoko Ueda

    Full Text Available Tannins, plant-derived polyphenols and other related compounds, have been utilized for a long time in many fields such as the food industry and manufacturing. In this study, we investigated the anti-viral effects of tannins on 12 different viruses including both enveloped viruses (influenza virus H3N2, H5N3, herpes simplex virus-1, vesicular stomatitis virus, Sendai virus and Newcastle disease virus and non-enveloped viruses (poliovirus, coxsachievirus, adenovirus, rotavirus, feline calicivirus and mouse norovirus. We found that extracts from persimmon (Diospyros kaki, which contains ca. 22% of persimmon tannin, reduced viral infectivity in more than 4-log scale against all of the viruses tested, showing strong anti-viral effects against a broad range of viruses. Other tannins derived from green tea, acacia and gallnuts were effective for some of the viruses, while the coffee extracts were not effective for any of the virus. We then investigated the mechanism of the anti-viral effects of persimmon extracts by using mainly influenza virus. Persimmon extracts were effective within 30 seconds at a concentration of 0.25% and inhibited attachment of the virus to cells. Pretreatment of cells with the persimmon extracts before virus infection or post-treatment after virus infection did not inhibit virus replication. Protein aggregation seems to be a fundamental mechanism underlying the anti-viral effect of persimmon tannin, since viral proteins formed aggregates when purified virions were treated with the persimmon extracts and since the anti-viral effect was competitively inhibited by a non-specific protein, bovine serum albumin. Considering that persimmon tannin is a food supplement, it has a potential to be utilized as a safe and highly effective anti-viral reagent against pathogenic viruses.

  20. A Broad Range of Dose Optima Achieve High-level, Long-term Gene Expression After Hydrodynamic Delivery of Sleeping Beauty Transposons Using Hyperactive SB100x Transposase

    Science.gov (United States)

    Podetz-Pedersen, Kelly M; Olson, Erik R; Somia, Nikunj V; Russell, Stephen J; McIvor, R Scott

    2016-01-01

    The Sleeping Beauty (SB) transposon system has been shown to enable long-term gene expression by integrating new sequences into host cell chromosomes. We found that the recently reported SB100x hyperactive transposase conferred a surprisingly high level of long-term expression after hydrodynamic delivery of luciferase-encoding reporter transposons in the mouse. We conducted dose-ranging studies to determine the effect of varying the amount of SB100x transposase-encoding plasmid (pCMV-SB100x) at a set dose of luciferase transposon and of varying the amount of transposon-encoding DNA at a set dose of pCMV-SB100x in hydrodynamically injected mice. Animals were immunosuppressed using cyclophosphamide in order to prevent an antiluciferase immune response. At a set dose of transposon DNA (25 µg), we observed a broad range of pCMV-SB100x doses (0.1–2.5 µg) conferring optimal levels of long-term expression (>1011 photons/second/cm2). At a fixed dose of 0.5 μg of pCMV-SB100x, maximal long-term luciferase expression (>1010 photons/second/cm2) was achieved at a transposon dose of 5–125 μg. We also found that in the linear range of transposon doses (100 ng), co-delivering the CMV-SB100x sequence on the same plasmid was less effective in achieving long-term expression than delivery on separate plasmids. These results show marked flexibility in the doses of SB transposon plus pCMV-SB100x that achieve maximal SB-mediated gene transfer efficiency and long-term gene expression after hydrodynamic DNA delivery to mouse liver. PMID:26784638

  1. A Broad Range of Dose Optima Achieve High-level, Long-term Gene Expression After Hydrodynamic Delivery of Sleeping Beauty Transposons Using Hyperactive SB100x Transposase.

    Science.gov (United States)

    Podetz-Pedersen, Kelly M; Olson, Erik R; Somia, Nikunj V; Russell, Stephen J; McIvor, R Scott

    2016-01-01

    The Sleeping Beauty (SB) transposon system has been shown to enable long-term gene expression by integrating new sequences into host cell chromosomes. We found that the recently reported SB100x hyperactive transposase conferred a surprisingly high level of long-term expression after hydrodynamic delivery of luciferase-encoding reporter transposons in the mouse. We conducted dose-ranging studies to determine the effect of varying the amount of SB100x transposase-encoding plasmid (pCMV-SB100x) at a set dose of luciferase transposon and of varying the amount of transposon-encoding DNA at a set dose of pCMV-SB100x in hydrodynamically injected mice. Animals were immunosuppressed using cyclophosphamide in order to prevent an antiluciferase immune response. At a set dose of transposon DNA (25 µg), we observed a broad range of pCMV-SB100x doses (0.1-2.5 µg) conferring optimal levels of long-term expression (>10(11) photons/second/cm(2)). At a fixed dose of 0.5 μg of pCMV-SB100x, maximal long-term luciferase expression (>10(10) photons/second/cm(2)) was achieved at a transposon dose of 5-125 μg. We also found that in the linear range of transposon doses (100 ng), co-delivering the CMV-SB100x sequence on the same plasmid was less effective in achieving long-term expression than delivery on separate plasmids. These results show marked flexibility in the doses of SB transposon plus pCMV-SB100x that achieve maximal SB-mediated gene transfer efficiency and long-term gene expression after hydrodynamic DNA delivery to mouse liver. PMID:26784638

  2. Public sector physiotherapists believe that staff supervision should be broad ranging, individualised, structured, and based on needs and goals: a qualitative study

    Directory of Open Access Journals (Sweden)

    Annabel A Redpath

    2015-10-01

    implementing effective physiotherapy supervision programs. [Redpath AA, Gill SD, Finlay N, Brennan F, Hakkennes S (2015 Public sector physiotherapists believe that staff supervision should be broad ranging, individualised, structured, and based on needs and goals: a qualitative study. Journal of Physiotherapy 61: 210–216

  3. Expression levels of the yeast alcohol acetyltransferase genes ATF1, Lg-ATF1, and ATF2 control the formation of a broad range of volatile esters.

    Science.gov (United States)

    Verstrepen, Kevin J; Van Laere, Stijn D M; Vanderhaegen, Bart M P; Derdelinckx, Guy; Dufour, Jean-Pierre; Pretorius, Isak S; Winderickx, Joris; Thevelein, Johan M; Delvaux, Freddy R

    2003-09-01

    Volatile aroma-active esters are responsible for the fruity character of fermented alcoholic beverages such as beer and wine. Esters are produced by fermenting yeast cells in an enzyme-catalyzed intracellular reaction. In order to investigate and compare the roles of the known Saccharomyces cerevisiae alcohol acetyltransferases, Atf1p, Atf2p and Lg-Atf1p, in volatile ester production, the respective genes were either deleted or overexpressed in a laboratory strain and a commercial brewing strain. Subsequently, the ester formation of the transformants was monitored by headspace gas chromatography and gas chromatography combined with mass spectroscopy (GC-MS). Analysis of the fermentation products confirmed that the expression levels of ATF1 and ATF2 greatly affect the production of ethyl acetate and isoamyl acetate. GC-MS analysis revealed that Atf1p and Atf2p are also responsible for the formation of a broad range of less volatile esters, such as propyl acetate, isobutyl acetate, pentyl acetate, hexyl acetate, heptyl acetate, octyl acetate, and phenyl ethyl acetate. With respect to the esters analyzed in this study, Atf2p seemed to play only a minor role compared to Atf1p. The atf1Delta atf2Delta double deletion strain did not form any isoamyl acetate, showing that together, Atf1p and Atf2p are responsible for the total cellular isoamyl alcohol acetyltransferase activity. However, the double deletion strain still produced considerable amounts of certain other esters, such as ethyl acetate (50% of the wild-type strain), propyl acetate (50%), and isobutyl acetate (40%), which provides evidence for the existence of additional, as-yet-unknown ester synthases in the yeast proteome. Interestingly, overexpression of different alleles of ATF1 and ATF2 led to different ester production rates, indicating that differences in the aroma profiles of yeast strains may be partially due to mutations in their ATF genes. PMID:12957907

  4. A novel Sarcocystis neurona genotype XIII is associated with severe encephalitis in an unexpectedly broad range of marine mammals from the northeastern Pacific Ocean

    OpenAIRE

    Barbosa, L; Johnson, CK; Lambourn, DM; Gibson, AK; Haman, KH; Huggins, JL; Sweeny, AR; Sundar, N.; Raverty, SA; Grigg, ME.

    2015-01-01

    © 2015 . Sarcocystis neurona is an important cause of protozoal encephalitis among marine mammals in the northeastern Pacific Ocean. To characterise the genetic type of S. neurona in this region, samples from 227 stranded marine mammals, most with clinical or pathological evidence of protozoal disease, were tested for the presence of coccidian parasites using a nested PCR assay. The frequency of S. neurona infection was 60% (136/227) among pinnipeds and cetaceans, including seven marine mamma...

  5. Cloning, expression, and purification of the His(6)-tagged hyper-thermostable dUTPase from Pyrococcus woesei in Escherichia coli: application in PCR

    DEFF Research Database (Denmark)

    Dabrowski, Slawomir; Ahring, Birgitte Kiær

    2003-01-01

    The gene encoding dUTPase from Pyrococcus woesei was cloned into Escherichia coli expression system. It shows 100% gene identity to homologous gene in Pyrococcus furiosus. The expression of N-terminal His(6)-tagged Pwo dUTPase was performed in E coli BL21(DE3)pLysS and E. coli Rosetta(DE3)p......LysS strain that contains plasmid encoding additional copies of rare E. coli tRNAs. E. coli Rosetta(pLysS) strain was found with two times higher expression yield of His(6)-tagged Pwo dUTPase than E. coli BL21(DE3)pLysS. The His(6)-tagged Pwo dUTPase was purified on Ni2+-IDA-Sepharose, dialyzed...

  6. 一种热激PCR法高效鉴定重组克隆%A highly effective heat shock PCR screening method for recombination clone

    Institute of Scientific and Technical Information of China (English)

    顾洪雁; 袁晓伟

    2010-01-01

    利用热激PCR法和菌落直接PCR法进行大肠杆菌和农杆菌的鉴定,筛选含有GFP-linker-C-TAPa或wtGPA1-C-TAPa的pCAMBIA2300EC的阳性克隆,比较热激PCR法和菌落直接PCR法的优劣.热激PCR法阳性检出率是100%,菌落直接PCR法阳性检出率是60%左右.热激PCR法是一种快速可靠的鉴定重组阳性克隆的方法.

  7. Why Clone?

    Science.gov (United States)

    ... How might cloning be used in medicine? Cloning animal models of disease Much of what researchers learn ... the first place, such as habitat destruction and hunting. But cloning may be one more tool that ...

  8. Elucidating the identity of Anisakis larvae from a broad range of marine fishes from the Yellow Sea, China, using a combined electrophoretic-sequencing approach.

    Science.gov (United States)

    Du, Chunxia; Zhang, Luping; Shi, Meiqing; Ming, Zhu; Hu, Min; Gasser, Robin B

    2010-01-01

    Larval nematodes were collected from marine fishes from the Yellow Sea, China. Specimens (n=1731) of Anisakis type I from 311 fishes (representing 40 species) were each identified based on morphological characters. From the genomic DNA from individual specimens, a region of nuclear ribosomal DNA was amplified by PCR, followed by digestion with restriction endonuclease HinfI, TaqI or HhaI. Subsequently, the ITS-1 and ITS-2 regions of selected samples were sequenced. The results revealed three species of Anisakis, namely Anisakis pegreffii (n=1709), A. typica (n=3) and a genotype (n=19) proposed, also based on comparison with previous studies, to be a "hybrid" between A. pegreffii and A. simplex sensu stricto. Thus, A. pegreffii was the dominant species, accounting for 98.7% of the total number of specimens examined herein. This is the first report of A. typica and the "hybrid" genotype from fishes from the Yellow Sea. This study provides important basic information on Anisakis in this region and suggests that the genus Anisakis has substantial host and geographical distributions. PMID:20108262

  9. A novel Sarcocystis neurona genotype XIII is associated with severe encephalitis in an unexpectedly broad range of marine mammals from the northeastern Pacific Ocean.

    Science.gov (United States)

    Barbosa, Lorraine; Johnson, Christine K; Lambourn, Dyanna M; Gibson, Amanda K; Haman, Katherine H; Huggins, Jessica L; Sweeny, Amy R; Sundar, Natarajan; Raverty, Stephen A; Grigg, Michael E

    2015-08-01

    Sarcocystis neurona is an important cause of protozoal encephalitis among marine mammals in the northeastern Pacific Ocean. To characterise the genetic type of S. neurona in this region, samples from 227 stranded marine mammals, most with clinical or pathological evidence of protozoal disease, were tested for the presence of coccidian parasites using a nested PCR assay. The frequency of S. neurona infection was 60% (136/227) among pinnipeds and cetaceans, including seven marine mammal species not previously known to be susceptible to infection by this parasite. Eight S. neurona fetal infections identified this coccidian parasite as capable of being transmitted transplacentally. Thirty-seven S. neurona-positive samples were multilocus sequence genotyped using three genetic markers: SnSAG1-5-6, SnSAG3 and SnSAG4. A novel genotype, referred to as Type XIII within the S. neurona population genetic structure, has emerged recently in the northeastern Pacific Ocean and is significantly associated with an increased severity of protozoal encephalitis and mortality among multiple stranded marine mammal species.

  10. Novel genus-specific broad range primers for the detection of furoviruses, hordeiviruses and rymoviruses and their application in field surveys in South-East Australia.

    Science.gov (United States)

    Zheng, Linda; Tang, Joe; Clover, Gerard R G; Spackman, Merrin E; Freeman, Angela J; Rodoni, Brendan C

    2015-03-01

    A number of viruses from the genera Furovirus, Hordeivirus and Rymovirus are known to infect and damage the four major temperate cereal crops, wheat, barley, sorghum and oats. Currently, there is no active testing in Australia for any of these viruses, which pose a significant biosecurity threat to the phytosanitary status of Australia's grains industry. To address this, broad spectrum PCR assays were developed to target virus species within the genera Furovirus, Hordeivirus and Rymovirus. Five sets of novel genus-specific primers were designed and tested in reverse-transcription polymerase chain reaction assays against a range of virus isolates in plant virus diagnostic laboratories in both Australia and New Zealand. Three of these assays were then chosen to screen samples in a three-year survey of cereal crops in western Victoria, Australia. Of the 8900 cereal plants screened in the survey, all were tested free of furoviruses, hordeiviruses and rymoviruses. To date, there were no published genus-specific primers available for the detection of furoviruses, hordeiviruses and rymoviruses. This study shows for the first time a broad-spectrum molecular test being used in a survey for exotic grain viruses in Australia. Results from this survey provide important evidence of the use of this method to demonstrate the absence of these viruses in Victoria, Australia. The primer pairs reported here are expected to detect a wide range of virus species within the three genera.

  11. A novel Sarcocystis neurona genotype XIII is associated with severe encephalitis in an unexpectedly broad range of marine mammals from the northeastern Pacific Ocean.

    Science.gov (United States)

    Barbosa, Lorraine; Johnson, Christine K; Lambourn, Dyanna M; Gibson, Amanda K; Haman, Katherine H; Huggins, Jessica L; Sweeny, Amy R; Sundar, Natarajan; Raverty, Stephen A; Grigg, Michael E

    2015-08-01

    Sarcocystis neurona is an important cause of protozoal encephalitis among marine mammals in the northeastern Pacific Ocean. To characterise the genetic type of S. neurona in this region, samples from 227 stranded marine mammals, most with clinical or pathological evidence of protozoal disease, were tested for the presence of coccidian parasites using a nested PCR assay. The frequency of S. neurona infection was 60% (136/227) among pinnipeds and cetaceans, including seven marine mammal species not previously known to be susceptible to infection by this parasite. Eight S. neurona fetal infections identified this coccidian parasite as capable of being transmitted transplacentally. Thirty-seven S. neurona-positive samples were multilocus sequence genotyped using three genetic markers: SnSAG1-5-6, SnSAG3 and SnSAG4. A novel genotype, referred to as Type XIII within the S. neurona population genetic structure, has emerged recently in the northeastern Pacific Ocean and is significantly associated with an increased severity of protozoal encephalitis and mortality among multiple stranded marine mammal species. PMID:25997588

  12. A novel Sarcocystis neurona genotype XIII is associated with severe encephalitis in an unexpectedly broad range of marine mammals from the northeastern Pacific Ocean

    Science.gov (United States)

    Barbosa, Lorraine; Johnson, Christine K.; Lambourn, Dyanna M.; Gibson, Amanda K.; Haman, Katherine H.; Huggins, Jessica L.; Sweeny, Amy R.; Sundar, Natarajan; Raverty, Stephen A.; Grigg, Michael E.

    2015-01-01

    Sarcocystis neurona is an important cause of protozoal encephalitis among marine mammals in the northeastern Pacific Ocean. To characterize the genetic type of S. neurona in this region, samples from 227 stranded marine mammals, most with clinical or pathological evidence of protozoal disease, were tested for the presence of coccidian parasites using a nested PCR assay. The frequency of S. neurona infection was 60% (136/227) among pinnipeds and cetaceans, including seven marine mammal species not previously known to be susceptible to infection by this parasite. Eight S. neurona fetal infections identified this coccidian parasite as capable of being transmitted transplacentally. Thirty-seven S. neurona-positive samples were multilocus sequence genotyped using three genetic markers: SnSAG1-5-6, SnSAG3 and SnSAG4. A novel genotype, referred to as Type XIII within the S. neurona population genetic structure, has emerged recently in the northeastern Pacific Ocean and is significantly associated with an increased severity of protozoal encephalitis and mortality among multiple stranded marine mammal species. PMID:25997588

  13. Gene Cloning of PME from Citrus Peels by RT-PCR%RT-PCR法克隆柑橘皮果胶酯酶基因

    Institute of Scientific and Technical Information of China (English)

    叶华; 马力

    2011-01-01

    试验利用RT-PCR技术将新鲜柑橘皮果胶酯酶基因克隆到pGEM T-Easy载体上,并进行了鉴定和序列测定.结果表明:该基因为克隆成功的果胶酯酶基因,全长1797bp,开放阅读框架长1785bp,共编码594个氨基酸.该序列含有PMEI和Pectinseterase两个保守序列.该序列与Coyadonga R发表的citrus CsPME4 3'端序列氨基酸同源性100%.%The PME gene was amplified from citrus peels by RT-PCR technique and inserted into plasmid Pgem T-Easy. The interest fragment was identified and sequenced. The results showed that it presented 100% identity with the 3'extremitycitrus of CsPME4. It has 1797bp and its ORF is 1785bp which coding 594 amino acid. It has two conserved sequences: PMEI and Pectinseterase. These suggest that is PME gene from citrus peels.

  14. Molecular cloning of three pyranose dehydrogenase-encoding genes from Agaricus meleagris and analysis of their expression by real-time RT-PCR.

    Science.gov (United States)

    Kittl, Roman; Sygmund, Christoph; Halada, Petr; Volc, Jindrich; Divne, Christina; Haltrich, Dietmar; Peterbauer, Clemens K

    2008-02-01

    Sugar oxidoreductases such as cellobiose dehydrogenase or pyranose oxidase are widespread enzymes among fungi, whose biological function is largely speculative. We investigated a similar gene family in the mushroom Agaricus meleagris and its expression under various conditions. Three genes (named pdh1, pdh2 and pdh3) putatively encoding pyranose dehydrogenases were isolated. All three genes displayed a conserved structure and organization, and the respective cDNAs contained ORFs translating into polypeptides of 602 or 600 amino acids. The N-terminal sections of all three genes encode putative signal peptides consistent with the enzymes extracellular secretion. We cultivated the fungus on different carbon sources and analyzed the mRNA levels of all three genes over a period of several weeks using real-time RT-PCR. The glyceraldehyde-3-phosphate dehydrogenase gene from A. meleagris was also isolated and served as reference gene. pdh2 and pdh3 are essentially transcribed constitutively, whereas pdh1 expression is upregulated upon exhaustion of the carbon source; pdh1 appears to be additionally regulated under conditions of oxygen limitation. These data are consistent with an assumed role in lignocellulose degradation. PMID:18097667

  15. Reproductive cloning : can cloning harm the clone?

    OpenAIRE

    Pattinson, S.D.

    2002-01-01

    Since the creation of Dolly the sheep was reported in February 1997, the possibility of a cloned child has elicited powerful declarations of condemnation. A widely held view is that cloning a human being would be immoral and ought to be prohibited by legislation. This paper outlines the regulatory approaches taken in the EU countries (with particular reference to the UK), Canada and the US, before examining the claim that creating a clone would be a wrong to the resultant clone. It is argued ...

  16. Multiplex PCR:a powerful and affordable tool for laboratory and field analysis in developing countries

    Institute of Scientific and Technical Information of China (English)

    Mohamed; O; Ahmed

    2014-01-01

    To the editor,Since the introduction of multiplex-PCR(mPCR)in1988,this technique has emerged as a highly efficient and sensitive molecular tool for nucleic acid-based diagnosis and monitoring,it is applicable to a broad range of physiological,metabolic and infectious conditions affecting human,animal

  17. HTCC: Broad Range Inhibitor of Coronavirus Entry.

    Directory of Open Access Journals (Sweden)

    Aleksandra Milewska

    Full Text Available To date, six human coronaviruses have been known, all of which are associated with respiratory infections in humans. With the exception of the highly pathogenic SARS and MERS coronaviruses, human coronaviruses (HCoV-NL63, HCoV-OC43, HCoV-229E, and HCoV-HKU1 circulate worldwide and typically cause the common cold. In most cases, infection with these viruses does not lead to severe disease, although acute infections in infants, the elderly, and immunocompromised patients may progress to severe disease requiring hospitalization. Importantly, no drugs against human coronaviruses exist, and only supportive therapy is available. Previously, we proposed the cationically modified chitosan, N-(2-hydroxypropyl-3-trimethylammonium chitosan chloride (HTCC, and its hydrophobically-modified derivative (HM-HTCC as potent inhibitors of the coronavirus HCoV-NL63. Here, we show that HTCC inhibits interaction of a virus with its receptor and thus blocks the entry. Further, we demonstrate that HTCC polymers with different degrees of substitution act as effective inhibitors of all low-pathogenic human coronaviruses.

  18. Clones above the unary clone

    OpenAIRE

    Goldstern, Martin; Sági, Gábor; Shelah, Saharon

    2011-01-01

    Let c be the cardinality of the continuum. We give a family of pairwise incomparable clones (on a countable base set) 2^c members, all with the same unary fragment, namely the set of all unary operations. We also give, for each n, a family of 2^c clones all with the same n-ary fragment, and all containing the set of all unary operations.

  19. Solid-phase plate-reader quantification of specific PCR products by measurement of band-specific ethidium bromide fluorescence.

    Science.gov (United States)

    McCarthy, Michael T; O'Callaghan, Christopher A

    2014-02-15

    Real-time PCR is widely employed to quantify PCR products across a range of applications. However, accurate real-time PCR is not always technically feasible, and alternative methods for PCR product quantification can be expensive and time consuming to validate. We have developed an inexpensive, rapid, and immediately accessible protocol to quantify PCR products, by measuring ethidium bromide fluorescence of PCR products excised from agarose gels. This protocol has relevance to a broad range of methods in molecular biology where quantification of PCR products is necessary.

  20. Identification of CTX-M15-, SHV-28-producing Klebsiella pneumoniae ST15 as an epidemic clone in the Copenhagen area using a semi-automated Rep-PCR typing assay

    DEFF Research Database (Denmark)

    Nielsen, J B; Skov, M N; Jørgensen, R L;

    2011-01-01

    pneumoniae (K. pneumoniae) producing extended spectrum β-lactamases (ESBLs) and their relation to recognized Danish outbreak strains. PFGE and Rep-PCR produced similar clustering among isolates. Individual isolates from each cluster were further characterized by PCR amplification and sequencing of bla (TEM......), bla (SHV), and bla (CTX-M), and multilocus sequence typing (MLST). Thirty-five out of 52 ESBL-producing K. pneumoniae isolates were ST15 and bla (CTX-M15), bla (SHV-28), and bla (TEM-1) positive by PCR. Ten out of 52 were ST16 and tested positive for bla (CTX-M15), bla (SHV-1), and bla (TEM-1...

  1. IVA cloning: A single-tube universal cloning system exploiting bacterial In Vivo Assembly

    OpenAIRE

    Javier García-Nafría; Watson, Jake F.; Greger, Ingo H.

    2016-01-01

    In vivo homologous recombination holds the potential for optimal molecular cloning, however, current strategies require specialised bacterial strains or laborious protocols. Here, we exploit a recA-independent recombination pathway, present in widespread laboratory E.coli strains, to develop IVA ( In Vivo Assembly) cloning. This system eliminates the need for enzymatic assembly and reduces all molecular cloning procedures to a single-tube, single-step PCR, performed in

  2. Self-Cloning CRISPR.

    Science.gov (United States)

    Arbab, Mandana; Sherwood, Richard I

    2016-01-01

    CRISPR/Cas9-gene editing has emerged as a revolutionary technology to easily modify specific genomic loci by designing complementary sgRNA sequences and introducing these into cells along with Cas9. Self-cloning CRISPR/Cas9 (scCRISPR) uses a self-cleaving palindromic sgRNA plasmid (sgPal) that recombines with short PCR-amplified site-specific sgRNA sequences within the target cell by homologous recombination to circumvent the process of sgRNA plasmid construction. Through this mechanism, scCRISPR enables gene editing within 2 hr once sgRNA oligos are available, with high efficiency equivalent to conventional sgRNA targeting: >90% gene knockout in both mouse and human embryonic stem cells and cancer cell lines. Furthermore, using PCR-based addition of short homology arms, we achieve efficient site-specific knock-in of transgenes such as GFP without traditional plasmid cloning or genome-integrated selection cassette (2% to 4% knock-in rate). The methods in this paper describe the most rapid and efficient means of CRISPR gene editing. © 2016 by John Wiley & Sons, Inc. PMID:27532819

  3. Cloning-free CRISPR

    Science.gov (United States)

    Arbab, Mandana; Srinivasan, Sharanya; Hashimoto, Tatsunori; Geijsen, Niels; Sherwood, Richard I.

    2015-01-01

    Summary We present self-cloning CRISPR/Cas9 (scCRISPR), a technology that allows for CRISPR/Cas9-mediated genomic mutation and site-specific knockin transgene creation within several hours by circumventing the need to clone a site-specific single-guide RNA (sgRNA) or knockin homology construct for each target locus. We introduce a self-cleaving palindromic sgRNA plasmid and a short double-stranded DNA sequence encoding the desired locus-specific sgRNA into target cells, allowing them to produce a locus-specific sgRNA plasmid through homologous recombination. scCRISPR enables efficient generation of gene knockouts (∼88% mutation rate) at approximately one-sixth the cost of plasmid-based sgRNA construction with only 2 hr of preparation for each targeted site. Additionally, we demonstrate efficient site-specific knockin of GFP transgenes without any plasmid cloning or genome-integrated selection cassette in mouse and human embryonic stem cells (2%–4% knockin rate) through PCR-based addition of short homology arms. scCRISPR substantially lowers the bar on mouse and human transgenesis. PMID:26527385

  4. Cloning-free CRISPR

    Directory of Open Access Journals (Sweden)

    Mandana Arbab

    2015-11-01

    Full Text Available We present self-cloning CRISPR/Cas9 (scCRISPR, a technology that allows for CRISPR/Cas9-mediated genomic mutation and site-specific knockin transgene creation within several hours by circumventing the need to clone a site-specific single-guide RNA (sgRNA or knockin homology construct for each target locus. We introduce a self-cleaving palindromic sgRNA plasmid and a short double-stranded DNA sequence encoding the desired locus-specific sgRNA into target cells, allowing them to produce a locus-specific sgRNA plasmid through homologous recombination. scCRISPR enables efficient generation of gene knockouts (∼88% mutation rate at approximately one-sixth the cost of plasmid-based sgRNA construction with only 2 hr of preparation for each targeted site. Additionally, we demonstrate efficient site-specific knockin of GFP transgenes without any plasmid cloning or genome-integrated selection cassette in mouse and human embryonic stem cells (2%–4% knockin rate through PCR-based addition of short homology arms. scCRISPR substantially lowers the bar on mouse and human transgenesis.

  5. Molecular cloning, expression and in vitro analysis of soluble cationic synthetic antimicrobial peptide from salt-inducible Escherichia coli GJ1158

    Directory of Open Access Journals (Sweden)

    Jawahar Babu Peravali

    2013-01-01

    Full Text Available Antimicrobial peptides are the upcoming therapeutic molecules as alternative drugs to the existing antibiotics owing to their potent action against pathogenic microorganisms. In this study, to obtain an antimicrobial peptide with a broad range of activity, the synthetic cationic antimicrobial peptide was designed by using in silico tools viz., antimicrobial peptide database, protparam, hierarchical neural network. Later, the peptide was translated back into a core nucleotide sequence and the gene for the peptide was constructed by overlapping PCR. The amplified gene was cloned into pRSET–A vector and transformed into salt inducible expression host E. coli GJ1158. The expression results show high yields of soluble recombinant fusion peptide (0.52 g/L from salt-inducible E. coli. The recombinant peptide was purified by the IMAC purification system and cleaved by enterokinase. The digested product was further purified and 0.12 g/L of biologically active recombinant cationic antimicrobial peptide was obtained. In vitro analysis of the purified peptide demonstrated high antimicrobial activity against both Gram positive and Gram negative bacteria devoid of hemolytic activity. Therefore, this synthetic cationic antimicrobial peptide could serves as an promising agent over chemical antibiotics. In this study, a synthetic cationic antimicrobial peptide was designed, cloned and expressed from salt-inducible E. coli GJ1158 using cost effective media in the large scale production of antimicrobial peptide and its biological activity was analysed against different Gram positive and negative organisms.

  6. Reproductive Cloning

    OpenAIRE

    Neves, D.

    2010-01-01

    ABSTRACT Man desires to perpetuate himself and thereby will cross ethical barriers in the attempt to preserve his genetic heritage and thus to immortalize himself. To create a being in one’s own image has been a dream of man since the dawn of civilization and since the advent of the cloned sheep Dolly (05/07/1996) it now seems possible. The great challenge now is too reconcile human knowledge and scientific knowledge in the search for happiness, as the fron...

  7. Applying Touchdown-PCR and Clone-based Sequencing to Detect the Methylation of IGF1R Gene Promoter in the Peripheral Leukocyte of Type 2 Diabetes Mellitus%应用降落PCR及克隆测序检测2型糖尿病外周血白细胞胰岛素样生长因子受体IGF1R基因甲基化

    Institute of Scientific and Technical Information of China (English)

    陈玲; 严世荣; 胡培; 陈永梅; 程龙海

    2011-01-01

    Objective To apply touchdown-PCR and clone-based sequencing detecting the methylation sites of IGF1R gene promoter in the peripheral leukocyte of type 2 diabetes mellitus. Methods After the bisulfite treatment of the DNA extracted from the peripheral leukocyte in patients with type 2 diabetes mellitus, the primer was design to amplify the target fragments by general PCR and touchdown-PCR,then the target fragments were used to direct sequencing and clone sequencing. Re-SUltS Compared the amplify results betweem touchdown-PCR and general PCR,the former had clearer fragment,more products, less dimers and saved time to explore the annealing temperature. The results of clone sequencing displayed clearly and accurately of every base. Conclusion Touchdown-PCR were recommend to be used to detect the methylation status after the DNA underwent the bisulfite treatment, the clone sequencing is a advisable choice.%目的:比较应用降落PCR(TD-PCR)及克隆测序检测2型糖尿病患者外周血白细胞中胰岛素样生长因子受体( IGF1 R)基因启动子区DNA甲基化位点的方法.方法:提取2型糖尿病患者外周血白细胞DNA进行亚硫酸氢盐处理,设计引物扩增IGF1R基因启动子区富含CG位点序列,分别行普通PCR和TD-PCR扩增,对含目的条带产物进行直接测序和克隆后测序.结果:与普通PCR扩增结果相比,TD-PCR扩增条带清晰、产物量多、二聚体少;且TD-PCR减少了对退火温度不断摸索的过程.克隆后测序峰图清晰,碱基丢失错判频率减少.结论:推荐应用TD-PCR检测亚硫酸氢盐处理的DNA甲基化位点,并进行克隆后测序.

  8. PCR thermocycler

    Science.gov (United States)

    Benett, William J.; Richards, James B.

    2003-01-01

    A sleeve-type silicon polymerase chain reaction (PCR) chamber or thermocycler having improved thermal performance. The silicon sleeve reaction chamber is improved in thermal performance by etched features therein that reduce thermal mass and increase the surface area of the sleeve for cooling. This improved thermal performance of the thermocycler enables an increase in speed and efficiency of the reaction chamber. The improvement is accomplished by providing grooves in the faces of the sleeve and a series of grooves on the interior surfaces that connect with grooves on the faces of the sleeve. The grooves can be anisotropically etched in the silicon sleeve simultaneously with formation of the chamber.

  9. The Cloning of the Human Tumor Supressor Gene INGI: DNA Cloning into Plasmid Vector and DNA Analysis by Restriction Enzymes

    Directory of Open Access Journals (Sweden)

    Elza Ibrahim Auerkari

    2015-11-01

    Full Text Available DNA cloning is one of the most important techniques In the field of molecular biology, with a critical role in analyzing the structure and function of genes and their adjacent regulatory regions. DNA cloning is helpful in learning fundamental molecular biological techniques, since DNA cloning involves a series of them, such as polymerase chain reaction (PCR, DNA ligation, bacterial transformation, bacterial culture, plasmid DNA extraction, DNA digestion with restriction enzymes and agarose gel electrophoresis. In this paper the cloning of the human tumor suppressor gene INGI has been used to illustrate the methodology. The gene was amplified by PCR, cloned into a TA-cloning vectore, and restriction enzyme mapping was used to distinguish the sense INGI construct from the antisense INGI construct.

  10. Molecular cloning of gluconobacter oxydans DSM 2003 xylitol dehydrogenase gene

    OpenAIRE

    Sadeghi, H. Mir Mohammad; Ahmadi, R; Aghaabdollahian, S.; Mofid, M.R.; Ghaemi, Y.; Abedi, D

    2011-01-01

    Due to the widespread applications of xylitol dehydrogenase, an enzyme used for the production of xylitol, the present study was designed for the cloning of xylitol dehydrogenase gene from Glcunobacter oxydans DSM 2003. After extraction of genomic DNA from this bacterium, xylitol dehydrogenase gene was replicated using polymerase chain reaction (PCR). The amplified product was entered into pTZ57R cloning vector by T/A cloning method and transformation was performed by heat shocking of the E. ...

  11. Quantum cloning

    International Nuclear Information System (INIS)

    It is impossible to make perfect copies or 'clones' of unknown quantum states, but approximate copies could still have many uses in quantum computing. A computer is a physical device that consists of components that are all subject to the laws of physics. Since computers deal exclusively in information, there is a close connection between information and physical systems. But what happens if the components inside the computer become so small that they must be described by quantum mechanics rather than classical physics? The seemingly unstoppable decrease in the size of transistors and other components will force the computer industry to confront this question in the near future. However, a small band of far-sighted physicists has been thinking about these problems for almost two decades. Starting with the work of Paul Benioff, Richard Feynman, David Deutsch and Charles Bennett in the mid-1980s, the field of 'quantum information' has grown to become one of the most exciting areas of modern physics. These early pioneers realized that the representation of information by quantum systems, such as single electrons or photons, was an opportunity rather than a problem. (U.K.)

  12. Broad Range of Hepatitis B Virus (HBV) Patterns, Dual Circulation of Quasi-Subgenotype A3 and HBV/E and Heterogeneous HBV Mutations in HIV-Positive Patients in Gabon

    Science.gov (United States)

    Bivigou-Mboumba, Berthold; François-Souquière, Sandrine; Deleplancque, Luc; Sica, Jeanne; Mouinga-Ondémé, Augustin; Amougou-Atsama, Marie; Chaix, Marie-Laure; Njouom, Richard; Rouet, François

    2016-01-01

    Integrated data on hepatitis B virus (HBV) patterns, HBV genotypes and mutations are lacking in human immunodeficiency virus type 1 (HIV-1) co-infected patients from Africa. This survey was conducted in 2010–2013 among 762 HIV-1-positive adults from Gabon who were predominantly treated with 3TC-based antiretroviral treatment. HBV patterns were identified using immunoassays detecting total antibody to hepatitis B core antigen (HBcAb), hepatitis B surface antigen (HBsAg), IgM HBcAb, hepatitis B e antigen (HBeAg), antibody to HBsAg (HBsAb) and an in-house real-time PCR test for HBV DNA quantification. Occult hepatitis B (OBI) was defined by the presence of isolated anti-HBc with detectable serum HBV DNA. HBV genotypes and HBV mutations were analyzed by PCR-direct sequencing method. Seventy-one (9.3%) patients tested positive for HBsAg, including one with acute hepatitis B (0.1%; 95% CI, 0.0%-0.2%), nine with HBeAg-positive chronic hepatitis B (CHB) (1.2%; 95% CI, 0.6%–2.2%), 16 with HBeAg-negative CHB (2.1%; 95% CI, 1.2%–3.3%) and 45 inactive HBV carriers (5.9%; 95% CI, 4.4%–7.8%). Sixty-one (8.0%; 95% CI, 6.2%–10.1%) patients showed OBI. Treated patients showed similar HBV DNA levels to those obtained in untreated patients, regardless of HBV patterns. Around 15.0% of OBI patients showed high (>1,000 UI/mL) viremia. The mutation M204V/I conferring resistance to 3TC was more common in HBV/A (47.4%) than in HBV/E isolates (0%) (P = .04). Our findings encouraged clinicians to promote HBV vaccination in patients with no exposure to HBV and to switch 3TC to universal TDF in those with CHB. PMID:26764909

  13. Broad Range of Hepatitis B Virus (HBV) Patterns, Dual Circulation of Quasi-Subgenotype A3 and HBV/E and Heterogeneous HBV Mutations in HIV-Positive Patients in Gabon.

    Science.gov (United States)

    Bivigou-Mboumba, Berthold; François-Souquière, Sandrine; Deleplancque, Luc; Sica, Jeanne; Mouinga-Ondémé, Augustin; Amougou-Atsama, Marie; Chaix, Marie-Laure; Njouom, Richard; Rouet, François

    2016-01-01

    Integrated data on hepatitis B virus (HBV) patterns, HBV genotypes and mutations are lacking in human immunodeficiency virus type 1 (HIV-1) co-infected patients from Africa. This survey was conducted in 2010-2013 among 762 HIV-1-positive adults from Gabon who were predominantly treated with 3TC-based antiretroviral treatment. HBV patterns were identified using immunoassays detecting total antibody to hepatitis B core antigen (HBcAb), hepatitis B surface antigen (HBsAg), IgM HBcAb, hepatitis B e antigen (HBeAg), antibody to HBsAg (HBsAb) and an in-house real-time PCR test for HBV DNA quantification. Occult hepatitis B (OBI) was defined by the presence of isolated anti-HBc with detectable serum HBV DNA. HBV genotypes and HBV mutations were analyzed by PCR-direct sequencing method. Seventy-one (9.3%) patients tested positive for HBsAg, including one with acute hepatitis B (0.1%; 95% CI, 0.0%-0.2%), nine with HBeAg-positive chronic hepatitis B (CHB) (1.2%; 95% CI, 0.6%-2.2%), 16 with HBeAg-negative CHB (2.1%; 95% CI, 1.2%-3.3%) and 45 inactive HBV carriers (5.9%; 95% CI, 4.4%-7.8%). Sixty-one (8.0%; 95% CI, 6.2%-10.1%) patients showed OBI. Treated patients showed similar HBV DNA levels to those obtained in untreated patients, regardless of HBV patterns. Around 15.0% of OBI patients showed high (>1,000 UI/mL) viremia. The mutation M204V/I conferring resistance to 3TC was more common in HBV/A (47.4%) than in HBV/E isolates (0%) (P = .04). Our findings encouraged clinicians to promote HBV vaccination in patients with no exposure to HBV and to switch 3TC to universal TDF in those with CHB.

  14. The Cloning of the Human Tumor Supressor Gene INGI: DNA Cloning into Plasmid Vector and DNA Analysis by Restriction Enzymes

    OpenAIRE

    Elza Ibrahim Auerkari; Mamoru Ouchida; Mehmet Gunduz

    2015-01-01

    DNA cloning is one of the most important techniques In the field of molecular biology, with a critical role in analyzing the structure and function of genes and their adjacent regulatory regions. DNA cloning is helpful in learning fundamental molecular biological techniques, since DNA cloning involves a series of them, such as polymerase chain reaction (PCR), DNA ligation, bacterial transformation, bacterial culture, plasmid DNA extraction, DNA digestion with restriction enzymes and agarose g...

  15. 赤拟谷盗HSP70基因克隆和竞争定量PCR检测%Cloning and quantitative competitive PCR assay of HSP70 gene in Tribolium castaneum ( Coleoptera: Tenebrionidae)

    Institute of Scientific and Technical Information of China (English)

    苏丽娟; 董晓慧; 尹新明

    2011-01-01

    To study the expression changes of heat shock protein 70 (a highly conserved protein) in Tribolium castaneum after exposure to heat stress, a fragment of 681 bp encoding for HSP70 was amplified and sequenced from T.castaneum.The fragment encoded 227 amino acid residues with the GenBank accession no.HM345948.The result of homology analysis showed that this fragment shared 97% identity with hsp70 from L.decemlineata (AF322911.1 ).Comparison of the deduced amino acid sequences of HSP70 in T.castaneum with those in Leptinotarsa decemlineata, Mamestra brassicae, Drosophila melanogaster and Liriomyza sativae indicated that they shared more than 94% identity.The internal competitor used in quantitative competitive PCR was obtained by RT-PCR.The detection system of hsp70 was constructed by PCR amplification using the same quantity of target cDNA and a series of diluted internal competitor as template.The linear equation of standard curve was Y= 1.032X- 1.618 (r2 =0.975).This study provides a very convenient method for the quantitation of the hsp70 expression changes in T.castaneum and offers the basic data for the prevention and control of pests using thermal control technology.%为研究赤拟谷盗Tribolium castaneum受到热胁迫后高度保守的热激蛋白70(heat shock protein 70,HSP70)基因的表达变化,本研究扩增了681 bp的赤拟谷盗hsp70片段,编码227个氨基酸残基,GenBank登录号为HM345948.同源性分析表明:赤拟谷盗hsp70核苷酸序列与马铃薯甲虫Leptinotarsa decemlineata的hsp70(GenBank登录号:AF322911.1)同源性最高,为97%;其推测的蛋白序列与马铃薯甲虫、甘蓝夜蛾Mamestra brassicae、黑腹果蝇Drosophila melanogaster和美洲斑潜蝇Liriomyza,sativae的HSP70蛋白均有94%以上的同源性.利用RT-PCR技术得到与赤拟谷盗hsp70进行竞争定量的内部竞争物,以等量的目标cDNA和一系列稀释的竞争模板进行竞争PCR扩增,构建了hsp70的竞争定量PCR检测体系,该

  16. The Clone Factory

    Science.gov (United States)

    Stoddard, Beryl

    2005-01-01

    Have humans been cloned? Is it possible? Immediate interest is sparked when students are asked these questions. In response to their curiosity, the clone factory activity was developed to help them understand the process of cloning. In this activity, students reenact the cloning process, in a very simplified simulation. After completing the…

  17. Cloning a novd catalase gene of Sporothrix schenckii with degenerate PCR and RACE%简并PCR结合RACE技术克隆申克孢子丝菌未知过氧化氢酶基因

    Institute of Scientific and Technical Information of China (English)

    王晓慧; 刘伟; 李若瑜

    2011-01-01

    Objective To isolate a novel catalase homologous gene from yeast-form Sporothrix schenckii and to make a designation. Methods Oligonucleotide primers were designed according to the conserved areas of the other 7 fungal catalase genes. Partial Sscat cDNA was amplified by PCR, and special primers were designed by RACE method to amplify the 3'cDNA and 5'cDNA. ResultsThe full-length Sscat cDNA sequence was 1 746 bp with an open reading frame of1 500 bp encoding 499 amino acids. The predicted molecular mass of Sscat was 56.07 kDa. The deduced amino acid sequence of Sscat showed 66.3% and 56.6% identity with those of Aspergillus oryzae and A. clavatus . An intron was identified within the 933-1 063 bp Sscat genomic DNA sequence ofS. schenckii. Conclusions Degenerate PCR combined with RACE is effective in searching and isolating novel genes of 5. schenckii.%目的 克隆孢子丝菌未知过氧化氢酶基因,命名为Sscat基因.方法 根据生物信息库中7种已知真菌过氧化氢酶氨基酸序列的高度保守区域设计简并引物,PCR扩增获得部分Sscat基因cDNA片段,随后应用RACE技术分别扩增其3’端和5’端未知序列.结果 Sscat基因cDNA序列全长1746 bp,其中包括5’端121 bp的非编码区、1500 bp的编码区和109 bp的3’端非编码区.该基因编码499个氨基酸,分子量为56.07 kDa,其氨基酸序列与其他真菌过氧化氢酶氨基酸高度同源,其中与米曲霉、黑曲霉同源性分别为66.3%和56.6%,Sscat基因为申克孢子丝菌过氧化氢酶cDNA.结论 简并PCR结合RACE技术成功克隆了孢子丝菌未知过氧化氢酶基因.

  18. PCR Amplification,Cloning and Sequencing of ITS rDNA of Fasciola Gigantica from Longyan%羊大片吸虫龙岩分离株ITS基因的克隆及序列分析

    Institute of Scientific and Technical Information of China (English)

    谢宝明; 陈永锋; 陈仁锋; 黄翠琴

    2012-01-01

    In the paper,the samples of Fasciola(Platyhelminthes: Trematoda: Digenea) from sheep host in Longyan,Fujian,China were characterized genetically by sequences of the first(ITS-1) and second(ITS-2) internal transcribed spacers(ITS) of nuclear ribosomal DNA(rDNA).The ITS rDNA was amplified by polymerase chain reaction(PCR),and the amplification was cloned and then sequenced.The lengths of the ITS-1 and ITS-2 sequences were 421 bp and 361 bp respectively.Comparison of the ITS sequences of Longyan Fasciola sample with that of Fasciola hepatica,Fasciola gigantica and the "intermediate Fasciola" revealed that Longyan Fasciola samples examined represent F.gigantica(named FgLY).The genetic relationship of FgLY is closest to the samples from Yunnan,China by phylogenetic analysis.The result has laid foundation for studying the population genetic structure of F.gigantica and for the diagnosis and control of the disease it causes.%应用PCR方法扩增龙岩地区羊片形吸虫分离株ITS序列,经克隆、测序后获得ITS全长序列944bp,其中ITS-1为421bp,ITS-2为361bp;通过在肝片吸虫和大片吸虫ITS种间鉴别位点上的序列分析表明,从龙岩地区羊体内分离的片形吸虫虫种属大片吸虫(命名为FgLY)。与国内外大片吸虫的进化分析表明,FgLY与中国云南的2个分离株处在一个小分支,亲缘关系最近。该结果为羊大片吸虫的进一步生物学研究和片形吸虫病的预防奠定了基础。

  19. 靶向克隆法构建NY-ESO-1基因的原核表达载体%Construction of NY-ESO-1 Gene Prokaryotic Expression Vector by LP Recco PCR Cloning

    Institute of Scientific and Technical Information of China (English)

    俞远东; 徐少勇; 王斌; 王家宁; 黄永章

    2009-01-01

    目的:利用PCR产物靶向克隆法构建人癌-睾丸抗原NY-ESO-1的原核表达载体.方法:从人新鲜的食管癌组织中提取总RNA,通过RT-PCR技术扩增NY-ESO-1基因3'端的340 bp片段,采用靶向克隆法将目的基因插入到原核表达载体pET-15b中,得到重组表达质粒pET-15b-NY-ESO-1,经过筛选,挑选出阳性克隆进行Xho Ⅰ和BamHⅠ双酶切图谱分析、PCR检测和扩增产物核苷酸序列分析等,鉴定所构建的原核表达载体.结果:扩增得到NY-ESO-1基因片段,经测序证实与GenBank公布的序列一致,重组的质粒经过PCR,酶切鉴定获得了一个大小为340 bp的特征性片段,证明重组质粒中已成功的插入了目的基因NY-ESO-1.结论:靶向克隆法可快速、高效地构建人NY-ESO-1基因的原核表达载体,为制备pET-15b-NY-ESO-1融合蛋白奠定了基础.

