...bacteria from the elliptical, purified and amplified the total community DNA, and then analyzed the sequenced DNA with Mi Seq Software. A revised protocol was used to extract, purify, and sequence the community DNA; these methods were followed without deviation (1). The procedure to sequence and configure the data is described on Blackboard (2). Results PCR amplification of the community DNA product was unsuccessful. There was no evidence of PCR amplified DNA on the gel (Figure 1.1). An alternate gel from Molecular Microbiology Laboratory was used as a model to perform gel electrophoresis of the community DNA (2). A plot of migration distance vs. size that includes the Invitrogen ladder can be used to determine the size of the PCR amplified community DNA (Figure 1.2). [Figure 1.2] Base Pairs vs. Migration Distance of Invitrogen Low DNA Mass Ladder. The distance these standardized fragments is associated with a quantity of base pairs. The graph created from a plot of base pairs vs. migration distance produces an equation that can be used to determine the size of the PCR amplified community DNA. The length of the amplicon was determined by using lane 36 of the alternate gel (2). The estimated migration distance of the amplicon in lane 36 is...
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...[pic] Biological control of Fusarium oxysporum f.sp. cubense using non-pathogenic F. oxysporum endophytes by Aneen Belgrove 动感之星 Submitted in partial fulfilment of the requirements for the degree of Magister Scientiae In the Facul ty of Natural and Agricultural Science University of Pretoria Pretoria Date October 2007 PROMOTOR: Prof. A. Viljoen CO-PROMOTOR: Dr. C. Steinberg I © University of Pretoria [pic] Declaration I, the undersigned, declare that the work contained in this thesis is my own and original work and that it has not previously in its entirety or part submitted for a degree to any other university. _________________________________ II [pic] TABLE OF CONTENTS Acknowledgements XII Preface XIII Chapter 1: Biological control of Fusarium wilt diseases ABSTRACT 2 INTRODUCTION 3 THE FUSARIUM WILT PATHOGEN 4 THE DISEASE 6 CONTROL OF FUSARIUM WILT 7 Chemical control 7 Cultural control 9 Disease resistance 10 Biological control 12 BIOLOGICAL CONTROL OF FUSARIUM WILT 12 Suppressive soils 12 Mechanisms of biological control 13 Antibiosis 13 Competition ...
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...repeats (STRs) which use PCR primers close to the STR repeat region and single nucleotide polymorphisms (Forensic DNA, 2014)....
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...by charge and/or size (IEF agarose, essentially size independent) and in biochemistry and molecular biology to separate a mixed population of DNA and RNA fragments by length, to estimate the size of DNA and RNA fragments or to separate proteins by charge.[1] Nucleic acid molecules are separated by applying an electric field to move the negatively charged molecules through an agarose matrix. Shorter molecules move faster and migrate farther than longer ones because shorter molecules migrate more easily through the pores of the gel. This phenomenon is called sieving.[2] Proteins are separated by charge in agarose because the pores of the gel are too large to sieve proteins. Gel electrophoresis can also be used for separation of nanoparticles. Gel electrophoresis uses a gel as an anticonvective medium and/or sieving medium during electrophoresis, the movement of a charged particle in an electrical field. Gels suppress the thermal convection caused by application of the electric field, and can also act as a sieving medium, retarding the passage of molecules; gels can also simply serve to maintain the finished separation, so that a post electrophoresis stain can be applied.[3] DNA Gel electrophoresis is usually performed for analytical purposes, often after amplification of DNA via PCR, but may be used as a preparative technique prior to use of other methods such as mass spectrometry, RFLP, PCR, cloning, DNA sequencing, or Southern blotting for further characterization. Physical basis ...
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...ABBREVIATIONS VIII 1 INTRODUCTION 1 1.1 HEPATITIS C VIRUS 1 1.1.1 DISCOVERY 1 1.1.2 EPIDEMIOLOGY 2 1.1.3 PATHOGENESIS 2 1.1.4 TREATMENT 3 1.2 MOLECULAR BIOLOGY 3 1.2.1 STRUCTURE OF GENOME 3 1.2.2 GENETIC VARIATION 6 1.2.3 GENOTYPIC DIFFERENCES 8 1.3 RNA DEPENDENT RNA POLYMERASE ACTIVITY 9 1.3.1 POLYMERASE FUNCTION 9 1.3.2 MODEL SYSTEMS OF HCV REPLICATION 11 1.3.3 GENOTYPE SPECIFIC STUDIES 11 1.3.4 BIOCHEMICAL PROPERTIES 12 1.4 KUNJIN VIRUS RNA DEPENDENT RNA POLYMERASE 13 1.5 CONCLUSION 15 1.6 AIMS AND HYPOTHESIS 16 2 MATERIALS AND METHODS 17 2.1 HCV POSITIVE SERA SAMPLES 17 2.2 RNA EXTRACTION 17 2.3 CDNA SYNTHESIS 17 2.4 HCV PRIMER DESIGN AND USAGE 18 2.5 NESTED POLYMERASE CHAIN REACTION (NPCR) 21 2.5.1 REACTION AND CYCLING CONDITIONS 21 2.5.2 PCR PRODUCT PURIFICATION 22 2.6 AGAROSE GEL VISUALISATION 22 2.7 DNA SEQUENCING 22 2.8 DNA SEQUENCE AND PHYLOGENETIC ANALYSIS 23 2.9 KUNJIN VIRUS PLASMID 23 2.10 KUN PRIMER DESIGN AND USAGE 23 2.11 CLONING PCR PRODUCTS 24 2.11.1 RESTRICTION DIGEST 24 2.11.2 LIGATION 24 2.11.3 TRANSFORMATION 24 2.11.4 COLONY PCR 24 2.12...
