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Journal articles on the topic 'Cloning, Molecular – methods'

Author: Grafiati

Published: 4 June 2021

Last updated: 17 February 2022

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1

Tan, Lendl, Emily J. Strong, Kyra Woods, and Nicholas P. West. "Homologous alignment cloning: a rapid, flexible and highly efficient general molecular cloning method." PeerJ 6 (June 29, 2018): e5146. http://dx.doi.org/10.7717/peerj.5146.

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Homologous alignment cloning (HAC) is a rapid method of molecular cloning that facilitates low-cost, highly efficient cloning of polymerase chain reaction products into any plasmid vector in approximately 2 min. HAC facilitates insert integration due to a sequence alignment strategy, by way of short, vector-specific homology tails appended to insert during amplification. Simultaneous exposure of single-stranded fragment ends, utilising the 3′→5′ exonuclease activity of T4 DNA polymerase, creates overlapping homologous DNA on each molecule. The exonuclease activity of T4 polymerase is quenched

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2

Silverman, Sanford J. "Methods for molecular cloning and analysis of eukaryotic genes." Analytical Biochemistry 192, no. 1 (1991): 254. http://dx.doi.org/10.1016/0003-2697(91)90217-h.

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3

Alfaresi, Mubarak, and Bassam Mahboub. "Identification of Bacteria in the Sputum of a Cystic Fibrosis patient; A Comparison of Phenotypic and Molecular Methods." Open Microbiology Journal 11, no. 1 (2017): 384–86. http://dx.doi.org/10.2174/1874285801711010384.

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Background: Cystic fibrosis (CF), caused by mutations in the CF transmembrane conductance regulator gene, is a common autosomal recessive disease. Accurate isolation and identification of the bacteria underlying these infections are is critical to the therapeutic management of CF. Objective: To compare phenotypic bacterial identification with a molecular method in a CF patient sputum. Methods: Bacterial identification done by standard microbiological method from a CF patient. Same sample underwent a molecular method involving 16S rDNA amplification, cloning, and sequencing. Results: All isolat

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4

Karn, Jonathan. "Methods in enzymology, vol. 152: guide to molecular cloning techniques." Trends in Genetics 4, no. 9 (1988): 268. http://dx.doi.org/10.1016/0168-9525(88)90035-2.

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Cline, Steven W., Wan L. Lam, Robert L. Charlebois, Leonard C. Schalkwyk, and W. Ford Doolittle. "Transformation methods for halophilic archaebacteria." Canadian Journal of Microbiology 35, no. 1 (1989): 148–52. http://dx.doi.org/10.1139/m89-022.

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We present a practical description of polyethylene glycol mediated spheroplast transformation of Halobacterium halobium and Halobacterium volcanii. This method has been applied to phage DNA transfection, plasmid DNA transformation, and transformation with linear fragments of high molecular weight genomic DNA. Efficient spheroplast regeneration allows uncomplicated recovery of transformed progeny. Transformations can be performed equally well using fresh or frozen cell preparations. These methods should find application in molecular cloning, genetic fine mapping, and strain construction.Key wor

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Миненко, I. Minenko, Сердюков, and D. Serdyukov. "To The Question of the Cloninig History." Journal of New Medical Technologies. eJournal 8, no. 1 (2014): 1–9. http://dx.doi.org/10.12737/2907.

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Cloning in biology - cloning in biology is getting both asexually by natural means, including vegetative reproduction, and by means of biotechnological methods genetically identical organisms, cells or molecules. In the XXI century, in the conditions of the impetuous growth of the population and the food problem aggravation, humanity faces a growing and more demanding challenge of creating the necessary quantity of living organisms-plants and animals, with pre-defined properties: resistant to disease, climate fluctuations, high productivity, fertility, desired flavoring, aromatic, nourishing,

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Martinez-Picado, Javier, Lorraine Sutton, Maria Pia De Pasquale, Anu V. Savara, and Richard T. D’Aquila. "Human Immunodeficiency Virus Type 1 Cloning Vectors for Antiretroviral Resistance Testing." Journal of Clinical Microbiology 37, no. 9 (1999): 2943–51. http://dx.doi.org/10.1128/jcm.37.9.2943-2951.1999.

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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 specimens and their application to generate infectious recombinant virus clones for virus phenotyping

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Taylor, Stephen J. C., Rob C. Brown, Phil A. Keene, and Ian N. Taylor. "Novel screening methods—the key to cloning commercially successful biocatalysts." Bioorganic & Medicinal Chemistry 7, no. 10 (1999): 2163–68. http://dx.doi.org/10.1016/s0968-0896(99)00146-7.