  20. Identification of Env-specific monoclonal antibodies from Chinese HIV-1 infected person by magnetic beads separating B cells and single cell RT-PCR cloning%利用磁珠分选和单细胞RT-PCR筛选HIV-1 Env特异性单克隆抗体的研究

    Institute of Scientific and Technical Information of China (English)

    黄湘滢; 余双庆; 程湛; 叶景荣; 徐柯; 冯霞; 曾毅

    2013-01-01

    Objective To establish a simple and practical method for screening of Env-specific monoclonal antibodies from HIV-1 infected individuals.Methods Human B cells were purified by negative sorting from PBMCs and memory B cells were further enriched using anti-CD27 microbeads.Gp120 antigen labbled with biotin was incubated with memory B cells to specifically bind IgG on cells membrane.The memory B cells expressing the Env-specific antibody were harvested by magnetic beads separating,counted and diluted to the level of single cell in each PCR well that loading with catch buffer containing RNase inhibitor to get RNAs.The antibody genes were amplified by single cell RT-PCR and nested PCR,cloned into eukaryotic expression vectors and transfected into 293T cells.The binding activity of recombinant antibodies to Env were tested by ELISA.Results Three monocolonal Env-specific antibodies were isolated from one HIV-1 infected individual.Conclusion We can obtain Env-specific antibody by biotin labbled antigen,magnetic beads separating technique coupled with single cell RT-PCR and expression cloning.%目的 建立一种简单易行的从HIV-1感染者中筛选包膜糖蛋白(envelope glycoprotein,Env)特异性单克隆抗体的方法.方法 采集HIV-1感染者抗凝全血,分离外周血单个核细胞,利用生物素标记的HIV Gp120抗原与B细胞膜上的IgG特异性结合,然后用链霉亲和素标记的磁珠分选出能够产生Env特异性抗体的记忆性B细胞.用单细胞RT-PCR法从记忆性B细胞中扩增抗体的重链可变区基因与轻链可变区的基因并克隆到表达载体中,将携带重链基因的质粒与携带轻链基因的质粒共转染293T细胞,获得HIV-1特异性人单克隆抗体,并进行抗体结合活性的鉴定.结果 从1例我国HIV-1感染者记忆性B细胞中筛选出3株对HIV-1 Env抗原有结合活性的单克隆抗体.结论 利用生物素标记抗原与记忆性B细胞特异结合,并用亲和素标记的磁珠对细胞

  1. Expression-PCR: A rapid method for in vitro expression of PCR products

    International Nuclear Information System (INIS)

    We present a rapid and simple method called Expression-PCR (E-PCR) for in vitro synthesis of protein from genomic, plasmid or reverse transcribed DNA. Expression-PCR is a procedure for installing transcription and translation signals to genes of interest allowing their efficient expression in vitro. These signals are contained in an in vitro expression cassette (EC) containing an untranslated leader sequence from alfalfa mosaic virus (AMV-UTL) directly downstream form the T7 bacteriophage promoter site. When this EC is spliced to a PCR product, it produces a suitable template for direct in vitro transcription and translation. This methodology permits the rapid analysis of gene products without the need for cloning or in vivo expression. E-PCR represents a significant improvement over current in vitro expression systems, most notably in time-savings, versatility of gene expression and compatibility with rapid PCR-based site-directed mutagenesis procedures. (author). 20 refs, 2 figs

  2. A Guide to Using STITCHER for Overlapping Assembly PCR Applications.

    Science.gov (United States)

    O'Halloran, Damien M

    2017-01-01

    Overlapping PCR is commonly used in many molecular applications that include stitching PCR fragments together, generating fluorescent transcriptional and translational fusions, inserting mutations, making deletions, and PCR cloning. Overlapping PCR is also used for genotyping and in detection experiments using techniques such as loop-mediated isothermal amplification (LAMP). STITCHER is a web tool providing a central resource for researchers conducting all types of overlapping assembly PCR experiments with an intuitive interface for automated primer design that's fast, easy to use, and freely available online.

  3. A Guide to Using STITCHER for Overlapping Assembly PCR Applications.

    Science.gov (United States)

    O'Halloran, Damien M

    2017-01-01

    Overlapping PCR is commonly used in many molecular applications that include stitching PCR fragments together, generating fluorescent transcriptional and translational fusions, inserting mutations, making deletions, and PCR cloning. Overlapping PCR is also used for genotyping and in detection experiments using techniques such as loop-mediated isothermal amplification (LAMP). STITCHER is a web tool providing a central resource for researchers conducting all types of overlapping assembly PCR experiments with an intuitive interface for automated primer design that's fast, easy to use, and freely available online. PMID:27671928

  4. Restriction endonucleases digesting DNA in PCR buffer

    Institute of Scientific and Technical Information of China (English)

    LIU Xue-dong; ZHENG Dong; ZHOU Yan-na; MAO Wei-wei; MA Jian-zhang

    2005-01-01

    Six commonly used restriction endonucleases (Res) (Acc I, Ban II, EcoR I, Hind III, Sac I, Sca I) were tested for their ability to directly digest DNA completely in the Polymerase Chain Reaction (PCR) buffers. The results showed that: with the requirement for additional magnesium supplemented as activator, Res, except EcoR I appeared star activity, completely digested unmethylated lambda DNA after overnight incubation in PCR buffer and functioned as equally well as in recommended Restriction Enzyme Buffer provided with each enzyme; all Res tested completely digested PCR products in PCR buffer, it implied digestion of PCR products may often be performed directly in the PCR tube without the requirement for any precipitation or purification steps; and the concentration of MgCl2 from 2.5 mmol·L-1 to 10 mmol·L-1 did not significantly affect activity of Res in PCR buffer. This simplified method for RE digestion of PCR products could have applications in restriction fragment length polymorphism (RFLP) analysis and single-stranded conformational polymorphism (SSCP) analysis of large PCR products. However, usage of this procedure for cloning applications needs further data.

  5. Ethical issues in cloning.

    Science.gov (United States)

    Satris, S

    2000-01-01

    There is great public concern with the ethics of human cloning. This paper briefly examines some of what I identify as pseudo-problems or myths associated with cloning, and some of the more substantial ethical concerns.

  6. Cloning,Characterization and Real-time RT-PCR Analysis of a Key Gene beta-Amyrin synthase for Saponin Biosynthesis in Barbarea vulgaris%欧洲山芥皂苷合成关键酶基因Bv-beta-AS克隆及表达分析

    Institute of Scientific and Technical Information of China (English)

    魏小春; 张晓辉; 吴青君; 王海平; 沈镝; 邱杨; 宋江萍; 李锡香

    2012-01-01

    G-type Barbarea vulgaris R.Br. which produce saponins is a rare insect resistant vegetable in Cruciferae. A beta-amyrin synthase gene which codes a key enzyme of saponin biosynthesis pathway was cloned from Barbarea vulgaris R.Br. using RT-PCR and RACE(Rapid Amplification of cDNA Ends) method,and named as Bv-beta-AS. The Bv-beta-AS contained a coding sequence of 2 289 bp(GenBank accession number:JQ172795),which encoded 762 amino acids. The gene of 4 107 bp from genomic DNA was further cloned,which contained 15 introns embedded in its coding sequences. The deduced protein of this gene contained the conserved characteristic motif of beta-amyrin synthase -DCTAE and QW. And thehigh similarity of this gene with the beta-amyrin synthase from other plants indicated it was a homologue of beta-amyrin synthase. Multiple sequence alignments and phylogenetic tree analyses showed that Bv-beta-AS was clustered with Arabidopsis beta-amyrin synthase and showed the highly similarity(74%) in amino acid sequences. The expression of Bv-beta-AS under the diamondback moth(Plutella xylostella) attack was determined by real-time RT-PCR. The results showed that Bv-beta-AS gene expression was up-regulated within 12 h of diamondback moth attack,but decline tendency appeared after 12 hours. Both the sequences analysis results and the real-time RT-PCR data indicated that Bv-beta-AS may be an important candidate gene of saponin biosynthesis pathway.%以能够产生抗虫皂苷的高抗小菜蛾资源G型欧洲山芥(Barbarea vulgaris R.Br.)B44为材料,利用RACE技术克隆出皂苷合成关键酶beta–香树脂合成酶的基因(Barbarea vulgaris beta-amyrin synthase,Bv-beta-AS)。该基因编码区序列长为2289bp(GenBank登录号JQ172795),推导其编码762个氨基酸;在基因组水平上长度为4107bp(GenBank登录号JQ172796),含有15个内含子。Bv-beta-AS编码的氨基酸具有beta–香树脂合成酶基因家族的保守序列,即DCTAE序列

  7. Generating in vivo cloning vectors for parallel cloning of large gene clusters by homologous recombination.

    Directory of Open Access Journals (Sweden)

    Jeongmin Lee

    Full Text Available A robust method for the in vivo cloning of large gene clusters was developed based on homologous recombination (HR, requiring only the transformation of PCR products into Escherichia coli cells harboring a receiver plasmid. Positive clones were selected by an acquired antibiotic resistance, which was activated by the recruitment of a short ribosome-binding site plus start codon sequence from the PCR products to the upstream position of a silent antibiotic resistance gene in receiver plasmids. This selection was highly stringent and thus the cloning efficiency of the GFPuv gene (size: 0.7 kb was comparable to that of the conventional restriction-ligation method, reaching up to 4.3 × 10(4 positive clones per μg of DNA. When we attempted parallel cloning of GFPuv fusion genes (size: 2.0 kb and carotenoid biosynthesis pathway clusters (sizes: 4 kb, 6 kb, and 10 kb, the cloning efficiency was similarly high regardless of the DNA size, demonstrating that this would be useful for the cloning of large DNA sequences carrying multiple open reading frames. However, restriction analyses of the obtained plasmids showed that the selected cells may contain significant amounts of receiver plasmids without the inserts. To minimize the amount of empty plasmid in the positive selections, the sacB gene encoding a levansucrase was introduced as a counter selection marker in receiver plasmid as it converts sucrose to a toxic levan in the E. coli cells. Consequently, this method yielded completely homogeneous plasmids containing the inserts via the direct transformation of PCR products into E. coli cells.

  8. Clones on regular cardinals

    OpenAIRE

    Goldstern, Martin; Shelah, Saharon

    2000-01-01

    We investigate the structure of the lattice of clones on an infinite set X. We first observe that ultrafilters naturally induce clones; this yields a simple proof of Rosenberg's theorem: "there are 2^2^kappa many maximal (=precomplete) clones on a set of size kappa." The clones we construct here do not contain all unary functions. We then investigate clones that do contain all unary functions. Using a strong negative partition theorem we show that for many cardinals kappa there are 2^2^kappa ...

  9. Rainbow Vectors for Broad-Range Bacterial Fluorescence Labeling.

    Directory of Open Access Journals (Sweden)

    Mariette Barbier

    Full Text Available Since their discovery, fluorescent proteins have been widely used to study protein function, localization or interaction, promoter activity and regulation, drug discovery or for non-invasive imaging. They have been extensively modified to improve brightness, stability, and oligomerization state. However, only a few studies have focused on understanding the dynamics of fluorescent proteins expression in bacteria. In this work, we developed a set plasmids encoding 12 fluorescent proteins for bacterial labeling to facilitate the study of pathogen-host interactions. These broad-spectrum plasmids can be used with a wide variety of Gram-negative microorganisms including Escherichia coli, Pseudomonas aeruginosa, Burkholderia cepacia, Bordetella bronchiseptica, Shigella flexneri or Klebsiella pneumoniae. For comparison, fluorescent protein expression and physical characteristics in Escherichia coli were analyzed using fluorescence microscopy, flow cytometry and in vivo imaging. Fluorescent proteins derived from the Aequorea Victoria family showed high photobleaching, while proteins form the Discosoma sp. and the Fungia coccina family were more photostable for microscopy applications. Only E2-Crimson, mCherry and mKeima were successfully detected for in vivo applications. Overall, E2-Crimson was the fastest maturing protein tested in E. coli with the best overall performance in the study parameters. This study provides a unified comparison and comprehensive characterization of fluorescent protein photostability, maturation and toxicity, and offers general recommendations on the optimal fluorescent proteins for in vitro and in vivo applications.

  10. Rainbow Vectors for Broad-Range Bacterial Fluorescence Labeling.

    Science.gov (United States)

    Barbier, Mariette; Damron, F Heath

    2016-01-01

    Since their discovery, fluorescent proteins have been widely used to study protein function, localization or interaction, promoter activity and regulation, drug discovery or for non-invasive imaging. They have been extensively modified to improve brightness, stability, and oligomerization state. However, only a few studies have focused on understanding the dynamics of fluorescent proteins expression in bacteria. In this work, we developed a set plasmids encoding 12 fluorescent proteins for bacterial labeling to facilitate the study of pathogen-host interactions. These broad-spectrum plasmids can be used with a wide variety of Gram-negative microorganisms including Escherichia coli, Pseudomonas aeruginosa, Burkholderia cepacia, Bordetella bronchiseptica, Shigella flexneri or Klebsiella pneumoniae. For comparison, fluorescent protein expression and physical characteristics in Escherichia coli were analyzed using fluorescence microscopy, flow cytometry and in vivo imaging. Fluorescent proteins derived from the Aequorea Victoria family showed high photobleaching, while proteins form the Discosoma sp. and the Fungia coccina family were more photostable for microscopy applications. Only E2-Crimson, mCherry and mKeima were successfully detected for in vivo applications. Overall, E2-Crimson was the fastest maturing protein tested in E. coli with the best overall performance in the study parameters. This study provides a unified comparison and comprehensive characterization of fluorescent protein photostability, maturation and toxicity, and offers general recommendations on the optimal fluorescent proteins for in vitro and in vivo applications. PMID:26937640

  11. MOLECULAR CLONING OF HUMAN NEUROTROPHIN-4 GENE

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Objective Cloning and sequencing of the human neurotrophin-4(hNT-4) gene.Methods With the chromosomal DNA of human blood lymphocytes as template,hNT-4 coding genes were amplified by polymerase chain reaction(PCR) and recombinated into phage vector pGEM-T Easy,which were sequenced by using Sanger's single stranded DNA terminal termination method.Results The sequence of the cloned gene is completely the same as that reported in the literature(GenBank data base,M86528).Conclusion This study successfully cloning and sequenced the gene of mhNT-4,and it would be convenient for us to study the expression of mhNT-4 in eukaryote,and to continue the research on the gene therapy of Alzheimer's disease intensively.This study indicate that the hNT-4 is conservative in different races and individuals.

  12. THE CLONING OF HUMAN NEUROTROPHIN-3 GENE

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    In the present study, we have cloned the gene of human neurotrophin-3 (hNT-3) from the genomic DNA of white blood cells (WBC) by polymerase chain reaction (PCR). The amplification products were cloned into pUC19 and sequenced. Genomic sequence comparison of the cloned fragment and the reported hNT-3 (GenBank M61180) reveals 7 base differences: 1 in the signal peptide, 3 in the prepro peptide, and 3 in the mature hNT-3. Except the 2 varied bases (16th, T to G; 285th, A to C) in the signal peptide and pro-sequence resulted in the change of their encoded amino-acids (Tyr→Asp; Gln→His), the other varied bases have no influence on their respective encoded amino-acids, and all the changes have no influence on the open reading frame (ORF) of the hNT-3.

  13. 克隆缺失连接片段——一种基于PCR技术的缺失型假肥大型肌营养不良症的携带者检测%Cloning of deletion junctions: a method of PCR for detecting the deletional pseudohypertrophic muscular dystrophy carriers

    Institute of Scientific and Technical Information of China (English)

    钟敏; 潘速跃; 陆兵勋; 李伟

    2008-01-01

    Objective Dystrophin gene deletion junction is the tmique DNA sequence resulted from illegitimate recombination after the gene deletion.A novel accurate approach is presented here for the detection of deletional pseudohypertrophic muscular dystrophy carriers with the deletion junctions.Methods A Becker muscular dystrophy (BMD)family from Zhaoqing,Guangdong,China was used.Two males in the family were diagnosed as BMD patients,3 phenotypically normal females and 1 charionic villi sample of an artificial abortion were waiting for diagnosis.The index patient was identified as exons 3-5 deletion of the dystrophin gene.Then a PCR-based genome-walking method was used to locate the breakpoints in corresponding introns.Finally,deletion junctions of the 6 family members were amplified by PCR with primers adjacent to breakpoints and sequenced.Results The deletion junctions of all patients and carriers of the BMD family were cloned and sequenced.The 3 females and 1 ehorionic tissue were diagnosed as female carriers.Conclusion In this study researchers have successfully carried out accurate geno diagnosis of delefional pseudohypertrophic carriers by cloning and sequencing the deletion junctions,and explored the prospect of using deletion junctions in prenatal diagnosis of BMD.%目的 依据dystrophin基因缺失后断端重接可形成一段变异的DNA序列,提出一种利用缺失连接片段进行缺失型假肥大型肌营养不良症携带者检测的新方法.方法 实验以来自广东省肇庆地区的一个Becker型肌营养不良(Becket muscular dystrophy,BMD)家系为研究对象,其中2例确诊的男性BMD患者,3例待诊的女性携带者,1例待诊的人工流产绒毛.先证者经外显子PCR检测确定第3~5外显子缺失,随后采用PCR步移法在相应内含子设计引物定位断裂点的位点,最后利用靠近断裂点设计的引物直接对家系的6例基因组DNA进行缺失连接片段的PCR扩增和测序.结果 6例基因组DNA均扩增

  14. Identification of Env-specific Monoclonal Antibodies from Chinese HIV-1 Infected Person by B cell Activation and RT-PCR Cloning%利用B细胞培养和RT-PCR技术从我国HIV-1感染者中筛选膜蛋白特异性单克隆抗体的初步研究

    Institute of Scientific and Technical Information of China (English)

    汪慧敏; 管永军; 曾毅; 徐柯; 余双庆; 丁林林; 罗海艳; Robin Flinko; George K lewis; 冯霞; 邵继荣

    2012-01-01

    To obtain protective human monoclonal antibody from HIV-1 infected person, we adapted a technology for isolating antigen specific monoclonal antibody from human memory B cells through in vitro B cell activation coupled with RT-PCT and expression cloning. Human B cells were purified by negative sorting from PBMCs of HIV-1 infected individuals and memory B cells were further enriched using anti-CD27 microbeads. Two hundred memory B cells per well were cultured in 96-well round-bottom plates with feeder cells in medium containing EBV and CpG. Env-specific antibodies in supernatants were screened by ELISA after 1~2 weeks' culture. Cells from positive wells of Env-specific antibody were harvested and total RNA was isolated. Human VH and Vκ or VX genes were amplified by RT-PCR and cloned into IgG1 and κ or γ expressing vectors. Functional VH and Vk or VX were identified by cotransfecting 293T cells with individual heavy chain and light chain clones followed by analysis of culture supernatants by ELISA for Env-specific antibodies. Finally, corresponding mAb was produced by transient transfection of 293T cells with the identified VH and V κ/γ pair and purified by protein A affinity chromatography. Purified monocolonal antibodies were used for HIV-1 specific antibody-dependent cell-mediated cytotoxicity (ADCC) and neutralizing activity assay. Four monocolonal Env-specific antibodies were isolated from one HIV-1 subtype B' infected individual. Two of them showed strong ADCC activity and one showed weak neutralizing activity against HIV-1. Its further studies on their application in therapeutic or prophylactic vaccines against HIV-1 should be grounded.%本研究通过采集1型人类免疫缺陷病毒(Human immunodeficiency virus-1,HIV-1)感染者抗凝全血,分离出外周血单个核细胞,然后用磁珠分选纯化记忆性B细胞和体外活化记忆性B细胞,促使其分泌抗体,用ELISA法识别阳性B细胞克隆,并提取阳性B细胞

  15. Cloning of Minor Autolysin of Streptococcus Pneumoniae

    OpenAIRE

    Mahboobi, R. (MSc); Fallah Mehrabadi, J. (PhD); MR Pourmand; R Mashhadi; Haddadi, A. (MD

    2015-01-01

    Background and Objective: Increased antibiotic resistant strains and inadequacy of current vaccines against pneumococcal infections necessitate the study of novel protein antigens. It seems that minor autolysin of Streptococcus pneumoniae may have antigenicity. Thus, we aimed at cloning its gene for the first time. Material and Methods: After DNA extraction of Streptococcus pneumoniae (ATCC 49619), Specific primers were designed for amplifying minor autolysin gene fragment, using PCR. The pur...

  16. Molecular cloning and comparative responses of Toll-like receptor 22 following ligands stimulation and parasitic infection in yellowtail (Seriola lalandi).

    Science.gov (United States)

    Reyes-Becerril, Martha; Ascencio-Valle, Felipe; Alamillo, Erika; Hirono, Ikuo; Kondo, Hidehiro; Jirapongpairoj, Walissara; Angulo, Carlos

    2015-10-01

    TLR22 is exclusively present in teleosts and amphibians and is expected to play the distinctive role in innate immunity. In this study, we cloned the full-length cDNA sequence of yellowtail (Seriola lalandi) TLR22 (SlTLR22). The complete cDNA sequence of SlTLR22 was 4208 bp and encodes a polypeptide of 961 amino acids. Analysis of the deduced amino acid sequence indicated that SlTLR22 has typical structural features of proteins belonging to the TLR family. These included 17 LRR domains (residues 91-633) and one C-terminal LRR domain (LRR-CT, residues 693-744) in the extracellular region, and a TIR domain (residues 800-943) in the cytoplasmic region. Comparison with homologous proteins showed that the deduced SlTLR22 has the highest sequence identity to turbot TLR22 (76%). Quantitative real-time PCR (qPCR) analysis demonstrated the constitutive expression of SlTLR22 mRNA in all examined tissues with higher levels in the head kidney, intestine, skin and spleen. Further, SlTLR22 expression was significantly up-regulated following TLR ligands injection with lipopolysaccharide (LPS), CpG ODN2006 and polyinosinic: polycytidylic acid (poly I:C) in spleen and liver. Amyloodinium ocellatum infection also induced a high expression of SlTLR22 in spleen, intestine, muscle, skin and gill, with maximum increases ranging from 1000 to 100 fold upon different ligands and organs. Finally, histological examination in gill tissue confirmed infection by the parasite and histopathological lesion was observed also in spleen and skin. These findings suggest a possible role of SlTLR22 in the immune responses to the infections of a broad range of pathogens that include DNA and RNA viruses and parasites. PMID:26102460

  17. DNA Cloning Using In Vitro Site-Specific Recombination

    OpenAIRE

    Hartley, James L.; Temple, Gary F.; Brasch, Michael A.

    2000-01-01

    As a result of numerous genome sequencing projects, large numbers of candidate open reading frames are being identified, many of which have no known function. Analysis of these genes typically involves the transfer of DNA segments into a variety of vector backgrounds for protein expression and functional analysis. We describe a method called recombinational cloning that uses in vitro site-specific recombination to accomplish the directional cloning of PCR products and the subsequent automatic...

  18. Statement on Human Cloning

    Science.gov (United States)

    ... as our understanding of this technology advances. Support Stem Cell Research (including Research Cloning) AAAS supports stem cell research, including the use of nuclear transplantation techniques (also ...

  19. An Alternative Method to Facilitate cDNA Cloning for Expression Studies in Mammalian Cells by Introducing Positive Blue White Selection in Vaccinia Topoisomerase I-Mediated Recombination

    OpenAIRE

    Udo, Hiroshi

    2015-01-01

    One of the most basic techniques in biomedical research is cDNA cloning for expression studies in mammalian cells. Vaccinia topoisomerase I-mediated cloning (TOPO cloning by Invitrogen) allows fast and efficient recombination of PCR-amplified DNAs. Among TOPO vectors, a pcDNA3.1 directional cloning vector is particularly convenient, since it can be used for expression analysis immediately after cloning. However, I found that the cloning efficiency was reduced when RT-PCR products were used as...

  20. Cloning and sequencing genes related to preeclampsia

    Institute of Scientific and Technical Information of China (English)

    SHI Juan-zi; LIU Yan-fang; YAO Yuan-qing; YAN Wei; ZHU Feng; ZHAO Zhong-liang

    2001-01-01

    To clone genes specifically expressed in the placenta of patients with preeclampsia, and to explain the mechanism in the etiopathology ofpreeclampsia. Methods: The placentae ofpreeclamptic and normotensive subjects with pregnancy were used as models, and the cDNA Library was constructed and 20 differentially expressed fragments were cloned after a new version of PCR-based subtractive hybridization. The false positive clones were identified by reverse dot blot analysis. With one of the obtained gene taken as the probe, the placentas of 10 normal pregnant women and 10 preeclamptic patients were studied by using dot hybridization methods. Results: Six false positive clones were identified by reverse dot blot, and the rest 14 clones were identified as preeclampsia-related genes. These clones were sequenced, and analyzed with BLAST analysis system. Eleven of 14 clones were genes already known, among which one belongs to necdin family; the rest 3 were identified as novel genes. These 3 genes were acknowledged by GenBank, with the accession numbers AF232216, AF232217, AF233648. The results of dot hybridization using necdin gene as probe were as follows: (1) There was this mRNA in the placental tissues of normal pregnancy as well as in that ofpreeclampsia.(2) The intensity of transcription of this mRNA in the placental tissues of preeclampsia increased significantly compared with that of the normal pregnancy (P<0.05). Conclusions: This study for the first time reported this group of genes, especially necdin-expressing gene, which are related to the etiopathology of preeclampsia. In addition, the overtranscription ofnecdin gene has been found in preeclampsia. It is helpful in further studies of the etiology ofpreeclampsia.

  1. Genetic stability of pestivirus genomes cloned into BACs

    DEFF Research Database (Denmark)

    Rasmussen, Thomas Bruun; Reimann, Ilona; Uttenthal, Åse;

    Infectious cDNA clones are a prerequisite for directed genetic manipulations of pestivirus genomes to obtain attenuated pestiviruses designed as new modified live DIVA vaccine candidates against classical swine fever. However, the construction of new infectious pestivirus cDNA clones has been...... hampered due to the large size of the pestivirus genome and due to genetic instability of the cloned cDNA, which in combination with plasmid vectors tend to be unstable and deleterious in the bacterial host. Therefore, new strategies are needed to facilitate construction of stable infectious cDNA clones...... of pestivirus strains. In a collaborative research project, between DTU Vet and FLI, on the establishment of genetically modified pestiviruses engineered specifically for the DIVA principle, we cloned a series of complete pestivirus genomes, obtained by full-length RT-PCR, directly into the bacterial artificial...

  2. Rapid Construction of Recombinant Plasmids by QuickStep-Cloning.

    Science.gov (United States)

    Jajesniak, Pawel; Wong, Tuck Seng

    2017-01-01

    QuickStep-Cloning is a novel molecular cloning technique that builds upon the concepts of asymmetric PCR and megaprimer-based amplification of whole plasmid. It was designed specifically to address the major drawbacks of previously reported cloning methods. The fully optimized protocol allows for a seamless integration of a long DNA fragment into any position within a plasmid of choice, in a time-efficient and cost-effective manner, without the need of a tedious DNA gel purification, a restriction digestion, and an enzymatic ligation. QuickStep-Cloning can be completed in less than 6 h, significantly faster than most of the existing cloning methods, while retaining high efficiency. PMID:27671943

  3. IVA cloning: A single-tube universal cloning system exploiting bacterial In Vivo Assembly.

    Science.gov (United States)

    García-Nafría, Javier; Watson, Jake F; Greger, Ingo H

    2016-06-06

    In vivo homologous recombination holds the potential for optimal molecular cloning, however, current strategies require specialised bacterial strains or laborious protocols. Here, we exploit a recA-independent recombination pathway, present in widespread laboratory E.coli strains, to develop IVA (In Vivo Assembly) cloning. This system eliminates the need for enzymatic assembly and reduces all molecular cloning procedures to a single-tube, single-step PCR, performed in IVA is a complete system, and offers significant advantages over alternative methods for all cloning procedures (insertions, deletions, site-directed mutagenesis and sub-cloning). Significantly, IVA allows unprecedented simplification of complex cloning procedures: five simultaneous modifications of any kind, multi-fragment assembly and library construction are performed in approximately half the time of current protocols, still in a single-step fashion. This system is efficient, seamless and sequence-independent, and requires no special kits, enzymes or proprietary bacteria, which will allow its immediate adoption by the academic and industrial molecular biology community.

  4. Cloning-free CRISPR

    NARCIS (Netherlands)

    Arbab, Mandana; Srinivasan, Sharanya; Hashimoto, Tatsunori; Geijsen, Niels; Sherwood, Richard I.

    2015-01-01

    We present self-cloning CRISPR/Cas9 (scCRISPR), a technology that allows for CRISPR/Cas9-mediated genomic mutation and site-specific knockin transgene creation within several hours by circumventing the need to clone a site-specific single-guide RNA (sgRNA) or knockin homology construct for each targ

  5. Cloning of the segment of flavonoid 3′-hydroxylasegene from the gDNA of Prunus mume by degenerate PCR%梅花类黄酮3'-羟化酶基因片段基于基因组DNA的简并PCR法克隆

    Institute of Scientific and Technical Information of China (English)

    赵昶灵; 杨清; 陈俊愉

    2006-01-01

    The gDNA was extracted from the tender leaves of P.mume with "PredeimpuritySDS method"developed in this study. Based on the highly conserved amino acid regions of the 11 deduced amino acid sequences of the cDNAs of the flavonoid 3'hydroxylase (F3'H)genes which had been openly published and submitted in the GenBank databases,2 forward degenerate primers and 3 reverse degenerate primers were designed and consisted of 6 sets of primer pair. Only one primer pair could be used in degenerate PCR to amplify three 469 bp segments from the gDNAs of P.mume'Nanjing Hongxu',P.mume'Nanjing Hong'and P.mume'Fenpi Gongfen'respectively. Sequence analysis indicated that the 3 segments shared 99.72% identity among each other and 65.57% identity with the corresponding regions of the 11 cDNAs as a whole. Furthermore,the"GGEK"motif is pointed out not to be the characteristic sequence of F3'H. It is the first time for the segment of F3'H gene to be cloned from the gDNA of ligneous plant. This study can underlay the cloning of the full length of F3'H gene from P.mume.%用本研究设计的"预先去杂-SDS法"从梅花嫩叶提取到高质量的基因组DNA.根据11条已公开发表的并提交到GenBank的类黄酮3'-羟化酶基因cDNA的假定氨基酸序列的保守区设计2个正向简并引物和3个反向简并引物组成6对引物,仅有1对引物能以PCR法同时从梅花'南京红须'、'南京红'和'粉皮宫粉'的基因组DNA扩增到一个469 bp的核苷酸片段,这3个片段在总体上有99.72%的一致性,与11条类黄酮3'-羟化酶基因cDNA的相应区域有65.57%的一致性.同时,"GGEK"并非类黄酮3'-羟化酶的特征性模体.这是首次从木本植物的基因组DNA克隆到类黄酮3'-羟化酶基因片段.本研究结果可为梅花类黄酮3'-羟化酶基因全长的克隆奠定基础.

  6. Frequent occurrence of highly expanded but unrelated B-cell clones in patients with multiple myeloma.

    Science.gov (United States)

    Kriangkum, Jitra; Motz, Sarah N; Debes Marun, Carina S; Lafarge, Sandrine T; Gibson, Spencer B; Venner, Christopher P; Johnston, James B; Belch, Andrew R; Pilarski, Linda M

    2013-01-01

    Clonal diversity in multiple myeloma (MM) includes both MM-related and MM-unrelated clonal expansions which are subject to dominance exerted by the MM clone. Here we show evidence for the existence of minor but highly expanded unrelated B-cell clones in patients with MM defined by their complementary determining region 3 (CDR3) peak. We further characterize these clones over the disease and subsequent treatment. Second clones were identified by their specific IgH-VDJ sequences that are distinct from those of dominant MM clones. Clonal frequencies were determined through semi-quantitative PCR, quantitative PCR and single-cell polymerase chain reaction of the clone-specific sequence. In 13/74 MM patients, more than one dominant CDR3 peak was identified with 12 patients (16%) being truly biclonal. Second clones had different frequencies, were found in different locations and were found in different cell types from the dominant MM clone. Where analysis was possible, they were shown to have chromosomal characteristic distinct from those of the MM clone. The frequency of the second clone also changed over the course of the disease and often persisted despite treatment. Molecularly-defined second clones are infrequent in monoclonal gammopathy of undetermined significance (MGUS, 1/43 individuals or 2%), suggesting that they may arise at relatively late stages of myelomagenesis. In further support of our findings, biclonal gammopathy and concomitant MM and CLL (chronic lymphocytic leukemia) were confirmed to originate from two unrelated clones. Our data supports the idea that the clone giving rise to symptomatic myeloma exerts clonal dominance to prevent expansion of other clones. MM and second clones may arise from an underlying niche permissive of clonal expansion. The clinical significance of these highly expanded but unrelated clones remains to be confirmed. Overall, our findings add new dimensions to evaluating related and unrelated clonal expansions in MM and the

  7. Frequent occurrence of highly expanded but unrelated B-cell clones in patients with multiple myeloma.

    Directory of Open Access Journals (Sweden)

    Jitra Kriangkum

    Full Text Available Clonal diversity in multiple myeloma (MM includes both MM-related and MM-unrelated clonal expansions which are subject to dominance exerted by the MM clone. Here we show evidence for the existence of minor but highly expanded unrelated B-cell clones in patients with MM defined by their complementary determining region 3 (CDR3 peak. We further characterize these clones over the disease and subsequent treatment. Second clones were identified by their specific IgH-VDJ sequences that are distinct from those of dominant MM clones. Clonal frequencies were determined through semi-quantitative PCR, quantitative PCR and single-cell polymerase chain reaction of the clone-specific sequence. In 13/74 MM patients, more than one dominant CDR3 peak was identified with 12 patients (16% being truly biclonal. Second clones had different frequencies, were found in different locations and were found in different cell types from the dominant MM clone. Where analysis was possible, they were shown to have chromosomal characteristic distinct from those of the MM clone. The frequency of the second clone also changed over the course of the disease and often persisted despite treatment. Molecularly-defined second clones are infrequent in monoclonal gammopathy of undetermined significance (MGUS, 1/43 individuals or 2%, suggesting that they may arise at relatively late stages of myelomagenesis. In further support of our findings, biclonal gammopathy and concomitant MM and CLL (chronic lymphocytic leukemia were confirmed to originate from two unrelated clones. Our data supports the idea that the clone giving rise to symptomatic myeloma exerts clonal dominance to prevent expansion of other clones. MM and second clones may arise from an underlying niche permissive of clonal expansion. The clinical significance of these highly expanded but unrelated clones remains to be confirmed. Overall, our findings add new dimensions to evaluating related and unrelated clonal expansions in

  8. IVA cloning: A single-tube universal cloning system exploiting bacterial In Vivo Assembly.

    Science.gov (United States)

    García-Nafría, Javier; Watson, Jake F; Greger, Ingo H

    2016-01-01

    In vivo homologous recombination holds the potential for optimal molecular cloning, however, current strategies require specialised bacterial strains or laborious protocols. Here, we exploit a recA-independent recombination pathway, present in widespread laboratory E.coli strains, to develop IVA (In Vivo Assembly) cloning. This system eliminates the need for enzymatic assembly and reduces all molecular cloning procedures to a single-tube, single-step PCR, performed in library construction are performed in approximately half the time of current protocols, still in a single-step fashion. This system is efficient, seamless and sequence-independent, and requires no special kits, enzymes or proprietary bacteria, which will allow its immediate adoption by the academic and industrial molecular biology community. PMID:27264908

  9. The terminal 5′ phosphate and proximate phosphorothioate promote ligation-independent cloning

    OpenAIRE

    Liu, Xi-Peng; LIU, JIAN-HUA

    2010-01-01

    Function studies of many proteins are waited to develop after genome sequencing. High-throughout technology of gene cloning will strongly promote proteins' function studies. Here we describe a ligation-independent cloning (LIC) method, which is based on the amplification of target gene and linear vector by PCR using phosphorothioate-modified primers and the digestion of PCR products by λ exonuclease. The phosphorothioate inhibits the digestion and results in the generation of 3′ overhangs, wh...

  10. Human Immunodeficiency Virus Type 1 Cloning Vectors for Antiretroviral Resistance Testing

    OpenAIRE

    Martinez-Picado, Javier; Sutton, Lorraine; De Pasquale, Maria Pia; Savara, Anu V.; D’Aquila, Richard T.

    1999-01-01

    Better detection of minority human immunodeficiency virus type 1 (HIV-1) populations containing gene mutations may improve the usefulness of antiretroviral resistance testing for clinical management. Molecular cloning of HIV-1 PCR products which might improve minority detection can be slow and difficult, and commercially available recombinant virus assays test drug susceptibility of virus pools. We describe novel plasmids and simple methods for rapid cloning of HIV-1 PCR products from patient...

  11. Systematic Cloning of Treponema pallidum Open Reading Frames for Protein Expression and Antigen Discovery

    OpenAIRE

    McKevitt, Matthew; Patel, Krupa; Smajs, David; Marsh, Michael; McLoughlin, Melanie; Norris, Steven J; Weinstock, George M.; Palzkill, Timothy

    2003-01-01

    A topoisomerase-based method was used to clone PCR products encoding 991 of the 1041 open reading frames identified in the genome sequence of the bacterium that causes syphilis, Treponema pallidum subsp. pallidum. Cloning the open reading frames into the univector plasmid system permitted the rapid conversion of the original clone set to other functional vectors containing a variety of promoters or tag sequences. A computational prediction of signal sequences identifie...

  12. Characterization of an Unusual Cytoplasmic Chimera Detected in Bolting Garlic (Allium sativum L.) Clones

    Science.gov (United States)

    Production of a visible flower stalk or bolting has been used as a major trait to categorize garlic clones. Analysis of mitochondrial genome variation with PCR revealed differences between bolting and non-bolting clones of garlic. Screening 333 garlic accessions from diverse geographic origins rev...

  13. Construction and characterization of human chromosome 2-specific cosmid, fosmid, and PAC clone libraries

    Energy Technology Data Exchange (ETDEWEB)

    Gingrich, J.C.; Boehrer, D.M.; Garnes, J.A. [Lawrence Livermore National Lab., CA (United States)] [and others

    1996-02-15

    This article discusses the construction and characterization of three human chromosome 2-specific clone libraries. A chromosome 2-specific PAC library was also constructed from a hybrid cell line. The chromosome 2 coverage of each of the three libraries was further determined by PCR screening clone pools with 82 chromosome 2-specific STSs. 47 refs., 3 figs., 1 tab.

  14. Prevalence of Adhesion and Regulation of Biofilm-Related Genes in Different Clones of Staphylococcus aureus

    Directory of Open Access Journals (Sweden)

    Salman Sahab Atshan

    2012-01-01

    Full Text Available Clinical information about genotypically different clones of biofilm-producing Staphylococcus aureus is largely unknown. We examined whether different clones of methicillin-sensitive and methicillin-resistant S. aureus (MSSA and MRSA differ with respect to staphylococcal microbial surface components recognizing adhesive matrix molecules (MSCRAMMs in biofilm formation. The study used 60 different types of spa and determined the phenotypes, the prevalence of the 13 MSCRAMM, and biofilm genes for each clone. The current investigation was carried out using a modified Congo red agar (MCRA, a microtiter plate assay (MPA, polymerase chain reaction (PCR, and reverse transcriptase polymerase chain reaction (RT-PCR. Clones belonging to the same spa type were found to have similar properties in adheringto thepolystyrene microtiter plate surface. However, their ability to produce slime on MCRA medium was different. PCR experiments showed that 60 clones of MSSA and MRSA were positive for 5 genes (out of 9 MSCRAMM genes. icaADBC genes were found to be present in all the 60 clones tested indicating a high prevalence, and these genes were equally distributed among the clones associated with MSSA and those with MRSA. The prevalence of other MSCRAMM genes among MSSA and MRSA clones was found to be variable. MRSA and MSSA gene expression (MSCRAMM and icaADBC was confirmed by RT-PCR.

  15. Cloning of Leishmania Major P4 Gene

    Directory of Open Access Journals (Sweden)

    Minoo Shaddel

    2008-01-01

    Full Text Available Objective: Leishmania major P4 gene is normally expressed during amastigote form ofthe parasite and can be good candidate for producing an effective vaccine. In this study wecloned this gene in suitable vector (pQE-30 for further vaccine preparation studies.Materials and Methods: Leishmania promastigotes were grown in N.N.N.medium and culturein RPMI 1640 cell culture medium. Total genomic DNA was extracted by centrifugationof promastigotes. The pellet was suspended in lysis buffer and followed by boiling method.PCR was carried out using P4 gene specific primers. PCR product was detected by agarosgel electrophoresis and cloned into Bluescript plasmid via T/A cloning method. Reactionwas transformed into XL1- Blue competent cell and recombinant plasmid screened usingagar plate contained X-gal and IPTG. The product was extracted, digested by restrictionenzyme and electrophoresed on agarose gel.Results: Plasmid was extracted and cloned gene was released by restriction enzyme andsubcloned into pQE-30 expression vector.Conclusion: This construct is ready for protein expression in in-vitro.

  16. Enzyme free cloning for high throughput gene cloning and expression

    NARCIS (Netherlands)

    de Jong, R.N.; Daniëls, M.; Kaptein, R.; Folkers, G.E.

    2006-01-01

    Structural and functional genomics initiatives significantly improved cloning methods over the past few years. Although recombinational cloning is highly efficient, its costs urged us to search for an alternative high throughput (HTP) cloning method. We implemented a modified Enzyme Free Cloning (EF

  17. The effect of high-fat diet on the composition of the gut microbiota in cloned and non-cloned pigs of lean and obese phenotype

    DEFF Research Database (Denmark)

    Pedersen, Rebecca; Andersen, Anders Daniel; Hermann-Bank, Marie Louise;

    2013-01-01

    overall composition of their gut microbiota. The colon of lean cloned pigs contained relatively more bacteria belonging to the phylum Firmicutes and less from the phylum Bacteroidetes than obese cloned pigs as estimated by qPCR. Fluidigm qPCR results revealed differences in specific bacterial groups...... in the gut microbiota of both lean and obese pigs. Our results suggest that high-far-high-energy diet is associated with changes in the gut microbiota even in the absence of obesity. Overall, the cloned pigs had a different gut microbiota from that of non-cloned pigs. To our knowledge this is the first study...... to investigate the gut microbiota of cloned domestic pigs of lean and obese phenotype....

  18. Nanoparticle PCR: A New Approach of DNA Amplification

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    @@ The polymerase chain reaction (PCR) is a technique for quickly "cloning" a particular piece of DNA in the test tube (rather than in living cells like E.coli). Thanks to this procedure, one can make virtually unlimited copies of a single DNA molecule even though it is initially present in a mixture containing many different DNA molecules.

  19. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing

    DEFF Research Database (Denmark)

    Binladen, Jonas; Gilbert, M Thomas P; Bollback, Jonathan P;

    2007-01-01

    BACKGROUND: The invention of the Genome Sequence 20 DNA Sequencing System (454 parallel sequencing platform) has enabled the rapid and high-volume production of sequence data. Until now, however, individual emulsion PCR (emPCR) reactions and subsequent sequencing runs have been unable to combine...... template DNA from multiple individuals, as homologous sequences cannot be subsequently assigned to their original sources. METHODOLOGY: We use conventional PCR with 5'-nucleotide tagged primers to generate homologous DNA amplification products from multiple specimens, followed by sequencing through...... be applied to PCR-based assays of multiple homologous PCR products. The new approach will be of value to a broad range of research areas, such as those of comparative genomics, complete mitochondrial analyses, population genetics, and phylogenetics....

  20. Main: Clone Detail [KOME

    Lifescience Database Archive (English)

    Full Text Available Clone Detail Mapping Pseudomolecule data detail Detail information Mapping to the TIGR japonica Pseudomolecu...les kome_mapping_pseudomolecule_data_detail.zip kome_mapping_pseudomolecule_data_detail ...

  1. Placentation in cloned cattle

    DEFF Research Database (Denmark)

    Miglino, M A; Pereira, F T V; Visintin, J A;

    2007-01-01

    To elucidate the morphological differences between placentas from normal and cloned cattle pregnancies reaching term, the umbilical cord, placentomes and interplacentomal region of the fetal membranes were examined macroscopically as well as by light and scanning electron microscopy. In pregnancies...

  2. Do Managers Clone Themselves?

    Science.gov (United States)

    Baron, Alma S.

    1981-01-01

    A recent questionnaire survey provides statistics on male managers' views of female managers. The author recommends that male managers break out of their cloning behavior and that the goal ought to be a plurality in management. (Author/WD)

  3. Asymmetric quantum cloning machines

    International Nuclear Information System (INIS)

    A family of asymmetric cloning machines for quantum bits and N-dimensional quantum states is introduced. These machines produce two approximate copies of a single quantum state that emerge from two distinct channels. In particular, an asymmetric Pauli cloning machine is defined that makes two imperfect copies of a quantum bit, while the overall input-to-output operation for each copy is a Pauli channel. A no-cloning inequality is derived, characterizing the impossibility of copying imposed by quantum mechanics. If p and p' are the probabilities of the depolarizing channels associated with the two outputs, the domain in (√p,√p')-space located inside a particular ellipse representing close-to-perfect cloning is forbidden. This ellipse tends to a circle when copying an N-dimensional state with N→∞, which has a simple semi-classical interpretation. The symmetric Pauli cloning machines are then used to provide an upper bound on the quantum capacity of the Pauli channel of probabilities px, py and pz. The capacity is proven to be vanishing if (√px, √py, √pz) lies outside an ellipsoid whose pole coincides with the depolarizing channel that underlies the universal cloning machine. Finally, the tradeoff between the quality of the two copies is shown to result from a complementarity akin to Heisenberg uncertainty principle. (author)

  4. Ion pair-reversed phase HPLC approach facilitates subcloning of PCR products and screening of recombinant colonies.

    Science.gov (United States)

    Shaw-Bruha, C M; Lamb, K A

    2000-04-01

    The isolation of a single DNA molecule for cloning is technically difficult, and the subsequent screening of colonies for recombinant DNA clones is time consuming. Ion pair-reversed phase HPLC (IP-RP-HPLC) analysis of nucleic acids improves the resolution and isolation of PCR products to be cloned. We demonstrate that PCR products analyzed and collected using the IP-RP-HPLC approach (WAVE DNA Fragment Analysis System) can be cloned directly into a plasmid vector. In addition, we demonstrate that when IP-RP-HPLC analysis is extended to the colony screening process, the time required for these procedures is reduced.

  5. CLONING AND SEQUENCING OF MATURED FRAGMENT OF HUMAN NEVER GROWTH FACTOR GENE

    Institute of Scientific and Technical Information of China (English)

    马巍; 吴玲; 王德利; 刘淼; 任惠民; 杨广笑; 王全颖

    2003-01-01

    Objective Molecular cloning and sequencing of the human matured fragment of human nerve growth factor(NGF) gene. Methods Extracting the human genomic DNA from the white blood cells as templates, the gene of NGF was cloned by using PCR and T-vector cloning method. Screening the positive clones and identified by the restriction enzymes, and then the cloned amplified fragment was sequenced and analyzed. Results DNA sequence comparison the cloned gene of NGF with the GenBank (V01511) sequence demonstrated that both of sequences were identical, 354bp length. Conclusion Cloning the NGF gene from the human genomic DNA has paved the way for further study on gene therapy of nerve system injury.

  6. Culture independent PCR: an alternative enzyme discovery strategy

    DEFF Research Database (Denmark)

    Jacobsen, Jonas; Lydolph, Magnus; Lange, Lene

    2005-01-01

    Degenerate primers were designed for use in a culture-independent PCR screening of DNA from composite fungal communities, inhabiting residues of corn stovers and leaves. According to similarity searches and alignments amplified clone sequences affiliated with glycosyl hydrolase family 7 and glyco......Degenerate primers were designed for use in a culture-independent PCR screening of DNA from composite fungal communities, inhabiting residues of corn stovers and leaves. According to similarity searches and alignments amplified clone sequences affiliated with glycosyl hydrolase family 7...... and glycosyl hydrolase family 45 though significant sequence divergence was observed. Glycosyl hydrolases from families 7 and 45 play a crucial role in biomass conversion to fuel ethanol. Research in this renewable energy source has two objectives: (i) To contribute to development of a renewable alternative...... the value of culture-independent PCR in microbial diversity studies and could add to development of a new enzyme screening technology....

  7. Screening of YAC clones and building a map of the chromosome 13 region often deleted during chronic B-cell lymphocytic leucosis

    NARCIS (Netherlands)

    Brodyanskii, VM; Sulimova, GE; Udina, IG; Aitova, SS; Shaikhaev, GO; Sharikova, OA; Zakharev, VM; Fedorova, LI; Zelenin, AV; Eikhorn, S; Baush, C; Laland, M; Ross, M; Yankovskii, NK

    1995-01-01

    Pools of YAC clones from the ICRF library were analyzed by PCR using PBKpt, MGG15, and D13S25 markers that flank the chromosome 13 region often deleted during chronic lymphocytic leukemia. Ten clones were found and described. Nine mega-YAC clones from the CEPH library flanking the region of interest

  8. Cloning and expression of Neisseria meningitides luxS gene

    Institute of Scientific and Technical Information of China (English)

    Bahram Kazemi; Nazila Baghalzadeh-Mohammadi; Reza Hadavi; Mojgan Bandehpour; Elham Ghayour; Majid Moghbeli; Kazem Parivar

    2008-01-01

    Neisseria meningitides is a Gram-negative bacterium which is an important causative agent of septicemia and meningitis.Numerous pathogenic bacteria contain luxS,which is required for autoinducer-2 production.Neis-seria meningitides contains a functional copy of luxS that is necessary for full meningococcal virulence.Neisse-ria meningitides DNA was extracted and its luxS gene was amplified by nested PCR.PCR product was purified and cloned in to pQE-30 expression vector.Recombinant plasmid was transformed and mass cultured.luxS was expressed in E.coli and confirmed by western blot analysis.In this study,N.meningitides luxS was amplified, cloned and expressed successfully.The sequencing of PCR product confirmed that amplified gene was luxS. Gene was expressed and observed in SDS-PAGE.Protein was reacted by his tag monoclonal antibody through western blot analysis.

