scholarly journals Molecular Characterization of Post Harvest Fungus Associated with Spoilt Broccoli

2021 ◽  
pp. 47-51
Author(s):  
Ikechi – Nwogu, Chinyerum Gloria ◽  
B. A. Odogwu ◽  
O. G. Obiakoeze
Keyword(s):  
Aspergillus Niger ◽  
Fungal Pathogens ◽  
Sequence Similarity ◽  
Local Alignment ◽  
Control Approach ◽  
Post Harvest ◽  
Morphological Studies ◽  
Search Tool ◽  
Fungal Organisms ◽  
Post Harvest Deterioration

Broccoli (Brassica oleracea var. italica) is a nutritional vegetable that looks like a small tree. Despite the fact that it is extensively loaded with arrays of vitamins, minerals, fiber and antioxidants, it has been observed that it has a short lifespan of not more than 2-5 days due to post-harvest deterioration. A study was conducted to isolate and identify the common fungal pathogens causing post-harvest deterioration of broccoli crown. Diseased broccoli crowns were collected from Ogunabali Fruit Garden Market in D-Line, Port Harcourt Local Government Area of Rivers State. Fungal isolates were collected and morphologically identified. The DNA of the most common fungal isolate, BC-3B was molecularly characterized using Internal Transcribed Spacer 4 and 5 (ITS-4 and 5) molecular markers. The morphological studies revealed that the BC-3B isolate was an Aspergillus niger. The BC-3B isolate DNA sequence was aligned using Basic Local Alignment Search Tool for Nucleotide (BLASTN) 2.8.0 version of National Center for Biotechnology Information (NCBI) database. The molecular weight of the DNA of the isolates was over 600base pairs. Based on sequence similarity, it was observed that the broccoli isolate BC-3B was 93% identical to Aspergillus niger. From the above results, these findings showed that Aspergillus niger is the causal fungal pathogen of post-harvest rot of broccoli. Phylogenetic tree was constructed to access the relationship between the isolates obtained from this study. This study has provided information on some of the fungal organisms found in broccoli. It is anticipated that this result will provide information for disease control approach for alleviating the post-harvest losses of broccoli caused by Aspergillus niger and provide a foundation for further study of possible harm of consuming diseased broccoli.

scholarly journals Molecular characterization of fungi associated with stored soybean (Glycine max L) seeds

2020 ◽  
Vol 36 (2) ◽  
pp. 27-32
Author(s):  
C.G. Ikechi-Nwogu ◽  
F.C. Okene
Keyword(s):  
Fungal Pathogens ◽  
Fungal Species ◽  
Molecular Techniques ◽  
Local Alignment ◽  
Post Harvest ◽  
High Quality Protein ◽  
Search Tool ◽  
Food And Feed ◽  
Glycine Max L

Soybean is an important legume that has high quality protein and oil for food and feed. Despite the importance of this legume, the crop is affected by several post-harvest diseases caused by fungi. A study was carried out to identify the fungal species associated with the seeds of soybean using molecular techniques. The DNA of the isolate, was molecularly characterized using Internal Transcribed Spacer 1 (ITS-1) molecular marker. The isolate DNA sequence, was aligned using the Basic Local Alignment Search Tool for nucleotide (BLASTN) 2.8.0 version of the National Center for Biotechnology Information (NCBI) database. The results showed that the isolate sequence was 98% identical to Diaporthe spp. Voucher VP51, 98% identical to Diaporthe schini isolate L5N71 and 98% identical to Diaporthe schini strain B125. These findings showed that Diaporthe spp. is one of the causal fungal pathogens of post-harvest diseases of soybean seeds. It is anticipated that these results will provide information on culturing Diaporthe species also provide the basis for further study to show their antibiotic and anti-cancerous, enzymes and secondary metabolites producing ability. Keywords: Soybean, Diaporthe schini and RBCL marker

scholarly journals Predicting bacteriophage hosts based on sequences of annotated receptor-binding proteins

