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All Journal Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences Jurnal Pendidikan Biologi Undiksha Agrikultura Bioedukasi BIOTROPIA - The Southeast Asian Journal of Tropical Biology Alchemy : Journal of Chemistry Jurnal Harpodon Borneo Biogenesis: Jurnal Ilmiah Biologi Biotropika Jurnal Pendidikan Biologi Indonesia Jurnal IPTEK QUANTUM: Jurnal Inovasi Pendidikan Sains Jurnal Pengabdian Pada Masyarakat Bioedukasi: Jurnal Pendidikan Biologi Edubiotik : Jurnal Pendidikan, Biologi dan Terapan Jurnal Pengabdian Masyarakat Borneo Jurnal Borneo Saintek Jurnal Riset Biologi dan Aplikasinya Soeropati: Journal of Community Service Bioscientist : Jurnal Ilmiah Biologi Proceeding Biology Education Conference Berkala Penelitian Hayati Borneo Journal of Biology Education (BJBE) Biopedagogia Al Kawnu : Science and Local Wisdom Journal Journal of Fisheries & Marine Biosaintifika: Journal of Biology & Biology Education Edubiotik : Jurnal Pendidikan, Biologi dan Terapan
Endik Deni Nugroho
Jurusan Biologi, Universitas Borneo Tarakan
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Molecular Analysis and Morphological Characterization of Tor sp. using DNA Barcode COI from Telaga Rambut Monte, Blitar, East Java, Indonesia Damayanti, Ayu Elysia; Rabbani, Calista Naya; Sulung, Cahya Ajeng Valenta Tresna; Rusdianto, Rusdianto; Nugroho, Endik Deni; Mamat, Noorhidayah Binti; Rahayu, Dwi Anggorowati
Biotropika: Journal of Tropical Biology Vol. 13 No. 2 (2025)
Publisher : Universitas Brawijaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.biotropika.2025.013.02.011

Abstract

The genus Tor (Cyprinidae) comprises highly diverse freshwater fishes widely distributed in Southeast Asia, including Indonesia. However, information on Tor species in several regions remains limited. This study aimed to identify Tor species from Telaga Rambut Monte, Blitar, using morphological analysis and molecular approaches based on COI DNA barcoding. Fish were collected through purposive sampling at depths of 1–2 m, and fin tissues were preserved in ethanol for DNA extraction. PCR amplification employed LCO1490 and HCO2198 primers, with sequence analysis conducted using BLAST and the BOLD System. Phylogenetic reconstruction applied Neighbour-Joining and Maximum Likelihood methods under the Kimura 2-Parameter model, supported by p-distance analysis with MEGA, Clustal X, BioEdit, and ABGD. Morphological characterisation confirmed the specimens as Tor tambra. COI gene amplification produced a 477 bp sequence, which showed 92% genetic similarity to the reference T. tambra. The phylogenetic tree revealed a distinct clade with a high bootstrap value (96%), clearly separating T. tambra from other congeners. Integrating morphological and molecular data provides robust evidence confirming the presence of T. tambra in Telaga Rambut Monte. This research represents the first study combining genetic identification, morphological analysis, and phylogenetic reconstruction of T. tambra from this locality. The findings contribute to understanding freshwater fish biodiversity in Indonesia and provide important baseline information on the distribution of local fish resources.
Morphology and Molecular Identification of Cyprinidae from the Sumber Umbulan Ngenep, Malang Regency, East Java Naya Rabbani, Calista; Damayanti, Ayu Elysia; Tresna Sulung, Cahya Ajeng Valenta; Rahayu, M.Si, Dwi Anggorowati; Nugroho, Endik Deni; Rusdianto, Rusdianto; Binti Mamat, Noorhidayah
Jurnal Riset Biologi dan Aplikasinya Vol. 7 No. 2 (2025)
Publisher : Universitas Negeri Surabaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.26740/jrba.v7n2.p142-159

