scholarly journals Genetic Identification of Edible Bird’s Nest in Thailand Based on ARMS-PCR

2021 ◽  
Vol 12 ◽  
Author(s):  
Dongyong Lv ◽  
Yaohua Fan ◽  
Wanhua Zhong ◽  
Piyanuch Lonan ◽  
Kunfeng Liu ◽  
...  
Keyword(s):  
Genetic Information ◽  
Phylogenetic Trees ◽  
Sodium Dodecyl ◽  
Genetic Identification ◽  
Gene Sequences ◽  
Simple Method ◽  
Guanidinium Isothiocyanate ◽  
Arms Pcr ◽  
Edible Bird’S Nest ◽  
Nd2 Gene

Edible bird’s nest (EBN) is a popular delicacy in the Asian Pacific region originating from Indonesia, Malaysia, Thailand and Vietnam, which consist of various potential medicine value in Traditional Chinese Medicine (TCM). Thailand is one of the main exporters of EBN. However, the genetic information of EBN, a key part of molecular biology, has yet to be reported in Thailand. It is necessary to explore the genetic information of EBN in Thailand based on a quick and simple method to help protect the rights and interests of consumers. This research aimed to systematically evaluate different methods of extracting EBN DNA to improve the efficiency of the analysis of cytochrome b (Cytb) and NADH dehydrogenase subunit 2 (ND2) gene sequences, the establishment of phylogenetic trees, and the genetic information of EBN in Thailand. Additionally, we aimed to develop a quick and simple method for identifying EBN from different species based on the genetic information and amplification-refractory mutation system PCR (ARMS-PCR). By comparing the four methods [cetyltrimethylammonium bromide (CTAB), sodium dodecyl sulfate (SDS), kit and guanidinium isothiocyanate methods] for EBN extraction, we found that the guanidinium isothiocyanate method was the optimal extraction method. Phylogenetic trees generated on the basis of Cytb and ND2 gene analyses showed that 26 samples of house EBN and 4 samples of cave EBN came from Aerodramus fuciphagus and Aerodramus maximus, respectively. In addition, to distinguish different samples from different species of Apodiformes, we designed 4 polymerase chain reaction (PCR) amplification primers based on the ND2 gene sequences of A. fuciphagus and A. maximus. The ARMS-PCR results showed band lengths for A. fuciphagus EBN of 533, 402, and 201 bp, while those for A. maximus EBN were 463, 317, and 201 bp. Collectively, the results showed that ARMS-PCR is a fast and simple method for the genetic identification of EBN based on designing specific original identification primers.

scholarly journals Distribution and recombination of Wolbachia endosymbionts in Korean coleopteran insects

2019 ◽  
Vol 43 (1) ◽  
Author(s):  
Gilsang Jeong ◽  
Taeman Han ◽  
Haechul Park ◽  
Soyeon Park ◽  
Pureum Noh
Keyword(s):  
16S Rrna ◽  
Phylogenetic Trees ◽  
Surface Protein ◽  
Rrna Gene ◽  
Infection Frequency ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Endosymbiotic Bacteria ◽  
Molecular Machinery ◽  
Broad Scale

Abstract Background Wolbachia are among the most prevalent endosymbiotic bacteria and induce reproductive anomalies in various invertebrate taxa. The bacterium has huge impacts on host reproductive biology, immunity, evolution, and molecular machinery. However, broad-scale surveys of Wolbachia infections at the order scale, including the order Coleoptera, are limited. In this study, we investigated the Wolbachia infection frequency in 201 Coleopteran insects collected in Korea. Results A total of 26 species (12.8%) belonging to 11 families harbored Wolbachia. The phylogenetic trees of based on partial 16S rRNA gene sequences and partial Wolbachia surface protein (wsp) gene sequences were largely incongruent to that of their hosts. This result confirms that Wolbachia evolved independently from their hosts, Conclusion Phylogenetic trees suggest that complex horizontal gene transfer and recombination events occurred within and between divergent Wolbachia subgroups.

