Identification of Microorganisms Associated to the Biodegradation of Historic Masonry Structure in San Francisco de Campeche City, México

2012 ◽  
Vol 1374 ◽  
pp. 187-194
Author(s):  
Rocío G. Escamilla Pérez ◽  
Javier Reyes Trujeque ◽  
Tezozomoc Pérez López ◽  
Víctor Monteón Padilla ◽  
Ruth López Alcántara
Keyword(s):  
Microbial Communities ◽  
San Francisco ◽  
Ribosomal Rna ◽  
Pcr Amplification ◽  
Masonry Structure ◽  
Historic Masonry ◽  
Nucleotide Database ◽  
Polymerase Chain ◽  
San Carlos ◽  
Rna Genes

ABSTRACTTropical climate create ideal conditions for the development of microbial communities associated with biodegradation of historic buildings made with stony materials. This is the case of Fort San Carlos, a historic colonial building representative of military tendencies during the XVII century in San Francisco de Campeche City. In this study the Polymerase Chain Reaction (PCR), was used to identify microorganisms related with the biodegradation of its masonry structure. Specific primers for amplification of 16S and 18S ribosomal RNA genes were used for organisms identification by PCR. Amplification products were sequenced and after that compared with GENBANK nucleotide database using-BLASTn. Results indicated that microbial communities associated to biodegradation of the Fort San Carlos are bacteria from the Phyla Cyanobacteria, Proteobacteria and Actinobacteria.

Molecular differentiation of Trichinella spiralis, T. pseudospiralis, T. papuae and T. zimbabwensis by pyrosequencing

2013 ◽  
Vol 89 (1) ◽  
pp. 118-123 ◽  
Author(s):  
L. Sadaow ◽  
C. Tantrawatpan ◽  
P.M. Intapan ◽  
V. Lulitanond ◽  
T. Boonmars ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Trichinella Spiralis ◽  
Large Subunit ◽  
Pcr Amplification ◽  
Epidemiological Studies ◽  
Chain Reaction ◽  
Target Region ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Zoonotic Parasites

AbstractNematodes of the genus Trichinella which infect wildlife and domestic animals show a cosmopolitan distribution. These zoonotic parasites are the aetiological agents of a severe human disease, trichinellosis. Twelve taxa are recognized in the Trichinella genus, but they cannot be identified by morphology since they are sibling species/genotypes. For epidemiological studies, it is extremely important to identify each taxon since they have different distribution areas and host ranges. In the present study, polymerase chain reaction (PCR) amplification of the mitochondrial large subunit ribosomal RNA (lsu-RNA) gene coupled with a pyrosequencing technique was developed to distinguish among four Trichinella species: Trichinella spiralis, T. pseudospiralis, T. papuae and T. zimbabwensis. A PCR method was used to amplify the lsu-RNA of Trichinella sp. larvae in mouse muscles and single larvae collected from infected muscles by digestion. The results show that the four Trichinella species can be distinguished by using 26 nucleotides in the target region and the method is sensitive enough to identify individual larvae. The pyrosequencing provides a simple, rapid and high-throughput tool for the differentiation of Trichinella species.

scholarly journals The Microbiome of the Reef Macroalga Sargassum ilicifolium in Singapore

2021 ◽  
Vol 9 (5) ◽  
pp. 898
Author(s):  
Ren Min Oh ◽  
Elena Bollati ◽  
Prasha Maithani ◽  
Danwei Huang ◽  
Benjamin J. Wainwright
Keyword(s):  
Coral Reef ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Microbial Community Composition ◽  
Pcr Amplification ◽  
Rrna Gene ◽  
Benthic Organisms ◽  
Polymerase Chain ◽  
Microbial Change ◽  
The 16S Rrna Gene

The large canopy-forming macroalga, Sargassum ilicifolium, provides shelter and food for numerous coral reef species, but it can also be detrimental at high abundances where it outcompetes other benthic organisms for light and space. Here, we investigate the microbial communities associated with S. ilicifolium in Singapore, where it is an abundant and important member of coral reef communities. We collected eight complete S. ilicifolium thalli from eight island locations along an approximate 14 km east-to-west transect. Each thallus was dissected into three separate parts: holdfast, vesicles, and leaves. We then characterized the bacterial communities associated with each part via polymerase chain reaction (PCR) amplification of the 16S rRNA gene V4 region. We then inferred predicted metagenome functions using METAGENassist. Despite the comparatively short distances between sample sites, we show significant differences in microbial community composition, with communities further differentiated by part sampled. Holdfast, vesicles and leaves all harbor distinct microbial communities. Functional predictions reveal some separation between holdfast and leaf communities, with higher representation of sulphur cycling taxa in the holdfast and higher representation of nitrogen cycling taxa in the leaves. This study provides valuable baseline data that can be used to monitor microbial change, and helps lay the foundation upon which we can begin to understand the complexities of reef-associated microbial communities and the roles they play in the functioning and diversity of marine ecosystems.