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Liang, Yaping, Yu Zhang, and Liangwei Liu. "Intra-Molecular Homologous Recombination of Scarless Plasmid." International Journal of Molecular Sciences 21, no. 5 (2020): 1697. http://dx.doi.org/10.3390/ijms21051697.

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Although many methods have been reported, plasmid construction compromises transformant efficiency (number of transformants per ng of DNAs) with plasmid accuracy (rate of scarless plasmids). An efficient method is two-step PCR serving DNA amplification. An accurate method is ExnaseII cloning serving homology recombination (HR). We combine DNA amplification and HR to develop an intra-molecular HR by amplifying plasmid DNAs to contain homology 5′- and 3′-terminus and recombining the plasmid DNAs in vitro. An example was to construct plasmid pET20b-AdD. The generality was checked by constructing

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10

Hussain, Mushtaq, and Joanna B. Wilson. "ID:2026 Investigating Molecular Interactions of EBV Oncogene, EBNA1, by Heterologous Cloning and Peptide Array System." Biomedical Research and Therapy 4, S (2017): 57. http://dx.doi.org/10.15419/bmrat.v4is.267.

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Background: EBNA1 is an important latent genes that is involved in the oncogenesis associated with Epstein Barr Virus. The protein is highly promiscuous in terms of its interaction with the several proteins including EBP2 and USP7, a p53 stabilizer. Herein, we aim to investigate the interactions points of molecular complexes of EBNA1, an EBV oncogene, in order to design potential therapeutic peptides. Methods: Full length EBNA1, EBP2 and USP7 models were constructed employing iterative threading. After proper refinements of models, EBNA1 dimer was constructed employing geometrical and st

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11

Creager, Angela N. H. "Recipes for recombining DNA: A history of Molecular Cloning: A Laboratory Manual." BJHS Themes 5 (2020): 225–43. http://dx.doi.org/10.1017/bjt.2020.5.

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AbstractLaboratory instructions and recipes are sometimes edited into books with a wide circulation. Even in the late twentieth century, publications of this nature remained influential. For example, protocols from a 1980 summer course on gene cloning at Cold Spring Harbor Laboratory provided the basis for a bestselling laboratory manual by Tom Maniatis, Ed Fritsch and Joe Sambrook. Not only did the Molecular Cloning: A Laboratory Manual become a standard reference for molecular biologists (commonly called the ‘bible’), but also its recipes and clear instructions made gene cloning and recombin

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Kathir, Pushpa, Matthew LaVoie, William J. Brazelton, Nancy A. Haas, Paul A. Lefebvre, and Carolyn D. Silflow. "Molecular Map of the Chlamydomonas reinhardtii Nuclear Genome." Eukaryotic Cell 2, no. 2 (2003): 362–79. http://dx.doi.org/10.1128/ec.2.2.362-379.2003.

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ABSTRACT We have prepared a molecular map of the Chlamydomonas reinhardtii genome anchored to the genetic map. The map consists of 264 markers, including sequence-tagged sites (STS), scored by use of PCR and agarose gel electrophoresis, and restriction fragment length polymorphism markers, scored by use of Southern blot hybridization. All molecular markers tested map to one of the 17 known linkage groups of C. reinhardtii. The map covers approximately 1,000 centimorgans (cM). Any position on the C. reinhardtii genetic map is, on average, within 2 cM of a mapped molecular marker. This molecular

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Kincaid, R. L., P. R. Giri, S. Higuchi, et al. "Cloning and characterization of molecular isoforms of the catalytic subunit of calcineurin using nonisotopic methods." Journal of Biological Chemistry 265, no. 19 (1990): 11312–19. http://dx.doi.org/10.1016/s0021-9258(19)38593-x.

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Stankov, Karmen, and Giovanni Romeo. "Cloning of the genes for non-medullary thyroid cancer: Methods and advances." Archive of Oncology 14, no. 1-2 (2006): 30–34. http://dx.doi.org/10.2298/aoo0602030s.

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In last ten years, significant advances have occurred in thyroid endocrinology, as a consequence of the generalized use of molecular biology techniques. New genes involved in the development of thyroid cancer have been identified, which had a great impact on our understanding of thyroid cancer predisposition. All cancers are genetic in origin because they arise from mutations in a single somatic cell, but the genetic changes in sporadic cancers are confined to a particular tissue. In inherited cancers, a predisposing mutation is present in all somatic cells and in the germ line, which enables

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Clegg, MT, and ML Durbin. "Molecular approaches to the study of plant biosystematics." Australian Systematic Botany 3, no. 1 (1990): 1. http://dx.doi.org/10.1071/sb9900001.

