Pub Date : 2022-07-06DOI: 10.35118/apjmbb.2022.030.3.02
M. Al-Zubaidi, R. Ameen, Reem Husam Al-Tabra, Ban Ameen
Specialized class of short tandem repeats located on human Y (male) chromosomes called Y-chromosome short tandem repeats (Y-STRs) are transferred from one generation to the next with unchanged (barring a mutation). Also, these loci have high discriminatory capacities among individuals of the same population or ethnicity due to the non-recombining nature of it. Peripheral blood sample from 160 unrelated Iraqi males in Baghdad are collected and DNA was extracted from it. Amplification of 23 Y-STR markers (DYS576, DYS3891, DYS448, DYS389II ,DYS19, DYS481, DYS549, DYS533, DYS438, DYS437, DYS570, DYS635, DYS390, DYS439, DYS392, DYS643, DYS393, DYS458a/b, DYS456 and YGATAH4) was performed using PowerPlex Y 23 System (Promega Corporation), PCR amplicons were analyzed on 4-capillary ABI Prism® 3100 Genetic Analyzer. Collected data were analyzed and haplotypes were obtained using Gene Mapper ID-X software version 1.4 (Applied Biosystems). Results indicated that the most polymorphic loci were DYS385a/b with 43 alleles and The GD value was 0.929, while 4 alleles at the DYS576 and DYS391, with the genetic diversity of 0.459 and 0.480 respectively. At the loci DYS570 and DYS458 the allele frequency were 10 and 12 alleles with a genetic diversity 0.780 and 0.844 respectively. Gene diversity values for the South of Iraq males ranged from 0.447 to 0.844. The highest GD was detected at DYS458loci with a value of 0.856 and the lowest GD at DYS448 locus with a value of 0.447, 143 Haplotype was identified, 130 (81, 25%) as a unique Haplotype and 13 (18, 75%) as replicated haplotype among individuals. The highest haplotype were found in sample H19, H43, H72 and H122 at frequency 0.01875, While 130 haplotype with 0.00625 frequency and haplotype diversity was 0.99835 with a discrimination capacity 0.91. The study revealed that the loci under study and the used kit are suitable for use in identification, discrimination and forensic applications in the Iraqi population.
{"title":"Estimation of allele and haplotype frequencies for 23 YSTR markers of Iraqi populations in Baghdad","authors":"M. Al-Zubaidi, R. Ameen, Reem Husam Al-Tabra, Ban Ameen","doi":"10.35118/apjmbb.2022.030.3.02","DOIUrl":"https://doi.org/10.35118/apjmbb.2022.030.3.02","url":null,"abstract":"Specialized class of short tandem repeats located on human Y (male) chromosomes called Y-chromosome short tandem repeats (Y-STRs) are transferred from one generation to the next with unchanged (barring a mutation). Also, these loci have high discriminatory capacities among individuals of the same population or ethnicity due to the non-recombining nature of it. Peripheral blood sample from 160 unrelated Iraqi males in Baghdad are collected and DNA was extracted from it. Amplification of 23 Y-STR markers (DYS576, DYS3891, DYS448, DYS389II ,DYS19, DYS481, DYS549, DYS533, DYS438, DYS437, DYS570, DYS635, DYS390, DYS439, DYS392, DYS643, DYS393, DYS458a/b, DYS456 and YGATAH4) was performed using PowerPlex Y 23 System (Promega Corporation), PCR amplicons were analyzed on 4-capillary ABI Prism® 3100 Genetic Analyzer. Collected data were analyzed and haplotypes were obtained using Gene Mapper ID-X software version 1.4 (Applied Biosystems). Results indicated that the most polymorphic loci were DYS385a/b with 43 alleles and The GD value was 0.929, while 4 alleles at the DYS576 and DYS391, with the genetic diversity of 0.459 and 0.480 respectively. At the loci DYS570 and DYS458 the allele frequency were 10 and 12 alleles with a genetic diversity 0.780 and 0.844 respectively. Gene diversity values for the South of Iraq males ranged from 0.447 to 0.844. The highest GD was detected at DYS458loci with a value of 0.856 and the lowest GD at DYS448 locus with a value of 0.447, 143 Haplotype was identified, 130 (81, 25%) as a unique Haplotype and 13 (18, 75%) as replicated haplotype among individuals. The highest haplotype were found in sample H19, H43, H72 and H122 at frequency 0.01875, While 130 haplotype with 0.00625 frequency and haplotype diversity was 0.99835 with a discrimination capacity 0.91. The study revealed that the loci under study and the used kit are suitable for use in identification, discrimination and forensic applications in the Iraqi population.","PeriodicalId":8566,"journal":{"name":"Asia-pacific Journal of Molecular Biology and Biotechnology","volume":"34 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78170266","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 : 2022-06-30DOI: 10.35118/apjmbb.2022.030.2.07
Umaiyal Munusamy, Zailani Khuzaimah, S. Kong, S. Abdullah