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...29808279 RELIGION: CHRISTIAN MARITAL STATUS: SINGLE LANGUAGES: ENGLISH, KISWAHILI (both spoken and written) SUMMARY A hard-working and motivated BSC Biochemistry and Molecular Biology graduate with proven communication, organization and numeracy skills seeking to gain relevant experience to diversify and excel in varying fields. Looking to apply solid knowledge of biochemistry and molecular biology practices to setting and building on skills developed during course work studies. Eager to share the knowledge I have gained. Pro-active and keen to learn, ready to back up the knowledge I have gained with relevant experience .Wishing to make a positive contribution to production and research institutions. EDUCATION BACKGROUND 2012-2015: BSC BIOCHEMISTRY (MOLECULAR BIOLOGY) JOMO KENYATTA UNIVERSITY OF AGRICULTURE AND TECHNOLOGY, SECOND CLASS HONOURS (UPPER DIVISION) Jan 2007 –Nov 2010: KENYA CERTIFICATE OF SECONDARY EDUCATION St JOSEPH’S MUTITO BOYS SECONDARY SCHOOL GRADE ATTAINED: B (64 POINTS). 1997-2006: KENYA CERTIFICATE OF PRIMARY EDUCATION IKANGA PRIMARY SCHOOL ATTAINED 349 MARKS OUT OF 500 MARKS BIOCHEMISTRY AND MOLECULAR BIOLOGY EXPERIENCE Sept-Dec 2013: Attachment at Machakos Level-5 Hospital laboratory where I gained experience in department of biochemistry, microbiology and...
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...ornamental Squat shrimp Thor amboinensis using mtCO1 from Gulf of Mannar coastal waters V.Priyalakshmi1, S.Dhanasekaran1, M.A.Badhul Haq2*, M.Nirosh Banu2, S.Vaitheeswari2 and P.Vengadesan2 1P.G and Research Department of Zoology, Yadava College, Madurai Kamaraj University, 2Marine Virology Laboratory, Faculty of Marine Sciences, CAS in Marine Biology, Annamalai University, Parangipettai - 608 502, Email*:drhaqmarinevirology@gmail.com Abstract Marine shrimp are among the most popular invertebrates in the marine ornamental aquarium trade. In this study exclusively focused in addressing the phylogenetic location of genus Thor amboinensis. A molecular phylogeny of the marine ornamental shrimp species based on...
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...ABSTRACT Real-time quantitative PCR represents a highly sensitive and powerful technique for the quantitation of nucleic acids. It has a tremendous potential for the high-throughput analysis of gene expression in research and routine diagnostics. However, the major hurdle is not the practical performance of the experiments themselves but rather the efficient evaluation and the mathematical and statistical analysis of the enormous amount of data gained by this technology, as these functions are not included in the software provided by the manufacturers of the detection systems. In this work, we focus on the mathematical evaluation and analysis of the data generated by real-time quantitative PCR, the calculation of the final results, the propagation of experimental variation of the measured values to the final results, and the statistical analysis. We developed a Microsoft® Excel®-based software application coded in Visual Basic for Applications, called Q-Gene, which addresses these points. Q-Gene manages and expedites the planning, performance, and evaluation of real-time quantitative PCR experiments, as well as the mathematical and statistical analysis, storage, and graphical presentation of the data. The Q-Gene software application is a tool to cope with complex realtime quantitative PCR experiments at a high-throughput scale and considerably expedites and rationalizes the experimental setup, data analysis, and data management while ensuring...