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Genetic relationships among organisms can be estimated from the pattern of DNA sequence change between hereditary molecules. The methods of molecular biology are increasingly being employed in systematic and evolutionary research to study genetic relationships and phylogeny. The investigator is faced with a variety of choices in initiating research in 'molecular biosystematics'. First, a gene or genome that provides a level of genetic resolution appropriate for the materials under study must be selected. Common choices in plants include the chloroplast genome (cpDNA) or components of the chlor

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Dalonso, N., M. Savoldi, P. H. C. França, T. F. Reis, G. H. Goldman, and R. M. M. Gern. "Sequence-independent cloning methods for long DNA fragments applied to synthetic biology." Analytical Biochemistry 530 (August 2017): 5–8. http://dx.doi.org/10.1016/j.ab.2017.04.018.

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17

Harshman, Keith, Russell Bell, Judith Rosenthal, et al. "Comparison of the positional cloning methods used to isolate the BRCA1 gene." Human Molecular Genetics 4, no. 8 (1995): 1259–66. http://dx.doi.org/10.1093/hmg/4.8.1259.

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18

NAKAGAWA, Tamotsu, Kaoru GOTO, and Hisatake KONDO. "Cloning and characterization of a 92 kDa soluble phosphatidylinositol 4-kinase." Biochemical Journal 320, no. 2 (1996): 643–49. http://dx.doi.org/10.1042/bj3200643.

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A phosphatidylinositol (PtdIns) 4-kinase cDNA cloned from a rat brain cDNA library encoded a protein of 816 amino acids with a calculated molecular mass of 91654 Da. This molecule contained a lipid-kinase-unique domain and a presumed lipid/protein kinase homology domain that are found in other PtdIns 4-kinases and PtdIns 3-kinases. Furthermore, this kinase molecule had 43.3% shared identity with the presumed catalytic domain of yeast PtdIns 4-kinase, PtdInsK1, and the two molecules had a region of similarity that is not conserved in other lipid kinases. By examining PtdIns kinase activity in t

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19

Dinka, Stephen J., and Manish N. Raizada. "Inexpensive fine mapping and positional cloning in plants using visible, mapped transgenes." Canadian Journal of Botany 84, no. 2 (2006): 179–88. http://dx.doi.org/10.1139/b05-170.

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Vast numbers of crop, fungal, and animal accessions as well as insect vectors and evolving eukaryotic pathogens await molecular analysis. Inexpensive methods are required to make map-based gene isolation accessible to more of the world’s researchers. Today, positional cloning relies on genotyping and phenotyping large numbers of progeny to detect chromosome recombination events that break linkage between the trait of interest and flanking molecular markers following meiosis. In the postgenome era, positional cloning will no longer be limited by the availability of high-density molecular marker

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Hnatiuk, I. S., O. I. Varchenko, M. F. Parii, and Yu V. Symonenko. "Creation of a genetic vector carrying a synthesis bacterial protein gene CAS9 for plant genome editing." Faktori eksperimental'noi evolucii organizmiv 26 (September 1, 2020): 176–82. http://dx.doi.org/10.7124/feeo.v26.1263.

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Aim. To create a genetic construct carrying the bacterial protein Cas9 gene, the reporter β-glucuronidase gus gene, as well as the marker phosphinotricin-N-acetyltransferase bar gene for plant genome editing. Methods. Molecular-biological, biotechnological, microbiological and bioinformatic methods were used in the study; Golden Gate molecular cloning method was used to create genetic constructs. Results. The genetic construct pSPE2053 which carries the Cas9 endonuclease gene, the gus and bar genes was created; the assembly correctness of all vector elements was confirmed by polymerase chain r

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21

Yurkov, Andrey P., Alexey A. Kryukov, Anastasia O. Gorbunova, et al. "Molecular genetic identification of arbuscular mycorrhizal fungi." Ecological genetics 16, no. 2 (2018): 11–23. http://dx.doi.org/10.17816/ecogen16211-23.

