Pub Date : 2021-06-28DOI: 10.35118/apjmbb.2021.029.3.01
Ocktariyana, N. Hikmawati, A. Hestiantoro, R. Muharam, M. L. Marwali, A. Surur, T. Aninditha, G. Pratama, Anisah Zahrah, N. Naura, Asmarinah
Transient Receptor Ankyrin Member 1 (TRPA1) is an ion channel family protein that regulates pain sensation through sensory neurons' activity. This study's purpose to analyzes the DNA methylation and mRNA expression level of the TRPA1 gene in endometriosis and its correlation with pain level. Twenty samples of peritoneal endometriosis and endometrial samples were obtained from women with endometriosis, which was subsequently compared to 20 endometrial samples of women without endometriosis. The DNA methylation level of TRPA1 was analyzed using Methylation-specific PCR (MS-PCR) and ImageJ software, while the mRNA expression of TRPA1 was analyzed using qRT-PCR. Furthermore, the pain level was measured using the numeric rating scale (NRS) by interviewing all the women. This study showed that there was a significant difference in the mRNA expression of TRPA1 in peritoneal endometriosis. The TRPA1 was unmethylated in both peritoneal and endometrial samples in endometriosis. However, DNA Methylation level of TRPA1 in peritoneal and endometrial of endometriosis compared to normal endometrial were no significant difference. Additionally, there was no correlation between DNA methylation level and mRNA expression level of TRPA1 in all samples, along with the endometriosis-associated pain.
瞬时受体锚蛋白1 (Transient Receptor anchkyrin Member 1, TRPA1)是一种通过感觉神经元活动调节痛觉的离子通道家族蛋白。本研究旨在分析子宫内膜异位症中TRPA1基因的DNA甲基化和mRNA表达水平及其与疼痛程度的相关性。从患有子宫内膜异位症的女性中获得了20个腹膜子宫内膜异位症和子宫内膜样本，随后将其与未患有子宫内膜异位症的女性的20个子宫内膜样本进行了比较。采用甲基化特异性PCR (methyl- specific PCR, MS-PCR)和ImageJ软件分析TRPA1 DNA甲基化水平，采用qRT-PCR分析TRPA1 mRNA表达。此外，通过访谈所有女性，使用数字评定量表(NRS)测量疼痛水平。本研究显示，TRPA1 mRNA在腹膜子宫内膜异位症中的表达存在显著差异。在子宫内膜异位症的腹膜和子宫内膜样本中TRPA1均未甲基化。然而，与正常子宫内膜相比，子宫内膜异位症患者腹膜和子宫内膜中TRPA1的DNA甲基化水平无显著差异。此外，在所有样本中，DNA甲基化水平与TRPA1 mRNA表达水平以及子宫内膜异位症相关疼痛之间没有相关性。
{"title":"Analysis of DNA methylation level and mRNA expression of Transient Receptor Ankyrin Member 1 (TRPA1) in endometriosis-associated pain","authors":"Ocktariyana, N. Hikmawati, A. Hestiantoro, R. Muharam, M. L. Marwali, A. Surur, T. Aninditha, G. Pratama, Anisah Zahrah, N. Naura, Asmarinah","doi":"10.35118/apjmbb.2021.029.3.01","DOIUrl":"https://doi.org/10.35118/apjmbb.2021.029.3.01","url":null,"abstract":"Transient Receptor Ankyrin Member 1 (TRPA1) is an ion channel family protein that regulates pain sensation through sensory neurons' activity. This study's purpose to analyzes the DNA methylation and mRNA expression level of the TRPA1 gene in endometriosis and its correlation with pain level. Twenty samples of peritoneal endometriosis and endometrial samples were obtained from women with endometriosis, which was subsequently compared to 20 endometrial samples of women without endometriosis. The DNA methylation level of TRPA1 was analyzed using Methylation-specific PCR (MS-PCR) and ImageJ software, while the mRNA expression of TRPA1 was analyzed using qRT-PCR. Furthermore, the pain level was measured using the numeric rating scale (NRS) by interviewing all the women. This study showed that there was a significant difference in the mRNA expression of TRPA1 in peritoneal endometriosis. The TRPA1 was unmethylated in both peritoneal and endometrial samples in endometriosis. However, DNA Methylation level of TRPA1 in peritoneal and endometrial of endometriosis compared to normal endometrial were no significant difference. Additionally, there was no correlation between DNA methylation level and mRNA expression level of TRPA1 in all samples, along with the endometriosis-associated pain.","PeriodicalId":8566,"journal":{"name":"Asia-pacific Journal of Molecular Biology and Biotechnology","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89074035","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-06-28DOI: 10.35118/apjmbb.2021.029.3.02
Variena Intansari, A. Indrawati, S. Murtini
Ochratoxin A (OTA) is the most common toxin found in nature. Ochratoxin is a metabolic product by Aspergillus spp. and Penicillium spp. OTA produced by many Aspergillus or Penicicillium species that contaminate animal feeds can cause diseases. This study aims to determine the incidence of ochratoxin contamination in pig feed such as pellets, meat bone meal (MBM), and tofu by products. The sampling method used the disease detection formula to collect 36 samples 36 taken from several regions. North Sumatra, East Nusa Tenggara, Bali, Bulan Island, Solo, Lampung, Banten, Bogor and Jakarta. Ochratoxin contamination in animal feed was detected based on the Enzyme Linked Immunosorbent Assay (ELISA) using Agraquant® ochratoxin assay following the manufacturer’s protocol. The analysis showed that 6 of the 36 samples (16.7%) were tested positive for ochratoxin contamination. Pellets and MBM were the feed and feedstuff which were found to contain ochratoxin. The concentration of ochratoxin in MBM was below the limit set by the National Agency of Drug and Food Control of the Republic of Indonesia (5 ppb). The high contamination of ochratoxin was found in pellets from Lampung (19 ppb). The fungi found to dominates the culture media and come from pellet feed were Aspergillus flavus and Aspergillus niger.
