Molecular Identification Using ITS Sequences and Genome Shuffling to Improve 2-Deoxyglucose Tolerance and Xylanase Activity of Marine-Derived Fungus, Aspergillus Sp. NRCF5

2012 ◽  
Vol 167 (8) ◽  
pp. 2160-2173 ◽  
Author(s):  
Ahmed M. A. El-Bondkly
Keyword(s):  
Molecular Identification ◽  
Xylanase Activity ◽  
Genome Shuffling ◽  
Its Sequences ◽  
Aspergillus Sp

scholarly journals Confirmation of Tuntun Angin (Elaeocarpus floribundus) Taxonomic Status Using matK and ITS Sequences

2016 ◽  
Vol 8 (3) ◽  
pp. 393
Author(s):  
Dewi Indriyani Roslim ◽  
Siti Khumairoh ◽  
Herman Herman
Keyword(s):  
Molecular Identification ◽  
Intergenic Spacer ◽  
Biology Education ◽  
Taxonomic Status ◽  
Its Sequences ◽  
Morphological Identification ◽  
Its Sequence ◽  
Query Cover ◽  
Identification Techniques ◽  
Scientific Name

<p>Tuntun angin is one of important floodplain plants in and around Kajuik Lake located in Riau Province, Indonesia. Morphological identification shows that the scientific name of this plant is <em>Elaeocarpus floribundus. </em>The study aimed to confirm the taxonomic status of tuntun angin using <em>matK</em> and nuclear intergenic spacer (ITS) sequences. The methods included fresh leaf DNA isolation, polymerase chain reaction, electrophoresis, sequencing, and data analysis using BLASTn program and MEGA software version 6.06 programs. The results showed that the <em>matK</em> sequence (519 bp) of tuntun angin had highest similarity to <em>E. floribundus</em> <em>matK</em> sequence that was available in GenBank. It was supported by the high max score (937), low E-value (0.0), high identity value (100%), and high query cover (100%). However, the ITS sequence of tuntun angin did not show similarity to <em>E. floribundus </em>ITS sequence because there was no database of the sequence in GenBank. This study was able to confirm the taxonomic status of tuntun angin as <em>E. floribundus</em> using <em>matK</em> sequence and also showed that morphological and molecular identification techniques were complementary to each other. Moreover, this study enriched the DNA sequence database of <em>E. floribundus </em>in GenBank which will be useful for this species’ molecular identification.</p><p><strong>How to Cite</strong></p><p>Roslim, D. I., Khumairoh, S. &amp; Herman, H. (2016). Confirmation of Tuntun Angin (<em>Elaeocarpus floribundus</em>) Taxonomic Status Using <em>matK</em> and ITS Sequences. <em>Biosaintifika: Journal of Biology &amp; Biology Education</em>, 8(3), 393-400. </p>

scholarly journals The UNITE Database for Molecular Identification and for Communicating Fungal Species

2019 ◽  
Vol 3 ◽  
Author(s):  
Urmas Kõljalg ◽  
Kessy Abarenkov ◽  
R. Henrik Nilsson ◽  
Karl-Henrik Larsson ◽  
Andy F.S. Taylor
Keyword(s):  
Molecular Identification ◽  
High Throughput Sequencing ◽  
Its Region ◽  
Fungal Species ◽  
Its Sequences ◽  
Current Version ◽  
Community Members ◽  
Global Biodiversity Information Facility ◽  
Unique System ◽  
Fungal Sequence

UNITE (https://unite.ut.ee; Nilsson et al. 2018) is an international community of scientists and citizen scientists established in 2001. The ambition of UNITE is to develop: 1) datasets and tools for robust and reproducible molecular identification; 2) Persistent Identifiers based system for the communicating fungal species. Datasets of the nuclear ribosomal internal transcribed spacer (ITS) region, form the basis for UNITE. The current version includes nearly 1 million public fungal ITS sequences. Datasets are curated and annotated by community members. During the past 15 years, they made more than 275 000 improvements. In the complete absence of Latin names for species, UNITE offers a unique system where species hypotheses (SH) are provided with Digital Object Identifiers (DOIs). The current version 8 of UNITE offers more than 800 000 DOI-based SHs. One such SH DOI page is shown in Fig. 1. These DOI identifiers are also incorporated into the taxonomic backbone, making communication of taxa seamless in both directions. DOI identifiers of species hypotheses are also used by GBIF (Global Biodiversity Information Facility) in order to publish high-throughput sequencing taxon occurrence data in their data portal. UNITE serves as a data provider for a range of metabarcoding software pipelines and regularly exchanges data with all major fungal sequence databases and other community resources. Recent improvements include ITS-based species hypotheses for all eukaryotes and aggregation of full-length, high-quality ITS sequences generated by the PacBio Sequel system (https://www.pacb.com/products-and-services/sequel-system) from diverse material samples.

