Identification of an Amylomaltase from the Halophilic Archaeon Haloquadratum walsbyi by Functional Metagenomics: Structural and Functional Insights

Amylomaltases are prokaryotic 4-α-glucanotransferases of the GH77 family. Thanks to the ability to modify starch, they constitute a group of enzymes of great interest for biotechnological applications. In this work we report the identification, by means of a functional metagenomics screening of the crystallization waters of the saltern of Margherita di Savoia (Italy), of an amylomaltase gene from the halophilic archaeon Haloquadratum walsbyi, and its expression in Escherichia coli cells. Sequence analysis indicated that the gene has specific insertions yet unknown in homologous genes in prokaryotes, and present only in amylomaltase genes identified in the genomes of other H. walsbyi strains. The gene is not part of any operon involved in the metabolism of maltooligosaccharides or glycogen, as it has been found in bacteria, making it impossible currently to assign a precise role to the encoded enzyme. Sequence analysis of the H. walsbyi amylomaltase and 3D modelling showed a common structure with homologous enzymes characterized in mesophilic and thermophilic bacteria. The recombinant H. walsbyi enzyme showed starch transglycosylation activity over a wide range of NaCl concentrations, with maltotriose as the best acceptor substrate compared to other maltooligosaccharides. This is the first study of an amylomaltase from a halophilic microorganism.

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Nucleotide sequence analysis of beta tubulin gene in a wide range of dermatophytes

Medical Mycology ◽

10.1093/mmy/myu033 ◽

2014 ◽

Vol 52 (7) ◽

pp. 674-688 ◽

Cited By ~ 30

Author(s):

Ali Rezaei-Matehkolaei ◽

Hossein Mirhendi ◽

Koichi Makimura ◽

G. Sybren de Hoog ◽

Kazuo Satoh ◽

...

Keyword(s):

Sequence Analysis ◽

Nucleotide Sequence ◽

Nucleotide Sequence Analysis ◽

Tubulin Gene ◽

Beta Tubulin ◽

Wide Range ◽

Beta Tubulin Gene

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Prevalence and new genotypes of Enterocytozoon bieneusi in sheltered dogs and cats in Sichuan province, southwestern China

Parasite ◽

10.1051/parasite/2021029 ◽

2021 ◽

Vol 28 ◽

pp. 31

Author(s):

Yalin Zhong ◽

Ziyao Zhou ◽

Lei Deng ◽

Haifeng Liu ◽

Zhijun Zhong ◽

...

Keyword(s):

Sequence Analysis ◽

Internal Transcribed Spacer ◽

Companion Animals ◽

Sichuan Province ◽

Enterocytozoon Bieneusi ◽

Southwestern China ◽

Intracellular Parasite ◽

Type Iv ◽

Wide Range ◽

Epidemiological Information

Enterocytozoon bieneusi is a common intracellular parasite that infects a wide range of hosts, including humans and companion animals, raising concerns of zoonotic transmission. However, there is limited epidemiological information on the prevalence and genotypes of E. bieneusi in sheltered dogs and cats in Sichuan province, southwestern China. A total of 880 fecal samples were collected from shelters in different cities of Sichuan province, including 724 samples from dogs, and 156 samples from cats. Enterocytozoon bieneusi was determined by sequence analysis of the ribosomal internal transcribed spacer (ITS). Overall, the prevalence of E. bieneusi was 18% (158/880), and the parasite was detected in 18.8% (136/724) and 14.1% (22/156) of the dogs and cats examined, respectively. Sequence analysis revealed the presence of five genotypes in dogs, including three known genotypes CD9 (n = 92), PtEb IX (n = 41), and Type IV (n = 1), and two novel genotypes SCD-1 (n = 1) and SCD-2 (n = 1). Similarly, four genotypes were identified in cats, including CD9 (n = 11), Type IV (n = 6), D (n = 4), and PtEb IX (n = 1). Genotypes D and Type IV have previously been identified in humans and are reported in sheltered dogs and cats in the present study, indicating that these animals could be as potential sources of human microsporidiosis infections.

