scholarly journals Antifungal strains and gene mapping of secondary metabolites in mangrove sediments from Semarang city and Karimunjawa islands, Indonesia

2021 ◽  
Vol 7 (4) ◽  
pp. 499-512
Author(s):  
Delianis Pringgenies ◽  
◽  
Wilis Ari Setyati
Keyword(s):  
Secondary Metabolites ◽  
Gene Mapping ◽  
Pathogenic Bacteria ◽  
Fungal Species ◽  
Mangrove Forests ◽  
Detection Approach ◽  
Sequencing Method ◽  
Genes Encoding ◽  
Pcr Method ◽  
Polymerase Chain

<abstract> <p>Infection caused by pathogenic fungal species is one of the most challenging disease to be tackled today. The antifungal bacteria candidate can be found in terrestrial as well as aquatic ecosystems, with mangrove forests being one of them. The purpose of this study is to obtain candidate isolates of antifungal strains with a detection approach and gene mapping simulation of bioactive compounds producers and screening to determine qualitative antifungal activity. The research will be carried out by collecting sediment samples from the mangrove ecosystems of Karimunjawa and Mangkang sub-district of Semarang city, isolating and purifying bacteria with Humic Acid Vitamin Agar (HVA), International Streptomyces Project 1 (ISP 1) and Zobell (Marine Agar). added with antibiotics, qualitative antifungal ability screening of each isolate obtained, detection of the presence of PKS gene and NRPS using special primers using the Polymerase Chain Reaction (PCR) method, and molecular identification of each isolate by 16s rRNA sequencing method. Of the total 59 isolates produced from the sample isolation process, 31 isolates from Karimunjawa sediments and 8 isolates from Semarang sediments showed activity against test pathogenic bacteria, namely <italic>Candida albicans</italic>, <italic>Trichoderma</italic> sp., and <italic>Aspergillus niger</italic>. Detection of Biosynthethic Gene Cluster (BGC) showed that the genes encoding secondary metabolites (NRPS, PKS 1 and PKS 2) were detected in KI 2-2 isolates from Karimunjawa. NRPS were detected only in isolates SP 3-9, SH 3-4, KI 1-6, KI 2-2, KI 2-4. The secondary metabolite-encoding gene, PKS1, was detected in isolates SP 3-5, SP 3-8, KI 2-2. PKS II genes were detected only on isolates SP 2-4, SH 3-8, KI 1-6, KI 2-2, and KI 2-4. Isolate SP 3-5 was revealed as <italic>Pseudomonas aeruginosa</italic> (93.14%), isolate SP 2-4 was <italic>Zhouia amylolytica</italic> strain HN-181 (100%) and isolate SP 3-8 was <italic>P. aeruginosa</italic> strain QK -2 (100%).</p> </abstract>

scholarly journals A revisit to a low-cost method for the isolation of microsatellite markers: the case of the endangered Malayan tapir (Tapirus indicus)

2018 ◽  
Author(s):  
Qi Luan Lim ◽  
Nurul Adilah Ismail ◽  
Ramitha Arumugam ◽  
Wei Lun Ng ◽  
Christina Seok Yien Yong ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Low Cost ◽  
Pcr Cloning ◽  
Chain Reaction ◽  
Sequencing Method ◽  
Rapid Polymerase Chain Reaction ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Tapirus Indicus

AbstractThere are many approaches to develop microsatellite markers. We revisited an easy and rapid Polymerase Chain Reaction (PCR)-cloning-sequencing method to design microsatellite markers for Tapirus indicus. Using six random amplified microsatellite (RAM) markers, this study had rapidly generated 45 unique genomic sequences containing microsatellites. After screening 15 terminal and seven intermediate microsatellite loci, we shortlisted five and seven which were amplified either by single- or multiplex PCR using the economical three-primer PCR method. Genotyping attempts were made with ten Tapirus indicus individuals using three of the terminal microsatellite loci and all seven intermediate loci. However, none of the terminal microsatellite loci were considered useful for population genotyping studies, while the seven intermediate loci showed good amplification but were monomorphic in the ten samples. Despite successful detection of amplified loci, we would like to highlight that, researchers who are interested in this alternative method for isolation of microsatellite loci to be cautious and be aware of the limitations and downfalls reported herein that could render these loci unsuitable for population genotyping.

scholarly journals Presence, Mode of Action, and Application of Pathway Specific Transcription Factors in Aspergillus Biosynthetic Gene Clusters

