scholarly journals Análisis del gen dhaT en cepas Colombianas de Clostridium sp. (Clostridia) productoras de 1,3-propanodiol.

2010 ◽  
Vol 15 (1) ◽  
pp. 17 ◽  
Author(s):  
Diana Milena Quilaguy Ayure ◽  
José David Montoya Solano ◽  
Zulma Rocío Suárez Moreno ◽  
José Mauricio Bernal Morales ◽  
Dolly Montoya Castaño
Keyword(s):  
Bioinformatics Analysis ◽  
Bacterial Species ◽  
Dna Amplification ◽  
Physical Structure ◽  
Clostridium Butyricum ◽  
Chain Reaction ◽  
Specific Primers ◽  
Native Strains ◽  
High Degree ◽  
Degree Of Similarity

<p><strong>Objective:</strong> to analyze the <em>dhaT </em>gene, one of the genes responsible for the 1,3-propanediol (1,3-PD) production, in two native <em>Clostridium</em> strains. <strong>Materials and methods: </strong>The <em>dhaT</em> gene was amplified by Polimerase Chain Reaction with specific primers designed from <em>Clostridium butyricum</em> VPI1718 operon. Bioinformatics tools like BLASTN, ORF finder, BLASTP and ClustalW were used to determine the identity of the sequence and to assign a function. <strong>Results:</strong> DNA amplification products were obtained from Colombian<em> Clostridium </em>sp. native strains (IBUN 13A and IBUN 158B) and the <em>Clostridium butyricum </em>DSM 2478 strain, which were sequenced. According to the bioinformatics analysis of the above sequences, a high degree of similarity was found with the <em>dhaT </em>gene of different bacterial species. The highest percentage of identity was obtained with the <em>Clostridium butyricum </em>VPI 1718 strain. <strong>Conclusion:</strong> knowledge of the physical structure of the 1,3-PD operon in native strains opens the way for developing genetic and metabolic engineering strategies for improving processes productivity.</p> <p><strong> </strong></p> <p><strong>Key words: </strong>1,3-propanediol, 1,3-propanediol dehydrogenase, <em>dhaT </em>gene, 1,3-propanediol operon.</p><br />

scholarly journals DNA Marker-based Study of Genetic Relatedness in United States Sweetpotato Cultivars

1996 ◽  
Vol 121 (6) ◽  
pp. 1059-1062 ◽  
Author(s):  
C.S. Prakash ◽  
Guohao He ◽  
Robert L. Jarret
Keyword(s):  
Ipomoea Batatas ◽  
Dna Marker ◽  
Genetic Relatedness ◽  
Genetic Relationships ◽  
Dna Amplification ◽  
Population Based ◽  
Pedigree Information ◽  
Polymerase Chain ◽  
High Degree ◽  
Degree Of Similarity

The polymerase chain reaction (PCR)-based DNA amplification fingerprinting (DAF) approach was used to investigate genetic relationships among 30 U.S. sweetpotato (Ipomoea batatas L. Lam.) genotypes including heirloom cultivars and recent releases. Phenogram, pairwise similarity matrix, and principal coordinate plots were developed based on Jaccard's coefficients using band-sharing data generated by seven octamer primers. All cultivars showed unique fingerprint patterns indicating the utility of DAF in cultivar identification. Many heirloom cultivars such as `Creole' and `Porto Rico' were readily differentiated from recently developed cultivars. Modern cultivars such as `Jewel', `Carver', `Nugget', and `Scarlet' exhibited a high degree of similarity reflecting ancestral relatedness. `Regal' and `Excel', recently developed using a population-based breeding approach, showed greater divergence from all other cultivars. Those cultivars, developed as a result of somatic mutations, exhibited high levels of genetic similarity to their normal-type parents and yet had distinct fingerprint profiles. With few exceptions, genetic relationships derived from DAF data appear to be consistent with available pedigree information.

scholarly journals Detection of chromosomal translocation t(14;18) within the minor cluster region of bcl-2 by polymerase chain reaction and direct genomic sequencing of the enzymatically amplified DNA in follicular lymphomas

Blood ◽  
1989 ◽  
Vol 73 (7) ◽  
pp. 1759-1762 ◽  
Author(s):  
BY Ngan ◽  
J Nourse ◽  
ML Cleary
Keyword(s):  
Polymerase Chain Reaction ◽  
Large Fraction ◽  
Dna Amplification ◽  
Nucleotide Sequencing ◽  
Chromosome 18 ◽  
Chain Reaction ◽  
Specific Primers ◽  
Cluster Region ◽  
Polymerase Chain ◽  
Follicular Lymphomas