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Arbuscular mycorrhiza (AM) is a widespread symbiosis formed by most land plants with fungi from Glomeromycotina subdivision. The main problem in study of AM fungi is the complication in identification, associated with high intra- and interspecific genetic polymorphism, as well as obligate status of AM fungi in relation to host plant. The methodology for AM fungi identification is constantly undergoing major changes. In the review the selection of optimal methods of molecular genetic identification for AM fungi is carried out. The sample preparation, selection of species-specific marker DNA fra

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22

Vella, Frank. "Methods in molecular biology and protein chemistry: Cloning and characterization of an enterotoxin subunit: Spangler, B. D." Biochemistry and Molecular Biology Education 31, no. 4 (2003): 272a—273. http://dx.doi.org/10.1002/bmb.2003.494031040230.

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23

Guzán, Plinio, and Joseph R. Ecker. "Development of large DNA methods for plants: molecular cloning of large segments ofArabidopsisand carrot DNA into yeast." Nucleic Acids Research 16, no. 23 (1988): 11091–105. http://dx.doi.org/10.1093/nar/16.23.11091.

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24

Wang, Aoxue, Fanjuan Meng, Xiangyang Xu, Yong Wang, and Jingfu Li. "Development of Molecular Markers Linked to Cladosporium fulvum Resistant Gene Cf-6 in Tomato by RAPD and SSR Methods." HortScience 42, no. 1 (2007): 11–15. http://dx.doi.org/10.21273/hortsci.42.1.11.

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Leaf mold, caused by the fungus Cladosporium fulvum, is a serious disease of tomato. In the current study, the main physiological races of C. fulvum collected from three northeastern provinces of China were identified using a set of identification hosts. The results showed that the prevalent pathogenic physiological races were 1.2.3, 1.3, 3, 1.2.3.4, and 1.2.4. F1, F2, and BC1 tomato plants were obtained by crossing C. fulvum-resistant cultivar 03748 carrying the Cf-6 gene and susceptible cultivar 03036. Three 10-mer oligonucleotide random amplified polymorphic DNA (RAPD) primers and two simpl

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Fotheringham, S., and W. K. Holloman. "Cloning and disruption of Ustilago maydis genes." Molecular and Cellular Biology 9, no. 9 (1989): 4052–55. http://dx.doi.org/10.1128/mcb.9.9.4052-4055.1989.

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We have demonstrated that genes from Ustilago maydis can be cloned by direct complementation of mutants through the use of genomic libraries made in a high-frequency transformation vector. We isolated a gene involved in amino acid biosynthesis as an illustrative example and showed that integrative and one-step disruption methods can be used to create null mutations in the chromosomal copy of the gene by homologous recombination. The results of this investigation make it clear that one-step gene disruption will be of general utility in investigations of U. maydis, since simple, precise replacem

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Ibarguchi, Gabriela, Vicki L. Friesen, and Stephen C. Lougheed. "Defeating numts: Semi-pure mitochondrial DNA from eggs and simple purification methods for field-collected wildlife tissues." Genome 49, no. 11 (2006): 1438–50. http://dx.doi.org/10.1139/g06-107.

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Mitochondrial DNA (mtDNA) continues to play a pivotal role in phylogeographic, phylogenetic, and population genetic studies. PCR amplification with mitochondrial primers often yields ambiguous sequences, in part because of the coamplification of nuclear copies of mitochondrial genes (numts) and true mitochondrial heteroplasmy arising from mutations, hybridization with paternal leakage, gene duplications, and recombination. Failing to detect numts or to distinguish the origin of such homologous sequences results in the incorrect interpretation of data. However, few studies obtain purified mtDNA

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Alon, Assaf, Hayden R. Schmidt, Michael D. Wood, James J. Sahn, Stephen F. Martin та Andrew C. Kruse. "Identification of the gene that codes for the σ2 receptor". Proceedings of the National Academy of Sciences 114, № 27 (2017): 7160–65. http://dx.doi.org/10.1073/pnas.1705154114.

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The σ2 receptor is an enigmatic protein that has attracted significant attention because of its involvement in diseases as diverse as cancer and neurological disorders. Unlike virtually all other receptors of medical interest, it has eluded molecular cloning since its discovery, and the gene that codes for the receptor remains unknown, precluding the use of modern biological methods to study its function. Using a chemical biology approach, we purified the σ2 receptor from tissue, revealing its identity as TMEM97, an endoplasmic reticulum-resident transmembrane protein that regulates the sterol

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Najafi, Akram, Maryam Moradinasab, Mohammad Seyedabadi, Mohammad A. Haghighi, and Iraj Nabipour. "First Molecular Identification of Symbiotic Archaea in a Sponge Collected from the Persian Gulf, Iran." Open Microbiology Journal 12, no. 1 (2018): 323–32. http://dx.doi.org/10.2174/1874285801812010323.