  9. Competitive PCR for quantification of minimal residual disease in acute lymphoblastic leukaemia

    DEFF Research Database (Denmark)

    Nyvold, C; Madsen, H O; Ryder, L P;

    2000-01-01

    under identical conditions. After restriction enzyme cleavage, the PCR products originating from the competitor and the malignant clone can be distinguished by size in a gel electrophoresis step and the amount of residual disease can be determined. The method is very sensitive with a detection limit......A very precise and reproducible polymerase chain reaction (PCR) method was developed in order to quantify minimal residual disease (MRD) in children with acute lymphoblastic leukaemia (ALL). A clone-specific competitor was constructed by introducing a restriction site in a PCR product identical...... to parts of the highly specific rearranged T-cell receptor delta (TCR-delta), T-cell receptor gamma (TCR-gamma), or immunoglobulin heavy chain (IgH) genes of the malignant clone. Using primers located externally to the restriction site the competitor and the DNA from the malignant clone will be amplified...

  10. Cloning of low dose radiation induced gene RIG1 by RACE based on non-cloned cDNA library

    International Nuclear Information System (INIS)

    Objective: To obtain full-length cDNA of radiation induced new gene RIG1 based on its EST fragment. Methods: Based on non-cloned cDNA library, enhanced nested RACE PCR and biotin-avidin labelled probe for magnetic bead purification was used to obtain full-length cDNA of RIG1. Results: About 1 kb of 3' end of RIG1 gene was successfully cloned by this set of methods and cloning of RIG1 5' end is proceeding well. Conclusion: The result is consistent with the design of experiment. This set of protocol is useful for cloning of full-length gene based on EST fragment

  11. [Advances in Molecular Cloning].

    Science.gov (United States)

    Ashwini, M; Murugan, S B; Balamurugan, S; Sathishkumar, R

    2016-01-01

    "Molecular cloning" meaning creation of recombinant DNA molecules has impelled advancement throughout life sciences. DNA manipulation has become easy due to powerful tools showing exponential growth in applications and sophistication of recombinant DNA technology. Cloning genes has become simple what led to an explosion in the understanding of gene function by seamlessly stitching together multiple DNA fragments or by the use of swappable gene cassettes, maximizing swiftness and litheness. A novel archetype might materialize in the near future with synthetic biology techniques that will facilitate quicker assembly and iteration of DNA clones, accelerating the progress of gene therapy vectors, recombinant protein production processes and new vaccines by in vitro chemical synthesis of any in silico-specified DNA construct. The advent of innovative cloning techniques has opened the door to more refined applications such as identification and mapping of epigenetic modifications and high-throughput assembly of combinatorial libraries. In this review, we will examine the major breakthroughs in cloning techniques and their applications in various areas of biological research that have evolved mainly due to easy construction of novel expression systems. PMID:27028806

  12. Software-Supported USER Cloning Strategies for Site-Directed Mutagenesis and DNA Assembly

    DEFF Research Database (Denmark)

    Genee, Hans Jasper; Bonde, Mads Tvillinggaard; Bagger, Frederik Otzen;

    2015-01-01

    USER cloning is a fast and versatile method for engineering of plasmid DNA. We have developed a user friendly Web server tool that automates the design of optimal PCR primers for several distinct USER cloning-based applications. Our Web server, named AMUSER (Automated DNA Modifications with USER...... cloning), facilitates DNA assembly and introduction of virtually any type of site-directed mutagenesis by designing optimal PCR primers for the desired genetic changes. To demonstrate the utility, we designed primers for a simultaneous two-position site-directed mutagenesis of green fluorescent protein...... (GFP) to yellow fluorescent protein (YFP), which in a single step reaction resulted in a 94% cloning efficiency. AMUSER also supports degenerate nucleotide primers, single insert combinatorial assembly, and flexible parameters for PCR amplification. AMUSER is freely available online at ....

  13. Selection vector for direct cloning of proof reading polymerase chain reaction products based on the lethal ccdB gene in Escherichia Coli

    OpenAIRE

    Weibel, Pascal; Ender, Miriam; Madon, Jerzy; Zinkernagel, Annelies; Schuepbach, Reto

    2013-01-01

    Introducing PCR products into plasmids vectors is key for molecular techniques. Ideally cloning vectors are easy to construct, modify and propagate, neither require advanced techniques nor special equipment or reagents and efficiently incorporate PCR products at close to zero empty vector background. We provide an easy to engineer self-made cloning vector, neither requiring sophisticated tools or techniques nor advanced cloning knowledge. Through recombination we obtained the pUC18ccdB vector...

  14. Genetic diversity analysis with ISSR PCR on green algae Chlorella vulgaris and Chlorella pyrenoidosa

    Institute of Scientific and Technical Information of China (English)

    SHEN Songdong

    2008-01-01

    In the present study, genetic polymorphism and diversity in unicellular clones of Chlorella vulgaris Beijerinck and Chlorella pyrenoidosa Chick were studied with Inter Simple Sequence Repeats PCR (ISSR PCR). Samples including four clones of C. vulgaris and three clones of C. pyrenoidosa were purified by single-clone-choice method. For four C. vulgaris unicellular clones, the total number of the bands scored for 18 primers was 298; and the number of the polymorphic bands was 118, of which 39.6% were polymorphic. The size of PCR products ranged from 200 to 2 500 bp. The total number of bands scored for 18 primers, the number of polymorphic bands and the percentage of three C. pyrenoidosa unicellular clones was 194.83 and 30.8%, respectively. POPGENE analysis show that the average Nei genetic diversity (h *) and Shannon index of diversity (I *) in the four C. vulgaris unicellular clones was 0.2181 and 0.3208, respectively, which is slightly higher than those of the three C. pyrenoidosa unicellular clones (0.190 3 and 0.274 8), which agreed with the percentage of polymorphic bands in the mixed samples of the two species. The results suggest that ISSR is a useful method to Chlorella for intra-species genetic analysis.

  15. Tagging the expressed protein with 6 histidines: rapid cloning of an amplicon with three options.

    Directory of Open Access Journals (Sweden)

    Manika Indrajit Singh

    Full Text Available We report the designing of three expression vectors that can be used for rapid cloning of any blunt-end DNA segment. Only a single set of oligonucleotides are required to perform the amplification of the target DNA and its cloning in all three vectors simultaneously. The DNA thus cloned can express a protein either with or without a hexa-histidine tag depending upon the vector used. The expression occurs from T7 promoter when transformed into E. coli BL21(DE3. Two of the three plasmids have been designed to provide the expressed protein with either N- or C-terminus 6 histidine amino acids in tandem. The third plasmid, however, does not add any tag to the expressed protein. The cloning is achieved quickly with the requirement of phosphorylation of PCR product without any restriction digestion. Additionally, the generated clones can be confirmed with a single step PCR reaction carried out from bacterial colonies (generally termed as "colony PCR". We show the cloning, expression and purification of Green Fluorescent Protein (GFP as proof-of-concept. Additionally, we also show the cloning and expression of four sigma factors from Mycobacterium tuberculosis further demonstrating the utility of the designed plasmids. We strongly believe that the vectors and the strategy that we have developed will facilitate the rapid cloning and expression of any gene in E. coli BL21(DE3 with or without a hexa-histidine tag.

  16. Tagging the expressed protein with 6 histidines: rapid cloning of an amplicon with three options.

    Science.gov (United States)

    Singh, Manika Indrajit; Jain, Vikas

    2013-01-01

    We report the designing of three expression vectors that can be used for rapid cloning of any blunt-end DNA segment. Only a single set of oligonucleotides are required to perform the amplification of the target DNA and its cloning in all three vectors simultaneously. The DNA thus cloned can express a protein either with or without a hexa-histidine tag depending upon the vector used. The expression occurs from T7 promoter when transformed into E. coli BL21(DE3). Two of the three plasmids have been designed to provide the expressed protein with either N- or C-terminus 6 histidine amino acids in tandem. The third plasmid, however, does not add any tag to the expressed protein. The cloning is achieved quickly with the requirement of phosphorylation of PCR product without any restriction digestion. Additionally, the generated clones can be confirmed with a single step PCR reaction carried out from bacterial colonies (generally termed as "colony PCR"). We show the cloning, expression and purification of Green Fluorescent Protein (GFP) as proof-of-concept. Additionally, we also show the cloning and expression of four sigma factors from Mycobacterium tuberculosis further demonstrating the utility of the designed plasmids. We strongly believe that the vectors and the strategy that we have developed will facilitate the rapid cloning and expression of any gene in E. coli BL21(DE3) with or without a hexa-histidine tag. PMID:23691118

  17. Development of a real-time PCR method for Thalassiosira rotula rapid detection

    Institute of Scientific and Technical Information of China (English)

    HE Shanying; YU Zhigang; MI Tiezhu

    2007-01-01

    Gene specific primers and DNA probe were designed based on the sequence of 18S rDNA cloned from the red tide alga Thalassiosira rotula. A real-time fluorescent quantitative PCR (RFQ - PCR) method was developed for quantitative detection of T. rotula. The RFQ - PCR assay data showed that the results obtained with the RFQ - PCR quite good agreement with those with the light microscope (LM) counting method, which suggested that the RFQ - PCR could be a useful method for red tide alga detection.

  18. Cloning-free CRISPR

    OpenAIRE

    Mandana Arbab; Sharanya Srinivasan; Tatsunori Hashimoto; Niels Geijsen; Richard I. Sherwood

    2015-01-01

    Summary We present self-cloning CRISPR/Cas9 (scCRISPR), a technology that allows for CRISPR/Cas9-mediated genomic mutation and site-specific knockin transgene creation within several hours by circumventing the need to clone a site-specific single-guide RNA (sgRNA) or knockin homology construct for each target locus. We introduce a self-cleaving palindromic sgRNA plasmid and a short double-stranded DNA sequence encoding the desired locus-specific sgRNA into target cells, allowing them to produ...

  19. Gene Cloning of Iranian Leishmania major Mannose-1-Phosphate Guanyltransferase

    Directory of Open Access Journals (Sweden)

    R Salehi

    2009-07-01

    Full Text Available "nBackground: Leishmania is an obligatory intracellular protozoan parasite, which infects human be­ings when infected sand fly vector takes a blood meal.  Most efforts are towards designing an effective vaccine to prevent leishmaniasis. In this way, development of candidate antigen for vaccine has spe­cial im­portant. In this study, we cloned mannose-1-phosphate guanyltransferase gene of Iranian L .major in pET32a expression vector. "nMethods: Primers based on L. major mannose-1-phosphate guanyltransferase sequence gene was de­signed and synthesized. DNA of Leishmania promastigotes was extracted and PCR reaction was done. PCR product was cloned into pTZ57R and sub cloned into pET32a expression vector. "nResults: Recombinant plasmid containing 1140 bp as L. major mannose-1-phosphate guanyltrans­ferase gene was extracted and confirmed by restriction analysis. PCR product was sequenced and de­posited to GenBank. There were some differences in amino acid sequences between Iranian L. major mannose-1-phosphate guanyltransferase and others previously accepted in GenBank "nConclusion: We amplified and cloned Iranian L. major mannose-1-phosphate guanyltransferase successfully.

  20. Rapid Amplification of 5′ cDNA End of S. Liaotungensis Choline Monooxygenase Using Inverse PCR RACE

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Based on part of a known cDNA sequence of Suaeda Liaotungensis choline monooxygenase, the authors successfully cloned the 5′ cDNA end of Suaeda Lianotungensis choline monooxygenase using Inverse PCR RACE with a specially designed 5′-phosphated RT primer and two pairs of specific inverse PCR primers. Compared with the anchored PCR RACE, inverse PCR RACE has better specificity and higher amplification.

  1. A Seminar on Human Cloning: Cloning in Reproductive Medicine

    OpenAIRE

    Illmensee, Karl

    2001-01-01

    This review article summarizes the historical development of mammalian cloning, presents current advances and presumed risk factors in the field of reproductive cloning, discusses possible clinical applications of therapeutic and diagnostic cloning and outlines prospective commercial trends in pharmacytical cloning. Predictable progress in biotechnology and stem cell engineering should prove to be advantageous for patients' health and for novel benefits in reproductive and regenerative medicine.

  2. cDNA cloning and sequencing of ostrich Growth hormone

    Directory of Open Access Journals (Sweden)

    Doosti Abbas

    2012-01-01

    Full Text Available In recent years, industrial breeding of ostrich (Struthio camelus has been widely developed in Iran. Growth hormone (GH is a peptide hormone that stimulates growth and cell reproduction in different animals. The aim of this study was to clone and sequence the ostrich growth hormone gene in E. coli, done for the first time in Iran. The cDNA that encodes ostrich growth hormone was isolated from total mRNA of the pituitary gland and amplified by RT-PCR using GH specific PCR primers. Then GH cDNA was cloned by T/A cloning technique and the construct was transformed into E. coli. Finally, GH cDNA sequence was submitted to the GenBank (Accession number: JN559394. The results of present study showed that GH cDNA was successfully cloned in E. coli. Sequencing confirmed that GH cDNA was cloned and that the length of ostrich GH cDNA was 672 bp; BLAST search showed that the sequence of growth hormone cDNA of the ostrich from Iran has 100% homology with other records existing in GenBank.

  3. Molecular diagnostic PCR handbook

    International Nuclear Information System (INIS)

    The uses of nucleic acid-directed methods have increased significantly in the past five years and have made important contributions to disease control country programmes for improving national and international trade. These developments include the more routine use of PCR as a diagnostic tool in veterinary diagnostic laboratories. However, there are many problems associated with the transfer and particularly, the application of this technology. These include lack of consideration of: the establishment of quality-assured procedures, the required set-up of the laboratory and the proper training of staff. This can lead to a situation where results are not assured. This book gives a comprehensive account of the practical aspects of PCR and strong consideration is given to ensure its optimal use in a laboratory environment. This includes the setting-up of a PCR laboratory; Good Laboratory Practice and standardised PCR protocols to detect animal disease pathogens. Examples of Standard Operating Procedures as used in individual specialist laboratories and an outline of training materials necessary for PCR technology transfer are presented. The difficulties, advantages and disadvantages in PCR applications are explained and placed in context with other test systems. Emphasis is placed on the use of PCR for detection of pathogens, with a particular focus on diagnosticians and scientists from the developing world. It is hoped that this book will enable readers from various disciplines and levels of expertise to better judge the merits of PCR and to increase their skills and knowledge in order to assist in a more logical, efficient and assured use of this technology

  4. Secure the Clones

    Science.gov (United States)

    Jensen, Thomas; Kirchner, Florent; Pichardie, David

    Exchanging mutable data objects with untrusted code is a delicate matter because of the risk of creating a data space that is accessible by an attacker. Consequently, secure programming guidelines for Java stress the importance of using defensive copying before accepting or handing out references to an internal mutable object. However, implementation of a copy method (like clone()) is entirely left to the programmer. It may not provide a sufficiently deep copy of an object and is subject to overriding by a malicious sub-class. Currently no language-based mechanism supports secure object cloning. This paper proposes a type-based annotation system for defining modular copy policies for class-based object-oriented programs. A copy policy specifies the maximally allowed sharing between an object and its clone. We present a static enforcement mechanism that will guarantee that all classes fulfill their copy policy, even in the presence of overriding of copy methods, and establish the semantic correctness of the overall approach in Coq. The mechanism has been implemented and experimentally evaluated on clone methods from several Java libraries.

  5. Clip, Connect, Clone

    DEFF Research Database (Denmark)

    Fujima, Jun; Lunzer, Aran; Hornbæk, Kasper Anders Søren;

    2010-01-01

    using three mechanisms: clipping of input and result elements from existing applications to form cells on a spreadsheet; connecting these cells using formulas, thus enabling result transfer between applications; and cloning cells so that multiple requests can be handled side by side. We demonstrate...

  6. Asian Yellow Goat Cloned

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    @@ It was released on August 24,2005 by Prof. CHEN Dayuan (Da-Yuan Chen) from the CAS Institute of Zoology that the first success in cloning the Asian Yellow Goat by nuclear transfer had recently been achieved in east China's Shandong Province.

  7. Animal Cloning and Food Safety

    Science.gov (United States)

    ... Products For Consumers Home For Consumers Consumer Updates Animal Cloning and Food Safety Share Tweet Linkedin Pin it ... This conclusion stems from an extensive study of animal cloning and related food safety, culminating in the release ...

  8. The First Human Cloned Embryo.

    Science.gov (United States)

    Cibelli, Jose B.; Lanza, Robert P.; West, Michael D.; Ezzell, Carol

    2002-01-01

    Describes a process known as parthenogenesis which produces cloned, early-stage embryos and human embryos generated only from eggs. Speculates that this technology puts therapeutic cloning within reach. (DDR)

  9. Cloning and prokaryotic expression of HGLP cDNA

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    A novel cDNA, HGLP, which encodes a G- protein coupled receptor (GPCR) like protein, has been isolated and cloned. The coding region of the human HGLP predicts a 7-transmembrane region protein with motifs of rhodopsin-like GPCR superfamily. Northern blot analysis reveals a 3-kb transcript in various human tissues examined. The N- and C-terminal coding regions of HGLP, which are deduced as non-transmembrane regions, have been amplified by PCR and cloned into pET30a+ vector. Then the recombinant proteins are highly expressed in E. coli.

  10. Sequential cloning of chromosomes

    Energy Technology Data Exchange (ETDEWEB)

    Lacks, S.A.

    1991-12-31

    A method for sequential cloning of chromosomal DNA and chromosomal DNA cloned by this method are disclosed. The method includes the selection of a target organism having a segment of chromosomal DNA to be sequentially cloned. A first DNA segment, having a first restriction enzyme site on either side. homologous to the chromosomal DNA to be sequentially cloned is isolated. A first vector product is formed by ligating the homologous segment into a suitably designed vector. The first vector product is circularly integrated into the target organism`s chromosomal DNA. The resulting integrated chromosomal DNA segment includes the homologous DNA segment at either end of the integrated vector segment. The integrated chromosomal DNA is cleaved with a second restriction enzyme and ligated to form a vector-containing plasmid, which is replicated in a host organism. The replicated plasmid is then cleaved with the first restriction enzyme. Next, a DNA segment containing the vector and a segment of DNA homologous to a distal portion of the previously isolated DNA segment is isolated. This segment is then ligated to form a plasmid which is replicated within a suitable host. This plasmid is then circularly integrated into the target chromosomal DNA. The chromosomal DNA containing the circularly integrated vector is treated with a third, retrorestriction enzyme. The cleaved DNA is ligated to give a plasmid that is used to transform a host permissive for replication of its vector. The sequential cloning process continues by repeated cycles of circular integration and excision. The excision is carried out alternately with the second and third enzymes.

  11. HUMAN CLONING AND FDA REGULATION

    OpenAIRE

    Vosk, Ted

    1998-01-01

    In the February 27, 1997 issue of the journal Nature scientists from Scotland's Roslin Institute reported their successful efforts to clone an adult sheep using differentiated somatic cells from the animal. The clone, named Dolly, was the first instance of the successful cloning of an adult mammal. The shock waves created by the possible ramifications of this development were immediately felt around the world. For the first time, the cloning of an adult human being was no longer being conside...

  12. Probabilistic Cloning and Quantum Computation

    Institute of Scientific and Technical Information of China (English)

    GAO Ting; YAN Feng-Li; WANG Zhi-Xi

    2004-01-01

    @@ We discuss the usefulness of quantum cloning and present examples of quantum computation tasks for which the cloning offers an advantage which cannot be matched by any approach that does not resort to quantum cloning.In these quantum computations, we need to distribute quantum information contained in the states about which we have some partial information. To perform quantum computations, we use a state-dependent probabilistic quantum cloning procedure to distribute quantum information in the middle of a quantum computation.

  13. Unique inclusions of maximal C-clones in maximal clones

    OpenAIRE

    Behrisch, Mike; Vargas-García, Edith

    2014-01-01

    $\\mathit{C}$-clones are polymorphism sets of so-called clausal relations, a special type of relations on a finite domain, which first appeared in connection with constraint satisfaction problems in [Creignou et al. 2008]. We completely describe the relationship w.r.t. set inclusion between maximal $\\mathit{C}$-clones and maximal clones. As a main result we obtain that for every maximal $\\mathit{C}$-clone there exists exactly one maximal clone in which it is contained. A precise description of...

  14. Target-selective homologous recombination cloning for high-throughput generation of monoclonal antibodies from single plasma cells

    OpenAIRE

    Isobe Masaharu; Yoshioka Megumi; Kurosawa Nobuyuki

    2011-01-01

    Abstract Background Molecular cloning of functional immunoglobulin genes from single plasma cells is one of the most promising technologies for the rapid development of monoclonal antibody drugs. However, the proper insertion of PCR-amplified immunoglobulin genes into expression vectors remains an obstacle to the high-throughput production of recombinant monoclonal antibodies. Results We developed a single-step cloning method, target-selective homologous recombination (TS-HR), in which PCR-am...

  15. Expression of Innate Immune Response Genes in Liver and Three Types of Adipose Tissue in Cloned Pigs

    DEFF Research Database (Denmark)

    Højbøge, Tina Rødgaard; Skovgaard, Kerstin; Stagsted, Jan;

    2012-01-01

    remain unaffected by the cloning process. We investigated the expression of 40 innate immune factors by high-throughput quantitative real-time PCR in samples from liver, abdominal subcutaneous adipose tissue (SAT), visceral adipose tissue (VAT), and neck SAT in cloned pigs compared to normal outbred pigs...

  16. Phage display used for gene cloning of human recombinant antibody against the erythrocyte surface antigen, rhesus D

    DEFF Research Database (Denmark)

    Dziegiel, M; Nielsen, L K; Andersen, P S;

    1995-01-01

    A novel phage display system has been developed for PCR amplification and cloning of the Fab fragments of human immunoglobulin genes. Using this system, we have cloned an antibody from a mouse-human hybridoma cell line directed against the erythrocyte antigen rhesus D. Intact erythrocytes were used...

  17. 猪新基因KCNJ12编码区电子克隆、RT-PCR验证和组织表达分析%In Silico Cloning,RT-PCR Verification and Tissues Expression of Coding Region Sequence of Novel Swine Gene KCNJ12

    Institute of Scientific and Technical Information of China (English)

    秦彩艳; 霍金龙; 王配; 王淑燕; 苗永旺; 潘伟荣; 査星琴; 曾养志

    2014-01-01

    The KCNJ12 sequences of allied species of pig were downloaded from NCBI and compared by online BLAST to obtain the EST sequences,the referenced genomic sequences and high-throughput genomic sequences of pig. Subsequently we used silicon cloning strategy to gain the coding sequence and a few flanking sequence of KC-NJ12 through Lasergene software. According to the coding regions,we designed specific primers and conducted ex-perimental verification using Banna mini-pig inbred line ( BMI) . Meanwhile,the expression of KCNJ12 in 31 impor-tant tissues of BMI was analyzed by semi-quantitative RT-PCR. The research obtained 1 290 bp coding sequence ( GenBank accession number:KC505155 , the corresponding amino acid accession number:AGK36093 ) of swine KCNJ12 . Bioinformatics analysis showed that the KCNJ12 gene encoded a protein of 429 amino acids with a predic-ted molecular weight (Mw) of 48. 63 kDa and isoelectric point (pI) 5. 66. Protein structural analysis suggested that it contained two conserved domains,three transmembrane regions and no signal peptide;hydrophobicity analysis in-dicated that both N-terminal and C-terminal of the protein were hydrophilic;and it was a cytosolic protein with a probability of 94 . 1%. Phylogenetic analysis demonstrated that pig had the closest relationship with cattle and sheep. The analysis of tissue expression showed that the expression of KCNJ12 examined in 31 tissues had obvious differences. It was highly abundant in the cerebellum;moderately expressed in muscle, colon, cecum, esophagus, skin,brain,hypothalamus and spinal cord;and weakly expressed in thymus,liver,rectum and brain stem;while un-detected in submandibular gland, testis, thyroid, epididymis, lung, heart, spleen, adrenal gland, lymph nodes, kid-neys,pancreas,duodenum,jejunum,ileum,stomach,pituitary,pineal gland and sublingual gland. These results will provide a basis for the study of KCNJ12 function in swine.%通过NCBI下载猪近缘物种的KCNJ12基因序列,在

  18. Ethical issues in livestock cloning.

    Science.gov (United States)

    Thompson, P B

    1999-01-01

    Although cloning may eventually become an important technology for livestock production, four ethical issues must be addressed before the practice becomes widespread. First, researchers must establish that the procedure is not detrimental to the health or well-being of affected animals. Second, animal research institutions should evaluate the net social benefits to livestock producers by weighing the benefits to producers against the opportunity cost of research capacity lost to biomedical projects. Third, scientists should consider the indirect effects of cloning research on the larger ethical issues surrounding human cloning. Finally, the market structure for products of cloned animals should protect individual choice, and should recognize that many individuals find the prospect of cloning (or consuming cloned animals) repugnant. Analysis of these four issues is complicated by spurious arguments alleging that cloning will have a negative impact on environment and genetic diversity.

  19. Biodiversity versus cloning

    International Nuclear Information System (INIS)

    The announcement has been made on the cloning of mice in these days and he doesn't stop to miss, because the world lives a stage where conscience of the protection is creating that should be given to the biodiversity. It is known that alone we won't subsist and the protection of the means and all that contains that environment is of vital importance for the man. But it is also known that the vegetables and animal transgenic that they come to multiply the species have appeared that we prepare. The transgenic has been altered genetically, for substitution of one or more genes of other species, inclusive human genes. This represents an improvement compared with the investigations that gave origin to the cloning animal. But it is necessary to notice that to it you arrived through the cloning. This year 28 million hectares have been sowed in cultivations of transgenic seeds and there is around 700 bovine transgenic whose milk contains a necessary protein in the treatment of the man's illnesses

  20. Cloning and sequence analysis of Wadi sheep defensin sBD-1 gene and establishment and application of SYBR green Ⅰ real-time fluorescence quantitative PCR method%洼地绵羊防御素sBD-1基因克隆、序列分析及SYBR Green Ⅰ实时荧光定量检测方法的建立与应用

    Institute of Scientific and Technical Information of China (English)

    王金良; 郭显坡; 沈志强; 李敏; 任艳玲

    2011-01-01

    根据GenBank上登录的绵羊防御素基因序列,经多重比较后,设计1对引物,从洼地绵羊舌上皮组织中扩增到防御素sBD-1基因,克隆到pMD18-T载体中进行测序.结果表明,扩增基因全长215 bp,编码64个氨基酸.基因进化树分析表明,与蒙古绵羊sBD-1基因有较近的亲缘关系,核苷酸同源性为98.5%;而与黄牛的亲缘关系最远,核苷酸同源性84.6%.氨基酸序列分析表明,序列内无信号肽区域,具有3个潜在的抗原表位.以pMD18-T/sBD-1质粒为模板建立了sBD-1基因SYBR Green Ⅰ荧光定量PCR检测方法,核酸电泳、扩增动力学曲线、溶解曲线及重复性试验表明,检测方法具有良好的稳定性和特异性,得到的回归方程(R2=0.998)表明PCR产物量的对数值与起始模板量之间存在良好的线性关系,从舌、盲肠及输卵管等组织中可以进行有效的检测,检测灵敏度为83.9 copies/μL.该方法为进一步研究防御素sBD-1基因在洼地绵羊抗逆性过程中的作用奠定了基础.%According to the published gene sequences of defensin gene of sheep on GenBank,one pair of primers were designed and defensin Sbd-1 gene was amplified by RT-PCR from tongue epithelial tissue of Wadi sheep. PCR product was cloned into the Pmd18-T vector and sequenced. The results showed that gene amplication of full-length was 215 bp, encoding 64 amino acids. Phylogenetic tree analysis showed that Wadi sheep and Menggu sheep had close phylogenetic relationship,nucleotide homology was 98. 5%;kinship with the Bos taurus as far as the nucleotide ho-mology of 84. 6%. Amino acid sequence analysis showed no signal peptide amino acid sequence in the region, with three potential antigenic epitopes. Sbd-1 gene SYBR Green I fluorescence quantitative PCR method was set up u-sing Pmd18-T/Sbd-l plasmid as a template. Nucleic acid electrophoresis,amplification kinetics,dissolution curve and repeatability tests showed that the methods had good stability and

  1. Advanced lymphoblastic clones detection in T-cell leukemia.

    Science.gov (United States)

    Minervina, A A; Komkov, A Y; Mamedov, I Z; Lebedev, Y B

    2016-03-01

    T cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignant neoplasm of the lymphocyte precursors that suffered malignant transformation arresting the lymphoid cell differentiation. Clinical studies revealed monoor, more rarely, oligoclonal nature of the disease. A precise identification of malignant clone markers is both the crucial stage of early diagnostics and the essential prognostic factor for therapeutic treatment. Here we present an improved system for unbiased detection of lymphoblastic clones in bone marrow aspirates of T-ALL patients. The system based on multiplex PCR of rearranged T-cell receptor locus (TRB) and straightforward sequencing of the resulted PCR fragments. Testing of the system on genomic DNA from Jurkat cell line and four clinical bone marrow aspirates revealed a set of unique TRB rearrangements that precisely characterize each of tested samples. Therefore, the outcome of the system produces highly informative molecular genetic markers for further monitoring of minimal residual disease in T-ALL patients. PMID:27193704

  2. PCR performance of a thermostable heterodimeric archaeal DNA polymerase

    OpenAIRE

    Tom eKillelea; Celine eRalec; Audrey eBosse; Ghislaine eHenneke

    2014-01-01

    International audience DNA polymerases are versatile tools used in numerous important molecular biological core technologies like the ubiquitous polymerase chain reaction (PCR), cDNA cloning, genome sequencing, and nucleic acid based diagnostics. Taking into account the multiple DNA amplification techniques in use, different DNA polymerases must be optimized for each type of application. One of the current tendencies is to reengineer or to discover new DNA polymerases with increased perfor...

  3. Cloning and expression of the enzymatic region of Streptococcal hyaluronidase

    OpenAIRE

    Nafiseh Al-Sadat Mirjamali; Safieh Soufian; Neda Molaee; Shabnam Sadoogh Abbasian; Hamid Abtahi

    2014-01-01

    Objective(s): Streptococcus pyogenes produces extracellular hyaluronidase enzyme. This enzyme is directly associated with the spread of the organism during infection. The objective of the present study was to clone and express the nucleotide sequence of the enzyme which is involved in hyaluronidase enzymatic activity. Materials and Methods: The enzymatic region of hyaluronidase gene was detected by bioinformatics method. The PCR method was used to amplify enzymatic region of hyaluronidase gen...

  4. Ethical issues in animal cloning.

    Science.gov (United States)

    Fiester, Autumn

    2005-01-01

    The issue of human reproductive cloning has recently received a great deal attention in public discourse. Bioethicists, policy makers, and the media have been quick to identify the key ethical issues involved in human reproductive cloning and to argue, almost unanimously, for an international ban on such attempts. Meanwhile, scientists have proceeded with extensive research agendas in the cloning of animals. Despite this research, there has been little public discussion of the ethical issues raised by animal cloning projects. Polling data show that the public is decidedly against the cloning of animals. To understand the public's reaction and fill the void of reasoned debate about the issue, we need to review the possible objections to animal cloning and assess the merits of the anti-animal cloning stance. Some objections to animal cloning (e.g., the impact of cloning on the population of unwanted animals) can be easily addressed, while others (e.g., the health of cloned animals) require more serious attention by the public and policy makers.

  5. Molecular cloning of gluconobacter oxydans DSM 2003 xylitol dehydrogenase gene

    Science.gov (United States)

    Sadeghi, H. Mir Mohammad; Ahmadi, R.; Aghaabdollahian, S.; Mofid, M.R.; Ghaemi, Y.; Abedi, D.

    2011-01-01

    Due to the widespread applications of xylitol dehydrogenase, an enzyme used for the production of xylitol, the present study was designed for the cloning of xylitol dehydrogenase gene from Glcunobacter oxydans DSM 2003. After extraction of genomic DNA from this bacterium, xylitol dehydrogenase gene was replicated using polymerase chain reaction (PCR). The amplified product was entered into pTZ57R cloning vector by T/A cloning method and transformation was performed by heat shocking of the E. coli XL1-blue competent cells. Following plasmid preparation, the cloned gene was digested out and ligated into the expression vector pET-22b(+). Electrophoresis of PCR product showed a 789 bp band. Recombinant plasmid (rpTZ57R) was then constructed. This plasmid was double digested with XhoI and EcoRI resulting in 800 bp and 2900 bp bands. The obtained insert was ligated into pET-22b(+) vector and its orientation was confirmed with XhoI and BamHI restriction enzymes. In conclusion, in the present study the recombinant expression vector containing xylitol dehydrogenase gene has been constructed and can be used for the production of this enzyme in high quantities. PMID:22110522

  6. RT-PCR Protocols - Methods in Molecular Biology

    Directory of Open Access Journals (Sweden)

    Manuela Monti

    2011-03-01

    Full Text Available “The first record I have of it, is when I made a computer file which I usually did whenever I had an idea, that would have been on the Monday when I got back, and I called it Chain Reaction.POL, meaning polymerase. That was the identifier for it and later I called the thing the Polymerase Chain Reaction, which a lot of people thought was a dumb name for it, but it stuck, and it became PCR”. With these words the Nobel prize winner, Kary Mullis, explains how he named the PCR: one of the most important techniques ever invented and currently used in molecular biology. This book “RT-PCR Protocols” covers a wide range of aspects important for the setting of a PCR experiment for both beginners and advanced users. In my opinion the book is very well structured in three different sections. The first one describes the different technologies now available, like competitive RT-PCR, nested RT-PCR or RT-PCR for cloning. An important part regards the usage of PCR in single cell mouse embryos, stressing how important...........

  7. A-T linker adapter polymerase chain reaction for determining flanking sequences by rescuing inverse PCR or thermal asymmetric interlaced PCR products.

    Science.gov (United States)

    Trinh, Quoclinh; Zhu, Pengyu; Shi, Hui; Xu, Wentao; Hao, Junran; Luo, Yunbo; Huang, Kunlun

    2014-12-01

    The polymerase chain reaction (PCR)-based genome walking method has been extensively used to isolate unknown flanking sequences, whereas nonspecific products are always inevitable. To resolve these problems, we developed a new strategy to isolate the unknown flanking sequences by combining A-T linker adapter PCR with inverse PCR (I-PCR) or thermal asymmetric interlaced PCR (TAIL-PCR). The result showed that this method can be efficiently achieved with the flanking sequence from the Arabidopsis mutant and papain gene. Our study provides researchers with an additional method for determining genomic DNA flanking sequences to identify the target band from bulk of bands and to eliminate the cloning step for sequencing.

  8. Characterization of a retinoic acid responsive element isolated by whole genome PCR.

    OpenAIRE

    Costa-Giomi, M P; Gaub, M P; Chambon, P; Abarzúa, P

    1992-01-01

    We have used whole PCR in an attempt to isolate novel retinoic acid (RA) responsive genes. We cloned several small genomic fragments from total human DNA containing putative retinoic acid responsive elements (RAREs) selected by direct binding to the retinoic acid receptor alpha (RAR alpha). We report here that an oligonucleotide containing a sequence from one of the cloned human DNA fragments, and referred to as alpha 1, functions as an authentic RARE. It is shown that both RAR alpha and RAR ...

  9. DETECTION OF CROSS-PROJECT BENEFICIAL CLONES

    OpenAIRE

    Ms.Kavitha Esther Rajakumari; Dr.T.Jebarajan

    2014-01-01

    Duplicate codes are also known as code clones. They are considered as one of the main factors that deteriorate the quality of software. They are usually discarded by using automatic clone detection tools. In this paper the clones are detected using a data mining approach. The clones are well analyzed and the beneficial code clones are retained. These clones are maintained separately and are used in software maintenance. The beneficial clones will definitely help in reducing the overall time s...

  10. A note on clones with nullary operations

    OpenAIRE

    Behrisch, Mike

    2013-01-01

    This report discusses clones with nullary operations and the corresponding relational clones, both defined on arbitrary non-empty sets. The relationship between such clones and clones in the usual sense, i.e. without nullary operations, is investigated, and in particular the latter type of clones is located in the lattice of all clones. By means of two pairs of kernel and closure operators, a framework is developed that allows to transfer statements about usual clones to statements about clon...

  11. A new implementation of high-throughput five-dimensional clone pooling strategy for BAC library screening

    Directory of Open Access Journals (Sweden)

    Deal Karin R

    2010-12-01

    Full Text Available Abstract Background A five-dimensional (5-D clone pooling strategy for screening of bacterial artificial chromosome (BAC clones with molecular markers utilizing highly-parallel Illumina GoldenGate assays and PCR facilitates high-throughput BAC clone and BAC contig anchoring on a genetic map. However, this strategy occasionally needs manual PCR to deconvolute pools and identify truly positive clones. Results A new implementation is reported here for our previously reported clone pooling strategy. Row and column pools of BAC clones are divided into sub-pools with 1~2× genome coverage. All BAC pools are screened with Illumina's GoldenGate assay and the BAC pools are deconvoluted to identify individual positive clones. Putative positive BAC clones are then further analyzed to find positive clones on the basis of them being neighbours in a contig. An exhaustive search or brute force algorithm was designed for this deconvolution and integrated into a newly developed software tool, FPCBrowser, for analyzing clone pooling data. This algorithm was used with empirical data for 55 Illumina GoldenGate SNP assays detecting SNP markers mapped on Aegilops tauschii chromosome 2D and Ae. tauschii contig maps. Clones in single contigs were successfully assigned to 48 (87% specific SNP markers on the map with 91% precision. Conclusion A new implementation of 5-D BAC clone pooling strategy employing both GoldenGate assay screening and assembled BAC contigs is shown here to be a high-throughput, low cost, rapid, and feasible approach to screening BAC libraries and anchoring BAC clones and contigs on genetic maps. The software FPCBrowser with the integrated clone deconvolution algorithm has been developed and is downloadable at http://avena.pw.usda.gov/wheatD/fpcbrowser.shtml.

  12. A recombination based method to rapidly assess specificity of two-hybrid clones in yeast.

    OpenAIRE

    Petermann, R; Mossier, B M; Aryee, D N; Kovar, H.

    1998-01-01

    The yeast two-hybrid system is frequently used to identify protein-protein interactions. Confirming the specificity of candidate clones requires separation and isolation of yeast plasmids, propagation in bacteria and testing combinations of DNA-binding and activation domain hybrids in yeast. In order to simplify this procedure, we developed a rapid method based on PCR amplification of library insert DNAs and in vivo cloning into the activation domain hybrid vector. Reporter gene activity is a...

  13. Cloning of the sea urchin mitochondrial RNA polymerase and reconstitution of the transcription termination system

    OpenAIRE

    Polosa, Paola Loguercio; Deceglie, Stefania; Falkenberg, Maria; Roberti, Marina; Di Ponzio, Barbara; Gadaleta, Maria Nicola; Cantatore, Palmiro

    2007-01-01

    Termination of transcription is a key process in the regulation of mitochondrial gene expression in animal cells. To investigate transcription termination in sea urchin mitochondria, we cloned the mitochondrial RNA polymerase (mtRNAP) of Paracentrotus lividus and used a recombinant form of the enzyme in a reconstituted transcription system, in the presence of the DNA-binding protein mtDBP. Cloning of mtRNAP was performed by a combination of PCR with degenerate primers and library screening. T...

  14. Molecular cloning and functional analysis of an ethylene receptor gene from sugarcane (Saccharum spp.) by hormone and environmental stresses

    Science.gov (United States)

    Ethylene receptor (ethylene response sensor, ERS) is the primary component involving in the ethylene biosynthesis and ethylene signal transduction pathway. In the present study, a GZ-ERS gene encoding ERS was cloned from a sugarcane cv. YL17 (Saccharum spp.) using RT-PCR and ligation-mediated PCR wi...

  15. Therapeutic cloning in the mouse

    OpenAIRE

    Mombaerts, Peter

    2003-01-01

    Nuclear transfer technology can be applied to produce autologous differentiated cells for therapeutic purposes, a concept termed therapeutic cloning. Countless articles have been published on the ethics and politics of human therapeutic cloning, reflecting the high expectations from this new opportunity for rejuvenation of the aging or diseased body. Yet the research literature on therapeutic cloning, strictly speaking, is comprised of only four articles, all in the mouse. The efficiency of d...

  16. Evaluation of PCR and multiplex PCR in relation to nested PCR for diagnosing Theileria equi

    Directory of Open Access Journals (Sweden)

    Danielle C. Leal

    2011-07-01

    Full Text Available Conventional PCR (PCRTeq for diagnosing Theileria equi and multiplex PCR (M/PCRTeq-Bc for diagnosing T. equi and Babesia caballi were comparatively evaluated with nested PCR (N/PCR-Teq for diagnosing equine piroplasmosis. In DNA sensitivity determinations, in multiple dilutions of equine blood that had tested positive for T. equi, PCR-Teq and N/PCR-Teq detected hemoparasite DNA in the larger dilutions (1:128, but did not differ significantly from the M/PCRTeq-Bc (1:64. In analyses on equine serum tested by ELISA, there was high agreement between this serological test and PCR-Teq (k = 0.780 and moderate agreement with N/PCR-Teq (k = 0.562 and M/PCRTeq-Bc (k = 0.488. PCR-Teq found a higher frequency of T. equi both in extensively and intensively reared horses, but this was not significant in relation to N/PCR-Teq (P>0.05, and both PCRs indicated that there was an endemic situation regarding T. equi in the population of horses of this sample. PCR-Teq was only significantly different from M/PCR-Teq-Bc (P<0.05. PCR-Teq presented high sensitivity and specificity, comparable to N/PCR-Teq, but with the advantage of higher speed in obtaining results and lower costs and risks of laboratory contamination. This accredits PCR-Teq for epidemiological studies and for determinations on affected horses.

  17. Therapeutic cloning: The ethical limits

    International Nuclear Information System (INIS)

    A brief outline of stem cells, stem cell therapy and therapeutic cloning is given. The position of therapeutic cloning with regard to other embryonic manipulations - IVF-based reproduction, embryonic stem formation from IVF embryos and reproductive cloning - is indicated. The main ethically challenging stages in therapeutic cloning are considered to be the nuclear transfer process including the source of eggs for this and the destruction of an embryo to provide stem cells for therapeutic use. The extremely polarised nature of the debate regarding the status of an early human embryo is noted, and some potential alternative strategies for preparing immunocompatible pluripotent stem cells are indicated

  18. PCR in forensic genetics

    DEFF Research Database (Denmark)

    Morling, Niels

    2009-01-01

    Since the introduction in the mid-1980s of analyses of minisatellites for DNA analyses, a revolution has taken place in forensic genetics. The subsequent invention of the PCR made it possible to develop forensic genetics tools that allow both very informative routine investigations and still more...... and more advanced, special investigations in cases concerning crime, paternity, relationship, disaster victim identification etc. The present review gives an update on the use of DNA investigations in forensic genetics....

  19. Mitochondrial DNA heteroplasmy in ovine fetuses and sheep cloned by somatic cell nuclear transfer

    Directory of Open Access Journals (Sweden)

    Müller Mathias

    2007-12-01

    Full Text Available Abstract Background The mitochondrial DNA (mtDNA of the cloned sheep "Dolly" and nine other ovine clones produced by somatic cell nuclear transfer (SCNT was reported to consist only of recipient oocyte mtDNA without any detectable mtDNA contribution from the nucleus donor cell. In cattle, mouse and pig several or most of the clones showed transmission of nuclear donor mtDNA resulting in mitochondrial heteroplasmy. To clarify the discrepant transmission pattern of donor mtDNA in sheep clones we analysed the mtDNA composition of seven fetuses and five lambs cloned from fetal fibroblasts. Results The three fetal fibroblast donor cells used for SCNT harboured low mtDNA copy numbers per cell (A: 753 ± 54, B: 292 ± 33 and C: 561 ± 88. The ratio of donor to recipient oocyte mtDNAs was determined using a quantitative amplification refractory mutation system (ARMS PCR (i.e. ARMS-qPCR. For quantification of SNP variants with frequencies below 0.1% we developed a restriction endonuclease-mediated selective quantitative PCR (REMS-qPCR. We report the first cases (n = 4 fetuses, n = 3 lambs of recipient oocyte/nuclear donor mtDNA heteroplasmy in SCNT-derived ovine clones demonstrating that there is no species-effect hindering ovine nucleus-donor mtDNA from being transmitted to the somatic clonal offspring. Most of the heteroplasmic clones exhibited low-level heteroplasmy (0.1% to 0.9%, n = 6 indicating neutral transmission of parental mtDNAs. High-level heteroplasmy (6.8% to 46.5% was observed in one case. This clone possessed a divergent recipient oocyte-derived mtDNA genotype with three rare amino acid changes compared to the donor including one substitution at an evolutionary conserved site. Conclusion Our study using state-of-the-art techniques for mtDNA quantification, like ARMS-qPCR and the novel REMS-qPCR, documents for the first time the transmission of donor mtDNA into somatic sheep clones. MtDNA heteroplasmy was detected in seven of 12 clones

  20. Potato virus X isolation and purification and coat protein gene cloning

    Directory of Open Access Journals (Sweden)

    L. Duplat

    2011-12-01

    Full Text Available In this work we describe the construction of potato virus X coat protein (PVX-CP gene clones from a Colombian isolate. Virus was isolated from field potato plants cultured at páramo de San Jorge. PVX particles were purified from Nicotiana tabacum leaves infected with a local lesion taken from Datura stramonium plants. The genomic RNA present in the virus particles consisted of a single species of about 6 Kb. cDNA synthesis representing genomic RNA was followed by Digoxigenin incorporation after priming with oligonucleotide 4DT/KPN. PCR amplification of CP gene sequence was made by using oligonucleotides OX6 and L/Kpn. An expected fragment of 870 bp, besides some 600-123 bp fragments, was obtained after PCR. The blunt-ended fragments were clonned into the PCR cloning pMOSblue plasmid. The insert size of the selected recombinant cDNA clones was determined by restriction analysis of the plasmidDNAwith Sma I and Hind III enzymes. Positive clones were also screened by direct colony PCR screening. The selected recombinant cDNA clones were stored in glycerol at .70 °C.

  1. 一种高特异性的改良降落PCR%Modified Touchdown PCR as a High Efficient Approach to Improve the Specificity of PCR

    Institute of Scientific and Technical Information of China (English)

    张贵星; 袁保梅; 许培荣; 王建民; 薛乐勋

    2002-01-01

    To improve the specificity of PCR in detection of genes in genomic DNA, a modified touchdown PCR method was designed by using the common Taq DNA polymerase and the Pfu DNA polymerase with proofreading ability. Genomic DNA was extracted from Dunaliella bardawil, a unicellular and wall-less alga being able to propagate in solution of high concentration of NaCl. Two kinds of PCR using Taq and Pfu DNA polymerases were carried out, utilizing the genomic DNA mentioned above as a template, to amplify the upstream promoter sequence of the cbr (carotene biosynthesis-related) gene. Traditional PCR was used as control. Electrophoresis of the PCRs using Taq DNA polymerase demonstrated that TD-PCR produced a single band of 1 272 bp which was corresponding to the expected cbr promoter, in contrast, however, in the lane of common PCR, two extra nonspecific bands appeared as well as the expected 1 272 bp band. PCRs using the Pfu DNA polymerase displayed that common PCR program generated two bands of 1 272 bp and 500 bp, while the TD-PCR program brought about only the expected 1 272 bp band. PCRs using modified touchdown PCR program with both kinds of polymerase were of higher specificity than common PCR. The modified TD-PCR program can efficiently improve the specificity of PCR. Similar programs are expected to clone gene fragments that are difficult to be cloned by the common PCR method, or to raise the specificity of PCR in which the false positives are difficult to be eliminated.%为提高基因组DNA中的基因PCR检出的特异性,设计了一种改良的降落PCR程序,并分别用TaqDNA聚合酶及高保真Pfu DNA聚合酶进行实验.自盐藻Dunaliella bardawil中提取基因组DNA作为PCR模板,使用Taq DNA聚合酶及Pfu DNA聚合酶,运用普通PCR和降落PCR程序,扩增胡萝卜素生物合成相关基因(cbr)上游启动子序列,并电泳比较PCR扩增产物的特异性.结果显示,使用普通Taq酶PCR,普通PCR程序产生200bp,500bp和1272 bp长的三条

  2. [Construction of RNAi vectors for SmNAC1 transcription factors of Salvia miltiorrhiza using Gateway cloning technology].

    Science.gov (United States)

    Zhao, Rong; Rong, Qi-Xian; Liu, Yu-Zhong; Shen, Ye; Huang, Lu-Qi

    2014-05-01

    NAC transcription factors involved in plant growth and development, as well as responses to biotic and abiotic stress. RNAi Vectors for SmNAC transcription factors of Salvia miltiorrhiza was constructed by using Gateway cloning technology, in order to further study the function of SmNAC1 transcription factor. According to Gateway cloning technology, the specific fragments of SmNAC1 containing attB adapter was amplified by PCR using ultra-fideling phusion polymerase of NEB. By the BP recombination reaction, the PCR product containing attB was transferred to an donor vector (pENTR/SD/D-TOPO). Finally, SmNACi specific gene was cloned into pK7GWIWG2D plant expression vectors by LR recombination reaction. Experimental results showed that Gateway cloning technology provide a rapid and highly efficient way to clone the interested gene. PMID:25095362

  3. Recombinant expression library of Pyrococcus furiosus constructed by high-throughput cloning: a useful tool for functional and structural genomics

    Directory of Open Access Journals (Sweden)

    Hui eYuan

    2015-09-01

    Full Text Available Hyperthermophile Pyrococcus furiosus grows optimally near 100°C and is an important resource of many industrial and molecular biological enzymes. To study the structure and function of Pyrococcus furiosus proteins at whole genome level, we constructed expression plasmids of each Pyrococcus furiosus gene using a ligase-independent cloning method, which was based on amplifying target gene and vector by PCR using phosphorothioate-modified primers and digesting PCR products by λ exonuclease. Our cloning method had a positive clone percentage of ≥ 80% in 96-well plate cloning format. Small-scale expression experiment showed that 55 out of 80 genes were efficiently expressed in Escherichia coli Strain Rosetta 2(DE3pLysS. In summary, this recombinant expression library of Pyrococcus furiosus provides a platform for functional and structural studies, as well as developing novel industrial enzymes. Our cloning scheme is adaptable to constructing recombinant expression library of other sequenced organisms.