Phosphate is an important macronutrient essential for various enzymatic reactions, biological processes and biosynthesis of different compounds in plants. There are multiple factors affecting phosphate uptake such as crop physiology, soil structure and texture, plantation management and environmental conditions. There is no specific solution that can be employed for better phosphate uptake by plants but clearly, sustainable agriculture management facilitated by precision crop assessment could be an effective solution. The ability for a better phosphate uptake by plants and that information will ensure the success of small and big scale farmers role in securing the demand for food by the growing population. Therefore, various approach has been taken to identify the phosphate uptake hence with the help of digitalization, we believe there will be innovated phosphate uptake studies compared to how these were previously carried out. In the next decade, more phosphate uptake information data with seamless accessibility will be available to various users. However, data alone will not be able to produce anything, analysis and advisory services are required in helping farmers to use and apply those obtained information for subsequent application in the field. Software applications with advance machine learning will customized the interactions between devices and data for the user. As they interact, they provide an untapped opportunity for better farm decision-making in real time. In this review, we will discuss how digitalization has improved to change the overall plant phosphate uptake studies and by what means the generated information can be efficiently utilized by the farmers and the various stakeholders.
{"title":"Progression in plant phosphate uptake studies","authors":"Umaiyal Munusamy, Zailani Khuzaimah, S. Kong, S. Abdullah","doi":"10.35118/apjmbb.2022.030.2.07","DOIUrl":"https://doi.org/10.35118/apjmbb.2022.030.2.07","url":null,"abstract":"Phosphate is an important macronutrient essential for various enzymatic reactions, biological processes and biosynthesis of different compounds in plants. There are multiple factors affecting phosphate uptake such as crop physiology, soil structure and texture, plantation management and environmental conditions. There is no specific solution that can be employed for better phosphate uptake by plants but clearly, sustainable agriculture management facilitated by precision crop assessment could be an effective solution. The ability for a better phosphate uptake by plants and that information will ensure the success of small and big scale farmers role in securing the demand for food by the growing population. Therefore, various approach has been taken to identify the phosphate uptake hence with the help of digitalization, we believe there will be innovated phosphate uptake studies compared to how these were previously carried out. In the next decade, more phosphate uptake information data with seamless accessibility will be available to various users. However, data alone will not be able to produce anything, analysis and advisory services are required in helping farmers to use and apply those obtained information for subsequent application in the field. Software applications with advance machine learning will customized the interactions between devices and data for the user. As they interact, they provide an untapped opportunity for better farm decision-making in real time. In this review, we will discuss how digitalization has improved to change the overall plant phosphate uptake studies and by what means the generated information can be efficiently utilized by the farmers and the various stakeholders.","PeriodicalId":8566,"journal":{"name":"Asia-pacific Journal of Molecular Biology and Biotechnology","volume":"91 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78074901","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 : 2022-06-30DOI: 10.35118/apjmbb.2022.030.2.08
Nur Adila Muradi, Dayang Salwani Awang Adeni, N. Suhaili
Bioethanol fermentation under very high gravity (VHG) conditions by using sago hampas hydrolysate (SHH) supplemented with yeast extract as a fermentation medium has resulted in an incomplete metabolism of glucose, leading to relatively low bioethanol production in comparison to the theoretical titre. Therefore, additional supplementation of the fermentation medium is necessary to increase the yeast tolerance towards inhibitors and high concentration of glucose and bioethanol. This work investigates the effect of supplementing SHH media with various nutrients on bioethanol fermentation under VHG conditions. The nutrients included magnesium sulphate (0.12 g/L), urea (3 g/L), glutamic acid (5 g/L), and peptone (5 g/L). Our results showed that culture supplemented with peptone has significantly improved the yeast growth by 0.9-fold and glucose consumption efficiency by 10% compared to the control cultures. Besides that, the media formulation has also increased bioethanol production by 13%, with a maximum concentration of 126.20 ± 3.0 g/L. In general, the results suggest an improved formulation of fermentation medium consisting of SHH for bioethanol production under VHG conditions. These results will provide useful insights into the development of bioethanol production from sago-based feedstock in the future.