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Dimitri Boeckaerts ◽  
Michiel Stock ◽  
Bjorn Criel ◽  
Hans Gerstmans ◽  
Bernard De Baets ◽  
...  
Keyword(s):  
Machine Learning ◽  
Predictive Model ◽  
Receptor Binding ◽  
Bacterial Infections ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Area Under The Curve ◽  
Local Alignment ◽  
Search Tool ◽  
Different Levels

AbstractNowadays, bacteriophages are increasingly considered as an alternative treatment for a variety of bacterial infections in cases where classical antibiotics have become ineffective. However, characterizing the host specificity of phages remains a labor- and time-intensive process. In order to alleviate this burden, we have developed a new machine-learning-based pipeline to predict bacteriophage hosts based on annotated receptor-binding protein (RBP) sequence data. We focus on predicting bacterial hosts from the ESKAPE group, Escherichia coli, Salmonella enterica and Clostridium difficile. We compare the performance of our predictive model with that of the widely used Basic Local Alignment Search Tool (BLAST). Our best-performing predictive model reaches Precision-Recall Area Under the Curve (PR-AUC) scores between 73.6 and 93.8% for different levels of sequence similarity in the collected data. Our model reaches a performance comparable to that of BLASTp when sequence similarity in the data is high and starts outperforming BLASTp when sequence similarity drops below 75%. Therefore, our machine learning methods can be especially useful in settings in which sequence similarity to other known sequences is low. Predicting the hosts of novel metagenomic RBP sequences could extend our toolbox to tune the host spectrum of phages or phage tail-like bacteriocins by swapping RBPs.

scholarly journals Isolation and Identification of Fungi Associated with Habanero Pepper (Capsicum chinense jacq) Using Basic Molecular Techniques

2021 ◽  
Vol 25 (7) ◽  
pp. 1121-1125
Author(s):  
G.C. Ikechi-Nwogu ◽  
A.B. Odogwu ◽  
J. Ukomadu ◽  
E.P. Usiakponebro
Keyword(s):  
Fungal Pathogens ◽  
Molecular Techniques ◽  
Local Alignment ◽  
Capsicum Chinense ◽  
Isolation And Identification ◽  
Post Harvest ◽  
Habanero Pepper ◽  
Mucor Irregularis ◽  
Identification Of Fungi ◽  
Rhizomucor Variabilis

Habanero pepper (Capsicum chinense Jacq.) is an economically important vegetable. It is used as spices for foods and for medicinal purposes in many parts of the country. Despite the importance of the crop, it has been observed that during storage, the fruits of the Habanero pepper (HP) shelf-life is reduced by several post-harvest diseases caused by fungal pathogens. A study was conducted to identify the common fungal pathogens causing post-harvest rot of Habanero fruits at the daily market in Omoko Aluu Town, Rivers State. The DNA of the most common fungal isolate HP-02 was molecularly characterized using Internal Transcribed Spacer 1 (ITS-1) molecular marker. The HP-02 isolate DNA sequence was aligned using the Basic Local Alignment Search Tool for nucleotide (BLASTN) 2.8.0 version of the National Center for Biotechnology Information (NCBI) database. The results indicated that the HP-02 isolate sequence was 79% identical to Mucor irregularis and also Rhizomucor viriabilis isolate SAPB3. These findings showed that Mucor irregularis, which was formerly known as Rhizomucor variabilis is one of the emerging causal fungal pathogens of post-harvest Habanero pepper.

scholarly journals A Study of Pathogenic Fungi Causing Post Harvest Losses of Pineapple Sold at Wudil and Yan Lemo Markets of Kano State

2019 ◽  
pp. 1-6
Author(s):  
S. M. Yahaya ◽  
A. B. Kamalu ◽  
M. U. Ali ◽  
M. Lawan ◽  
Y. S. Ajingi ◽  
...  
Keyword(s):  
Aspergillus Niger ◽  
Fungal Pathogen ◽  
Fungal Pathogens ◽  
Pathogenic Fungi ◽  
Potato Dextrose Agar ◽  
Frequency Of Occurrence ◽  
Post Harvest ◽  
Fungal Isolates ◽  
Microbiological Methods ◽  
Two Samples