2021 ◽  
Vol 22 (16) ◽  
pp. 8709
Author(s):  
Wenjie Wang ◽  
Yuchao Yu ◽  
Nancy P. Keller ◽  
Pinmei Wang
Keyword(s):  
Transcription Factor ◽  
Secondary Metabolites ◽  
Gene Clusters ◽  
Fungal Species ◽  
Relative Location ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Genes Encoding ◽  
Depth View ◽  
Fungal Secondary Metabolites

Fungal secondary metabolites are renowned toxins as well as valuable sources of antibiotics, cholesterol-lowering drugs, and immunosuppressants; hence, great efforts were levied to understand how these compounds are genetically regulated. The genes encoding for the enzymes required for synthesizing secondary metabolites are arranged in biosynthetic gene clusters (BGCs). Often, BGCs contain a pathway specific transcription factor (PSTF), a valuable tool in shutting down or turning up production of the BGC product. In this review, we present an in-depth view of PSTFs by examining over 40 characterized BGCs in the well-studied fungal species Aspergillus nidulans and Aspergillus fumigatus. Herein, we find BGC size is a predictor for presence of PSTFs, consider the number and the relative location of PSTF in regard to the cluster(s) regulated, discuss the function and the evolution of PSTFs, and present application strategies for pathway specific activation of cryptic BGCs.

scholarly journals Investigation of the presence of G354A (Cys87Tyr) mutation in osteoprotegerin gene in women with osteoporosis in Chaharmahal and Bakhtiari province

2019 ◽  
Vol 21 (6) ◽  
pp. 250-253
Author(s):  
Seyedeh Zahra Mousavi ◽  
Morteza Dehghan ◽  
Razieh Pourahmad
Keyword(s):  
Gel Electrophoresis ◽  
Analytical Study ◽  
Competitive Inhibitor ◽  
Osteoclast Formation ◽  
Bone Diseases ◽  
Mineral Density ◽  
Sequencing Method ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Osteoprotegerin Gene

Background and aims: Osteoprotegerin (OPG) is a competitive inhibitor of the differentiation and activity of osteoclasts, which inhibits the final stages of osteoclast formation and induces its apoptosis. In addition, OPG is considered as one of the most important candidate genes in the pathogenesis of bone diseases such as osteoporosis and idiopathic hyperphosphatasia. The G354A (Cys87Tyr) mutation in the OPG gene leads to idiopathic hyperphosphatasia. This mutation is probably related to osteoporosis. The purpose of this study was to investigate the presence of G354A (Cys87Tyr) in women with osteoporosis in Chaharmahal and Bakhtiari province. Methods: In this descriptive-analytical study, the bone mineral density (BMD) of the femoral neck and lumbar spine of women referring to Shahrekord bone densitometry centers was measured by the X-ray absorptiometry technique in 2013-2014. Based on T-scores, people with osteoporosis were identified and 70 patients were enrolled in the study after receiving their consent. Finally, DNA was extracted from blood samples, amplified by polymerase chain reaction (PCR) technique, and sequenced by DNA sequencing method. Results: After DNA extraction from the blood, the quality and quantity were determined by gel electrophoresis and spectrophotometry, respectively. Then, the gene was amplified by the PCR method and the product was detected by gel electrophoresis, followed by sequencing the samples to investigate the presence of the mutation. Eventually, genotypes associated with Cys87Tyr mutation were not observed in the studied population. Conclusion: In the present study, the G354A (Cys87Tyr) mutation associated with idiopathic hyperphosphatasia was not found in women with osteoporosis.

scholarly journals Prevalence and distribution of resistance and enterotoxins/enterotoxin-like genes in different clinical isolates of coagulase-negative Staphylococcus

2020 ◽  
Vol 25 (1) ◽  
Author(s):  
Mona Nasaj ◽  
Zahra Saeidi ◽  
Hamed Tahmasebi ◽  
Sanaz Dehbashi ◽  
Mohammad Reza Arabestani
Keyword(s):  
Selective Advantage ◽  
Diffusion Method ◽  
Coagulase Negative Staphylococcus ◽  
Disk Diffusion Method ◽  
Genes Encoding ◽  
Sequence Elements ◽  
Insertion Elements ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Encoding Genes