{"title":"Effect of medium supplementation on very high gravity bioethanol fermentation using sago hampas hydrolysate as a feedstock","authors":"Nur Adila Muradi, Dayang Salwani Awang Adeni, N. Suhaili","doi":"10.35118/apjmbb.2022.030.2.08","DOIUrl":"https://doi.org/10.35118/apjmbb.2022.030.2.08","url":null,"abstract":"Bioethanol fermentation under very high gravity (VHG) conditions by using sago hampas hydrolysate (SHH) supplemented with yeast extract as a fermentation medium has resulted in an incomplete metabolism of glucose, leading to relatively low bioethanol production in comparison to the theoretical titre. Therefore, additional supplementation of the fermentation medium is necessary to increase the yeast tolerance towards inhibitors and high concentration of glucose and bioethanol. This work investigates the effect of supplementing SHH media with various nutrients on bioethanol fermentation under VHG conditions. The nutrients included magnesium sulphate (0.12 g/L), urea (3 g/L), glutamic acid (5 g/L), and peptone (5 g/L). Our results showed that culture supplemented with peptone has significantly improved the yeast growth by 0.9-fold and glucose consumption efficiency by 10% compared to the control cultures. Besides that, the media formulation has also increased bioethanol production by 13%, with a maximum concentration of 126.20 ± 3.0 g/L. In general, the results suggest an improved formulation of fermentation medium consisting of SHH for bioethanol production under VHG conditions. These results will provide useful insights into the development of bioethanol production from sago-based feedstock in the future.","PeriodicalId":8566,"journal":{"name":"Asia-pacific Journal of Molecular Biology and Biotechnology","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89452775","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 : 2022-06-27DOI: 10.35118/apjmbb.2022.030.2.06
J. Ng, Zhi Xuan Low, L. Alessandro, Jung Yin Fong, Au Yong, Minn-E Ng, Michelle Yee Mun Teo, Hokchai Yam, L. L. In
One of the drivers for early carcinogenesis involves specific somatic point substitution mutations in the KRAS gene which damages its ability to conduct signal transduction. Although antibodies can be used for the targeting of KRAS antigen, their localization along the cell’s inner membrane serves as a barrier against the accessibility of the antibodies. This study describes the evaluation of two internalization strategies, namely the endocytosis-based cell penetrating peptide (CPP) approach and the adenoviral-based intrabody (IB) approach, for the delivery of an anti-mutant KRAS single-chain variable fragment (scFv) into the cell. Splicing by overhang extension polymerase chain reaction (SOE-PCR) was used for the fusion of scFv with an enhanced green fluorescence protein (eGFP) and Antennapedia-PTD (Antp), a cell penetrating signal peptide. The fused construct (Antp-scFv-eGFP) at a concentration of 0.085 mg/ml was expressed in E. coli (BL21), while recombinant adenoviral particles containing the scFv-eGFP gene were harvested from HEK 293 cells. Both SW480 and HeLa cells were treated with Antp-scFv-eGFP and recombinant adenoviral particles, and their eGFP localization and intensity were compared to determine their scFv binding efficiencies. The IB approach was shown to exhibit a 3-fold higher fluorescence signal intensity compared to the CPP approach. This proof-of-concept study demonstrated that both antigens for either screening, diagnostic approaches can be potentially adopted when targeting various intracellular or therapeutic purposes.