{"title":"Ochratoxin contamination in pig feed from pig farming centres in Indonesia","authors":"Variena Intansari, A. Indrawati, S. Murtini","doi":"10.35118/apjmbb.2021.029.3.02","DOIUrl":"https://doi.org/10.35118/apjmbb.2021.029.3.02","url":null,"abstract":"Ochratoxin A (OTA) is the most common toxin found in nature. Ochratoxin is a metabolic product by Aspergillus spp. and Penicillium spp. OTA produced by many Aspergillus or Penicicillium species that contaminate animal feeds can cause diseases. This study aims to determine the incidence of ochratoxin contamination in pig feed such as pellets, meat bone meal (MBM), and tofu by products. The sampling method used the disease detection formula to collect 36 samples 36 taken from several regions. North Sumatra, East Nusa Tenggara, Bali, Bulan Island, Solo, Lampung, Banten, Bogor and Jakarta. Ochratoxin contamination in animal feed was detected based on the Enzyme Linked Immunosorbent Assay (ELISA) using Agraquant® ochratoxin assay following the manufacturer’s protocol. The analysis showed that 6 of the 36 samples (16.7%) were tested positive for ochratoxin contamination. Pellets and MBM were the feed and feedstuff which were found to contain ochratoxin. The concentration of ochratoxin in MBM was below the limit set by the National Agency of Drug and Food Control of the Republic of Indonesia (5 ppb). The high contamination of ochratoxin was found in pellets from Lampung (19 ppb). The fungi found to dominates the culture media and come from pellet feed were Aspergillus flavus and Aspergillus niger.","PeriodicalId":8566,"journal":{"name":"Asia-pacific Journal of Molecular Biology and Biotechnology","volume":"19 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78275826","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-06-28DOI: 10.35118/apjmbb.2021.029.3.03
S. Z. Abdullah, W. Tong, C. Leong, S. Rashid, Nur Amiera Syuhada Rozman, Nur Humaira Mohammad Hamid, S. Karim, Najua Delaila Tumin, S. A. Muda, Lily Suhaila Yacob
The increased incidence of food spoilage has exacerbated the need to enhance the protection of processed foods. Food packaging incorporated with bioactive components can be exploited to improve the security of food products from microbiological contamination. Thus, this study aimed to generate an alginate-based film loaded with cinnamaldehyde for use in food packaging. Aspergillus niger ATCC 9029 was utilised to assess the biodegradability of the film. The fungal growth on the plate with alginate film was evident after 21 days of incubation period and 29.7% of weight loss was monitored. The mechanical characterisation of the film indicated that the resulting film was sturdy and flexible. In the cinnamaldehyde release test, no burst release was observed. The release was slow and gradual. Out of 8 test microorganisms, only 6 microorganisms were inhibited by the film with cinnamaldehyde during the cross streak test. The growth inhibition test signified that there were 4 Gram-positive bacteria with 100% growth inhibition. The application of the film showed a notable reduction of bacterial load in the cooked rice. Besides, it exhibited 5.0-log suppression of bacterial growth, which relative to control. The results indicated that the alginate film incorporated with cinnamaldehyde could be potentially used as an eco-friendly food packaging material.