scholarly journals Phylogenetic relationships within the family Halobacteriaceae inferred from rpoB′ gene and protein sequences

2007 ◽  
Vol 57 (10) ◽  
pp. 2289-2295 ◽  
Author(s):  
Madalin Enache ◽  
Takashi Itoh ◽  
Tadamasa Fukushima ◽  
Ron Usami ◽  
Lucia Dumitru ◽  
...  
Keyword(s):  
16S Rrna ◽  
Molecular Marker ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Protein Sequences ◽  
Rpob Gene ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
The Family

In order to clarify the current phylogeny of the haloarchaea, particularly the closely related genera that have been difficult to sort out using 16S rRNA gene sequences, the DNA-dependent RNA polymerase subunit B′ gene (rpoB′) was used as a complementary molecular marker. Partial sequences of the gene were determined from 16 strains of the family Halobacteriaceae. Comparisons of phylogenetic trees inferred from the gene and protein sequences as well as from corresponding 16S rRNA gene sequences suggested that species of the genera Natrialba, Natronococcus, Halobiforma, Natronobacterium, Natronorubrum, Natrinema/Haloterrigena and Natronolimnobius formed a monophyletic group in all trees. In the RpoB′ protein tree, the alkaliphilic species Natrialba chahannaoensis, Natrialba hulunbeirensis and Natrialba magadii formed a tight group, while the neutrophilic species Natrialba asiatica formed a separate group with species of the genera Natronorubrum and Natronolimnobius. Species of the genus Natronorubrum were split into two groups in both the rpoB′ gene and protein trees. The most important advantage of the use of the rpoB′ gene over the 16S rRNA gene is that sequences of the former are highly conserved amongst species of the family Halobacteriaceae. All sequences determined so far can be aligned unambiguously without any gaps. On the other hand, gaps are necessary at 49 positions in the inner part of the alignment of 16S rRNA gene sequences. The rpoB′ gene and protein sequences can be used as an excellent alternative molecular marker in phylogenetic analysis of the Halobacteriaceae.

scholarly journals Variovorax gossypii sp. nov., isolated from Gossypium hirsutum

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4335-4340 ◽  
Author(s):  
Peter Kämpfer ◽  
Hans-Jürgen Busse ◽  
John A. McInroy ◽  
Stefanie P. Glaeser
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gossypium Hirsutum ◽  
Dna Hybridization ◽  
Phylogenetic Trees ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Polar Lipid Profile ◽  
The 16S Rrna Gene

A beige-pigmented bacterial strain (JM-310T), isolated from the healthy internal root tissue of 4-week-old cotton (Gossypium hirsutum, cultivar ‘DES-119’) in Tallassee (Macon county), Alabama, USA, was studied taxonomically. The isolate produced small rod-shaped cells, which showed a Gram-negative staining behaviour. A comparison of the 16S rRNA gene sequence of the isolate revealed 99.2, 98.8, 98.7, 98.7, 98.1 and 97.6 % similarity to the 16S rRNA gene sequences of the type strains of Variovorax paradoxus, Variovorax boronicumulans, Variovorax ginsengisoli, Variovorax soli, Variovorax defluvii and Variovorax dokdonensis, respectively. In phylogenetic trees based on 16S rRNA gene sequences, strain JM-301T was placed within the monophyletic cluster of Variovorax species. The fatty acid profile of strain JM-310T consisted mainly of the major fatty acids C16 : 0, C10 : 0 3-OH and summed feature 4 (iso-C15 : 0 2-OH/C16 : 1ω7c/t). The quinone system of strain JM-310T contained predominantly ubiquinone Q-8 and lesser amounts of Q-7 and Q-9. The major polyamine was putrescine and the diagnostic polyamine 2-hydroxyputrescine was detected as well. The polar lipid profile consisted of the major lipids phosphatidylethanolamine, phosphatidylglycerol, diphospatidylglycerol and several unidentified lipids. DNA–DNA hybridization experiments with V. paradoxus LMG 1797T, V. boronicumulans 1.22T, V. soli KACC 11579T and V. ginsengisoli 3165T gave levels of relatedness of < 70 %. These DNA–DNA hybridization results in addition to differential biochemical properties indicate clearly that strain JM-310T is a member of a novel species, for which the name Variovorax gossypii sp. nov. is proposed. The type strain is JM-310T ( = LMG 28869T = CIP 110912T = CCM 8614T).