Abstract Background Coagulase-negative staphylococcus (CoNS) is considered to be the major reservoirs for genes facilitating the evolution of S. aureus as a successful pathogen. The present study aimed to determine the occurrence of genes conferring resistance to fluoroquinolone, determining of the prevalence of insertion sequence elements IS256, IS257 and different superantigens (SAgs) among CoNS isolates obtained from various clinical sources. Materials and methods The current study conducted on a total of the 91 CoNS species recovered from clinical specimens in Hamadan hospitals in western Iran in 2017–2019. The antimicrobial susceptibility testing was performed using disk diffusion method and the presence of the IS256 and IS257, genes conferring resistance to fluoroquinolone and enterotoxins/enterotoxin-like encoding genes were investigated by polymerase chain reaction (PCR) method. Results Among genes encoding classic enterotoxins, sec was the most frequent which was carried by 48.4% of the 91 isolates, followed by seb in 27.5% of the isolates. None of the CoNS isolates was found to be positive to enterotoxin-like encoding genes. In 11(12%) of all isolates that were phenotypically resistant to levofloxacin, 9 isolates (81.8%) were positive for gyrB, 8 isolates (72.7%) were positive for gyrA, 8 isolates (72.7%) harbored grlB and 7 isolates (63.6%) were found to carry grlA. The IS256 and IS257 were identified in 31.8% and 74.7% of the isolates, respectively. The results of statistical analysis showed a significant association between the occurrence of staphylococcal enterotoxins (SEs) encoding genes and antimicrobial resistance. Conclusion Antimicrobial resistant determinants and SEs are co-present in clinical CoNS isolates that confer selective advantage for colonization and survival in hospital settings. The coexistence of insertion elements and antibiotic resistance indicate their role in pathogenesis and infectious diseases.

scholarly journals Goat Colostrum—Source of Toxigenic Bacillus Cereus

2019 ◽  
Vol 63 (3) ◽  
pp. 27-33
Author(s):  
Š. Bursová ◽  
D. Nečasová ◽  
K. Dorotíková ◽  
L. Necidová ◽  
L. Vorlová
Keyword(s):  
Polymerase Chain Reaction ◽  
Bacillus Cereus ◽  
Toxin Production ◽  
Gyrb Gene ◽  
Gene Detection ◽  
Chain Reaction ◽  
Genes Encoding ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Toxigenic Strains

Abstract The aim of this study was to evaluate the toxigenic potential of Bacillus cereus strains isolated from frozen goat colostrum. Of the 50 phenotypically suspected B. cereus isolates, 39 (78.0 %) were confirmed as B. cereus by the polymerase chain reaction (PCR) method based on the gyrB gene detection. In these isolates, genes encoding the production of haemolysin BL (Hbl), a complex of non-haemolytic enterotoxins (Nhe) and emetic toxin were detected by the PCR method. In 36 (92.3 %) confirmed B. cereus isolates, genes encoding at least one type of toxins of interest were detected. In all toxigenic isolates, we found the presence of genes for Nhe production, and in 16 (41.0 %) of the isolates, genes encoding both Nhe and haemolysin BL were shown. Eight (20.5 %) of the emetic strains of B. cereus were identified. The emetic toxin production gene was always detected simultaneously with genes encoding non-haemolytic enterotoxin production. The ability to produce BL haemolysin and non-haemolytic enterotoxins were confirmed by the immunochromatographic method. In summary, goat colostrum can be a significant source of toxigenic strains of B. cereus.

scholarly journals Prevalence and Distribution of Resistance and Enterotoxins/Enterotoxin-likes Genes in Different Clinical Isolates of Coagulase-negative Staphylococcus

2020 ◽  
Author(s):  
Mona Nasaj ◽  
Zahra Saeidi ◽  
Hamed Tahmasebi ◽  
Sanaz Dehbashi ◽  
Mohammad Arabestani
Keyword(s):  
Selective Advantage ◽  
Diffusion Method ◽  
Coagulase Negative Staphylococcus ◽  
Disk Diffusion Method ◽  
Genes Encoding ◽  
Sequence Elements ◽  
Insertion Elements ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Encoding Genes

