scholarly journals Nucleic acids in mummified plant seeds: biochemistry and molecular genetics of pre-Columbian maize

1991 ◽  
Vol 58 (3) ◽  
pp. 193-201 ◽  
Author(s):  
Franco Rollo ◽  
Franco Maria Venanzi ◽  
Augusto Amici
Keyword(s):  
Nucleic Acids ◽  
Polyacrylamide Gel Electrophoresis ◽  
Dna Amplification ◽  
Degree Of Polymerization ◽  
Base Pairs ◽  
Plant Seeds ◽  
Maize Seeds ◽  
Maize Populations ◽  
Polymerase Chain ◽  
Seed Dna

SummaryNucleic acids fractions were isolated from pre-Columbian maize seeds and characterized using different approaches such as polyacrylamide gel electrophoresis, anti-DNA antibody binding, HPLC fractionation, molecular hybridization with cloned genes, and DNA amplification by the polymerase chain reaction. The nucleic acids were found to be very depolymerized (≤140 base pairs in length) and composed mainly of ribosomal RNA. Despite the very low amount and degree of polymerization of seed DNA, specific maize nuclear Mul, Mu4, Mu8 and, possibly, Mu5 element components could be detected, thanks to the use of amplification systems as short as 90 bp. The results suggest that evaluation of the relative proportions of Mu-type element components and, possibly, other maize genomic components in single mummified kernels, may offer a new key to the study of ancient maize populations.

scholarly journals Methods for identification of causative agents of dangerous and particularly dangerous infections based on the analysis of nucleic acids

2018 ◽  
Vol 2 (4) ◽  
pp. 22-35
Keyword(s):  
Nucleic Acids ◽  
Dna Amplification ◽  
Rapid Identification ◽  
Chain Reaction ◽  
Biological Contamination ◽  
Laboratory Facilities ◽  
Trained Personnel ◽  
Causative Agents ◽  
Polymerase Chain ◽  
Goals And Objectives

One of the main tasks of the NBC Protection Troops is accurate and rapid identification of infectious disease causative agents in case of establishing the fact of biological contamination. Different methods based on the analysis of nucleic acids are most preferred for this purpose. Most of them are based on DNA amplification by polymerase chain reaction (PCR). The result is detected by electrophoretic separation of amplification products, as well as by registration of endpoint fluorescent signal (FLASH modification) or in real time (PCR-RT). Other methods of DNA amplification, such as ligase chain reaction (LCR) and isothermal amplification, are also applicable in practice. The article also describes some identification methods based on nucleic acid sequencing: multilocus sequence typing (MLST) method, sequencing of individual genes and complete genome sequencing. It is concluded that the choice of identification method should be based on the goals and objectives, laboratory facilities, availability of trained personnel and funding levels. Despite the fact that the most informative are methods based on sequencing nucleotide sequences, their implementation in the field is difficult so far due to technological requirements

Separation of Nucleic Acids Using Single- and Multimodal Chromatography

2018 ◽  
Vol 20 (1) ◽  
pp. 49-55 ◽  
Author(s):  
Tiago Matos ◽  
Leif Bülow
Keyword(s):  
Nucleic Acids ◽  
Chemical Properties ◽  
Single Mode ◽  
Major Groove ◽  
Base Pairs ◽  
Chromatographic Separations ◽  
Multimodal Chromatography ◽  
Phosphate Backbone ◽  
Target Molecules ◽  
Polymerase Chain

The needs for purified nucleic acids for preparative and analytical applications have increased constantly, demanding for the development of new and more efficient methods for their recovery and isolation. DNA molecules harbour some intrinsic chemical properties that render them suitable for chromatographic separations. These include a negatively charged phosphate backbone as well as a hydrophobic character originating mainly from the major groove of DNA which exposes the base pairs on the surface of the molecule. In addition, single stranded DNA often allows for a free exposure of the hydrophobic aromatic bases. In this review, multimodal chromatography (MMC) has been evaluated as an alternative tool for complex separations of nucleic acids. MMC embraces more than one kind of interaction between the chromatographic ligand and the target molecules. These resins have often proved superior to conventional single-mode chromatographic materials for DNA isolation, including, e.g., the purification of plasmid DNA from crude cell lysates and for the preparation of DNA fragments before or after a polymerase chain reaction (PCR).