scholarly journals SHOOT: phylogenetic gene search and ortholog inference

2021 ◽  
Author(s):  
David Emms ◽  
Steven Kelly
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Phylogenetic Trees ◽  
Query Sequence ◽  
Gene Tree ◽  
Biological Research ◽  
Gene Sequences ◽  
Multiple Sequence ◽  
Gene Search

Determining the evolutionary relationships between gene sequences is fundamental to comparative biological research. However, conducting such analyses requires a high degree of technical proficiency in several computational tools including gene family construction, multiple sequence alignment, and phylogenetic inference. Here we present SHOOT, an easy to use phylogenetic search engine for fast and accurate phylogenetic analysis of biological sequences. SHOOT searches a user-provided query sequence against a database of phylogenetic trees of gene sequences (gene trees) and returns a gene tree with the given query sequence correctly grafted within it. We show that SHOOT can perform this search and placement with comparable speed to a conventional BLAST search. We demonstrate that SHOOT phylogenetic placements are as accurate as conventional multiple sequence alignment and maximum likelihood tree inference approaches. We further show that SHOOT can be used to identify orthologs with equivalent accuracy to conventional orthology inference methods. In summary, SHOOT is an accurate and fast tool for complete phylogenetic analysis of novel query sequences. An easy to use webserver is available online at www.shoot.bio.

scholarly journals GENETIC IDENTIFICATION OF AQUATIC INVERTEBRATES OF KAZAKHSTAN AS INDICATORS OF ORGANIC POLLUTANTS

2018 ◽  
pp. 139-148
Author(s):  
Alexandr Anatoljevich Volkov ◽  
Larisa Anatoljevna Kovaljova ◽  
Tatjana Timofeevna Troshina ◽  
Zhanara Omirbekovna Mazhibaeva ◽  
Dmitrij Valerjevich Pilin ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Phylogenetic Trees ◽  
Aquatic Invertebrates ◽  
Species Abundance ◽  
Ecological Status ◽  
Taxonomic Status ◽  
Organic Pollution ◽  
Water Bodies ◽  
Genetic Identification ◽  
Morphological Identity

The article deals with carrying out DNA barcoding of aquatic invertebrates of Kazakhstan to identify their taxonomic status as organic pollution indicators. 33 species of the Balkhash-Alakol basin and the Zhayik river were analyzed. 21 species correlate (95-100%) with previously published sequences of invertebrates with well-known classifications in the GenBank and BOLD databases. The taxonomic discrepancy in morphometric and genetic parameters in certain species has been revealed. The discrepancy may be caused by the morphological identity in chironomids at a larval stage. The phylogenetic trees of the investigated species within the families Chironomidae and Moinidae have been indicated. Chironomids are represented by ten clades of different types of genetic polymorphism of DNA gene. Genetic links of Moinidae are detected in four groups including a cryptic species from Lake Alakol. It has been stated that in distribution of cryptic taxons in Moina family factors of salinity and depth of the lake are important, as well as differences in depth. Molecular DNA-barcoding of invertebrates of Kazakhstan should be continued with covering a greater number of species and several replications, with qualified primary fixation of subjects of research and a sufficient number of samples. Authenticity of composition defining, species abundance, species characteristics of aquatic invertebrates from the water bodies of poorly explored arid regions is necessary for using them as indicators of the ecological status of water bodies.