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Emergence of Bacterial Soft Rot in Cucumber Caused by Pectobacterium carotovorum subsp. brasiliense in China

Plant Disease ◽

10.1094/pdis-05-16-0763-re ◽

2017 ◽

Vol 101 (2) ◽

pp. 279-287 ◽

Cited By ~ 14

Author(s):

Xianglong Meng ◽

Ali Chai ◽

Yanxia Shi ◽

Xuewen Xie ◽

Zhanhong Ma ◽

...

Keyword(s):

Sequence Analysis ◽

Soft Rot ◽

Economic Losses ◽

Pectobacterium Carotovorum ◽

Bacterial Soft Rot ◽

Bacterial Strains ◽

Phenotypic Properties ◽

Gene Sequence Analysis ◽

Wide Range ◽

Carotovorum Subsp

During 2014 to 2015, a devastating bacterial soft rot on cucumber stems and leaves occurred in Shandong, Shanxi, Hebei, Henan, and Liaoning provinces of China, resulting in serious economic losses for cucumber production. The gummosis emerged on the surface of leaves, stems, petioles, and fruit of cucumber. The basal stem color was dark brown and the stem base turned to wet rot. Yellow spots and wet rot emerged at the edge of the infected cucumber leaves and gradually infected the leaf centers. In total, 45 bacterial strains were isolated from the infected tissues. On the basis of phenotypic properties of morphology, physiology, biochemistry, and 16S ribosomal RNA gene sequence analysis, the pathogen was identified as Pectobacterium carotovorum. Multilocus sequence analysis confirmed that the isolates were P. carotovorum subsp. brasiliense, and the pathogens fell in clade II. The pathogenicity of isolated bacteria strains was confirmed. The strains reisolated were the same as the original. The host range test confirmed that strains had a wide range of hosts. As far as we know, this is the first report of cucumber stem soft rot caused by P. carotovorum subsp. brasiliense in China as well as in the world, which has a significant economic impact on cucumber production.

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Evaluating telemedicine systems and services

Journal of Telemedicine and Telecare ◽

10.1258/1357633054068955 ◽

2005 ◽

Vol 11 (4) ◽

pp. 167-177 ◽

Cited By ~ 36

Author(s):

Paul Taylor

Keyword(s):

Cost Effective ◽

Appropriate Technology ◽

Sufficient Evidence ◽

Safe Alternative ◽

Telemedicine Service ◽

Common Structure ◽

Wide Range ◽

Cost Effective Alternative ◽

New Community ◽

Clinical Conditions

The evaluation of telemedicine involves attempts to answer a wide range of questions involved in making decisions about safety, about practicality and about utility. Roughly speaking, if we wish to provide a telemedicine service we should first establish that it is safe, next that it is practical and finally that it is worthwhile. In establishing safety, most laboratory studies of telemedicine have a common structure, and consist of the following steps: (1) selection of cases; (2) interpretation; (3) comparison with a gold standard; (4) statistical analyses. Most of the studies to establish the practicality of telemedicine have been carried out as demonstrations, to show that a proposed application can be implemented in a chosen setting. In terms of utility, telemedicine has been used to improve the efficiency of an existing service or to make an existing service available to a new community. One of the difficulties is that the vendors of relatively expensive telemedicine systems and services disseminate much of the information on the topic. We have to focus not on the glamorous technology but on the underlying issue of how the participants in health care (patients, general practitioners, specialists) can communicate more effectively, using the range of technological options open to them. Ensuring that the most appropriate technology is used in the most effective way should be the primary aim of telemedicine research. There is now sufficient evidence for us to be confident that telemedicine is a safe alternative to conventional care in a variety of situations and for a number of clinical conditions. Reliable evidence that it is a practical and cost-effective alternative is, at the time of writing, harder to find.

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The seamless and multi-model coupling between atmosphere, land, hydrology, ocean, waves and sea-ice models based on SURFEX surface model using OASIS3-MCT

10.5194/gmd-2017-91 ◽

2017 ◽

Cited By ~ 3

Author(s):

Aurore Voldoire ◽

Bertrand Decharme ◽

Joris Pianezze ◽

Cindy Lebeaupin Brossier ◽

Florence Sevault ◽

...

