I. Crespo, Augusto Arindra, Jessica Tashia Lualdi, Phoebe Anadita Rimba, Agus Budiawan Naro Putra, R. Rahardja
Indonesia has many types of tubers, some of them are gembolo tuber (Dioscorea bulbifera), lesser yam (Dioscorea esculenta), yam bean (Pachyrhizus erosus), and dahlia tuber (Dahlia pinnata); which are the sources of prebiotics. The term of prebiotics has been used since 1995 to describe the non-digestible components in food that positively alter gut microbiota activity and exhibit beneficial properties to the human body. One of the prebiotics that can be found in tubers is inulin. This review was aimed to compare inulin content in the above-mentioned tubers and their roles towards the growth of gut microbiota. Library searches using Semantic Scholar database was done. Findings showed that gembolo tuber contains the highest inulin content, followed by lesser yam, dahlia tuber, and yam bean. Moreover, inulin increases the population of Lactobacillus, Bifidobacterium, and Bacteroides while inhibits the growth of Escherichia coli and reduce the growth of Clostridium.
{"title":"Inulin from Several Tubers Available in Indonesia and the Growth of Gut Microbiota","authors":"I. Crespo, Augusto Arindra, Jessica Tashia Lualdi, Phoebe Anadita Rimba, Agus Budiawan Naro Putra, R. Rahardja","doi":"10.54250/IJLS.V2I1.33","DOIUrl":"https://doi.org/10.54250/IJLS.V2I1.33","url":null,"abstract":"Indonesia has many types of tubers, some of them are gembolo tuber (Dioscorea bulbifera), lesser yam (Dioscorea esculenta), yam bean (Pachyrhizus erosus), and dahlia tuber (Dahlia pinnata); which are the sources of prebiotics. The term of prebiotics has been used since 1995 to describe the non-digestible components in food that positively alter gut microbiota activity and exhibit beneficial properties to the human body. One of the prebiotics that can be found in tubers is inulin. This review was aimed to compare inulin content in the above-mentioned tubers and their roles towards the growth of gut microbiota. Library searches using Semantic Scholar database was done. Findings showed that gembolo tuber contains the highest inulin content, followed by lesser yam, dahlia tuber, and yam bean. Moreover, inulin increases the population of Lactobacillus, Bifidobacterium, and Bacteroides while inhibits the growth of Escherichia coli and reduce the growth of Clostridium.","PeriodicalId":375737,"journal":{"name":"Indonesian Journal of Life Sciences | ISSN: 2656-0682 (online)","volume":"os-37 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127778803","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}
A. A. Parikesit, Gabriella Patricia, Nanda Rizqia Pradana Ratnasari
The prediction of protein subcellular localization (SCL) has been a long-running challenge in bioinformatics. Protein SCL is crucial for a protein to exercise its functions properly. The reliance of protein localization on signaling peptides and the information available in gene ontology (GO) databases makes it possible to use computational approaches to predict protein SCL. SCL methods can be classified as either sequence-based or annotation-based. Machine learning algorithms and classifiers are used in protein SCL prediction tools. This review presents a list of protein SCL predictors published in the last 5 years.
{"title":"Prediction Methods of the Protein Subcellular Localization: A Systematic Reviews","authors":"A. A. Parikesit, Gabriella Patricia, Nanda Rizqia Pradana Ratnasari","doi":"10.54250/ijls.v1i2.20","DOIUrl":"https://doi.org/10.54250/ijls.v1i2.20","url":null,"abstract":"The prediction of protein subcellular localization (SCL) has been a long-running challenge in bioinformatics. Protein SCL is crucial for a protein to exercise its functions properly. The reliance of protein localization on signaling peptides and the information available in gene ontology (GO) databases makes it possible to use computational approaches to predict protein SCL. SCL methods can be classified as either sequence-based or annotation-based. Machine learning algorithms and classifiers are used in protein SCL prediction tools. This review presents a list of protein SCL predictors published in the last 5 years.","PeriodicalId":375737,"journal":{"name":"Indonesian Journal of Life Sciences | ISSN: 2656-0682 (online)","volume":"76 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123599797","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}
Shania Foustine, Andre Andre, Bastian Setiadi, L. Hartiadi, Agnes Anania Triavika Sahamastuti
Background: Ginger (Zingiber officinale) is one of the most well-known spices with antimicrobial activity. However, different extraction methods of ginger will result in different antimicrobial properties due to the various substances extracted. This study aimed to compare antimicrobial activity between ethanolic extract and essential oil of ginger against food-borne bacteria grown in 2.1% Mueller Hinton agar. Methods: Fresh ginger rhizomes were extracted either by using vapor distillation method or maceration using ethanol to obtain ginger essential oils (GEO) and ginger ethanolic extract (GEE), respectively. Ethanolic extract and essential oil of ginger at different concentrations were then tested for their antimicrobial activity using disk diffusion method against Escherichia coli, Bacillus subtilis, Salmonella typhi, and Staphylococcus aureus. Tetracycline was also used as a standard of antibacterial agent. Results: Ginger essential oil in 25%, 50%, and 100% showed significant growth inhibition of four types of bacteria compared to ginger ethanolic extract. This antimicrobial effect of ginger essential oil was shown to be dose-dependent. However, it has been demonstrated that ginger ethanolic extract 50% and 100% has a stronger antimicrobial effect against B.subtilis. Conclusion: Ginger essential oil and ethanolic extract showed different degree of antibacterial activity against food-borne bacteria due to compound contained within respective extracts, with a higher degree of activity found in ginger essential oil. These may show that different ginger extract may have different antibacterial activity.