{"title":"Recombinant cell penetrating peptides and intrabodies targeting membrane-bound mutated KRAS antigens","authors":"J. Ng, Zhi Xuan Low, L. Alessandro, Jung Yin Fong, Au Yong, Minn-E Ng, Michelle Yee Mun Teo, Hokchai Yam, L. L. In","doi":"10.35118/apjmbb.2022.030.2.06","DOIUrl":"https://doi.org/10.35118/apjmbb.2022.030.2.06","url":null,"abstract":"One of the drivers for early carcinogenesis involves specific somatic point substitution mutations in the KRAS gene which damages its ability to conduct signal transduction. Although antibodies can be used for the targeting of KRAS antigen, their localization along the cell’s inner membrane serves as a barrier against the accessibility of the antibodies. This study describes the evaluation of two internalization strategies, namely the endocytosis-based cell penetrating peptide (CPP) approach and the adenoviral-based intrabody (IB) approach, for the delivery of an anti-mutant KRAS single-chain variable fragment (scFv) into the cell. Splicing by overhang extension polymerase chain reaction (SOE-PCR) was used for the fusion of scFv with an enhanced green fluorescence protein (eGFP) and Antennapedia-PTD (Antp), a cell penetrating signal peptide. The fused construct (Antp-scFv-eGFP) at a concentration of 0.085 mg/ml was expressed in E. coli (BL21), while recombinant adenoviral particles containing the scFv-eGFP gene were harvested from HEK 293 cells. Both SW480 and HeLa cells were treated with Antp-scFv-eGFP and recombinant adenoviral particles, and their eGFP localization and intensity were compared to determine their scFv binding efficiencies. The IB approach was shown to exhibit a 3-fold higher fluorescence signal intensity compared to the CPP approach. This proof-of-concept study demonstrated that both antigens for either screening, diagnostic approaches can be potentially adopted when targeting various intracellular or therapeutic purposes.","PeriodicalId":8566,"journal":{"name":"Asia-pacific Journal of Molecular Biology and Biotechnology","volume":"109 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85702401","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 : 2022-06-22DOI: 10.35118/apjmbb.2022.030.2.05
Michelle Ngassy Mering, M. H. Bolhassan, D. S. Awg-Adeni
In Malaysia, sawdust is widely used as a substrate for the cultivation of grey oyster mushrooms (Pleurotus sajor-caju). Due to the scarcity and increasing cost of sawdust, this research investigated the feasibility of employing sago hampas as an alternative substrate for the cultivation of P. sajor-caju. In Sarawak, sago hampas were discarded into the river together with wastewater or incinerated, causing water and air pollution. In this study, P. sajor-caju was grown in five different formulations which are 100% sawdust (100SD) as control, 100% sago hampas (100SH), 75% sawdust + 25% sago hampas (75SD:25SH), 50% sawdust + 50% sago hampas (50SD:50SH), and 25% sawdust + 75% sago hampas (25SD:75SH). The substrate was mixed with rice bran and calcium carbonate at a dry matter basis in the ratio of 100:10:1. For the biological efficiency, 50SD:50SH recorded the highest yield (115.07%) compared to singular substrate 100SD (19.52%) and 100SH (37.04%). The higher lignin content and moisture-holding capacity in 100SD might not give better physical characteristics of P. sajor-caju. At the end of the study, supplementation sawdust with sago hampas especially formulation 50SD:50SH is recommended as the best formulation to reduce sawdust and utilise sago hampas as an alternative substrate for P. sajor-caju.
{"title":"The physical characteristics and yield of grey oyster mushroom (Pleurotus sajor-caju) cultivated on sawdust and sago hampas as substrate","authors":"Michelle Ngassy Mering, M. H. Bolhassan, D. S. Awg-Adeni","doi":"10.35118/apjmbb.2022.030.2.05","DOIUrl":"https://doi.org/10.35118/apjmbb.2022.030.2.05","url":null,"abstract":"In Malaysia, sawdust is widely used as a substrate for the cultivation of grey oyster mushrooms (Pleurotus sajor-caju). Due to the scarcity and increasing cost of sawdust, this research investigated the feasibility of employing sago hampas as an alternative substrate for the cultivation of P. sajor-caju. In Sarawak, sago hampas were discarded into the river together with wastewater or incinerated, causing water and air pollution. In this study, P. sajor-caju was grown in five different formulations which are 100% sawdust (100SD) as control, 100% sago hampas (100SH), 75% sawdust + 25% sago hampas (75SD:25SH), 50% sawdust + 50% sago hampas (50SD:50SH), and 25% sawdust + 75% sago hampas (25SD:75SH). The substrate was mixed with rice bran and calcium carbonate at a dry matter basis in the ratio of 100:10:1. For the biological efficiency, 50SD:50SH recorded the highest yield (115.07%) compared to singular substrate 100SD (19.52%) and 100SH (37.04%). The higher lignin content and moisture-holding capacity in 100SD might not give better physical characteristics of P. sajor-caju. At the end of the study, supplementation sawdust with sago hampas especially formulation 50SD:50SH is recommended as the best formulation to reduce sawdust and utilise sago hampas as an alternative substrate for P. sajor-caju.","PeriodicalId":8566,"journal":{"name":"Asia-pacific Journal of Molecular Biology and Biotechnology","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91054007","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 : 2022-06-22DOI: 10.35118/apjmbb.2022.030.2.03
