scholarly journals Molecular Characterization of Fungi Associated with Cowdung-impacted Soil

2020 ◽  
pp. 3819-3827
Author(s):  
Iyanyi N. G. ◽  
Ataga A. E. ◽  
Akinido C. E. ◽  
Udobong E.
Keyword(s):  
Disease Transmission ◽  
Pcr Amplification ◽  
Geotrichum Candidum ◽  
Fungal Species ◽  
Cow Dung ◽  
Base Pairs ◽  
Universal Primer ◽  
Absidia Corymbifera ◽  
Fungal Organisms

Dung is the undigested remains of food taken in by herbivores. It is a combination of faeces and urine at a ratio of 3:1. It mostly consists of cellulose, hemicelluloses and lignin. Cow dung harbours several microorganisms, including various species of fungi. The aim of this study was to isolate and characterize the fungal organisms associated with cow dung-impacted soil using both traditional cultural techniques and molecular method. DNA extraction was carried out using Zymo Quick DNA Fungal/Bacterial Mini prep kit. The Polymerase Chain Reaction (PCR) amplification of the Internal Transcribed Spacer (ITS) genes, using the universal primer pair; ITS4 and ITS5, generated amplicon sizes of 372 and 834 base pairs. The amplicons were sequenced using Sanger sequencing and the isolates were identified as Lichtheimia ramosa and Galactomyces pseudocandidus. Phylogenetic analysis showed the relationship that exists between the fungal species and other closely-related species in GenBank such as: Aspergillus amstelodami, Absidia corymbifera, Mycocladus corymbiferus and Geotrichum candidum. This study has provided information on some of the fungal organisms harboured by cowdung-impacted soil which will help predict the possibility for disease transmission to plants or humans through cow dung.

scholarly journals Molecular identification of fungi associated with avocado (Persea americana Mill.) fruits

Agro-Science ◽  
2021 ◽  
Vol 20 (1) ◽  
pp. 80-86
Author(s):  
N.G. Iyanyi ◽  
A.E. Ataga ◽  
I.S. Rotimi ◽  
I. Blessing
Keyword(s):  
Pcr Amplification ◽  
Fungal Species ◽  
Persea Americana ◽  
Molecular Techniques ◽  
Control Measures ◽  
Universal Primer ◽  
Identification Of Fungi ◽  
Pcr Products ◽  
Fungal Organisms ◽  
Health Complications

Avocado (Persea americana Mill.) is grown for its nutritious fruit. However, the quantity and quality of these fruits are threatened by some fungal organisms which can cause health complications when it is consumed by man. DNA extraction provides a unique tool for identification of organisms. This study was conducted to isolate and identify fungal species associated with avocado fruit using both morphological and molecular techniques. Fungal species were isolated from Persea americana purchased from Choba market, Port Harcourt, Rivers State, Nigeria using Potato Dextrose Agar (PDA) as a growth medium. The morphology of isolated fungi on PDA were cotton-like blackish grey spots, white villous colonies, greyish powdery spores and black spores for isolates 1 to 4 respectively. Extraction of DNA from fungal isolates was carried out using Zymo Fungal/Bacteria DNA Miniprep Kit. PCR amplification of the ITS1-2 regions of isolates was carried out using fungal universal primer pair; ITS4 and ITS5.PCR amplification of the ITS1-2 gene sequences yielded amplicons between 537-580 base pairs. PCR products were sequenced and the sequencing result after BLAST search revealed the identity of the four fungal species as follows: Lasiodiplodia theobromae, Fusarium proliferatum, Penicillium sp. and Aspergillus niger. This study will promote the knowledge of specific fungal species associated with Persea americanna and help plant pathologists to proffer preventive and control measures to enhance fruit protection and yield quality.

scholarly journals Molecular characterisation of fungi associated with sewage-impacted soil

2021 ◽  
Vol 27 (2) ◽  
pp. 107-113
Author(s):  
N. G. Iyanyi ◽  
A. E. Ataga ◽  
E. A Obichi ◽  
S. C. Agbasoga
Keyword(s):  
Pcr Amplification ◽  
Its Region ◽  
Fungal Species ◽  
Molecular Techniques ◽  
Septic Tank ◽  
Nucleotide Sequence Analysis ◽  
Molecular Method ◽  
Base Pairs ◽  
Universal Primer ◽  
Fungal Isolates