Keyword(s):

Weather Prediction ◽

Ocean Waves ◽

Coupled Systems ◽

Surface Model ◽

Atmospheric Models ◽

Common Structure ◽

Wide Range ◽

Wave Models ◽

Prediction Systems ◽

Component Models

Abstract. This study presents the principles of the new coupling interface based on the SURFEX multi-surface model and the OASIS3-MCT coupler. As SURFEX can be plugged into several atmospheric models, it can be used in a wide range of applications, from global and regional coupled climate systems to high-resolution Numerical Weather Prediction systems or very fine scale systems dedicated to process studies. The objective of this development is to build and share a common structure for all these applications for the atmosphere-surface coupling, between atmospheric models and ocean, ice, hydrology, and wave models. The numerical and physical principles of the SURFEX interface between the different component models are described, and the different coupled systems into which the SURFEX OASIS3-MCT-based coupling interface is already applied are presented.

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Multilocus sequence analysis reveals different lineages of Pseudomonas anguilliseptica associated with disease in farmed lumpfish (Cyclopterus lumpus L.)

PLoS ONE ◽

10.1371/journal.pone.0259725 ◽

2021 ◽

Vol 16 (11) ◽

pp. e0259725

Author(s):

Even Bysveen Mjølnerød ◽

Hanne Katrine Nilsen ◽

Snore Gulla ◽

Andreas Riborg ◽

Kirsten Liland Bottolfsen ◽

...

Keyword(s):

Population Structure ◽

Sequence Analysis ◽

Fish Species ◽

Vaccine Development ◽

Geographic Origin ◽

Housekeeping Genes ◽

Cyclopterus Lumpus ◽

Wide Range ◽

Phylogenetic Lineages ◽

High Degree

The bacterium Pseudomonas anguilliseptica has in recent years emerged as a serious threat to production of lumpfish in Norway. Little is known about the population structure of this bacterium despite its association with disease in a wide range of different fish species throughout the world. The phylogenetic relationships between 53 isolates, primarily derived from diseased lumpfish, but including a number of reference strains from diverse geographical origins and fish species, were reconstructed by Multi-Locus Sequence Analysis (MLSA) using nine housekeeping genes (rpoB, atpD, gyrB, rpoD, ileS, aroE, carA, glnS and recA). MLSA revealed a high degree of relatedness between the studied isolates, altough the seven genotypes identified formed three main phylogenetic lineages. While four genotypes were identified amongst Norwegian lumpfish isolates, a single genotype dominated, irrespective of geographic origin. This suggests the existence of a dominant genotype associated with disease in production of lumpfish in Norwegian aquaculture. Elucidation of the population structure of the bacterium has provided valuable information for potential future vaccine development.

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Estimation of Similarity between DNA Sequences and Its Graphical Representation

International Journal of Recent Technology and Engineering - 2 ◽

10.35940/ijrte.f9389.059120 ◽

2020 ◽

Vol 9 (1) ◽

pp. 43-51

Keyword(s):

Sequence Analysis ◽

Molecular Biology ◽

Dna Sequence ◽

Dna Sequences ◽

Graphical Representation ◽

Similarity Analysis ◽

Biological Sequence ◽

Field Of Study ◽

Biological Sequence Analysis ◽

Wide Range

Bioinformatics, which is now a well known field of study, originated in the context of biological sequence analysis. Recently graphical representation takes place for the research on DNA sequence. Research in biological sequence is mainly based on the function and its structure. Bioinformatics finds wide range of applications specifically in the domain of molecular biology which focuses on the analysis of molecules viz. DNA, RNA, Protein etc. In this review, we mainly deal with the similarity analysis between sequences and graphical representation of DNA sequence.

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Structural analyses of the two cysteine desulfurases from Aquifex aeolicus

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s205327331408351x ◽

2014 ◽

Vol 70 (a1) ◽

pp. C1648-C1648

Author(s):

Kei Hirabayashi ◽

Tomoko Iwanaga ◽

Makoto Yamakawa ◽

Naoyuki Tanaka ◽

Keiichi Fukuyama ◽

...