May Naji Alkhanaq, Ghadeer Thamer Al-Hadidi
Cryptosporidium is a coccidian protozoan parasite infecting alimentary system and epithelial respiratory tract of humans and a wide range of vertebrates such as mammals, birds, reptiles, and fish. This study was carried out in Al-Kut city, Iraq, in two major hospitals: Al-Kut Hospital for Gynecology, Obstetric and Pediatric and Al-Karama Teaching Hospital, which included collection of stool samples from diarrheal patients. 96 stool samples taken from patients with different ages and both genders were examined by multiplex PCR technique. The results showed that the percentage of Cryptosporidium spp. infection was 39.6% and 4.2% for C. parvum and C. hominis, respectively. There are no statistically significant associates between gender and Cryptosporidium infection. The higher infection for C. parvum (41.2%) appeared in females, while the higher infection for C. hominis was found in male (4.8%). The study showed that the percentage of C. parvum infection in the rural areas is more than the urban, where the percentage in rural areas (52.9%) showed a significant difference at p = 0.004, while the infection rate for C. hominis was 6.7% in urban area. Regarding the water source, higher cryptosporidiosis rate was found in participants who used bottled water than in those who used tap water, and there is statistical significant between C. parvum infection and water source (p = 0.03), while the high infection in individuals who used bottled water were 58%. The present study aimed to determine the common Cryptosporidium species in diarrhea samples.
{"title":"Molecular study of Cryptosporidium spp. among diarrheal patients at Wasit province, Iraq","authors":"May Naji Alkhanaq, Ghadeer Thamer Al-Hadidi","doi":"10.35118/apjmbb.2022.030.2.03","DOIUrl":"https://doi.org/10.35118/apjmbb.2022.030.2.03","url":null,"abstract":"Cryptosporidium is a coccidian protozoan parasite infecting alimentary system and epithelial respiratory tract of humans and a wide range of vertebrates such as mammals, birds, reptiles, and fish. This study was carried out in Al-Kut city, Iraq, in two major hospitals: Al-Kut Hospital for Gynecology, Obstetric and Pediatric and Al-Karama Teaching Hospital, which included collection of stool samples from diarrheal patients. 96 stool samples taken from patients with different ages and both genders were examined by multiplex PCR technique. The results showed that the percentage of Cryptosporidium spp. infection was 39.6% and 4.2% for C. parvum and C. hominis, respectively. There are no statistically significant associates between gender and Cryptosporidium infection. The higher infection for C. parvum (41.2%) appeared in females, while the higher infection for C. hominis was found in male (4.8%). The study showed that the percentage of C. parvum infection in the rural areas is more than the urban, where the percentage in rural areas (52.9%) showed a significant difference at p = 0.004, while the infection rate for C. hominis was 6.7% in urban area. Regarding the water source, higher cryptosporidiosis rate was found in participants who used bottled water than in those who used tap water, and there is statistical significant between C. parvum infection and water source (p = 0.03), while the high infection in individuals who used bottled water were 58%. The present study aimed to determine the common Cryptosporidium species in diarrhea samples.","PeriodicalId":8566,"journal":{"name":"Asia-pacific Journal of Molecular Biology and Biotechnology","volume":"20 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85370675","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 : 2022-06-22DOI: 10.35118/apjmbb.2022.030.2.04
D. Kingsley, J. Abraham
This study is undertaken to prove the antimicrobial potential of the methanolic extracts of the seeds of cowpea (Vigna unguiculata) for the antimicrobial assay and biochemical characterization. The knowledge about the type of compound and its nature were obtained using characterizations including UV-Visible analysis and GC-MS. The extracts of cowpea displayed a zone of inhibition which is 13-17 mm, against Staphylococcus aureus being the most sensitive. Thin-layer chromatography, GC-MS and UV-Vis results showed the presence of methyl esters in higher amounts in the extracts with small amounts of sterols, suggesting that methyl esters can be the cause of the biological activity seen in the present work. SwissADME tool helped in screening the absorption, distribution, metabolism and excretion parameters of the identified phytoligands. Molecular docking results were following the in vitro studies performed. Protein-ligand docking using AutoDock 4.0 software was used for the validation of the wet-lab results. Binding energies were calculated for each ligand and its interaction with amino acids in the active site of the target protein. Among all the ligands tested 9-Octadecenoic Acid has emerged most promising against DNA topoisomerase of Staphylococcus aureus. The molecular dynamic simulation was also done to access the stability of the docked complex concerning temperature, hydrogen bonds, and hydrophobic interactions. Cowpea could be used as an effective antimicrobial agent in human welfare.