This research was conducted to determine the fungal pathogens responsible for post harvest losses of pineapple sold at Wudil and Yen lemo markets.  Two samples of pineapples were purchased twice a week from both Wudil and Yanlemo markets for four months. The samples were investigated for the presence of fungal pathogen using standard microbiological methods. The methods involve mounting small portion of pineapple in the plate containing Potato dextrose agar to isolate the fungi. Three fungal pathogens belonging to Aspergillus species were isolated, and Aspergillus niger had the highest frequency of occurrence of (50%). Followed by A. flavus with (27%). The A. fumigatus had the lowest frequency of occurrence of (23%). The differences between the fungal isolates recorded were significantly different (P<0.05) between the two markets, where higher fungal isolates were recorded at Yanlemo market 159 (40.6%) and Wudil 38 (9.71%). The study showed that the post harvest losses of pine apple in the two markets are attributed to fungal infection. Therefore, safe guarding the two markets from debris and dumps of rotten fruits and vegetable may assist in reducing fungal inoculums in the two markets.

scholarly journals HBLAST: Parallelised sequence similarity – A Hadoop MapReducable basic local alignment search tool

2015 ◽  
Vol 54 ◽  
pp. 58-64 ◽  
Author(s):  
Aisling O’Driscoll ◽  
Vladislav Belogrudov ◽  
John Carroll ◽  
Kai Kropp ◽  
Paul Walsh ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Local Alignment ◽  
Search Tool

scholarly journals Evaluation of Pathogenic Potentials of Microbial Contaminants from Naira Notes in Nigeria

2021 ◽  
pp. 180-188
Author(s):  
Ifeoma Bessie Enweani ◽  
Chinyere Nkemjika Anyanwu ◽  
Emmanuel Ifeanyi Obeagu
Keyword(s):  
Escherichia Coli ◽  
Aspergillus Niger ◽  
Proteus Mirabilis ◽  
Base Pair ◽  
Alveolar Epithelium ◽  
Local Alignment ◽  
Histopathological Study ◽  
E Coli ◽  
Watery Stool ◽  
Search Tool

The study was done to determine burden of fiat currencies. A total of Six hundred and twenty four pieces of different denominations of naira notes obtained from banks in Enugu metropolis and samples of nose swabs aseptically collected from fifty two note counters from those banks were examined for similar bacterial and fungal contaminants. All sequences were identified using the Basic Local Alignment Search Tool (BLAST) on National Center for Biotechnology Information (NCBI) website. While the fungi amplicons yielded DNA bands of approximately 650 base pair, that of the bacterial isolates were approximately 850 base pair. Proteus mirabilis (NR11449.1) and Escherichia coli (LN831043.1) were identical and selected from the bacterial category while Aspergillus fumigatus (MK910068), Aspergillus flavus (JQ860302) and Aspergillus niger (MK461093) were identical and selected from the fungal category. Rats inoculated orally with Escherichia coli and Proteus mirabilis presented with watery stool and reduction of weight by 16+0.4g after two weeks of commencement of inoculation. They showed reduction in activity and reduced locomotion when compared with the control. There were no physically observable changes in the other test groups. In the hematological investigation, the mean PCV in % were 39±1.0 for the E. coli, 40±0.4 for P. mirabilis, 35±0.2 for A. niger, 40±0.7 for A. fumigatus and 37±0.1 for A .flavus. These varied significantly at p<0.05 with the control which has mean PCV of 45±0.3. The differential leucocyte count showed a marked increase in the % neutrophil (E. coli 73±0.1, P. mirabilis 70±0.1, A. niger 78±1.1, A. fumigatus 59±0.3 and A. flavus 62±1.0) when compared with the control rats with percentage neutrophil of 20±0.2. There was also an increase in the white blood cell count of the test groups when compared with the control. Histopathological study of the lungs of the rats inoculated nasally with Aspergillus niger showed necrosis of the alveolar epithelium. This study has shown that naira notes could be a reservoir of microorganisms of medical importance which in turn could become vectors for the transmission of diseases in the society.