{"title":"Development of cinnamaldehyde loaded-alginate based film for food packaging","authors":"S. Z. Abdullah, W. Tong, C. Leong, S. Rashid, Nur Amiera Syuhada Rozman, Nur Humaira Mohammad Hamid, S. Karim, Najua Delaila Tumin, S. A. Muda, Lily Suhaila Yacob","doi":"10.35118/apjmbb.2021.029.3.03","DOIUrl":"https://doi.org/10.35118/apjmbb.2021.029.3.03","url":null,"abstract":"The increased incidence of food spoilage has exacerbated the need to enhance the protection of processed foods. Food packaging incorporated with bioactive components can be exploited to improve the security of food products from microbiological contamination. Thus, this study aimed to generate an alginate-based film loaded with cinnamaldehyde for use in food packaging. Aspergillus niger ATCC 9029 was utilised to assess the biodegradability of the film. The fungal growth on the plate with alginate film was evident after 21 days of incubation period and 29.7% of weight loss was monitored. The mechanical characterisation of the film indicated that the resulting film was sturdy and flexible. In the cinnamaldehyde release test, no burst release was observed. The release was slow and gradual. Out of 8 test microorganisms, only 6 microorganisms were inhibited by the film with cinnamaldehyde during the cross streak test. The growth inhibition test signified that there were 4 Gram-positive bacteria with 100% growth inhibition. The application of the film showed a notable reduction of bacterial load in the cooked rice. Besides, it exhibited 5.0-log suppression of bacterial growth, which relative to control. The results indicated that the alginate film incorporated with cinnamaldehyde could be potentially used as an eco-friendly food packaging material.","PeriodicalId":8566,"journal":{"name":"Asia-pacific Journal of Molecular Biology and Biotechnology","volume":"229 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77588423","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-06-26DOI: 10.35118/apjmbb.2021.029.3.07
E. Ali, Nurul Hamizah Hamidon, R. Issa
Tuberculosis (TB) is mainly caused by Mycobacterium tuberculosis (MTB) and remains as a key public health problem worldwide. Most of MTB clinical strains are resistant to rifampicin (RIF), the first-line anti-tuberculosis drug. RIF resistance to MTB is due to mutations that mainly found in RIF resistance-determining region (RRDR) in drug target gene, RNA polymerase β subunit (rpoB). Therefore, the aim of the study is to extend the identification of variants in rpoB gene and to elucidate the effect of variants to the RIF resistance. Four of the strains, MTBR1/09, MTBR2/09, MTBR3/09 and MTB221/11 were subjected to drug susceptibility test (DST). All of the strains sequenced and submitted to the National Center for Biotechnology Information Sequence Read Archive were analyzed to identify the variants in the rpoB gene. The identified new variants were then subjected to docking to examine the drug-protein interactions. DST analysis revealed MTBR1/09, MTBR2/09 and MTBR3/09 were resistant to the RIF drug, while MTB221/11 was a presumptive susceptible strain. Two new variants were observed, the deletion (Phe433_Met434delinsLeu in MTBR1/09) and missense (Lys37Arg in MTBR3/09) variants. Meanwhile, the His445Leu, Ser450Leu, Asp103Asp, Ala1075Ala were reported variants. Docking of RIF to MTBR1/09 and MTBR3/09 mutant models revealed the RIF bound to the RIF binding site at different binding affinity and conformation. Concurrently, the new variants caused the RIF to bind to the different active site and neighboring residues. Findings from DST and docking analyses indicate that new variants potentially disturb the RIF inhibition in RpoB mutant proteins, and thus might be responsible to cause the RIF resistance.
{"title":"In silico mutational analysis in RNA polymerase β subunit (rpoB) gene of rifampicin-resistant in Mycobacterium tuberculosis from Malaysia","authors":"E. Ali, Nurul Hamizah Hamidon, R. Issa","doi":"10.35118/apjmbb.2021.029.3.07","DOIUrl":"https://doi.org/10.35118/apjmbb.2021.029.3.07","url":null,"abstract":"Tuberculosis (TB) is mainly caused by Mycobacterium tuberculosis (MTB) and remains as a key public health problem worldwide. Most of MTB clinical strains are resistant to rifampicin (RIF), the first-line anti-tuberculosis drug. RIF resistance to MTB is due to mutations that mainly found in RIF resistance-determining region (RRDR) in drug target gene, RNA polymerase β subunit (rpoB). Therefore, the aim of the study is to extend the identification of variants in rpoB gene and to elucidate the effect of variants to the RIF resistance. Four of the strains, MTBR1/09, MTBR2/09, MTBR3/09 and MTB221/11 were subjected to drug susceptibility test (DST). All of the strains sequenced and submitted to the National Center for Biotechnology Information Sequence Read Archive were analyzed to identify the variants in the rpoB gene. The identified