Characterization of a novel high-pH-tolerant laccase-like multicopper oxidase and its sequence diversity in Thioalkalivibrio sp

2015 ◽  
Vol 99 (23) ◽  
pp. 9987-9999 ◽  
Author(s):  
Luka Ausec ◽  
Miha Črnigoj ◽  
Marko Šnajder ◽  
Nataša Poklar Ulrih ◽  
Ines Mandic-Mulec
Keyword(s):  
Multicopper Oxidase ◽  
Sequence Diversity ◽  
Its Sequence ◽  
High Ph

scholarly journals Molecular Characterization of Ciliate Diversity in Stream Biofilms

2008 ◽  
Vol 74 (6) ◽  
pp. 1740-1747 ◽  
Author(s):  
Andrew Dopheide ◽  
Gavin Lear ◽  
Rebecca Stott ◽  
Gillian Lewis
Keyword(s):  
18S Rrna ◽  
Pcr Primers ◽  
18S Rrna Gene ◽  
Sequence Diversity ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Specific Pcr ◽  
Stream Biofilms

ABSTRACT Free-living protozoa are thought to be of fundamental importance in aquatic ecosystems, but there is limited understanding of their diversity and ecological role, particularly in surface-associated communities such as biofilms. Existing eukaryote-specific PCR primers were used to survey 18S rRNA gene sequence diversity in stream biofilms but poorly revealed protozoan diversity, demonstrating a need for protozoan-targeted primers. Group-specific PCR primers targeting 18S rRNA genes of the protozoan phylum Ciliophora were therefore designed and tested using DNA extracted from cultured protozoan isolates. The two most reliable primer combinations were applied to stream biofilm DNA, followed by cloning and sequencing analysis. Of 44 clones derived from primer set 384F/1147R, 86% were of probable ciliate origin, as were 25% of 44 clones detected by primer set 121F/1147R. A further 29% of 121F/1147R-detected clones matched sequences from the closely related phylum Apicomplexa. The highly ciliate-specific primer set 384F/1147R was subsequently used in PCRs on biofilm DNA from four streams exhibiting different levels of human impact, revealing differences in ciliate sequence diversity in samples from each site. Of a total of 240 clones, 73% were of probable ciliate origin; 54 different putative ciliate sequences were detected from throughout seven taxonomic ciliate classes. Sequences from Oligohymenophorea were most commonly detected in all samples, followed by either Spirotrichea or Phyllopharyngea. Restriction fragment length polymorphism profile-based analysis of clones suggested a potentially higher level of diversity than did sequencing. Nevertheless, newly designed PCR primers 384F/1147R were considered to provide an effective molecular basis for characterization of ciliate diversity in stream biofilms.

scholarly journals Crystallization and preliminary X-ray characterization of the 2,4′-dihydroxyacetophenone dioxygenase fromAlcaligenessp. 4HAP

2014 ◽  
Vol 70 (6) ◽  
pp. 823-826 ◽  
Author(s):  
G. Beaven ◽  
A. Bowyer ◽  
P. Erskine ◽  
S. P. Wood ◽  
A. McCoy ◽  
...  
Keyword(s):  
Synchrotron Radiation ◽  
Formic Acid ◽  
Molecular Oxygen ◽  
Aromatic Ring ◽  
Bond Cleavage ◽  
Its Sequence ◽  
Hydroxybenzoic Acid ◽  
X Ray

The enzyme 2,4′-dihydroxyacetophenone dioxygenase (or DAD) catalyses the conversion of 2,4′-dihydroxyacetophenone to 4-hydroxybenzoic acid and formic acid with the incorporation of molecular oxygen. Whilst the vast majority of dioxygenases cleave within the aromatic ring of the substrate, DAD is very unusual in that it is involved in C—C bond cleavage in a substituent of the aromatic ring. There is evidence that the enzyme is a homotetramer of 20.3 kDa subunits each containing nonhaem iron and its sequence suggests that it belongs to the cupin family of dioxygenases. By the use of limited chymotrypsinolysis, the DAD enzyme fromAlcaligenessp. 4HAP has been crystallized in a form that diffracts synchrotron radiation to a resolution of 2.2 Å.