Use of mitochondrial RNA genes for the differentiation of four Trichinella species by multiplex PCR amplification

2009 ◽  
Vol 83 (2) ◽  
pp. 121-128 ◽  
Author(s):  
R. Blaga ◽  
BaoQuan Fu ◽  
D. Le Rhun ◽  
E. Le Naour ◽  
A. Heckman ◽  
...  
Keyword(s):  
Multiplex Pcr ◽  
Dna Sequences ◽  
Trichinella Spiralis ◽  
Pcr Amplification ◽  
Mitochondrial Rna ◽  
Mitochondrial Rrna ◽  
Polymerase Chain ◽  
Rna Genes ◽  
Rdna Amplification ◽  
Mitochondrial Rdna

AbstractUntil now, four species of the Trichinella genus have been identified in Europe: Trichinella spiralis, T. nativa, T. britovi and T. pseudospiralis. The aim of this work was to establish a sound polymerase chain reaction (PCR)-based method to differentiate these four species using mitochondrial rDNA as a reliable genetic marker and to evaluate the sensitivity of this method. Full-length DNA sequences coding for the small and large mitochondrial rRNA (mt-rrnS and mt-rrnL) of the four species are described. A multiplex PCR was designed and successfully tested on 24 European isolates. As few as one larva, or 100 pg of genomic DNA was detected, providing equivalent sensitivity to previously described PCR methods. The PCR-based method of mitochondrial rDNA amplification was thereby established as a sensitive and reproductive diagnostic method for the four European Trichinella species.

What Molecular Biology has to Tell us at the Species Level in Lichenized Fungi

1998 ◽  
Vol 30 (4-5) ◽  
pp. 307-320 ◽  
Author(s):  
Paul D. Bridge ◽  
David L. Hawksworth
Keyword(s):  
Ribosomal Rna ◽  
Pcr Amplification ◽  
Fungal Genome ◽  
Species Boundaries ◽  
Chain Reaction ◽  
Variable Regions ◽  
Fungal Partner ◽  
Large Numbers ◽  
Polymerase Chain ◽  
Pcr Techniques

AbstractMolecular biological techniques now provide many opportunities for determining relationships between organisms. In lichen-forming fungi, polymerase chain reaction (PCR) amplification can be undertaken with primers that have enhanced specificity for fungi, allowing the recovery of precise regions of the genome of the fungal partner. Such PCR techniques are suitable for the analysis of both fresh and dried specimens of great age, and as the techniques require only minimal amounts of starting material, they are suitable for the analysis of large numbers of specimens. PCR can be used to examine both conserved and variable regions of the fungal genome that may be taxonomically significant, and variability in these sequences can be used to describe species boundaries. The ease of analysis of large numbers of specimens without the need to purify or culture the fungal partner makes analysis and comparison of infra- and inter-specific relationships possible, and provides valuable information into their genetic background. Most molecular analyses undertaken with lichen-forming fungi have considered variation within ribosomal RNA clusters, and in this paper we consider the application and interpretation of such PCR-based analysis in the circumscription of species and in determining concepts for individuality and infra-specific groupings.

DNA fingerprinting of tabanids (Diptera: Tabanidae) and their respective egg masses using PCR – restriction fragment profiling

2004 ◽  
Vol 136 (5) ◽  
pp. 605-619 ◽  
Author(s):  
M. Iranpour ◽  
A.M. Schurko ◽  
G.R. Klassen ◽  
T.D. Galloway
Keyword(s):  
Restriction Fragment ◽  
Ribosomal Rna ◽  
Intergenic Spacer ◽  
Interspecific Variation ◽  
Egg Masses ◽  
Polymerase Chain ◽  
High Level ◽  
Rna Genes ◽  
Profiling Analysis ◽  
Respective Species

AbstractPolymerase chain reaction and subsequent restriction fragment profiling analysis were used to associate collected tabanid egg masses with their respective species of adult horse flies and deer flies (Diptera: Tabanidae) in Manitoba, Canada. The ribosomal DNA (rDNA) intergenic spacer between the 28S and 18S ribosomal RNA genes was used successfully to differentiate 34 species of adult tabanids representing five genera: Atylotus (1 sp.), Chrysops (10 spp.), Haematopota (1 sp.), Hybomitra (17 spp.), and Tabanus (5 spp.). rDNA was a suitable molecular target for identifying tabanid species because of the high level of interspecific variation when comparing fragment profiles among different species, and the corresponding minimal intraspecific variation among individuals of the same species. Restriction fragment profiles from 56 field-collected tabanid egg masses were compared with those previously obtained from adults of known species. Egg masses of five species were identified: Hybomitra lasiophthalma (Macquart), Hybomitra nitidifrons nuda (McDunnough), Chrysops aestuans van der Wulp, Chrysops excitans Walker, and Chrysops mitis Osten Sacken. We also provide physical descriptions of these tabanid egg masses along with pictures.

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