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  1. Article: Implementation of machine learning in DNA barcoding for determining the plant family taxonomy.

    Riza, Lala Septem / Zain, Muhammad Iqbal / Izzuddin, Ahmad / Prasetyo, Yudi / Hidayat, Topik / Abu Samah, Khyrina Airin Fariza

    Heliyon

    2023  Volume 9, Issue 10, Page(s) e20161

    Abstract: The DNA barcoding approach has been used extensively in taxonomy and phylogenetics. The differences in certain DNA sequences are able to differentiate and help classify organisms into taxa. It has been used in cases of taxonomic disputes where morphology ...

    Abstract The DNA barcoding approach has been used extensively in taxonomy and phylogenetics. The differences in certain DNA sequences are able to differentiate and help classify organisms into taxa. It has been used in cases of taxonomic disputes where morphology by itself is insufficient. This research aimed to utilize hierarchical clustering, an unsupervised machine learning method, to determine and resolve disputes in plant family taxonomy. We take a case study of Leguminosae that historically some classify into three families (Fabaceae, Caesalpiniaceae, and Mimosaceae) but others classify into one family (Leguminosae). This study is divided into several phases, which are: (i) data collection, (ii) data preprocessing, (iii) finding the best distance method, and (iv) determining disputed family. The data used are collected from several sources, including National Center for Biotechnology Information (NCBI), journals, and websites. The data for validation of the methods were collected from NCBI. This was used to determine the best distance method for differentiating families or genera. The data for the case study in the Leguminosae group was collected from journals and a website. From the experiment that we have conducted, we found that the Pearson method is the best distance method to do clustering ITS sequence of plants, both in accuracy and computational cost. We use the Pearson method to determine the disputed family between Leguminosae. We found that the case study of Leguminosae should be grouped into one family based on our research.
    Language English
    Publishing date 2023-09-21
    Publishing country England
    Document type Journal Article
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2023.e20161
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  2. Article: Allometric models for above- and below-ground biomass of Sonneratia spp

    Kusmana, Cecep / Hidayat, Topik / Tiryana, Tatang / Rusdiana, Omo / Istomo

    Global ecology and conservation. 2018 July, v. 15

    2018  

    Abstract: Allometric models are needed to estimate the stored carbon stocks in a mangrove forest ecosystem (blue carbon). Nevertheless, the development of allometric models for above- and below-ground biomass models for Sonneratia spp. species specifically has not ...

    Abstract Allometric models are needed to estimate the stored carbon stocks in a mangrove forest ecosystem (blue carbon). Nevertheless, the development of allometric models for above- and below-ground biomass models for Sonneratia spp. species specifically has not yet been carried out either at global, regional and local scale and therefore it is very important to conduct a research on it. This is because this species is a pioneer species in the mangrove forests and a CO2 absorber, has a very important role in reducing wave energy and retain sediments. Therefore this research was conducted to formulate an allometric model for the above- and below-ground biomass of Sonneratia spp. The biomass data of Sonneratia spp. (S.alba and S. caseolaris) were acquired through destructive sampling technique of 30 tree samples that have a stem diameter (diameter breast height/DBH)) within the range of 1.27–20.06 cm. The allometric model is obtained through non-linear regression analysis (using GNLS function in R), with a combination of the stem diameter, tree heights and wood density as estimated variables. The largest biomass proportion is found on the part of the stem (31.28%), which was followed by the below-ground roots (23.40%), twig (13.35%), branches (12.96%), foliage (12.50%), while the smallest proportion is present on the pneumatophore (6.51%). The biomass comparison of the above- and below-ground is 3:1 (76.60%:23.40%). The result of the analysis indicate that the belowground, aboveground and total biomass can be estimated well with the power function. The aboveground and total biomass can be estimated with just the stem diameter variable, while the belowground biomass can be well estimated with a combination of the stem diameter, tree height, and wood density. Overall, the addition of the tree heights or wood density variable in biomass allometric model development can increase the accuracy of the model, however the results are not significantly different than the model that uses only the stem diameter variable.
    Keywords Sonneratia caseolaris ; allometry ; belowground biomass ; blue carbon ; branches ; carbon dioxide ; carbon sinks ; forest ecosystems ; leaves ; mangrove forests ; models ; pioneer species ; pneumatophores ; regression analysis ; sampling ; sediments ; tree height ; trees ; water power ; wood density
    Language English
    Dates of publication 2018-07
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 2814786-8
    ISSN 2351-9894
    ISSN 2351-9894
    DOI 10.1016/j.gecco.2018.e00417
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  3. Article: Molecular biodiversity of selected mango cultivars based on DNA sequences of internal transcribed spacer region.