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...vary in length between individuals, particularly between unrelated individuals, allowing exact individuals to be identified. One major use of DNA fingerprinting is in crime scene investigations in order to identify suspects or also victims based on DNA samples from blood or hair present in the crime scene. Another use is in paternity testing that compares the DNA of the mother and offspring to the potential fathers in order to identify the father. The first step in DNA fingerprinting involves isolating DNA from a tissue sample such as blood or hair. Very often, particularly when tissue samples are obtained from crime scenes, the amount of DNA available for DNA fingerprinting is extremely small. Fortunately, a molecular biology technique known as polymerase chain reaction (PCR) allows the DNA sample to be amplified considerably. In essence, this technique is an artificial version of DNA replication. The DNA sample is firstly added to a mixture of DNA nucleotides and DNA polymerase that is then heated 95°C. This high temperature breaks the hydrogen bonds holding the two strands of DNA together. The sample DNA is now single stranded. Short sequences of DNA known as primers are then added to the mixture. The temperature is then reduced to 55°C allowing the primers to hydrogen bond to the sample DNA at...
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...Introduction: Vitamin D is critical for embryonic skeletal formation and long bone growth. Without vitamin D, the hypertrophic cell zone will expand because the cartilage fails to calcify leading to rickets. Protein disulfide isomerase A3 (PDIA3), also known as ERp60, ERp57, Grp58, and 1,25-MARRS, is a multifunctional protein that has been associated with rapid membrane-initiated signaling by 1α,25-dihydroxyvitamin D3 (1α,25(OH)2D3) in several cell types. Knockdown of PDIA3 in osteoblast-like cell line MC3T3 showed that reduction of PDIA3 expression led to remarkable decrease of PKC activation with 1,25 (OH) 2VitD3 treatment as well as a decrease in expression of several osteogenic genes compared to wild type cells, which indicated the important role of PDIA3 in vitamin D-regulated cartilage and bone development. However, the mechanism involved still remains unclear. The fact motivate us to generate the PDIA3 knockout mice which will serve as a good model to further explore the physiological function of PDIA3 and to understand the mechanism involved in PDIA3-mediated 1,25VitD3 signal pathway. To date, the major problems we are facing during the generation an ERp60 Knockout mice is the lack of a liable genotyping method to distinguish the Knockout mice from the heterozygous mice. No knockout mice available from the previous breeding along with very lower percentage of wild type mice which did not match to the Mendel’s rule of Segregation. Therefore, the object...
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...Welcome to Biol 342 Molecular Biotechnology 1 Dr. Michael D.J. Lynch Biology 342 Molecular Biotechnology 1 Instructor: Dr. Michael D.J. Lynch Room: B2 - 249D e-mail: mdjlynch@uwaterloo.ca office hours: Thursdays 1:00 – 2:30 pm If you need to speak with me outside scheduled lecture time, please contact me via email to make an appointment – that way I can be sure to set aside time for you. Prerequisites: Biol 130, 239, 240, 309. Biol 241 recommended Required textbook: Glick & Pasternak Molecular Biotechnology 4th edition, 2010. ASM Press. Available from UWaterloo Bookstore. 2 copies on reserve at Davis library. Students find this textbook very useful, and I refer to it often for lectures. A worthwhile purchase. This text is also used in Biol 432. LEARN ● ● ● ● ● ● lecture notes (slides in .pdf) Podcasts (screencasts) of lectures course info, important dates tutorial information practice exams announcements Use your Quest/UWdir ID and password Accessing the podcasts…….. Check that you are using a LEARN-approved browser! Goals for this course: ● Understand the fundamentals of molecular biotechnology, primarily in the context of the methods that are employed in the field ● Develop skills in the designing of molecular approaches to biotechnology ● Develop critical thinking skills ● Effectively communicate concepts learned Assigned readings and student notes: Readings from the text will be assigned in lecture notes on...
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...Agarose Gel Electrophoresis for the Separation of DNA Fragments Pei Yun Lee, John Costumbrado, Chih-Yuan Hsu, Yong Hoon Kim Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles Video Article Chapters 0:05 Title 1:31 Preparation of the Gel 3:21 Setting up Gel Apparatus and Separating DNA Fragments 4:55 Observing Separated DNA Fragments 5:43 Results: Agarose Gel Electrophoresis of PCR Products 6:23 Conclusion Cite this Article Lee, P. Y., Costumbrado, J., Hsu, C. Y., Kim, Y. H. Agarose Gel Electrophoresis for the Separation of DNA Fragments. J. Vis. Exp. (62), e3923, doi:10.3791/3923 (2012). Abstract Agarose gel electrophoresis is the most effective way of separating DNA fragments of varying sizes ranging from 100 bp to 25 kb1. Agarose is isolated from the seaweed genera Gelidium and Gracilaria, and consists of repeated agarobiose (L- and D-galactose) subunits2. During gelation, agarose polymers associate non-covalently and form a network of bundles whose pore sizes determine a gel's molecular sieving properties. The use of agarose gel electrophoresis revolutionized the separation of DNA. Prior to the adoption of agarose gels, DNA was primarily separated using sucrose density gradient centrifugation, which only provided an approximation of size. To separate DNA using agarose gel electrophoresis, the DNA is loaded into pre-cast wells in the gel and a current applied. The phosphate backbone of the DNA (and RNA) molecule...