{"title":"Comparison of Antimicrobial Activity between Ethanolic Extract and Essential Oil of Ginger (Zingiber officinale) against Food-borne Bacteria","authors":"Shania Foustine, Andre Andre, Bastian Setiadi, L. Hartiadi, Agnes Anania Triavika Sahamastuti","doi":"10.54250/ijls.v1i2.21","DOIUrl":"https://doi.org/10.54250/ijls.v1i2.21","url":null,"abstract":"Background: Ginger (Zingiber officinale) is one of the most well-known spices with antimicrobial activity. However, different extraction methods of ginger will result in different antimicrobial properties due to the various substances extracted. This study aimed to compare antimicrobial activity between ethanolic extract and essential oil of ginger against food-borne bacteria grown in 2.1% Mueller Hinton agar. Methods: Fresh ginger rhizomes were extracted either by using vapor distillation method or maceration using ethanol to obtain ginger essential oils (GEO) and ginger ethanolic extract (GEE), respectively. Ethanolic extract and essential oil of ginger at different concentrations were then tested for their antimicrobial activity using disk diffusion method against Escherichia coli, Bacillus subtilis, Salmonella typhi, and Staphylococcus aureus. Tetracycline was also used as a standard of antibacterial agent. Results: Ginger essential oil in 25%, 50%, and 100% showed significant growth inhibition of four types of bacteria compared to ginger ethanolic extract. This antimicrobial effect of ginger essential oil was shown to be dose-dependent. However, it has been demonstrated that ginger ethanolic extract 50% and 100% has a stronger antimicrobial effect against B.subtilis. Conclusion: Ginger essential oil and ethanolic extract showed different degree of antibacterial activity against food-borne bacteria due to compound contained within respective extracts, with a higher degree of activity found in ginger essential oil. These may show that different ginger extract may have different antibacterial activity.","PeriodicalId":375737,"journal":{"name":"Indonesian Journal of Life Sciences | ISSN: 2656-0682 (online)","volume":"21 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122205367","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}
Raymond Christanto, Andre Andre, Shania Foustine, L. Hartiadi
Introduction: Oral health awareness in Indonesia is still low with more and more oral and/or dental infection becomes more prevalent such as gingivitis, endodontitis, and pericoronitis. These infections could be caused by mouth microflora such as lactobacilli, Streptococcus mutans, Streptococcus mitis, Streptococcus oralis, and Streptococcus sobrinus. As time goes by, these bacteria could also become more problematic as antibacterial resistance emerges. Betel nut and betel leaf are well known traditional herbs that is often used in combination for "nyirih"; an Indonesian tradition to chew both plants often after meal. It is believed that these plants treat bad breath and also increases oral health as it could inhibit bacterial growth. Method: Betel nut and betel leaf were dried, powdered and macerated using 96% ethanol. The extract was tested on mouth microflora of volunteers grown in BHI using agar using disk diffusion test and modified E-test strip. Results: The betel leaves extract showed antibacterial activity in most of concentration used (1.25%, 2.5%, 5%, 10%) while betel nuts only gave antimicrobial effect in 10% concentration. The E-test results also showed the synergistic action between Piper betel leaves and Areca catechu nuts with some giving significant difference compared to the single treatment (P<0.05). Conclusion: Piper betel leaves gives antimicrobial effect with MIC value of 1.25% while Areca catechu have MIC value of 10%. Furthermore, combination of both resulted in synergistic effect as indicated with larger diameter of inhibition compared to the single treatments.