Taxonomic study of the genus Salinicola: transfer of Halomonas salaria and Chromohalobacter salarius to the genus Salinicola as Salinicola salarius comb. nov. and Salinicola halophilus nom. nov., respectively

2010 ◽  
Vol 60 (4) ◽  
pp. 963-971 ◽  
Author(s):  
Rafael R. de la Haba ◽  
Cristina Sánchez-Porro ◽  
M. Carmen Márquez ◽  
Antonio Ventosa
Keyword(s):  
16S Rrna ◽  
Type Strain ◽  
Phylogenetic Trees ◽  
23S Rrna ◽  
Rrna Gene ◽  
Gene Sequences ◽  
The Family ◽  
23S Rrna Gene ◽  
Single Genus ◽  
Type Strains

We have carried out a polyphasic taxonomic characterization of the type strains of the species with the recently validated name Salinicola socius, together with two species that were phylogenetically closely related, Halomonas salaria and Chromohalobacter salarius. 16S rRNA gene sequence analyses showed that they constituted a coherent cluster, with sequence similarities between 98.7 and 97.7 %. We have determined the almost complete 23S rRNA gene sequences of these three type strains, and the percentage of similarity between them was 99.2–97.6 %. Phylogenetic trees based on the 16S rRNA and 23S rRNA gene sequences, obtained by using three different algorithms, were consistent and showed that these three species constituted a cluster separated from the other species of the genera of the family Halomonadaceae, supporting their placement in a single genus. All three species have ubiquinone 9 as the major respiratory quinone, and showed similar fatty acid and polar lipid profiles. The level of DNA–DNA hybridization between Salinicola socius DSM 19940T, Halomonas salaria DSM 18044T and Chromohalobacter salarius CECT 5903T was 41–21 %, indicating that they are different species of the genus Salinicola. A comparative phenotypic study of these strains following the proposed minimal standards for describing new taxa of the family Halomonadaceae has been carried out. The phenotypic data are consistent with the placement of these three species in a single genus and support their differentiation at the species level. On the basis of these data we have emended the description of the species Salinicola socius and we propose to transfer the species Halomonas salaria and Chromohalobacter salarius to the genus Salinicola, as Salinicola salarius comb. nov. (type strain M27T =KCTC 12664T =DSM 18044T) and Salinicola halophilus nom. nov. (type strain CG4.1T =CECT 5903T =LMG 23626T), respectively.

scholarly journals A New Subclade of Leptosphaeria biglobosa Identified from Brassica rapa

2019 ◽  
Vol 20 (7) ◽  
pp. 1668 ◽  
Author(s):  
Zhongwei Zou ◽  
Xuehua Zhang ◽  
Paula Parks ◽  
Lindsey du Toit ◽  
Angela Van de Wouw ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Phylogenetic Trees ◽  
Single Gene ◽  
Leptosphaeria Maculans ◽  
Stem Canker ◽  
Willamette Valley ◽  
Gene Sequences ◽  
Distance Analysis ◽  
Pathogenicity Tests ◽  
Leptosphaeria Biglobosa

Blackleg (Phoma stem canker) of crucifers is a globally important disease caused by the ascomycete species complex comprising of Leptosphaeria maculans and Leptosphaeria biglobosa. Six blackleg isolates recovered from Brassica rapa cv. Mizspoona in the Willamette Valley of Oregon were characterized as L. biglobosa based on standard pathogenicity tests and molecular phylogenetic analysis. These isolates were compared to 88 characterized L. biglobosa isolates from western Canada, 22 isolates from Australia, and 6 L. maculans isolates from Idaho, USA using maximum parsimony and distance analysis of phylogenetic trees generated from the ITS rDNA (internal transcribed spacer rDNA) sequence, and the actin and β-tubulin gene sequences. The L. biglobosa isolates derived from B. rapa collected in Oregon formed a separate subclade based on concatenated gene sequences or a single gene sequence, regardless of the analyses. Pathogenicity tests showed that these isolates failed to infect either resistant or susceptible B. napus cultivars, but caused severe symptoms on three B. rapa cultivars (Accession number: UM1113, UM1112, and UM1161), a B. oleracea var. capitata (cabbage) cultivar (Copenhagen Market), and two B. juncea cultivars (CBM, a common brown Mustard, and Forge). These findings demonstrated that the L. biglobosa isolates derived from a B. rapa crop in Oregon were genetically distinct from existing species of L. biglobosa, and constitute a new subclade, herein proposed as L. biglobosa ‘americensis’.