new variants were then subjected to docking to examine the drug-protein interactions. DST analysis revealed MTBR1/09, MTBR2/09 and MTBR3/09 were resistant to the RIF drug, while MTB221/11 was a presumptive susceptible strain. Two new variants were observed, the deletion (Phe433_Met434delinsLeu in MTBR1/09) and missense (Lys37Arg in MTBR3/09) variants. Meanwhile, the His445Leu, Ser450Leu, Asp103Asp, Ala1075Ala were reported variants. Docking of RIF to MTBR1/09 and MTBR3/09 mutant models revealed the RIF bound to the RIF binding site at different binding affinity and conformation. Concurrently, the new variants caused the RIF to bind to the different active site and neighboring residues. Findings from DST and docking analyses indicate that new variants potentially disturb the RIF inhibition in RpoB mutant proteins, and thus might be responsible to cause the RIF resistance.","PeriodicalId":8566,"journal":{"name":"Asia-pacific Journal of Molecular Biology and Biotechnology","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90105238","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-06-15DOI: 10.35118/APJMBB.2021.029.2.10
L. Vengidasan, Choong Soo Sin, Chen Kok Siong, K. Ibrahim
Acute lymphoblastic leukemia (ALL) is the most frequent cancer among children. Regardless of the advances in disease treatments, approximately 10-20 % of childhood ALL (cALL) have an incidence of relapse. Therefore, identification of additional prognostic variables is essential to provide specific therapeutic intervention for each patient. TERF2 is one of the main components of the shelterin complex (telosome) that plays a crucial role in the protective activity of telomeres. This research aims to investigate the expression level of TERF2 and its potential as a prognostic marker in cALL patients. 88 bone marrow samples and 6 peripheral blood were used to isolated cDNA samples. Real time PCR were used to study the gene expression of TERF2 in cALL. Results were standardized using B2M transcripts as an internal control. Relative quantification of the gene expression was calculated by using the delta-delta Ct method. TERF2 was up-regulated significantly in cALL patients compared to control samples of which p-value=0.002859, (p<0.05). Over-expression of TERF2 was observed in TEL-AML1 subgroup of which p-value=0.0002, (p<0.05). In contrast, under-expression of TERF2 was found in those having BCR-ABL1 fusion transcripts of which p-value=0.0221, (p<0.05). TERF2 also have found to have a better survival advantages for cALL patients. Over-expression of TERF2 is associated with good prognosis in cALL whilst under-expression is associated with poor prognosis in cALL patients. Measurement of TERF2 gene expression allows proper stratification of cALL subtypes into its respective prognostic indicator classification.
急性淋巴细胞白血病(ALL)是儿童中最常见的癌症。无论疾病治疗的进展如何，大约10- 20%的儿童ALL (cALL)有复发的发生率。因此，确定额外的预后变量对于为每位患者提供特定的治疗干预至关重要。TERF2是保护蛋白复合物(端粒)的主要成分之一，在端粒的保护活性中起着至关重要的作用。本研究旨在探讨TERF2的表达水平及其作为cALL患者预后指标的潜力。88份骨髓样本和6份外周血样本分离cDNA样本。采用Real - time PCR技术研究TERF2基因在cALL中的表达。使用B2M转录本作为内部控制对结果进行标准化。采用δ - δ Ct法计算基因表达的相对定量。与对照组相比，cALL患者中TERF2显著上调，p值=0.002859，(p<0.05)。TEL-AML1亚组中TERF2过表达，p值=0.0002，(p<0.05)。相比之下，TERF2在BCR-ABL1融合转录本中低表达，p值=0.0221，(p<0.05)。TERF2也被发现对cALL患者有更好的生存优势。TERF2过表达与cALL患者预后良好相关，而过表达与cALL患者预后不良相关。TERF2基因表达的测量允许将cALL亚型适当分层为其各自的预后指标分类。
{"title":"Expression of telomeric repeat binding factor 2 (TERF2) in childhood acute lymphoblastic leukemia","authors":"L. Vengidasan, Choong Soo Sin, Chen Kok Siong, K. Ibrahim","doi":"10.35118/APJMBB.2021.029.2.10","DOIUrl":"https://doi.org/10.35118/APJMBB.2021.029.2.10","url":null,"abstract":"Acute lymphoblastic leukemia (ALL) is the most frequent cancer among children. Regardless of the advances in disease treatments, approximately 10-20 % of childhood ALL (cALL) have an incidence of relapse. Therefore, identification of additional prognostic variables is essential to provide specific therapeutic intervention for each patient. TERF2 is one of the main components of the shelterin complex (telosome) that plays a crucial role in the protective activity of telomeres. This research aims to investigate the expression level of TERF2 and its potential as a prognostic marker in cALL patients. 88 bone marrow samples and 6 peripheral blood were used to isolated cDNA samples. Real time PCR were used to study the gene expression of TERF2 in cALL. Results were standardized using B2M transcripts as an internal control. Relative quantification of the gene expression was calculated by using the delta-delta Ct method. TERF2 was up-regulated significantly in cALL patients compared to control samples of which p-value=0.002859, (p<0.05). Over-expression of TERF2 was observed in TEL-AML1 subgroup of which p-value=0.0002, (p<0.05). In contrast, under-expression of TERF2 was found in those having BCR-ABL1 fusion transcripts of which p-value=0.0221, (p<0.05). TERF2 also have found to have a better survival advantages for cALL patients. Over-expression of TERF2 is associated with good prognosis in cALL whilst under-expression is associated with poor prognosis in cALL patients. Measurement of TERF2 gene expression allows proper stratification of cALL subtypes into its respective prognostic indicator classification.","PeriodicalId":8566,"journal":{"name":"Asia-pacific Journal of Molecular Biology and Biotechnology","volume":"1 1","pages":"98-106"},"PeriodicalIF":0.0,"publicationDate":"2021-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41795957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-06-08DOI: 10.35118/APJMBB.2021.029.2.07