The decay of faecal matter from a septic system causes the arousal of fungi in the surrounding soil. These fungi can cause diseases if there is sewage spillage containing untreated or improperly treated wastewaters. Molecular techniques of identification of fungi have shown to be more dependable than traditional methods of identifying fungal species. This study was carried out to identify the fungal species associated with soil obtained from sewage-impacted soil near a septic tank using both traditional cultural techniques and molecular method. Fungi associated with the soil samples were isolated using serial dilution and Potato Dextrose Agar (PDA) method. Deoxyribonucleic Acid (DNA) was extracted from the pure cultures of fungal isolates using Quick DNA Fungal/Bacterial Miniprep kit. Polymerase Chain Reaction (PCR) amplification of internal transcribed spacer (ITS) region of the fungal isolates was carried out using universal primer pair; ITS4 and ITS5. The PCR products were sequenced and the sequences were blasted against National Centre for Biotechnology Information database. The result of the nucleotide sequence analysis revealed the identity of the isolates as Trichoderma harzanium with 580 base pairs and Aspergillus welwitschiae with 560 base pairs. Sequences of the isolates were aligned and compared with sequences on GenBank and a phylogenetic tree was constructed. The cultural method only aided in suggesting the suspected genera of the isolates while the molecular method was able to identify the isolates to the species level. This study will promote the knowledge of the fungal species associated with sewage-impacted soil and also aid researchers in proffering ways to enhance the prevention/control of diseases associated with sewage spill. Keyword: Septic tank, fungi, soil, phylogeny, sequencing

scholarly journals Molecular Characterization of 12 Mango Germplasm Using RAPD markers

2010 ◽  
Vol 20 (1) ◽  
pp. 91-99
Author(s):  
R. C. Jena ◽  
K. C. Samal ◽  
P. K. Chand ◽  
B. K. Das
Keyword(s):  
Molecular Characterization ◽  
Rapd Markers ◽  
Mangifera Indica ◽  
Pcr Amplification ◽  
Similarity Coefficient ◽  
Group Method ◽  
Base Pairs ◽  
Relationship Analysis ◽  
Pair Group

Randomly amplified polymorphic DNA (RAPD) markers were used for the genetic variation and relationship analysis among 12 Mango (Mangifera indica L.) germplasm. Five oligonucleotide primers were employed to amplify DNA from 12 cultivars. PCR amplification with five primers generated 45 reproducible, clear and distinct bands, out of which 41 bands are considered polymorphic and the remaining four fragments (8.88%)  monomorphic. The size of amplified product ranged from 200 (RPI-5) to 3000 base pairs (RPI-1) with an average of nine bands per primer. The average polymorphism in all the 12 cultivars using the five primers was found to be 91.91%. Among all the primers RPI-2 and RPI-4 have shown 100% polymorphism while RPI-5 was found to be least polymorphism (81.81%). One specific band, namely was found with RPI-5, in a particular variety, Chiratpuri. The UPGMA (Unweighted Pair Group Method of Arithmetic Mean) dendrogram based on Jaccard’s similarity coefficient segregated the 12 mango germplasm into two clusters. Langra, Chiratpuri, Pravasankar, Alphanso, Sindhu and Kesar formed one cluster and rest six mango germplasm grouped together into another cluster. Sindhu and Alphanso cultivar pair was very close to each other with highest similarity coefficient (0.78), which was comparatively higher than all other cultivar pairs. On the other hand, Pravasankar and Neelam cultivar pair was more distinct to each other with the lowest intervarietal similarity coefficient 0.38. This study showed clearly that cultivars from Orissa unveiled maximum diversity and indicated the potential of RAPD markers for the identification of management of mango germplasm for breeding purposes.  Key words: Molecular characterization, Mango germplasm, Dversity  D.O.I. 10.3329/ptcb.v20i1.5972 Plant Tissue Cult. & Biotech. 20(1): 91-99, 2010 (June)

Characterization of a cDNA for Rhesus Monkey Protein C Inhibitor – Evidence for N-Terminal Involvement in Heparin Stimulation

1995 ◽  
Vol 74 (04) ◽  
pp. 1079-1087 ◽  
Author(s):  
Klaus-P Radtke ◽  
José A Fernández ◽  
Bruno O Villoutreix ◽  
Judith S Greengard ◽  
John H Griffin
Keyword(s):  
Rhesus Monkey ◽  
Protein C ◽  
Activated Protein C ◽  
Pcr Amplification ◽  
Amino Acid Sequences ◽  
Heparin Binding ◽  
Reactive Center ◽  
Protein C Inhibitor ◽  
Polymerase Chain

SummarycDNAs for protein C inhibitor (PCI) were cloned from human and rhesus monkey 1 liver RNAs by reverse transcription and polymerase chain reaction (PCR) amplification. Sequencing showed that rhesus monkey and human PCI cDNAs were 93% identical. Predicted amino acid sequences differed at 26 of 387 residues. Pour of these differences (T352M, N359S, R362K, L3631) were in the reactive center loop that is important for inhibitory specificity, and two were in the N-terminal helix (M8T, E13K) that is implicated in glycosaminoglycan binding. PCI in human or rhesus monkey plasma showed comparable inhibitory activity towards human activated protein C in the presence of 10 U/ml heparin. However, maximal acceleration of the inhibition of activated protein C required 5-fold lower heparin concentration for rhesus monkey than for human plasma, consistent with the interpretation that the additional positive charge (E13K) in a putative-heparin binding region increased the affinity for heparin.