  4. Recombinant laccase: I. Enzyme cloning and characterization.

    Science.gov (United States)

    Nicolini, Claudio; Bruzzese, Debora; Cambria, Maria Teresa; Bragazzi, Nicola Luigi; Pechkova, Eugenia

    2013-03-01

    We obtained structural and functional characterization of a recombinant Laccase from Rigidoporus lignosus (formerly Rigidoporus microporus), a white-rot basidiomycete, by means of circular dichroism (CD) spectra, cyclic voltammetry (CV) and biochemical assays. Here we report the optimization of expression and purification procedures of a recombinant Laccase expressed in supercompetent Escherichia coli cells. We amplified the coding sequence of Laccase using PCR from cDNA and cloned into a bacterial expression system. The resulting expression plasmid, pET-28b, was under a strong T7/Lac promoter induced by IPTG (isopropyl-β-d-thiogalactoipyranoside). We obtained purification by fast protein liquid chromatography (FPLC) method. We recorded the variation of the current of a solution containing purified Laccase with increasing Syringaldazine (SGZ) concentration using a potentiometer as proof of principle, showing its compatibility with the development of a new enzymatic biosensor for medical purposes, as described in Part II. PMID:22991171

  5. Construction of infectious cDNA clones for RNA viruses: Turnip crinkle virus.

    Science.gov (United States)

    Ryabov, Eugene V

    2008-01-01

    Reverse genetic approach is widely used in virology as it makes possible direct identification of viral gene function and uses RNA genomes as vectors. Production of infectious cDNA clones is an essential step in developing a reverse genetic system for an RNA virus. Here, we present rapid method for generation of infectious cDNA clone for Turnip crinkle virus (TCV). The infectious cDNA clone could be used for production of in vitro transcripts with the T7 RNA polymerase which could be used for infection of plants or plant cell protoplasts. The procedure described here includes purification of TCV, viral RNA extraction, reverse transcription, PCR amplification of the full-length cDNA copy of TCV linked to a T7 RNA polymerase promoter, cloning into a plasmid vector, in vitro transcription, and selection of infectious clones. PMID:18370276

  6. Molecular cloning, chromosomal mapping, and functional expression of human brain glutamate receptors

    Energy Technology Data Exchange (ETDEWEB)

    Sun, W.; Ferrer-Montiel, A.V.; Schinder, A.F.; Montal, M. (Univ. of California, San Diego, La Jolla (United States)); McPherson, J.P. (Univ. of California, Irvine (United States)); Evans, G.A. (Salk Inst. for Biological Studies, La Jolla, CA (United States))

    1992-02-15

    A full-length cDNA clone encoding a glutamate receptor was isolated from a human brain cDNA library, and the gene product was characterized after expression in Xenopus oocytes. Degenerate PCR primers to conserved regions of published rat brain glutamate receptor sequences amplified a 1-kilobase fragment from a human brain cDNA library. This fragment was used as a probe for subsequent hybridization screening. Two clones were isolated that, based on sequence information, code for different receptors: a 3-kilobase clone, HBGR1, contains a full-length glutamate receptor cDNA highly homologous to the rat brain clone GluR1, and a second clone, HBGR2, contains approximately two-thirds of the coding region of a receptor homologous to rat brain clone GluR2. Southern and PCr analysis of a somatic cell-hybrid panel mapped HBGR1 to human chromosome 5q31.3-33.3 and mapped HBGR2 to chromosome 4q25-34.3. Xenopus oocytes injected with in vitro-synthesized HBGR1 cRNA expressed currents activated by glutamate receptor agonists. These results indicate that clone HBGR1 codes for a glutamate receptor of the kainate subtype cognate to members of the glutamate receptor family from rodent brain.

  7. Cloning of Vibrio cholerae outer membrane protein W in Pichia pastoris.

    Directory of Open Access Journals (Sweden)

    Javad Alizadeh

    2013-09-01

    Full Text Available The outer membrane protein W (ompW of Vibrio cholerae is involved in stimulating the immune response via induction of protective immunity. It also plays an important role in bacterial pathogenesis by increasing the adaptability of pathogenic strains. In this study we aimed to clone V. cholerae ompW gene in the strain X-33 of Pichia pastoris.A gene encoding ompW was cloned into the Ppicza vector downstream of alcohol oxidase promoter. Then recombinant vector was transformed into the genome of the strain X-33 of P. pastoris. After growth of zeocin-resistant transformants, clones were selected and subsequently confirmed for cloning by PCR enzymatic digestion and sequencing.PCR, enzymatic digestion and sequencing showed that the ompW gene was correctly cloned into P. pastoris genome.Results of our study showed that the methylotrophic yeast P. pastoris can be considered as an appropriate host instead of mammalian and prokaryotic systems for cloning of ompW. As far as data show, this is the first time that ompW of V. cholera is cloned into the methylotrophic P. pastoris.

  8. Evaluation of PCR and multiplex PCR in relation to nested PCR for diagnosing Theileria equi

    OpenAIRE

    Danielle C. Leal; Cláudio R. Madruga; Paulo F. de Matos; Bárbara M. P. da S. Souza; Carlos R. Franke

    2011-01-01

    Conventional PCR (PCRTeq) for diagnosing Theileria equi and multiplex PCR (M/PCRTeq-Bc) for diagnosing T. equi and Babesia caballi were comparatively evaluated with nested PCR (N/PCR-Teq) for diagnosing equine piroplasmosis. In DNA sensitivity determinations, in multiple dilutions of equine blood that had tested positive for T. equi, PCR-Teq and N/PCR-Teq detected hemoparasite DNA in the larger dilutions (1:128), but did not differ significantly from the M/PCRTeq-Bc (1:64). In analyses on equ...

  9. CATO: The Clone Alignment Tool.

    Directory of Open Access Journals (Sweden)

    Peter V Henstock

    Full Text Available High-throughput cloning efforts produce large numbers of sequences that need to be aligned, edited, compared with reference sequences, and organized as files and selected clones. Different pieces of software are typically required to perform each of these tasks. We have designed a single piece of software, CATO, the Clone Alignment Tool, that allows a user to align, evaluate, edit, and select clone sequences based on comparisons to reference sequences. The input and output are designed to be compatible with standard data formats, and thus suitable for integration into a clone processing pipeline. CATO provides both sequence alignment and visualizations to facilitate the analysis of cloning experiments. The alignment algorithm matches each of the relevant candidate sequences against each reference sequence. The visualization portion displays three levels of matching: 1 a top-level summary of the top candidate sequences aligned to each reference sequence, 2 a focused alignment view with the nucleotides of matched sequences displayed against one reference sequence, and 3 a pair-wise alignment of a single reference and candidate sequence pair. Users can select the minimum matching criteria for valid clones, edit or swap reference sequences, and export the results to a summary file as part of the high-throughput cloning workflow.

  10. [The discrete horror of cloning].

    Science.gov (United States)

    Guibourg, Ricardo A

    2009-01-01

    The author raises the topic of cloning after the decision of the Argentine government, which concerned for the "dignity of the human person", passed a decree of need and urgency, No. 200/97 (Annex), prohibiting cloning experiments with human beings. Therefore, considering that the topic is so terribly urgent and necessary, the author feels it is timely to consider it.

  11. Polimeraz Zincir Reaksiyonu (PCR) Optimizasyonu

    OpenAIRE

    KAHYA, Serpil; BUYUKCANGAZ, Esra; Carli, K. Tayfun

    2013-01-01

    Polymerase chain reaction (PCR), a deoxyribonucleic acid (DNA) that lies between two known chain enzymatically amplify a specific DNA region as an in vitro technique becoming common everyday. PCR method, used for many purposes such as diagnosis, epidemiology and studies to determine the amount of DNA, are still under development. Microbiology is taking a significant proportion in PCR usage, like innovations of application in other fields. Furthermore, PCR is the fundamental molecular method t...

  12. PCR performance of a thermostable heterodimeric archaeal DNA polymerase

    Directory of Open Access Journals (Sweden)

    Tom eKillelea

    2014-05-01

    Full Text Available DNA polymerases are versatile tools used in numerous important molecular biological core technologies like the ubiquitous polymerase chain reaction (PCR, cDNA cloning, genome sequencing and nucleic acid based diagnostics. Taking into account the multiple DNA amplification techniques in use, different DNA polymerases must be optimized for each type of application. One of the current tendencies is to reengineer or to discover new DNA polymerases with increased performance and broadened substrate spectra. At present, there is a great demand for such enzymes in applications, e.g., forensics or paleogenomics. Current major limitations hinge on the inability of conventional PCR enzymes, such as Taq, to amplify degraded or low amounts of template DNA. Besides, a wide range of PCR inhibitors can also impede reactions of nucleic acid amplification. Here we looked at the PCR performances of the proof-reading D-type DNA polymerase from P. abyssi, Pab-polD. Fragments, 3 kilobases in length, were specifically PCR-amplified in its optimized reaction buffer. Pab-polD showed not only a greater resistance to high denaturation temperatures than Taq during cycling, but also a superior tolerance to the presence of potential inhibitors. Proficient proof-reading Pab-polD enzyme could also extend a primer containing up to two mismatches at the 3’ primer termini. Overall, we found valuable biochemical properties in Pab-polD compared to the conventional Taq, which makes the enzyme ideally suited for cutting-edge PCR-applications.

  13. Quantum probabilistically cloning and computation

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    In this article we make a review on the usefulness of probabilistically cloning and present examples of quantum computation tasks for which quantum cloning offers an advantage which cannot be matched by any approach that does not resort to it.In these quantum computations,one needs to distribute quantum information contained in states about which we have some partial information.To perform quantum computations,one uses state-dependent probabilistic quantum cloning procedure to distribute quantum information in the middle of a quantum computation.And we discuss the achievable efficiencies and the efficient quantum logic network for probabilistic cloning the quantum states used in implementing quantum computation tasks for which cloning provides enhancement in performance.

  14. An improved allele-specific PCR primer design method for SNP marker analysis and its application

    OpenAIRE

    Liu Jing; Huang Shunmou; Sun Meiyu; Liu Shengyi; Liu Yumei; Wang Wanxing; Zhang Xiurong; Wang Hanzhong; Hua Wei

    2012-01-01

    Abstract Background Although Single Nucleotide Polymorphism (SNP) marker is an invaluable tool for positional cloning, association study and evolutionary analysis, low SNP detection efficiency by Allele-Specific PCR (AS-PCR) still restricts its application as molecular marker like other markers such as Simple Sequence Repeat (SSR). To overcome this problem, primers with a single nucleotide artificial mismatch introduced within the three bases closest to the 3’end (SNP site) have been used in ...

  15. A survey of polymerase chain reaction (PCR) amplification studies of unicellular protists using single-cell PCR.

    Science.gov (United States)

    Lynn, Denis H; Pinheiro, Marcel

    2009-01-01

    We surveyed a variety of studies that have used single-cell polymerase chain reaction (SC-PCR) to examine the gene sequences of a diversity of unicellular protists. Representatives of all the Super-Groups of eukaryotes have been subjected to SC-PCR with ciliates and dinoflagellates being most commonly examined. The SC-PCR was carried out either by directly amplifying a single lysed cell or by first extracting DNA and following this with amplification of the DNA extract. Cell lysis methods included heating, freezing, mechanical rupture, and enzyme digestion. Cells fixed or preserved with ethanol, methanol, and Lugol's have also been used successfully. Heminested or seminested PCR might follow the initial PCR, whose products were then directly sequenced or cloned and then sequenced. The methods are not complicated. This should encourage protistologists to use SC-PCR in the description of new or revised taxa, especially rare and unculturable forms, and it should also enable the probing of gene expression in relation to life history stages.

  16. PCR, exit stage left ...

    CERN Multimedia

    2004-01-01

    The Prevessin Control Room during LEP's start up in 1989. The Prévessin Control Room (PCR) was recently engulfed in a wave of nostalgia. The PCR, scene of some of the greatest moments in CERN's history, is being dismantled to prepare for a complete overhaul. In February 2006, a new combined control centre for all the accelerators will open its doors on the same site, together with a new building currently under construction (see Bulletin issue 27/2004 of 28 June 2004). This marks the end of an important chapter in CERN's history. The Prévessin Control Room saw its first momentous event 28 years ago when the 400 GeV beam for the SPS was commissioned in the presence of Project Leader John Adams. It was also here that the first proton-antiproton collisions were observed, in 1981. Eight years later, in 1989, operators and directors alike jumped for joy at the announcement of the first electron-positron collisions at the start up of LEP, the biggest accelerator in the world. Today the 80 terminals and PCs have b...

  17. Clone Networks, Clone Extensions and Biregularizations of Varieties of Algebras

    Institute of Scientific and Technical Information of China (English)

    J. Plonka

    2001-01-01

    We consider algebras of type τ- without nullary operations. An identity ψ≈ψ of type τ is clone compatible if ψ and ψ are the same variable or the sets of fundamental operation symbols in ψ and ψ are non-empty and identical. For a variety V, we denote by Vc the variety defined by all clone compatible identities from Id(V). In this paper, we give a construction of algebras called a clone network. Under some assumptions, we describe algebras from Vc by means of this construction. We find some properties of Vc and applications.

  18. Targeted isolation and cloning of 100-kb microbial genomic sequences by Cas9-assisted targeting of chromosome segments.

    Science.gov (United States)

    Jiang, Wenjun; Zhu, Ting F

    2016-05-01

    Cloning of long microbial genomic sequences is an essential tool in synthetic biology and genome engineering. Such long sequences are often difficult to obtain directly by traditional PCR or restriction enzyme digestion, and therefore the cloning of these sequences has remained a technical obstacle in molecular biology. Based on the in vitro application of RNA-guided Cas9 nuclease, the method of Cas9-assisted targeting of chromosome segments (CATCH) cleaves target DNA in vitro from intact bacterial chromosomes embedded in agarose plugs, which can be subsequently ligated with cloning vector through Gibson assembly. Here we describe an optimized protocol of CATCH cloning for the targeted cloning of long genomic sequences of up to 100 kb from microorganisms. The protocol uses standard laboratory equipment and takes ∼8 h of bench time over several days, and it may potentially simplify and accelerate efforts to isolate and clone large gene clusters from microorganisms. PMID:27101517

  19. Isolation and Identification of Haemophilus parasuis, Cloning and Sequence Analysis of aroA Gene and Institution of Two Program of Triplex PCR Assay%副猪嗜血杆菌aroA基因的克隆与序列分析及2种三重PCR检测方法的建立

    Institute of Scientific and Technical Information of China (English)

    牟和平; 王兴美; 叶亚琼; 李家伟; 李玉谷

    2012-01-01

    本试验对分离的5株副猪嗜血杆菌进行了“卫星”生长试验、生化鉴定和PCR检测.通过对aroA基因序列进行分析,发现这5株菌同标准菌株相比,其核苷酸序列相似性为96.3%~99.8%,氨基酸序列相似性为98.2%~99.5%.此外,还建立了分别针对副猪嗜血杆菌(Hps)、猪伪狂犬病病毒(PRV)、猪细小病毒(PPV)及猪圆环病毒2型(PCV2)、猪细小病毒、猪伪狂犬病病毒的三重PCR检测方法;敏感性试验表明,三重PCR最低能检出Hps、PPV、PRV、PCV2的DNA分别为12、16、7.6和6.3 pg.%In this study, 5 strains of Haemophilus parasuis( Hps) were identified by 'satellite' growing test, biochemical and PCR assay. The results showed that aroA gene of the isolated Hps had a high degree of similarity with classical culture strain in the sequence of nucleotide and amino acid sequence, which was between 96. 3% to 99. 8% and 98. 2% to 99. 5% respectively. We implemented two program of triplex PCR assay, one group was used to detect simultaneously infections of Hps, PCV2 and PPV, the other group was developed to detect the PCV2, PPV and PRV. The sensitivity tests indicated that the triplex PCR assay may be used for detecting Hps, PPV, PRV and PCV2 of 105 dilute strength) the DNA minimun detectable quantity of Hps, PPV, PRV, PCV2 was 12, 16, 7.6 and 6. 3 pg respectively.

  20. Cloning of Integral Mature Peptide Gene of Human GDF-5

    Institute of Scientific and Technical Information of China (English)

    王万山; 顾为望; 王启伟; 朴仲贤; 朴英杰

    2004-01-01

    Summary: The integral mature peptide gene of human growth differentiation factor-5 (GDF-5) was cloned to provide the essential foundation for study on the biological characteristics of GDF-5 at gene and protein levels. Two primers were chemosynthesized according to the hGDF-5 sequence reported in Genbank. The hGDF-5 gene was gained by RT-PCR methods from the total RNA extracted from human fetus cartilage tissue, and was cloned into vector pMD18-T. The sequence of recombinant plasmid pMD18-T-hGDF-5 was analyzed by sequence analysis. DNA agarose gel electrophoresis showed that the product of RT-PCR was about 380bp, and double enzyme digestion of the recombinant plasmid corresponded with it. The result of sequence assay was in agreement with the reported hGDF-5 sequence in Genbank. Our results showed that the integral mature peptide gene of human GDF-5 was cloned successfully from human fetal cartilage tissue, and totally identified with the sequence of human GDF-5 in Genbank.

  1. Biomimetic Cloning of Quantum Observables

    CERN Document Server

    Alvarez-Rodriguez, U; Lamata, L; Solano, E

    2013-01-01

    We propose a bio-inspired sequential quantum protocol for the cloning and preservation of the statistics associated to quantum observables of a given system. It combines the cloning of a set of commuting observables, permitted by the no-cloning and no-broadcasting theorems, with a controllable propagation of the initial state coherences to the subsequent generations. The protocol mimics the scenario in which an individual in an unknown quantum state copies and propagates its quantum information into an environment of blank qubits. Finally, we propose a realistic experimental implementation of this protocol in trapped ions.

  2. Cloning: revisiting an old debate.

    Science.gov (United States)

    Verhey, Allen D

    1994-09-01

    The debate about cloning that took place 25 years ago, although directed toward a different sort of cloning, elucidates fundamental issues currently at stake in reproductive technologies and research. Paul Ramsey and Joseph Fletcher were participants in this early debate. The differences between Ramsey and Fletcher about the meaning and sufficiency of freedom, the understanding and weighing of good and evil, the connection between embodiment and personhood, the relationship of humans with nature, and the meaning of parenthood suggest both a broader agenda for the debate about cloning and a cautious move forward in the development of embryo-splitting.

  3. Target-selective homologous recombination cloning for high-throughput generation of monoclonal antibodies from single plasma cells

    Directory of Open Access Journals (Sweden)

    Isobe Masaharu

    2011-04-01

    Full Text Available Abstract Background Molecular cloning of functional immunoglobulin genes from single plasma cells is one of the most promising technologies for the rapid development of monoclonal antibody drugs. However, the proper insertion of PCR-amplified immunoglobulin genes into expression vectors remains an obstacle to the high-throughput production of recombinant monoclonal antibodies. Results We developed a single-step cloning method, target-selective homologous recombination (TS-HR, in which PCR-amplified immunoglobulin variable genes were selectively inserted into vectors, even in the presence of nonspecifically amplified DNA. TS-HR utilizes Red/ET-mediated homologous recombination with a target-selective vector (TS-vector with unique homology arms on its termini. Using TS-HR, immunoglobulin variable genes were cloned directly into expression vectors by co-transforming unpurified PCR products and the TS-vector into E. coli. Furthermore, the high cloning specificity of TS-HR allowed plasmids to be extracted from pools of transformed bacteria without screening single colonies for correct clones. We present a one-week protocol for the production of recombinant mouse monoclonal antibodies from large numbers of single plasma cells. Conclusion The time requirements and limitations of traditional cloning procedures for the production of recombinant immunoglobulins have been significantly reduced with the development of the TS-HR cloning technique.

  4. A simple, rapid and efficient way to obtain infectious clones of potyviruses.

    Science.gov (United States)

    Desbiez, C; Chandeysson, C; Lecoq, H; Moury, B

    2012-07-01

    The availability of an infectious cDNA clone is a prerequisite for genetic studies on RNA viruses. However, despite important improvement in molecular biology techniques during the last decades, obtaining such clones often remains tedious, time-consuming and rather unpredictable. In the case of potyviruses, cDNA clones are frequently unstable due to the toxicity of some viral proteins for bacteria. The problem can be overcome by inserting introns into the viral sequence but this requires additional steps in the cloning process and depends on the availability of suitable restriction sites in the viral sequence or adjunction of such sites by mutagenesis. Homologous recombination in yeast rather than in vitro restriction and ligation can be used to build infectious clones or other viral constructs. This paper describes how, by using recombination in yeast and fusion PCR, infectious intron-containing clones were obtained within a few weeks for two strains of watermelon mosaic virus (WMV, Potyvirus), whereas previous attempts using "classical" cloning techniques had failed repeatedly. Using the same approach, intronless infectious clones of two other potyviruses, zucchini yellow mosaic virus (ZYMV) and papaya ringspot virus (PRSV), were obtained in less than two weeks. PMID:22498260

  5. Separation of DNA Fragments with a Broad Range of Molecular Weight by Capillary Electrophoresis with Sieving Matrix of Poly (ethylene oxide)%聚环氧乙烷无胶筛分毛细管电泳分离宽分子量范围DNA片段

    Institute of Scientific and Technical Information of China (English)

    李玉荣; 陈长宝; 周杰

    2011-01-01

    在无胶筛分毛细管电泳中,以聚环氧乙烷为筛分介质,用硅烷化处理的毛细管柱(31.2 cm×75 μm i.d.,有效长度21.0 cm)分离DL5000 DNA Marker(DNA长度为100~5000 bp),考察了筛分介质浓度、缓冲液pH值、分离电压和溴化乙锭浓度对分离双链DNA片段的影响,优化得到分离100~5000 bp DNA片段的最佳条件.毛细管电泳的最佳条件为PEO浓度5 mg/mL,缓冲液pH值8.0,电压-12.0 kV及溴化乙锭浓度3.0 μg/mL.在此条件下,可对山梨醇脱氢酶基因(SDH)和乙烯受体基因(ETR1)的聚合酶链式反应(PCR)扩增产物同时进行检测,分离和鉴定效果良好.%DL5000 DNA marker fragments( 100-5000 bp) were separated by non-gel sieve capillary electrophoresis on a silanized fused silica capillary column(31.2 cm ×75 μm i.d. with effective length 21.0 cm)using poly( ethylene oxide) as sieve matrix. The influences of poly( ethylene oxide) concentration, pH value of running buffer, separation voltage and ethidium bromide concentration on the separation efficiency of different lengths of double-strand DNA fragments were investigated. The optimum conditions for separation of 100-5000 bp DNA fragments were established as 5 mg/mL poly ( ethylene oxide), pH = 8.0, 3.0 μg/mL ethidium bromide and voltage of - 12.0 kV. Under these conditions, the multiplex polymerase chain reaction (PCR) magnified products from the sorbitol dehydrogenase gene (SDH) and the ethylene receptor gene (ETR1) were simultaneously detected, and good identification and resolution were obtained.

  6. Cloning and expression of islandisin, a new thermostable subtilisin from Fervidobacterium islandicum, in Escheria coli

    NARCIS (Netherlands)

    Godde, C.; Sahm, K.; Brouns, S.J.J.; Kluskens, L.D.; Oost, van der J.; Vos, de W.M.; Antranikian, G.

    2005-01-01

    A gene encoding a subtilisin-like protease, designated islandisin, from the extremely thermophilic bacterium Fervidobacterium islandicum (DSMZ 5733) was cloned and actively expressed in Escherichia coli. The gene was identified by PCR using degenerated primers based on conserved regions around two o

  7. Molecular cloning and genomic organization of an allatostatin preprohormone from Drosophila melanogaster

    DEFF Research Database (Denmark)

    Lenz, C; Williamson, M; Grimmelikhuijzen, C J

    2000-01-01

    insect allatostatins. This resulted in alignment with a DNA sequence coding for some Drosophila allatostatins (drostatins). Using PCR with oligonucleotide primers directed against the presumed exons of this Drosophila allatostatin gene and subsequent 3'- and 5'-RACE, we were able to clone its c...

  8. CDNA cloning, characterization and expression of an endosperm-specific barley peroxidase

    DEFF Research Database (Denmark)

    Rasmussen, Søren Kjærsgård; Welinder, K.G.; Hejgaard, J.

    1991-01-01

    -terminal amino acid residues of mature BP 1. The clone pcR7 encodes an additional C-terminal sequence of 22 residues, which apparently are removed during processing. BP 1 is less than 50% identical to other sequenced plant peroxidases. Analyses of RNA and protein from aleurone, endosperm and embryo tissue showed...

  9. A Clone of Your Own.

    Science.gov (United States)

    Bilodeau, Kirsten

    1997-01-01

    Describes an activity used at the Washington Park Arboretum that helps students understand cloning through plant propagation. Students also learn how to make a pot from recycled newspapers and how to make soil that is appropriate for the plants. (DDR)

  10. Human cloning and 'posthuman' society.

    Science.gov (United States)

    Blackford, Russell

    2005-01-01

    Since early 1997, when the creation of Dolly the sheep by somatic cell nuclear transfer was announced in Nature, numerous government reports, essays, articles and books have considered the ethical problems and policy issues surrounding human reproductive cloning. In this article, I consider what response a modern liberal society should give to the prospect of human cloning, if it became safe and practical. Some opponents of human cloning have argued that permitting it would place us on a slippery slope to a repugnant future society, comparable to that portrayed in Aldous Huxley's novel, Brave New World. I conclude that, leaving aside concerns about safety, none of the psychological or social considerations discussed in this article provides an adequate policy justification for invoking the state's coercive powers to prevent human cloning.

  11. Construction of adenovirus vectors encoding the lumican gene by gateway recombinant cloning technology

    Science.gov (United States)

    Wang, Gui-Fang; Qi, Bing; Tu, Lei-Lei; Liu, Lian; Yu, Guo-Cheng; Zhong, Jing-Xiang

    2016-01-01

    AIM To construct adenovirus vectors of lumican gene by gateway recombinant cloning technology to further understand the role of lumican gene in myopia. METHODS Gateway recombinant cloning technology was used to construct adenovirus vectors. The wild-type (wt) and mutant (mut) forms of the lumican gene were synthesized and amplified by polymerase chain reaction (PCR). The lumican cDNA fragments were purified and ligated into the adenovirus shuttle vector pDown-multiple cloning site (MCS)-/internal ribozyme entry site (IRES)/enhanced green fluorescent protein (EGFP). Then the desired DNA fragments were integrated into the destination vector pAV.Des1d yielding the final expression constructs pAV.Ex1d-cytomegalovirus (CMV)>wt-lumican/IRES/EGFP and pAV.Ex1d-CMV>mut-lumican/IRES /EGFP, respectively. RESULTS The adenovirus plasmids pAV.Ex1d-CMV>wt-lumican/IRES/EGFP and pAV.Ex1d-CMV>mut-lumican/IRES/EGFP were successfully constructed by gateway recombinant cloning technology. Positive clones identified by PCR and sequencing were selected and packaged into recombinant adenovirus in HEK293 cells. CONCLUSION We construct adenovirus vectors containing the lumican gene by gateway recombinant cloning technology, which provides a basis for investigating the role of lumican gene in the pathogenesis of high myopia. PMID:27672590

  12. Cloning and expression of special F protein from human liver

    Institute of Scientific and Technical Information of China (English)

    Shu-Ye Liu; Xin-Da Yu; Chun-Juan Song; Wei Lu; Jian-Dong Zhang; Xin-Rong Shi; Ying Duan; Ju Zhang

    2007-01-01

    AIM:To clone human liver special F protein and to express it in a prokaryotic system.METHODS:Total RNA was isolated from human liver tissue and first-strand cDNA was reverse transcribed using the PCR reverse primer. Following this,cDNA of the F protein was ligated into the clone vector pUCm-T. The segment of F protein's cDNA was subcloned into the expression vector pET-15b and transformed into E coli BL21 (DEB) pLyss. Isopropy-β-D-thiogalactoside (IPTG) was then used to induce expression of the target protein.RESULTS:The cDNA clone of human liver special F protein (1134bp) was successfully produced,with the cDNA sequence being published in Gene-bank:DQ188836. We confirmed the expression of F protein by Western blot with a molecular weight of 43 kDa. The expressed protein accounted for 40% of the total protein extracted.CONCLUSION:F protein expresses cDNA clone in a proKaryotic system,which offers a relatively simple way of producing sufficient quantities of F protein and contributes to understanding the principal biological functions of this protein.

  13. Artificial cloning of domestic animals

    OpenAIRE

    Keefer, Carol L.

    2015-01-01

    Domestic animals can be cloned using techniques such as embryo splitting and nuclear transfer to produce genetically identical individuals. Although embryo splitting is limited to the production of only a few identical individuals, nuclear transfer of donor nuclei into recipient oocytes, whose own nuclear DNA has been removed, can result in large numbers of identical individuals. Moreover, clones can be produced using donor cells from sterile animals, such as steers and geldings, and, unlike ...

  14. Animal cloning: advances and prospects

    OpenAIRE

    Chuaire Lilian; Sánchez Magda Carolina; Franco María Liliana

    2004-01-01

    Few recent advances have revolutionized the developmental biology as the animal cloning has. Since the birth of Dolly, the sheep, in 1996, which was the first derived clone of a mature animal, a new scientific era began. It has been characterized by growing demystification that differentiated cells are unalterable entities in its nuclear organization and chromatin structure, and by a better understanding of the mechanisms that regulate the development. Throughout this paper, we will review ...

  15. Therapeutic cloning: promises and issues

    OpenAIRE

    Kfoury, Charlotte

    2007-01-01

    Advances in biotechnology necessitate both an understanding of scientific principles and ethical implications to be clinically applicable in medicine. In this regard, therapeutic cloning offers significant potential in regenerative medicine by circumventing immunorejection, and in the cure of genetic disorders when used in conjunction with gene therapy. Therapeutic cloning in the context of cell replacement therapy holds a huge potential for de novo organogenesis and the permanent treatment o...

  16. Cloning, expression, and polymorphism of the porcine calpain10 gene

    Institute of Scientific and Technical Information of China (English)

    Xiuqin Yang; Di Liu; Hao Yu; Lijuan Guo; Hui Liu

    2008-01-01

    Calpains are calcium-regulated protcases involved in cellular functions that include muscle proteolysis both ante- and postmortem. This study was designed to clone the complete coding sequence of the porcine calpain10 gene, CAPN10, to analyze its expression characteristics and to investigate its polymorphism. Two isoforms of the CAPN10 gene, CAPN10A and CAPN10B, were obtained by reverse transcriptionpolymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends methods combined with in silico cloning. RT-PCR results indicated that CAPN10 mRNA was ubiquitously expressed in all tissues examined and, with increasing age,the expression level increased in muscles at six different growth points. In the same tissues, the expression level of CAPN10A was higher than that of CAPN10B. In addition,three single nucleotide polymorphisms were detected by the PCR-single-stranded conformational polymorphism method and by comparing the sequences of Chinese Min pigs with those of Yorkshire pigs. C527T mutation was a missense mutation and led to transforming Pro into Leu at the 176th amino acid. The results of the current study provided basic molecular information for further study of the function of the porcine CAPN10 gene.

  17. Inverse PCR and Quantitative PCR as Alternative Methods to Southern Blotting Analysis to Assess Transgene Copy Number and Characterize the Integration Site in Transgenic Woody Plants.

    Science.gov (United States)

    Stefano, Biricolti; Patrizia, Bogani; Matteo, Cerboneschi; Massimo, Gori

    2016-06-01

    One of the major unanswered questions with respect to the commercial use of genetic transformation in woody plants is the stability of the transgene expression over several decades within the same individual. Gene expression is strongly affected by the copy number which has been integrated into the plant genome and by the local DNA features close to the integration sites. Because woody plants cannot be subjected to selfing or backcrossing to modify the transgenic allelic structure without affecting the valuable traits of the cultivar, molecular characterization of the transformation event is therefore crucial. After assessing the transgene copy number of a set of apple transgenic clones with Southern blotting, we describe two alternative methods: the first is based on inverse PCR (i-PCR) and the second on the quantitative PCR (q-PCR). The methods produced comparable results with the exception of the data regarding a high copy number clone, but while the q-PCR-based system is rapid and easily adaptable to high throughput systems, the i-PCR-based method can provide information regarding the transformation event and the characteristics of the sequences flanking the transgenic construct.

  18. Artificial cloning of domestic animals.

    Science.gov (United States)

    Keefer, Carol L

    2015-07-21

    Domestic animals can be cloned using techniques such as embryo splitting and nuclear transfer to produce genetically identical individuals. Although embryo splitting is limited to the production of only a few identical individuals, nuclear transfer of donor nuclei into recipient oocytes, whose own nuclear DNA has been removed, can result in large numbers of identical individuals. Moreover, clones can be produced using donor cells from sterile animals, such as steers and geldings, and, unlike their genetic source, these clones are fertile. In reality, due to low efficiencies and the high costs of cloning domestic species, only a limited number of identical individuals are generally produced, and these clones are primarily used as breed stock. In addition to providing a means of rescuing and propagating valuable genetics, somatic cell nuclear transfer (SCNT) research has contributed knowledge that has led to the direct reprogramming of cells (e.g., to induce pluripotent stem cells) and a better understanding of epigenetic regulation during embryonic development. In this review, I provide a broad overview of the historical development of cloning in domestic animals, of its application to the propagation of livestock and transgenic animal production, and of its scientific promise for advancing basic research.

  19. Towards Clone Detection in UML Domain Models

    DEFF Research Database (Denmark)

    Störrle, Harald

    2010-01-01

    , we discuss how model clones arise by analyzing several practical scenarios. We propose a formal definition of models and clones, that allows us to specify a generic clone detection algorithm. Through a thorough analysis of the detail structure of sample UML domain models, recommendations for clone...

  20. Structured Review of Code Clone Literature

    NARCIS (Netherlands)

    Hordijk, Wiebe; Ponisio, María Laura; Wieringa, Roel

    2008-01-01

    This report presents the results of a structured review of code clone literature. The aim of the review is to assemble a conceptual model of clone-related concepts which helps us to reason about clones. This conceptual model unifies clone concepts from a wide range of literature, so that findings ab

  1. Cloning of Omp1 Gene from Chlamydia trachomatis F Genotype

    Institute of Scientific and Technical Information of China (English)

    QI Manli(齐蔓莉); LIU Quanzhong(刘全中); JIAO Wenling(缴稳苓); TIAN Jingqun(田敬群); CHEN Jinying(陈锦英)

    2002-01-01

    Objectives: To directionally clone the omp1 gene fromChlamydia trachomatis (Ct) F genotype onto a plasmid vectorfor constructing a rudimentary DNA vaccine.Methods: The complete omp1 gene from genomic DNA of CtF genotype wild species was amplified with primers designedby computer. The recombinant gene was obtained byrestriction enzyme cutting, linking the gene with the plasmidvector in vitro, transforming the recombinant gene intobacteria, and extracting the DNA from the bacteria.Results: DNA extracted from the bacteria was composed ofthe omp1 gene and plasmid, which is identified by threemethods of singular restrictive enzyme cutting, doublerestrictive enzyme cutting and PCR.Conclusion: Cloning of the omp1 gene from the Ct Fgenotype means that a rudimentary DNA vaccine wassuccessfully constructed.

  2. Preliminary screening and identification of stem cell-like sphere clones in a gallbladder cancer cell line GBC-SD*

    Institute of Scientific and Technical Information of China (English)

    Bao-bing YIN; Shuang-jie WU; Hua-jie ZONG; Bao-jin MA; Duan CAI

    2011-01-01

    This paper aims to screen and identify sphere clone cells with characteristics similar to cancer stem cellsin human gallbladder cancer cell line GBC-SD. GBC-SD cells were cultured in a serum-free culture medium with different concentrations of the chemotherapeutic drug cisplatin for generating sphere clones. The mRNA expressions of stem cell-related genes CD133, OCT-4, Nanog, and drug resistance genes ABCG2 and MDR-1 in sphere clones were detected by quantitative real-time polymerase chain reaction (PCR). Stem cell markers were also analyzed by flow cytometry and immunofluorescent staining. Different amounts of sphere clones were injected into nude mice to test their abilities to form tumors. Sphere clones were formed in serum-free culture medium containing cisplatin (30 pmol/L).Flow cytometry results demonstrated that the sphere clones expressed high levels of stem cell markers CD133+ (97.6%) and CD44+ (77.9%) and low levels of CD24+ (2.3%). These clones also overexpressed the drug resistance genes ABCG2 and MDR-1. Quantitative real-time PCR showed that sphere clones expressed stem cell genes Nanog and OCT-4 284 and 266 times, respectively, more than those in the original GBC-SD cells. Immunofluorescent staining showed that sphere clones overexpressed OCT-4, Nanog, and SOX-2, and Iow expressed MUG1 and vimentin. Tumor formation experiments showed that 1 x 103 sphere clone cells could induce much larger tumors in nude mice than 1 x 105 GBC-SD cells. In conclusion, sphere clones of gallbladder cancer with stem cell-like characteristics can be obtained using suspension cultures of GBC-SD cells in serum-free culture medium containing cisplatin.

  3. Sequence Homologies between Mycoplasma and Chlamydia spp. Lead to False-Positive Results in Chlamydial Cell Cultures Tested for Mycoplasma Contamination with a Commercial PCR Assay▿

    OpenAIRE

    Maass, Viola; Kern, Jan Marco; Poeckl, Matthias; Maass, Matthias

    2011-01-01

    Mycoplasma contamination is a frequent problem in chlamydial cell culture. After obtaining contradictory contamination results, we compared three commercial PCR kits for mycoplasma detection. One kit signaled contamination in mycoplasma-free Chlamydia pneumoniae cultures. Sequencing of cloned PCR products revealed primer homology with the chlamydial genome as the basis of this false-positive result.

  4. QuickStep-Cloning: a sequence-independent, ligation-free method for rapid construction of recombinant plasmids

    OpenAIRE

    Jajesniak, Pawel; Wong, Tuck Seng

    2015-01-01

    Background Molecular cloning is an essential step in biological engineering. Methods involving megaprimer-based PCR of a whole plasmid are promising alternatives to the traditional restriction-ligation-based molecular cloning. Their widespread use, however, is hampered by some of their inherent characteristics, e.g., linear amplification, use of self-annealing megaprimers and difficulty with performing point insertion of DNA. These limitations result in low product yield and reduced flexibili...

  5. Turbo cloning: a fast, efficient method for cloning PCR products and other blunt-ended DNA fragments into plasmids.

    OpenAIRE

    Boyd, A C

    1993-01-01

    The method uses a novel plasmid vector, p9lox5, containing a site-specific recombination sequence lox from the lox/Cre recombinase system of bacteriophage P1. There are two distinct stages. Firstly, vector and fragment DNAs are ligated intermolecularly under conditions of macromolecular crowding (15% polyethylene glycol 6000) which accelerate blunt-end joining a thousandfold. Secondly, circular recombinant molecules are efficiently excised from the ligation products by Cre recombinase acting ...

  6. 用mRNA RT-PCR差异显示技术克隆拟除虫菊酯抗性家蝇细胞色素P450基因片段%CLONING OF CYTOCHROME P450 ESTs FROM A DELTAMETHRIN-RESISTANT STRAIN OF HOUSEFLY, MUSCA DOMESTICA, USING mRNA DIFFERENTIAL DISPLAY RT-PCR TECHNIQUE

    Institute of Scientific and Technical Information of China (English)

    马彩霞; 李梅; 邱星辉; 何凤琴; 刘惠霞

    2005-01-01

    细胞色素P450单加氧酶系是一类广泛分布在生物有机体中的重要酶系,具有多样的功能.细胞色素P450介导的杀虫剂代谢解毒作用的增强是昆虫对杀虫剂产生抗性的普遍机制.为揭示家蝇对拟除虫菊酯类杀虫剂的分子基础,我们利用mRNA差异显示技术(DD RT-PCR)从溴氰菊酯抗性品系家蝇Musca domestica中分离出2个新的基因片段(M1,M2).序列比对(BlastP)结果表明,M1与黑腹果蝇Drosophila melanogaster中的Cyp6A9在氨基酸水平上具有54%的相似性,M2分别与果蝇Drosophila simulans中的Cyp6g1有65%的相似性.M1和M2包含P450的特征序列,并与细胞色素P450具有最高程度的序列相似性,是为细胞色素P450基因片段.

  7. Molecular cloning and enzymatic characterization of sheep CYP2J

    OpenAIRE

    Messina, Andrea; Nencioni, Simona; Gervasi, Pier Giovanni; Gotlinger, K. H.; Schwartzman, Michael Linado; Longo, Vincenzo

    2010-01-01

    Abstract 1. Cytochrome P450 (CYP) 2Js have been studied in various mammals, but not in sheep, as an animal model used to test veterinary drug metabolism. 2. Sheep CYP2J was cloned from liver messenger RNA (mRNA) by RACE. The cDNA, after modification at its N- and C-terminals, was expressed in Escherichia coli and the sheep CYP2J protein, purified by chromatography, was 80% homologous to human and monkey CYP2J2. 3. Reverse transcriptase-polymerase chain reaction (RT-PCR) experiments showed tha...

  8. Cloning of an agr homologue of Staphylococcus saprophyticus.

    Science.gov (United States)

    Sakinc, Türkan; Kulczak, Pawel; Henne, Karsten; Gatermann, Sören G

    2004-08-01

    An agr homologue of Staphylococcus saprophyticus was identified, cloned and sequenced. The gene locus shows homologies to other staphylococcal agr systems, especially to those of S. epidermidis and S. lugdunensis. A putative RNAIII was identified and found to be differentially expressed during the growth phases. In contrast to the RNAIII molecules of S. epidermidis and S. aureus it does not contain an open reading frame that codes for a protein with homologies to the delta-toxin. Using PCR, the agr was found to be present in clinical isolates of S. saprophyticus.

  9. An asymmetric PCR-based, reliable and rapid single-tube native DNA engineering strategy

    Directory of Open Access Journals (Sweden)

    Bi Yanzhen

    2012-07-01

    Full Text Available Abstract Background Widely used restriction-dependent cloning methods are labour-intensive and time-consuming, while several types of ligase-independent cloning approaches have inherent limitations. A rapid and reliable method of cloning native DNA sequences into desired plasmids are highly desired. Results This paper introduces ABI-REC, a novel strategy combining asymmetric bridge PCR with intramolecular homologous recombination in bacteria for native DNA cloning. ABI-REC was developed to precisely clone inserts into defined location in a directional manner within recipient plasmids. It featured an asymmetric 3-primer PCR performed in a single tube that could robustly amplify a chimeric insert-plasmid DNA sequence with homologous arms at both ends. Intramolecular homologous recombination occurred to the chimera when it was transformed into E.coli and produced the desired recombinant plasmids with high efficiency and fidelity. It is rapid, and does not involve any operational nucleotides. We proved the reliability of ABI-REC using a double-resistance reporter assay, and investigated the effects of homology and insert length upon its efficiency. We found that 15 bp homology was sufficient to initiate recombination, while 25 bp homology had the highest cloning efficiency. Inserts up to 4 kb in size could be cloned by this method. The utility and advantages of ABI-REC were demonstrated through a series of pig myostatin (MSTN promoter and terminator reporter plasmids, whose transcriptional activity was assessed in mammalian cells. We finally used ABI-REC to construct a pig MSTN promoter-terminator cassette reporter and showed that it could work coordinately to express EGFP. Conclusions ABI-REC has the following advantages: (i rapid and highly efficient; (ii native DNA cloning without introduction of extra bases; (iii restriction-free; (iv easy positioning of directional and site-specific recombination owing to formulated primer design. ABI

  10. An Alternative Method to Facilitate cDNA Cloning for Expression Studies in Mammalian Cells by Introducing Positive Blue White Selection in Vaccinia Topoisomerase I-Mediated Recombination.

    Directory of Open Access Journals (Sweden)

    Hiroshi Udo

    Full Text Available One of the most basic techniques in biomedical research is cDNA cloning for expression studies in mammalian cells. Vaccinia topoisomerase I-mediated cloning (TOPO cloning by Invitrogen allows fast and efficient recombination of PCR-amplified DNAs. Among TOPO vectors, a pcDNA3.1 directional cloning vector is particularly convenient, since it can be used for expression analysis immediately after cloning. However, I found that the cloning efficiency was reduced when RT-PCR products were used as inserts (about one-quarter. Since TOPO vectors accept any PCR products, contaminating fragments in the insert DNA create negative clones. Therefore, I designed a new mammalian expression vector enabling positive blue white selection in Vaccinia topoisomerase I-mediated cloning. The method utilized a short nontoxic LacZα peptide as a linker for GFP fusion. When cDNAs were properly inserted into the vector, minimal expression of the fusion proteins in E. coli (harboring lacZΔM15 resulted in formation of blue colonies on X-gal plates. This method improved both cloning efficiency (75% and directional cloning (99% by distinguishing some of the negative clones having non-cording sequences, since these inserts often disturbed translation of lacZα. Recombinant plasmids were directly applied to expression studies using GFP as a reporter. Utilization of the P2A peptide allowed for separate expression of GFP. In addition, the preparation of Vaccinia topoisomerase I-linked vectors was streamlined, which consisted of successive enzymatic reactions with a single precipitation step, completing in 3 hr. The arrangement of unique restriction sites enabled further modification of vector components for specific applications. This system provides an alternative method for cDNA cloning and expression in mammalian cells.

  11. Quantum superposition of multiple clones and the novel cloning machine

    OpenAIRE

    Pati, Arun Kumar

    1999-01-01

    we envisage a novel quantum cloning machine, which takes an input state and produces an output state whose success branch can exist in a linear superposition of multiple copies of the input state and the failure branch exist in a superposition of composite state independent of the input state. We prove that unknown non-orthogonal states chosen from a set $\\cal S$ can evolve into a linear superposition of multiple clones by a unitary process if and only if the states are linearly independent. ...

  12. Allele Specific Locked Nucleic Acid Quantitative PCR (ASLNAqPCR): An Accurate and Cost-Effective Assay to Diagnose and Quantify KRAS and BRAF Mutation

    Science.gov (United States)

    Morandi, Luca; de Biase, Dario; Visani, Michela; Cesari, Valentina; De Maglio, Giovanna; Pizzolitto, Stefano; Pession, Annalisa; Tallini, Giovanni

    2012-01-01

    The use of tyrosine kinase inhibitors (TKIs) requires the testing for hot spot mutations of the molecular effectors downstream the membrane-bound tyrosine kinases since their wild type status is expected for response to TKI therapy. We report a novel assay that we have called Allele Specific Locked Nucleic Acid quantitative PCR (ASLNAqPCR). The assay uses LNA-modified allele specific primers and LNA-modified beacon probes to increase sensitivity, specificity and to accurately quantify mutations. We designed primers specific for codon 12/13 KRAS mutations and BRAF V600E, and validated the assay with 300 routine samples from a variety of sources, including cytology specimens. All were analyzed by ASLNAqPCR and Sanger sequencing. Discordant cases were pyrosequenced. ASLNAqPCR correctly identified BRAF and KRAS mutations in all discordant cases and all had a mutated/wild type DNA ratio below the analytical sensitivity of the Sanger method. ASLNAqPCR was 100% specific with greater accuracy, positive and negative predictive values compared with Sanger sequencing. The analytical sensitivity of ASLNAqPCR is 0.1%, allowing quantification of mutated DNA in small neoplastic cell clones. ASLNAqPCR can be performed in any laboratory with real-time PCR equipment, is very cost-effective and can easily be adapted to detect hot spot mutations in other oncogenes. PMID:22558339

  13. Particle infectivity of HIV-1 full-length genome infectious molecular clones in a subtype C heterosexual transmission pair following high fidelity amplification and unbiased cloning

    Energy Technology Data Exchange (ETDEWEB)

    Deymier, Martin J., E-mail: mdeymie@emory.edu [Emory Vaccine Center, Yerkes National Primate Research Center, 954 Gatewood Road NE, Atlanta, GA 30329 (United States); Claiborne, Daniel T., E-mail: dclaibo@emory.edu [Emory Vaccine Center, Yerkes National Primate Research Center, 954 Gatewood Road NE, Atlanta, GA 30329 (United States); Ende, Zachary, E-mail: zende@emory.edu [Emory Vaccine Center, Yerkes National Primate Research Center, 954 Gatewood Road NE, Atlanta, GA 30329 (United States); Ratner, Hannah K., E-mail: hannah.ratner@emory.edu [Emory Vaccine Center, Yerkes National Primate Research Center, 954 Gatewood Road NE, Atlanta, GA 30329 (United States); Kilembe, William, E-mail: wkilembe@rzhrg-mail.org [Zambia-Emory HIV Research Project (ZEHRP), B22/737 Mwembelelo, Emmasdale Post Net 412, P/BagE891, Lusaka (Zambia); Allen, Susan, E-mail: sallen5@emory.edu [Zambia-Emory HIV Research Project (ZEHRP), B22/737 Mwembelelo, Emmasdale Post Net 412, P/BagE891, Lusaka (Zambia); Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA (United States); Hunter, Eric, E-mail: eric.hunter2@emory.edu [Emory Vaccine Center, Yerkes National Primate Research Center, 954 Gatewood Road NE, Atlanta, GA 30329 (United States); Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA (United States)

    2014-11-15

    The high genetic diversity of HIV-1 impedes high throughput, large-scale sequencing and full-length genome cloning by common restriction enzyme based methods. Applying novel methods that employ a high-fidelity polymerase for amplification and an unbiased fusion-based cloning strategy, we have generated several HIV-1 full-length genome infectious molecular clones from an epidemiologically linked transmission pair. These clones represent the transmitted/founder virus and phylogenetically diverse non-transmitted variants from the chronically infected individual's diverse quasispecies near the time of transmission. We demonstrate that, using this approach, PCR-induced mutations in full-length clones derived from their cognate single genome amplicons are rare. Furthermore, all eight non-transmitted genomes tested produced functional virus with a range of infectivities, belying the previous assumption that a majority of circulating viruses in chronic HIV-1 infection are defective. Thus, these methods provide important tools to update protocols in molecular biology that can be universally applied to the study of human viral pathogens. - Highlights: • Our novel methodology demonstrates accurate amplification and cloning of full-length HIV-1 genomes. • A majority of plasma derived HIV variants from a chronically infected individual are infectious. • The transmitted/founder was more infectious than the majority of the variants from the chronically infected donor.