Nneoma Confidence JeanStephanie Anyanwu, A. Suleiman, Elijah Ekah Ella, H. M. Kazeem, M. Aminu
Although mutation in the RAS genes has become important in the evaluation of haematologic malignancies worldwide, developing countries like Nigeria are yet to integrate it as a diagnostic tool and prognostic indicator for improved therapy. This study determined mutations in codons 12 and 13 of NRAS gene in blood donors and haematologic malignant individuals using multiplex (AS-PCR) and Sanger sequencing, thus highlighting the mutations as helpful diagnostic and prognostic tool. AS-PCR was used to selectively amplify mutation-specific synthetic oligonucleotides from the cfDNA of 100 study participants (50 cancer patients and 50 blood donors). Percentage mutation of 31.0% was seen in NRAS_G12D gene while NRAS_G13C had 17.0%. Twenty nine (29.0%) of the NRAS_G12D mutations were found in haematopoietic malignant patients and 2.0% were found in blood donors, while 15.0% of the NRAS_G13C were found in the malignant patients, confirming the occurrence of NRAS gene mutations in haematologic cancers and predominance of the G-A transition. The highest rate of mutation was observed in leukaemia patients, having a significant association with codon 13 (p = 0.042). Stages 3 and 2 cancers each had the highest mutation rates of NRAS_G12D and NRAS_G13C, revealing possible link between these mutations and susceptibility and progression of haematologic malignancies, which is higher in leukaemia. Further NRAS mutation studies and its role in other cancers are advocated, especially targeted towards ameliorating diagnosis and prognostic therapy. Challenges related to diagnosis and management of haematologic cancer continue to persist in developing countries like Nigeria. Thus, there is a need to go beyond studying the incidence and distribution pattern of these malignancies to capturing immunogenetic parameters of affected individuals.
{"title":"Mutations in two neuroblastoma rat sarcoma oncogenes are associated with progression of haematologic malignancies in Nigeria","authors":"Nneoma Confidence JeanStephanie Anyanwu, A. Suleiman, Elijah Ekah Ella, H. M. Kazeem, M. Aminu","doi":"10.35118/APJMBB.2021.029.2.07","DOIUrl":"https://doi.org/10.35118/APJMBB.2021.029.2.07","url":null,"abstract":"Although mutation in the RAS genes has become important in the evaluation of haematologic malignancies worldwide, developing countries like Nigeria are yet to integrate it as a diagnostic tool and prognostic indicator for improved therapy. This study determined mutations in codons 12 and 13 of NRAS gene in blood donors and haematologic malignant individuals using multiplex (AS-PCR) and Sanger sequencing, thus highlighting the mutations as helpful diagnostic and prognostic tool. AS-PCR was used to selectively amplify mutation-specific synthetic oligonucleotides from the cfDNA of 100 study participants (50 cancer patients and 50 blood donors). Percentage mutation of 31.0% was seen in NRAS_G12D gene while NRAS_G13C had 17.0%. Twenty nine (29.0%) of the NRAS_G12D mutations were found in haematopoietic malignant patients and 2.0% were found in blood donors, while 15.0% of the NRAS_G13C were found in the malignant patients, confirming the occurrence of NRAS gene mutations in haematologic cancers and predominance of the G-A transition. The highest rate of mutation was observed in leukaemia patients, having a significant association with codon 13 (p = 0.042). Stages 3 and 2 cancers each had the highest mutation rates of NRAS_G12D and NRAS_G13C, revealing possible link between these mutations and susceptibility and progression of haematologic malignancies, which is higher in leukaemia. Further NRAS mutation studies and its role in other cancers are advocated, especially targeted towards ameliorating diagnosis and prognostic therapy. Challenges related to diagnosis and management of haematologic cancer continue to persist in developing countries like Nigeria. Thus, there is a need to go beyond studying the incidence and distribution pattern of these malignancies to capturing immunogenetic parameters of affected individuals.","PeriodicalId":8566,"journal":{"name":"Asia-pacific Journal of Molecular Biology and Biotechnology","volume":"1 1","pages":"62-74"},"PeriodicalIF":0.0,"publicationDate":"2021-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42526559","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-06-08DOI: 10.35118/APJMBB.2021.029.2.05