    Hidayat, Topik / Arif, Shahkila Mohd / Samad, Azman Abd

    Pakistan journal of biological sciences : PJBS

    2014  Volume 16, Issue 19, Page(s) 1072–1075

    Abstract: The mango (Mangifer indica L.) is an important species of the family Anacardiaceae and is one of the most important crops cultivated commercially in many parts of the world. Hence, a better understanding of the phylogeny in this species is crucial as it ... ...

    Abstract The mango (Mangifer indica L.) is an important species of the family Anacardiaceae and is one of the most important crops cultivated commercially in many parts of the world. Hence, a better understanding of the phylogeny in this species is crucial as it is the basis knowledge of improving its genetic resources which is beneficial for breeding programs. Phylogenetic relationships among 13 mango cultivars from Indonesia, Malaysia and Taiwan were carried out by comparing DNA sequence data sets derived from the Internal Transcribed Spacer (ITS) region pfnuclear ribosomal DNA (nrDNA). Analysis using parsimony method showed that the cultivars were classified into three major groups. The first group composed almost Malaysian cultivars although with low bootstrap value, the second group consisted of mainly Taiwan cultivars and the last group included mostly Indonesia one. The results indicated that some cultivars have a close relationships with each other even it is originated from different countries. With regards to the relationship among these cultivars, this gives better insight for generating new cultivar.
    MeSH term(s) Base Sequence ; Biodiversity ; DNA, Plant/genetics ; DNA, Ribosomal/genetics ; Mangifera/genetics ; Phylogeny ; Transcription, Genetic
    Chemical Substances DNA, Plant ; DNA, Ribosomal
    Language English
    Publishing date 2014-01-30
    Publishing country Pakistan
    Document type Journal Article
    ISSN 1028-8880
    ISSN 1028-8880
    DOI 10.3923/pjbs.2013.1072.1075
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  4. Article: Molecular Phylogenetic Screening of Withania somnifera Relative From Indonesia Based on Internal Transcribed Spacer Region

    Hidayat, Topik / Didik Priyandoko / Dina Karina Islami / Putri Yunita Wardiny

    Institut Pertanian Bogor HAYATI Journal of Biosciences. 2016,

    2016  

    Abstract: Withania somnifera (family Solanaceae), known commonly as Ashwaganda, is one of the important medicinal plants, and recent studies reported that Withanone, one of the chemical components in this plant, has ability to kill cancer cell. Because of endemic ... ...

    Abstract Withania somnifera (family Solanaceae), known commonly as Ashwaganda, is one of the important medicinal plants, and recent studies reported that Withanone, one of the chemical components in this plant, has ability to kill cancer cell. Because of endemic state of this plant to South Asia, exploring plant species under the same family which grow well in Indonesia has been of interest. Thus, main objective of this study was to screen the Indonesian plant which has strong phylogenetic relationship with Ashwaganda. To do this, phylogenetic analysis using DNA sequences of internal transcribed spacer (ITS) region was conducted. DNAs from living material of 19 species of Solanaceae and two species of Convolvulaceae (as outgroup) were extracted, and the ITS region were amplified and sequenced. Five ITS regions of Ashwaganda retrieved from GenBank were included in the phylogenetic tree reconstruction. The phylogenetic analysis based on parsimony method showed that Indonesia Solanaceae comprises seven groups which is consistent with the global Solanaceae relationship that has been previously reported. Furthermore, our study revealed that two species, Physalis angulata and Physalis peruviana, are relative to W. somnifera. This relationship is supported by several morphological characters especially their flower and fruit. This result indicated that these two species are potential to have similar chemical properties as Ashwaganda, thus we can have new variants of Withanone originated from Indonesia with similar effect.
    Keywords Convolvulaceae ; DNA ; flowers ; fruits ; internal transcribed spacers ; medicinal plants ; neoplasm cells ; phylogeny ; Physalis angulata ; Physalis peruviana ; physicochemical properties ; screening ; Withania somnifera ; Indonesia ; South Asia
    Language English
    Size p. .
    Publishing place Elsevier B.V.
    Document type Article
    Note Pre-press version
    ZDB-ID 2621600-0
    ISSN 2086-4094 ; 1978-3019
    ISSN (online) 2086-4094
    ISSN 1978-3019
    DOI 10.1016/j.hjb.2016.02.002
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  5. Article: Decolorization of Azo, Triphenylmethane and Anthraquinone Dyes by Laccase of a Newly Isolated Armillaria sp. F022