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Background: Marine sponges are associated with numerically vast and phylogenetically diverse microbial communities at different geographical locations. However, little is known about the archaeal diversity of sponges in the Persian Gulf. The present study was aimed to identify the symbiotic archaea with a sponge species gathered from the Persian Gulf, Iran. Methods: Sponge sample was collected from a depth of 3 m offshore Bushehr, Persian Gulf, Iran. Metagenomic DNA was extracted using a hexadecyl trimethyl ammonium bromide (CTAB) method. The COI mtDNA marker was used for molecular taxonomy id

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Okegawa, Yuki, and Ken Motohashi. "Evaluation of seamless ligation cloning extract preparation methods from an Escherichia coli laboratory strain." Analytical Biochemistry 486 (October 2015): 51–53. http://dx.doi.org/10.1016/j.ab.2015.06.031.

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Cronn, Richard, and Jonathan F. Wendel. "Simple methods for isolating homoeologous loci from allopolyploid genomes." Genome 41, no. 6 (1998): 756–62. http://dx.doi.org/10.1139/g98-078.

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During allopolyploid formation, divergent sets of chromosomes are combined in a common nucleus. Accordingly, loci that are single-copy in progenitor diploid genomes become duplicated, homoeologous loci in allopolyploids. Although homoeologous loci have been identified using classical genetic and linkage mapping approaches, there are few examples of the isolation and molecular characterization of homoeologous loci from allopolyploids. Here we describe two methods for the isolation of orthologous duplicated loci and demonstrate the feasibility of the techniques using allotetraploid cotton. The m

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Stevenson, Zachary C., Megan J. Moerdyk-Schauwecker, Brennen Jamison, and Patrick C. Phillips. "Rapid Self-Selecting and Clone-Free Integration of Transgenes into Engineered CRISPR Safe Harbor Locations in Caenorhabditis elegans." G3: Genes|Genomes|Genetics 10, no. 10 (2020): 3775–82. http://dx.doi.org/10.1534/g3.120.401400.

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Precision genome editing for model organisms has revolutionized functional analysis and validation of a wide variety of molecular systems. To date, the capacity to insert single-copy transgenes into the model nematode Caenorhabditis elegans has focused on utilizing either transposable elements or CRISPR-based safe harbor strategies. These methods require plate-level screening processes to avoid selecting heritable extrachromosomal arrays or rely on co-CRISPR markers to identify knock-in events. As a result, verification of transgene insertion requires anti-array selection screening methods and

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Rodriguez, Benjamin A. T., and Tim H. M. Huang. "Tilling the chromatin landscape: emerging methods for the discovery and profiling of protein–DNA interactions." Biochemistry and Cell Biology 83, no. 4 (2005): 525–34. http://dx.doi.org/10.1139/o05-055.

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Interactions between protein and DNA are essential for cellular function. The incremental process of developing global approaches to study chromatin began with the in vitro characterization of chromatin structural components and modifications of the versatile chromatin immunoprecipitation (ChIP) assay, capable of analyzing protein–DNA interactions in vivo. Among the emerging global approaches are ChIP cloning, ChIP display, differential chromatin scanning, ChIP–chip, DamID chromatin profiling, and chromatin array. These methods have been used to assess transcription-factor binding and (or) his

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Green, Michael R., and Joseph Sambrook. "A Guide to Cloning the Products of Polymerase Chain Reactions." Cold Spring Harbor Protocols 2021, no. 9 (2021): pdb.top101345. http://dx.doi.org/10.1101/pdb.top101345.

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This introduction outlines various methods to clone amplified DNAs and to facilitate the construction of complex multicomponent genetic units. Because of the ease with which the termini of amplified DNAs can be tailored by polymerase chain reaction (PCR), many of the methods outlined here use PCR not only to synthesize DNAs but also to link them together into purpose-designed constructs. The most recent refinements however have been the development of modular genetic units that can be harnessed to target DNAs not by PCR but by site-specific recombination enzymes.

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Li, J., Y. H. Zhang, Y. T. Du, et al. "61 EFFICIENCY OF TWO ENUCLEATION METHODS FOR THE PRODUCTION OF TRANSGENIC PIG EMBRYOS BY HANDMADE CLONING." Reproduction, Fertility and Development 19, no. 1 (2007): 148. http://dx.doi.org/10.1071/rdv19n1ab61.