Yuliana, U. Saepuloh, Suryani
Taq DNA polymerase is a thermostable enzyme widely used for DNA amplification in the PCR technique. It was initially characterized and isolated from thermophilic bacteria, Thermus aquaticus. It was difficult to developed in this enzyme using a native host system. Therefore, the development of the recombinant Taq DNA polymerase expressed using a synthetic gene is important to improve production efficiency. In this study, we developed the in house Taq DNA polymerase recombinant based on a codon-optimized using E. coli expression system. We cloned 2685 bp of the Taq DNA polymerase gene in the pET151/D-TOPO vector. The gene was synthesized and the expression was analyzed with SDS-PAGE technique which indicated with a 100.9 kDa specific target protein. The concentration and activity of this purified enzyme were 5.17 mg/mL and 4.647 U/µL, respectively. The application of this enzyme to the PCR technique showed that this enzyme could amplify the target genes from 200 bp to 3500 bp amplicons with a minimum DNA concentration template 10 ng/µL. This assumes that the in house recombinant Taq DNA polymerase based on synthetic genes is successfully expressed, purified, and was functional and comparable to the commercial Taq polymerase.
{"title":"Development of a recombinant Taq DNA polymerase enzyme expressed using a synthetic gene and its comparison with a commercial enzyme","authors":"Yuliana, U. Saepuloh, Suryani","doi":"10.35118/APJMBB.2021.029.2.05","DOIUrl":"https://doi.org/10.35118/APJMBB.2021.029.2.05","url":null,"abstract":"Taq DNA polymerase is a thermostable enzyme widely used for DNA amplification in the PCR technique. It was initially characterized and isolated from thermophilic bacteria, Thermus aquaticus. It was difficult to developed in this enzyme using a native host system. Therefore, the development of the recombinant Taq DNA polymerase expressed using a synthetic gene is important to improve production efficiency. In this study, we developed the in house Taq DNA polymerase recombinant based on a codon-optimized using E. coli expression system. We cloned 2685 bp of the Taq DNA polymerase gene in the pET151/D-TOPO vector. The gene was synthesized and the expression was analyzed with SDS-PAGE technique which indicated with a 100.9 kDa specific target protein. The concentration and activity of this purified enzyme were 5.17 mg/mL and 4.647 U/µL, respectively. The application of this enzyme to the PCR technique showed that this enzyme could amplify the target genes from 200 bp to 3500 bp amplicons with a minimum DNA concentration template 10 ng/µL. This assumes that the in house recombinant Taq DNA polymerase based on synthetic genes is successfully expressed, purified, and was functional and comparable to the commercial Taq polymerase.","PeriodicalId":8566,"journal":{"name":"Asia-pacific Journal of Molecular Biology and Biotechnology","volume":"1 1","pages":"43-50"},"PeriodicalIF":0.0,"publicationDate":"2021-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45270556","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-06-08DOI: 10.35118/APJMBB.2021.029.2.06
K. Swamy, N. Chandrashekar, R. Subramanian, S. Sukumaran, S. Chandra
Cerium oxide nanoparticle (CeO2NPs) has wide applications in pharmaceutical, biomedical and chemical industries. Albeit of their uses, bioavailability followed by toxicity of CeO2NPs in fresh water fishes, are yet to be understood in detail. In this evaluation, we have synthesized, characterized and assessed the biological effects (hematology, ionoregulatory, oxidative stress, histological and glutamate indices) of CeO2NPs at different doses (2.5mg/L and 25mg/L based on 1/10th LC50) on freshwater carps Cirrhinus mrigala, for short term exposure of 96 h. Impact of CeO2NPs at low concentration (2.5mg/L) confirmed a significant decrease in hematological parameters and also affecting serum Na+, Cl-, K+ levels along with gill Na+/K+-ATPase activity. The indicated variations oxidative stress enzymes superoxide dismutase, Catalase, glutathione peroxidase with relative elevation in lipid peroxidation (LPO) (22.47±0.198) compared to control groups. CeO2NPs at high concentration (25mg/L) revealed the alterations in neurotransmitter glutamate levels compared to control groups. Rise in glucose and decrease in plasma protein levels in response to both the concentrations was noted. Microscopic observations confirmed the tissue damages and alterations in gill architecture. By integrating all results obtained by short term exposure of juvenile carps to CeO2NPs at different doses, we reported nanoparticles have considerable deleterious effects on physiological and morphological condition of fishes.