Molecular Identification and Morphological Characterization of Ficus sp. (Moraceae) in Bogor Botanic Gardens

2021 ◽  
Vol 6 (1) ◽  
pp. 36-44
Author(s):  
Muhammad Rifqi Hariri ◽  
Peniwidiyanti Peniwidiyanti ◽  
Arifin Surya Dwipa Irsyam ◽  
Rina Ratnasih Irwanto ◽  
Irfan Martiansyah ◽  
...  
Keyword(s):  
Molecular Identification ◽  
Morphological Characterization ◽  
Species Level ◽  
Herbarium Specimen ◽  
Morphological Observation ◽  
Its Sequence ◽  
Botanic Gardens ◽  
Molecular Approaches ◽  
Vegetative Characters

Ficus spp. belongs to the tribe Ficeae in the Moraceae family. Many members of this genus have been collected and grown in Bogor Botanic Gardens. There are 519 living collections of Ficus conserved since 1817, and 13 of them have not been identified until the species level. This research aimed to identify the Ficus sp. originated from Kaur Selatan (Bengkulu) using morphological and molecular approaches. Morphological characterization and herbarium specimen observation have been carried out to identify the Ficus sp. The molecular approach was conducted through DNA barcoding using ITS primer. The molecular identification using ITS sequence showed that Ficus sp. is Ficus crassiramea with 99.87% similarity to the sequence in NCBI. Morphological observation through herbarium specimen showed that there are 9 vegetative characters specific to Ficus crassiramea.

scholarly journals Isolation and Characterization of 2,3-Dichloro-1-Propanol-Degrading Rhizobia

2000 ◽  
Vol 66 (7) ◽  
pp. 2882-2887 ◽  
Author(s):  
Agus J. Effendi ◽  
Steven D. Greenaway ◽  
Brian N. Dancer
Keyword(s):  
Molecular Weight ◽  
High Ph ◽  
Molecular Weights ◽  
Isolation And Characterization ◽  
Complete Mineralization ◽  
Native Molecular Weight

ABSTRACT 2,3-Dichloro-1-propanol is more chemically stable than its isomer, 1,3-dichloro-2-propanol, and is therefore more difficult to degrade. The isolation of bacteria capable of complete mineralization of 2,3-dichloro-1-propanol was successful only from enrichments at high pH. The bacteria thus isolated were found to be members of the α division of the Proteobacteria in the Rhizobiumsubdivision, most likely Agrobacterium sp. They could utilize both dihaloalcohol substrates and 2-chloropropionic acid. The growth of these strains in the presence of 2,3-dichloro-1-propanol was strongly affected by the pH and buffer strength of the medium. Under certain conditions, a ladder of four active dehalogenase bands could be visualized from this strain in activity gels. The enzyme involved in the complete mineralization of 2,3-dichloro-1-propanol was shown to have a native molecular weight of 114,000 and consisted of four subunits of similar molecular weights.

Genotypic Characterization of Rhizopus Spp. Tempeh and Usar: Traditional Inoculum of Tempeh in Indonesia

2020 ◽  
Vol 14 (3) ◽  
pp. 3
Author(s):  
Tati Barus ◽  
Jason Wiranata Sanjaya ◽  
Anastasia Tatik Hartanti ◽  
Adi Yulandi ◽  
Vivitri Dewi Prasasty ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Internal Transcribed Spacer ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Its Sequence ◽  
Rhizopus Microsporus ◽  
Rhizopus Delemar

Abstract. Soybeans tempeh (tempeh) is processed by fermentation using Rhizopus spp. Tempeh is an important source of protein in Indonesia. The traditional inoculum in fermentation locally is known as Usar which is made from the leaves of Hibiscus tiliaceus. However, Rhizopus information from Usar is still limited. Therefore, this study aims to identify and investigate the genetic diversity of Rhizopus species from Usar and tempeh based on the Internal Transcribed Spacer (ITS) sequence and the Random Amplified Polymorphic DNA (RAPD) markers. Twenty-three Rhizopus strains were isolated from Usar and ten Rhizopus strains were isolated from tempeh. Based on ITS sequences, the isolates were similar to R Rhizopus microsporus (30 isolates) and Rhizopus delemar (3 isolates) with 98-99% similarity. The genetics of R. microsporus and R. delemar are varied and different from the genetics of R. microsporus from tempeh. The growth temperature of R. microsporus varies from 33 to 48°C and R. delemar can grow to a maximum at 33°C. The role of R. microsporus and R. delemar from Usar in determining the quality of tempeh is still limited. Therefore, it needs to be investigated further.

scholarly journals Characterization of Soymar1, a Mariner Element in Soybean

Genetics ◽  
1998 ◽  
Vol 149 (3) ◽  
pp. 1569-1574 ◽  
Author(s):  
Tyler Jarvik ◽  
Karl G Lark
Keyword(s):  
Glycine Max ◽  
Transposable Elements ◽  
Its Sequence ◽  
Transformation Vector ◽  
Starting Point ◽  
Glycine Max L ◽  
Inverted Terminal Repeats ◽  
Terminal Repeats

Abstract Mariner elements, a family of DNA-mediated transposable elements with short, inverted terminal repeats, have been reported in a wide variety of arthropods, as well as planarians, nematodes, and humans. No such element has been reported in a plant. Here we report a mariner element in the plant soybean (Glycine max (L.) Merr.). Although this sequence belongs to the mariner family, it is clearly distinct from previously reported mariner-like elements, as well as from the Tc1 transposon family. Novel aspects of its sequence could be useful as a starting point to identify mariner-like elements in new organisms, and it may prove useful in creating a transformation vector for plants.