  14. Particle infectivity of HIV-1 full-length genome infectious molecular clones in a subtype C heterosexual transmission pair following high fidelity amplification and unbiased cloning

    International Nuclear Information System (INIS)

    The high genetic diversity of HIV-1 impedes high throughput, large-scale sequencing and full-length genome cloning by common restriction enzyme based methods. Applying novel methods that employ a high-fidelity polymerase for amplification and an unbiased fusion-based cloning strategy, we have generated several HIV-1 full-length genome infectious molecular clones from an epidemiologically linked transmission pair. These clones represent the transmitted/founder virus and phylogenetically diverse non-transmitted variants from the chronically infected individual's diverse quasispecies near the time of transmission. We demonstrate that, using this approach, PCR-induced mutations in full-length clones derived from their cognate single genome amplicons are rare. Furthermore, all eight non-transmitted genomes tested produced functional virus with a range of infectivities, belying the previous assumption that a majority of circulating viruses in chronic HIV-1 infection are defective. Thus, these methods provide important tools to update protocols in molecular biology that can be universally applied to the study of human viral pathogens. - Highlights: • Our novel methodology demonstrates accurate amplification and cloning of full-length HIV-1 genomes. • A majority of plasma derived HIV variants from a chronically infected individual are infectious. • The transmitted/founder was more infectious than the majority of the variants from the chronically infected donor

  15. Cloning and Expression of Highly Pathogenic Avian Influenza Virus Full-Length Nonstructural Gene in Pichia pastoris

    OpenAIRE

    Abubakar, M. B.; I. Aini; Omar, A. R.; Hair-Bejo, M

    2011-01-01

    Avian influenza (AI) is a highly contagious and rapidly evolving pathogen of major concern to the poultry industry and human health. Rapid and accurate detection of avian influenza virus is a necessary tool for control of outbreaks and surveillance. The AI virus A/Chicken/Malaysia/5858/2004 (H5N1) was used as a template to produce DNA clones of the full-length NS1 genes via reverse transcriptase synthesis of cDNA by PCR amplification of the NS1 region. Products were cloned into pCR2.0 TOPO TA...

  16. Animal cloning: advances and prospects

    Directory of Open Access Journals (Sweden)

    Chuaire Lilian

    2004-05-01

    Full Text Available Few recent advances have revolutionized the developmental biology as the animal cloning has. Since the birth of Dolly, the sheep, in 1996, which was the first derived clone of a mature animal, a new scientific era began. It has been characterized by growing demystification that differentiated cells are unalterable entities in its nuclear organization and chromatin structure, and by a better understanding of the mechanisms that regulate the development. Throughout this paper, we will review some of the achievements and limitations of the techniques used, both in therapeutic and in the reproductive cloning, as well as the perspectives that its application allows to glimpse within a close future. At the same time, we will point out some considerations regarding the ethical debate that surrounds such a controversial issue.

  17. Public perceptions of animal cloning

    DEFF Research Database (Denmark)

    Jelsøe, Erling; Vincentsen, Ulla; Andersen, Ida-Elisabeth;

    What was from the outset meant to be a survey testing predefined categories of ethical positions related to new biotechnologies with animal cloning as an example was subsequently developed into a process of broader involvement of groups of citizens in the issue. The survey was conducted at meetings...... in four different cities in Denmark. The participants were introduced to animal cloning and after that they filled out the questionnaire. Finally, the issue was discussed in focus groups. The process as a whole was run in a dialogue oriented way. Through the information they received in combination...... with reflecting on the survey questions the participants were well prepared for discussions in the focus groups. This approach made it possible, on the one hand to get a measure of the citizen's perceptions of the ethical aspects of animal cloning, but also to go deeper into their own thoughts of the issue...

  18. Public perceptions of animal cloning

    DEFF Research Database (Denmark)

    Jelsøe, Erling; Vincentsen, Ulla; Andersen, Ida-Elisabeth;

    What was from the outset meant to be a survey testing predefined categories of ethical positions related to new biotechnologies with animal cloning as an example was subsequently developed into a process of broader involvement of groups of citizens in the issue. The survey was conducted at meetings...... in four different cities in Denmark. The participants were introduced to animal cloning and after that they filled out the questionnaire. Finally, the issue was discussed in focus groups. The process as a whole was run in a dialogue oriented way. Through the information they received in combination...... with reflecting on the survey questions the participants were well prepared for discussions in the focus groups. This approach made it possible, on the one hand to get a measure of the citizen's perceptions of the ethical aspects of animal cloning, but also to go deeper into their own thoughts of the...

  19. Transcripts from a single full-length cDNA clone of hepatitis C virus are infectious when directly transfected into the liver of a chimpanzee

    OpenAIRE

    Yanagi, Masayuki; Purcell, Robert H.; Emerson, Suzanne U.; Bukh, Jens

    1997-01-01

    We have succeeded in constructing a stable full-length cDNA clone of strain H77 (genotype 1a) of hepatitis C virus (HCV). We devised a cassette vector with fixed 5′ and 3′ termini and constructed multiple full-length cDNA clones of H77 in a single step by cloning of the entire ORF, which was amplified by long reverse transcriptase–PCR, directly into this vector. The infectivity of two complete full-length cDNA clones was tested by the direct intrahepatic injection of a chimpanzee with RNA tra...

  20. Phage display used for gene cloning of human recombinant antibody against the erythrocyte surface antigen, rhesus D

    DEFF Research Database (Denmark)

    Dziegiel, Morten Hanefeld; Nielsen, L K; Andersen, P S;

    1995-01-01

    A novel phage display system has been developed for PCR amplification and cloning of the Fab fragments of human immunoglobulin genes. Using this system, we have cloned an antibody from a mouse-human hybridoma cell line directed against the erythrocyte antigen rhesus D. Intact erythrocytes were used...... for absorption of the Fab phages. Soluble Fab fragments produced from the cloned material showed identical performance to the parental antibody in agglutination assays. Gel filtration confirmed that the Fab fragment consists of a kappa-Fd heterodimer. The successful use of intact cells for selection of specific...

  1. [Cloning alphavirus and flavivirus sequences for use as positive controls in molecular diagnostics].

    Science.gov (United States)

    Camacho, Daría; Reyes, Jesús; Franco, Leticia; Comach, Guillermo; Ferrer, Elizabeth

    2016-06-01

    The purpose of the study was to obtain a positive control to validate molecular techniques (reverse transcription- polymerase chain reaction [RT-PCR]) used in the diagnosis and research of viral infections. From strains of Chikungunya virus (CHIKV), Zika virus, and Dengue virus (DENV-1, DENV-2, DENV- 3, and DENV-4) viral RNAs were extracted to obtain complementary DNA using RT-PCR from the nsP4 (CHIKV), NS5 (Zika virus), C/prM-M, and 5'UTR-C (DENV-1, DENV-2, DENV-3, DENV-4) sequences, which were cloned into pGEM®-T Easy. Cloning was confirmed through colony PCR, from which plasmid DNA was extracted for fragment cloning verification. Cloning of cDNA corresponding to nsP4, NS5, C/prM-M, and 5'UTR-C of the different viral agents was achieved. In conclusion, recombinant plasmids were obtained with each of the sequences specified for further assessment as positive controls in molecular techniques in an effort to avoid the use of cell cultures, which can be costly, time-consuming, and potentially dangerous.

  2. [Cloning alphavirus and flavivirus sequences for use as positive controls in molecular diagnostics].

    Science.gov (United States)

    Camacho, Daría; Reyes, Jesús; Franco, Leticia; Comach, Guillermo; Ferrer, Elizabeth

    2016-06-01

    The purpose of the study was to obtain a positive control to validate molecular techniques (reverse transcription- polymerase chain reaction [RT-PCR]) used in the diagnosis and research of viral infections. From strains of Chikungunya virus (CHIKV), Zika virus, and Dengue virus (DENV-1, DENV-2, DENV- 3, and DENV-4) viral RNAs were extracted to obtain complementary DNA using RT-PCR from the nsP4 (CHIKV), NS5 (Zika virus), C/prM-M, and 5'UTR-C (DENV-1, DENV-2, DENV-3, DENV-4) sequences, which were cloned into pGEM®-T Easy. Cloning was confirmed through colony PCR, from which plasmid DNA was extracted for fragment cloning verification. Cloning of cDNA corresponding to nsP4, NS5, C/prM-M, and 5'UTR-C of the different viral agents was achieved. In conclusion, recombinant plasmids were obtained with each of the sequences specified for further assessment as positive controls in molecular techniques in an effort to avoid the use of cell cultures, which can be costly, time-consuming, and potentially dangerous. PMID:27656926

  3. A Bac Library and Paired-PCR Approach to Mapping and Completing the Genome Sequence of Sulfolobus Solfataricus P2

    DEFF Research Database (Denmark)

    She, Qunxin; Confalonieri, F.; Zivanovic, Y.;

    2000-01-01

    screening. The PCR approaches included a novel chromosome walking method termed “paired-PCR”. 21 gaps were filled by BAC end sequence analyses and 6 gaps were filled by PCR including three large ones by paired-PCR. The complete map revealed that 0.9 Mb remained to be sequenced and 34 BAC clones were......The original strategy used in the Sulfolobus solfatnricus genome project was to sequence non overlapping, or minimally overlapping, cosmid or lambda inserts without constructing a physical map. However, after only about two thirds of the genome sequence was completed, this approach became counter......-productive because there was a high sequence bias in the cosmid and lambda libraries. Therefore, a new approach was devised for linking the sequenced regions which may be generally applicable. BAC libraries were constructed and terminal sequences of the clones were determined and used for both end mapping and PCR...

  4. One-step generation of error-prone PCR libraries using Gateway® technology

    Directory of Open Access Journals (Sweden)

    Gruet Antoine

    2012-01-01

    Full Text Available Abstract Background Error-prone PCR (epPCR libraries are one of the tools used in directed evolution. The Gateway® technology allows constructing epPCR libraries virtually devoid of any background (i.e., of insert-free plasmid, but requires two steps: the BP and the LR reactions and the associated E. coli cell transformations and plasmid purifications. Results We describe a method for making epPCR libraries in Gateway® plasmids using an LR reaction without intermediate BP reaction. We also describe a BP-free and LR-free sub-cloning method for in-frame transferring the coding sequence of selected clones from the plasmid used to screen the library to another one devoid of tag used for screening (such as the green fluorescent protein. We report preliminary results of a directed evolution program using this method. Conclusions The one-step method enables producing epPCR libraries of as high complexity and quality as does the regular, two-step, protocol for half the amount of work. In addition, it contributes to preserve the original complexity of the epPCR product.

  5. Biological activity evaluation of cloned and expressed caprine growth hormone from local Pakistani goat breed beetal

    International Nuclear Information System (INIS)

    Growth hormone cDNA of local goat breed-beetal was amplified by RT PCR and gene including leader sequence was cloned in pTZR57 cloning vector. The cGH-pTZR57 clone was confirmed by restriction digestion and sequence analyses before finally sub-cloning the gene in pND- a mammalian expression vector. The clones were again confirmed by restriction digestion and PCR analyses. Highly purified, supercoiled cGH-pND construct was used to transfect Vero cell lines for expression studies. The in vitro expression of cGH was checked by dot-ELISA technique. After confirming its in vitro cell line based expression, the construct was injected to 4 weeks old balb/c mice intramuscularly. Two animals were euthanized per week till four weeks to monitor the in vivo biological activity by evaluating the tibia epiphyseal width and body weight gain assays. Significant increase in tibia epiphyseal width and gain in body weight was observed from vaccinated animals. The study supports the concept that DNA based therapeutics are an efficient and cost effective method for gene delivery and in vivo transgene expressions. (author)

  6. Symmetrical directional cloning:An efficient method to prepare hairpin RNA interference constructs

    Institute of Scientific and Technical Information of China (English)

    ZHANG Zhonglin; Everett COOK; ZHAO Huayan; SONG Yanru; Qingxi J. SHEN

    2004-01-01

    RNA interference (RNAi) is a loss-of-function approach by which double-stranded RNA (dsRNA) initiates degradation of homologous mRNAs in a sequence specific manner. The dsRNA molecules can be produced in vitro or in vivo, and can be introduced to cells in a number of ways. Here we report a more efficient method for the cloning of inverted repeat DNA fragments into expression vectors that can be transcribed into effective dsRNA molecules in vivo or in vitro. This method, named Symmetrical Directional Cloning (SDC), takes the advantage of compatible non-palindromic restriction enezyme sites, which allow one to directionally clone a single PCR product in both the sense and antisense orientations together into a vector. SDC allows for the directional cloning of inverted repeats using a single PCR product; it requires only one cut site on each side of the loop. Hence this method is more cost effective and less time-consuming. At least 21 commercially available restriction endonucleases can be used as cloning sites for the SDC method. The efficacy of dsRNA expression vectors prepared by SDC has been demonstrated by targeting a negative regulator of the signaling pathway mediating the response of cells to phytohormone, gibberellins (GA), in the aleurone cells.

  7. Quantum cloning machines and the applications

    Energy Technology Data Exchange (ETDEWEB)

    Fan, Heng, E-mail: hfan@iphy.ac.cn [Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China); Collaborative Innovation Center of Quantum Matter, Beijing 100190 (China); Wang, Yi-Nan; Jing, Li [School of Physics, Peking University, Beijing 100871 (China); Yue, Jie-Dong [Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China); Shi, Han-Duo; Zhang, Yong-Liang; Mu, Liang-Zhu [School of Physics, Peking University, Beijing 100871 (China)

    2014-11-20

    No-cloning theorem is fundamental for quantum mechanics and for quantum information science that states an unknown quantum state cannot be cloned perfectly. However, we can try to clone a quantum state approximately with the optimal fidelity, or instead, we can try to clone it perfectly with the largest probability. Thus various quantum cloning machines have been designed for different quantum information protocols. Specifically, quantum cloning machines can be designed to analyze the security of quantum key distribution protocols such as BB84 protocol, six-state protocol, B92 protocol and their generalizations. Some well-known quantum cloning machines include universal quantum cloning machine, phase-covariant cloning machine, the asymmetric quantum cloning machine and the probabilistic quantum cloning machine. In the past years, much progress has been made in studying quantum cloning machines and their applications and implementations, both theoretically and experimentally. In this review, we will give a complete description of those important developments about quantum cloning and some related topics. On the other hand, this review is self-consistent, and in particular, we try to present some detailed formulations so that further study can be taken based on those results.

  8. Positional cloning of deafness genes

    NARCIS (Netherlands)

    Kremer, H.; Cremers, F.P.M.

    2009-01-01

    The identification of the majority of the known causative genes involved in nonsyndromic sensorineural hearing loss (NSHL) started with linkage analysis as part of a positional cloning procedure. The human and mouse genome projects in combination with technical developments on genotyping, transcript

  9. EasyClone-MarkerFree

    DEFF Research Database (Denmark)

    Fabre, Mathew Malcolm Jessop; Jakociunas, Tadas; Stovicek, Vratislav;

    2016-01-01

    Clone-MarkerFree. The integration of linearized expression cassettes into defined genomic loci is facilitated by CRISPR/Cas9. Cas9 is recruited to the chromosomal location by specific guide RNAs (gRNAs) expressed from a set of gRNA helper vectors. Using our genome engineering vector suite, single and triple insertions are obtained...

  10. Clone Poems and the Microcomputer.

    Science.gov (United States)

    Irizarry, Estelle

    1989-01-01

    Describes how students can use the computer to study and create clone poems (altering original Spanish-language poems by substituting words and expressions), and how students can gain a deeper appreciation of the original poem's poetic structure and semantics. (CB)

  11. Expression of chromatin modification genes in organs of cloned cattle that died within hours after birth

    Institute of Scientific and Technical Information of China (English)

    LI Shijie; LIAN Zhengxing; LI Dongjie; YU Shuyang; ZHANG Lei; DAI Yunping; LI Rong; FEI Jing; LI Ning

    2006-01-01

    Cloning by somatic nuclear transfer is an inefficient process in which many of the cloned animals died shortly after birth and displayed organ abnormalities. In an effort to determine the possible genetic causes of neonatal death and organ abnormalities, we have examined expression patterns of four genes that modified chromatin (DNMT1, PCAF,MeCP2 and EED) in six organs (heart, liver, spleen, lung, kidney and brain) of both neonatal death cloned bovines (n=9) and normal control calves produced by artificial insemination (AI) using real-time quantitative RT-PCR. The effect of the age of the fibroblast donor cell on the gene expression profiles was also investigated. Aberrant expressions of DNMT1 and PCAF were found in some studied tissues, but the expression of MeCP2 and EED had similar levels to those of the normal controls. The expression of DNMT1 showed a higher level in heart, liver and brain of both cloned bovines. A higher expression level of PCAF was seen in heart and liver of both cloned bovines, but a lower level was seen only in spleen of adult fibroblast (AF) cell-derived clones. Our results suggest that aberrant expression in gene that modified chromatins were found in cloned bovine tissues of neonatal death. Because DNMT1 and PCAF play an important role in DNA methylation and histone acetylation on nuclear chromatin respectively, and normal expression of DNMT1 and PCAF is needed for precious reprogramming of donor nuclear, the aberrant transcription patterns of DNMT1 and PCAF in these clones 5 contribute to the defects of organs reported in neonatal death of clones.

  12. Cloning and sequencing of the ferredoxin gene of blue-green alga Anabaena siamensis

    Science.gov (United States)

    Li, Shou-Dong; Song, Li-Rong; Liu, Yong-Ding; Zhao, Jin-Dong

    1998-03-01

    The structure gene for ferredoxin, petFI, from Anabaena siamensis has been amplified by polymerase chain reaction(PCR) and cloned into cloning vector pGEM-3zf(+). The nucleotide sequence of petFI has been determined with silver staining sequencing method. There is 96.8% homology between coding region of petFI from A. siamensis and that of petFI from A. sp. 7120. Amino acid sequences of seven strains of blue-green algae are compared.

  13. Human cloning in film: horror, ambivalence, hope

    OpenAIRE

    O'Riordan, Kate

    2008-01-01

    Fictional filmic representations of human cloning have shifted in relation to the 1997 announcement of the birth of Dolly the cloned sheep, and since therapeutic human cloning became a scientific practice in the early twentieth century. The operation and detail of these shifts can be seen through an analysis of the films The Island (2005) and Aeon Flux (2005). These films provide a site for the examination of how these changes in human cloning from fiction to practice, and from horror to hope...

  14. ETHICAL PROBLEMS OF CLONING HUMANS (SCNT)

    OpenAIRE

    SAVVINA O.V.

    2015-01-01

    The article analyses ethical problems of cloning of human beings. Today scientists have opportunity to clone animals and human embryos by somatic cell nuclear transfer (SCNT), and the author considers this technology and ethical problems generated by it. The author maintains that we must divide two types of cloning of human beings: therapeutic and reproductive. The therapeutic cloning does not generate any new ethical problems or dilemmas, but it exacerbates the problems which have already ex...

  15. Mice cloned from embryonic stem cells

    OpenAIRE

    Wakayama, Teruhiko; Rodriguez, Ivan; Perry, Anthony C F; Yanagimachi, Ryuzo; Mombaerts, Peter

    1999-01-01

    Cloning allows the asexual reproduction of selected individuals such that the offspring have an essentially identical nuclear genome. Cloning by nuclear transfer thus far has been reported only with freshly isolated cells and cells from primary cultures. We previously reported a method of cloning mice from adult somatic cells after nuclear transfer by microinjection. Here, we apply this method to clone mice from widely available, established embryonic stem (ES) cell ...

  16. Genome modifications and cloning using a conjugally transferable recombineering system

    Directory of Open Access Journals (Sweden)

    Mohammad J Hossain

    2015-12-01

    Full Text Available The genetic modification of primary bacterial disease isolates is challenging due to the lack of highly efficient genetic tools. Herein we describe the development of a modified PCR-based, λ Red-mediated recombineering system for efficient deletion of genes in Gram-negative bacteria. A series of conjugally transferrable plasmids were constructed by cloning an oriT sequence and different antibiotic resistance genes into recombinogenic plasmid pKD46. Using this system we deleted ten different genes from the genomes of Edwardsiella ictaluri and Aeromonas hydrophila. A temperature sensitive and conjugally transferable flp recombinase plasmid was developed to generate markerless gene deletion mutants. We also developed an efficient cloning system to capture larger bacterial genetic elements and clone them into a conjugally transferrable plasmid for facile transferring to Gram-negative bacteria. This system should be applicable in diverse Gram-negative bacteria to modify and complement genomic elements in bacteria that cannot be manipulated using available genetic tools.

  17. Development and comparison of a real-time PCR assay for detection of Dichelobacter nodosus with culturing and conventional PCR: harmonisation between three laboratories

    DEFF Research Database (Denmark)

    Frosth, Sara; Slettemeås, Jannice S.; Jørgensen, Hannah J.;

    2012-01-01

    is fundamental to diagnosis of footrot, but D. nodosus should also be detected to confirm the diagnosis. PCR-based detection using conventional PCR has been used at our institutes, but the method was laborious and there was a need for a faster, easier-to-interpret method. The aim of this study was to develop...... a TaqMan-based real-time PCR assay for detection of D. nodosus and to compare its performance with culturing and conventional PCR. METHODS: A D. nodosus-specific TaqMan based real-time PCR assay targeting the 16S rRNA gene was designed. The inclusivity and exclusivity (specificity) of the assay...... samples, and to a conventional PCR method by analysing 224 samples. A selection of PCR-products was cloned and sequenced in order to verify that they had been identified correctly. RESULTS: The developed assay had a detection limit of 3.9 fg of D. nodosus genomic DNA. This result was obtained at all three...

  18. A General Duality Theory for Clones

    OpenAIRE

    Kerkhoff, Sebastian

    2011-01-01

    In this thesis, we generalize clones (as well as their relational counterparts and the relationship between them) to categories. Based on this framework, we introduce a general duality theory for clones and apply it to obtain new results for clones on finite sets.

  19. EVALUATION OF Eucalyptus CLONES FOR CHARCOAL PRODUCTION

    Directory of Open Access Journals (Sweden)

    Paulo Fernando Trugilho

    2001-01-01

    Full Text Available Charcoal is economically representative in the Brazilian economy, specially in Minas Gerais, the main producer, and consumer of this product. A problem related to the charcoal utilization is its heterogeneous quality, which is influenced both for the wood and the production process. This variability causes waste of material and make it difficult to handle the blast furnaces. The objective of this work was to evaluate the wood of ten clones: seven of Eucalyptus grandis and three of Eucalyptus saligna: both directed to charcoal production. Also, it was looked for to select clones with highercapacity for the establishment of a forestry improvement program. During the assessment it was considered the quantitative and qualitative characteristics of the charcoal. According to the results it was verified that there exists a large variation among the assessed clones, which is higher in Eucalyptus grandis. The production of dry mass, associated to the estimation of mass of both lignin and charcoal proportionate a classification of the clones considered as the superior (clones number five, six and two, median (clones number ten, three, one and eight and inferior (clones number nine, four and seven. Clone seven was the worsen for the charcoal production due to its low growth rate. The classification of the clones based on both the wood chemical characteristics and charcoal yield was not satisfactory. The growth rate was fundamental for the clones classification, being recommendable to incorporate it in future assessment of wood quality. Eucalyptus grandis clones were superior to Eucalyptus saligna clones.

  20. No-cloning theorem in thermofield dynamics

    CERN Document Server

    Prudencio, Thiago

    2011-01-01

    Here we apply the no-cloning theorem from quantum information in the thermofield dynamics (TFD) scenario, relating the doubling procedure of TFD to a cloning machine process. As a consequence we use the no-cloning theorem to demonstrate that the thermal vaccuum state defined in TFD is necessarilly a mixed state.

  1. Cloning and expression of human colon mast cell carboxypeptidase

    Institute of Scientific and Technical Information of China (English)

    Zhang-Quan Chen; Shao-Heng He

    2004-01-01

    AIM: To clone and express the human colon mast cell METHODS: Total RNA was extracted from colon tissue, and the cDNA encoding human colon mast cell carboxypeptidase was amplified by reverse-transcription PCR (RT-PCR). The product cDNA was subcloned into the prokaryotic expression vector pMAL-c2x and eukaryotic expression vector pPIC9K to conrtruct prokaryotic expression vector pMAL/human MC-CP (hMC-CP) and eukaryotic pPIC9K/hMC-CP. The recombinant fusion protein expressed in E.coli was induced with IPTG and purified by amylose affinity chromatography. After digestion with factor Xa, recombinant hMC-CP was purified by heparin agarose chromatography. The recombinant hMC-CP expressed in Pichia pastoris (P.pastoris) was induced with methanol and analyzed by SDS-PAGE, Western blot, N-terminal amino acid RESULTS: The cDNA encoding the human colon mast cell carboxypeptidase was cloned, which had five nucleotide variations compared with skin MC-CP cDNA. The recombinant hMC-CP protein expressed in E.coli was purified with amylose affinity chromatography and heparin agarose chromatogphy.SDS-PAGE and Western blot analysis showed that the recombinant protein expressed by E. coli had a molecular weight of 36 kDa and reacted to the anti-native hMC-CP monoclonal antibody (CA5). The N-terminal amino acid sequence confirmed further the product was hMC-CP. E. coli generated hMC-CP showed a very low level of enzymatic activity, but P. pastoris produced hMC-CP had a relatively high enzymatic activity towards a synthetic substrate hippuryl-L-phenylalanine.carboxypeptidase can be successfully cloned and expressed in E.coli and P. pastoris, which will contribute greatly to the fonctional study on hMC-CP.

  2. PCR for diagnosis of male Trichomonas vaginalis infection with chronic prostatitis and urethritis.

    Science.gov (United States)

    Lee, Jong Jin; Moon, Hong Sang; Lee, Tchun Yong; Hwang, Hwan Sik; Ahn, Myoung-Hee; Ryu, Jae-Sook

    2012-06-01

    The aim of this study was to assess the usefulness of PCR for diagnosis of Trichomonas vaginalis infection among male patients with chronic recurrent prostatitis and urethritis. Between June 2001 and December 2003, a total of 33 patients visited the Department of Urology, Hanyang University Guri Hospital and were examined for T. vaginalis infection by PCR and culture in TYM medium. For the PCR, we used primers based on a repetitive sequence cloned from T. vaginalis (TV-E650). Voided bladder urine (VB1 and VB3) was sampled from 33 men with symptoms of lower urinary tract infection (urethral charge, residual urine sensation, and frequency). Culture failed to detect any T. vaginalis infection whereas PCR identified 7 cases of trichomoniasis (21.2%). Five of the 7 cases had been diagnosed with prostatitis and 2 with urethritis. PCR for the 5 prostatitis cases yielded a positive 330 bp band from bothVB1 and VB3, whereas positive results were only obtained from VB1 for the 2 urethritis patients. We showed that the PCR method could detect T. vaginalis when there was only 1 T. vaginalis cell per PCR mixture. Our results strongly support the usefulness of PCR on urine samples for detecting T. vaginalis in chronic prostatitis and urethritis patients.

  3. Simple and versatile molecular method of copy-number measurement using cloned competitors.

    Science.gov (United States)

    Kim, Hyun-Kyoung; Hwang, Hai-Li; Park, Seong-Yeol; Lee, Kwang Man; Park, Won Cheol; Kim, Han-Seong; Um, Tae-Hyun; Hong, Young Jun; Lee, Jin Kyung; Joo, Sun-Young; Seoh, Ju-Young; Song, Yeong-Wook; Kim, Soo-Youl; Kim, Yong-Nyun; Hong, Kyeong-Man

    2013-01-01

    Variations and alterations of copy numbers (CNVs and CNAs) carry disease susceptibility and drug responsiveness implications. Although there are many molecular methods to measure copy numbers, sensitivity, reproducibility, cost, and time issues remain. In the present study, we were able to solve those problems utilizing our modified real competitive PCR method with cloned competitors (mrcPCR). First, the mrcPCR for ERBB2 copy number was established, and the results were comparable to current standard methods but with a shorter assay time and a lower cost. Second, the mrcPCR assays for 24 drug-target genes were established, and the results in a panel of NCI-60 cells were comparable to those from real-time PCR and microarray. Third, the mrcPCR results for FCGR3A and the FCGR3B CNVs were comparable to those by the paralog ratio test (PRT), but without PRT's limitations. These results suggest that mrcPCR is comparable to the currently available standard or the most sensitive methods. In addition, mrcPCR would be invaluable for measurement of CNVs in genes with variants of similar structures, because combination of the other methods is not necessary, along with its other advantages such as short assay time, small sample amount requirement, and applicability to all sequences and genes.

  4. Heterogeneity of clones from a human metastatic melanoma detected by autologous cytotoxic T lymphocyte clones

    OpenAIRE

    1986-01-01

    The possibility that a single human tumor may be composed of an heterogeneous population of cells with respect to susceptibility to lysis by autologous CTL clones was investigated by testing six cytolytic clones derived by micromanipulation against the autologous metastatic melanoma, Me28, and against 31 clones derived from Me28 by cloning in soft agar. Highly significant differences in the lysis of many tumor clones were observed by three of the CTL effectors in comparison with the cytotoxic...

  5. Cloning, sequencing and expression of cDNA encoding growth hormone from Indian catfish (Heteropneustes fossilis)

    Indian Academy of Sciences (India)

    Vikas Anathy; Thayanithy Venugopal; Ramanathan Koteeswaran; Thavamani J Pandian; Sinnakaruppan Mathavan

    2001-09-01

    A tissue-specific cDNA library was constructed using polyA+ RNA from pituitary glands of the Indian catfish Heteropneustes fossilis (Bloch) and a cDNA clone encoding growth hormone (GH) was isolated. Using polymerase chain reaction (PCR) primers representing the conserved regions of fish GH sequences the 3′ region of catfish GH cDNA (540 bp) was cloned by random amplification of cDNA ends and the clone was used as a probe to isolate recombinant phages carrying the full-length cDNA sequence. The full-length cDNA clone is 1132 bp in length, coding for an open reading frame (ORF) of 603 bp; the reading frame encodes a putative polypeptide of 200 amino acids including the signal sequence of 22 amino acids. The 5′ and 3′ untranslated regions of the cDNA are 58 bp and 456 bp long, respectively. The predicted amino acid sequence of H. fossils GH shared 98% homology with other catfishes. Mature GH protein was efficiently expressed in bacterial and zebrafish systems using appropriate expression vectors. The successful expression of the cloned GH cDNA of catfish confirms the functional viability of the clone.

  6. Cloning, sequencing and expression of cDNA encoding growth hormone from Indian catfish (Heteropneustes fossilis)

    Indian Academy of Sciences (India)

    Vikas Anathy; Thayanithy Venugopal; Ramanathan Koteeswaran; Thavamani J Pandian; Sinnakaruppan Mathavan

    2013-03-01

    A tissue-specific cDNA library was constructed using polyA+ RNA from pituitary glands of the Indian catfish Heteropneustes fossilis (Bloch) and a cDNA clone encoding growth hormone (GH) was isolated. Using polymerase chain reaction (PCR) primers representing the conserved regions of fish GH sequences the 3′ region of catfish GH cDNA (540 bp) was cloned by random amplification of cDNA ends and the clone was used as a probe to isolate recombinant phages carrying the full-length cDNA sequence. The full-length cDNA clone is 1132 bp in length, coding for an open reading frame (ORF) of 603 bp; the reading frame encodes a putative polypeptide of 200 amino acids including the signal sequence of 22 amino acids. The 5′ and 3′ untranslated regions of the cDNA are 58 bp and 456 bp long, respectively. The predicted amino acid sequence of H. fossils GH shared 98% homology with other catfishes. Mature GH protein was efficiently expressed in bacterial and zebrafish systems using appropriate expression vectors. The successful expression of the cloned GH cDNA of catfish confirms the functional viability of the clone.

  7. Single primer-mediated circular polymerase chain reaction for hairpin DNA cloning and plasmid editing.

    Science.gov (United States)

    Huang, Jiansheng; Khan, Inamullah; Liu, Rui; Yang, Yan; Zhu, Naishuo

    2016-05-01

    We developed and validated a universal polymerase chain reaction (PCR) method, single primer circular (SPC)-PCR, using single primer to simultaneously insert and amplify a short hairpin sequence into a vector with a high success rate. In this method, the hairpin structure is divided into two parts and fused into a vector by PCR. Then, a single primer is used to cyclize the chimera into a mature short hairpin RNA (shRNA) expression vector. It is not biased by loop length or palindromic structures. Six hairpin DNAs with short 4-nucleotide loops were successfully cloned. Moreover, SPC-PCR was also applied to plasmid editing within 3 h with a success rate higher than 95%. PMID:26792375

  8. Single primer-mediated circular polymerase chain reaction for hairpin DNA cloning and plasmid editing.

    Science.gov (United States)

    Huang, Jiansheng; Khan, Inamullah; Liu, Rui; Yang, Yan; Zhu, Naishuo

    2016-05-01

    We developed and validated a universal polymerase chain reaction (PCR) method, single primer circular (SPC)-PCR, using single primer to simultaneously insert and amplify a short hairpin sequence into a vector with a high success rate. In this method, the hairpin structure is divided into two parts and fused into a vector by PCR. Then, a single primer is used to cyclize the chimera into a mature short hairpin RNA (shRNA) expression vector. It is not biased by loop length or palindromic structures. Six hairpin DNAs with short 4-nucleotide loops were successfully cloned. Moreover, SPC-PCR was also applied to plasmid editing within 3 h with a success rate higher than 95%.

  9. Combined subtractive cDNA cloning and array CGH: an efficient approach for identification of overexpressed genes in DNA amplicons

    Directory of Open Access Journals (Sweden)

    De Paepe Anne

    2004-02-01

    Full Text Available Abstract Background Activation of proto-oncogenes by DNA amplification is an important mechanism in the development and maintenance of cancer cells. Until recently, identification of the targeted genes relied on labour intensive and time consuming positional cloning methods. In this study, we outline a straightforward and efficient strategy for fast and comprehensive cloning of amplified and overexpressed genes. Results As a proof of principle, we analyzed neuroblastoma cell line IMR-32, with at least two amplification sites along the short arm of chromosome 2. In a first step, overexpressed cDNA clones were isolated using a PCR based subtractive cloning method. Subsequent deposition of these clones on a custom microarray and hybridization with IMR-32 DNA, resulted in the identification of clones that were overexpressed due to gene amplification. Using this approach, amplification of all previously reported amplified genes in this cell line was detected. Furthermore, four additional clones were found to be amplified, including the TEM8 gene on 2p13.3, two anonymous transcripts, and a fusion transcript, resulting from 2p13.3 and 2p24.3 fused sequences. Conclusions The combinatorial strategy of subtractive cDNA cloning and array CGH analysis allows comprehensive amplicon dissection, which opens perspectives for improved identification of hitherto unknown targeted oncogenes in cancer cells.

  10. Large intervals in the clone lattice

    OpenAIRE

    Goldstern, Martin; Shelah, Saharon

    2002-01-01

    We give three examples of large intervals in the lattice of (local) clones on an infinite set X, by exhibiting clones C_1, C_2, C_3 such that: (1) the interval [C_1, O] in the lattice of local clones is (as a lattice) isomorphic to {0,1,2, ...} under the divisibility relation, (2) the interval [C_2, O] in the lattice of local clones is isomorphic to the congruence lattice of an arbitrary semilattice, (3) the interval [C_3, O] in the lattice of all clones is isomorphic to the lattice of all fi...

  11. No-cloning theorem on quantum logics

    Science.gov (United States)

    Miyadera, Takayuki; Imai, Hideki

    2009-10-01

    This paper discusses the no-cloning theorem in a logicoalgebraic approach. In this approach, an orthoalgebra is considered as a general structure for propositions in a physical theory. We proved that an orthoalgebra admits cloning operation if and only if it is a Boolean algebra. That is, only classical theory admits the cloning of states. If unsharp propositions are to be included in the theory, then a notion of effect algebra is considered. We proved that an atomic Archimedean effect algebra admitting cloning operation is a Boolean algebra. This paper also presents a partial result, indicating a relation between the cloning on effect algebras and hidden variables.

  12. RAPID SCREENING OF AN ARRAYED cDNA LIBRARY BY IMPROVED PCR-BASED METHOD

    Institute of Scientific and Technical Information of China (English)

    杜光伟; 潘美辉; 袁建刚; 周彦; 强伯勤; 梁植权

    1998-01-01

    Tbe present study reports an improved PCR-based technique that allows quick and effecfive screening of eDNA libraries. First, the eDNA library was arrayed as follows: about 3×106 cDNA clones were multiplied as individual plsques on solid medium in 24-well culture dishes at 1 200 plaque forming units per well.The phage suspension of each well was transferred to an individual micrccentrifuge tube in 72-tube box. Then,box pool, row pools and column pools were set up that respectively represent a 72-tube box,rows and columns within the box. To screen a specific target cDNA,primers specific for novel ESTs obtained in our laboratory were eznployed to conduct PCR in a fiierarchy mode. PCR began with the box pools, resulting in the identification of some positive box pools. Then PCR went down to the row and column pools of the positive box. Tbe intersection of the positive row(s) and column(s) revealed the candidate positive tubes. The specificity of PCR products were meanwhile checked hy restriction enzyme digestion. Finally, hybridization was carried out to get single specific eDNA clones-from the positive tlabes. This PCR-hased technique features high specificity, high efficiency and Les-cost in large-scale cDNA library screening. Our initial implementation of the technique resulted in the isolation of three longer different cDNA clones from a hnman fetal brain eDNA library. Thus this improved technique can serve as an alternative to the time-consuming and laborious conventional hybridization-hased metfiod for screening cDNA library.

  13. Application of restriction display PCR technique in the preparation of cDNA microarray probes

    Institute of Scientific and Technical Information of China (English)

    Zhao-Hui Sun; Wen-Li Ma; Bao Zhang; Yi-Fei Peng; Wen-Ling Zheng

    2005-01-01

    AIM: To develop a simplified and efficient method for the preparation of hepatitis C virus (HCV) cDNA microarray probes.METHODS: With the technique of restriction display PCR (RD-PCR), restriction enzyme Sau3A I was chosen to digest the full-length HCV cDNAs. The products were classified and re-amplified by RD-PCR. We separated the differential genes by polyacrylamide gel electrophoresis and silver staining. Single bands cut out from the polyacrylamide gel were isolated. The third-round PCR was performed using the single bands as PCR template.The RD-PCR fragments were purified and cloned into the pMD18-T vector. The recombinant plasmids were extracted from positive clones, and the target gene fragments were sequenced. The cDNA microarray was prepared by spotting RD-PCR products to the surface of amino-modified glass slides using a robot. We validated the detection of microarray by hybridization and sequence analysis.RESULTS: A total of 24 different cDNA fragments ranging from 200 to 800 bp were isolated and sequenced,which were the specific gene fragments of HCV. These fragments could be further used as probes in microarray preparation. The diagnostic capability of the microarray was evaluated after the washing and scanning steps. The results of hybridization and sequence analysis showed that the specificity, sensitivity, accuracy, reproducibility,and linearity in detecting HCV RNA were satisfactory.CONCLUSION: The RD-PCR technique is of great value in obtaining a large number of size-comparable gene probes, which provides a speedy protocol in generating probes for the preparation of microarrays. Microarray prepared as such could be further optimized and applied in the clinical diagnosis of HCV.

  14. A real-time PCR assay for the specific identification of serotype O : 9 of Yersinia enterocolitica

    DEFF Research Database (Denmark)

    Jacobsen, N.R.; Bogdanovich, T.; Skurnik, M.;

    2005-01-01

    A real-time PCR assay was developed based on a 18 1 -bp fragment of the recently cloned per gene, including an internal amplification control (124 bp), for the detection of Yersinia enterocolitica 0:9 (Ye 0:9). The validation included 48 Ye 0:9, 33 Y enterocolitica non-0:9 and 35 other closely...

  15. Underestimation of ammonia-oxidizing bacteria abundance by amplification bias in amoA-targeted qPCR

    DEFF Research Database (Denmark)

    Dechesne, Arnaud; Musovic, Sanin; Palomo, Alejandro;

    2016-01-01

    quantitative PCR methods to enumerate ammonia-oxidizing bacteria (AOB): one targeting the phylogenetic gene 16S rRNA and the other, the functional gene amoA. Cloning-sequencing with both primer sets on DNA from two waterworks revealed contrasting images of AOB diversity. The amoA-based approach preferentially...

  16. Conotoxins Are Purified and Cloned

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    @@ A group of CAS scientists have succeeded in purifying many conotoxins and cloning more than 100 new genes from six species of cone snails living in waters off the coast of the South China Sea, paving the way for the development of new drugs to relieve neuropathic pains. The work has been honored with a first prize from the 2005 Awards for S&T Progress in Shanghai.

  17. Rice's Salt Tolerance Gene Cloned

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    @@ In cooperation with US colleagues, CAS researchers have made significant progress in their studies into functional genes for key agronomic traits by cloning SKC1, a salt-tolerant functional gene of rice and making clear its biological functions and mechanisms. This pioneering work,which was reported in the Oct. issue of Nature Genetics (37:1141-1146), is believed to hold promise to increase the output of the crop plant in this country.

  18. Cloning of Thermostable DNA Polymerase Gene from a Thermophilic Brevibacillus sp. Isolated from Sikidang Crater, Dieng Plateu, Central Java

    Directory of Open Access Journals (Sweden)

    Lucia Dhiantika Witasari

    2015-11-01

    Full Text Available Thermostable DNA polymerase has an important role for amplifying small amount of DNA through polymerase chain reaction (PCR. Thermophillic bacteria Brevibacillus sp. was isolated from Sikidang Crater, Dieng Plateu, Central Java. Previous study showed that crude protein of the isolate could be used in PCR. Unfortunately, like most native thermostable enzymes, the thermostable DNA polymerase of the isolate is synthesized in a very low level and therefore is cumbersome to purify. The purpose of this research is to clone thermostable DNA polymerase gene of the isolate. The DNA polymerase gene was amplified by means of PCR using spesific primers. The amplified fragment was then isolated, purified, and ligated into the pGEM-T cloning vector. The recombinant plasmid was then transformed to competent E. coli JM109 cells using heat shock method. The cloned thermostable DNA polymerase gene from the thermophilic isolate was then characterized for its nucleotide base sequence. The result showed that the DNA Pol I gene was successfully be amplified from the isolate DNA genom, resulting in ± 2,7 kb DNA fragment in length. Sequence analysis of segment of targeted gene showed high similarity to that of thermostable DNA polymerase genes from other Bacillus.Key words : Thermostable DNA Pol I, Brevibacillus sp., PCR, cloning

  19. Cloning and sequencing of protein L-isoaspartyl O-methyl transferase of Salmonella Typhimurium isolated from poultry

    Directory of Open Access Journals (Sweden)

    S. K. Dixit

    2014-09-01

    Full Text Available Aim: To clone the Salmonella Typhimurium protein L-isoaspartyl O-methyl transferase (PIMT enzyme and to analyze the sequence with PIMT gene of other pathogenic serovars of Salmonella. Materials and Methods: Salmonella Typhimurium strain E-2375 was procured from the National Salmonella Center, IVRI. The genomic DNA was isolated from Salmonella Typhimurium. Polymerase chain reaction (PCR was carried out to amplify PIMT gene using the designed primers. The PCR product was cloned into pET28c plasmid vector and transformed into Escherichia coli DH5α cells. The plasmid was isolated from E. coli and was sequenced. The sequence was analyzed and submitted in Genbank. Results: The PCR product revealed a distinct amplicon of 627 bp. The clone was confirmed by PCR. Sequencing data revealed 100% homology between PIMT sequences from Salmonella Typhimurium strain E-2375 (used in the current study and PIMT sequences of standard reported strain (Salmonella Typhimurium str. LT2 in NCBI data base. This submitted sequence in Genbank having accession no. KJ575536. Conclusions: PIMT gene of Salmonella is highly conserved in most of the pathogenic Salmonella serovars. The PIMT clone can be used to isolate PIMT protein. This PIMT protein will be helpful to identify isoaspartate containing proteins thus can help in study Salmonella virulence.

  20. Cloning and functional expression in Escherichia coli of the gene encoding the di- and tripeptide transport protein of Lactobacillus helveticus

    NARCIS (Netherlands)

    Nakajima, H.; Hagting, A; Kunji, E.R S; Poolman, B.; Konings, W.N

    1997-01-01

    The gene encoding the di- and tripeptide transport protein (DtpT) of Lactobacillus helveticus (DtpT(LH)) was cloned with the aid of the inverse PCR technique and used to complement the dipeptide transport-deficient and proline-auxotrophic Escherichia coil E1772. Functional expression of the peptide

  1. Cloning expeditions: risky but rewarding.

    Science.gov (United States)

    Lodish, Harvey

    2013-12-01

    In the 1980s, a good part of my laboratory was using the then-new recombinant DNA techniques to clone and characterize many important cell surface membrane proteins: GLUT1 (the red cell glucose transporter) and then GLUT2 and GLUT4, the red cell anion exchange protein (Band 3), asialoglycoprotein receptor subunits, sucrase-isomaltase, the erythropoietin receptor, and two of the subunits of the transforming growth factor β (TGF-β) receptor. These cloned genes opened many new fields of basic research, including membrane insertion and trafficking of transmembrane proteins, signal transduction by many members of the cytokine and TGF-β families of receptors, and the cellular physiology of glucose and anion transport. They also led to many insights into the molecular biology of several cancers, hematopoietic disorders, and diabetes. This work was done by an exceptional group of postdocs and students who took exceptionally large risks in developing and using novel cloning technologies. Unsurprisingly, all have gone on to become leaders in the fields of molecular cell biology and molecular medicine.

  2. Methylation-Specific PCR Unraveled

    Directory of Open Access Journals (Sweden)

    Sarah Derks

    2004-01-01

    Full Text Available Methylation‐specific PCR (MSP is a simple, quick and cost‐effective method to analyze the DNA methylation status of virtually any group of CpG sites within a CpG island. The technique comprises two parts: (1 sodium bisulfite conversion of unmethylated cytosine's to uracil under conditions whereby methylated cytosines remains unchanged and (2 detection of the bisulfite induced sequence differences by PCR using specific primer sets for both unmethylated and methylated DNA. This review discusses the critical parameters of MSP and presents an overview of the available MSP variants and the (clinical applications.

  3. A colony multiplex quantitative PCR-Based 3S3DBC method and variations of it for screening DNA libraries.

    Directory of Open Access Journals (Sweden)

    Yang An

    Full Text Available A DNA library is a collection of DNA fragments cloned into vectors and stored individually in host cells, and is a valuable resource for molecular cloning, gene physical mapping, and genome sequencing projects. To take the best advantage of a DNA library, a good screening method is needed. After describing pooling strategies and issues that should be considered in DNA library screening, here we report an efficient colony multiplex quantitative PCR-based 3-step, 3-dimension, and binary-code (3S3DBC method we used to screen genes from a planarian genomic DNA fosmid library. This method requires only 3 rounds of PCR reactions and only around 6 hours to distinguish one or more desired clones from a large DNA library. According to the particular situations in different research labs, this method can be further modified and simplified to suit their requirements.

  4. Construction and evaluation of reference standards for detection and quantification of Klebsiella pneumoniae using real-time PCR

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Objective To construct reference standards for detection and quantification of Klebsiella pneumoniae(K.pneumoniae)with SYBR Green I-based real-time PCR assay.Methods Primers were designed based on the published sequence of the phoE gene of K.pneumoniae.The standard was prepared by cell culture,PCR and T-A clone methods,and was identified by colony PCR and DNA sequencing.Results The standard curve showed a very good linear negative regression between threshold cycle(Ct)and Log starting quantity of copy numbe...