{"title":"Combination of Piper betel Leaves and Areca catechu Nuts Ethanolic Extract Effects on In Vitro Antimicrobial Test against Aerobic Mouth Microbiota","authors":"Raymond Christanto, Andre Andre, Shania Foustine, L. Hartiadi","doi":"10.54250/ijls.v1i2.24","DOIUrl":"https://doi.org/10.54250/ijls.v1i2.24","url":null,"abstract":"Introduction: Oral health awareness in Indonesia is still low with more and more oral and/or dental infection becomes more prevalent such as gingivitis, endodontitis, and pericoronitis. These infections could be caused by mouth microflora such as lactobacilli, Streptococcus mutans, Streptococcus mitis, Streptococcus oralis, and Streptococcus sobrinus. As time goes by, these bacteria could also become more problematic as antibacterial resistance emerges. Betel nut and betel leaf are well known traditional herbs that is often used in combination for \"nyirih\"; an Indonesian tradition to chew both plants often after meal. It is believed that these plants treat bad breath and also increases oral health as it could inhibit bacterial growth. Method: Betel nut and betel leaf were dried, powdered and macerated using 96% ethanol. The extract was tested on mouth microflora of volunteers grown in BHI using agar using disk diffusion test and modified E-test strip. Results: The betel leaves extract showed antibacterial activity in most of concentration used (1.25%, 2.5%, 5%, 10%) while betel nuts only gave antimicrobial effect in 10% concentration. The E-test results also showed the synergistic action between Piper betel leaves and Areca catechu nuts with some giving significant difference compared to the single treatment (P<0.05). Conclusion: Piper betel leaves gives antimicrobial effect with MIC value of 1.25% while Areca catechu have MIC value of 10%. Furthermore, combination of both resulted in synergistic effect as indicated with larger diameter of inhibition compared to the single treatments.","PeriodicalId":375737,"journal":{"name":"Indonesian Journal of Life Sciences | ISSN: 2656-0682 (online)","volume":"15 2","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"113935843","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}
Agnes Anania Triavika Sahamastuti, Andre Andre, Shania Foustine, Anton Sumarpo, L. Hartiadi
Background: Lemongrass and ginger are traditional food ingredients in Asian countries, including Indonesia, Thailand, India, and Malaysia. Although their single essential oil has been assessed for its antibacterial activities, no report has been done for their combination. Material and methods: Our study evaluated single and combination of these herbs for their antibacterial properties against food-borne bacteria E. coli (NEB® catalog No. C2989K), B. subtilis (ATCC 6633), S. typhi (ATCC 14028) and S. aureus (InaCC B4). Essential oil of lemongrass and ginger were obtained by steam distillation and their antimicrobial were evaluated using disk diffusion assay with chloramphenicol as the standard antibiotic. Synergistic activity was assessed using the combination of materials at two or four-fold dilution from their respected MIC value. Results: We confirmed that single lemongrass and ginger essential oils inhibited the bacteria growth with MIC value of about 1-5% and 2.5-5%, respectively. Moreover, their synergism activities were observed when both were mixed at two-fold dilution from their respective MIC. Conclusion: We conclude that the combination of the ginger essential oils and lemongrass essential oils may have potential as a natural preservative to prevent food-borne diseases.
{"title":"Synergistic Antibacterial Activities of Ginger and Lemongrass Essential Oils as an Alternative Prevention to Food-Borne Disease","authors":"Agnes Anania Triavika Sahamastuti, Andre Andre, Shania Foustine, Anton Sumarpo, L. Hartiadi","doi":"10.54250/ijls.v1i2.25","DOIUrl":"https://doi.org/10.54250/ijls.v1i2.25","url":null,"abstract":"Background: Lemongrass and ginger are traditional food ingredients in Asian countries, including Indonesia, Thailand, India, and Malaysia. Although their single essential oil has been assessed for its antibacterial activities, no report has been done for their combination. Material and methods: Our study evaluated single and combination of these herbs for their antibacterial properties against food-borne bacteria E. coli (NEB® catalog No. C2989K), B. subtilis (ATCC 6633), S. typhi (ATCC 14028) and S. aureus (InaCC B4). Essential oil of lemongrass and ginger were obtained by steam distillation and their antimicrobial were evaluated using disk diffusion assay with chloramphenicol as the standard antibiotic. Synergistic activity was assessed using the combination of materials at two or four-fold dilution from their respected MIC value. Results: We confirmed that single lemongrass and ginger essential oils inhibited the bacteria growth with MIC value of about 1-5% and 2.5-5%, respectively. Moreover, their synergism activities were observed when both were mixed at two-fold dilution from their respective MIC. Conclusion: We conclude that the combination of the ginger essential oils and lemongrass essential oils may have potential as a natural preservative to prevent food-borne diseases.","PeriodicalId":375737,"journal":{"name":"Indonesian Journal of Life Sciences | ISSN: 2656-0682 (online)","volume":"22 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114983560","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}
Dengue is a major public health problem in tropical urban areas, not only because it can quickly progress from the mild dengue fever to the deadly dengue hemorrhagic fever, but also because there is no single cure or licensed vaccine available to this day. To control the disease, the World Health Organization has recommended insecticides to control the number of mosquito vectors Aedes aegypti and Aedes albopictus. One of the main insecticides used is temephos, which inhibits the progression of the mosquito life cycle at the larvae stadium. Temephos is a member of the organophosphorus group of insecticides which is known to exhibit neurotoxicity through a common cholinergic pathway to insects and mammals. Despite its possible toxicity towards humans and other non-target organisms, temephos has been used widely to treat household water, including drinking-water and bath-water. Although clinical studies have yet shown any detrimental effects due to chronic consumption of temephos, studies on animal models have shown neurodevelopmental toxicity, while at the molecular level, exposure to tempehos has demonstrated genotoxic effects. Temephos is also considered an environmental contaminant and accumulation in soil and water have caused toxicity towards water organisms. Considering the extensive and repeated usage of temephos in public health, understanding and confirming the safety of temephos towards human health is crucial. Therefore, the objective of this paper is to review the current body of work available on the toxicity of temephos as a common dengue vector control.