scholarly journals BIOCHEMICAL CHARACTERIZATION OF RECOMBINANT PHYTASE ENZYME (phyK) FROM Klebsiella sp. ASR1 ENCAPSULATED WITH ALGINATE

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Muhammad Eka Hidayatullah ◽  
. Sajidan ◽  
Ari Susilowati ◽  
Baraka Stewart Mkumbe ◽  
Ralf Greiner
Keyword(s):  
Metal Ion ◽  
Biochemical Characterization ◽  
Extreme Conditions ◽  
Optimum Temperature ◽  
High Ph ◽  
Recombinant Phytase ◽  
Ion Effects ◽  
Metal Ion Effects

Karakterisasi Biokimia Enzim Fitase Rekombinan (phyK) dari Klebsiella sp. ASR1 Yang Dienkapsulasi Dengan AlginatEnzim fitase melepas molekul fosfor pada atom C dari benzena Inositol fitat. Tetapi fitase memiliki kelemahan tidak mampu bertahan terhadap kondisi ekstrim dalam lambung nonruminansia. Solusi dalam penelitian ini yaitu fitase dienkapsulasi menggunakan alginat. Penelitian ini bertujuan mengkarakterisasi fitase setelah dienkapsulasi menggunakan alginate. Hasil penelitian ini yaitu fitase yang dienkapsulasi memiliki aktivitas tertinggi pada pH 6,0, sedangkan fitase tanpa enkapsulasi pada pH 5,0. Suhu optimum untuk aktivitas tertinggi fitase yang dienkapsulasi yaitu 70ºC, sedangkan fitase tanpa enkapsulasi 37ºC. Untuk perlakuan penambahan ion logam, aktivitas tertinggi fitase yang dienkapsulasi terjadi dengan penambahan 0,1 mM Fe2+ dan 1,0 mM Ca2+, sedangkan fitase tanpa enkapsulasi dengan penambahan 0,1 mM Fe2+. Berdasarkan hasil penelitian ini, fitase yang dienkapsulasi memiliki keunggulan lebih banyak dibandingkan dengan fitase tanpa enkapsulasi, karena mampu bertahan pada pH dan suhu tinggi, dan beberapa efek ion logam.Kata Kunci: alginat, asam fitat, enkapsulasi, fitase, fitase rekombinanABSTRACTPhytase enzymes release phosphorus molecules on the C atom from benzene inositol phytate. But phytase has the disadvantage of being unable to withstand extreme conditions in the non-ruminant stomach. The solution in this research was phytase encapsulated using alginate. This study aims to characterize phytase after being encapsulated using alginate. The results of this study were the encapsulated phytase had the highest activity at pH 6.0, while the unencapsulated phytase at pH 5.0. The optimum temperature for the highest activity of the encapsulated phytase was 70ºC, while the unencapsulated phytase 37ºC. For treatment of metal ion addition, the highest activity of the encapsulated phytase occurred with the addition of 0.1 mM Fe2+ and 1.0 mM Ca2+, while the unencapsulated phytase with the addition of 0.1 mM Fe2+. Based on the results of this study, the encapsulated phytase had more advantages compared to the unencapsulated phytase, as the former withstand high pH and temperature, and some metal ion effects.

scholarly journals Molecular characterization and pathogenicity of isolates of Beauveria spp. to fall armyworm

2008 ◽  
Vol 43 (4) ◽  
pp. 513-520 ◽  
Author(s):  
Andréa Almeida Carneiro ◽  
Eliane Aparecida Gomes ◽  
Claudia Teixeira Guimarães ◽  
Fernando Tavares Fernandes ◽  
Newton Portilho Carneiro ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Spodoptera Frugiperda ◽  
Sequence Comparison ◽  
Rapd Markers ◽  
Fall Armyworm ◽  
Its Sequence ◽  
Its Sequencing ◽  
Host Insect ◽  
Rdna Its

The objective of this work was to evaluate the pathogenicity of 24 Beauveria isolates to Spodoptera frugiperda larvae, and characterize them molecularly through rDNA-ITS sequencing and RAPD markers. Sequencing of rDNA-ITS fragments of 570 bp allowed the identification of isolates as B. bassiana or B. brongniarti by sequence comparison to GenBank. Sixty seven polymorphic RAPD fragments were capable to differentiate 20 among 24 Beauveria isolates, grouping them according to the derived host insect and to pathogenicity against maize fall armyworm larvae. Three RAPD markers were highly associated to the pathogenicity against S. frugiperda, explaining up to 67% of the phenotypic variation. Besides identification and molecular characterization of Beauveria isolates, ITS sequence and RAPD markers proved to be very useful in selecting the isolates potentially effective against S. frugiperda larvae and in monitoring field release of these microorganisms in biocontrol programs.

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