{"title":"Cerium oxide nanoparticles induced physio-biochemical, neurochemical, and morphological responses in Cirrhinus mrigala during short term exposure","authors":"K. Swamy, N. Chandrashekar, R. Subramanian, S. Sukumaran, S. Chandra","doi":"10.35118/APJMBB.2021.029.2.06","DOIUrl":"https://doi.org/10.35118/APJMBB.2021.029.2.06","url":null,"abstract":"Cerium oxide nanoparticle (CeO2NPs) has wide applications in pharmaceutical, biomedical and chemical industries. Albeit of their uses, bioavailability followed by toxicity of CeO2NPs in fresh water fishes, are yet to be understood in detail. In this evaluation, we have synthesized, characterized and assessed the biological effects (hematology, ionoregulatory, oxidative stress, histological and glutamate indices) of CeO2NPs at different doses (2.5mg/L and 25mg/L based on 1/10th LC50) on freshwater carps Cirrhinus mrigala, for short term exposure of 96 h. Impact of CeO2NPs at low concentration (2.5mg/L) confirmed a significant decrease in hematological parameters and also affecting serum Na+, Cl-, K+ levels along with gill Na+/K+-ATPase activity. The indicated variations oxidative stress enzymes superoxide dismutase, Catalase, glutathione peroxidase with relative elevation in lipid peroxidation (LPO) (22.47±0.198) compared to control groups. CeO2NPs at high concentration (25mg/L) revealed the alterations in neurotransmitter glutamate levels compared to control groups. Rise in glucose and decrease in plasma protein levels in response to both the concentrations was noted. Microscopic observations confirmed the tissue damages and alterations in gill architecture. By integrating all results obtained by short term exposure of juvenile carps to CeO2NPs at different doses, we reported nanoparticles have considerable deleterious effects on physiological and morphological condition of fishes.","PeriodicalId":8566,"journal":{"name":"Asia-pacific Journal of Molecular Biology and Biotechnology","volume":"1 1","pages":"51-61"},"PeriodicalIF":0.0,"publicationDate":"2021-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43246323","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-06-08DOI: 10.35118/APJMBB.2021.029.2.08
M. Salih, A. Al-Assie, M. Sabbah
Short tandem repeats (STRs) have been recommended as the highest polymorphic loci among the humana DNA regions. Therefore, STRs are agreeable to many genetic fields like forensic, population genetics and anthropological studies. The main aim of this research is to evaluate the autosomal STRs in Tikrit city-Iraq, to expand the human genetics database and forensic genetics analysis. The DNA database was obtained from 306 unrelated volunteers from native Tikrit population-Iraq, using 15 autosomal STR loci. The current study determined the allele frequencies in the Tikrit population and then compared them with other national Iraqi populations as well as with populations in the Middle East, Africa, and Europe. The highest level of heterozygosity was observed in D8S1179 and TH01 loci (0.797), while the less level was shown by CSF1PO (0.48). The departure from HWE Equilibrium was recorded in only 3 STR loci from a total of 15 loci analyzed (p<0.003). The Combined Match Probability (CMP) for 15 autosomal STR was 1 in 7.89208×10-19 and the Combined Discrimination Power (CDP) was 0.9999999997. The discrimination power (DP) was especially high in D2S1338, D18S51, D19S433 and D21S11. Based on the results observed in a Dendrogram, Tikrit population was clustered with other populations, likely reflecting the historical and geographical factors. D2S1338, D18S51, D19S433 and D21S11 markers were recognized as suitable for forensic genetics analysis in Tikrit population. Also, the 15 STRs markers provide information for the studies of genetic distances between the current study and other included populations to be compared with this study.