Preliminary Treatment of Urinary Proteins Improves Electrophoretic Analysis and Immunodetection

1992 ◽  
Vol 38 (6) ◽  
pp. 860-863 ◽  
Author(s):  
J M Verdier ◽  
B Dussol ◽  
P Dupuy ◽  
Y Berland ◽  
J C Dagorn
Keyword(s):  
Protein Pattern ◽  
Protein A ◽  
Sodium Dodecyl ◽  
Complex Mixture ◽  
Electrophoretic Analysis ◽  
Renal Physiology ◽  
Preliminary Treatment ◽  
Urinary Proteins ◽  
Simple Method ◽  
Electrophoretic Migration

Abstract Analysis of urinary protein composition is an important tool in studies on renal physiology and physiopathology. Urine is, however, a complex mixture containing, besides protein, a variety of compounds such as salts, peptides, oligosaccharides, and glycosaminoglycans. Some of these compounds interfere with the electrophoretic migration of protein in sodium dodecyl sulfate-polyacrylamide gels and prevent correct analysis of the protein pattern. We describe a simple method for extracting urinary proteins that considerably improves their electrophoretic migration and subsequent immunodetection. This treatment involves ammonium sulfate fractionations (for precipitating proteins), EDTA (for inhibiting protein aggregation), and HCl hydrolysis (for removing glycosylaminoglycans). Recovery during extraction was found to be almost quantitative for total protein and three representative proteins: albumin, alpha 1-glycoprotein acid, and beta 2-microglobulin.

scholarly journals Distribution of Viable Bacteria in the Dust-Generating Natural Source Area of the Gobi Region, Mongolia

Atmosphere ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 893
Author(s):  
Katsuro Hagiwara ◽  
Tamaki Matsumoto ◽  
Purevsuren Tsedendamba ◽  
Kenji Baba ◽  
Buho Hoshino
Keyword(s):  
Phylogenetic Trees ◽  
Surface Soil ◽  
Sequence Data ◽  
Source Area ◽  
Soil Surface ◽  
Genetic Identification ◽  
Gobi Desert ◽  
Health Concept ◽  
Dry Lake ◽  
Live Bacteria

The Gobi Desert is a major source of dust events, whose frequency of occurrence and damage caused have recently significantly increased. In the present study, we investigated the types of live bacteria present in the surface soil of the Gobi Desert in Mongolia, and determined their genetic identification as well as their geographical distribution. During the survey, four different topographies (dry lake bed, wadi, well, and desert steppe) were selected, and land characteristics were monitored for moisture and temperature. The surface soil was aerobically cultured to isolate bacterial colonies, and their 16s rDNA regions were sequenced. The sequence data were identified through NCBI-BLAST analysis and generated phylogenetic trees. The results revealed two phyla and seven families of isolates from the sample points. Each isolate was characterized by their corresponding sample site. The characteristics of land use and soil surface bacteria were compared. Most of the bacteria originated from the soil, however, animal-derived bacteria were also confirmed in areas used by animals. Our findings confirmed the existence of live bacteria in the dust-generating area, suggesting that their presence could affect animal and human health. Therefore, it is necessary to further investigate dust microbes based on the One Health concept.

Sign in / Sign up

Export Citation Format

Share Document