scholarly journals Morphological and molecular identification of cellulolytic fungi associated with local raru species

2019 ◽  
Vol 20 (8) ◽  
Author(s):  
Deni Elfiati ◽  
ARIDA SUSILOWATI ◽  
CELVIA MODES ◽  
HENTI HENDALASTUTI RACHMAT
Keyword(s):  
Molecular Identification ◽  
Aspergillus Terreus ◽  
Methyl Cellulose ◽  
Fungal Species ◽  
Polymer Materials ◽  
Cellulolytic Activity ◽  
Cellulolytic Fungi ◽  
Identification Of Fungi ◽  
Pure Cultures ◽  
Aspergillus Sp

Abstract. Elfiati D, Susilowati A, Modes C, Rachmat HH. 2019. Morphological and molecular identification of cellulolytic fungi associated with local raru species. Biodiversitas 20: 2348-2354. This study is aimed to isolate and identify cellulolytic fungi from different local Raru species in Central Tapanuli, North Sumatra, Indonesia. Cellulolytic fungi are fungi that can degrade natural polymer materials such as cellulose. The fungal species were isolated from soil under three local raru species. The samples inoculating (1 mL) from serial dilutions (10-2 to 10-5) on Carboxy Methyl Cellulose (CMC) plates. The plates were incubated at 28 ̊C for one week, then the fungal colonies were observed and pure cultures were maintained. Fungi with cellulolytic activity were characterized by the formation of clear zones around the colonies on CMC media plus congo red (0.1%). The identification of fungi was carried out by molecular identification of the isolated fungi at the species level. The extracted fungal DNA was amplified by PCR using specific internal transcribed spacer primer (ITS1/ITS4). The PCR products were sequenced and compared with the other related sequences in Gen Bank (NCBI). 20 isolates were successfully isolated and nine isolates had cellulolytic activity. Six fungal species from 20 isolates were identified as: Aspergillus sp., Penicillium sp., Aspergillus terreus, Penicillium mariae-crucis, Aspergillus tanneri and Penicillium citrinum. The results showed that Aspergillus terreus was the most abundant fungus obtained from all the raru stand.

scholarly journals Molecular identification of coprophilous microfungi from Banyumas District, Central Java, Indonesia

2021 ◽  
Vol 22 (3) ◽  
Author(s):  
Aris Mumpuni ◽  
Adi Amurwanto ◽  
Daniel Joko Wahyono
Keyword(s):  
Organic Matter ◽  
Molecular Identification ◽  
Animal Waste ◽  
Mechanical Degradation ◽  
Lignocellulosic Material ◽  
Coprophilous Fungi ◽  
Central Java ◽  
Comprehensive Picture ◽  
Herbivorous Animal ◽  
Aspergillus Sp

Abstract. Mumpuni A, Amurwanto A, Wahyono DJ. 2021. Molecular identification of coprophilous microfungi from Banyumas District, Central Java, Indonesia. Biodiversitas 22: 1550-1557. Coprophilous microfungi are a group of fungi that are ecologically interesting in relation to herbivores. These fungi play a predominant role in the decomposition of organic matter, in which the organic matter passes through a series of events involving mechanical degradation, as well as physical and biological processes. The role of coprophilous fungi as the main decomposers of the lignocellulosic material of herbivorous animal waste, which is widespread in nature, is very important. Previous research on the inventory and identification of coprophilous fungi in the Banyumas district has been limited to macroscopic genera, so the results have not been able to provide a comprehensive picture of the presence of coprophilous fungi in the region. Identification of the types of microscopic coprophilous fungi that live in herbivorous animal waste, such as lignocellulosic material, is necessary to understand the taxonomy of these fungi. This study aimed to investigate and identify microscopic coprophilous fungi obtained in the Banyumas district of Central Java, Indonesia. Based on the purposive random sampling method, the obtained fungi were analyzed using the molecular methods of DNA isolation, gene amplification, DNA sequencing and phylogenetic analysis of fungal cultures. The following species and genera were identified: Ceriporia lacerata, Trichosporon insectorum, Lentinus squarrosulus, Fusarium sp., Aspergillus sp., and Trichosporon sp.

scholarly journals Morphological and Molecular Identification of Mycobiota Associated with Juniperus monosperma (Engelm.) Sarg. Blight in Mexico