Abstract

The genus Tor comprises freshwater fish belonging to the Cyprinidae family, recognized for their remarkable diversity and broad distribution across Southeast Asia, including Indonesia. Despite this, data on Tor species in certain regions are limited, highlighting the need for additional research to confirm their presence. Therefore, this study aims to examine the genetic diversity and phylogenetic reconstruction of the species observed in Sumber Umbulan Ngenep using the COI gene as a DNA barcode marker. The research was conducting using the Purposive Random Sampling method and fin tissues were preserved in 96% ethanol for DNA analysis. The species found at Sumber Umbulan Ngenep were observed morphologically using a phenetic approach. Fins from each fish sample were collected and subjected to PCR, sequence analysis using the BOLD System, phylogenetic tree reconstruction, ABGD analysis, and QR barcoding. The results of morphological, genetic, and phylogenetic tree reconstruction based on the COI gene indicate that three species have been identified at Sumber Umbulan Ngenep, namely Tor douronensis, Tor tambra, and Barbonymus gonionotus. Based on the phenetic approach, three apomorphies and five automorphies were identified, indicating the relatedness of the observed species with the reference species. The phylogenetic tree topology shows an unambiguous branching pattern for the observed sample cluster with Poecilia reticulata as the outgroup. This study is the first to identify the species present at Sumber Umbulan Ngenep, Malang Regency, East Java, Indonesia. The findings provide new information about the existence of these species and can serve as a basis for future conservation and management strategies.
Pengaruh Model Pembelajaran Problem Based Learning Berbasis Mind Mapping Terhadap Kemampuan Berpikir Kritis Siswa FADILAH; Safitri, Nur Lina; Nugroho, Endik Deni
Al Kawnu : Science and Local Wisdom Journal Vol. 5 No. 1 (2025): Oktober 2025
Publisher : Tadris Biologi, Tadris Fisika, and Tadris Kimia, Universitas Islam Negeri Antasari

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.18592/ak.v5i1.13747

Abstract

Kemampuan berpikir kritis berperan penting dalam meningkatkan kemampuan berpikir tingkat tinggi serta menjadi landasan utama bagi siswa dalam menghadapi perkembangan dunia yang penuh dengan keberagaman informasi dan tantangan . Penelitian ini bertujuan untuk mengetahui pengaruh penerapan model pembelajaran Problem Based Learning (PBL) berbasis mind mapping terhadap kemampuan berpikir kritis siswa. Metode penelitian menggunakan kuasi eksperimen dengan desain pretest-posttest control group. Teknik pengambilan sampel menggunakan purposive sampling, yaitu dengan pertimbangan berdasarkan nilai rata-rata kelas siswa yang sama atau mendekati. Siswa kelas X-3 digunakan sebagai kelas eksperimen dan X-5 digunakan sebagai kelas kontrol. Analisis data menggunakan Independent sample t-test setelah melalui uji prasyarat yaitu uji normalitas dan homogenitas . Hasil penelitian ini menunjukkan bahwa hasil uji Independent sample t-test kemampuan berpikir kritis siswa menyatakan dengan nilai sig. (2-tailed) sebesar 0,000. Hasil tersebut mengarah pada kesimpulan bahwa penerapan model pembelajaran Problem Based Learning berbasis mind mapping mimiliki pengaruh terhadap kemampuan berpikir kritis siswa pada materi perubahan lingkungan kelas X SMA Negeri 1 Gondangwetan. Model ini juga mendorong siswa untuk aktif mengonstruksi pengetahuan melalui visualisasi konsep dan pemecahan masalah autentik, sehingga dapat diterapkan pada berbagai mata pelajaran untuk mengembangkan keterampilan abad 21.
The assistance of Pesanggem in the Prevention of Coffee Pests through Vegetable Pesticides Coffee from Amethyst Mountain (Brugmansia Suaveolens Bercht. & J. Presl) at Taman Kehati Sapen Nusantara Mount Arjuno Pasuruan: Pendampingan Pesanggem dalam Pencegahan Hama Kopi melalui Pestisida Nabati Kopi dari Kecubung Gunung (Brugmansia Suaveolens Bercht. & J. Presl) di Taman Kehati Sapen Nusantara Gunung Arjuno Pasuruan Wibisono, Mulyono; Fafit Rahmat Aji; Amang Fathurrohman; Endik Deni Nugroho
Jurnal Soeropati Vol 4 No 2: Mei 2022
Publisher : LPPM Universitas Yudharta Pasuruan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.35891/js.v4i2.3422