A majority of t(14;18) translocations have been shown to cluster at one of two sites on chromosome 18, called the major breakpoint region (mbr) or the minor cluster region, (mcr), which map within or flanking the bcl-2 proto-oncogene, respectively. We have determined the nucleotide sequence for a portion of the mcr, and constructed oligonucleotides that were used to perform the polymerase chain reaction (PCR) in conjunction with universal immunoglobulin primers to specifically amplify t(14;18) breakpoints in DNA obtained from follicular lymphomas. Eight of ten breakpoints that were detectable on Southern blots using DNA probes for the mcr could be detected due to specific amplification by the PCR technique using an mcr-specific primer. Direct nucleotide sequencing of the enzymatically amplified DNAs showed that the breakpoints clustered within a 500 nucleotide region, and five occurred within three nucleotides of each other. These data show a remarkable clustering of some t(14;18) breakpoints at a site on chromosome 18, at least a 30-kb distance from the bcl-2 gene. Our findings also indicate that mcr-specific primers may be used in conjunction with previously described mbr-specific primers in a highly sensitive DNA amplification technique to detect a large fraction of t(14;18) breakpoints.

scholarly journals Detection of chromosomal translocation t(14;18) within the minor cluster region of bcl-2 by polymerase chain reaction and direct genomic sequencing of the enzymatically amplified DNA in follicular lymphomas

Blood ◽  
1989 ◽  
Vol 73 (7) ◽  
pp. 1759-1762 ◽  
Author(s):  
BY Ngan ◽  
J Nourse ◽  
ML Cleary
Keyword(s):  
Polymerase Chain Reaction ◽  
Large Fraction ◽  
Dna Amplification ◽  
Nucleotide Sequencing ◽  
Chromosome 18 ◽  
Chain Reaction ◽  
Specific Primers ◽  
Cluster Region ◽  
Polymerase Chain ◽  
Follicular Lymphomas

Abstract A majority of t(14;18) translocations have been shown to cluster at one of two sites on chromosome 18, called the major breakpoint region (mbr) or the minor cluster region, (mcr), which map within or flanking the bcl-2 proto-oncogene, respectively. We have determined the nucleotide sequence for a portion of the mcr, and constructed oligonucleotides that were used to perform the polymerase chain reaction (PCR) in conjunction with universal immunoglobulin primers to specifically amplify t(14;18) breakpoints in DNA obtained from follicular lymphomas. Eight of ten breakpoints that were detectable on Southern blots using DNA probes for the mcr could be detected due to specific amplification by the PCR technique using an mcr-specific primer. Direct nucleotide sequencing of the enzymatically amplified DNAs showed that the breakpoints clustered within a 500 nucleotide region, and five occurred within three nucleotides of each other. These data show a remarkable clustering of some t(14;18) breakpoints at a site on chromosome 18, at least a 30-kb distance from the bcl-2 gene. Our findings also indicate that mcr-specific primers may be used in conjunction with previously described mbr-specific primers in a highly sensitive DNA amplification technique to detect a large fraction of t(14;18) breakpoints.

scholarly journals Perancangan Primer Spesifik Subspesies Berbasis Gen Endoglukanase untuk Deteksi Ralstonia syzygii subsp. syzygii

2018 ◽  
Vol 22 (2) ◽  
pp. 124
Author(s):  
Bambang Trianom ◽  
Triwidodo Arwiyanto ◽  
Tri Joko
Keyword(s):  
Polymerase Chain Reaction ◽  
Ralstonia Solanacearum ◽  
Species Complex ◽  
Control Strategies ◽  
Bacterial Species ◽  
Pcr Primers ◽  
Chain Reaction ◽  
Specific Primers ◽  
Minimum Concentration ◽  
Polymerase Chain