scholarly journals PITA, a pre-bilaterian p75NTR, is the evolutionary ancestor of TNF receptors

2021 ◽  
Author(s):  
Mark J Cumming ◽  
Julien Gibon ◽  
Wayne S Sossin ◽  
Philip A Barker
Keyword(s):  
Large Scale ◽  
Sequence Similarity ◽  
Evolutionary Model ◽  
Neurotrophin Receptor ◽  
Local Alignment ◽  
P75 Neurotrophin Receptor ◽  
Death Domain ◽  
Search Tool ◽  
Health And Disease ◽  
Tnfr Superfamily

Tumor necrosis factor receptors (TNFRs) regulate a diverse array of biological functions, including adaptive immunity, neurodevelopment, and many others. Although TNFRs are expressed in all metazoan phyla, a coherent model of the molecular origins of mammalian TNFRs—and how they relate to TNFRs in other phyla—has remained elusive. To address this, we executed a large-scale, systematic Basic Local Alignment Search Tool (BLAST)-based approach to trace the evolutionary ancestry of all 29 human TNFRs. We discovered that all human TNFRs are descendants of a single pre-bilaterian TNFR with strong sequence similarity to the p75 neurotrophin receptor (p75NTR), which we designate as PITA for ‘ p75NTR is the TNFR Ancestor’ . A distinct subset of human TNFRs—including EDAR, XEDAR and TROY—share a unique history as descendants of EDAR-XEDAR-TROY (EXT), which diverged from PITA in a bilaterian ancestor.  Most PITA descendants possess a death domain (DD) within their intracellular domain (ICD) but EXTs do not. PITA descendants are expressed in all bilaterian phyla and Cnidaria, but not in non-planulozoan ParaHoxozoa, suggesting that PITA originated in an ancestral planulozoan. Drosophila melanogaster TNFRs (Wengen (Wgn) and Grindelwald (Grnd)) were identified as divergent PITA descendants, providing the first evolutionary link between this model TNFR system and the mammalian TNFR superfamily. This study reveals PITA as the ancestor to human and Drosophila TNFR systems and describes an evolutionary model that will facilitate deciphering TNF-TNFR functions in health and disease.

scholarly journals Application of internal transcribed spacer of nuclear ribosomal DNA for identification of Echinops mandavillei Kit Tan

2014 ◽  
Vol 21 (1) ◽  
pp. 33-42 ◽  
Author(s):  
Fahad M.A. Al-Hemaid ◽  
M. Ajmal Ali ◽  
Joongku Lee ◽  
Gábor Gyulai ◽  
Arun K. Pandey
Keyword(s):  
Ribosomal Dna ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Local Alignment ◽  
The Novel ◽  
Search Tool ◽  
Plant Taxon ◽  
High Level

The present study explored the use of internal transcribed spacers (ITS) sequences (ITS1-5.8S-ITS2) of nuclear ribosomal DNA (nrDNA) for identification of Echinops mandavillei Kit Tan, an endemic species to Saudi Arabia. The sequence similarity search using Basic Local Alignment Search Tool (BLAST) and phylogenetic analyses of the ITS sequence of E. mandavillei Kit Tan showed high level of sequence similarity (98%) with E. glaberrimus DC. (section Ritropsis). The novel primary sequence and the secondary structure of ITS2 of E. mandavillei could have a potential use for molecular genotyping.DOI: http://dx.doi.org/10.3329/bjpt.v21i1.19256Bangladesh J. Plant Taxon. 21(1): 33-42, 2014 (June)

scholarly journals Alignment-Free Approaches for Predicting Novel Nuclear Mitochondrial Segments (NUMTs) in the Human Genome