  5. Protocol: Streamline cloning of genes into binary vectors in Agrobacterium via the Gateway® TOPO vector system

    Directory of Open Access Journals (Sweden)

    Xu Ruqiang

    2008-01-01

    Full Text Available Abstract Background In plant functional genomic studies, gene cloning into binary vectors for plant transformation is a routine procedure. Traditionally, gene cloning has relied on restriction enzyme digestion and ligation. In recent years, however, Gateway® cloning technology (Invitrogen Co. has developed a fast and reliable alternative cloning methodology which uses a phage recombination strategy. While many Gateway- compatible vectors are available, we frequently encounter problems in which antibiotic resistance genes for bacterial selection are the same between recombinant vectors. Under these conditions, it is difficult, if not sometimes impossible, to use antibiotic resistance in selecting the desired transformants. We have, therefore, developed a practical procedure to solve this problem. Results An integrated protocol for cloning genes of interest from PCR to Agrobacterium transformants via the Gateway® System was developed. The protocol takes advantage of unique characteristics of the replication origins of plasmids used and eliminates the necessity for restriction enzyme digestion in plasmid selections. Conclusion The protocol presented here is a streamlined procedure for fast and reliable cloning of genes of interest from PCR to Agrobacterium via the Gateway® System. This protocol overcomes a key problem in which two recombinant vectors carry the same antibiotic selection marker. In addition, the protocol could be adapted for high-throughput applications.

  6. Construction of Agropyrum intermedium 2Ai-2 Chromosome DNA Library and Cloning of Species-Specific DNA Sequences

    Institute of Scientific and Technical Information of China (English)

    HE Cong-fen; MA You-zhi; XIN Zhi-yong; XU Qiong-fang; LI Lian-cheng

    2004-01-01

    The univalent from the meiosis-metaphase spreads of F1 (Z2× wheat variety Wan7107) was identified to be Agropyrum intermedium 2Ai-2 chromosome by GISH. The 2Ai-2 chromosomes were microisolated and collected. After two rounds of PCR amplification, the PCR products were ranged from 150 - 3 000 bp,with predominant fragments at about 200 - 2 000 bp. Using Ag.intermediumgenomic DNA as a probe, Southern blotting analysis confirmed the products originated from Ag. intermediumgenome. The products were purified, ligated to pUC18 and then transformed into competence E.coli DH5α to produce a 2Ai-2 chromosome DNA library. The microcloning experiments produced approximately 5×105 clones, the size range of the cloned inserts was 200- 1 500 bp, with an average of 580bp. Using Ag. intermediumgenomic DNA as a probe, dot blotting results showed that 56% clones are unique/low copy sequences, 44% are repetitive sequences in the library. Four Ag. intermedium clones were screened from the library by RFLP, and three clones(Mag065, Mag088, Mag139)belong to low/single sequences, one clone(Mag104)was repetitive sequence, and GISH results indicated that Mag104 was Ag.intermedium species-specific repetitive DNA sequence.

  7. A simplified approach to construct infectious cDNA clones of a tobamovirus in a binary vector.

    Science.gov (United States)

    Junqueira, Bruna Rayane Teodoro; Nicolini, Cícero; Lucinda, Natalia; Orílio, Anelise Franco; Nagata, Tatsuya

    2014-03-01

    Infectious cDNA clones of RNA viruses are important tools to study molecular processes such as replication and host-virus interactions. However, the cloning steps necessary for construction of cDNAs of viral RNA genomes in binary vectors are generally laborious. In this study, a simplified method of producing an agro-infectious Pepper mild mottle virus (PMMoV) clone is described in detail. Initially, the complete genome of PMMoV was amplified by a single-step RT-PCR, cloned, and subcloned into a small plasmid vector under the T7 RNA polymerase promoter to confirm the infectivity of the cDNA clone through transcript inoculation. The complete genome was then transferred to a binary vector using a single-step, overlap-extension PCR. The selected clones were agro-infiltrated to Nicotiana benthamiana plants and showed to be infectious, causing typical PMMoV symptoms. No differences in host responses were observed when the wild-type PMMoV isolate, the T7 RNA polymerase-derived transcripts and the agroinfiltration-derived viruses were inoculated to N. benthamiana, Capsicum chinense PI 159236 and Capsicum annuum plants.

  8. A simplified approach to construct infectious cDNA clones of a tobamovirus in a binary vector.

    Science.gov (United States)

    Junqueira, Bruna Rayane Teodoro; Nicolini, Cícero; Lucinda, Natalia; Orílio, Anelise Franco; Nagata, Tatsuya

    2014-03-01

    Infectious cDNA clones of RNA viruses are important tools to study molecular processes such as replication and host-virus interactions. However, the cloning steps necessary for construction of cDNAs of viral RNA genomes in binary vectors are generally laborious. In this study, a simplified method of producing an agro-infectious Pepper mild mottle virus (PMMoV) clone is described in detail. Initially, the complete genome of PMMoV was amplified by a single-step RT-PCR, cloned, and subcloned into a small plasmid vector under the T7 RNA polymerase promoter to confirm the infectivity of the cDNA clone through transcript inoculation. The complete genome was then transferred to a binary vector using a single-step, overlap-extension PCR. The selected clones were agro-infiltrated to Nicotiana benthamiana plants and showed to be infectious, causing typical PMMoV symptoms. No differences in host responses were observed when the wild-type PMMoV isolate, the T7 RNA polymerase-derived transcripts and the agroinfiltration-derived viruses were inoculated to N. benthamiana, Capsicum chinense PI 159236 and Capsicum annuum plants. PMID:24388933

  9. Cloning and Structural Analysis of Calmodulin Gene from the Mangrove Plant Sonneratia Paracaseolaris

    Institute of Scientific and Technical Information of China (English)

    Xiong Lingyuan; Lin Tao; Zhou Hantao; Xu Jinsen; Ge Yunsheng; Chen Muchuan; Chen Liang

    2002-01-01

    Calmodulin is a calcium binding protein that modulates the activity of diverse groups of protein including some protein kinase, adenylate cyclases and ATPase. Here we use the total DNA of Sonneratiaparacaseolaris as the template ofthe polymerase chain reaction (PCR). The PCR primers have been designed and synthesized according to the 5-and 3-terminal oligonucleotide sequences of Calmodulin gene of plants in Genbank and ligated with cloning vector pBsk(+).The recombinant clones have been obtained from the selected medium. The results of DNA sequences analysis show that the nucleotide sequences of ORF share more than 85% homologies as compared with those ofcalmodulin genes of several other plants. Similar to rice and apple, the ORF is interrupted by an intron behind the 75th nucleotide.

  10. [Cloning and analyzing of the female-specific marker in the dioecious species Asparagus officinalis L].

    Science.gov (United States)

    Lu, Long Dou; Li, Rui Li; Gao, Wu Jun; Deng, Chuan Liang; Wang, Lian Jun

    2006-06-01

    Sex-linked molecular markers are being obtained, which would be essential to be used in the screening of different sex of dioecious plants at the seedling stage. Furthermore, it is important in cloning the gene related to the sex. In this study the random amplified polymorphic DNA (RAPD) technique was employed with the objective to find markers linked to sex determination in Asparagus. A total of 100 primers were tested with the same PCR cycling procedure. A female-associated fragment with a length of about 867bp was generated with S12 primer. The fragment was cloned and sequenced, showing it is abundant in AT and contains 2 shorter open reading frames. In order to convert the RAPD marker into SCAR (sequence characterized amplified regions) marker, 24bp specific primers were constructed and used for PCR amplifying. The female-linked dominant SCAR marker was obtained, which would be efficient to identify the different sex of Asparagus officinalis L. PMID:16944605

  11. Identification and molecular cloning of glutamate decarboxylase gene from Lactobacillus casei

    Directory of Open Access Journals (Sweden)

    Yasaman Tavakoli

    2015-09-01

    Full Text Available Gamma-amino butyric acid (GABA possesses several physiological functions such as neurotransmission, induction of hypotension, diuretic and tranquilizer effects. Production of GABA-enriched products by lactic acid bacteria has been a focus of different researches in recent years because of their safety and health-promoting specifities. In this study, glutamate decarboxylase (gad gene of a local strains Lactobacillus casei was identified and cloned. In order to clone the gad gene from this strain, the PCR was carried out using primers designed based on conserved regions. The PCR product was purified and ligated into PGEM-T vector. Comparison of obtained sequences shows that this fragment codes the pyridoxal 5′-phosphate binding region. This strain could possibly be used for the industrial GABA production and also for development of functional fermented foods. Gad gene manipulation can also either decrease or increase the activity of enzyme in bacteria.

  12. Cloning of human 15ku selenoprotein gene from H9 T cells

    Institute of Scientific and Technical Information of China (English)

    Ke-Jun Nan; Chun-Li Li; Yong-Chang Wei; Chen-Guang Sui; Zhao Jing; Hai-Xia Qin; Li-Jun Zhao; Bo-Rong Pan

    2003-01-01

    AIM: To clone human 15ku selenoprotein gene.METHODS: H9 human T cells were cultured in RPMI1640medium supplemented with 100 mL/L fetal calf serum. mRNA was isolated from the cells. cDNA library was constructed by RT-PCR. The human 15ku selenoprotein gene was obtained by PCR and cloned into T vector and sequenced.RESULTS: A unique cDNA fragment about 1 244 bp was obtained. Sequence analysis identified an open reading frame within the cDNA. The gene had an in-frame TGA, which encoded selenocysteine (Sec), and a 3′-UTR SECIS element,which was required for synthesis of selenoprotein. The predicted protein molecular mass was about 15ku (162residues). The result was identical with human liver 15ku selenoprotein gene published in Genbank.CONCLUSION: Human 15ku selenoprotein gene can be successfully obtained from T cell line.

  13. Map-Based Cloning of Genes Important for Maize Anther Development

    Science.gov (United States)

    Anaya, Y.; Walbot, V.; Nan, G.

    2012-12-01

    Map-Based cloning for maize mutant MS13 . Scientists still do not understand what decides the fate of a cell in plants. Many maize genes are important for anther development and when they are disrupted, the anthers do not shed pollen, i.e. male sterile. Since the maize genome has been fully sequenced, we conduct map-based cloning using a bulk segregant analysis strategy. Using PCR (polymerase chain reaction), we look for biomarkers that are linked to our gene of interest, Male Sterile 13 (MS13). Recombinations occur more often if the biomarkers are further away from the gene, therefore we can estimate where the gene is and design more PCR primers to get closer to our gene. Genetic and molecular analysis will help distinguish the role of key genes in setting cell fates before meiosis and for being in charge of the switch from mitosis to meiosis.

  14. HMW glutenin subunits in multiploid Aegilops species: composition analysis and molecular cloning of coding sequences

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The Aegilops genus contains species closely related to wheat. Incommon with wheat, Aegilops species accumulate high molecular weight (HMW) glutenin subunits in their endospermic tissue. In this study, we investigated the composition of HMW glutenin subunits in four multiploid Aegilops species using SDS-PAGE analysis. Furthermore, by working with Ae. ventricosa, we established an efficient genomic PCR condition for simultaneous amplification of DNA sequences coding for either x-ory-type HMW glutenin subunits from polyploid Aegilops species. Using the genomic PCR condition, we amplified and subsequently cloned two DNA fragments that may code for HMW glutenin subunits in Ae. ventricosa. Based on an analysis of the deduced amino acid sequences, we concluded that the two cloned sequences encode one x- and one y-type of HMW glutenin subunit, respectively.

  15. Design, calibration and application of broad-range optical nanosensors for determining intracellular pH

    DEFF Research Database (Denmark)

    Søndergaard, Rikke Vicki; Henriksen, Jonas Rosager; Andresen, Thomas Lars

    2014-01-01

    Particle-based nanosensors offer a tool for determining the pH in the endosomal-lysosomal system of living cells. Measurements providing absolute values of pH have so far been restricted by the limited sensitivity range of nanosensors, calibration challenges and the complexity of image analysis...

  16. Discovery of parvovirus-related sequences in an unexpected broad range of animals

    Science.gov (United States)

    François, S.; Filloux, D.; Roumagnac, P.; Bigot, D.; Gayral, P.; Martin, D. P.; Froissart, R.; Ogliastro, M.

    2016-01-01

    Our knowledge of the genetic diversity and host ranges of viruses is fragmentary. This is particularly true for the Parvoviridae family. Genetic diversity studies of single stranded DNA viruses within this family have been largely focused on arthropod- and vertebrate-infecting species that cause diseases of humans and our domesticated animals: a focus that has biased our perception of parvovirus diversity. While metagenomics approaches could help rectify this bias, so too could transcriptomics studies. Large amounts of transcriptomic data are available for a diverse array of animal species and whenever this data has inadvertently been gathered from virus-infected individuals, it could contain detectable viral transcripts. We therefore performed a systematic search for parvovirus-related sequences (PRSs) within publicly available transcript, genome and protein databases and eleven new transcriptome datasets. This revealed 463 PRSs in the transcript databases of 118 animals. At least 41 of these PRSs are likely integrated within animal genomes in that they were also found within genomic sequence databases. Besides illuminating the ubiquity of parvoviruses, the number of parvoviral sequences discovered within public databases revealed numerous previously unknown parvovirus-host combinations; particularly in invertebrates. Our findings suggest that the host-ranges of extant parvoviruses might span the entire animal kingdom. PMID:27600734

  17. A color discriminating broad range cell staining technology for early detection of cell transformation

    Directory of Open Access Journals (Sweden)

    Sagiv Idit

    2009-01-01

    Full Text Available Background: Advanced diagnostic tools stand today at the heart of successful cancer treatment. CellDetect® is a new histochemical staining technology that enables color discrimination between normal cells and a wide variety of neoplastic tissues. Using this technology, normal cells are colored blue/green, while neoplastic cells color red. This tinctorial difference coincides with clear morphological visualization properties, mainly in tissue samples. Here we show that the CellDetect® technology can be deployed to distinguish normal cells from transformed cells and most significantly detect cells in their early pre-cancerous transformed state. Materials and Methods: In tissue culture, we studied the ability of the CellDetect® technology to color discriminate foci in a number of two stage transformation systems as well as in a well defined cellular model for cervical cancer development, using HPV16 transformed keratinocytes. Results: In all these cellular systems, the CellDetect® technology was able to sensitively show that all transformed cells, including pre-cancerous HPV 16 transformed cells, are colored red, whereas normal cells are colored blue/green. The staining technology was able to pick up: (i early transformation events in the form of small type 1 foci (non-invasive, not piled up small, with parallel alignment of cells, and (ii early HPV16 transformed cells, even prior to their ability to form colonies in soft agar. The study shows the utility of the CellDetect® technology in early detection of transformation events.

  18. Discovery of parvovirus-related sequences in an unexpected broad range of animals.

    Science.gov (United States)

    François, S; Filloux, D; Roumagnac, P; Bigot, D; Gayral, P; Martin, D P; Froissart, R; Ogliastro, M

    2016-01-01

    Our knowledge of the genetic diversity and host ranges of viruses is fragmentary. This is particularly true for the Parvoviridae family. Genetic diversity studies of single stranded DNA viruses within this family have been largely focused on arthropod- and vertebrate-infecting species that cause diseases of humans and our domesticated animals: a focus that has biased our perception of parvovirus diversity. While metagenomics approaches could help rectify this bias, so too could transcriptomics studies. Large amounts of transcriptomic data are available for a diverse array of animal species and whenever this data has inadvertently been gathered from virus-infected individuals, it could contain detectable viral transcripts. We therefore performed a systematic search for parvovirus-related sequences (PRSs) within publicly available transcript, genome and protein databases and eleven new transcriptome datasets. This revealed 463 PRSs in the transcript databases of 118 animals. At least 41 of these PRSs are likely integrated within animal genomes in that they were also found within genomic sequence databases. Besides illuminating the ubiquity of parvoviruses, the number of parvoviral sequences discovered within public databases revealed numerous previously unknown parvovirus-host combinations; particularly in invertebrates. Our findings suggest that the host-ranges of extant parvoviruses might span the entire animal kingdom. PMID:27600734

  19. Improve Motor System Efficiency for a Broad Range of Motors with MotorMaster+ International

    Energy Technology Data Exchange (ETDEWEB)

    None

    2005-05-01

    Available at no charge, MotorMaster+ International is designed to support motor systems improvement planning at industrial facilities by identifying the most cost-effective choice when deciding to repair or replace older motor models.

  20. Granular Solid Hydrodynamics (GSH): a broad-ranged macroscopic theory of granular media

    OpenAIRE

    Jiang, Yimin; Liu, Mario

    2014-01-01

    A unified continuum-mechanical theory has been until now lacking for granular media, some believe it could not exist. Derived employing the hydrodynamic approach, GSH is such a theory, though as yet a qualitative one. The behavior being accounted for includes static stress distribution, elastic wave, elasto-plastic motion, the critical state and rapid dense flow. The equations and application to a few typical experiments are presented here.

  1. Theoretical Study of Radiation from a Broad Range of Impurity Ions for Magnetic Fusion Diagnostics

    Energy Technology Data Exchange (ETDEWEB)

    Safronova, Alla [Univ. of Nevada, Reno, NV (United States)

    2014-03-14

    Spectroscopy of radiation emitted by impurities plays an important role in the study of magnetically confined fusion plasmas. The measurements of these impurities are crucial for the control of the general machine conditions, for the monitoring of the impurity levels, and for the detection of various possible fault conditions. Low-Z impurities, typically present in concentrations of 1%, are lithium, beryllium, boron, carbon, and oxygen. Some of the common medium-Z impurities are metals such as iron, nickel, and copper, and high-Z impurities, such as tungsten, are present in smaller concentrations of 0.1% or less. Despite the relatively small concentration numbers, the aforementioned impurities might make a substantial contribution to radiated power, and also influence both plasma conditions and instruments. A detailed theoretical study of line radiation from impurities that covers a very broad spectral range from less than 1 Å to more than 1000 Å has been accomplished and the results were applied to the LLNL Electron Beam Ion Trap (EBIT) and the Sustained Spheromak Physics Experiment (SSPX) and to the National Spherical Torus Experiment (NSTX) at Princeton. Though low- and medium-Z impurities were also studied, the main emphasis was made on the comprehensive theoretical study of radiation from tungsten using different state-of-the-art atomic structure codes such as Relativistic Many-Body Perturbation Theory (RMBPT). The important component of this research was a comparison of the results from the RMBPT code with other codes such as the Multiconfigurational Hartree–Fock developed by Cowan (COWAN code) and the Multiconfiguration Relativistic Hebrew University Lawrence Atomic Code (HULLAC code), and estimation of accuracy of calculations. We also have studied dielectronic recombination, an important recombination process for fusion plasma, for variety of highly and low charged tungsten ions using COWAN and HULLAC codes. Accurate DR rate coefficients are needed for describing the ionization balance of plasmas, which in turn determines the lines contributing to the spectral emission and the radiative power loss. In particular, we have calculated relativistic atomic data and corresponding dielectronic satellite spectra of highly ionized W ions, such as, for example, Li-like W (with the shortest wavelength of x-ray radiation of about 0.2 Å) that might exist in ITER core plasmas at very high temperatures of 30-40 keV. In addition, we have completed relativistic calculations of low ionized W ions from Lu-like (W3+) to Er-like (W6+) and for Sm-like(W12+) and Pm-like (W13+) that cover a spectral range from few hundred to thousand Å and are more relevant to the edge plasma diagnostics in tokamak.

  2. Discovery of parvovirus-related sequences in an unexpected broad range of animals

    Science.gov (United States)

    François, S.; Filloux, D.; Roumagnac, P.; Bigot, D.; Gayral, P.; Martin, D. P.; Froissart, R.; Ogliastro, M.

    2016-09-01

    Our knowledge of the genetic diversity and host ranges of viruses is fragmentary. This is particularly true for the Parvoviridae family. Genetic diversity studies of single stranded DNA viruses within this family have been largely focused on arthropod- and vertebrate-infecting species that cause diseases of humans and our domesticated animals: a focus that has biased our perception of parvovirus diversity. While metagenomics approaches could help rectify this bias, so too could transcriptomics studies. Large amounts of transcriptomic data are available for a diverse array of animal species and whenever this data has inadvertently been gathered from virus-infected individuals, it could contain detectable viral transcripts. We therefore performed a systematic search for parvovirus-related sequences (PRSs) within publicly available transcript, genome and protein databases and eleven new transcriptome datasets. This revealed 463 PRSs in the transcript databases of 118 animals. At least 41 of these PRSs are likely integrated within animal genomes in that they were also found within genomic sequence databases. Besides illuminating the ubiquity of parvoviruses, the number of parvoviral sequences discovered within public databases revealed numerous previously unknown parvovirus-host combinations; particularly in invertebrates. Our findings suggest that the host-ranges of extant parvoviruses might span the entire animal kingdom.

  3. Oxidative Stress and Mitochondrial Dysfunction across Broad-Ranging Pathologies: Toward Mitochondria-Targeted Clinical Strategies

    OpenAIRE

    Giovanni Pagano; Annarita Aiello Talamanca; Giuseppe Castello; Mario D Cordero; Marco d’Ischia; Maria Nicola Gadaleta; Federico V Pallardó; Sandra Petrović; Luca Tiano; Adriana Zatterale

    2014-01-01

    Beyond the disorders recognized as mitochondrial diseases, abnormalities in function and/or ultrastructure of mitochondria have been reported in several unrelated pathologies. These encompass ageing, malformations, and a number of genetic or acquired diseases, as diabetes and cardiologic, haematologic, organ-specific (e.g., eye or liver), neurologic and psychiatric, autoimmune, and dermatologic disorders. The mechanistic grounds for mitochondrial dysfunction (MDF) along with the occurrence of...

  4. Investigations of Saturn’s Main Rings over Broad Range of Wavelengths

    Science.gov (United States)

    Spilker, Linda J.; Deau, Estelle; Morishima, Ryuji; Filacchione, Gianrico; Hedman, Matt; Nicholson, Phil; Colwell, Josh; Bradley, Todd; Showalter, Mark; Pilorz, Stu; Brooks, Shawn; Ciarniello, Mauro

    2015-11-01

    An abundance of information about the characteristics of Saturn’s ring particles and their regolith can be obtained by comparing the changes in their brightness, color and temperature with changing viewing geometry over a wide range of wavelengths from ultraviolet through the thermal infrared. Data from Cassini’s Composite Infrared Spectrometer (CIRS), Visual and Infrared Mapping Spectrometer (VIMS), Imaging Science Subsystem (ISS) and Ultraviolet Imaging Spectrograph (UVIS) are jointly studied using data from the lit and unlit main rings at multiple geometries and solar elevations over 11 years of the Cassini mission. Using multi-wavelength data sets allows us to test different thermal models by combining the effects of particle albedo, regolith grain size and surface roughness with thermal emissivity and inertia, particle spin rate and spin axis orientation.CIRS temperatures, ISS colors and UVIS brightness appear to vary noticeably with phase angle, but are not a strong function of spacecraft elevation angle. Color, temperature and brightness dependence on solar elevation angle are also observed. VIMS observations show that the infrared ice absorption band depths change with the solar phase angle, in particular between 0-20° and at high phase. This trend indicates that single scattering approximation is correct only at low phases (Copyright 2015 California Institute of Technology. Government sponsorship is acknowledged.

  5. Development of Broad Range Scan Capabilities with Jet Cooled Cavity Ringdown Spectroscopy

    Science.gov (United States)

    Codd, Terrance J.; Chen, Ming-Wei; Miller, Terry A.

    2011-06-01

    We have developed a technique for obtaining broad scans, >100 Cm-1, for jet cooled cavity ringdown spectroscopy (CRDS) spectra. Previously the scans of the jet cooled, CRDS apparatus were limited to <10 Cm-1 due to the use of a narrow linewidth radiation source. However, by coupling our jet cooled, CRDS apparatus with a moderate resolution (≃q 0.05 Cm-1) dye laser we are able to greatly increase our rate of data acquisition thereby gaining the capability to perform broad spectral surveys of jet cooled molecules. As a test of the capabilities of the technique we have scanned the tilde{A}-tilde{X} transition of NO_3 previously reported by Deev et al. at room temperature. We believe that this will be a very useful technique to search for transitions of cold molecules whose frequencies are not well known and which later can be studied using high resolution methods. A. Deev, J. Sommar, and M. Okumura, J. Chem. Phys. 122, 224305 (2005).

  6. Leptospirosis in animals and human contacts in Egypt: broad range surveillance

    OpenAIRE

    Ahmed Samir; Rafik Soliman; Mahmoud El-Hariri; Khaled Abdel-Moein; Mahmoud Essam Hatem

    2015-01-01

    INTRODUCTION: Leptospirosis is a re-emerging zoonotic disease of humans and animals worldwide. The disease is caused by pathogenic species of the genus Leptospira. These organisms are maintained in nature via chronic renal infection of carrier animals, which excrete the organisms in their urine. Humans become infected through direct or indirect exposure to infected animals and their urine or through contact with contaminated water and soil. This study was conducted to investigate Leptospira i...

  7. Dried Saliva Spots: A Robust Method for Detecting Streptococcus pneumoniae Carriage by PCR

    Directory of Open Access Journals (Sweden)

    Cassandra L. Krone

    2016-03-01

    Full Text Available The earliest studies in the late 19th century on Streptococcus pneumoniae (S. pneumoniae carriage used saliva as the primary specimen. However, interest in saliva declined after the sensitive mouse inoculation method was replaced by conventional culture, which made isolation of pneumococci from the highly polymicrobial oral cavity virtually impossible. Here, we tested the feasibility of using dried saliva spots (DSS for studies on pneumococcal carriage. Saliva samples from children and pneumococcus-spiked saliva samples from healthy adults were applied to paper, dried, and stored, with and without desiccant, at temperatures ranging from −20 to 37 °C for up to 35 days. DNA extracted from DSS was tested with quantitative-PCR (qPCR specifically for S. pneumoniae. When processed immediately after drying, the quantity of pneumococcal DNA detected in spiked DSS from adults matched the levels in freshly spiked raw saliva. Furthermore, pneumococcal DNA was stable in DSS stored with desiccant for up to one month over a broad range of temperatures. There were no differences in the results when spiking saliva with varied pneumococcal strains. The collection of saliva can be a particularly useful in surveillance studies conducted in remote settings, as it does not require trained personnel, and DSS are resilient to various transportation conditions.

  8. Cloning and expression of swine myostatin gene and its application in animal immunization trial

    Institute of Scientific and Technical Information of China (English)

    MA Xianyong; CAO Yongchang; SHU Dingming; BI Yingzuo

    2005-01-01

    We have amplified swine myostatin (MSTN) gene by reverse transcription polymerase chain reaction (RT-PCR) and cloned it into pGEM-T Easy vector. The cloned swine MSTN gene consists of 1128 nucleotides, which has been submitted to GenBank (acquired registered code- AY448008). The cloned swine MSTN gene was successfully expressed in E. coli without the first 25 amino acids. Crude extraction of the expressed recombinant MSTN protein was used to immunize mice to investigate the effects on their bodyweights. We show here that the body weights of the immunized mice were higher than that of the controls, even though the difference was not significant. Surprisingly, the progenies of the immunized mice also were heavier than the controls. Especially at day 3, the average body weight of the immunized mice was 10.5% higher than that of the controls , which is significant (p < 0.05).

  9. Solid-phase cloning for high-throughput assembly of single and multiple DNA parts

    DEFF Research Database (Denmark)

    Lundqvist, Magnus; Edfors, Fredrik; Sivertsson, Åsa;

    2015-01-01

    is needed or where multiple inserts are to be assembled. In this approach, the solid support allows for head-to-tail assembly of DNA fragments based on hybridization and polymerase fill-in. The usefulness of head-to-tail SPC was demonstrated by assembly of >150 constructs with up to four DNA parts......We describe solid-phase cloning (SPC) for high-throughput assembly of expression plasmids. Our method allows PCR products to be put directly into a liquid handler for capture and purification using paramagnetic streptavidin beads and conversion into constructs by subsequent cloning reactions. We...... present a robust automated protocol for restriction enzyme based SPC and its performance for the cloning of >60 000 unique human gene fragments into expression vectors. In addition, we report on SPC-based single-strand assembly for applications where exact control of the sequence between fragments...

  10. Cloning and alignment of WaaF gene of Campylobacter jejuni Lulei

    Directory of Open Access Journals (Sweden)

    XING Cong-cong

    2012-04-01

    Full Text Available Objective To clone the WaaF gene of Campylobacter jejuni, and analyse its relationship with WaaF genetic evolution. Methods Amplified WaaF gene of Campylobacter jejuni Lulei by PCR, and constructed pGEM-T-WaaF cloning plasmid. Downloaded five WaaF associated with Guillain-Barré syndrome (GBS and one WaaF not associated with GBS, and then constructed phylogenetic tree. Results pGEM-T-WaaF cloning plasmid was constructed successfully. WaaF presented cluster phenomenon in Campylobacter jejuni associated with GBS. Conclusion WaaF gene of Campylobacter jejuni Lulei is the fragment of 807 bp, and has the nearest relationship with the genetic evolution of Lichang.

  11. Cloning and expression of nucleocapsid protein gene of TGEV HB06 strain

    Institute of Scientific and Technical Information of China (English)

    FAN Jinghui; ZUO Yuzhu; ZHAO Yuelan; LI Tanqing; ZHANG Xiaobo

    2007-01-01

    The nucleocapsid protein gene of transmissible gastroenteritis virus,1 149 bp in length,was amplified by RT-PCR from isolated strain HB06 and cloned into pMD 18T.Sequence comparison with other transmissible gastroenteritis virus (TGEV) strains selected from the Gene Bank revealed that the homology of N gene complete sequence shares more than 97% in nucleotide.N gene was cloned into BamHI and EcoRI multiple cloning sites of the prokaryotic expression vector pET 20 b,and named pETN.After being induced by isopropyl-β-D-thiogalactopyranoside (IPTG),the recombinant nucleocapsid protein was expressed.The result of SDS-PAGE and Western-blot showed that the recombinant nucleocapsid protein was 47 kDa and had strong positive reactions with TGEV-specific antibody.

  12. Investigation of T-cell receptor-γ gene rearrangement in gastrointestinal lymphomas by PCR-SSCP analysis

    Institute of Scientific and Technical Information of China (English)

    Xi-Qun Han; Li He; Lan-Ying Shong; Hui-Yong Jiang; Mei-Gang Zhu; Tong Zhao

    2004-01-01

    AIM: To analyze the characterization of T-cell receptor-γ (TCR-γ) gene rearrangement in the gastrointestinal lymphomas and evaluate the value of PCR-SSCP analysis in gastrointestinal lymphomas investigation.METHODS: TCR-γgene rearrangement segments of gastrointestinal lymphomas were cloned and sequenced.Single clone plasmid and mixed clone plsamids were subsequently submitted to PCR-SSCP analysis to investigate the relationship between the number of amplified clones and band patterns of the amplified products. The PCR products of TCR-γgene rearrangement of 40 gastrointestinal lymphomas were electrophoresed on agarose gels and the positive cases on agarose gels were studied by SSCP analysis.RESULTS: The sequencing showed that TCR-γ gene rearrangement of the gastrointestinal lymphomas included functional gene and pseudogene with extensive variety in the junctional regions. In SSCP analysis, the number of the single-stranded bands was about two times of the number of amplified clones, and double-stranded band became broad with the increased number of the amplified clones. Thirteen of the 25 B-cell gastrointestinal lymphomas and 14 of the 15 gastrointestinal T-cell lymphomas were positive detected on agarose gel electrophoresis. Of the positive cases detected by SSCP analysis, 3 B-cell lymphomas and 13 T-cell lymphomas showed positive bands. The other cases showed only smears. The rearranged pattern included 13 monoallelic gene rearrangements and 3 biallelic or oligoclonal gene rearrangements.CONCLUSION: The pattern of TCR-γ, gene rearrangement in gastrointestinal lymphomas are similar to that of the nodular lymphomas. PCR-SSCP analysis for TCR-γ gene rearrangement can be applied both for adjuvant diagnosis of gastrointestinal lymphomas and analysis of the gene rearrangement pattern. The ratio of TCR-γ gene rearrangements occurred in T-cell gastrointestinal lymphomas is significantly higher than that in B-cell gastrointestinal lymphomas. The gene rearrangement

  13. Rapid Identification and Enumeration of Saccharomyces cerevisiae Cells in Wine by Real-Time PCR

    OpenAIRE

    Martorell, P.; Querol, A.; Fernández-Espinar, M. T.

    2005-01-01

    Despite the beneficial role of Saccharomyces cerevisiae in the food industry for food and beverage production, it is able to cause spoilage in wines. We have developed a real-time PCR method to directly detect and quantify this yeast species in wine samples to provide winemakers with a rapid and sensitive method to detect and prevent wine spoilage. Specific primers were designed for S. cerevisiae using the sequence information obtained from a cloned random amplified polymorphic DNA band that ...

  14. Multiplex PCR for Rapid Detection of Staphylococcus aureus Isolates Suspected to Represent Community-Acquired Strains▿

    OpenAIRE

    Strommenger, B.; Braulke, C.; Pasemann, B.; Schmidt, C.; Witte, W.

    2007-01-01

    The continuous spread of community-acquired methicillin-resistant Staphylococcus aureus (caMRSA) and the introduction of these highly virulent isolates into hospitals represent increasing threats. The timely recognition of caMRSA strains is crucial for infection control purposes. Thus, we developed a PCR-based assay for the easy and rapid determination of those caMRSA clones that currently are the most prevalent in Germany and Central Europe. This assay was able to correctly identify the majo...

  15. Rapid Characterization of Garlic Clones with Locus-Specific DNA Markers

    OpenAIRE

    İPEK, Meryem; İPEK, AHMET; Simon, Philipp W

    2008-01-01

    Maintenance of redundant garlic (Allium sativum L.) accessions is expensive due to the necessity of yearly regenerating garlic accessions in germplasm centers. Therefore, rapid characterization of garlic accessions is important for avoiding duplicated genotypes. For this purpose we developed several locus-specific polymerase chain reaction (PCR)-based DNA markers, and tested them for the characterization of garlic clones that were previously analyzed using amplified fragment length polymorphi...

  16. Preparation of North American Type II PRRSV Infectious Clone Expressing Green Fluorescent Protein

    OpenAIRE

    Liyue Wang; Kao Zhang; Hongyu Lin; Wenyan Li; Jiexia Wen; Jianlou Zhang; Yonghong Zhang; Xiujin Li; Fei Zhong

    2014-01-01

    Porcine reproductive and respiratory syndrome virus (PRRSV) is still one of the most important infectious diseases threatening the swine industry. To construct North American type II PRRSV infectious clone containing green fluorescent protein (GFP) gene, we amplify gfp gene, flanked by PRRSV Nsp2 gene fragments upstream and downstream, using overlap PCR method from pcDNA-EF1-GFP plasmid and FL12 plasmid containing PRRSV infectious genome as the templates. The Nsp2 fragment-flanked gfp gene wa...

  17. Cloning and functional characterization of endo-β-1,4-glucanase gene from metagenomic library of vermicompost.

    Science.gov (United States)

    Yasir, Muhammad; Khan, Haji; Azam, Syed Sikander; Telke, Amar; Kim, Seon Won; Chung, Young Ryun

    2013-06-01

    In the vermicomposting of paper mill sludge, the activity of earthworms is very dependent on dietetic polysaccharides including cellulose as energy sources. Most of these polymers are degraded by the host microbiota and considered potentially important source for cellulolytic enzymes. In the present study, a metagenomic library was constructed from vermicompost (VC) prepared with paper mill sludge and dairy sludge (fresh sludge, FS) and functionally screened for cellulolytic activities. Eighteen cellulase expressing clones were isolated from about 89,000 fosmid clones libraries. A short fragment library was constructed from the most active positive clone (cMGL504) and one open reading frame (ORF) of 1,092 bp encoding an endo-β-1,4-glucanase was indentified which showed 88% similarity with Cellvibrio mixtus cellulase A gene. The endo-β-1,4-glucanase cmgl504 gene was overexpressed in Escherichia coli. The purified recombinant cmgl504 cellulase displayed activities at a broad range of temperature (25-55°C) and pH (5.5-8.5). The enzyme degraded carboxymethyl cellulose (CMC) with 15.4 U, while having low activity against avicel. No detectable activity was found for xylan and laminarin. The enzyme activity was stimulated by potassium chloride. The deduced protein and three-dimensional structure of metagenome-derived cellulase cmgl504 possessed all features, including general architecture, signature motifs, and N-terminal signal peptide, followed by the catalytic domain of cellulase belonging to glycosyl hydrolase family 5 (GHF5). The cellulases cloned in this work may play important roles in the degradation of celluloses in vermicomposting process and could be exploited for industrial application in future. PMID:23812813

  18. Fluorescence-PCR Assays and Isolation of Luminescent Bacterial Clones Using an Automated Plate Reader

    Science.gov (United States)

    Crowley, Thomas E.

    2011-01-01

    The genes responsible for luminescence in various species of the marine microorganism "Photobacterium", have been used for many years as a tool by researchers and instructors. In particular, the "lux" operon of "Photobacterium fischeri" has been used by many instructors to teach recombinant DNA techniques. Two methods using an automated plate…

  19. Recombinant thermostable AP exonuclease from Thermoanaerobacter tengcongensis: cloning, expression, purification, properties and PCR application

    DEFF Research Database (Denmark)

    Dabrowski, Slawomir; Brillowska-Dabrowska, Anna; Ahring, Birgitte Kiær

    2013-01-01

    ) of fully active and soluble His6-tagged Tte AP enzyme with His6-tag on C-terminal end was obtained in Escherichia coli Rosetta (DE3) pLysS. The active enzyme was purified up to 98% homogeneity in one chromatographic step using metal-affinity chromatography on Ni(2+)-IDA-Sepharose resin. The yield was 90 mg...

  20. Cloning of TRP Gene of Bombyx mori%家蚕TPR基因的克隆

    Institute of Scientific and Technical Information of China (English)

    牛伟涛

    2011-01-01

    [ Objective ] The aim was to clone Bornbyx rnori TRP gene. [ Method ] The total RNA of Bombyx mori was extracted during its pupal pedod with Trizol method, and then the TRP gene was cloned by RT-PCR. [ Result] The full-length cDNA of TRP gene was successfully obtained, and the ORF fragment (858 bp) of TRP gene was cloned by PCR. [ Conclusion] TRP gene of Bombyx mori was cloned for the first time,which could provide solid basis for the study on its function.%[目的]克隆家蚕TPR基因,为研究该基因功能提供依据.[方法]利用Trizol法提取家蚕蛹期总RNA,再用RT-PCR的方法对家蚕TPR基因进行克隆.[结果]成功得到家蚕TPR基因全cDNA序列,并用PCR扩增得到了TPR基因的ORF,全长858 bp.[结论]首次对家蚕TPR家族基因进行了克隆,为今后对该基因功能研究奠定了坚实的基础.

  1. Cloning of TRP Gene of Bombyx mori%家蚕TPR基因的克隆

    Institute of Scientific and Technical Information of China (English)

    牛伟涛

    2011-01-01

    [ Objective ] The aim was to clone Bombyx mori TRP gene. [ Method ] The total RNA of Bombyx mori was extracted during its pupal period with Trizol method, and then the TRP gene was cloned by RT-PCR. [ Result] The full-length cDNA of TRP gene was successfully obtained, and the ORF fragment (858 bp) of TRP gene was cloned by PCR. [Conclusion] TRP gene of Bombyx mori was cloned for the first time, which could provide solid basis for the study on its function.%[目的]克隆家蚕TPR基因,为研究该基因功能提供依据.[方法]利用Trizol法提取家蚕蛹期总RNA,再用RT-PCR方法对家蚕TPR基因进行克隆.[结果]成功得到家蚕TPR基因全cDNA序列,并用PCR扩增得到了TPR基因的ORF,全长858 bp.[结论]首次对家蚕TPR家族基因进行了克隆,为今后对该基因功能研究奠定了坚实的基础.

  2. RAPD markers for genetic fingerprinting of elite clones and land races of root crops

    International Nuclear Information System (INIS)

    Molecular markers such as restriction fragment length polymorphisms (RFLPs) and polymerase chain reaction (PCR) based markers such as random amplified polymorphic DNAs (RAPDs) are being widely used for genetic analysis and DNA fingerprinting. In addition to biochemical markers for isozyme analysis, combined with morphological, physiological and pest and disease reactions, we have established RAPD markers as tools for assessing the genetic diversity in cassava (Manihot esculenta Crantz L.) and yam (Dioscorea species). In cassava, a preparatory study was conducted to characterize 24 cassave elite clones. A preliminary survey of 60 different commercially available primers from Operon, Alameda, California, United States of America (OPA, B and C series) was performed to identify those primers that gave good DNA fingerprinting. The results obtained show a relatively low degree of polymorphism. Nevertheless, the detected polymorphism allowed us to distinguish clones from one another. In yam (Dioscorea species), PCR-RAPD analysis was carried out to detect DNA polymorphism in the improved clones and land races of cultivated yams D. rotundata as well as in 11 wild species of the genus Dioscorea from Africa. Eight primers from the OPB and C series revealed polymorphism in the International Institute of Tropical Agriculture elite clones and land races. Two random primers (OPB-1 and OPB-2) gave excellent scorable polymorphism, allowing us to detect 17 different fragments that were scored as unit characters and used to draw phylogenetic relationships in Dioscorea using the computer program PAUP (phylogenetic analysis using parsimony)

  3. Molecular Cloning and Preliminary Analysis of a Fragile Site Associated Gene

    Institute of Scientific and Technical Information of China (English)

    YI-WEN CAO; CHUAN-LU JIANG; TAO JIANG

    2006-01-01

    Objective To analyze the molecular colning of a fragile site-associated gene. Methods Genomic Chinese hamster ovary (CHO) DNA library was constructed using high molecular weight CHO DNA partially digested with MboI restriction enzyme from cultured CHO cells. Screening of genomic DNA library followed the established procedures. Genomic CHO in the positive clones was sequenced. Appropriate primers were designed for the reverse transcriptase-polymerase chain reactions (RT-PCR). The RT-PCR products were cloned into a pCRⅡ TOPO vector and confirmed by DNA sequencing. Antibodies were prepared using synthetic peptides as antigens by immunizing the rabbits. Immunohistochemical analyses were performed to evaluate the expression of the novel gene in different tissues. Results To investigate the molecular mechanism underlying the initial events of mdrla amplification, we cloned 1q31 fragile site DNA. Strikingly, we found that this fragile site contained a novel gene which was designated as a fragile site-associated (FSA) gene. FSA encoded an unusually large mRNA of ~16 kb. Full-length human FSA cDNA was cloned. FSA mRNA was expressed in many cultured cells and tissue types. Immunohistochemical analyses also revealed an expression pattern of the encoded proteins in postmitotic, well-differentiated epithelial compartments of many organs, including colon, mammary glands, ovary, prostate, and bladder. Conclusion FSA plays an important role in regulating mammalian epithelial cell growth and differentiation.

  4. Cloning

    Science.gov (United States)

    ... Care Online Health Resources For Health Professionals Competency & Curricular Resources Genetics 101 Genomic Medicine and Health Care ... as bacteria , produce genetically identical offspring through a process called asexual reproduction. In asexual reproduction, a new ...

  5. Cloning

    Institute of Scientific and Technical Information of China (English)

    彭荣华

    2002-01-01

    As we come near to the 21st century, it is clear than ever that science and technology are changing the way we live and work. The breakthroughs1 in bioengineering2 science are helping to uncover the mysteries of life, holding out new hope for life-saving cures to some of our greatly terrible diseases.

  6. Determination of human papillomavirus type 16 genotype and construction of cloning vector pTZ57R encoding HPV16 E7 gene

    International Nuclear Information System (INIS)

    To isolate and construct a cloning vector contain the human papillomavirus (HPV) 16-E7 gene as a target for application as a DNA vaccine. The study was performed in 2005 in Iran. The E7 gene, one of the most important HPV oncoproteins and a target molecule for therapeutic vaccine, was amplified by polymerase chain reaction (PCR). The PCR product was cloned into a suitable cloning vector and confirmed by colony-PCR, restriction enzyme analysis and sequenced. The desired plasmid was sequenced and indicated 99% homology with those mentioned in the Genbank. The Iranian HPV16 E7 gene sequence is very similar to other sequences in the Genbank and it can be used as candidate gene in a therapeutic vaccine for Iranian patients with cervical cancer. (author)

  7. Construction of a BAC library from cucumber (Cucumis sativus L.) and identification of linkage group specific clones

    Institute of Scientific and Technical Information of China (English)

    Yuan Guan; Qi Chen; Junsong Pan; Zheng Li; Huanle He; Aizhong Wu; Rentao Song; Run Cai

    2008-01-01

    A bacterial artificial chromosome (BAC) library consisting of 19,200 clones with an average insert size of 105 kb has been constructed from a cucumber (Cucumis sativus L.) inbred line S94, derived from a cultivar in North China. The entire library was equivalent to approximately 5 haploid cucumber genomes. To facilitate chromosome engineering and anchor the cucumber genetic linkage map to its chromosomes, 15 sequence-characterized amplified regions (SCAR) and seven simple sequence repeats (SSR) markers from each link-age group of cucumber were used to screen an ordered array of pooled BAC DNA with polymerase chain reaction (PCR). Fifteen mark-ers gave at least two positive clones. As a result, 22 BAC clones representing 7 linkage groups of cucumber were identified, which further validated the genome coverage and utility of the library. This BAC library and linkage group specific clones provide essential resources for future research of the cucumber genome.

  8. Molecular detection of Mycoplasma pneumoniae by quantitative real-time PCR in patients with community acquired pneumonia

    Directory of Open Access Journals (Sweden)

    Rama Chaudhry

    2013-01-01

    Full Text Available Background & objectives: Mycoplasma pneumoniae is the most important and common cause of community-acquired pneumonia (CAP. The conventional detection methods (culture and serology lack sensitivity. PCR offers a better approach for rapid detection but is prone to carry over contamination during manipulation of amplification products. Quantitative real-time PCR (qRT-PCR method offers an attractive alternative detection method. In the present study, qRT-PCR, PCR and serology methods were used to detect M. pneumoniae infection in cases of pneumonias and findings compared. Methods: A total of 134 samples consisting of blood (for serology and respiratory secretions (for PCR and qRT-PCR from 134 patients were collected. The blood samples were tested for IgG, IgM and IgA using commercially available kits. For standardization of PCR of M. pneumoniae P1 gene was cloned in pGEMTEasy vector. Specific primers and reporter sequence were designed and procured for this fragment. The qRT-PCR assay was performed to prepare the standard curve for M. pneumoniae positive control DNA template and detection in patient samples. Results: Of the 134 patients, 26 (19% were positive for antibodies against M. pneumoniae. IgG was positive in 14.92 per cent (20 cases, IgM in 4.47 per cent (6 and IgA was positive in 5.22 per cent (7 cases. In the qRT-PCR assay 19 per cent (26 samples were positive. Of the 26 qRT-PCR positive samples, nine could be detected by serology. PCR was positive for 25 samples. An extra sample negative by PCR was detected by qRT-PCR. Thus, real-time PCR assay, PCR and serology in combination could detect M. pneumoniae infection in 43 patients. Interpretation & conclusions: The study shows that 17 patients were detected by serology alone, 17 were detected by qRT-PCR only and nine patients were positive by both serology and real-time PCR. Of the 134 samples tested, 25 were positive by conventional PCR, but qRT-PCR could detect one more sample that was

  9. Effective and efficient model clone detection

    DEFF Research Database (Denmark)

    Störrle, Harald

    2015-01-01

    Code clones are a major source of software defects. Thus, it is likely that model clones (i.e., duplicate fragments of models) have a significant negative impact on model quality, and thus, on any software created based on those models, irrespective of whether the software is generated fully...... automatically (“MDD-style”) or hand-crafted following the blueprint defined by the model (“MBSD-style”). Unfortunately, however, model clones are much less well studied than code clones. In this paper, we present a clone detection algorithm for UML domain models. Our approach covers a much greater variety...... of model types than existing approaches while providing high clone detection rates at high speed....

  10. Multiplex PCR detection of GSTM1, GSTT1, and GSTP1 gene variants: simultaneously detecting GSTM1 and GSTT1 gene copy number and the allelic status of the GSTP1 Ile105Val genetic variant

    DEFF Research Database (Denmark)

    Buchard, Anders; Sanchez Sanchez, Juan Jose; Dalhoff, Kim;

    2007-01-01

    The glutathione S-transferase (GST) genes GSTM1, GSTT1, and GSTP1 are involved in the detoxification of a broad range of toxic substances. Genetic polymorphisms in these genes have been studied intensively for their potential role in cancer susceptibility and drug response. In Caucasians, the...... none, one, or two copies of the GSTM1 and GSTT1 genes and simultaneously detects the allelic status of the GSTP1 Ile105Val genetic variant. A total of 200 Danes, 100 Somalis, and 100 Greenlanders were genotyped. This multiplex PCR assay enables future large-scale studies to investigate the role of GSTs....

  11. Growth and nutrition of willow clones.

    OpenAIRE

    ViherÀ-Aarnio, Anneli; Saarsalmi, Anna

    1994-01-01

    Growth and nutrition of 20 clones representing different species and interspecific hybrids of willows growing on an abandoned field were studied. There were highly significant differences between the clones as regards the survival, number of sprouts/stool, sprout mean height and diameter and stem biomass production/stool. The differences between the clones in the concentrations of all nutrients in both the leaves and stems were highly significant.