Ralstonia syzygii subsp. syzygii that belong to Ralstonia solanacearum species complex is the cause of Sumateran disease of clove. The disease was reported to cause widespread devastation on clove plantings in Indonesia. One of the control strategies is to reduce the spread of the disease through early detection on clove seedlings. The study aimed to design the specific primers based on endoglucanase (egl) gene of R. syzygii subsp. syzygii as a tool for early diagnosis. The analyses were conducted on development of specific primers design using egl sequences retrieved from GenBank, Polymerase Chain Reaction (PCR), primers sensitivity and specificity test. The pair of primers UGMRss-F (5’-GCTCACCATCGC CAAGGACAGCG-3’) and UGMRss-R (5’-TTCGATCGAACGCCTGGTTGAGC-3’) could amplify R. syzygii subsp. syzygii at ~378 base pairs with 0.8 ng/µl minimum concentration of DNA. The primers was specific to R. syzygii subsp. syzygii but not to other bacterial species even in the same phylotype. IntisariRalstonia syzygii subsp. syzygii merupakan bakteri yang termasuk dalam kelompok Ralstonia solanacearum species complex yang menyebabkan penyakit Sumatera pada tanaman cengkih. Penyakit ini menyebabkan kerugian yang sangat besar dan sampai saat ini belum ditemukan cara pengendalian yang efektif. Salah satu  upaya pencegahan penyakit adalah melalui deteksi dini dan mencegah penyebaran penyakit melalui peredaran bibit dari areal yang endemis. Penelitian ini bertujuan untuk merancang primer spesifik berbasis gen endoglukanase (egl) sebagai upaya deteksi dini penyakit Sumatera. Analisis yang dilakukan  meliputi  desain primer spesifik dengan menggunakan data sekuens gen egl dari GenBank, Polymerase Chain Reaction (PCR), uji kepekaan primer dan uji kekhususan primer. Desain primer yang berhasil dirancang terdiri dari UGMRss-F (5’- GCTCACCATCGCCAAGGACAGCG-3’) dan UGMRss-R (5’-TTC GATCGAACGCCTGGTTGAGC-3’) dengan amplikon ~378 pasang basa. Pada konsentrasi DNA 0,8 ng/µl, secara peka R. syzygii subsp. syzygii masih dapat teramplifikasi dengan baik. Primer ini juga hanya dapat mendeteksi R. syzygii subsp. syzygii dan tidak untuk bakteri lain bahkan pada filotipe yang sama.

scholarly journals Comparison of three qPCR-based commercial tests for detection of periodontal pathogens

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Fridus Van der Weijden ◽  
Mirella Rijnen ◽  
Cees Valkenburg
Keyword(s):  
The Netherlands ◽  
Bacterial Species ◽  
Clinical Samples ◽  
Bacterial Cells ◽  
Periodontal Pathogens ◽  
Target Species ◽  
High Degree ◽  
Test Outcomes ◽  
Degree Of Similarity ◽  
Detection And Quantification

AbstractIn periodontal practice microbial results of periodontal test kits for identification of key pathogens are an aid in the treatment planning. Information on the performance of commercially available test kits is therefore essential for the clinician. In this retrospective analysis three commercially available qPCR kits for detection and quantification of selected periodontal bacterial species were compared, using 100 clinical samples from patients with untreated periodontitis. The analysis involved two separate comparisons in which kit A (LabOral Diagnostics, The Netherlands) was compared with kit B (Advanced Dental Diagnostics, The Netherlands), and with kit C (OralDent diagnostics, The Netherlands). Analytic procedures for detection and quantification of selected periodontal bacterial species were carried out according to the instructions of the laboratories. Kit A detected target species more often, and absolute numbers of bacterial cells were higher than with kit B. A high degree of similarity was found between the test outcomes by kit A and kit C. All three kits performed satisfactory but small and significant differences exist between kits.

scholarly journals Circulating miR-146a as a possible candidate biomarker in the indeterminate phase of Chagas disease

2021 ◽  
Vol 54 (1) ◽  
Author(s):  
Martha Alicia Ballinas-Verdugo ◽  
Rogelio Frank Jiménez-Ortega ◽  
Eduardo Martínez-Martínez ◽  
Nancy Rivas ◽  
Erick Abraham Contreras-López ◽  
...  
Keyword(s):  
Chagas Disease ◽  
Extracellular Vesicles ◽  
Bioinformatics Analysis ◽  
Chronic Phase ◽  
Heart Tissue ◽  
Detailed Knowledge ◽  
Total Plasma ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Relevant Finding