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...working on the common problem of identifying an unknown bacterium. This lab helps students develop an understanding of the biochemical and molecular differences in bacteria and introduces the concept of identifying species based on characeristic gene sequences. Students work through two types of identification procedures, one classical and one involving DNA sequencing, then compare the results of the two methods. Educational Context The lab was created to accompany lecture topics in bacterial genetics and biochemistry. The main topics covered in lecture that relate to this lab are prokaryotic replication, transcription, and translation, enzyme function, and cellular respiration. This lab was tailored for second semester freshmen who are in their first semester of a three-semester introductory biology course. The first semester focuses on molecular biology, bacterial genetics, and introductory biochemistry. This lab was designed for 500 students split into lab sections of 20. However, this curriculum is easily adaptable to accommodate any number of students. In this lab, students identify an unknown bacteria using a biochemical method and a molecular method. For the biochemical method, students use a combination of differential growth tests and enzyme tests developed for clinical use. For the molecular method, students PCR amplify and sequence the 16S rRNA gene from their bacteria, then use BLAST to search the bacterial database and identify the species that...
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...Introduction Wheat (Triticum aestivum) is the most important and considered cereal crop for major part of global population. In Pakistan, wheat is most important crop of agricultural economy. It is grown each year on 8.3 million hectares that is 36% of total area cropped in Pakistan. It accounts for 40% of total value added of major crops. It is essential part of diet for population as it contributes 60% of daily diet of common masses in Pakistan. Average per capita consumption is around 125kg and possess a central position in agricultural policies of government. If area under wheat crop remains same then wheat requirement would be about about 34.25 million tonnes in 2030. It means additional 10 million tonnes wheat have to be produced during next 20 years. It would require to improve national average yield from 2.8 to 3.8 t/ha (2030). There is 60% yield gap in wheat that is required to be tapered. There are several agronomic, physiological, political and managerial factors responsible for low yield in Pakistan. Among them ill management is more conspicuous of all. Since management skills vary from area to area, productivity also vary from region to region. In addition there is yield gap between progressive and common farmers which may attribute to several ignorance factors. Conventional plant breeding has been practicing successfully since 1960’s for production of improved wheat varieties but has limited potential to meet such a great challenge with limited gene pool. Genetic...
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...ABBREVIATIONS VIII 1 INTRODUCTION 1 1.1 HEPATITIS C VIRUS 1 1.1.1 DISCOVERY 1 1.1.2 EPIDEMIOLOGY 2 1.1.3 PATHOGENESIS 2 1.1.4 TREATMENT 3 1.2 MOLECULAR BIOLOGY 3 1.2.1 STRUCTURE OF GENOME 3 1.2.2 GENETIC VARIATION 6 1.2.3 GENOTYPIC DIFFERENCES 8 1.3 RNA DEPENDENT RNA POLYMERASE ACTIVITY 9 1.3.1 POLYMERASE FUNCTION 9 1.3.2 MODEL SYSTEMS OF HCV REPLICATION 11 1.3.3 GENOTYPE SPECIFIC STUDIES 11 1.3.4 BIOCHEMICAL PROPERTIES 12 1.4 KUNJIN VIRUS RNA DEPENDENT RNA POLYMERASE 13 1.5 CONCLUSION 15 1.6 AIMS AND HYPOTHESIS 16 2 MATERIALS AND METHODS 17 2.1 HCV POSITIVE SERA SAMPLES 17 2.2 RNA EXTRACTION 17 2.3 CDNA SYNTHESIS 17 2.4 HCV PRIMER DESIGN AND USAGE 18 2.5 NESTED POLYMERASE CHAIN REACTION (NPCR) 21 2.5.1 REACTION AND CYCLING CONDITIONS 21 2.5.2 PCR PRODUCT PURIFICATION 22 2.6 AGAROSE GEL VISUALISATION 22 2.7 DNA SEQUENCING 22 2.8 DNA SEQUENCE AND PHYLOGENETIC ANALYSIS 23 2.9 KUNJIN VIRUS PLASMID 23 2.10 KUN PRIMER DESIGN AND USAGE 23 2.11 CLONING PCR PRODUCTS 24 2.11.1 RESTRICTION DIGEST 24 2.11.2 LIGATION 24 2.11.3 TRANSFORMATION 24 2.11.4 COLONY PCR 24 2.12...
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