    Hadibarata, Tony / Yusoff, Abdull Rahim Mohd / Aris, Azmi / Salmiati / Hidayat, Topik / Kristanti, Risky Ayu

    Water, air and soil pollution. 2012 Mar., v. 223, no. 3

    2012  

    Abstract: A newly isolated white-rot fungus, Armillaria sp. strain F022, was isolated from the decayed wood in a tropical rain forest. Strain F022 was capable of decolorizing a variety of synthetic dyes, including azo, triphenylmethane, and anthraquinone dyes, ... ...

    Abstract A newly isolated white-rot fungus, Armillaria sp. strain F022, was isolated from the decayed wood in a tropical rain forest. Strain F022 was capable of decolorizing a variety of synthetic dyes, including azo, triphenylmethane, and anthraquinone dyes, with an optimal efficiency of decolorization obtained when dyes added after 96 h of culture, with the exception of Brilliant Green. All of the tested dyes were decolorized by the purified laccase in the absence of any redox mediators, but only a few were completely removed, while others were not completely removed even when decolorization time was increased. The laccase, with possible contributions from unknown enzymes, played a role in the decolorization process carried out by Armillaria sp. F022 cultures, and this biosorption contributed a negligible part to the decolorization by cultures. The effect of dye to fungal growth was also investigated. When dyes were added at 0 h of culture, the maximum dry mycelium weight (DMW) values in the medium containing Brilliant Green were 1/6 of that achieved by the control group. For other dyes, the DMW was similar with control. The toxic tolerance of dye for the cell beads was excellent at least up to a concentration of 500 mg/l. The optimum conditions for decolorization of three synthetic dyes are at pH 4 and 40°C.
    Keywords Armillaria ; decayed wood ; decolorization ; dyes ; laccase ; microbial growth ; pH ; tropical rain forests ; tropical wood ; white-rot fungi
    Language English
    Dates of publication 2012-03
    Size p. 1045-1054.
    Publishing place Springer-Verlag
    Document type Article
    ZDB-ID 120499-3
    ISSN 1573-2932 ; 0049-6979 ; 0043-1168
    ISSN (online) 1573-2932
    ISSN 0049-6979 ; 0043-1168
    DOI 10.1007/s11270-011-0922-6
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  6. Article ; Online: Identification of naphthalene metabolism by white rot fungus Pleurotus eryngii.

    Hadibarata, Tony / Teh, Zee Chuang / Rubiyatno / Zubir, Meor Mohd Fikri Ahmad / Khudhair, Ameer Badr / Yusoff, Abdull Rahim Mohd / Salim, Mohd Razman / Hidayat, Topik

    Bioprocess and biosystems engineering

    2013  Volume 36, Issue 10, Page(s) 1455–1461

    Abstract: The use of biomaterials or microorganisms in PAHs degradation had presented an eye-catching performance. Pleurotus eryngii is a white rot fungus, which is easily isolated from the decayed woods in the tropical rain forest, used to determine the ... ...