scholarly journals Integrity and Amplification of Nucleic Acids From Snap-Frozen Prostate Tissues From Robotic-Assisted Laparoscopic and Open Prostatectomies

2013 ◽  
Vol 137 (4) ◽  
pp. 525-530 ◽  
Author(s):  
Barbara L. Voss ◽  
Kristine Santiano ◽  
Mary Milano ◽  
Kathy A. Mangold ◽  
Karen L. Kaul
Keyword(s):  
Polymerase Chain Reaction ◽  
Nucleic Acid ◽  
Nucleic Acids ◽  
Polymerase Chain Reaction Amplification ◽  
Chain Reaction ◽  
Base Pairs ◽  
Robotic Assisted ◽  
Rna Integrity ◽  
Reaction Amplification ◽  
Polymerase Chain

Context.—Recently, robotic-assisted laparoscopic prostatectomy has replaced open retropubic radical prostatectomy as the surgical procedure of choice. This less-invasive approach offers many advantages but exposes prostate tissue to longer periods of warm ischemia that may affect subsequent analysis of biomarkers. Objective.—To analyze the nucleic acid quality and quantity isolated from open versus laparoscopic prostatectomies. Design.—Nucleic acids were isolated from 10 open-obtained and 10 laparoscopic-obtained tissues stored in our prostate sample repository. Nucleic acid integrity was assessed via electrophoresis and polymerase chain reaction amplification of RNA and DNA targets ranging in size from 125 to 939 base pairs. Results.—The DNA yield, integrity, and polymerase chain reaction amplification were identical between samples obtained from both surgical approaches. The RNA integrity number and yield were similar, as was β-2 microglobulin mRNA amplification up to 652 base pairs. However, 2 of 10 samples (20%) collected robotically showed decreased real-time reverse transcriptase-polymerase chain reaction amplification of prostate-specific antigen messenger RNA, especially with targets larger than 300 base pairs. Conclusions.—Generally, the quality and quantity of nucleic acids isolated from prostate tissue obtained via open or laparoscopic approaches are equivalent, suggesting that procurement of tissues is appropriate from either procedure. However, some loss of reverse transcriptase-polymerase chain reaction amplification of larger RNA targets was noted in the laparoscopic samples; appropriate design of assays to keep amplicon sizes small and the use of internal controls to assess RNA integrity is recommended.

Detection of the Glanzmann's Thrombasthenia Mutations in Arab and Iraqi-Jewish Patients by Polymerase Chain Reaction and Restriction Analysis of Blood or Urine Samples

1991 ◽  
Vol 66 (04) ◽  
pp. 500-504 ◽  
Author(s):  
H Peretz ◽  
U Seligsohn ◽  
E Zwang ◽  
B S Coller ◽  
P J Newman
Keyword(s):  
Polymerase Chain Reaction ◽  
Base Pair ◽  
Restriction Analysis ◽  
Urine Samples ◽  
Chain Reaction ◽  
Base Pairs ◽  
Glanzmann’S Thrombasthenia ◽  
Glanzmann's Thrombasthenia ◽  
Base Pair Deletion ◽  
Polymerase Chain

SummarySevere Glanzmann's thrombasthenia is relatively frequent in Iraqi-Jews and Arabs residing in Israel. We have recently described the mutations responsible for the disease in Iraqi-Jews – an 11 base pair deletion in exon 12 of the glycoprotein IIIa gene, and in Arabs – a 13 base pair deletion at the AG acceptor splice site of exon 4 on the glycoprotein IIb gene. In this communication we show that the Iraqi-Jewish mutation can be identified directly by polymerase chain reaction and gel electrophoresis. With specially designed oligonucleotide primers encompassing the mutation site, an 80 base pair segment amplified in healthy controls was clearly distinguished from the 69 base pair segment produced in patients. Patients from 11 unrelated Iraqi-Jewish families had the same mutation. The Arab mutation was identified by first amplifying a DNA segment consisting of 312 base pairs in controls and of 299 base pairs in patients, and then digestion by a restriction enzyme Stu-1, which recognizes a site that is absent in the mutant gene. In controls the 312 bp segment was digested into 235 and 77 bp fragments, while in patients there was no change in the size of the amplified 299 bp segment. The mutation was found in patients from 3 out of 5 unrelated Arab families. Both Iraqi-Jewish and Arab mutations were detectable in DNA extracted from blood and urine samples. The described simple methods of identifying the mutations should be useful for detection of the numerous potential carriers among the affected kindreds and for prenatal diagnosis using DNA extracted from chorionic villi samples.