2017 ◽  
Author(s):  
Wentian Li ◽  
Jerome Freudenberg ◽  
Jan Freudenberg
Keyword(s):  
Human Genome ◽  
Similarity Search ◽  
Sequence Similarity ◽  
Local Alignment ◽  
Sequence Similarity Search ◽  
Alignment Free ◽  
Search Tool ◽  
Manhattan Plot ◽  
Mitochondrial Origin ◽  
Jensen Shannon Divergence

AbstractThe nuclear human genome harbors sequences of mitochondrial origin, indicating an ancestral transfer of DNA from the mitogenome. Several Nuclear Mitochondrial Segments (NUMTs) have been detected by alignment-based sequence similarity search, as implemented in the Basic Local Alignment Search Tool (BLAST). Identifying NUMTs is important for the comprehensive annotation and understanding of the human genome. Here we explore the possibility of detecting NUMTs in the human genome by alignment-free sequence similarity search, such as k-mers (k-tuples, k-grams, oligos of length k) distributions. We find that when k=6 or larger, the k-mer approach and BLAST search produce almost identical results, e.g., detect the same set of NUMTs longer than 3kb. However, when k=5 or k=4, certain signals are only detected by the alignment-free approach, and these may indicate yet unrecognized, and potentially more ancestral NUMTs. We introduce a “Manhattan plot” style representation of NUMT predictions across the genome, which are calculated based on the reciprocal of the Jensen-Shannon divergence between the nuclear and mitochondrial k-mer frequencies. The further inspection of the k-mer-based NUMT predictions however shows that most of them contain long-terminal-repeat (LTR) annotations, whereas BLAST-based NUMT predictions do not. Thus, similarity of the mitogenome to LTR sequences is recognized, which we validate by finding the mitochondrial k-mer distribution closer to those for transposable sequences and specifically, close to some types of LTR.

The Influence of Memory-Aware Computation on Distributed BLAST

2019 ◽  
Vol 14 (2) ◽  
pp. 157-163
Author(s):  
Majid Hajibaba ◽  
Mohsen Sharifi ◽  
Saeid Gorgin
Keyword(s):  
Search Time ◽  
Genomic Research ◽  
Local Alignment ◽  
Negative Effects ◽  
Sequencing Technologies ◽  
Percent Improvement ◽  
Fast Processing ◽  
Search Tool ◽  
Memory Awareness ◽  
Generation Sequencing

Background: One of the pivotal challenges in nowadays genomic research domain is the fast processing of voluminous data such as the ones engendered by high-throughput Next-Generation Sequencing technologies. On the other hand, BLAST (Basic Local Alignment Search Tool), a longestablished and renowned tool in Bioinformatics, has shown to be incredibly slow in this regard. Objective: To improve the performance of BLAST in the processing of voluminous data, we have applied a novel memory-aware technique to BLAST for faster parallel processing of voluminous data. Method: We have used a master-worker model for the processing of voluminous data alongside a memory-aware technique in which the master partitions the whole data in equal chunks, one chunk for each worker, and consequently each worker further splits and formats its allocated data chunk according to the size of its memory. Each worker searches every split data one-by-one through a list of queries. Results: We have chosen a list of queries with different lengths to run insensitive searches in a huge database called UniProtKB/TrEMBL. Our experiments show 20 percent improvement in performance when workers used our proposed memory-aware technique compared to when they were not memory aware. Comparatively, experiments show even higher performance improvement, approximately 50 percent, when we applied our memory-aware technique to mpiBLAST. Conclusion: We have shown that memory-awareness in formatting bulky database, when running BLAST, can improve performance significantly, while preventing unexpected crashes in low-memory environments. Even though distributed computing attempts to mitigate search time by partitioning and distributing database portions, our memory-aware technique alleviates negative effects of page-faults on performance.

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