Abstract

Pesanggem Taman Kehati Sapen Nusantara (TKSN) is a farming community in the Sapen Forest Area of ​​Mount Arjuno, Pasuruan. Coffee agroforestry is the main commodity for forest farmers in the TKSN area. For pest prevention, they have been using chemical pesticides to prevent the Coffee Fruit Borer. Through the Community Based Research approach, the companion team together with the community have succeeded in innovating vegetable pesticides coffee by utilizing Brugmansia Suaveolens Bercht. & J. Presl and Swietenia macrophylla King. as the main ingredients that are easily found in Taman Kehati Sapen Nusantara into environmentally friendly coffee pesticide products.
Diversity of bird agroforestry species in Sapen Nusantara Conservation Park of Mount Arjuno, Pasuruan Nugroho, Endik Deni; Rahayu, Dwi Anggorowati; Ainiyah, Roisatul; Fathurrohman, Amang; Ahwan, Zainul; Dayat, Muhammad; Wibisono, Mulyono; Aji, Fafit Rahmat; Kasiman, Kasiman
Edubiotik : Jurnal Pendidikan, Biologi dan Terapan Vol. 8 No. 01 (2023): Edubiotik : Jurnal Pendidikan, Biologi dan Terapan
Publisher : Biology Education Department, Universitas Insan Budi Utomo, Malang, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33503/ebio.v8i01.1059

Abstract

The Sapen Nusantara Conservation Park is agroforestry that has certain vegetation. The vegetation in Sapen Nusantara Protected forest park seems to support the existence of birds as wildlife that need a living habitat. The presence of birds in the Sapen Nusantara Protected Forest Park is very important in supporting agroforestry vegetation. However, until now the diversity of bird species there has not been identified and recorded properly. The forest is one of the buffer forests of Mount Arjuno protection forest, the ecosystem must be protected. This study aims to analyze the diversity of bird species in the agroforest forest area in Sapen Nusantara Conservation forest park, Ledug Village, Pasuruan. The research was conducted in July 2021 using the direct observation method (point count) on ecotourism routes by calculating and recording the trails traversed using GPS, sampling by observing walking along the path/road accompanied by predetermined observation points, identification primarily based totally on MacKinnon et al., (2010) and information on the status of its protection. Data analysis used the Shannon-Wiener diversity index, evenness index, and species richness index. The results of the study identified 18 bird species from 16 families with a total of 169 individuals. Of all the birds found, 18 species are listed in IUCN status, and 4 are listed in the protected status PP No. P.106 of 2018 and 3 species are listed in the CITES category Appendix II. It is known that the Shannon diversity index (H'=2,547) is in the medium diversity category. species evenness index (E=0.9) with a high evenness category and stable community. Then the specific wealth index (R=3.31) with the category of species richness is classified as medium. The presence of birds in the Sapen Nusantara Conservation Park Forest indicates that the ecosystem in the forest is still maintained and this cannot be separated from the role of the community, especially the Ledug Lembaga Masyarakat Desa Hutan (LMDH), which manages and maintains the forest.
Identifikasi Kandungan Volatil Ekstrak Etanol Benalu Alpukat (Dendrophthoe pentandra) Sebagai Kandidat Antibiotik Alami Tuberkulosis Ainiyah, Roisatul; Nugroho, Endik Deni; Ardiansyah, Reza; Hamdani, Khoirul; Tarmudi, Imam; Kuswanto, Wawan; Hadi, Lukman
Bioscientist : Jurnal Ilmiah Biologi Vol. 12 No. 2 (2024): December
Publisher : Department of Biology Education, FSTT, Mandalika University of Education, Indonesia.