  12. Test of high land potato clones

    OpenAIRE

    Handayani, Tri; Kusmana

    2011-01-01

    Potatoes farming in Indonesia were still dominated by Granola variety. New varieties with high yield are still needed. The objective this study was to obtain high yield clones. The study was conducted at Ciwidey, Bandung that located at altitude of 1300 m above sea level and there conducted from February to June 2007. The study applied completely randomized block design with three replications. Treatments were 15 clones include 4 controls that are tested. Among 11 clones tes...

  13. Economic Aspects of Human Cloning and Reprogenetics

    OpenAIRE

    Saint-Paul, Gilles

    2002-01-01

    This paper analyses the economic issues associated with human cloning and new reproductive technologies. We analyze the incentives for human cloning and its implications for the long run distribution of skills and income. We analyse models of human cloning for different motives, focusing on those which tend to produce new human beings with improved ability. We thus ignore purely therapeutic applications, which may well be the most likely ones to happen in the near future, but have no first-or...

  14. Benefits and problems with cloning animals.

    OpenAIRE

    Smith, L. C.; Bordignon, V.; Babkine, M; Fecteau, G; Keefer, C.

    2000-01-01

    Animal cloning is becoming a useful technique for producing transgenic farm animals and is likely to be used to produce clones from valuable adults. Other applications will also undoubtedly be discovered in the near future, such as for preserving endangered breeds and species. Although cloning promises great advantages for commerce and research alike, its outcome is not always certain due to high pregnancy losses and high morbidity and mortality during the neonatal period. Research into the m...

  15. Meat and milk compositions of bovine clones

    OpenAIRE

    Tian, X. Cindy; Kubota, Chikara; Sakashita, Kunihito; IZAIKE, Yoshiaki; OKANO, Ryoichi; Tabara, Norio; Curchoe, Carol; Jacob, Lavina; Zhang, Yuqin; Smith, Sadie; Bormann, Charles; Xu, Jie; Sato, Masumi; Andrew, Sheila; Yang, Xiangzhong

    2005-01-01

    The technology is now available for commercial cloning of farm animals for food production, but is the food safe for consumers? Here, we provide data on >100 parameters that compare the composition of meat and milk from beef and dairy cattle derived from cloning to those of genetic- and breed-matched control animals from conventional reproduction. The cloned animals and the comparators were managed under the same conditions and received the same diet. The composition of the meat and milk from...

  16. Recombination-assisted megaprimer (RAM) cloning

    OpenAIRE

    Jacques Mathieu; Emilia Alvarez; Alvarez, Pedro J. J.

    2014-01-01

    No molecular cloning technique is considered universally reliable, and many suffer from being too laborious, complex, or expensive. Restriction-free cloning is among the simplest, most rapid, and cost-effective methods, but does not always provide successful results. We modified this method to enhance its success rate through the use of exponential amplification coupled with homologous end-joining. This new method, recombination-assisted megaprimer (RAM) cloning, significantly extends the app...

  17. Ultra-Low Background DNA Cloning System

    OpenAIRE

    Goto, Kenta; Nagano, Yukio

    2013-01-01

    Yeast-based in vivo cloning is useful for cloning DNA fragments into plasmid vectors and is based on the ability of yeast to recombine the DNA fragments by homologous recombination. Although this method is efficient, it produces some by-products. We have developed an “ultra-low background DNA cloning system” on the basis of yeast-based in vivo cloning, by almost completely eliminating the generation of by-products and applying the method to commonly used Escherichia coli vectors, particularly...

  18. Metabolomic phenotyping of a cloned pig model

    Directory of Open Access Journals (Sweden)

    Callesen Henrik

    2011-08-01

    Full Text Available Abstract Background Pigs are widely used as models for human physiological changes in intervention studies, because of the close resemblance between human and porcine physiology and the high degree of experimental control when using an animal model. Cloned animals have, in principle, identical genotypes and possibly also phenotypes and this offer an extra level of experimental control which could possibly make them a desirable tool for intervention studies. Therefore, in the present study, we address how phenotype and phenotypic variation is affected by cloning, through comparison of cloned pigs and normal outbred pigs. Results The metabolic phenotype of cloned pigs (n = 5 was for the first time elucidated by nuclear magnetic resonance (NMR-based metabolomic analysis of multiple bio-fluids including plasma, bile and urine. The metabolic phenotype of the cloned pigs was compared with normal outbred pigs (n = 6 by multivariate data analysis, which revealed differences in the metabolic phenotypes. Plasma lactate was higher for cloned vs control pigs, while multiple metabolites were altered in the bile. However a lower inter-individual variability for cloned pigs compared with control pigs could not be established. Conclusions From the present study we conclude that cloned and normal outbred pigs are phenotypically different. However, it cannot be concluded that the use of cloned animals will reduce the inter-individual variation in intervention studies, though this is based on a limited number of animals.

  19. Cloning of spin-coherent states

    International Nuclear Information System (INIS)

    We consider optimal cloning of the spin coherent states in Hilbert spaces of different dimensionality d. We give explicit form of optimal cloning transformation for spin coherent states in the three-dimensional space, analytical results for the fidelity of the optimal cloning in d=3 and d=4 as well as numerical results for higher dimensions. In the low-dimensional case we construct the corresponding completely positive maps and exhibit their structure with the help of Jamiolkowski isomorphism. This allows us to formulate some conjectures about the form of optimal coherent cloning completely positive maps in arbitrary dimension

  20. Quantum cloning disturbed by thermal Davies environment

    Science.gov (United States)

    Dajka, Jerzy; Łuczka, Jerzy

    2016-06-01

    A network of quantum gates designed to implement universal quantum cloning machine is studied. We analyze how thermal environment coupled to auxiliary qubits, `blank paper' and `toner' required at the preparation stage of copying, modifies an output fidelity of the cloner. Thermal environment is described in terms of the Markovian Davies theory. We show that such a cloning machine is not universal any more but its output is independent of at least a part of parameters of the environment. As a case study, we consider cloning of states in a six-state cryptography's protocol. We also briefly discuss cloning of arbitrary input states.

  1. A single-copy galK promoter cloning vector suitable for cloning strong promoters

    DEFF Research Database (Denmark)

    Dandanell, Gert; Court, Donald L.; Hammer, Karin

    1986-01-01

    We report the construction of lambda galK promoter cloning vectors for cloning and characterization of strong promoters. This phage, which contains a unique HindIII cloning site, was applied to the cloning and analysis of transcription initiations of the regulatory region of the deo-operon of...... Escherichia coli and the PL promoter of bacteriophage lambda....

  2. Alloreactive cloned T cell lines. I. Interactions between cloned amplifier and cytolytic T cell lines

    OpenAIRE

    1980-01-01

    Several T cell clones have been derived by limiting dilution of secondary mixed leukocyte culture cells stimulated by H-2- and M locus (Mls)-disparate spleen cells. When examined for the expression of cytolytic activity and the ability to proliferate, these cell clones can be classified into two major categories. One type of cell is noncytolytic; when cultured with irradiated spleen cells, such clones proliferate in response to Mls determinants. Some, but not all, of these clones express Lyt-...

  3. General View on Gateway Cloning Technology: Faster, Easier, More Accurate Cloning Method

    OpenAIRE

    Meryem JEFFERIES; Mustafa HACIÖMEROĞLU

    2010-01-01

    Gateway Cloning Technology (GCT) is developed by the scientists James Hartley, Dominic Esposito and Mike Brasch. This technology is an universal cloning method based on the site-specific recombination properties of bacteriophage lambda. The Gateway Cloning is performed in two steps. The first step, called BP recombination, the reaction between an attB-flanked DNA fragment and an attP-containing donor vector to generate an entry clone by BP clonase. The second step is called as LR Reaction. I...

  4. Cloning and Sequence Analysis of Capsid Protein Gene of Iridovirus Indonesian Isolates

    Directory of Open Access Journals (Sweden)

    Murwantoko .

    2015-11-01

    Full Text Available generated by an Adobe application 11.5606 Iridovirus was known as agents that caused serious systemic disease in freshwater and marine fishes. The mortality up to 100% of orange-spotted grouper (Epinephelus coioides due to iridovirus infection has been reported in Indonesia. The gene encoding capsid protein of iridovirus is supposed to be conserved and has the potency for the development of control methods. The objectives of this study are to clone the gene encoding capsid protein iridovirus and to analyze their sequences. The   spleen tissues of orange-spotted grouper were collected and extracted their DNA. The DNA fragment of capsid protein of iridovirus genes were amplified by PCR using designed primers with the extraction DNA as templates. The amplified DNA fragments were cloned in pBSKSII and sequenced.  The genes encoding capsid protein of iridovirus from Jepara and Bali were successfully amplified and cloned. The Jepara clone (IJP03 contained complete open reading frame (ORF of the gene composed by 1362 bp nucleotides which encoded 453 amino acids. Those Jepara and Bali (IGD01 clones shared 99.8% similarity in nucleotide level and 99.4% at amino acid level. Based on those sequences, Indonesian iridovirus was belonged to genus Megalocystivirus and shared 99,6-99,9% similarity on nucleotide level with DGIV, ISKNV, MCIV, and ALIV Normal 0 36 false false false

  5. Cloning and sequencing of a DNA fragment encoding N37 apoptotic peptide derived from p53

    Institute of Scientific and Technical Information of China (English)

    Yan-xia Bai; Qing-yong Ma; Guang-xiao Yang

    2009-01-01

    Objective It was reported that p53 apoptotic peptide (N37) could inhibit p73 gene through being bound with iASPP, which could induce tumor cell apoptosis. To further explore the function of N37, we constructed the cloning plasmid of DNA fragment encoding p53 (N37) apoptotic peptide by using DNA synthesis and molecular biology methods. Methods According to human p53 sequence from the GenBank database, the primer of p53(N37) gene was designed using Primer V7.0 software. The DNA fragment encoding p53 (N37) apoptotic peptide was amplified by using self-complementation polymerase chain reaction (PCR) method and cloned into the pGEM-T Easy vector. The constructed plasmid was confirmed by endonuclease analysis and sequencing. Results The insertion of objective DNA fragment was confirmed by plasmid DNA enzyme spectrum analysis, p53 (N37) gene was successfully synthesized chemically in vitro. The sequencing result of positive clone was completely identical to the human p53(N37) sequence in GenBank using BLAST software (http://www. ncbi. him. nih. gov/cgi-bin /BLASTn). Conclusion The cloning of DNA fragment encoding p53(N37) apoptotic peptide was constructed by using DNA synthesis and pGEM-T Easy cloning methods. With the constructed plasmid, we could further investigate the function of N37 peptide.

  6. Functional genomics of maize submergence tolerance and cloning of the related gene Sicyp51

    Institute of Scientific and Technical Information of China (English)

    TANG; Wanhu; ZHANG; Zuxin; ZOU; Xiling; ZHENG; Yonglian

    2005-01-01

    In this study, SSH (Suppression Subtractive Hybridization) and cDNA microarray were used to identify genes associated with waterlogging response of maize roots. Mo17 and Hz32 are two maize inbred lines with differential tolerance to hypoxia. Seedlings of the inbred lines with two leaves were submerged in hypoxia buffer. SSH libraries were constructed with cDNA samples from roots. Both forward and reverse subtractions were performed for each inbred line, and 105 positive clones induced by hypoxia were selected by differential screening. The treated and control message RNA were hybridized with the cDNA microarray of Mo17, sequentially, 57 of 3-fold differentially expressed clones were obtained. A total of 162 positive clones were all sequenced. Bioinformatics analysis showed these positive clones represent 85 TUGs, including genes involved in several biochemistry pathways, such as glycolysis, protection, signal transduction, cell construction and energy metabolism and 41 EST with unknown function. Comparison between Mo17 and Hz32 indicates that genes related to hypoxia tolerance have different expression patterns in submerged roots. Several positive clones' expression patterns were revealed by Northern or RT-PCR, and a new gene (Sicyp51), which may contribute to hypoxia tolerance, was identified.

  7. CLONING AND EXPRESSION OF A cDNA SEQUENCE FOR HUMAN THIOREDOXIN

    Institute of Scientific and Technical Information of China (English)

    Liu Qingyong(刘庆勇); Ruan Xiyun(阮喜云); Liu Xiaogong(刘效恭); Ji Zongzheng(纪宗正); Dang Jiangong; Nan Xunyi(南勋义); Wang Quanying(王全颖); Yang Guangxiao(杨广笑)

    2003-01-01

    Objective To clone and determine the sequence and expression of a cDNA segment for human thioredoxin. Methods The cDNA segment of thioredoxin was obtained through amplification by RT-PCR cloning from 143 (TK-) human osteosarcoma cell. The amplified products were cloned into pGEM-T Easy vector and sequenced. Then the expressed vector pBV220-hTRX was constructed and transformed into E.coli strain DH5α for hTRX expression. The hTRX was purified by DEAE-Sephadex A-50 column and the activity of recombinant hTRX was determined by the insulin disulfide reduction assay. Results Comparison of cDNA sequence of the cloned fragments with that of the reported hTRX (GenBank J04026) demonstrated that there were two differences compared to the reported cDNA sequence for hTRX at bp180 and bp284, and the amino acids enceoded altered respectively, but motif of the sequence was identical to that of the reported hTRX. The recombinant hTRX can catalyze insulin reduction by DTT. Conclusion The successful cloning and expression of hTRX cDNA formed a basis for further study on biological functions and utilization of hTRX.

  8. Establishment of Real-Time TaqMan-Fluorescence Quantitative RT-PCR Assay for Detection and Quantification of Porcine Lipoprotein Lipase mRNA

    Institute of Scientific and Technical Information of China (English)

    LIAN Hong-xia; LU De-xun; GAO Min

    2009-01-01

    Porcine lipoprotein lipase (LPL) cDNA was cloned as the standard for real-time quantifying LPL mRNA and the TaqMan-fluorescence quantitative PCR assay for detection was established. The total RNA extracted from Longissimus dorsi of porcine was reverse-transcribed to cDNA. LPL cDNA was ligated with pGM-T vector and transformed into Escherichia coli TOP 10. Plasmid DNA extracted from positive clones was verified by PCR amplification and sequenced. LPL was amplified by real-time fluorescence quantitative PCR from the plasmid DNA. The concentration of DNA template purified was detected by analyzing absorbance in 260 nm and then the combined plasmid was diluted to series as standard for fluorescence quantitative PCR (FQ-PCR). The method of LPL mRNA real-time PCR was well established, which detected as low as 103 with the linear range 103 to 1010 copies. The standard curves showed high correlations (R2=0.9871). A series of standards for real-time PCR analysis have been constructed successfully, and real-time TaqMan-fluorescence quantitative RT-PCR is reliable to quantitatively evaluate FQ-PCR mRNA in L. dorsi of porcine.

  9. Cloning the Promoter of BcNA1 from Brassica napus and Fad2 Gene from Arabidopsis thaliana and Construction of the Plant Expression Vector

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The upstream regulatory region of a seed-specific gene was isolated from the genomic DNA of Brassica napus by PCR amplification. The cloned fragment contained 1755 nucleotides, and shared a sequence homology of 99.6% with the reported data. The coding region of oleic acid desaturase gene was then cloned from Arabidopsis thaliana. The sequencing analysis indicated that the sequence of the PCR product was just the same as reported before. In addition, the plant expression vector harboring the seed-specific promoter and trans-Fad2 gene was constructed.

  10. Cloning and molecular evolution research of porcine GAD65 gene

    Institute of Scientific and Technical Information of China (English)

    YU Hao; SONG Yuefen; LI Li; LIU Di

    2007-01-01

    Glutamate decarboxylase (GAD) has been found in animal and higher plant tissues as well as in yeasts and microorganisms.In animals the enzyme plays an important role in central nervous system activity because the enzyme substrate glutamic acid is a mediator of excitation process and the product, gamma-aminobutyric acid, is the most important mediator of inhibition process in the central nervous system. GAD65 is one form of the glutamate decarboxylases (GAD), GAD65 has been identified as a major autoantigen in type 1 diabetes, so the GAD65 gene of porcine was cloned by RT-PCR method to construct phylogenetic tree, the homology of 13glutamate decarboxylases (GAD) of different origin was analyzed by multiple alignment.

  11. ES cells derived from cloned embryos in monkey - a jump toward human therapeutic cloning

    Institute of Scientific and Technical Information of China (English)

    Xiangzhong Yang; Sadie L Smith

    2007-01-01

    @@ Therapeutic cloning refers to the derivation of embryonic stem cells (ntESC) from embryos derived from somatic cell nuclear transfer (SCNT) also known as cloning. Cloning involves transplanting a differentiated cell into an oocyte that has had its nucleus (DNA) removed.

  12. Comparison of Droplet Digital PCR to Real-Time PCR for Quantitative Detection of Cytomegalovirus

    OpenAIRE

    Hayden, R. T.; Gu, Z; Ingersoll, J; Abdul-Ali, D.; Shi, L; Pounds, S.; Caliendo, A. M.

    2013-01-01

    Quantitative real-time PCR (QRT-PCR) has been widely implemented for clinical viral load testing, but a lack of standardization and relatively poor precision have hindered its usefulness. Digital PCR offers highly precise, direct quantification without requiring a calibration curve. Performance characteristics of real-time PCR were compared to those of droplet digital PCR (ddPCR) for cytomegalovirus (CMV) load testing. Tenfold serial dilutions of the World Health Organization (WHO) and the Na...

  13. Cloning and Identification of Methionine Synthase Gene from Pichia pastoris

    Institute of Scientific and Technical Information of China (English)

    Lan HUANG; Dong-Yang LI; Shao-Xiao WANG; Shi-Ming ZHANG; Jun-Hui CHEN; Xiang-Fu WU

    2005-01-01

    Methionine synthase (MS) is grouped into two classes. Class One MS (MetH) and Class Two MS (MetE) share no homology and differ in their catalytic model. Based on the conserved sequences of metE genes from different organisms, a segment of the metE gene was first cloned from Pichia pastoris genomic DNA by PCR, and its 5' and 3' regions were further cloned by 5'- and 3'-rapid amplification of cDNA ends (RACE), respectively. The assembled sequence reveals an open reading frame encoding a polypeptide of 768 residues, and the deduced product shares 76% identity with MetE of Saccharomyces cerevisiae. P. pastoris methionine synthase (PpMetE) consists of two domains common to MetEs. The active site is located in the C-terminal domain, in which the residues involved in the interaction of zinc with substrates are conserved. Homologous expression of PpMetE in P. pastoris was achieved, and the heterologous expression of PpMetE in the S. cerevisiae strain XJB3-1D that is MetE-defective restored the growth of the mutant on methionine-free minimal media. The gene sequence has been submitted to GenBank/EMBL/DDBJ under accession No. AY601648.

  14. Two-temperature PCR for Microfluidics

    KAUST Repository

    Kodzius, Rimantas

    2010-05-01

    Since its invention in 1983, polymerase chain reaction (PCR) has been the method of choice for DNA amplification. Successful PCR depends on the optimization of several parameters, which is a cumbersome task due to the many variables (conditions and compon

  15. Rapid Cloning and Expression of Glutaryl-7-Aminocephalosporanic Acid Acylase Genes from Soil Samples

    Institute of Scientific and Technical Information of China (English)

    LUO Hui; YU Huimin; LI Qiang; SHEN Zhongyao

    2005-01-01

    A polymerase chain reaction (PCR)-based strategy was developed to rapidly obtain the gene encoding for an industrially important enzyme, glutaryl-7-aminocephalosporanic acid (GL-7-ACA) acylase. Different soil samples were cultured with a Pseudomonas selective medium to enrich specific microorganisms, and then the genomic DNA was extracted to serve as PCR templates. PCR primers for GL-7-ACA acylase gene amplification were designed on the basis of bioinformatics searches and analyses. The method was used to successfully amplify three GL-7-ACA acylase genes from different soil samples. The GL-7-ACA acylase genes were then cloned and overexpressed in Escherichia coli with a relatively high level of 266 unit·L-1.

  16. Utilization of Super BAC Pools and Fluidigm Access Array Platform for High-Throughput BAC Clone Identification: Proof of Concept

    Directory of Open Access Journals (Sweden)

    Peter J. Maughan

    2012-01-01

    Full Text Available Bacterial artificial chromosome (BAC libraries are critical for identifying full-length genomic sequences, correlating genetic and physical maps, and comparative genomics. Here we describe the utilization of the Fluidigm access array genotyping system in conjunction with KASPar genotyping technology to identify individual BAC clones corresponding to specific single-nucleotide polymorphisms (SNPs from an Amplicon Express seven-plate super pooled Amaranthus hypochondriacus BAC library. Ninety-six SNP loci, spanning the length of A. hypochondriacus linkage groups 1, 2, and 15, were simultaneously tested for clone identification from four BAC super pools, corresponding to 28 384-well plates, using a single Fluidigm integrated fluidic chip (IFC. Forty-six percent of the SNPs were associated with a single unambiguous identified BAC clone. PCR amplification and next-generation sequencing of individual BAC clones confirmed the IFC clone identification. Utilization of the Fluidigm Dynamic array platform allowed for the simultaneous PCR screening of 10,752 BAC pools for 96 SNP tag sites in less than three hours at a cost of ~$0.05 per reaction.

  17. Progress in interspecies cloning of mammals

    Institute of Scientific and Technical Information of China (English)

    WEN Duancheng; BI Chunming; CHEN Dayuan

    2004-01-01

    Interspecies mammalian cloning can be achieved by application of two key techniques, i.e.the technique of interspecies nuclear transfer and the technique of interspecies pregnancy.The general principles, problems and possible solutions, as well as the recent advances of interspecies mammalian cloning have been summarized in this review.

  18. Computerized adaptive testing with item cloning

    NARCIS (Netherlands)

    Glas, Cees A.W.; Linden, van der Wim J.

    2003-01-01

    To increase the number of items available for adaptive testing and reduce the cost of item writing, the use of techniques of item cloning has been proposed. An important consequence of item cloning is possible variability between the item parameters. To deal with this variability, a multilevel item

  19. No-cloning theorem in thermofield dynamics

    OpenAIRE

    Prudencio, Thiago

    2011-01-01

    We discuss the relation between the no-cloning theorem from quantum information and the doubling procedure used in the formalism of thermofield dynamics (TFD). We also discuss how to apply the no-cloning theorem in the context of thermofield states defined in TFD. Consequences associated to mixed states, von Neumann entropy and thermofield vacuum are also addressed.

  20. Challenges in regulating farm animal cloning

    DEFF Research Database (Denmark)

    Gunning, Jennifer; Hartlev, Mette; Gamborg, Christian

    Report from the project Cloning in Public: A specific support action within the 6th framework programme, priority 5: Food quality and safety......Report from the project Cloning in Public: A specific support action within the 6th framework programme, priority 5: Food quality and safety...

  1. Real Time PCR: Principles and Application

    OpenAIRE

    Safie Amini; Seyed-Moayed Alavian; Malek Hossein Ahmadipour

    2005-01-01

    The polymerase chain reaction (PCR) has been used as the new golden standard for detecting a wide variety of templates across a range of scientific specialties and also as an essential tool in research laboratories. PCR has completely revolutionized the detection of RNA and DNA viruses(1). Real Time vs. Traditional PCRReal time chemistry allows the detection of PCR amplification during the early phase of the reaction. Measuring the kinetic of the reaction in the early phase of PCR provides a ...

  2. Coconut clones through somatic embryogenesis

    OpenAIRE

    Verdeil, Jean-Luc; Buffard-Morel, Jacqueline; Rival, Alain; Grosdemange, Frédérique; Huet, Christine; Pannetier, Catherine

    1993-01-01

    Une étape importante a été atteinte dans la maîtrise de la propagation végétative #in vitro$ du cocotier : obtention reproductible de plantules à partir de 5 clones appartenant à différents génotypes. Deux sortes de tissus prélevés sur des arbres adultes sélectinnés ont été utilisés : explants foliaires et explants inflorenscenciels. La méthode développée comprend les étapes suivantes : induction de la callogénèse sur explants primaires, induction de l'embryogénèse sur les cals obtenus, matur...

  3. Cloning and expression of Mycobacterium bovis secreted protein MPB51 in Escherichia coli

    Institute of Scientific and Technical Information of China (English)

    JIANG Xiuyun; WANG Chunfeng; WANG Chunfang; HE Zhaoyang

    2007-01-01

    The purpose of this study is to clone,identify,and express the mature secreted protein MPB51 from Mycobacterium bovis and to lay a good foundation for the diagnosis of M.bovis,for applying M.bovis vaccine into clinical practice,and for detection of immunity effectiveness.The gene encoding MPB51 was amplified from M.bovis Valleel 11 chromosomal DNA by using PCR technique,PCR product was approximately 800 bp DNA segment.Clone vector pGEM-T-51 was successfully constructed by the PCR product that was cloned into pGEM-T vector by using T-A clone technique,pGEM-T-51 and pET28a(+)were digested by BamH I and EcoR I double enzymes.The prokaryotic expression vector pET28a-51 was constructed by using the purified MPB51 gene that was subcloned into the expression vector pET28a(+).Plasmid containing pET28a-51 was transformed into competence E.coli BL21(DE3).The bacterium was induced by IPTG and its lysates were loaded directly onto SDS-PAGE.An approximately 30 kDa exogenous protein was observed on the SDS-PAGE.The protein was analyzed by using Western-blotting and it had the antigenic activity ofM.bovis.These results could serve as a basis for further studies on the usefulness of the gene and its expression product in the development of subunit vaccine and DNA vaccine against bovine tuberculosis.

  4. Metabolomic phenotyping of af cloned pig model

    DEFF Research Database (Denmark)

    Clausen, Morten Rahr; Christensen, Kirstine Lykke; Hedemann, Mette Skou;

    2011-01-01

    Background Pigs are widely used as models for human physiological changes in intervention studies, because of the close resemblance between human and porcine physiology and the high degree of experimental control when using an animal model. Cloned animals have, in principle, identical genotypes...... and possibly also phenotypes and this offer an extra level of experimental control which could possibly make them a desirable tool for intervention studies. Therefore, in the present study, we address how phenotype and phenotypic variation is affected by cloning, through comparison of cloned pigs and normal...... outbred pigs. Results The metabolic phenotype of cloned pigs (n = 5) was for the first time elucidated by nuclear magnetic resonance (NMR)-based metabolomic analysis of multiple bio-fluids including plasma, bile and urine. The metabolic phenotype of the cloned pigs was compared with normal outbred pigs (n...

  5. Metabolomic phenotyping of a cloned pig model

    DEFF Research Database (Denmark)

    Clausen, Morten Rahr; Christensen, Kirstine Lykke; Hedemann, Mette Skou;

    2011-01-01

    Background Pigs are widely used as models for human physiological changes in intervention studies, because of the close resemblance between human and porcine physiology and the high degree of experimental control when using an animal model. Cloned animals have, in principle, identical genotypes and...... established. Conclusions From the present study we conclude that cloned and normal outbred pigs are phenotypically different. However, it cannot be concluded that the use of cloned animals will reduce the inter-individual variation in intervention studies, though this is based on a limited number of animals....... possibly also phenotypes and this offer an extra level of experimental control which could possibly make them a desirable tool for intervention studies. Therefore, in the present study, we address how phenotype and phenotypic variation is affected by cloning, through comparison of cloned pigs and normal...

  6. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing.

    Directory of Open Access Journals (Sweden)

    Jonas Binladen

    Full Text Available BACKGROUND: The invention of the Genome Sequence 20 DNA Sequencing System (454 parallel sequencing platform has enabled the rapid and high-volume production of sequence data. Until now, however, individual emulsion PCR (emPCR reactions and subsequent sequencing runs have been unable to combine template DNA from multiple individuals, as homologous sequences cannot be subsequently assigned to their original sources. METHODOLOGY: We use conventional PCR with 5'-nucleotide tagged primers to generate homologous DNA amplification products from multiple specimens, followed by sequencing through the high-throughput Genome Sequence 20 DNA Sequencing System (GS20, Roche/454 Life Sciences. Each DNA sequence is subsequently traced back to its individual source through 5'tag-analysis. CONCLUSIONS: We demonstrate that this new approach enables the assignment of virtually all the generated DNA sequences to the correct source once sequencing anomalies are accounted for (miss-assignment rate<0.4%. Therefore, the method enables accurate sequencing and assignment of homologous DNA sequences from multiple sources in single high-throughput GS20 run. We observe a bias in the distribution of the differently tagged primers that is dependent on the 5' nucleotide of the tag. In particular, primers 5' labelled with a cytosine are heavily overrepresented among the final sequences, while those 5' labelled with a thymine are strongly underrepresented. A weaker bias also exists with regards to the distribution of the sequences as sorted by the second nucleotide of the dinucleotide tags. As the results are based on a single GS20 run, the general applicability of the approach requires confirmation. However, our experiments demonstrate that 5'primer tagging is a useful method in which the sequencing power of the GS20 can be applied to PCR-based assays of multiple homologous PCR products. The new approach will be of value to a broad range of research areas, such as those of

  7. A PCR Assay To Discriminate Human and Ruminant Feces on the Basis of Host Differences in Bacteroides-Prevotella Genes Encoding 16S rRNA

    OpenAIRE

    Bernhard, Anne E.; Field, Katharine G.

    2000-01-01

    Our purpose was to develop a rapid, inexpensive method of diagnosing the source of fecal pollution in water. In previous research, we identified Bacteroides-Prevotella ribosomal DNA (rDNA) PCR markers based on analysis. These markers length heterogeneity PCR and terminal restriction fragment length polymorphism distinguish cow from human feces. Here, we recovered 16S rDNA clones from natural waters that were close phylogenetic relatives of the markers. From the sequence data, we designed spec...

  8. Molecular Characterization of Viable Legionella spp. in Cooling Tower Water Samples by Combined Use of Ethidium Monoazide and PCR

    Science.gov (United States)

    Inoue, Hiroaki; Fujimura, Reiko; Agata, Kunio; Ohta, Hiroyuki

    2015-01-01

    Viable Legionella spp. in environmental water samples were characterized phylogenetically by a clone library analysis combining the use of ethidium monoazide and quantitative PCR. To examine the diversity of Legionella spp., six cooling tower water samples and three bath water samples were collected and analyzed. A total of 617 clones were analyzed for their 16S rRNA gene sequences and classified into 99 operational taxonomic units (OTUs). The majority of OTUs were not clustered with currently described Legionella spp., suggesting the wide diversity of not-yet-cultured Legionella groups harbored in cooling tower water environments. PMID:25736979

  9. MOLECULAR GENE CLONING OF NICOTINE-DEHIDROGENASE FROM THE pAO1 MEGAPLASMID OF ARTHROBACTER NICOTINOVORANS

    Directory of Open Access Journals (Sweden)

    Andreea Andrei

    2013-10-01

    Full Text Available 6-hydroxi-L-nicotine (6HNic has an important potential as a drug for neuro-degenerative disorders and a  suitable simple and reliable method for obtaining contaminant-free 6HNic preparations is required. Here, we envision the in-vitro production of 6HNic by using purified nicotine-dehydrogenase (NDH followed by HPLC or capillary electrophoresis techniques and we focus on the isolation and cloning of the three genes coding the NDH enzyme.  A PCR protocol was established for easy amplification and the DNA fragment containing the ndhLSM genes was directionally cloned into the pART2 vector.

  10. Molecular cloning of the first metazoan beta-1,3 glucanase from eggs of the sea urchin Strongylocentrotus purpuratus.

    OpenAIRE

    Bachman, E S; McClay, D R

    1996-01-01

    We report the molecular cloning of the first beta-1,3 glucanase from animal tissue. Three peptide sequences were obtained from beta-1,3 glucanase that had been purified from eggs of the sea urchin Strongylocentrotus purpuratus and the gene was cloned by PCR using oligonucleotides deduced from the peptide sequences. The full-length cDNA shows a predicted enzyme structure of 499 aa with a hydrophobic signal sequence. A 3.2-kb message is present in eggs, during early embryogenesis, and in adult ...

  11. Real-time PCR in Food Science: PCR Diagnostics.

    Science.gov (United States)

    Rodriguez-Lazaro, David; Cook, Nigel; Hernandez, Marta

    2013-01-01

    A principal consumer demand is a guarantee of the safety and quality of food. The presence of foodborne pathogens and their potential hazard, the use of genetically modified organisms (GMOs) in food production, and the correct labelling in foods suitable for vegetarians are among the subjects where society demands total transparency. The application of controls within the quality assessment programmes of the food industry is a way to satisfy these demands, and is necessary to ensure efficient analytical methodologies are possessed and correctly applied by the Food Sector. The use of real-time PCR has become a promising alternative approach in food diagnostics. It possesses a number of advantages over conventional culturing approaches, including rapidity, excellent analytical sensitivity and selectivity, and potential for quantification. However, the use of expensive equipment and reagents, the need for qualified personnel, and the lack of standardized protocols are impairing its practical implementation for food monitoring and control.

  12. Human Interleukine-1 receptor antagonist:Cloning, Expression and Optimization in E.coli Host

    Directory of Open Access Journals (Sweden)

    Gh. Barati

    2014-07-01

    Full Text Available Introduction & Objective: Interleukine-1 receptor antagonist (IL-1RA is a powerful anti-inflammatory cytokine which limits the biological effects of IL-1. Due to structural similarity between IL-1 and its antagonist, IL-1RA competitively binds to IL-1 receptor which leads to no signal transduction. Therefore , it is applied in the treatment of patients with inflammatory diseases such as Rheumatoid Arthritis. The aim of this study is cloning, expression and op-timization of IL-1RA in E. coli. Materials & Methods: In this experimental study synthetically prepared cDNA was amplified by PCR. After double digestion with NdeI and XhoI restriction enzymes, this gene was cloned in pET28a expression vector. Expression of desired gene was analyzed at RNA level by RT-PCR and at protein level by SDS-PAGE and followed by western blot to confirm SDS-PAGE results. Optimization of recombinant protein expression was performed in dif-ferent IPTG concentrations and harvesting times after induction. Results: The presence of gene in pET28a was determined by colony-PCR and confirmed by restriction digestion. Transcription of cloned gene and expression of high yield recombinant protein were shown by RT-PCR and SDS-PAGE, respectively. The result of SDS-PAGE was confirmed by western blot. Expression was optimized in different induction time and IPTG concentrations Conclusion: The result of this study demonstrated expression of this recombinant protein at high level in E.coli system by pET28a expression vector. This study also showed a direct as-sociation between the increased level of expression and time of induction . Therefore, an overnight induction time with 0.1 mM IPTG concentration is recommended for a high level expression. (Sci J Hamadan Univ Med Sci 2014; 21 (2:145-151

  13. Cloning and characterization of a murine SIL gene

    Energy Technology Data Exchange (ETDEWEB)

    Collazo-Garcia, N.; Scherer, P.; Aplan, P.D. [Roswell Park Cancer Institute, Buffalo, NY (United States)

    1995-12-10

    The human SIL gene is disrupted by a site-specific interstitial deletion in 25% of children with T-cell acute lymphoblastic leukemia. Since transcriptionally active genes are prone to recombination events, the recurrent nature of this lesion suggests that the SIL gene product is transcriptionally active in the cell type that undergoes this interstitial deletion and that the SIL gene product may play a role in normal lymphoid development. To facilitate studies of SIL gene function, we have cloned and characterized a murine SIL gene. The predicted murine SIL protein is 75% identical to the human gene, with good homology throughout the open reading frame. An in vitro translated SIL cDNA generated a protein slightly larger than the predicted 139-kDa protein. Although a prior report detected SIL mRNA expression exclusively in hematopoietic tissues, a sensitive RT-PCR assay demonstrated SIL expression to be ubiquitous, detectable in all tissues examined. Since the RT-PCR assay suggested that SIL mRNA expression was higher in rapidly proliferating tissues, we assayed SIL mRNA expression using a murine erythroleukemia model of terminal differentiation and found it to be dramatically decreased in conjunction with terminal differentiation. These studies demonstrate that the human SIL gene product is quite well conserved in rodents and suggest that the SIL gene product may play a role in cell proliferation. 26 refs., 6 figs.

  14. [Cloning and functional characterization of phytoene desaturase in Andrographis paniculata].

    Science.gov (United States)

    Shen, Qin-qin; Li, Li-xia; Zhan, Peng-lin; Wang, Qiang

    2015-10-01

    A full-length cDNA of phytoene desaturase (PDS) gene from Andrographis paniculata was obtained through RACE-PCR. The cDNA sequence consists of 2 224 bp with an intact ORF of 1 752 bp (GeneBank: KP982892), encoding a ploypeptide of 584 amino acids. Homology analysis showed that the deduced protein has extensive sequence similarities to PDS from other plants, and contains a conserved NAD ( H) -binding domain of plant dehydrase cofactor binding-domain in N-terminal. Phylogenetic analysis demonstrated that ApPDS was more related to PDS of Sesamum indicum and Pogostemon cablin. The semi-quantitative RT-PCR analysis revealed that ApPDS expressed in whole aboveground tissues with the highest expression in leaves. Virus induced gene silencing (VIGS) was performed to characterize the functional of ApPDS in planta. Significant photobleaching was not observed in infiltrated leaves, while the PDS gene has been down-regulated significantly at the yellowish area. To the best of our knowledge, this represents the first report of PDS gene cloning and functional characterization from A. paniculata, which lays the foundation for further investigation of new genes, especially that correlative to andrographolide biosynthetic pathway. PMID:26975098

  15. Cloning and Expression Profiles of Myf5 Gene of Yak

    Directory of Open Access Journals (Sweden)

    Yaqiu Lin

    2015-01-01

    Full Text Available To reveal the sequence characteristic and expression pattern of Myf5 gene in Jiulong yaks (Bos grunniens, a full-length cDNA of Myf5 was cloned from yak muscle tisssue by RT-PCR. The cDNA obtained was 821bp nucleotide (nt long with an ORF of 768 bp which encoding 255 amino acids. Compared with cattle, sheep, pig, horse, human, pygmy chimpanzee, mouse, rat and dog, the homology of amino acid sequences were higher (89-9%, but lower in Zebrafish (60%. SQ RT-PCR analysis showed that Myf5 gene expression was observed only in longissimus muscle, but not be detected in heart, liver, kidney, spleen and adipose tissues. The expression level of Myf5 gene in longissium muscle of 0.5 and over 9 years old yaks was significantly higher than those of 3.5-5.5 years old yaks (p<0.05. These results suggest that Myf5 may play an important role in the regulation of muscle growth and development of yak.

  16. Real-Time PCR (qPCR) Primer Design Using Free Online Software

    Science.gov (United States)

    Thornton, Brenda; Basu, Chhandak

    2011-01-01

    Real-time PCR (quantitative PCR or qPCR) has become the preferred method for validating results obtained from assays which measure gene expression profiles. The process uses reverse transcription polymerase chain reaction (RT-PCR), coupled with fluorescent chemistry, to measure variations in transcriptome levels between samples. The four most…

  17. Aberrant DNA methylation in cloned ovine embryos

    Institute of Scientific and Technical Information of China (English)

    LIU Lei; HOU Jian; LEI TingHua; BAI JiaHua; GUAN Hong; AN XiaoRong

    2008-01-01

    By using the approach of immunofluorescence staining with an antibody against 5-methylcytosine (5MeC), the present study detected the DNA methylation patterns of cloned ovine embryos. The em-bryos derived from in vitro fertilization were also examined for reference purpose. The results showed that: (1) during the pre-implantation development, cloned embryos displayed a similar demethylation profile to the fertilized embryos; that is, the methylation level decreased to the lowest at 8-cell stage, and then increased again at morulae stage. However, methylation level was obviously higher in cloned embryos than in stage-matched fertilized embryos, especially at 8-cell stage and afterwards; (2) at blastocyst stage, the methylation pattern in cloned embryos was different from that in fertilized em-bryos. In cloned blastocyst, inner cell mass (ICM) exhibited a comparable level to trophectoderm cells (TE), while in in-vitro fertilized blastocyst the methylation level of ICM was lower than that of TE, which is not consistent with that reported by other authors. These results indicate that DNA methylation is abnormally reprogrammed in cloned embryos, implying that aberrant DNA methylation reprogramming may be one of the factors causing cloned embryos developmental failure.

  18. Human embryo cloning prohibited in Hong Kong.

    Science.gov (United States)

    Liu, Athena

    2005-12-01

    Since the birth of Dolly (the cloned sheep) in 1997, debates have arisen on the ethical and legal questions of cloning-for-biomedical-research (more commonly termed "therapeutic cloning") and of reproductive cloning using human gametes. Hong Kong enacted the Human Reproductive Technology Ordinance (Cap 561) in 2000. Section 15(1)(e) of this Ordinance prohibits the "replacing of the nucleus of a cell of an embryo with a nucleus taken from any other cell," i.e., nucleus substitution. Section 15(1)(f) prohibits the cloning of any embryo. The scope of the latter, therefore, is arguably the widest, prohibiting all cloning techniques such as cell nucleus replacement, embryo splitting, parthenogenesis, and cloning using stem cell lines. Although the Human Reproductive Technology Ordinance is not yet fully operative, this article examines how these prohibitions may adversely impact on basic research and the vision of the Hong Kong scientific community. It concludes that in light of recent scientific developments, it is time to review if the law offers a coherent set of policies in this area.

  19. PCR-based diversity estimates of artificial and environmental 18S rRNA gene libraries.

    Science.gov (United States)

    Potvin, Marianne; Lovejoy, Connie

    2009-01-01

    Environmental clone libraries constructed using small subunit ribosomal RNA (rRNA) or other gene-specific primers have become the standard molecular approach for identifying microorganisms directly from their environment. This technique includes an initial polymerase chain reaction (PCR) amplification step of a phylogenetically useful marker gene using universal primers. Although it is acknowledged that such primers introduce biases, there have been few studies if any to date systematically examining such bias in eukaryotic microbes. We investigated some implications of such bias by constructing clone libraries using several universal primer pairs targeting rRNA genes. Firstly, we constructed artificial libraries using a known mix of small cultured pelagic arctic algae with representatives from five major lineages and secondly we investigated environmental samples using several primer pairs. No primer pair retrieved all of the original algae in the artificial clone libraries and all showed a favorable bias toward the dinoflagellate Polarella glacialis and a bias against the prasinophyte Micromonas and a pennate diatom. Several other species were retrieved by only one primer pair tested. Despite this, sequences from nine environmental libraries were diverse and contained representatives from all major eukaryotic clades expected in marine samples. Further, libraries from the same sample grouped together using Bray-Curtis clustering, irrespective of primer pairs. We conclude that environmental PCR-based techniques are sufficient to compare samples, but the total diversity will probably always be underestimated and relative abundance estimates should be treated with caution.

  20. CLONING AND SEQUENCING OF MATURE FRAGMENT OF HUMAN BMP4 GENE

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Objective To study the cloning and sequencing of mature fragment of human bone morphogenetic protein-4 gene. Methods The template DNA was obtained from the human osteosarcoma cell line U2OS. By using RT- PCR method, the cDNA coding for the mature fragment of BMP-4 was amplified, cloned into the vector pUC19, and sequenced by Sanger Dideoxy-mediated Chain Termination method. Results The mature fragment of BMP4 cDNA was obtained by RT-PCR and determined by sequencing. Through the computer search on Genebank, the analysis showed that the homology of nucleotides and amino acids between cDNA of rhBMP4 mature fragment of this study and the published sequence was 99%. Sequence analysis showed that there were two differences, one was at base 1154 (201): G→C, which had no influence on the corresponding amino acids (Val). Another was at basel222 (269):C→T, the mutation at the base 1222 had the change of Ala to Val. Conclusion The mature fragment of BMP4 gene has been cloned. The results will be of great significance in treatment of skeletal injuries and diseases.

  1. Cloning and sequencing of cagA gene fragment of Helicobacter pylori with coccoid form

    Institute of Scientific and Technical Information of China (English)

    Ke-Xia Wang; Xue-Feng Wang

    2004-01-01

    AIM: To clone and sequence the cagA gene fragment of Helicobacter pylori ( H pylori) with coccoid form.METHODS: H pylori strain NCTC11637 were transformed to coccoid form by exposure to antibiotics in subinhibitory concentrations. The coccoid H pyloriwas collected. cagA gene of the coccoid H pylori strain was amplified by PCR.After purified, the target fragment was cloned into plasmid pMD-18T. The recombinant plasmid pMD-18T-cagA was transformed into E. coli JM109. Positive clones were screened and identified by PCR and digestion with restriction endonucleases. The sequence of inserted fragment was then analysed.RESULTS: cagA gene of 3 444 bp was obtained from the coccoid H pylori genome DNA. The recombinant plasmid pMD-18T-cagA was constructed, then it was digested by BamH Ⅰ+Sac Ⅰ, and the product of digestion was identical with the predicted one. Sequence analysis showed that the homology of coccoid and the reported original sequence H pylori was 99.7%.CONCLUSION: The recombinant plasmid containing cagA gene from coccoid H pylori has been constructed successfully.The coccoid H pylori contain completed cagA gene, which may be related to pathogenicity of them.

  2. Human embryo cloning prohibited in Hong Kong

    OpenAIRE

    Liu, Athena

    2005-01-01

    Since the birth of Dolly (the cloned sheep) in 1997, debates have arisen on the ethical and legal questions of cloning-for-biomedical-research (more commonly termed “therapeutic cloning”) and of reproductive cloning using human gametes. Hong Kong enacted the Human Reproductive Technology Ordinance (Cap 561) in 2000. Section 15(1)(e) of this Ordinance prohibits the “replacing of the nucleus of a cell of an embryo with a nucleus taken from any other cell,” i.e., nucleus substitution. Section 15...

  3. Simplified cryopreservation of porcine cloned blastocysts

    DEFF Research Database (Denmark)

    Du, Yutao; Zhang, Yunhai; Li, Juan;

    2007-01-01

    )â€"handmade cloning (HMC)â€"to establish a simplified and efficient cryopreservation system for porcine cloned embryos. In Experiment 1, zonae pellucidae of oocytes were partially digested with pronase, followed by centrifugation to polarize lipid particles. Ninety percent (173/192) oocytes were successfully......). Our results prove that porcine embryos produced from delipated oocytes by PA or HMC can be cryopreserved effectively by ultrarapid vitrification. Further experiments are required to assess the in vivo developmental competence of the cloned-vitrified embryos  ...

  4. Maximum confidence measurements via probabilistic quantum cloning

    Institute of Scientific and Technical Information of China (English)

    Zhang Wen-Hai; Yu Long-Bao; Cao Zhuo-Liang; Ye Liu

    2013-01-01

    Probabilistic quantum cloning (PQC) cannot copy a set of linearly dependent quantum states.In this paper,we show that if incorrect copies are allowed to be produced,linearly dependent quantum states may also be cloned by the PQC.By exploiting this kind of PQC to clone a special set of three linearly dependent quantum states,we derive the upper bound of the maximum confidence measure of a set.An explicit transformation of the maximum confidence measure is presented.

  5. A versatile bacterial expression vector designed for single-step cloning of multiple DNA fragments using homologous recombination.

    Science.gov (United States)

    Holmberg, Mats A; Gowda, Naveen Kumar Chandappa; Andréasson, Claes

    2014-06-01

    Production of recombinant proteins is the starting point for biochemical and biophysical analyses and requires methodology to efficiently proceed from gene sequence to purified protein. While optimized strategies for the efficient cloning of single-gene fragments for bacterial expression is available, efficient multiple DNA fragment cloning still presents a challenge. To facilitate this step, we have developed an efficient cloning strategy based on yeast homologous recombination cloning (YHRC) into the new pET-based bacterial expression vector pSUMO-YHRC. The vector supports cloning for untagged expression as well as fusions to His6-SUMO or His6 tags. We demonstrate that YHRC from single PCR products of 6 independent genes into the vector results in virtually no background. Importantly, in a quantitative assay for functional expression we find that single-step YHRC of 7 DNA fragments can be performed with very high cloning efficiencies. The method and reagents described in this paper significantly simplifies the construction of expression plasmids from multiple DNA fragments, including complex gene fusions, chimeric genes and polycistronic constructs. PMID:24631626

  6. Validation of Reference Genes for Quantitative Real-Time PCR in Laodelphax striatellus

    Institute of Scientific and Technical Information of China (English)

    HE Xiu-ting; LIU Cheng-cheng; LI Zhao-qun; ZHANG Zan; LI Guo-qing; LI Fei; DONG Shuang-lin

    2014-01-01

    The normalization of quantitative real-time PCR (qPCR) is important to obtain accurate gene expression data, and the most common method for qPCR normalization is to use reference genes. However, reference genes can be regulated under different conditions. qPCR has recently been used for gene expression study in Laodelphax striatellus, but there is no study on validation of the reference genes. In this study, ifve new housekeeping genes (LstrTUB1, LstrTUB2, LstrTUB3, LstrARF and LstrRPL9) in L. striatellus were cloned and deposited in the GenBank with accession numbers of JF728809, JF728810, JF728811, JF728807 and JF728806, respectively. Furthermore, mRNA expressions of the five genes and β-actin were measured by qPCR with insect samples of different instar at nymph stage, and the expression stabilities were determined by the software geNorm and NormFinder. As a result, ARF and RPL9 were consistently more stable thanβ-actin, while three TUB genes were less stable than β-actin. To determine the optimal number of reference genes used in qPCR, a pairwise variations analysis by geNorm indicated that two references ARF and RPL9 were required to obtain the accurate quantiifcation. These results were further conifrmed by the validation qPCR experiment with chitinase gene as the target gene, in which the standard error of the mRNA quantiifcation by using binary reference ARF-RPL9 was much lower than those by ARF, RPL9 orβ-actin alone. Taken together, our study suggested that the combination of ARF-RPL9 could replaceβ-actin as the reference genes for qPCR in L. striatellus.