Keyword(s):

Schiff Base ◽

Electron Density ◽

Small Molecule ◽

Active Site ◽

Thermophilic Bacteria ◽

Binary Complex ◽

Dependent Manner ◽

Aquifex Aeolicus ◽

Cysteine Desulfurase ◽

Wide Range

The cysteine desulfurase IscS is a highly conserved master enzyme initiating sulfur transfer to a wide range of acceptor proteins. IscS degrades L-cysteine into L-alanine and a sulfur atom in a pyridoxal 5'-phosphate (PLP) dependent manner. In this reaction, it is essential for a conserved Lys residue of IscS to form Schiff base (the covalent bonding interaction) with PLP. Recent accumulations of genomic information have revealed that some IscS homologues in archaea and thermophilic bacteria lack this invariant Lys. Here we report the crystal structures of two paralogous cysteine desulfurases, the canonical Aa IscS1 and the invariant Lys lacking Aa IscS2, from Aquifex aeolicus. Aa IscS1/Aa IscS2 were overproduced in E. coli, and purified by heat-treatment and several column chromatography, and crystallized. The structure of Aa IscS1 was determined at 2.00 Å (Rcryst= 19.4% and Rfree = 22.0%), and Aa IscS2 at 2.55 Å (Rcryst= 21.8% and Rfree = 27.0%). Overall structures as well as orientations of the residues in the active site were quite similar to each other. In Aa IscS1 the PLP adduct was anchored in the catalytic pocket of Aa IscS1 by the formation of the aldimine Schiff base with the invariant Lys. Whereas in Aa IscS2 the PLP was not seen in the active pocket, since the catalytic Lys was substituted by Leu. Alternatively, an electron density derived from unknown-small molecule was located in the catalytic site of Aa IscS2. The shape of this electron density was completely different from that of PLP. The Bijvoet difference map calculated from data collected at λ=1.7 Å overlapped with the electron density observed in the active site; the unknown-small molecule probably contains such metals as iron atoms. Furthermore, the ICP-MS analysis demonstrated that as-isolated Aa IscS2 harbored the iron atom in the solution state. More recently we obtained the experimental evidences that non-canonical Aa IscS2 was able to form the binary complex with Aa IscU, which is responsible for a scaffold for the assembly of a nascent Fe-S cluster. Base on the structural/biochemcal results, possible physiological functions of two cysteine desulfrurases will be discussed.

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Amplification and Direct Sequence Analysis of the 23S rRNA Gene from Thermophilic Bacteria

BioTechniques ◽

10.2144/01302rr05 ◽

2001 ◽

Vol 30 (2) ◽

pp. 414-420 ◽

Cited By ~ 11

Author(s):

Ashraf Ibrahim ◽

Jacob Hofman-Bang ◽

Birgitte K. Ahring

Keyword(s):

Sequence Analysis ◽

Thermophilic Bacteria ◽

23S Rrna ◽

Rrna Gene ◽

Direct Sequence ◽

23S Rrna Gene ◽

Direct Sequence Analysis

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Structure of plantaricin locus of Lactobacillus plantarum 8P-A3

Beneficial Microbes ◽

10.3920/bm2011.0030 ◽

2011 ◽

Vol 2 (4) ◽

pp. 255-261 ◽

Cited By ~ 13

Author(s):

A. Tsapieva ◽

N. Duplik ◽

A. Suvorov

Keyword(s):

Escherichia Coli ◽

Staphylococcus Aureus ◽

Pseudomonas Aeruginosa ◽

Antibacterial Activity ◽

Sequence Analysis ◽

Lactobacillus Plantarum ◽

Streptococcus Pyogenes ◽

Antagonistic Activity ◽

Wide Range ◽

Encoding Genes

Lactobacillus plantarum 8P-A3 is a strain which is well known on the Russian pharmaceutical market and it is included in several probiotic products. The strain has been widely used since 1973 but the mechanisms of its antibacterial activity were unknown. L. plantarum 8P-A3 expressed high antagonistic activity against the wide range of bacterial pathogens including Streptococcus agalactiae, Streptococcus pyogenes, Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa and Klebsiella pneumoniae strains. DNA sequence analysis of L. plantarum 8P-A3 genome revealed the presence of a complete plantaricin locus of about 20,000 bp encoding genes of at least two bacteriocins – plantaricins EF and NC8. The plantaricin locus found in L. plantarum 8P-A3 is homologous to the plantaricin cluster in L. plantarum J51.

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