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33394/bioscientist.v12i2.13326

Abstract

Tuberculosis is an infectious disease that spreads through the air and is caused by the bacterium Mycobacterium tuberculosis. To combat it, synthetic drugs are commonly used, which can have adverse effects, making natural alternatives like avocado mistletoe (Dendrophthoe pentandra) necessary. This study aims to explore potential tuberculosis compounds from D. pentandra. The method used in this research is an exploratory descriptive method. The identification of compound content in the ethanol extract of D. pentandra leaves was performed using GC-MS, along with potential testing as an antituberculosis agent through in silico molecular docking. The research results showed that there were 13 volatile compounds contained in the ethanol extract of D. Pentandra leaves, predominantly consisting of propane, 1-methoxy, with a concentration of 9.39%. D. pentandra has the potential as a ClpP1P2 antituberculosis agent with four promising compounds:2-amino-1-(5-bromo-2-pyridinyl)-4-(2,4-dichlorophenyl)-7,7-dimethyl-5-oxo-1,4,5,6,7,8-hexahydro-3-quinolinecarbonitrile, stigmasterol acetate, β-sitosterol acetate, and γ-sitosterol. PASSOnline predictions support the potential of ethanol extract of D. Pentandra leaves as anti-tuberculosis and anti-mycobacteria agent.
Morphological and Molecular Characterization of Pufferfish from Lekok Coastal Area, Pasuruan Indonesia Panjaitan, Viona Angelina Erlan; Rangga, Adam Dwi; Sulung, Cahya Ajeng Valenta Tresna; Rahayu, Dwi Anggorowati; Khaleyla, Firas; Nugroho, Endik Deni; Rusdianto, Rusdianto; Mamat, Noorhidayah Binti
Biosaintifika: Journal of Biology & Biology Education Vol. 17 No. 3 (2025): November 2025
Publisher : Universitas Negeri Semarang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15294/biosaintifika.v17i3.26663

Abstract

Pufferfish belong to the Tetraodontidae family, which consists of 28 genera and 184 species; however, there are limited studies on the species from East Java, especially Pasuruan. This indicates the need for the collection of more accurate morphological and genetic resources as an important step for its conservation. Therefore, this study was conducted to identify pufferfish species found in the Lekok Coastal Waters, Pasuruan District, through morphological characterization and molecular analysis using DNA barcoding of the COI gene. A total of 12 samples were collected from the Lekok Coastal Waters, Pasuruan Regency. Fin samples were stored in 96% absolute ethanol. DNA extraction, polymerase chain reaction (PCR), and sequence analysis were performed using bioinformatics tools, the BOLD system, and the Automatic Barcode Gap Discovery (ABGD) web platform. Phenetic taxonomy was further applied using Ntysc to enhance the robustness of genetic analysis. The results showed that there were identified five pufferfish species were identified: Lagocephalus spadiceus, Chelonodontops patoca, Cyclichthys orbicularis, Arothron stellatus, and Arothron reticularis. High haplotype diversity (Hd) of 1 and nucleotide diversity (π) of 0.1 indicate significant genetic variation. The frequency of parsimonious informative sites was 22.6%, with 13 polymorphic sites and an overall ts/tv ratio of 2.2. The phylogenetic tree showed unambiguous branching patterns among species. These findings are supported by morphological and molecular identification results, which indicate the presence of five species of pufferfish along the Lekok Coast, Pasuruan Regency.
FURTHER STUDY ON TWO SPECIES OF LOACH FISHES (Cypriniformes: Nemacheilidae: Nemacheilus) BASED ON MORPHOLOGY AND MOLECULAR DATA Rahayu, Dwi Anggorowati; Kuntjoro, Sunu; Budijastuti, Widowati; Winarsih, Winarsih; Ambarwati, Reni; Nugroho, Endik Deni; Basith, Abdul; Kurniawan, Nia; Haryono, Haryono
BIOTROPIA Vol. 30 No. 3 (2023): BIOTROPIA Vol. 30 No. 3 December 2023
Publisher : SEAMEO BIOTROP