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Since the successful production of transgenic pigs by somatic nuclear transfer (Lai et al. 2002 Science 295, 1089–1092), more efficient reproduction technologies for transgenic pigs have been in demand. The purpose of our work was to develop an efficient method for production of transgenic embryos by handmade cloning (HMC; Vajta et al. 2001 Cloning 3, 89–95) connected to oriented enucleation to eliminate potential harm of staining and UV illumination at cytoplast selection. After 41–42 h of in vitro maturation, oocytes were further cultured with or without 0.4 µg mL−1 demecolcine for 45 min (i

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Dunlap, Walter, Marcel Jaspars, Daslav Hranueli, et al. "New Methods for Medicinal Chemistry - Universal Gene Cloning and Expression Systems for Production of Marine Bioactive Metabolites." Current Medicinal Chemistry 13, no. 6 (2006): 697–710. http://dx.doi.org/10.2174/092986706776055643.

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Budziszewski, Gregory J., Sharon Potter Lewis, Lyn Wegrich Glover, et al. "Arabidopsis Genes Essential for Seedling Viability: Isolation of Insertional Mutants and Molecular Cloning." Genetics 159, no. 4 (2001): 1765–78. http://dx.doi.org/10.1093/genetics/159.4.1765.

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Abstract We have undertaken a large-scale genetic screen to identify genes with a seedling-lethal mutant phenotype. From screening ~38,000 insertional mutant lines, we identified &gt;500 seedling-lethal mutants, completed cosegregation analysis of the insertion and the lethal phenotype for &gt;200 mutants, molecularly characterized 54 mutants, and provided a detailed description for 22 of them. Most of the seedling-lethal mutants seem to affect chloroplast function because they display altered pigmentation and affect genes encoding proteins predicted to have chloroplast localization. A

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Tozaki, T. "Characterization of Equine Microsatellites and Microsatellite-Linked Repetitive Elements (eMLREs) by Efficient Cloning and Genotyping Methods." DNA Research 8, no. 1 (2001): 33–45. http://dx.doi.org/10.1093/dnares/8.1.33.

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Li, Min, Ling-Yan Jiang, Qin Liu, et al. "A method combining TA cloning and fluorescence screening for rapid acquisition of transgenic seeds." BioTechniques 68, no. 5 (2020): 251–56. http://dx.doi.org/10.2144/btn-2019-0141.

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The establishment of transgenic plants has greatly promoted the progress of plant research. However, traditional selection methods using antibiotics or herbicides may miss any positive transformants with growth defects. Additionally, screening with antibiotics/herbicides requires a huge amount of seeds, sterile work conditions and a large amount of space to germinate plants, making the selection process time- and labor-consuming. In this study, we constructed a novel stable transformation vector, plasmid of OLE1-GFP T-DNA vector (pOGT), which can shorten the steps of cloning foreign genes into

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Dourmishev, Lyubomir A., Assen L. Dourmishev, Diana Palmeri, Robert A. Schwartz, and David M. Lukac. "Molecular Genetics of Kaposi's Sarcoma-Associated Herpesvirus (Human Herpesvirus 8) Epidemiology and Pathogenesis." Microbiology and Molecular Biology Reviews 67, no. 2 (2003): 175–212. http://dx.doi.org/10.1128/mmbr.67.2.175-212.2003.

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SUMMARY Kaposi's sarcoma had been recognized as unique human cancer for a century before it manifested as an AIDS-defining illness with a suspected infectious etiology. The discovery of Kaposi's sarcoma-associated herpesvirus (KSHV), also known as human herpesvirus-8, in 1994 by using representational difference analysis, a subtractive method previously employed for cloning differences in human genomic DNA, was a fitting harbinger for the powerful bioinformatic approaches since employed to understand its pathogenesis in KS. Indeed, the discovery of KSHV was rapidly followed by publication of i

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Gulig, Paul A., Matthew S. Tucker, Patrick C. Thiaville, Jennifer L. Joseph, and Roslyn N. Brown. "USER Friendly Cloning Coupled with Chitin-Based Natural Transformation Enables Rapid Mutagenesis of Vibrio vulnificus." Applied and Environmental Microbiology 75, no. 15 (2009): 4936–49. http://dx.doi.org/10.1128/aem.02564-08.