Incidence and molecular characterization of fungi and yeast isolated from cultured catfish and Nile tilapia

2020 ◽  
Vol 21 (3) ◽  
pp. 61-66
Author(s):  
Ola Hashem ◽  
Viola Zaki ◽  
Rawia Adawy
Keyword(s):  
Molecular Characterization ◽  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
Clarias Gariepinus ◽  
Fungal Species ◽  
High Rate ◽  
Fish Farms ◽  
Isolation And Identification ◽  
Penicillium Spp

Objective: To study the incidence and seasonal dynamics of different fungi affected freshwater fishes in Lake Manzala with molecular identification of the isolated fungi. Animals: 300 Nile tilapia (Oreochromis niloticus) and 300 catfish (Clarias gariepinus). Design: Descriptive study. Procedures: Random samples of Oreochromis niloticus (O. niloticus) and Clarias gariepinus (C. gariepinus) were collected from Manzala fish farms. Clinical and postmortem examination of fish was applied. Isolation and identification of different fungi were performed by conventional methods. Furthermore, the molecular characterization of isolated fungi was carried out. Results: C. gariepinus had a higher rate of infection with different fungal species than O. niloticus. Aspergillus spp. (Aspergillus niger and Aspergillus flavus) were the most fungal isolated from the examined fishes, followed by Penicillium spp. and Candida albicans. Aspergillus spp were detected in all seasons with a higher rate in summer and spring. A. flavus, A. niger, Penicillium spp. and C.albicans isolates were amplified from both C. gariepinus and O. niloticus at the specified molecular weight using PCR. Conclusion and clinical relevance: Fungal infection affected the fish showing different external and internal lesions, all species of Aspergillus were found in all seasons with a high rate in, hot seasons, summer and spring. The Prevalence of Penicillium and C. albicans were also reported. All fungal isolates were identified on the phenotypic and molecular bases.

scholarly journals Morpho-molecular identification and first report of Fusarium equiseti in causing chilli wilt from Kashmir (Northern Himalayas)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ammarah Hami ◽  
Rovidha S. Rasool ◽  
Nisar A. Khan ◽  
Sheikh Mansoor ◽  
Mudasir A. Mir ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Pcr Amplification ◽  
Its Region ◽  
Fungal Species ◽  
Pathogenicity Test ◽  
Kashmir Valley ◽  
Fusarium Equiseti ◽  
Infected Root ◽  
Fusarium Sp ◽  
High Degree

AbstractChilli (Capsicum annuum L.) is one of the most significant vegetable and spice crop. Wilt caused by Fusarium Sp. has emerged as a serious problem in chilli production. Internal transcribed spacer (ITS) region is widely used as a DNA barcoding marker to characterize the diversity and composition of Fusarium communities. ITS regions are heavily used in both molecular methods and ecological studies of fungi, because of its high degree of interspecific variability, conserved primer sites and multiple copy nature in the genome. In the present study we focused on morphological and molecular characterization of pathogen causing chilli wilt. Chilli plants were collected from four districts of Kashmir valley of Himalayan region. Pathogens were isolated from infected root and stem of the plants. Isolated pathogens were subjected to DNA extraction and PCR amplification. The amplified product was sequenced and three different wilt causing fungal isolates were obtained which are reported in the current investigation. In addition to Fusarium oxysporum and Fusarium solani, a new fungal species was found in association with the chilli wilt in Kashmir valley viz., Fusarium equiseti that has never been reported before from this region. The studies were confirmed by pathogenicity test and re-confirmation by DNA barcoding.

scholarly journals Quantitative Characterization of Geotrichum candidum Growth in Milk

2021 ◽  
Vol 11 (10) ◽  
pp. 4619
Author(s):  
Petra Šipošová ◽  
Martina Koňuchová ◽  
Ľubomír Valík ◽  
Monika Trebichavská ◽  
Alžbeta Medveďová
Keyword(s):  
Growth Parameters ◽  
Mechanistic Model ◽  
Geotrichum Candidum ◽  
Activity Level ◽  
Effect Of Temperature ◽  
Operational Parameters ◽  
Quantitative Characterization ◽  
Essential Knowledge ◽  
Cardinal Temperatures