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11598/btb.2023.30.2.1942

Abstract

The identities of two local loaches, Nemacheilus chrysolaimos (Valenciennes, 1846) and N. fasciatus (Valenciennes, 1846) from six rivers, were obtained through a comprehensive examination of their morphology and molecular characteristics in Biltar Regency, East Java, Indonesia. Therefore, this study identified Nemacheilus spp. from Blitar based on morphology and partial sequence of COI. The meristic data obtained for N. chrysolaimos included DII. 7–8 (dorsal fin), AI. 3–5 (anal fin), PI. 9 (pectoral fin), VI. 6–7 (ventral fin), and C. 17 (caudal fin). On the other hand, N. fasciatus exhibited the following meristic data, namely D II 7–8 (dorsal fin), AI. 6 (anal fin), PI. 9–10 (pectoral fin), VI. 6–7 (ventral fin), and C. 17 (caudal fin). A significant difference was observed in the morphometric characteristics of N. fasciatus across various sampling sites, as determined by the Kruskal-Wallis Test. Furthermore, the nucleotide base composition sequences of Nemacheilus spp. consisted of Thiamine (T), Cytosine (C), Adenine (A), and Guanine (G) with a mean of 29.565%, 32.023%, 23.88%, and 16.244%. Maximum Likelihood (ML) and Minimum Evolution (ME) phylogenetic analysis was also conducted using the Kimura 2 Parameter model to establish two major clades on Nemacheilus spp. and one out-group significantly different from the Nemacheilus spp. The results showed that these major clades exhibited a close relationship at 100% bootstrap support and were grouped under the genus Nemacheilus. The study on Nemacheilus spp. from the Blitar locality differentiated COI sequences between N. fasciatus and N. chrysolaimos. Additionally, N. chrysolaimos, as inferred from reference sequences, was identified as the ancestral species to N. chrysolaimos MZB 26540 and MZB 26539. ABGD analyses, employing a prior maximal distance of 0.025, also indicated the separation of these species into distinct partitions. The integration of morphology and genetic data for Nemacheilus spp. should provide valuable insights for future genetic population studies and conservation initiatives.
Morphological and Molecular Characteristics of Pufferfish Using DNA Barcode COI Gene at Camplong Beach, Madura, Indonesia Adam Dwi Rangga; Viona Angelina Erlan Panjaitan; Endik Deni Nugroho; Rahayu, Dwi Anggorowati; Cahya Ajeng Valentina Sulung; Rusdianto, Rusdianto; Noorhidayah Binti Mamat
Jurnal Ilmiah Perikanan dan Kelautan 2026: IN PRESS ISSUE (JUST ACCEPTED MANUSCRIPT, 2026)
Publisher : Faculty of Fisheries and Marine Universitas Airlangga