scholarly journals COBAS AMPLICOR: fully automated RNA and DNA amplification and detection system for routine diagnostic PCR

1996 ◽  
Vol 42 (12) ◽  
pp. 1915-1923 ◽  
Author(s):  
N DiDomenico ◽  
H Link ◽  
R Knobel ◽  
T Caratsch ◽  
W Weschler ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Internal Control ◽  
Detection System ◽  
Dna Amplification ◽  
Cross Reactivity ◽  
Diagnostic Pcr ◽  
Thermal Cycler ◽  
Paramagnetic Microparticles ◽  
Rna And Dna ◽  
Single Reaction

Abstract The COBAS AMPLICOR system automates amplification and detection of target nucleic acids, making diagnostic PCR routine for a variety of infectious diseases. The system contains a single thermal cycler with two independently regulated heating/cooling blocks, an incubator, a magnetic particle washer, a pipettor, and a photometer. Amplified products are captured on oligonucleotide-coated paramagnetic microparticles and detected with use of an avidin-horseradish peroxidase (HRP) conjugate. Concentrated solutions of amplicon or HRP were pipetted without detectable carryover. Amplified DNA was detected with an intraassay CV of < 4.5%; the combined intraassay CV for amplification and detection was < 15%. No cross-reactivity was observed when three different target nucleic acids were amplified in a single reaction and detected with three target-specific capture probes. The initial COBAS AMPLICOR menu includes qualitative tests for diagnosing infections with Chlamydia trachomatis, Neisseria gonorrhoeae, Mycobacterium tuberculosis, and hepatitis C virus. All tests include an optional Internal Control to provide assurance that specimens are successfully amplified and detected.

Nucleic acids in two dimensions: layers of base pairs linked by carboxylate

2007 ◽  
Vol 31 (1) ◽  
pp. 21-24 ◽  
Author(s):  
Eva Corral ◽  
Huub Kooijman ◽  
Anthony L. Spek ◽  
Jan Reedijk
Keyword(s):  
Nucleic Acids ◽  
Two Dimensions ◽  
Base Pairs

PCR BY THERMAL CONVECTION

2004 ◽  
Vol 18 (16) ◽  
pp. 775-784 ◽  
Author(s):  
DIETER BRAUN
Keyword(s):  
Polymerase Chain Reaction ◽  
Thermal Convection ◽  
Dna Amplification ◽  
Reaction Vessel ◽  
Cold Region ◽  
Chain Reaction ◽  
Heating And Cooling ◽  
Highly Sensitive ◽  
Specific Amplification ◽  
Polymerase Chain

The Polymerase Chain Reaction (PCR) allows for highly sensitive and specific amplification of DNA. It is the backbone of many genetic experiments and tests. Recently, three labs independently uncovered a novel and simple way to perform a PCR reaction. Instead of repetitive heating and cooling, a temperature gradient across the reaction vessel drives thermal convection. By convection, the reaction liquid circulates between hot and cold regions of the chamber. The convection triggers DNA amplification as the DNA melts into two single strands in the hot region and replicates into twice the amount in the cold region. The amplification progresses exponentially as the convection moves on. We review the characteristics of the different approaches and show the benefits and prospects of the method.