{"title":"Molecular docking and simulation studies to prove the antimicrobial property of cowpea extract","authors":"D. Kingsley, J. Abraham","doi":"10.35118/apjmbb.2022.030.2.04","DOIUrl":"https://doi.org/10.35118/apjmbb.2022.030.2.04","url":null,"abstract":"This study is undertaken to prove the antimicrobial potential of the methanolic extracts of the seeds of cowpea (Vigna unguiculata) for the antimicrobial assay and biochemical characterization. The knowledge about the type of compound and its nature were obtained using characterizations including UV-Visible analysis and GC-MS. The extracts of cowpea displayed a zone of inhibition which is 13-17 mm, against Staphylococcus aureus being the most sensitive. Thin-layer chromatography, GC-MS and UV-Vis results showed the presence of methyl esters in higher amounts in the extracts with small amounts of sterols, suggesting that methyl esters can be the cause of the biological activity seen in the present work. SwissADME tool helped in screening the absorption, distribution, metabolism and excretion parameters of the identified phytoligands. Molecular docking results were following the in vitro studies performed. Protein-ligand docking using AutoDock 4.0 software was used for the validation of the wet-lab results. Binding energies were calculated for each ligand and its interaction with amino acids in the active site of the target protein. Among all the ligands tested 9-Octadecenoic Acid has emerged most promising against DNA topoisomerase of Staphylococcus aureus. The molecular dynamic simulation was also done to access the stability of the docked complex concerning temperature, hydrogen bonds, and hydrophobic interactions. Cowpea could be used as an effective antimicrobial agent in human welfare.","PeriodicalId":8566,"journal":{"name":"Asia-pacific Journal of Molecular Biology and Biotechnology","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81835148","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 : 2022-06-08DOI: 10.35118/apjmbb.2022.030.2.02
Rahayu Dian Eka Putri, Y. S. Pradana, M. Koerniawan, L. T. Suwanti, U. J. Siregar, A. Budiman, E. Suyono
Chlorella vulgaris and Dunaliella sp. are prominent microalgae that are generally used for natural pigment stocks. These species have been established as producer of valuable bio compounds such as chlorophyll, carotenoids, and astaxanthin. For this research, C. vulgaris and Dunaliella sp. were cultivated in mixed culture under nitrogen stress treatments. Total four treatments at distinct nitrate concentrations of 0.012, 0.025, 0.5 NaNO3 g/L, respectively including nitrogen starvation was incorporated in this study. Nitrogen limitation and nitrogen starvation are widely used techniques to manipulate metabolic pathways into secondary pigments biosynthesis in microalgae cells. In addition, spectrophotometric measurement was conducted to investigate every single pigment content in all four treatments of distinct nitrogen concentrations for 14 days. The highest chlorophyll-a (23.65 mg/L), chlorophyll-b (10.02 mg/L), and total carotenoids (7.61 mg/L) were obtained from mixed culture with a concentration of 0.025 g/L NaNO3 in the last period cultivation. Conversely, the highest content of astaxanthin (0.6 mg/L) in mixed culture of C. vulgaris and Dunaliella sp. in the last period cultivation was achieved from starvation of nitrogen as well. The microalgae demonstrated robust growth in the presence of diverse bacterial community in the culture. It is well known that microalgae are associated with the microbiota on its phycosphere biofilm. Yet, it is unclear which specific bacteria taxa have a role in supporting or inhibiting microalgae growth.