  7. PCR associated with hybridization with DNA radioactive probes for diagnosis of asymptomatic infection caused by Leishmania Chagasi; PCR associado a hibridizacao com sondas radioativas de DNA para a identificacao de infeccao subclinica causada por Leishmania Chagasi

    Energy Technology Data Exchange (ETDEWEB)

    Andrade, Antero Silva Ribeiro de [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN), Belo Horizonte, MG (Brazil); Moreno, Elizabeth Castro [Fundacao Nacional de Saude, Belo Horizonte, MG (Brazil). Coordenacao Regional de Minas Gerais; Gomes, Rosangela Fatima; Melo, Maria Norma de; Carneiro, Mariangela [Minas Gerais Univ., Belo Horizonte, MG (Brazil). Dept. de Parasitologia; Fernandes, Octavio [Fundacao Inst. Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, RJ (Brazil). Dept. de Medicina Tropical

    2002-07-01

    Detection systems for diagnosis of leishmaniasis based on PCR are very promising due to their sensitivity and specificity. Secondary detection by specific radioactive DNA probes, able to type the PCR amplified products, increase the specificity and raise about tem-fold the sensitivity of the assay. The aim of this work was evaluate PCR and hybridization as a tool to identify Leishmania (Leishmania) chagasi (the specie that cause the visceral leishmaniasis in Brazil) infection in asymptomatic persons living in a endemic area. Material and Methods: A group of 226 asymptomatic individuals, living in General Carneiro (MG), was selected. Blood samples were harvested and the DNA extracted from the mononucleate cells. PCR was performed using primers addressed to the kinetoplast DNA minicircles. This protocol gives a positive reaction for all Leishmania species. The amplified products were further hybridized with cloned L.chagasi minicircles labeled with {sup 32} P. Results: were identified 111 samples PCR positive, 2 of them hybridization negative and 133 samples hybridization positive, 24 of them PCR negative. The occurrence of samples with hybridization positive and PCR negative was expected since hybridization, with DNA probes labeled with {sup 32} P, increase the sensitivity of the assay. The samples that presented positive PCR and negative hybridization were probably due the presence of other Leishmania species, likely L. (V.) braziliensis (that produce tegumentary leishmaniasis in the region), since L. (L.) chagasi cloned minicircles were used as hybridization probe. We conclude that this procedure is a valuable tool to access subclinical L. (L.) chagasi infections in epidemiological studies. (author)

  8. Anchored PCR (A-PCR):A new method for chromosome walking

    Institute of Scientific and Technical Information of China (English)

    CHEN Bojun; SUN Chao; WANG Yong; HU Yuanlei; LIN Zhongping

    2004-01-01

    @@ PCR-based techniques are most popular methods for isolation of DNA sequences flanking a known region.Such techniques published to date mainly include three types: inverse PCR (IPCR)[1-3], ligation-mediated PCR (LM-PCR)[4-9] and randomly primed PCR (RP-PCR)[10-12].IPCR was the first method developed for this kind of purpose. However, it is now rarely used because of the difficulty in finding suitable restriction sites in the target region or poor circularization of the template molecule.LM-PCR and RP-PCR are more frequently used nowadays, yet they also have some limitations. For example,LM-PCR depends on restriction sites within a reasonable distance in the flanking regions, while the amplified products of RP-PCR are generally small (<1 kb). Moreover, both methods often result in excessive amplification of non-specific molecules, which greatly reduces their efficiencies in obtaining sequences of interest. To resolve these problems, some new strategies have emerged in the past few years, such as Vectorette-PCR[6], biotin-capture PCR[7], TAIL-PCR[l2] and T-linker PCR[9]. These improved methods are more efficient than their old versions;however, most of them are still limited by restriction digestion or ligation. Although the intervening steps are avoided in TAIL-PCR, the amplified fragments are often small because of the use of random primers.

  9. Insulated Isothermal Reverse Transcriptase PCR (iiRT-PCR) for Rapid and Sensitive Detection of Classical Swine Fever Virus.

    Science.gov (United States)

    Lung, O; Pasick, J; Fisher, M; Buchanan, C; Erickson, A; Ambagala, A

    2016-10-01

    Classical swine fever (CSF) is an OIE-listed disease that can have a severe impact on the swine industry. User-friendly, sensitive, rapid diagnostic tests that utilize low-cost field-deployable instruments for CSF diagnosis can be useful for disease surveillance and outbreak monitoring. In this study, we describe validation of a new probe-based insulated isothermal reverse transcriptase PCR (iiRT-PCR) assay for rapid detection of classical swine fever virus (CSFV) on a compact, user-friendly device (POCKIT(™) Nucleic Acid Analyzer) that does not need data interpretation by the user. The assay accurately detected CSFV RNA from a diverse panel of 33 CSFV strains representing all three genotypes plus an additional in vitro-transcribed RNA from cloned sequences representing a vaccine strain. No cross-reactivity was observed with a panel of 18 viruses associated with livestock including eight other pestivirus strains (bovine viral diarrhoea virus type 1 and type 2, border disease virus, HoBi atypical pestivirus), African swine fever virus, swine vesicular disease virus, swine influenza virus, porcine respiratory and reproductive syndrome virus, porcine circovirus 1, porcine circovirus 2, porcine respiratory coronavirus, vesicular exanthema of swine virus, bovine herpes virus type 1 and vesicular stomatitis virus. The iiRT-PCR assay accurately detected CSFV as early as 2 days post-inoculation in RNA extracted from serum samples of experimentally infected pigs, before appearance of clinical signs. The limit of detection (LOD95% ) calculated by probit regression analysis was 23 copies per reaction. The assay has a sample to answer turnaround time of less than an hour using extracted RNA or diluted or low volume of neat serum. The user-friendly, compact device that automatically analyses and displays results could potentially be a useful tool for surveillance and monitoring of CSF in a disease outbreak. PMID:25644051

  10. Analysis of bacterial communities in soil by use of denaturing gradient gel electrophoresis and clone libraries, as influenced by different reverse primers

    NARCIS (Netherlands)

    Brons, Jolanda; van Elsas, J.D.

    2008-01-01

    To assess soil bacterial diversity, PCR systems consisting of several slightly different reverse primers together with forward primer F968-GC were used along with subsequent denaturing gradient gel electrophoresis (DGGE) or clone library analyses. In this study, a set of 13 previously used and novel

  11. Cloning and characterization of new bioluminescent proteins

    Science.gov (United States)

    Szent-Gyorgyi, Christopher; Ballou, Byron T.; Dagnal, Erich; Bryan, Bruce

    1999-07-01

    Over the past two years Prolume has undertaken a comprehensive program to clone luciferases and associated 'green fluorescent proteins' (GFPs) from marine animals that use coelenterazine as the luciferin. To data we have cloned several bioluminescent proteins, including two novel copepod luciferases and two anthozoan GFPs. These four proteins have sequences that differ greatly form previously cloned analogous proteins; the sequence diversity apparently is due to independent evolutionary origins and unusual evolutionary constraints. Thus coelenterazine-based bioluminescent systems may also manifest a variety of useful properties. We discuss form this taxonomic perspective the initial biochemical and spectral characterization of our cloned proteins. Emphasis is placed on the anthozoan luciferase-GFP systems, whose efficient resonance energy transfer has elicited much current interest.

  12. A genetic system for direct selection of gene-positive clones during recombinational cloning in yeast

    OpenAIRE

    Noskov, Vladimir; Kouprina, Natalay; Leem, Sun-Hee; Koriabine, Maxim; Barrett, J. Carl; Larionov, Vladimir

    2002-01-01

    Transformation-associated recombination (TAR) is a cloning technique that allows specific chromosomal regions or genes to be isolated directly from genomic DNA without prior construction of a genomic library. This technique involves homologous recombination during spheroplast transformation between genomic DNA and a TAR vector that has 5′ and 3′ gene targeting sequences (hooks). Typically, TAR cloning produces positive YAC recombinants at a frequency of ∼0.5%; the positive clones are identifi...

  13. Application of Reverse Transcription-PCR and Real-Time PCR in Nanotoxicity Research

    Science.gov (United States)

    Mo, Yiqun; Wan, Rong; Zhang, Qunwei

    2016-01-01

    Reverse transcription-polymerase chain reaction (RT-PCR) is a relatively simple and inexpensive technique to determine the expression level of target genes and is widely used in biomedical science research including nanotoxicology studies for semiquantitative analysis. Real-time PCR allows for the detection of PCR amplification in the exponential growth phase of the reaction and is much more quantitative than traditional RT-PCR. Although a number of kits and reagents for RT-PCR and real-time PCR are commercially available, the basic principles are the same. Here, we describe the procedures for total RNA isolation by using TRI Reagent, for reverse transcription (RT) by M-MLV reverse transcriptase, and for PCR by GoTaq® DNA Polymerase. And real-time PCR will be performed on an iQ5 multicolor real-time PCR detection system by using iQ™ SYBR Green Supermix. PMID:22975959

  14. Cloning and Identification of A Novel Variant of Human Vascular Endothelial Growth Factor

    Institute of Scientific and Technical Information of China (English)

    GUO; Jianli; QU; Shen

    2001-01-01

    A novel variant of human vascular endothelial growth factor (h'VEGF165) cDNA was amplified by nested PCR method from the HL601 cells and was cloned into a eukaryotic expressing vector pcDNA3 to construct a recombinant plasmid pCD-h'VEGF165. The amplified h'VEGF165cDNA fragment was identified by enzyme digestion and DNA sequencing methods. Also, wild-type hVEGF165 cDNA was obtained, identified and cloned into a eukaryotic expressing vector pcDNA3by using the same methods. The results of DNA sequencing showed that h'VEGF165 cDNA cloned from HL601 was 600 bp in size with 8 % of the base sequence in h'VEGF165 cDNA being changed as compared with the base sequence in the wild-type hVEGF165 cDNA. The results of sequencing of hVEGF165 which was cloned from HL60 by us were consistent with the reports completely.

  15. cDNA Cloning and Sequence Analysis of Rice Sbel and Sbe3 Genes

    Institute of Scientific and Technical Information of China (English)

    CHENXiu-hua; LIUQiao-quan; WuHsin-kan; WANGZong-yang; GuMing-hong

    2004-01-01

    Two starch-branching enzyme (SBE) in rice, is known to be a key enzyme in amylopectin biosynthesis. The cDNA of two SBE(starch-branching enzyme) genes SheI and Shed encoding SBE Ⅰ and SBE Ⅲ (two major isoforms in rice) were cloned by an improved RT-PCR technique, from a template cDNA libray, derived from the total mRNAs extracted from the immature seeds of a japonica rice Wuyunjing 7. DNA sequence analysis showed that the size of the cloned SheI and Shed cDNAs were 2490 and 2481 bp long, respectively, including their entire coding sequences. Comparison analysis indicated that the nucleotide sequence of She3 was the same as that of shed (Genbank Accession No. D16201) as reported previously. There were only four base-pairs difference,which resulted in changes of two deduced amino acids between the cloned She1 cDNA and the reported she1 (Genbank Accession No. D11082). The cloned SheI and Shed cDNAs make it possible to improve rice starch quality through genetic engineering.

  16. cDNA Cloning and Sequence Analysis of Rice Sbe1 and Sbe3 Genes

    Institute of Scientific and Technical Information of China (English)

    CHEN Xiu-hua; LIU Qiao-quan; WU Hsin-kan; WANG Zong-yang; GU Ming-hong

    2004-01-01

    Two starch-branching enzyme (SBE) in rice, is known to be a key enzyme in amylopectin biosynthesis. The cDNA of two SBE(starch-branching enzyme) genes Sbe1 and Sbe3 encoding SBE I and SBE Ⅲ (two major isoforms in rice) were cloned by an improved RT-PCR technique, from a template cDNA library derived from the total mRNAs extracted from the immature seeds of a japonica rice Wuyunjing 7. DNA sequence analysis showed that the size of the cloned Sbe1 and Sbe3 cDNAs were 2490 and 2481 bp long, respectively, including their entire coding sequences. Comparison analysis indicated that the nucleotide sequence of Sbe3 was the same as that of sbe3 (Genbank Accession No. D16201) as reported previously. There were only four base-pairs difference,which resulted in changes of two deduced amino acids between the cloned Sbe1 cDNA and the reported sbe1 (Genbank Accession No. D11082). The cloned Sbe1 and Sbe3 cDNAs make it possible to improve rice starch quality through genetic engineering

  17. Recombinatorial Cloning Using Heterologous Lox Sites

    OpenAIRE

    Siegel, Robert W.; Velappan, Nileena; Pavlik, Peter; Chasteen, Leslie; Bradbury, Andrew

    2004-01-01

    Recombination systems based on λ and Cre/loxP have been described to facilitate gene transfer from one vector to another in a high-throughput fashion, avoiding the bottlenecks associated with traditional cloning. However, no system described to date is suitable for the cloning of affinity reagents selected from display libraries, which requires that the recombination signals flanking the affinity reagent are translated with a minimum impact on functionality. As affinity reagents will be essen...

  18. Teleportation using continuous variable quantum cloning machine

    OpenAIRE

    Adhikari, Satyabrata

    2008-01-01

    We show that an unknown quantum state in phase space can be teleported via three-mode entanglement generated by continuous variable quantum cloning machine (transformation). Further, proceeding with our teleportation protocol we are able to improve the fidelity of teleportation obtained by Loock et.al. [Phys.Rev.Lett. 84, 3482(2000)]. Also we study here the entanglement between the two output copies from cloning machine.

  19. Towards Clone Detection in UML Domain Models

    DEFF Research Database (Denmark)

    Störrle, Harald

    2013-01-01

    on the thorough analysis of practical scenarios. We propose a formal definition of model clones, specify a clone detection algorithm for UML domain models, and implement it prototypically. We investigate different similarity heuristics to be used in the algorithm, and report the performance of our approach. While...... we believe that our approach advances the state of the art significantly, it is restricted to UML models, its results leave room for improvements, and there is no validation by field studies....

  20. Is There a Constitutional Right to Clone?

    OpenAIRE

    Sunstein, Cass Robert

    2002-01-01

    Recent scientific innovations, and proposed legislation, have raised questions about the nature of the constitutional right to reproductive freedom, and in particular about whether there is a constitutional “right to clone.” This essay urges that as a matter of substantive due process, rationality review is probably appropriate, and that restrictions on both reproductive and therapeutic cloning would and should survive constitutional scrutiny. At the same time, many of the arguments for banni...

  1. Bacteriophage Lambda as a Cloning Vector

    OpenAIRE

    Chauthaiwale, V M; Therwath, A; Deshpande, V V

    1993-01-01

    Extensive research has been directed toward the development of multipurpose lambda vectors for cloning ever since the potential of using coliphage lambda as a cloning vector was recognized in the late 1970s. An understanding of the intrinsic molecular organization and of the genetic events which determine lysis or lysogeny in lambda has allowed investigators to modify it to suit the specific requirements of gene manipulations. Unwanted restriction sites have been altered and arranged together...

  2. Economical phase-covariant cloning with multiclones

    Institute of Scientific and Technical Information of China (English)

    Zhang Wen-Hai; Ye Liu

    2009-01-01

    This paper presents a very simple method to derive the explicit transformations of the optimal economical to M phase-covariant cloning. The fidelity of clones reaches the theoretic bound [D'Ariano G M and Macchiavello C 2003 Phys. Rcv. A 67 042306]. The derived transformations cover the previous contributions [Delgado Y,Lamata L et al,2007 Phys. Rev. Lett. 98 150502] in which M must be odd.

  3. Cloning and Homology Comparison of S Gene for Isolate TH-98 of Porcine Transmissible Gastroenteritis Virus

    Institute of Scientific and Technical Information of China (English)

    REN Xiao-feng; LI Yi-jing; LIU Bao-quan

    2003-01-01

    TH-98 isolate of transmissible gastroenteritis virus (TGEV) was propagated and harvested onswine testicle (ST) monolayer ceil. Two pairs of primers were designed to amplify S gene by RT-PCR accord-ing to the published sequence of TGEV'S gene cDNA with Oligo version 4.1 and DNasis software. The productsof PCR were named Sa and Sb, of 2.3 kb and 2.1 kb respectively. Sa was inserted in EcoR I and Kpn I sitesafter Sb was cloned in Kpn I and Pst I multiple cloning sites of the same pUC18 plasmid. The recombinantpUC-S plasmid was identified and analyzed by corresponding restriction endonuclease and nested PCR on thebasis of the genetic sites of S gene and pUC18 plasmid, which was identified as S gene of TGEV. RecombinantpUC-S was sequenced and analyzed in comparison with the other strains. Gene sequence comparison indicatedthat TH-98 shared 99, 97, 98, 97 and 94% identities with Purdue-115(US), Miller(US), TO14(Japan),FS772(British), 96-1933(British), respectively, their deduced amino acid homology was 99, 97, 97, 96 and93% correspondingly. In addition, the analysis report verified that pUC-S owned a complete open readingframe (ORF) including initiation codon, signal sequences, remaining sequences and termination codon aswell. Therefore, the results affirmed that S gene of TGEV TH-98 was extremely conservative.

  4. Partial and full PCR-based reverse genetics strategy for influenza viruses.

    Directory of Open Access Journals (Sweden)

    Hongjun Chen

    Full Text Available Since 1999, plasmid-based reverse genetics (RG systems have revolutionized the way influenza viruses are studied. However, it is not unusual to encounter cloning difficulties for one or more influenza genes while attempting to recover virus de novo. To overcome some of these shortcomings we sought to develop partial or full plasmid-free RG systems. The influenza gene of choice is assembled into a RG competent unit by virtue of overlapping PCR reactions containing a cDNA copy of the viral gene segment under the control of RNA polymerase I promoter (pol1 and termination (t1 signals - herein referred to as Flu PCR amplicons. Transfection of tissue culture cells with either HA or NA Flu PCR amplicons and 7 plasmids encoding the remaining influenza RG units, resulted in efficient virus rescue. Likewise, transfections including both HA and NA Flu PCR amplicons and 6 RG plasmids also resulted in efficient virus rescue. In addition, influenza viruses were recovered from a full set of Flu PCR amplicons without the use of plasmids.

  5. Do Clones Dream of Love? Images of Clones in Popular Culture

    Directory of Open Access Journals (Sweden)

    Dragana Antonijević

    2016-02-01

    Full Text Available Fantasies about clones, cyborgs and androids have become part and parcel of the mythology of modern times – the mythologies of the biotechnological era in which the achievements of genetic engineering have inflamed fears of possible abuse of scientific knowledge and the consequences of such abuse. The paper considers the phenomenon of reproductive cloning of human beings as it is represented in popular culture, especially film as it is one of the most important sources of representations and constructions of ideas about clones. After the introductory consideration of this phenomenon in scientific, ethical and media debates which are imbued with rejection of reproductive cloning, I have analyzed the different uses of the clone motif in selected movies. I have examined the structure and content of the genre formula of "social melodrama" which is present in films about clones, and have analyzed the mythical patterns pertaining to the topic of cloning, such as the myth of immortality, the myth of twins, the myth of the uniqueness of human kind etc. Ultimately, the nature and origins of the fear of clones and disgust that clones cause have been examined, and it has been shown that they mostly boil down to the fear of the dehumanization of human beings, the fear of the loss of difference and the transgression of biological, sociocultural and metaphysical boundaries.

  6. T-linker-specific ligation PCR (T-linker PCR): an advanced PCR technique for chromosome walking or for isolation of tagged DNA ends

    OpenAIRE

    Yuanxin, Yan; Chengcai, An; Li, Li; Jiayu, Gu; Guihong, Tan; Zhangliang, Chen

    2003-01-01

    Dozens of PCR-based methods are available for chromosome walking from a known sequence to an unknown region. These methods are of three types: inverse PCR, ligation-mediated PCR and randomly primed PCR. However, none of them has been generally applied for this purpose, because they are either difficult or inefficient. Here we describe a simple and efficient PCR strategy—T-linker-specific ligation PCR (T-linker PCR) for gene or chromosome walking. The strategy amplifies the template molecules ...

  7. Cloning of polyadenylated mRNA fragments of Escherichia coli with restriction display-polymerase chain reaction

    Institute of Scientific and Technical Information of China (English)

    HU Zi-you; MA Wen-li; SONG Yan-bin; ZHANG Bao; WU Qing-hua; GUO Qiu-ye; PENG Yi-fei; ZHENG Wen-ling

    2002-01-01

    Objective:To investigate the polyadenylation of mRNA in E. Coli. Methods: The mRNA of E. Coli was enriched from the total RNA with oligo(dT)-cellulose, prior to reverse transcription using oligo(dT)18as the primer. Double-stranded cDNA was subsequently synthesized, which was subjected to digestion with Sau3A I to produce multiple gene fragments for ligation with the adapters. PCR was carried out in 10 groups according to 10 different pairs of the selective primers, and the PCR products were then cloned into T-vectors. Results: More than 100 gene fragments had been cloned, 30 of which were sequenced. Conclusion:Polyadenylation of E. Coli mRNA may not be a biochemical curiosity but a general attribute of bacterial mRNA.

  8. Cloning and sequence analysis of hsf, an outer membrane protein gene of Pasteurella multocida serotype B:2

    Directory of Open Access Journals (Sweden)

    A. Priyadarshini

    2014-12-01

    Full Text Available Aim: The present study was undertaken to clone, sequence and analyze the hsf, an outer membrane protein gene of Pasteurella multocida serotype B:2 Materials and Methods: hsf gene was amplified from genomic DNA of P. multocida. Polymerase chain reaction (PCR product was cloned in pET-32a vector and was characterized. hsf gene was sequenced, analyzed and phylogenetic tree was constructed taking sequences of other strains. Results: Amplicon size was found to be 785 bp. Recombinant got characterized through colony PCR and restriction enzyme analysis. Conclusion: hsf gene of P. multocida serotype B is similar to serotype A, but different from serotype D. Further work is needed to evaluate role of Hsf protein in protection studies and to study the antigenic properties of this recombinant protein as a candidate for vaccine.

  9. Cloning and Sequence Analysis of a Novel Cold-Adapted Lipase Gene from Strain Iip35 (Pseudomonas sp.)

    Institute of Scientific and Technical Information of China (English)

    WANG Cai-hong; GUO Run-fang; YU Hong-wei; JIA Ying-min

    2008-01-01

    A combination method of the usual-PCR and reverse-PCR for the cloning of a novel lipase gene directly from the total genomic DNA of strain lip35 (Pseudomonas sp.) is described, whereby a lipase gene (lip) was cloned directly from genomic DNA. The sequence data have been deposited in the GenBank and EMBL data bank with the accession number EU414288. The nucleotide sequence showed a major open reading frame encoding a 59-kDa protein of 566 amino acid residues, which contained a lipase consensus sequence GXSXG. The lipase lip had 74 and 70% homologies with the Upases of an uncultured bacterium and P.fluorescens PfO-1, respectively, but it did not show any overall homology with lipases from other origins. The functional lipase was obtained when the lip gene was expressed in Pichia pastoris GS115.

  10. Spread of carbapenem-resistant international clones of Acinetobacter baumannii in Turkey and Azerbaijan: a collaborative study.

    Science.gov (United States)

    Ahmed, S S; Alp, E; Ulu-Kilic, A; Dinc, G; Aktas, Z; Ada, B; Bagirova, F; Baran, I; Ersoy, Y; Esen, S; Guven, T G; Hopman, J; Hosoglu, S; Koksal, F; Parlak, E; Yalcin, A N; Yilmaz, G; Voss, A; Melchers, W

    2016-09-01

    Epidemic clones of Acinetobacter baumannii, described as European clones I, II, and III, are associated with hospital epidemics throughout the world. We aimed to determine the molecular characteristics and genetic diversity between European clones I, II, and III from Turkey and Azerbaijan. In this study, a total of 112 bloodstream isolates of carbapenem-resistant Acinetobacter spp. were collected from 11 hospitals across Turkey and Azerbaijan. The identification of Acinetobacter spp. using conventional and sensitivity tests was performed by standard criteria. Multiplex polymerase chain reaction (PCR) was used to detect OXA carbapenemase-encoding genes (bla OXA-23-like, bla OXA-24-like, bla OXA-51-like, and bla OXA-58-like). Pulsed-field gel electrophoresis (PFGE) typing was used to investigate genetic diversity. The bla OXA-51-like gene was present in all 112 isolates, 75 (67 %) carried bla OXA-23-like, 7 (6.2 %) carried bla OXA-58-like genes, and 5 (4.5 %) carried bla OXA-24-like genes. With a 90 % similarity cut-off value, 15 clones and eight unique isolates were identified. The largest clone was cluster D, with six subtypes. Isolates from clusters D and I were widely spread in seven different geographical regions throughout Turkey. However, F cluster was found in the northern and eastern regions of Turkey. EU clone I was grouped within J cluster with three isolates found in Antalya, Istanbul, and Erzurum. EU clone II was grouped in the U cluster with 15 isolates and found in Kayseri and Diyarbakır. The bla OXA-24-like gene in carbapenemases was identified rarely in Turkey and has been reported for the first time from Azerbaijan. Furthermore, this is the first multicenter study in Turkey and Azerbaijan to identify several major clusters belonging to European clones I and II of A. baumannii. PMID:27259712

  11. Rapid Amplification of Flanking Sequences of a Known DNA Region by Partial Restriction Digestion and Hot Start PCR

    Institute of Scientific and Technical Information of China (English)

    LOU Qun-feng; LIU Qiang; YANG Yin-gui; CHEN Jin-feng

    2008-01-01

    A simple and efficient method for cloning the flanking genomic sequences of a known DNA region is reported in this study. This method combined partial restriction endonuclease digestion, adaptor ligation, and a single round polymerase chain reaction. Total genomic DNA was partially digested with the frequent-cutting restriction enzyme Mse Ⅰ. The partially digested products were ligated to an unphosphorylated adaptor. A hot start PCR amplification with Taq polymerase and dNTP was performed with a DNA-specific primer and the adaptor primer complementary to the adaptor and the Mse Ⅰ recognition site. The amplified products were fractionated, cloned and sequenced. By this method, we cloned the downstream region of a gynoecious marker TG/CAC234 from cucumber (Cucumis sativus L.).

  12. The polymerase chain reaction (PCR): general methods.

    Science.gov (United States)

    Waters, Daniel L E; Shapter, Frances M

    2014-01-01

    The polymerase chain reaction (PCR) converts very low quantities of DNA into very high quantities and is the foundation of many specialized techniques of molecular biology. PCR utilizes components of the cellular machinery of mitotic cell division in vitro which respond predictably to user inputs. This chapter introduces the principles of PCR and discusses practical considerations from target sequence definition through to optimization and application.

  13. Cloning: Past, Present, and the Exciting Future. Breakthroughs in Bioscience.

    Science.gov (United States)

    Di Berardino, Marie A.

    This document explores the history of cloning by focusing on Dolly the Sheep, one of the first large animal clonings. The disadvantages and advantages of transgenic clones are discussed as well as the future implications of cloning from the perspective of human health. (Contains 10 resources.) (YDS)

  14. Public perceptions of farm animal cloning in Europe

    OpenAIRE

    Lassen, Jesper

    2005-01-01

    This report presents a picture of European opinion on farm animal cloning. In the report, both agricultural and biomedical applications of farm animal cloning are considered. With the arrival of Dolly, animal cloning became an integral part of the biotech debate, but this debate did not isolate animal cloning as a single issue.

  15. Assessment of genetic diversity within sour cherry clones

    DEFF Research Database (Denmark)

    Clausen, Sabine Karin; Andersen, Sven Bode; Henriksen, K.;

    2013-01-01

    Harvested yields of sour cherry (Prunus cerasus) cultivar ‘Stevnsbaer’ clones grown in Denmark have been highly variable over the years, yet some propagated derived trees selected from within the two widely grown clones of ‘Stevnsbaer’ clone ‘Birgitte’ and clone ‘Viki’ have consistently produced...

  16. Universal Quantum Cloning Machines for Two Identical Mixed Qubits

    Institute of Scientific and Technical Information of China (English)

    YANG Shuai; ZHAO Mei-Sheng; LIU Nai-Le; CHEN Zeng-Bing

    2007-01-01

    We present a series of universal quantum cloning machines for two identical mixed qubits. Every machine is optimal in the sense that it achieves the optimal bound of the single copy shrinking factor. Unlike in the case of pure state cloning, the single copy shrinking factor does not uniquely determine the cloning map in the case of mixed state cloning.

  17. Public perceptions of farm animal cloning in Europe

    DEFF Research Database (Denmark)

    Lassen, Jesper

    This report presents a picture of European opinion on farm animal cloning. In the report, both agricultural and biomedical applications of farm animal cloning are considered. With the arrival of Dolly, animal cloning became an integral part of the biotech debate, but this debate did not isolate...... animal cloning as a single issue....

  18. Cloning and GST-fused expression in E. coli of mouse β-1,4-galactosyltransferase

    Institute of Scientific and Technical Information of China (English)

    龚兴国; 钟文涛; 吴文英

    2004-01-01

    β-1,4-galactosyltransferase (β4Gal-T) (EC 2.4.1.38) plays a multifunctional role in many aspects of normal cell physiology. By now, several dozens of β4Gal-T genes have been cloned, separated from mouse, chick, bovine, human, etc. This paper presents the cloning and GST-fused expression of mouse β4Gal-T gene in Escherichia coli (E. coli). The target gene was cloned by PCR, followed by identification by DNA sequencing and expression in E.coli with isopro-pyl-β-D-thiogalactoside (IPTG) gradient concentrations, products of which were separated on SDS-PAGE showing that the target protein had the same molecular weight as that of mouse β4Gal-T. The transcriptional product of β4Gal-T gene was proved by Western hybridization analysis to be due to GST-fusion.

  19. Phage display used for gene cloning of human recombinant antibody against the erythrocyte surface antigen, rhesus D

    DEFF Research Database (Denmark)

    Dziegiel, M; Nielsen, L K; Andersen, P S;

    1995-01-01

    A novel phage display system has been developed for PCR amplification and cloning of the Fab fragments of human immunoglobulin genes. Using this system, we have cloned an antibody from a mouse-human hybridoma cell line directed against the erythrocyte antigen rhesus D. Intact erythrocytes were used...... for absorption of the Fab phages. Soluble Fab fragments produced from the cloned material showed identical performance to the parental antibody in agglutination assays. Gel filtration confirmed that the Fab fragment consists of a kappa-Fd heterodimer. The successful use of intact cells for selection of specific...... Fab phages demonstrates that it is possible to by-pass purification of the antigen of interest. Comparison with published germline sequences demonstrated that the immunoglobulin coding regions had the highest homology to the VH 1.9III and V kappa Hum kappa v325 germline genes, respectively....

  20. Gene Cloning of Murine α-Fetoprotein Gene and Construction of Its Eukaryotic Expression Vector and Expression in CHO Cells

    Institute of Scientific and Technical Information of China (English)

    易继林; 田耕

    2003-01-01

    To clone the murine α-fetoprotein (AFP) gene, construct the eukaryotic expression vector of AFP and express in CHO cells, total RNA were extracted from Hepa 1-6 cells, and then the murine α-fetoprotein gene was amplified by RT-PCR and cloned into the eukaryotic expression vector pcDNA3.1. The recombinant of vector was identified by restriction enzyme analysis and sequencing. A fter transient transfection of CHO cells with the vector, Western blotting was used to detect the expression of AFP. It is concluded that the 1.8kb murine α-fetoprotein gene was successfully cloned and its eukaryotic expression vector was successfully constructed.

  1. Pitfalls in PCR troubleshooting: Expect the unexpected?

    Science.gov (United States)

    Schrick, Livia; Nitsche, Andreas

    2016-01-01

    PCR is a well-understood and established laboratory technique often used in molecular diagnostics. Huge experience has been accumulated over the last years regarding the design of PCR assays and their set-up, including in-depth troubleshooting to obtain the optimal PCR assay for each purpose. Here we report a PCR troubleshooting that came up with a surprising result never observed before. With this report we hope to sensitize the reader to this peculiar problem and to save troubleshooting efforts in similar situations, especially in time-critical and ambitious diagnostic settings.

  2. Detection of Eperythrozoon wenyoni by PCR assay

    Institute of Scientific and Technical Information of China (English)

    Jian WANG; Yutao ZHU; Jianhua QIN; Fumei ZHANG; Yuelan ZHAO

    2009-01-01

    The objective of this research was to develop a detection method for Eperythrozoon wenyoni infection using polymerase chain reaction (PCR) assay technique. A pair of primers was designed and synthesized according to the conservative sequence 16S rRNA. The PCR assay was performed with the primers. A 985-bp fragment was amplified by using PCR. The amplified fragments with the expected size were identified by EcoR I restriction digestion. The crossing-reaction, specific-reaction and duplicate-reaction indicated that the PCR method is a specific, sensitive, fast and effective method for diagnosing E. Wenyoni infection at group level.

  3. Assessment of the real-time PCR and different digital PCR platforms for DNA quantification

    OpenAIRE

    Pavšič, Jernej; Žel, Jana; Milavec, Mojca

    2015-01-01

    Digital PCR (dPCR) is beginning to supersede real-time PCR (qPCR) for quantification of nucleic acids in many different applications. Several analytical properties of the two most commonly used dPCR platforms, namely the QX100 system (Bio-Rad) and the 12.765 array of the Biomark system (Fluidigm), have already been evaluated and compared with those of qPCR. However, to the best of our knowledge, direct comparison between the three of these platforms using the same DNA material has not been do...

  4. Two metallothionein gene family members in buckwheat: Expression analysis in flooding stress using Real Time RT-PCR technology

    Directory of Open Access Journals (Sweden)

    Majić Dragana B.

    2008-01-01

    Full Text Available Metallothioneins (MTs are an extensive and diverse family of small cysteine-rich proteins with metal-binding ability that are involved in metal homeostasis and detoxification. Two cDNA clones of the MT3 type, differing in 3’ UTRs, were isolated from the developing buckwheat seed cDNA library. Following sequence analyses, expression profiles during flooding stress were monitored by Real Time RT PCR technology.

  5. Identification of the B-cell tumor-specific molecular fingerprint using non-radiolabelled PCR consensus primers

    OpenAIRE

    Paolucci, G.; Pileri, S. A.; Pession, A.; Zinzani, P L; Rodriguez-Calvillo, M. (Mercedes); Inoges, S. (Susana); Sartini, R. (R.); Turi, C. (C.); Botti, S.; R. Maffei; Tonelli, R; M. Bendandi

    2001-01-01

    Abstract BACKGROUND: The complementarity determining region 3 (CDR3) of the immunoglobulin (Ig) heavy chain variable region (VH) is the most reliable molecular fingerprint for most if not all human B cells. The nucleotide sequence encoding for any B-cell tumor-specific VH CDR3 is currently identified by PCR sequencing based on procedures involving the usage of either radioactive materials, patient/family-specific primers, or bacterial cloning. PATIENTS AND METHODS: In six consecut...

  6. [Ethical considerations on human cloning. A psychoanalytic perspective].

    Science.gov (United States)

    Alvarez, A

    2000-01-01

    A brief review of ethical issues related to two types of human cloning is presented: cloning embryonic cells not intended to culminate in the birth of a new individual and cloning human beings. Advantages and objections related to both types of human cloning are analyzed from an ethical point of view. Repercussions on individuals born by the technique of cloning are discussed from a psychoanalytical perspective. It can be concluded that cloning embryonic cells could be admissible, while not cloning considered as a reproductive option.

  7. Molecular cloning and expression of a human heat shock factor, HSF1

    Energy Technology Data Exchange (ETDEWEB)

    Rabindran, S.K.; Giorgi, G.; Clos, J.; Wu, C. (National Institutes of Health, Bethesda, MD (United States))

    1991-08-15

    Human cells respond to heat stress by inducing the binding of a preexisting transcriptional activator (heat shock factor, HSF) to DNA. The authors isolated recombinant DNA clones for a human cDNA fragment. The human HSF1 probe was produced by the PCR with primers deduced from conserved amino acids in the Drosophila and yeast HSF sequences. The human HSF1 mRNA is constitutively expressed in HeLa cells under nonshock conditions and encodes a protein with four conserved leucine zipper motifs. Like its counterpart in Drosophila, human HSF1 produced in Escherichia coli in the absence of heat shock is active as a DNA binding transcription factor, suggesting that the intrinsic activity of HSF is under negative control in human cells. Surprisingly, an independently isolated human HSF clone, HSF2, is related to but significantly different from HSF.

  8. Cloning and bioinformatics analysis of cDNA encoding cattle Smad4 gene

    Institute of Scientific and Technical Information of China (English)

    Xiaohui ZHANG; Shangzhong XU; Xue GAO; Hongyan REN; Jinbao CHEN

    2008-01-01

    The cDNA of cattle Smad4 gene was cloned by RT-PCR, 3' RACE and 5' RACE and got a 3503-bp full-long cDNA sequence. The cloned cattle Smad4 cDNA sequence had been send to GenBank and got an accession number: DQ494856. Cattle Smad4 gene consists of 12 exons and codes 553 amino acids. Cattle Smad4 cDNA shares 99%, 96%, 95%, 91% and 91% similarity in nucleic acid sequences, and 99%, 98%, 98%, 99% and 98% sim-ilarity in amino acid sequences with sheep, pig, human, rat and mouse, respectively. Smad4 cDNA was found in the testes, pancreas, liver, small intestine, ovary, lymph, car-diac muscle, skeleton muscle and thymus gland, which indicated that Smad4 was broadly expressed in cattle.

  9. Cloning and Analysis of Telomere-associated Sequences of Ginkgo biloba L.

    Institute of Scientific and Technical Information of China (English)

    Liu Di; Lu Hai; Ji Fei-teng; Li Feng-lan; Guo Hui-hong

    2005-01-01

    Total genomic DNA was extracted from leaves of Ginkgo biloba L. by the method of hot CTAB. After determining quantification of DNA sample by microclorimetric spectrophotography, Arabidopsis-type telomere primer and Sau3A I cassette primer were used to isolate telomere-associated sequences from G. biloba L. by the method of cassette-ligation-mediated polymerase chain reaction (PCR). Using this method, two telomere-associated sequences, TAS 1 and TAS2, were isolated. The authors preformed Southern hybridization ofEcoR I -treated G. biloba genomic DNA with each clone. The hybridization pattern showed that the clones obtained were derived from G. biloba genomic DNA. There are the Arabidopsis-type TTTAGGG tandem repeats in telomeres of G.biloba.

  10. MOLECULAR CLONING, EXPRESSION AND SUBCELLULAR LOCALIZATION OF HUMAN OCT-4 PROTEIN

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Objective To clone, express, purify human Oct-4 and detect its subcellular localization.Methods Human Oct-4 cDNA was amplified by RT-PCR strategy. Oct-4 protein was induced and expressed in BL21 (DE3) strain. Furthermore, the protein was purified with Ni-NTA resin. Subsequently, site-directed mutagenesis of Oct-4 (aa 236 -240) was introduced. Finally, the subcellular localization of wide type Oct-4 and mutant Oct-4 was examined by immunofluorescent cytochemistry staining and confocal laser scanning microscope analysis.Results The full length cDNA of human Oct-4 was 1083bp. Human Oct-4 encoded a 55 kd protein by prokaryotic vector in E coli. Compared with pure nuclear localization of wide type Oct-4, mutant Oct-4 was mostly enriched in the cytoplasm. Conclusion The cloning, expression and investigation of subcellular localization of human Oct-4 are basis of studying its biological function.

  11. Identification of a new HLA-G allele, HLA-G*01:19, by cloning and phasing.

    Science.gov (United States)

    Wang, W Y; Tian, W

    2016-08-01

    A new HLA-G allelic variant, HLA-G*01:19, was identified in a southern Chinese Han population by polymerase chain reaction-sequence-based typing (PCR-SBT), cloning and phasing. HLA-G*01:19 differs from HLA-G*01:04:01 by a nonsynonymous cytosine at position 99 in exon 2, resulting in amino acid change from valine to leucine at codon 34 of the mature HLA-G molecule. PMID:27277539

  12. Cloning, Characterization and Heterologous Expression of the Indolocarbazole Biosynthetic Gene Cluster from Marine-Derived Streptomyces sanyensis FMA

    OpenAIRE

    Wenli Li; Kui Hong; Weiming Zhu; Jingtao Zhang; Qiu Cui; Yuanyuan Du; Tong Li

    2013-01-01

    The indolocarbazole (ICZ) alkaloids have attracted much attention due to their unique structures and potential therapeutic applications. A series of ICZs were recently isolated and identified from a marine-derived actinomycete strain, Streptomyces sanyensis FMA. To elucidate the biosynthetic machinery associated with ICZs production in S. sanyensis FMA, PCR using degenerate primers was carried out to clone the FAD-dependent monooxygenase gene fragment for ICZ ring formation, which was used as...

  13. Cloning and Sequence Analysis on 3' Coding Region of Wild Boar and Cross Bred Pig Myostatin Gene

    Institute of Scientific and Technical Information of China (English)

    LIU Di; YANG Xiu-qin; YANG Jia-fang

    2004-01-01

    Myostatin, with a highly conservative gene among breeds is a negative regulator of muscle. The 3' coding regions of wild boar and crossbred pig myostatin were cloned by RT-PCR and sequenced respectively. The homology of the nucleotide sequence between wild boar and crossbred pig was 100% and there was no difference in this region compared with pig myostatin gene of Genbank. This indicated that there was not change of gene sequence in this region during the evolution processes.

  14. Neuromedin B and Its Receptor: Gene Cloning, Tissue Distribution and Expression Levels of the Reproductive Axis in Pigs

    OpenAIRE

    Zhiyu Ma; Juan Su; Tingting Guo; Mengmeng Jin; Xiang Li; Zhihai Lei; Yuanlong Hou; Xiaoliang Li; Cuicui Jia; Zheng Zhang; Ejlal Ahmed

    2016-01-01

    Neuromedin B is one member of a family of bombesin-like peptides, which performs a variety of physiological functions via their receptor (NMBR) in most mammals. However, the genes encoding NMB and NMBR and their functions especially reproduction of the pigs are currently not fully understood. To research the physiological functions of NMB, we cloned and analyzed the NMB and NMBR genes, and systematically investigated the expression levels of NMB and NMBR mRNA using relative real-time PCR and ...

  15. Cloning of a peroxidase gene from cassava with potential as a molecular marker for resistance to bacterial blight

    OpenAIRE

    Luiz Filipe Pereira; Goodwin, Paul H.; Larry Erickson

    2003-01-01

    Cassava bacterial blight (CBB), caused by Xanthomonas axonopodis pv. manihotis, is considered one of the most important bacterial diseases of cassava (Manihot esculenta Crantz). In order to characterize the cassava genes involved in resistance to this disease, a genomic clone of a cationic peroxidase gene, MEPX1, was isolated by PCR from cassava cultivar MCOL 22. The DNA sequence of MEPX1 showed high homology with other plant peroxidase genes and contained a large intron typical of peroxidase...

  16. Nonlocal quantum cloning via quantum dots trapped in distant cavities

    Institute of Scientific and Technical Information of China (English)

    Yu Tao; Zhu Ai-Dong; Zhang Shou

    2012-01-01

    A scheme for implementing nonlocal quantum cloning via quantum dots trapped in cavities is proposed.By modulating the parameters of the system,the optimal 1 → 2 universal quantum cloning machine,1 → 2 phase-covariant cloning machine,and 1 → 3 economical phase-covariant cloning machine are constructed.The present scheme,which is attainable with current technology,saves two qubits compared with previous cloning machines.

  17. Droplet digital PCR-aided screening and characterization of Pichia pastoris multiple gene copy strains.

    Science.gov (United States)

    Cámara, Elena; Albiol, Joan; Ferrer, Pau

    2016-07-01

    Pichia (syn. Komagataella) pastoris is a widely used yeast platform for heterologous protein production. Expression cassettes are usually stably integrated into the genome of this host via homologous recombination. Although increasing gene dosage is a powerful strategy to improve recombinant protein production, an excess in the number of gene copies often leads to decreased product yields and increased metabolic burden, particularly for secreted proteins. We have constructed a series of strains harboring different copy numbers of a Rhizopus oryzae lipase gene (ROL), aiming to find the optimum gene dosage for secreted Rol production. In order to accurately determine ROL gene dosage, we implemented a novel protocol based on droplet digital PCR (ddPCR), and cross validated it with conventional real-time PCR. Gene copy number determination based on ddPCR allowed for an accurate ranking of transformants according to their ROL gene dosage. Results indicated that ddPCR was particularly superior at lower gene dosages (one to five copies) over quantitative real-time PCR (qPCR). This facilitated the determination of the optimal ROL gene dosage as low as two copies. The ranking of ROL gene dosage versus Rol yield was consistent at both small scale and bioreactor chemostat cultures, thereby easing clone characterization in terms of gene dosage dependent physiological effects, which could be discriminated even among strains differing by only one ROL copy. A selected two-copy strain showed twofold increase in Rol specific production in a chemostat culture over the single copy strain. Conversely, strains harboring more than two copies of the ROL gene showed decreased product and biomass yields, as well as altered substrate consumption specific rates, compared to the reference (one-copy) strain. Biotechnol. Bioeng. 2016;113: 1542-1551. © 2015 Wiley Periodicals, Inc. PMID:26704939

  18. Rapid screening of an ordered fosmid library to clone multiple polyketide synthase genes of the phytopathogenic fungus Cladosporium phlei.

    Science.gov (United States)

    So, Kum-Kang; Kim, Jung-Mi; Nguyen, Ngoc-Luong; Park, Jin-Ah; Kim, Beom-Tae; Park, Seung-Moon; Hwang, Ki-Jun; Kim, Dae-Hyuk

    2012-12-01

    In previous studies, the biological characteristics of the fungus Cladosporium phlei and its genetic manipulation by transformation were assessed to improve production of the fungal pigment, phleichrome, which is a fungal perylenequinone that plays an important role in the production of a photodynamic therapeutic agent. However, the low production of this metabolite by the wild-type strain has limited its application. Thus, we attempted to clone and characterize the genes that encode polyketide synthases (PKS), which are responsible for the synthesis of fungal pigments such as perylenequinones including phleichrome, elsinochrome and cercosporin. Thus, we performed genomic DNA PCR using 11 different combinations of degenerate primers targeting conserved domains including β-ketoacyl synthase and acyltransferase domains. Sequence comparison of the PCR amplicons revealed a high homology to known PKSs, and four different PKS genes showing a high similarity to three representative types of PKS genes were amplified. To obtain full-length PKS genes, an ordered gene library of a phleichrome-producing C. phlei strain (ATCC 36193) was constructed in a fosmid vector and 4800 clones were analyzed using a simple pyramidal arrangement system. This hierarchical clustering method combines the efficiency of PCR with enhanced specificity. Among the three representative types of PKSs, two reducing, one partially reducing, and one non-reducing PKS were identified. These genes were subsequently cloned, sequenced, and characterized. Biological characterization of these genes to determine their roles in phleichrome production is underway, with the ultimate aim of engineering this pathway to overproduce the desired substance.

  19. Cloning and characterization of porcine aquaporin 1 water channel expressed extensively in gastrointestinal system

    Institute of Scientific and Technical Information of China (English)

    Shun-Ying Jin; Yan-Li Liu; Li-Na Xu; Yong Jiang; Ying Wang; Bao-Xue Yang; Hong Yang; Tong-Hui Ma

    2006-01-01

    AIM: To clone and characterize the porcine aquaporins (AQPs) in the gastrointestinal system.METHODS: A PCR-based cloning strategy and RACE were used to clone full-length AQP coding sequence from reversely transcribed pig liver cDNA. Stopped-flow light scattering and a YFP-based fluorescence method were used to measure the osmotic water permeability of erythrocytes and the stably transfected CHO cells.RT-PCR, Northern blot, and immunohistochemistry were used to determine the gastrointestinal expression and localization of cloned AQPs. Protein expression in transfected cells and red blood cells was analyzed by Western blot.RESULTS: An 813 bp cDNA encoding a 271 amino acid porcine aquaporin (designated pAQP1) was cloned from liver mRNA (pAQP1 has a 93% identity with human AQP1 and contains two NPA motifs conserved in AQP family, one consensus sequence for N-linked glycosylation, and one mercury-sensitive site at cysteine 191). RT-PCR analysis revealed extensive expression of pAQP1 mRNA in porcine digestive glands and gut.Northern blot showed a single 3.0 kb transcript in selected digestive organs, pAQP1 protein was localized at central lacteals of the small intestine, microvessles of salivary glands, as well as epithelium of intrahepatic bile ducts by immunoperoxydase. High osmotic water permeability that is inhibitable by HgCl2 was detected in porcine erythrocytes and CHO cells stably transfected with pAQP1 cDNA. Tmmunoblot analysis of porcine erythrocytes and pAQP-transfected CHO cells revealed an unglycosylated 28 ku band and larger glycosylated proteins.CONCLUSION: pAQP1 is the first porcine aquaporin that can be molecularly identified so far. The broad distribution of pAQP1 in epithelium and endothelium of porcine digestive organs may suggest an important role of channel-mediated water transport in fluid secretion/absorption as well as in digestive function and pathophysiology of the gastrointestinal system.

  20. Validation of RNAi by real time PCR

    DEFF Research Database (Denmark)

    Josefsen, Knud; Lee, Ying Chiu

    2011-01-01

    Real time PCR is the analytic tool of choice for quantification of gene expression, while RNAi is concerned with downregulation of gene expression. Together, they constitute a powerful approach in any loss of function studies of selective genes. We illustrate here the use of real time PCR to verify...