{"title":"Toxicity of the Organophosphorus Pesticide Temephos","authors":"Dina Satriawan, Wibi Sindjaja, Timmy Richardo","doi":"10.54250/ijls.v1i2.26","DOIUrl":"https://doi.org/10.54250/ijls.v1i2.26","url":null,"abstract":"Dengue is a major public health problem in tropical urban areas, not only because it can quickly progress from the mild dengue fever to the deadly dengue hemorrhagic fever, but also because there is no single cure or licensed vaccine available to this day. To control the disease, the World Health Organization has recommended insecticides to control the number of mosquito vectors Aedes aegypti and Aedes albopictus. One of the main insecticides used is temephos, which inhibits the progression of the mosquito life cycle at the larvae stadium. Temephos is a member of the organophosphorus group of insecticides which is known to exhibit neurotoxicity through a common cholinergic pathway to insects and mammals. Despite its possible toxicity towards humans and other non-target organisms, temephos has been used widely to treat household water, including drinking-water and bath-water. Although clinical studies have yet shown any detrimental effects due to chronic consumption of temephos, studies on animal models have shown neurodevelopmental toxicity, while at the molecular level, exposure to tempehos has demonstrated genotoxic effects. Temephos is also considered an environmental contaminant and accumulation in soil and water have caused toxicity towards water organisms. Considering the extensive and repeated usage of temephos in public health, understanding and confirming the safety of temephos towards human health is crucial. Therefore, the objective of this paper is to review the current body of work available on the toxicity of temephos as a common dengue vector control.","PeriodicalId":375737,"journal":{"name":"Indonesian Journal of Life Sciences | ISSN: 2656-0682 (online)","volume":"102 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132424671","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}
Michaela Maria Kanya Anindita, Agus Budiawan Naro Putra, T. Sugahara
Ikan peda is one of Indonesia’s traditional fermented food products. It uses mackerel fish (Rastrelliger sp.), also known as ikan kembung in Indonesia, as its main ingredient. It is made through fermentation by adding high concentration of salt in order to extend the shelf-life and bring out the desired flavor of the fish. Although fermented foods are known to be beneficial towards health, fewer studies have been reported regarding the actual health promoting potential of Indonesian fermented foods, especially ikan peda. Thus, the immunostimulatory effects of ikan peda extract were examined. Water-extract of ikan peda was tested to human-human hybridoma HB4C5 cells. It was found that ikan peda extract stimulates the production of IgM by HB4C5 cells according to ELISA results. Data from real-time RT-PCR result showed that ikan peda extract has the ability to increase IgM gene expression by 3-fold at the highest concentration treatment. Results from the heat and enzyme treatments showed that the active substance contained in the ikan peda extract was expected to be a heat-stable protein. Although, the active substance and the mechanism is yet to be determined, and can be considered for future experiments. Our findings suggest that consumption of ikan peda would contribute to the promotion of health.