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ABSTRACT Vibrio vulnificus is a bacterial contaminant of shellfish and causes highly lethal sepsis and destructive wound infections. A definitive identification of virulence factors using the molecular version of Koch's postulates has been hindered because of difficulties in performing molecular genetic analysis of this opportunistic pathogen. For example, conjugation is required to introduce plasmid DNA, and allelic exchange suicide vectors that rely on sucrose sensitivity for counterselection are not efficient. We therefore incorporated USER friendly cloning techniques into pCVD442-based all

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Morton, Newton E. "Genetic epidemiology, genetic maps and positional cloning." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 358, no. 1438 (2003): 1701–8. http://dx.doi.org/10.1098/rstb.2003.1357.

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Genetic epidemiology developed in the middle of the last century, focused on inherited causes of disease but with methods and results applicable to other traits and even forensics. Early success with linkage led to the localization of genes contributing to disease, and ultimately to the Human Genome Project. The discovery of millions of DNA markers has encouraged more efficient positional cloning by linkage disequilibrium (LD), using LD maps and haplotypes in ways that are rapidly evolving. This has led to large international programmes, some promising and others alarming, with laws about DNA

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TANABE, Atsushi, Yukari EGASHIRA, Shin-Ichi FUKUOKA, Katsumi SHIBATA, and Hiroo SANADA. "Purification and molecular cloning of rat 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase." Biochemical Journal 361, no. 3 (2002): 567–75. http://dx.doi.org/10.1042/bj3610567.

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2-Amino-3-carboxymuconate-6-semialdehyde decarboxylase (ACMSD; EC 4.1.1.45) is one of the important enzymes regulating tryptophan—niacin metabolism. In the present study, we purified the enzyme from rat liver and kidney, and cloned the cDNA encoding rat ACMSD. The molecular masses of rat ACMSDs purified from the liver and kidney were both estimated to be 39kDa by SDS/PAGE. Analysis of N-terminal amino acid sequences showed that these two ACMSDs share the same sequence. An expressed sequence tag (EST) of the mouse cited from the DNA database was found to be identical with this N-terminal sequen

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Habib, Peter T. "Vaccine Design, Adaptation, and Cloning Design for Multiple Epitope-Based Vaccine Derived From SARS-CoV-2 Surface Glycoprotein (S), Membrane Protein (M) and Envelope Protein (E): In silico approach." Frontiers in Health Informatics 10, no. 1 (2021): 67. http://dx.doi.org/10.30699/fhi.v10i1.279.

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Introduction: The SARS Coronavirus-2 (SARS-CoV-2) pandemic has become a global epidemic that has increased the scientific community's concern about developing and finding a counteraction against this lethal virus. So far, hundreds of thousands of people have been infected by the pandemic due to contamination and spread. This research was therefore carried out to develop potential epitope-based vaccines against the SARS-CoV-2 virus using reverse vaccinology and immunoinformatics approaches.Material and Methods: The material of SARS-COV2 Surface Glycoprotein (S), Membrane Protein (M), and Envelo

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Schwarz, Michael, Marius Welzel, Tolganay Kabdullayeva, Anke Becker, Bernd Freisleben, and Dominik Heider. "MESA: automated assessment of synthetic DNA fragments and simulation of DNA synthesis, storage, sequencing and PCR errors." Bioinformatics 36, no. 11 (2020): 3322–26. http://dx.doi.org/10.1093/bioinformatics/btaa140.

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Abstract Summary The development of de novo DNA synthesis, polymerase chain reaction (PCR), DNA sequencing and molecular cloning gave researchers unprecedented control over DNA and DNA-mediated processes. To reduce the error probabilities of these techniques, DNA composition has to adhere to method-dependent restrictions. To comply with such restrictions, a synthetic DNA fragment is often adjusted manually or by using custom-made scripts. In this article, we present MESA (Mosla Error Simulator), a web application for the assessment of DNA fragments based on limitations of DNA synthesis, amplif

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Tomita, M., H. Itoh, N. Ishikawa, et al. "Molecular cloning of mouse intestinal trefoil factor and its expression during goblet cell changes." Biochemical Journal 311, no. 1 (1995): 293–97. http://dx.doi.org/10.1042/bj3110293.

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A cDNA encoding mouse intestinal trefoil factor (mITF) was successfully cloned and sequenced from the small intestine of C57BL/6 mouse by using the combination of reverse transcription-PCR and rapid amplification of cDNA ends methods. The gene was, similar to rat and human ITFs, mainly expressed in the small and large intestine. The mITF expression was up-regulated during the recovery phase after depletion of goblet cells in acetic acid-induced colitis. On the other hand, the expression in the jejunum was not altered, while goblet cell hyperplasia was induced by Nippostrongylus brasiliensis in

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Mason, Robert J., Kelly Greene, and Dennis R. Voelker. "Surfactant protein A and surfactant protein D in health and disease." American Journal of Physiology-Lung Cellular and Molecular Physiology 275, no. 1 (1998): L1—L13. http://dx.doi.org/10.1152/ajplung.1998.275.1.l1.