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20473/jipk.v18i2.82924

Abstract

Graphical Abstract Highlight Research 1. Combining DNA barcoding with morphological variation analysis can enhance the accuracy of Pufferfish species identification. 2. This is the first study to examine the genetic diversity and phylogenetic relationships pufferfish from Madura, East Java, using partial COI sequences. 3. DNA barcoding confirms the morphological identification of this group (96%-100%) 4. The reliability using targeted DNA barcoding and phenetic taxonomy to study genetic variation and identify species differences in pufferfish.   Abstract Pufferfish are one of the most common fish species in the ocean particularly in Camplong Beach, Madura. Despite the abundant nature, there isn’t much information on this species in East Java, showing the need for identification. Therefore, this study sought to identify pufferfish species in Sampang Regency through morphological and molecular characterization utilizing DNA barcoding of the COI gene. Fins were kept in 96% absolute ethanol, and DNA extraction, polymerase chain reaction (PCR), and sequence analysis were performed using bioinformatics tools, including the BOLD system and the web-based Automatic Barcode Gap Discovery (ABGD) tool. To strengthen genetic study, phenetic taxonomy was again applied using Ntysc. Morphological identification revealed five distinct species of pufferfish, namely Chelonodontops patoca, Lagocephalus spadiceus, Arothron reticularis, Otracion rhinorhynchos, and Cyclichthys orbicularis. The high haplotype diversity (Hd) of 0.9 and nucleotide diversity (π) of 0.2 indicated substantial genetic variation. There were 11 polymorphic sites, and the overall ts/tv ratio was 2.2. The frequency of parsimonious informative sites was 21.6%. The phylogenetic tree displayed distinct branching patterns among species. Morphological and molecular identification data supported these results, demonstrating that five distinct pufferfish species occur at Camplong Beach in the Sampang District of Madura.
Co-Authors - Ibrahim, - Abdul Basith Achmad Zultan M Adam Dwi Rangga Adelyn Salurapa Adelyn Salurapa Ahwan, Zainul Aidil Adhani Ainiyah, Roisatul Aji, Fafit Rahmat Aji, Fatit Rahmar Alfrida Alfrida Amang Fathurrohman Andari, Kadek Dewi Wahyuni Andari, Kadek Dewi Wahyuni Azrianingzih, Rodiyati Azrianingzih, Rodliyati Binti Mamat, Noorhidayah Cahya Ajeng Valentina Sulung Candra, Puspa Mega Dahlia Dahlia Damayanti, Ayu Elysia Dayat, Muhammad Dwi Anggorowati Rahayu Dwi Anggorowati Rahayu Dwi Anggorowati Rahayu Dwi Anggorowati Rahayu Dwi Anggorowati Rahayu Dwi Anggorowati Rahayu Dwi Anggorowati Rahayu Dwi Anggorowati Rahayu DWI ANGGOROWATI RAHAYU Dwi Listyorini Fadhlan Muchlas Abrori Fadilah Fafit Rahmat Aji Fafit Rahmat Aji Fafit Rahmat Aji Fafit Rahmat Aji Fitriani Said Hamdani, Khoirul Haryono Haryono Haryono Haryono Ibrahim Ibrahim Ibrahim Ibrahim Ixora Sartika Mercuriani Kasiman Kasiman Kasiman Kasiman Kasiman, Kasiman Khaleyla, Firas Khoirul Anam KHOIRUL ANAM Kuswanto, Wawan Laila Rasidah H. Lukman Hadi, Lukman M Dayat Mamat, Noorhidayah Binti Matrani Maylina Ilhami Khurniyati Moh. Amin Muhammad Dayat Muhammad Dayat Mulyono Wibisono Mulyono Wibisono Mulyono Wibisono Nawir, Daud Naya Rabbani, Calista Nia Kurniawan Nia Kurniawan Nia Kurniawan Noorhidayah Binti Mamat Novianti, Nilam Nur Anisa Nur Anisa NUR LINA SAFITRI Nur'aini, Afifah Diyah Nursia Nursia Nursiah Nursiah, Nursiah Panjaitan, Viona Angelina Erlan Parada Agus Pasaribu, Aswin Poetri, Dini Andini Puspa Mega Candra Rabbani, Calista Naya Rahayu, M.Si, Dwi Anggorowati Rahayu, Tanti Rangga, Adam Dwi Rasidah H., Laila Reni Ambarwati Reza Ardiansyah Ribka Ribka Rodiyati Azrianingsih Rodiyati Azrianingsih Rodliyati Azrianingzih Roisatul Ainiyah Rupa, Darius Rusdianto Rusdianto, Rusdianto Salurapa, Adelyn Silfia Ilma Sulung, Cahya Ajeng Valenta Tresna Sunu Kuntjoro Sururi, Ahmad Misbakhus Syarifa Ramadhani Nurbaya Tarmudi, Imam Tresna Sulung, Cahya Ajeng Valenta Trio Ageng Prayitno, Trio Ageng Umie Lestari Viona Angelina Erlan Panjaitan Vlorensius Vlorensius Wanandi, Ichsan Bakhtiar Wibisono, Mulyono WIDOWATI BUDIJASTUTI Winarsih Winarsih Yuliawati, Witri Yunita Khilyatun Nisak Yusuf Tomy Harsoyo Zulfadli Zulfadli Zultan, Achmad