The study of microbial growth in relation to food environments provides essential knowledge for food quality control. With respect to its significance in the dairy industry, the growth of Geotrichum candidum isolate J in milk without and with 1% NaCl was investigated under isothermal conditions ranging from 6 to 37 °C. The mechanistic model by Baranyi and Roberts was used to fit the fungal counts over time and to estimate the growth parameters of the isolate. The effect of temperature on the growth of G. candidum in milk was modelled with the cardinal models, and the cardinal temperatures were calculated as Tmin = −3.8–0.0 °C, Topt = 28.0–34.6 °C, and Tmax = 35.2–37.2 °C. The growth of G. candidum J was slightly faster in milk with 1% NaCl and in temperature regions under 21 °C. However, in a temperature range that was close to the optimum, its growth was slightly inhibited by the lowered water activity level. The present study provides useful cultivation data for understanding the behaviour of G. candidum in milk and can serve as an effective tool for assessing the risk of fungal spoilage, predicting the shelf life of dairy products, or assessing the optimal conditions for its growth in relation to the operational parameters in dairy practices.

scholarly journals Isolation and characterization of two virulent Aeromonads associated with haemorrhagic septicaemia and tail-rot disease in farmed climbing perch Anabas testudineus

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Abhishek Mazumder ◽  
Hrishikesh Choudhury ◽  
Abhinit Dey ◽  
Dandadhar Sarma
Keyword(s):  
Natural Infection ◽  
Winter Season ◽  
Pcr Amplification ◽  
Body Parts ◽  
Anabas Testudineus ◽  
Climbing Perch ◽  
Isolation And Characterization ◽  
Biochemical Characterisation ◽  
Rot Disease

AbstractDiseased Anabas testudineus exhibiting signs of tail-rot and ulcerations on body were collected from a fish farm in Assam, India during the winter season (November 2018 to January 2019). Swabs from the infected body parts were streaked on sterilized nutrient agar. Two dominant bacterial colonies were obtained, which were then isolated and labelled as AM-31 and AM-05. Standard biochemical characterisation and 16S rRNA and rpoB gene sequencing identified AM-31 isolate as Aeromonas hydrophila and AM-05 as Aeromonas jandaei. Symptoms similar to that of natural infection were observed on re-infecting both bacteria to disease-free A. testudineus, which confirmed their virulence. LC50 was determined at 1.3 × 104 (A. hydrophila) and 2.5 × 104 (A. jandaei) CFU per fish in intraperitoneal injection. Further, PCR amplification of specific genes responsible for virulence (aerolysin and enterotoxin) confirmed pathogenicity of both bacteria. Histopathology of kidney and liver in the experimentally-infected fishes revealed haemorrhage, tubular degeneration and vacuolation. Antibiotic profiles were also assessed for both bacteria. To the best of our knowledge, the present work is a first report on the mortality of farmed climbing perch naturally-infected by A. hydrophila as well as A. jandaei, with no records of pathogenicity of the latter in this fish.

scholarly journals Characterization of a Novel Thermobifida fusca Bacteriophage P318

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1042
Author(s):  
Cheepudom ◽  
Lin ◽  
Lee ◽  
Meng
Keyword(s):  
Plant Cell Wall ◽  
Hydrolytic Enzymes ◽  
Thermobifida Fusca ◽  
Genome Replication ◽  
Putative Orfs ◽  
Base Pairs ◽  
Double Stranded Dna ◽  
Virion Morphogenesis ◽  
Genome Information

Thermobifida fusca is of biotechnological interest due to its ability to produce an array of plant cell wall hydrolytic enzymes. Nonetheless, only one T. fusca bacteriophage with genome information has been reported to date. This study was aimed at discovering more relevant bacteriophages to expand the existing knowledge of phage diversity for this host species. With this end in view, a thermostable T. fusca bacteriophage P318, which belongs to the Siphoviridae family, was isolated and characterized. P318 has a double-stranded DNA genome of 48,045 base pairs with 3′-extended COS ends, on which 52 putative ORFs are organized into clusters responsible for the order of genome replication, virion morphogenesis, and the regulation of the lytic/lysogenic cycle. In comparison with T. fusca and the previously discovered bacteriophage P1312, P318 has a much lower G+C content in its genome except at the region encompassing ORF42, which produced a protein with unknown function. P1312 and P318 share very few similarities in their genomes except for the regions encompassing ORF42 of P318 and ORF51 of P1312 that are homologous. Thus, acquisition of ORF42 by lateral gene transfer might be an important step in the evolution of P318.

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