{"title":"Analysis of allele frequencies of the selected 15 autosomal STR markers in Tikrit population – Iraq with comparison to Middle Eastern, African, and Europeans","authors":"M. Salih, A. Al-Assie, M. Sabbah","doi":"10.35118/APJMBB.2021.029.2.08","DOIUrl":"https://doi.org/10.35118/APJMBB.2021.029.2.08","url":null,"abstract":"Short tandem repeats (STRs) have been recommended as the highest polymorphic loci among the humana DNA regions. Therefore, STRs are agreeable to many genetic fields like forensic, population genetics and anthropological studies. The main aim of this research is to evaluate the autosomal STRs in Tikrit city-Iraq, to expand the human genetics database and forensic genetics analysis. The DNA database was obtained from 306 unrelated volunteers from native Tikrit population-Iraq, using 15 autosomal STR loci. The current study determined the allele frequencies in the Tikrit population and then compared them with other national Iraqi populations as well as with populations in the Middle East, Africa, and Europe. The highest level of heterozygosity was observed in D8S1179 and TH01 loci (0.797), while the less level was shown by CSF1PO (0.48). The departure from HWE Equilibrium was recorded in only 3 STR loci from a total of 15 loci analyzed (p<0.003). The Combined Match Probability (CMP) for 15 autosomal STR was 1 in 7.89208×10-19 and the Combined Discrimination Power (CDP) was 0.9999999997. The discrimination power (DP) was especially high in D2S1338, D18S51, D19S433 and D21S11. Based on the results observed in a Dendrogram, Tikrit population was clustered with other populations, likely reflecting the historical and geographical factors. D2S1338, D18S51, D19S433 and D21S11 markers were recognized as suitable for forensic genetics analysis in Tikrit population. Also, the 15 STRs markers provide information for the studies of genetic distances between the current study and other included populations to be compared with this study.","PeriodicalId":8566,"journal":{"name":"Asia-pacific Journal of Molecular Biology and Biotechnology","volume":"1 1","pages":"75-84"},"PeriodicalIF":0.0,"publicationDate":"2021-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41937634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-06-08DOI: 10.35118/APJMBB.2021.029.2.09
Vandana Nandal, Manu Solanki
Wheat (Triticum aestivum) is a major cereal crop grown worldwide. Most of the world population depends on wheat for their nutrient requirement. Zinc (Zn) is one of the most crucial elements required for the development of wheat plant. It is one of the micronutrients required in many biochemical cycles. It has been found that the concentration of Zn is below the required level in the soil and hence it remains deficient in the crops. To ameliorate the deficit, chemical fertilizers are added in the soil, where as biofertilizers are preferred over chemicals in sustainable agriculture. The paper describes the isolation, screening and molecular characterization of the zinc solubilizing bacteria (ZSB) to improve plant growth. A total of 100 soil samples were collected from the rhizospheric soil of wheat plants. ZSB were isolated by dilution plating on Bunt and Rovira media. The 50 isolates were selected and screened for their Zn solubilization. The zinc tolerance of all the isolates varied from 0.5% to 2% of insoluble Zn. Based on the Zn tolerance ability, 15 bacterial isolates were screened for Phosphate solubilization and further analyzed for the synthesis of IAA, NH3, siderophore production and chitinase activity. The three isolates were selected on the basis of the plant growth promoting characteristics for molecular characterization and were found to be homologous to Bacillus cereus, Pseudomonas aeruginosa and Bacillus tropicus. This study documented the establishment and survival of ZSB in the wheat rhizosphere and enhanced plant productivity, thus indicating the potential of isolates as commercial biofertilizers.
{"title":"Isolation screening and molecular characterization of zinc solubilizing bacteria and their effect on the growth of wheat (Triticum aestivum)","authors":"Vandana Nandal, Manu Solanki","doi":"10.35118/APJMBB.2021.029.2.09","DOIUrl":"https://doi.org/10.35118/APJMBB.2021.029.2.09","url":null,"abstract":"Wheat (Triticum aestivum) is a major cereal crop grown worldwide. Most of the world population depends on wheat for their nutrient requirement. Zinc (Zn) is one of the most crucial elements required for the development of wheat plant. It is one of the micronutrients required in many biochemical cycles. It has been found that the concentration of Zn is below the required level in the soil and hence it remains deficient in the crops. To ameliorate the deficit, chemical fertilizers are added in the soil, where as biofertilizers are preferred over chemicals in sustainable agriculture. The paper describes the isolation, screening and molecular characterization of the zinc solubilizing bacteria (ZSB) to improve plant growth. A total of 100 soil samples were collected from the rhizospheric soil of wheat plants. ZSB were isolated by dilution plating on Bunt and Rovira media. The 50 isolates were selected and screened for their Zn solubilization. The zinc tolerance of all the isolates varied from 0.5% to 2% of insoluble Zn. Based on the Zn tolerance ability, 15 bacterial isolates were screened for Phosphate solubilization and further analyzed for the synthesis of IAA, NH3, siderophore production and chitinase activity. The three isolates were selected on the basis of the plant growth promoting characteristics for molecular characterization and were found to be homologous to Bacillus cereus, Pseudomonas aeruginosa and Bacillus tropicus. This study documented the establishment and survival of ZSB in the wheat rhizosphere and enhanced plant productivity, thus indicating the potential of isolates as commercial biofertilizers.","PeriodicalId":8566,"journal":{"name":"Asia-pacific Journal of Molecular Biology and Biotechnology","volume":"1 1","pages":"85-97"},"PeriodicalIF":0.0,"publicationDate":"2021-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48431519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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