Abstract Background: Coagulase-negative staphylococcus (CoNS) are considered to be the major reservoirs for genes facilitating the evolution of S. aureus as a successful pathogen. The present study aimed to determine the occurrence of genes conferring resistance to fluoroquinolone, determining of the prevalence of insertion sequence elements IS256, IS257 and different superantigenes (SAgs) among CoNS isolates obtained from various clinical sources.Materials and Methods: The current study conducted on a total of the 91 CoNS species recovered from clinical specimens in Hamadan hospitals in western Iran in 2017-19. The antimicrobial susceptibility testing was performed using disk diffusion method and the presence of the IS256 and IS257, genes conferring resistance to fluoroquinolone and enterotoxins/enterotoxin-like encoding genes were investigated by Polymerase Chain Reaction (PCR) method. Results: Among genes encoding classic enterotoxins, sec was the most frequent which was carried by 48.4% of the 91 isolates, followed by seb in 27.5% of the isolates. None of the CoNS isolates was found to be positive to enterotoxin-like encoding genes. In 11(12%) of all isolates that were phenotypically resistant to levofloxacin, 9 isolates (81.8%) were positive for gyrB, 8 isolates (72.7%) were positive for gyrA, 8 isolates (72.7%) harbored grlB and 7 isolates (63.6%) were found to carry grlA. The IS256 and IS257 were identified in 31.8 % and 74.7% of the isolates, respectively. The results of statistical analysis showed a significant association between the occurrence of staphylococcal enterotoxins (SEs) encoding genes and antimicrobial resistance.Conclusion: Antimicrobial resistant determinants and SEs are co-present in clinical CoNS isolates that confer selective advantage for colonization and survival in hospital settings. The coexistence of insertion elements and antibiotic resistance indicate their role in pathogenesis and infectious diseases.

Investigation of duck plague virus in hoar areas of Bangladesh

2020 ◽  
Vol 26 (1-2) ◽  
pp. 73-78
Author(s):  
A Hossen ◽  
MH Rahman ◽  
MZ Ali ◽  
MA Yousuf ◽  
MZ Hassan ◽  
...  
Keyword(s):  
Cytopathic Effect ◽  
Clinical Sample ◽  
Chorioallantoic Membrane ◽  
Clinical Samples ◽  
Isolation And Identification ◽  
Duck Plague Virus ◽  
Pcr Method ◽  
Polymerase Chain ◽  
The Individual ◽  
Free Ranging

Duck plague (DP) is the most important infectious disease of geese, ducks and free-ranging water birds. The present study was conducted to determine the prevalence of duck plague virus followed by isolation and identification. For these purposes, a total of 155 cloacal swabs samples were collected randomly from duck of different haor areas of Bangladesh including 45 (41 surveillance and 4 clinical) samples from Netrokona; 42 (40 surveillance and 2 clinical) samples from Kishoregonj; 30 samples from Brahmanbaria and 38 samples from Sunamganj. The samples were processed and pooled (1:5 ratio) for initial screening of target polymerase gene of duck plague virus by polymerase chain reaction (PCR) method. All the samples of a positive pool were then tested individually for identifying the individual positive samples. The result showed that out of 155 samples, 41 (26.45%) were found positive in which 17 were from Netrokona, where 15 (36.58%) were from surveillance samples and 2 (50%) were from clinical sample; 16 were from Kishoregonj, where 14 (35%) were from surveillance samples and 2 (100%) were from clinical sample; 2 (6.6%) were from Brahmanbaria and 5 (13.15%) were from Sunamganj. These positive samples were inoculated into 9-10 days embryonated duck eggs (EDE) through chorioallantoic membrane (CAM) route for the isolation of virus. The EDE died earlier was also chilled, and in a similar way, the CAMs were collected and again performed PCR for id entification of virus. Out of 41 PCR positive samples, 26 samples were isolated and reconfirmed by PCR. Subsequently, DPV was isolated in primary duck embryo fibroblasts cell culture and confirmed by observing cytopathic effect (CPE). Bang. J. Livs. Res. Vol. 26 (1&2), 2019: P. 73-78

Prevalence of SHV-extended spectrum β-lactamase producing carbapenem –resistantKlebsiellapneumoniae among patients with lower respiratory tractinfections in Babylon Province-Iraq.