2020 ◽  
pp. 1-7
Author(s):  
Ma. E. Galindo-Cepeda ◽  
A. Sánchez-Arizpe ◽  
E. Castro-del Ángel ◽  
S. F. Velázquez-Morales ◽  
J. L. Arispe-Vázquez
Keyword(s):  
Dna Extraction ◽  
Molecular Identification ◽  
Culture Medium ◽  
Dna Amplification ◽  
Agarose Gel ◽  
Juniperus Monosperma ◽  
Morphological Criteria ◽  
Search Tool ◽  
Alternaria Sp ◽  
Aspergillus Sp

The aim of the investigation was to identify the agents associated with blight in Juniperus monosperma at Lirios region, Arteaga, Coahuila. Botanical material was collected at Lirios, Arteaga, and taken to the laboratory. Pathogens were isolated in ADP culture medium and identifying by morphological criteria and molecular using primers ITS1 and ITS4. DNA extraction by the Dellaporta method, the visualization of obtained DNA was performed by electrophoresis on a 2% (p/v) agarose gel. DNA quantification was performed on a NanoDrop 1000 spectrophotometer, and DNA amplification was carried out in the Veriti thermocycler. Obtained sequences were aligned and compared with those available in the GenBank database of the National Center for Biotechnology Information (NCBI), using the BLAST algorithm (Basic Local Aligment Search Tool) to find conserved sequences. Pathogens were inoculated in stems of J. monosperma. The agents associated with blight were Alternaria sp., Aspergillus sp. and Rosellinia sp. and the sequence obtained compared with BLAST coincided only with Alternaria sp. and Aspergillus sp. with the access codes KP027305.1 and MG551283.1, respectively. According to data taken in field, Alternaria sp. behaved as the highest prevalence species and severity associated with blight in J. monosperma, and Rosellinia sp. in laboratory conditions.

scholarly journals Molecular identification of Fusarium spp. isolated from tomato plant in Iraq and China

2017 ◽  
Vol 30 (1) ◽  
pp. 65-72
Author(s):  
Mohammed A. Fayyadh ◽  
Adnan I. Al-Badran ◽  
Iman S. Al-Jaafari
Keyword(s):  
Fusarium Oxysporum ◽  
Molecular Identification ◽  
Growth Pattern ◽  
Tomato Plant ◽  
Morphological Characteristics ◽  
Sensitivity Test ◽  
Its Sequences ◽  
Fusarium Spp

This study was conducted to identify Fusarium spp. isolated from tomato plant in Iraq and China. A total of 12 isolates from Iraq (1-12) and four isolates from China (M1-M4) were used in this study. Based on Morphological characteristics (color, growth pattern, Macro and Micro-conidia shape) high differences between Fusarium isolates were found. Sensitivity test to the fungicide carbendazim revealed that one third of isolates(4/12) from Iraq had EC50 values over than 1000?g/ml indicated that many Iraqi isolates have developed resistance to carbendazim. Based on ITS sequences, Fusarium isolates were identified as follow, isolates 1, 3, 5, 6, 7, 10 were identified as Fusarium oxysporum, isolates 8, 11 as F. solani, isolates 12, M1 and M3 as F. moniliforme, isolates 2, M2 and M4 as F. proliferatum, F. chlamydosporum and F. kyushuense , respectively.

Electron microscopy in diagnostic virology

1984 ◽  
Vol 42 ◽  
pp. 70-73
Author(s):  
S. E. Miller
Keyword(s):  
Electron Microscopy ◽  
Tissue Culture ◽  
Molecular Identification ◽  
Point Of View ◽  
Negative Stain ◽  
Viral Diagnosis ◽  
Electron Microscopist ◽  
Diagnostic Virology

The techniques for detecting viruses are many and varied including FAT, ELISA, SPIRA, RPHA, SRH, TIA, ID, IEOP, GC (1); CF, CIE (2); Tzanck (3); EM, IEM (4); and molecular identification (5). This paper will deal with viral diagnosis by electron microscopy and will be organized from the point of view of the electron microscopist who is asked to look for an unknown agent--a consideration of the specimen and possible agents rather than from a virologist's view of comparing all the different viruses. The first step is to ascertain the specimen source and select the method of preparation, e. g. negative stain or embedment, and whether the sample should be precleared by centrifugation, concentrated, or inoculated into tissue culture. Also, knowing the type of specimen and patient symptoms will lend suggestions of possible agents and eliminate some viruses, e. g. Rotavirus will not be seen in brain, nor Rabies in stool, but preconceived notions should not prejudice the observer into missing an unlikely pathogen.

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