Genetic diversity and phylogeny analysis of Azolla based on DNA amplification by arbitrary primers

Genome ◽  
1993 ◽  
Vol 36 (4) ◽  
pp. 686-693 ◽  
Author(s):  
Benoit Van Coppenolle ◽  
Iwao Watanabe ◽  
Charles Van Hove ◽  
Gerard Second ◽  
Ning Huang ◽  
...  
Keyword(s):  
Principal Component Analysis ◽  
Polymerase Chain Reaction ◽  
Principal Component ◽  
Dna Amplification ◽  
Component Analysis ◽  
Genetic Distances ◽  
Group Method ◽  
Chain Reaction ◽  
Arbitrary Primers ◽  
Polymerase Chain

The polymerase chain reaction was used to amplify random sequences of DNA from 25 accessions of Azolla to evaluate the usefulness of this technique for identification and phylogenetic analysis of this aquatic fern. Accessions were selected to represent all known species within the genus Azolla and to encompass the worldwide distribution of the fern. Primers of 10 nucleotides with 70% G + C content were used to generate randomly amplified polymorphic DNA from the symbiotic Azolla–Anabaena complex. Twenty-two primers were used and each primer gave 4–10 bands of different molecular weights for each accession. Bands were scored as present or absent for each accession and variation among accessions was quantified using Nei's genetic distances. A dendrogram summarizing phenetic relationships among the 25 accessions was generated using the unweighted pair-group method with arithmetic mean. Principal component analysis was also used to evaluate genetic similarities. Three distinct groups were identified: group 1 contains five species, group 2 contains the pinnata species, and group 3 contains the nilotica species. The analysis demonstrates that the major groups of Azolla species can be easily distinguished from one an other and, in addition, that closely related accessions within species can be identified. We further found that using 10 primers, a phylogeny that is essentially the same as that derived from 22 primers can be constructed. Our results suggest that total DNA extracted from the Azolla–Anabaena symbionts is useful for classification and phylogenetic studies of Azolla.Key words: Azolla–Anabaena symbiosis, genetic distances, polymerase chain reaction, principal component analysis.

SEROLOGICAL AND MOLECULAR EVALUATION OF MIGRATORY TRICHINELLA SPIRALIS LARVAE IN BLOOD OF HUMANS IN KADUNA METROPOLIS, NIGERIA

2021 ◽  
Vol 4 (4) ◽  
pp. 281-289
Author(s):  
Paul Isaac Ojodale ◽  
Helen Ileigo Inabo ◽  
Elijah Ekah Ella ◽  
Oluyinka Oluseyi Okubanjo
Keyword(s):  
Trichinella Spiralis ◽  
Enzyme Linked Immunosorbent Assay ◽  
Seroprevalence Rate ◽  
Base Pairs ◽  
Worldwide Distribution ◽  
Food Borne ◽  
Atp6 Gene ◽  
Amplicon Size ◽  
Polymerase Chain ◽  
Species Specific

Trichinellosis is an important food-borne zoonotic disease with public health implications and a worldwide distribution. In this study, Polymerase Chain Reaction (PCR) procedure using species specific ATP6 primers was used to detect the presence of migratory Trichinella spiralis larval mitochondrial ATP6 synthase F0 subunit (ATP6) gene, after detection of antibodies to Trichinella excretory-secretory (E/S) antigen using Enzyme-linked Immunosorbent Assay (ELISA), in blood of humans in Kaduna metropolis, Nigeria. The sera of 210 participants were tested for antibodies to Trichinella E/S antigen. Overall seroprevalence rate of 39% (82/210) was recorded using ELISA. Out of the 9 ELISA samples selected randomly, PCR detected migratory Trichinella spiralis larval ATP6 gene in 4 (44.4%) at the amplicon size of 250 base pairs using the whole blood of the participants.  The 9 samples comprised 7 seropositive and 2 seronegative. The bands at lanes 1, 2, 3 and 4 were positive for ATP6 while lanes 5,6,7,8 and 9 were negative for ATP6.  Lanes 4 and 5 were ELISA negative for anti-Trichinella antibodies. One in 5 of the 128 ELISA negative samples was positive for ATP6 representing a 25.6% prevalence rate by extrapolation.  PCR using ATP6 gene as a genetic marker is valuable for the detection of T. spiralis migratory larvae in blood samples of humans and consequently the early diagnosis of trichinellosis in humans.

Sign in / Sign up

Export Citation Format

Share Document