Abstract Background Chagas disease is considered important and presents intense inflammatory and fibrotic processes induced by the perpetuation of the parasite in the affected tissues and organs. Therefore, it is necessary to inquire about the host defense and attack mechanisms to have a more detailed knowledge about Chagas disease. MicroRNAs are found in blood, tissues and extracellular vesicles. These small regulators of gene expression are involved in physiological and pathological processes in both mammals and parasites. Several microRNAs have deregulated expression in chagasic heart disease, although little is known about their extracellular expression. Our main objective was to evaluate the involvement of miR-21, miR-146a and miR-155 in several samples from mice infected with the TcI Ninoa strain from the acute and indeterminate phases. We also explored a potential functional association of the selected microRNAs using STRING software. This software identified 23 pathways associated with Trypanosoma cruzi infection. In addition, eleven genes were identified through bioinformatics analysis, and we found that SMAD family member 5 was downregulated in both phases. This gene serves as a mediator in the TGF-β signaling pathway. Thus, forty female mice of the CD1 strain were distributed into 4 groups and the expression levels of miR-21, miR-146a and miR-155 were measured in samples of heart tissue, total plasma and plasma extracellular vesicles by quantitative real-time polymerase chain reaction. Results Overexpression of miR-21, miR-146a and miR-155 was observed in heart and plasma in both phases. Moreover, in extracellular vesicles miR-21 and miR-146a were also overexpressed in the acute phase, whereas in the indeterminate chronic phase we found only miR-146a up-regulated. Conclusions The expression of inflammatory microRNAs miR-21, miR-146a and miR-155 were up-regulated in each of the samples from acutely and chronically infected mice. The relevant finding was that miR-146a was up-regulated in each sample in both phases; therefore, this miRNA could be a possible candidate biomarker in Chagas disease.

Bacterial Species Identification after DNA Amplification with a Universal Primer Pair

1999 ◽  
Vol 66 (3) ◽  
pp. 205-211 ◽  
Author(s):  
Kevin M. McCabe ◽  
Yao-Hua Zhang ◽  
Bing-Ling Huang ◽  
Elizabeth A. Wagar ◽  
Edward R.B. McCabe
Keyword(s):  
Species Identification ◽  
Bacterial Species ◽  
Dna Amplification ◽  
Universal Primer

scholarly journals Development of a Genoserotyping Method for Salmonella Infantis Detection on the Basis of Pangenome Analysis

2020 ◽  
Vol 9 (1) ◽  
pp. 67
Author(s):  
Seung-Min Yang ◽  
Jiwon Baek ◽  
Eiseul Kim ◽  
Hyeon-Be Kim ◽  
Seyoung Ko ◽  
...  
Keyword(s):  
Public Health ◽  
Polymerase Chain Reaction ◽  
Bacterial Species ◽  
Cost Effective ◽  
The Other ◽  
Gene Marker ◽  
Diagnostic Assay ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Substantial Economic Burden

In recent years, Salmonella Infantis has become a predominant serovariant in clinical and poultry isolates, thereby imposing a substantial economic burden on both public health and the livestock industry. With the aim of coping with the steep increase in serovar Infantis prevalence, a polymerase chain reaction (PCR)-based rapid and accurate diagnostic assay was developed in this study through pangenome profiling of 60 Salmonella serovars. A gene marker, SIN_02055, was identified, which is present in the S. Infantis genome but not in the pangenome of the other serovars. Primers specific to SIN_02055 were used to accurately detect serovar Infantis, and to successfully differentiate Infantis from the other 59 serovars in real-time PCR with a R2 of 0.999 and an efficiency of 95.76%. The developed method was applied to 54 Salmonella strains belonging to eight dominant serovars, and distinguished Infantis from the other seven serovars with an accuracy of 100%. The diagnostic primer set also did not show false positive amplification with 32 strains from eight non-Salmonella bacterial species. This cost-effective and rapid method can be considered an alternative to the classic serotyping using antisera.

Using Cluster Analysis to Improve Marketing Experiments

1971 ◽  
Vol 8 (3) ◽  
pp. 340-347 ◽  
Author(s):  
George S. Day ◽  
Roger M. Heeler
Keyword(s):  
Cluster Analysis ◽  
Space Representation ◽  
Reduced Space ◽  
High Degree ◽  
Degree Of Similarity ◽  
Sensitive Experiment ◽  
Selection Of

When the selection of a sample of stores or cities requires a high degree of similarity among the test units in order to ensure a sensitive experiment, the sample may no longer represent the market. These conflicting requirements can be satisfied by choosing the sample from clusters displayed in a reduced space representation of the market.

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