    Abstract The use of biomaterials or microorganisms in PAHs degradation had presented an eye-catching performance. Pleurotus eryngii is a white rot fungus, which is easily isolated from the decayed woods in the tropical rain forest, used to determine the capability to utilize naphthalene, a two-ring polycyclic aromatic hydrocarbon as source of carbon and energy. In the meantime, biotransformation of naphthalene to intermediates and other by-products during degradation was investigated in this study. Pleurotus eryngii had been incubated in liquid medium formulated with naphthalene for 14 days. The presence of metabolites of naphthalene suggests that Pleurotus eryngii begin the ring cleavage by dioxygenation on C1 and C4 position to give 1,4-naphthaquinone. 1,4-Naphthaquinone was further degraded to benzoic acid, where the proposed terepthalic acid is absent in the cultured extract. Further degradation of benzoic acid by Pleurotus eryngii shows the existence of catechol as a result of the combination of decarboxylation and hydroxylation process. Unfortunately, phthalic acid was not detected in this study. Several enzymes, including manganese peroxidase, lignin peroxidase, laccase, 1,2-dioxygenase and 2,3-dioxygenase are enzymes responsible for naphthalene degradation. Reduction of naphthalene and the presence of metabolites in liquid medium showed the ability of Pleurotus eryngii to utilize naphthalene as carbon source instead of a limited glucose amount.
    MeSH term(s) Biotransformation ; Chromatography, Thin Layer ; Culture Media ; Gas Chromatography-Mass Spectrometry ; Naphthalenes/metabolism ; Phylogeny ; Pleurotus/classification ; Pleurotus/growth & development ; Pleurotus/metabolism ; Spectrophotometry, Ultraviolet
    Chemical Substances Culture Media ; Naphthalenes ; naphthalene (2166IN72UN)
    Language English
    Publishing date 2013-10
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1476357-6
    ISSN 1615-7605 ; 1432-0797 ; 1615-7591
    ISSN (online) 1615-7605 ; 1432-0797
    ISSN 1615-7591
    DOI 10.1007/s00449-013-0884-8
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  7. Article: Identification of naphthalene metabolism by white rot fungus Pleurotus eryngii

    Hadibarata, Tony / Teh, Zee Chuang / Rubiyatno / Zubir, Meor Mohd Fikri Ahmad / Khudhair, Ameer Badr / Yusoff, Abdull Rahim Mohd / Salim, Mohd Razman / Hidayat, Topik

    Bioprocess and biosystems engineering. 2013 Oct., v. 36, no. 10

    2013  

    Abstract: The use of biomaterials or microorganisms in PAHs degradation had presented an eye-catching performance. Pleurotus eryngii is a white rot fungus, which is easily isolated from the decayed woods in the tropical rain forest, used to determine the ... ...

    Abstract The use of biomaterials or microorganisms in PAHs degradation had presented an eye-catching performance. Pleurotus eryngii is a white rot fungus, which is easily isolated from the decayed woods in the tropical rain forest, used to determine the capability to utilize naphthalene, a two-ring polycyclic aromatic hydrocarbon as source of carbon and energy. In the meantime, biotransformation of naphthalene to intermediates and other by-products during degradation was investigated in this study. Pleurotus eryngii had been incubated in liquid medium formulated with naphthalene for 14 days. The presence of metabolites of naphthalene suggests that Pleurotus eryngii begin the ring cleavage by dioxygenation on C1 and C4 position to give 1,4-naphthaquinone. 1,4-Naphthaquinone was further degraded to benzoic acid, where the proposed terepthalic acid is absent in the cultured extract. Further degradation of benzoic acid by Pleurotus eryngii shows the existence of catechol as a result of the combination of decarboxylation and hydroxylation process. Unfortunately, phthalic acid was not detected in this study. Several enzymes, including manganese peroxidase, lignin peroxidase, laccase, 1,2-dioxygenase and 2,3-dioxygenase are enzymes responsible for naphthalene degradation. Reduction of naphthalene and the presence of metabolites in liquid medium showed the ability of Pleurotus eryngii to utilize naphthalene as carbon source instead of a limited glucose amount.
    Keywords Pleurotus eryngii ; benzoic acid ; biocompatible materials ; biotransformation ; byproducts ; carbon ; catechol ; decarboxylation ; energy ; fungi ; glucose ; hydroxylation ; laccase ; lignin peroxidase ; manganese peroxidase ; metabolism ; metabolites ; naphthalene ; phthalic acid ; polycyclic aromatic hydrocarbons ; tropical rain forests
    Language English
    Dates of publication 2013-10
    Size p. 1455-1461.
    Publishing place Springer-Verlag
    Document type Article
    ZDB-ID 1476357-6
    ISSN 1432-0797 ; 1615-7605 ; 1615-7591
    ISSN (online) 1432-0797 ; 1615-7605
    ISSN 1615-7591
    DOI 10.1007/s00449-013-0884-8
    Database NAL-Catalogue (AGRICOLA)

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