2018 ◽  
Vol 9 (SPL1) ◽  
Author(s):  
Fatima Moeen Abbas
Keyword(s):  
Resistance Rate ◽  
Combination Method ◽  
Diffusion Method ◽  
Disk Diffusion Method ◽  
Carbapenem Resistant ◽  
Extended Spectrum ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Tract Infections ◽  
Positive Results

This study was carried out to screen the prevalence of Klebsiella pneumoniae isolated from patients with lower respiratory tract infections in Babylon province.From December,2015 to the end of March,2016,a total of 100 sputum samples were collected from patients visited or hospitalized Merjan Teaching Hospital and Al- Hashimya General Hospital. Fifteenth (65%) isolates were identified as Klebsiellapneumoniae. All bacterial isolates were evaluated for extended spectrum β-lactamase (ESBL) production phenotypically using disk combination method. Eleven (73.3%) isolates were detected as ESBL-producers. Kirby-Bauer disk diffusion method was employed to determine resistance profile of ESBLs-positive isolates. Higher rates of resistance were observed for ampicillin and piperacillin antibiotics with (81.8%) and (72.7%) resistance rate, respectively, while the lowest rate was noticed for imipenem antibiotic (14.28%). Carbapenem-resistant isolates were investigated for blaSHV gene by Polymerase Chain Reaction (PCR) method, 2 (100%) isolates gave positive results.

Antimicrobial properties of actively purified secondary metabolites isolated from different marine organisms

2020 ◽  
Vol 21 ◽  
Author(s):  
Nilushi Indika Bamunu Arachchige ◽  
Fazlurrahman Khan ◽  
Young-Mog Kim
Keyword(s):  
Secondary Metabolites ◽  
Pathogenic Bacteria ◽  
Antimicrobial Agents ◽  
Bacterial Species ◽  
Antimicrobial Properties ◽  
Antimicrobial Effect ◽  
Cost Effective ◽  
Resistance Mechanisms ◽  
Marine Organisms ◽  
Antimicrobial Compounds

Background: The treatment of infection caused by pathogenic bacteria becomes one of the serious concerns globally. The failure in the treatment was found due to the exhibition of multiple resistance mechanisms against the antimicrobial agents. Emergence of resistant bacterial species has also been observed due to prolong treatment using conventional antibiotics. To combat these problems, several alternative strategies have been employed using biological and chemically synthesized compounds as antibacterial agents. Marine organisms considered as one of the potential sources for the isolation of bioactive compounds due to the easily available, cost-effective, and eco-friendly. Methods: The online search methodology was adapted for the collection of information related to the antimicrobial properties of marine-derived compounds. These compound has been isolated and purified by different purification techniques, and their structure also characterized. Furthermore, the antibacterial activities have been reported by using broth microdilution as well as disc diffusion assays. Results: The present review paper describes the antimicrobial effect of diverse secondary metabolites which are isolated and purified from the different marine organisms. The structural elucidation of each secondary metabolite has also been done in the present paper, which will help for the in silico designing of the novel and potent antimicrobial compounds. Conclusion: A thorough literature search has been made and summarizes the list of antimicrobial compounds that are isolated from both prokaryotic and eukaryotic marine organisms. The information obtained from the present paper will be helpful for the application of marine compounds as antimicrobial agents against different antibiotic-resistant human pathogenic bacteria.

Structure, expression, chromosomal location and product of the gene encoding Adh2 in Petunia.

Genetics ◽  
1993 ◽  
Vol 133 (4) ◽  
pp. 999-1007
Author(s):  
R G Gregerson ◽  
L Cameron ◽  
M McLean ◽  
P Dennis ◽  
J Strommer
Keyword(s):  
Chromosomal Location ◽  
Higher Plants ◽  
Gene Encoding ◽  
Genomic Libraries ◽  
Regulatory Strategy ◽  
Adh1 Gene ◽  
Adh Genes ◽  
Genes Encoding ◽  
Adh Gene ◽  
Polymerase Chain

Abstract In most higher plants the genes encoding alcohol dehydrogenase comprise a small gene family, usually with two members. The Adh1 gene of Petunia has been cloned and analyzed, but a second identifiable gene was not recovered from any of three genomic libraries. We have therefore employed the polymerase chain reaction to obtain the major portion of a second Adh gene. From sequence, mapping and northern data we conclude this gene encodes ADH2, the major anaerobically inducible Adh gene of Petunia. The availability of both Adh1 and Adh2 from Petunia has permitted us to compare their structures and patterns of expression to those of the well-studied Adh genes of maize, of which one is highly expressed developmentally, while both are induced in response to hypoxia. Despite their evolutionary distance, evidenced by deduced amino acid sequence as well as taxonomic classification, the pairs of genes are regulated in strikingly similar ways in maize and Petunia. Our findings suggest a significant biological basis for the regulatory strategy employed by these distant species for differential expression of multiple Adh genes.

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