{"title":"Immunostimulatory effect of ikan peda (fermented Rastrelliger sp.) water extract on IgM production by HB4C5 cells","authors":"Michaela Maria Kanya Anindita, Agus Budiawan Naro Putra, T. Sugahara","doi":"10.54250/ijls.v1i1.12","DOIUrl":"https://doi.org/10.54250/ijls.v1i1.12","url":null,"abstract":"Ikan peda is one of Indonesia’s traditional fermented food products. It uses mackerel fish (Rastrelliger sp.), also known as ikan kembung in Indonesia, as its main ingredient. It is made through fermentation by adding high concentration of salt in order to extend the shelf-life and bring out the desired flavor of the fish. Although fermented foods are known to be beneficial towards health, fewer studies have been reported regarding the actual health promoting potential of Indonesian fermented foods, especially ikan peda. Thus, the immunostimulatory effects of ikan peda extract were examined. Water-extract of ikan peda was tested to human-human hybridoma HB4C5 cells. It was found that ikan peda extract stimulates the production of IgM by HB4C5 cells according to ELISA results. Data from real-time RT-PCR result showed that ikan peda extract has the ability to increase IgM gene expression by 3-fold at the highest concentration treatment. Results from the heat and enzyme treatments showed that the active substance contained in the ikan peda extract was expected to be a heat-stable protein. Although, the active substance and the mechanism is yet to be determined, and can be considered for future experiments. Our findings suggest that consumption of ikan peda would contribute to the promotion of health.","PeriodicalId":375737,"journal":{"name":"Indonesian Journal of Life Sciences | ISSN: 2656-0682 (online)","volume":"62 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133273040","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}
Protein N-myristoylation is the covalent attachment of myrstate, via an amide bond, to the N-terminal glycine residue of a nascent polypeptide assisted by myristol-CoA protein: N-myristoltransferases (NMT). PROSITE motif describes 5 amino acid after glycine site that would give rise to myristoylation site. However, applied to whole database extract, this motif give too many false postive results. Therefore 2 new tools were developed for N-myristoylation prediction.Taking physical properties into consideration inceases prediction scores greatly. However, these algorithms still cannot predict myristoylated site correctly 100% of the time due to limited understanding of the real mechanims underlying N-myristoylation
{"title":"Bioinformatics tools to Predict N-myristoylation Site a Comparison Study","authors":"Muhammad Zainul Arifin, A. A. Parikesit","doi":"10.54250/ijls.v1i1.10","DOIUrl":"https://doi.org/10.54250/ijls.v1i1.10","url":null,"abstract":"Protein N-myristoylation is the covalent attachment of myrstate, via an amide bond, to the N-terminal glycine residue of a nascent polypeptide assisted by myristol-CoA protein: N-myristoltransferases (NMT). PROSITE motif describes 5 amino acid after glycine site that would give rise to myristoylation site. However, applied to whole database extract, this motif give too many false postive results. Therefore 2 new tools were developed for N-myristoylation prediction.Taking physical properties into consideration inceases prediction scores greatly. However, these algorithms still cannot predict myristoylated site correctly 100% of the time due to limited understanding of the real mechanims underlying N-myristoylation","PeriodicalId":375737,"journal":{"name":"Indonesian Journal of Life Sciences | ISSN: 2656-0682 (online)","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130654657","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}
Allelic dropout is a failed amplification of an allele which usually happens when the concentration of the DNA sample is low. As there is a missing genotype, the result of the DNA profiling will significantly be affected. One way to overcome this problem is by using computational software that considers thedropout event within its algorithm. This review is aimed to discuss several software that have been created to serve this purpose. All of the listed software turn to implement Maximum Likelihood (LR) algorithm within their calculation; however, they use different parameters and variables. This reviewshowed that allelic dropout should not be evaluated alone; it correlates with other events in creating a low quality of DNA. Therefore, a comprehensive algorithm that consider all of the factors should be built to best estimates the allelic dropout rate within a data.
{"title":"Computational Software for Assessing Allelic Droput","authors":"Jeremias Ivan, A. A. Parikesit","doi":"10.54250/ijls.v1i1.11","DOIUrl":"https://doi.org/10.54250/ijls.v1i1.11","url":null,"abstract":"Allelic dropout is a failed amplification of an allele which usually happens when the concentration of the DNA sample is low. As there is a missing genotype, the result of the DNA profiling will significantly be affected. One way to overcome this problem is by using computational software that considers thedropout event within its algorithm. This review is aimed to discuss several software that have been created to serve this purpose. All of the listed software turn to implement Maximum Likelihood (LR) algorithm within their calculation; however, they use different parameters and variables. This reviewshowed that allelic dropout should not be evaluated alone; it correlates with other events in creating a low quality of DNA. Therefore, a comprehensive algorithm that consider all of the factors should be built to best estimates the allelic dropout rate within a data.","PeriodicalId":375737,"journal":{"name":"Indonesian Journal of Life Sciences | ISSN: 2656-0682 (online)","volume":"70 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127558289","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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