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Surfactant protein (SP) A and SP-D are collagenous glycoproteins with multiple functions in the lung. Both of these proteins are calcium-dependent lectins and are structurally similar to mannose-binding protein and bovine conglutinin. Both form polyvalent multimeric structures for interactions with pathogens, cells, or other molecules. SP-A is an integral part of the surfactant system, binds phospholipids avidly, and is found in lamellar bodies and tubular myelin. Initially, most research interest focused on its role in surfactant homeostasis. Recently, more attention has been placed on the ro

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Williams, Nic A., David R. Dixon, Eve C. Southward, and Peter W. H. Holland. "Molecular evolution and diversification of the vestimentiferan tube worms." Journal of the Marine Biological Association of the United Kingdom 73, no. 2 (1993): 437–52. http://dx.doi.org/10.1017/s0025315400032987.

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The Vestimentifera, or deep-sea tube worms, comprise an ecologically and anatomically unusual group of marine invertebrates, with poorly understood biogeography, ecology, phylogenetic affinities and evolutionary radiation. To gain insight into evolutionary diversification within the group, we have used a molecular biological approach. We report the cloning of a region of 28S ribosomal DNA from representatives of five vestimentiferan genera plus, for comparison, a polychaete and a perviate pogonophore. Phylogenetic analyses using these DNA sequences confirm thatRidgeiaandTevniaare closely relat

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Cama, Alessandro, Maurizio Genuardi, Ginevra Guanti, Paolo Radice, and Liliana Varesco. "Molecular Genetics of Hereditary Non-Polyposis Colorectal Cancer (HNPCC)." Tumori Journal 82, no. 2 (1996): 122–35. http://dx.doi.org/10.1177/030089169608200206.

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The story of the molecular genetics of HNPCC is one of astonishingly rapid achievements. In just 16 months, from May 1993 to September 1994, four different genes, namely hMSH2, hMLH1, hPMS1 and hPMS2 have been identified and demonstrated to be associated with the disease. Their cloning was facilitated by the finding that tumor cells in HNPCC patients display a hypermutability of DNA short tandem repeats (microsatellite instability). In fact, HNPCC associated genes are the human counterparts of genetic elements known to control the fidelity of DNA replication in lower organisms. So far, more th

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Frenk, Sammy, Nadya Rakovitsky, Hadas Kon, et al. "OXA-900, a Novel OXA Sub-Family Carbapenemase Identified in Citrobacter freundii, Evades Detection by Commercial Molecular Diagnostics Tests." Microorganisms 9, no. 9 (2021): 1898. http://dx.doi.org/10.3390/microorganisms9091898.

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Using whole-genome sequencing and cloning of the target gene, we identified blaOXA-900 carbapenemase, a novel blaOXA belonging to a distant and distinct sub-family of blaOXA-48-like. The plasmid-mediated gene was identified in a C. freundii isolate with elevated carbapenem MICs that evaded detection by commercial DNA-based methods. The novel gene, an OXA-48 family carbapenem-hydrolyzing class D β-lactamase, OXA-900, likely originates from marine environmental Shewanella. Since this plasmid-mediated gene has entered a member of the Enterobacterales and evades detection by commonly used tests, i

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Zhang, Jiao, Si-yu Shao, Li-zu Li, Di Liu, and Xiu-qin Yang. "Molecular cloning and characterization of porcine interferon-induced protein with tetratricopeptide repeats (IFIT) 5." Canadian Journal of Animal Science 95, no. 4 (2015): 551–56. http://dx.doi.org/10.4141/cjas-2015-009.

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Zhang, J., Shao, S.-y., Li, L.-z., Liu, D. and Yang, X.-q. 2015. Molecular cloning and characterization of porcine interferon-induced protein with tetratricopeptide repeats (IFIT) 5. Can. J. Anim. Sci. 95: 551–556. Interferon-induced protein with tetratricopeptide repeats (IFIT) family members play important roles in host defense against viral infection. In the present study, the complete coding sequence (CDS) of porcine IFIT5 gene was cloned using molecular biology techniques, and the genomic structure was determined using the bioinformatic method. The porcine IFIT5 is located on chromosome 1

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