{"title":"Effect of distinct nitrate concentrations on pigment content of mixed culture of Chlorella vulgaris and Dunaliella sp.","authors":"Rahayu Dian Eka Putri, Y. S. Pradana, M. Koerniawan, L. T. Suwanti, U. J. Siregar, A. Budiman, E. Suyono","doi":"10.35118/apjmbb.2022.030.2.02","DOIUrl":"https://doi.org/10.35118/apjmbb.2022.030.2.02","url":null,"abstract":"Chlorella vulgaris and Dunaliella sp. are prominent microalgae that are generally used for natural pigment stocks. These species have been established as producer of valuable bio compounds such as chlorophyll, carotenoids, and astaxanthin. For this research, C. vulgaris and Dunaliella sp. were cultivated in mixed culture under nitrogen stress treatments. Total four treatments at distinct nitrate concentrations of 0.012, 0.025, 0.5 NaNO3 g/L, respectively including nitrogen starvation was incorporated in this study. Nitrogen limitation and nitrogen starvation are widely used techniques to manipulate metabolic pathways into secondary pigments biosynthesis in microalgae cells. In addition, spectrophotometric measurement was conducted to investigate every single pigment content in all four treatments of distinct nitrogen concentrations for 14 days. The highest chlorophyll-a (23.65 mg/L), chlorophyll-b (10.02 mg/L), and total carotenoids (7.61 mg/L) were obtained from mixed culture with a concentration of 0.025 g/L NaNO3 in the last period cultivation. Conversely, the highest content of astaxanthin (0.6 mg/L) in mixed culture of C. vulgaris and Dunaliella sp. in the last period cultivation was achieved from starvation of nitrogen as well. The microalgae demonstrated robust growth in the presence of diverse bacterial community in the culture. It is well known that microalgae are associated with the microbiota on its phycosphere biofilm. Yet, it is unclear which specific bacteria taxa have a role in supporting or inhibiting microalgae growth.","PeriodicalId":8566,"journal":{"name":"Asia-pacific Journal of Molecular Biology and Biotechnology","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85448356","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 : 2022-05-23DOI: 10.35118/apjmbb.2022.030.2.01
Mirushan Arunasalam, Vivian Chong, Sharanya Ranee Mareshvaran, Venessa Ngui Fern Yee, A. Gaurav, S. Salvamani, C. S. Lim, B. Gunasekaran
Dysregulation of the metabolic pathways is fundamental to cancer formation. The differential expression and activation of de novo fatty acid synthase (FASN) and lipogenesis enzymes ATP citrate lyase (ACLY) have been observed in various cancer types making them a promising metabolic target in cancer therapy. Natural products (NP) are a major contributor to the development of novel non-toxic anti-tumour drugs with greater efficiency. An attempt has been made in this study to identify potent orally active ACLY and FASN inhibitors from Universal Natural Product Database (UNPD) through virtual screening (VS). The VS resulted in the discovery of two hit compounds UNPD 80894 and UNPD 100156 as inhibitors of ACLY and FASN respectively. Molecular docking revealed that UNPD 80894 and UNPD 100156 bind at the substrate binding site of ACLY and the entry channel of FASN with a docking score of -8.0 kcal/mol and -5.0 kcal/mol, respectively. Identified hit compounds also obeyed the Rule of Three (RO3) thus making them possible candidates for future fragment-based drug design studies. In silico absorption, distribution, metabolism, excretion and toxicity (ADMET) analysis of the hits predicted desirable pharmacokinetic profiles with no aberrant toxicity. The anti-cancer potentialities of the hits were also analysed using the prediction of activity spectra for substances (PASS) prediction tool which predicted the potential of UNPD 80894 as an inhibitor of ubiquinol-cytochrome-c reductase and UNPD 100156 as a lipoprotein lipase inhibitor and probable application in preneoplastic conditions treatment. These two natural compounds are proposed as potential candidates for the development of a novel ACLY and FASN inhibitors in this study.
{"title":"Identification of natural product inhibitors of de novo lipogenesis enzymes as an anti-cancer strategy: An in silico approach","authors":"Mirushan Arunasalam, Vivian Chong, Sharanya Ranee Mareshvaran, Venessa Ngui Fern Yee, A. Gaurav, S. Salvamani, C. S. Lim, B. Gunasekaran","doi":"10.35118/apjmbb.2022.030.2.01","DOIUrl":"https://doi.org/10.35118/apjmbb.2022.030.2.01","url":null,"abstract":"Dysregulation of the metabolic pathways is fundamental to cancer formation. The differential expression and activation of de novo fatty acid synthase (FASN) and lipogenesis enzymes ATP citrate lyase (ACLY) have been observed in various cancer types making them a promising metabolic target in cancer therapy. Natural products (NP) are a major contributor to the development of novel non-toxic anti-tumour drugs with greater efficiency. An attempt has been made in this study to identify potent orally active ACLY and FASN inhibitors from Universal Natural Product Database (UNPD) through virtual screening (VS). The VS resulted in the discovery of two hit compounds UNPD 80894 and UNPD 100156 as inhibitors of ACLY and FASN respectively. Molecular docking revealed that UNPD 80894 and UNPD 100156 bind at the substrate binding site of ACLY and the entry channel of FASN with a docking score of -8.0 kcal/mol and -5.0 kcal/mol, respectively. Identified hit compounds also obeyed the Rule of Three (RO3) thus making them possible candidates for future fragment-based drug design studies. In silico absorption, distribution, metabolism, excretion and toxicity (ADMET) analysis of the hits predicted desirable pharmacokinetic profiles with no aberrant toxicity. The anti-cancer potentialities of the hits were also analysed using the prediction of activity spectra for substances (PASS) prediction tool which predicted the potential of UNPD 80894 as an inhibitor of ubiquinol-cytochrome-c reductase and UNPD 100156 as a lipoprotein lipase inhibitor and probable application in preneoplastic conditions treatment. These two natural compounds are proposed as potential candidates for the development of a novel ACLY and FASN inhibitors in this study.","PeriodicalId":8566,"journal":{"name":"Asia-pacific Journal of Molecular Biology and Biotechnology","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86660082","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 : 2022-04-13DOI: 10.35118/apjmbb.2022.030.1.06
F. Ismail, Yusmazura Zakaria, Nik Fakhuruddin Nik Hassan, M. L. MD ISA
Cancer is a complex disease and ranks as a leading cause of death globally. Despite many advances made in cancer therapeutics, adverse side effects and treatment resistance remain a great problem. In that sense, there are increasing demands to discover new anticancer agents from naturally-derived compounds. Medicinal plants represent a valuable source of new drugs with promising efficacy and safety. They produce various secondary metabolites, which exhibit unique structures and a pharmacological spectrum of activity, including antitumour activity. Clinacanthus nutans, Strobilanthes crispus, Ficus deltoidea, Curcuma longa, Centella asiatica and Piper betle are among the plants species commonly used to cure cancer in traditional medicine formulae in Malaysia. The present review aims to highlight the anticancer properties of the listed Malaysian herbs with a focus on their bioactive compounds and the mode of action. Overall, many studies have disclosed the presence of active metabolites in these plants, including phenols, alkaloids, flavonoids, terpenoids, saponin, curcumin and Asiatic acid. They possess significant cytotoxic or antiproliferative effects primarily via the induction of apoptosis, elevation of antioxidant activity and inhibition of cancer activating enzymes. Hence, further investigation into their clinical therapeutic potential may be noteworthy. Additionally, this review article also provides the reader with information concerning the conventional anticancer drugs and their limitations, recent developments and milestones achieved in plant- derived cancer therapeutics as well as different approaches to enhance the production of these anticancer molecules.
{"title":"Malaysian herbs as potential natural resources of anticancer drugs: From folklore to discovery","authors":"F. Ismail, Yusmazura Zakaria, Nik Fakhuruddin Nik Hassan, M. L. MD ISA","doi":"10.35118/apjmbb.2022.030.1.06","DOIUrl":"https://doi.org/10.35118/apjmbb.2022.030.1.06","url":null,"abstract":"Cancer is a complex disease and ranks as a leading cause of death globally. Despite many advances made in cancer therapeutics, adverse side effects and treatment resistance remain a great problem. In that sense, there are increasing demands to discover new anticancer agents from naturally-derived compounds. Medicinal plants represent a valuable source of new drugs with promising efficacy and safety. They produce various secondary metabolites, which exhibit unique structures and a pharmacological spectrum of activity, including antitumour activity. Clinacanthus nutans, Strobilanthes crispus, Ficus deltoidea, Curcuma longa, Centella asiatica and Piper betle are among the plants species commonly used to cure cancer in traditional medicine formulae in Malaysia. The present review aims to highlight the anticancer properties of the listed Malaysian herbs with a focus on their bioactive compounds and the mode of action. Overall, many studies have disclosed the presence of active metabolites in these plants, including phenols, alkaloids, flavonoids, terpenoids, saponin, curcumin and Asiatic acid. They possess significant cytotoxic or antiproliferative effects primarily via the induction of apoptosis, elevation of antioxidant activity and inhibition of cancer activating enzymes. Hence, further investigation into their clinical therapeutic potential may be noteworthy. Additionally, this review article also provides the reader with information concerning the conventional anticancer drugs and their limitations, recent developments and milestones achieved in plant- derived cancer therapeutics as well as different approaches to enhance the production of these anticancer molecules.","PeriodicalId":8566,"journal":{"name":"Asia-pacific Journal of Molecular Biology and Biotechnology","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83816465","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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