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All Journal HAYATI Journal of Biosciences Jurnal Ilmu Dasar AL KAUNIYAH BERKALA SAINSTEK REKAYASA UNEJ e-Proceeding REINWARDTIA Jurnal Biodjati Caraka Tani: Journal of Sustainable Agriculture BIOEDUKASI JPSCR : Journal of Pharmaceutical Science and Clinical Research Journal of Natural Sciences Makara Journal of Science Jurnal Malikussaleh Mengabdi Life Science and Biotechnology Biosaintifika: Journal of Biology & Biology Education Reinwardtia Jurnal Penelitian Sains dan Teknologi Indonesia Jurnal Hasil Pengabdian Kepada Masyarakat Universitas Jember Biodiversitas Journal of Biological Diversity
Fuad Bahrul Ulum
Department Of Biology, Faculty Of Mathematics And Natural Sciences, Universitas Jember. Jl. Kalimantan No. 37, Jember 68121, East Java, Indonesia
Religion Agriculture, Biological Sciences & Forestry Humanities Biochemistry, Genetics & Molecular Biology Chemistry Computer Science & IT Control & Systems Engineering Earth & Planetary Sciences Economics, Econometrics & Finance Education Electrical & Electronics Engineering Engineering Environmental Science Immunology & microbiology Industrial & Manufacturing Engineering Library & Information Science Materials Science & Nanotechnology Mathematics Physics Public Health Social Sciences Other

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Poiploidy induction of Indonesian Black Rice Oryza sativa L. Var. Cempo Ireng with Bio-catharantine Kurniawan, Ludfi; Laili, Alvina Nur; Angraeni, Devi Silvia; ‘Ain, Salsabila Qurrotu; Wulandari, Dyah Retno; Ulum, Fuad Bahrul
Life Science and Biotechnology Vol. 1 No. 2 (2023): November 2023
Publisher : Department of Biology, Faculty Mahematics and Natural Sciences, University of Jember

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.19184/lsb.v1i2.43753

Abstract

High demand on black rice Oryza sativa L. due to their high antioxydant content and better nutrition than the white rice. On the other hand this high price rice still less interest for the farmet to cultivate it. Therefore, improvement of plant characters was carried out through polyploid induction using the natural anti-mitotic compound bio-catharanthine. The purpose of this study was to test the effectiveness of bio-catharanthine in inducing polyploidy in Cemp ireng black rice. This study used a two-factor completely randomized design (CRD) method with three replications. The treatment factor of bio-catharanthine concentration was 1%, 1.5 %, 2 %, 2 %, 2.5 % and 3 % with the soaking time of 48 hours. The germination rate, ploidy level, stomatal size and density, and antioxidant were measuret to observed the characteristic of the mutan. The results showed that the treatments of 3 % bio-catharanthine enhanced the chromosome number of black rice Cempo ireng. Biocatharantine did not affected the germination rate through the treatments. Out mutants shows alternation on the stomatal size and density. The antioxidant of leaf sample did not changed after the treatment. Bio-catharanthine on high concentration migh be possible to be applied on polyploidy induction in black rice
In Silico Study of Genus Marchantia using matK loci for DNA Barcoding Farhan, Abdillah Maulana; Ulum, Fuad Bahrul
Life Science and Biotechnology Vol. 2 No. 2 (2024): November 2024
Publisher : Department of Biology, Faculty Mahematics and Natural Sciences, University of Jember

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.19184/lsb.v2i2.53527

Abstract

Marchantia is a genus of liverworts that can be found in the Asia-Europe Region. Some of the types that can be found are Marchantia polymorpha subsp. montivagans, Marchantia polymorpha subsp. ruderalis, Marchantia paleacea subsp. diptera. All of these species have different levels of kinship, this is due to differences in their nucleotide structure. The purpose of this study was to identify the intolerance between Marchantia species in genomic studies using the NCBI Database. The method used in this research is the collection of nucleotides on NCBI and then construction with Mega 11 software. The marker used in this study is Maturase K (matK), this is because the marker is very optimal in the identification of a molecular-based species. The results of this study are Marchantia paleacea subsp. diptera matK (MP 58 and MP 54) has the highest level of kinship with a score of 99 (Neighbor-Joining Tree) and 100 (Maximum Likelihood Tree) and the outgroup of this phylogenetic is Dumortiera hirsuta. Keywords: Marchantia, matK, NCBI, Phylogenetic.
In Silico Biological Activity Prediction of Bioactive Compounds from Dumortiera hirsuta (Sw.) Nees. Using Way2Drug PASS Online Farhan, Abdillah Maulana; Rosida, Waki'atil; Ulum, Fuad Bahrul
Life Science and Biotechnology Vol. 3 No. 1 (2025): May 2025
Publisher : Department of Biology, Faculty Mahematics and Natural Sciences, University of Jember

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Abstract

The liverwort Dumortiera hirsuta (Sw.) Nees. is recognized as a potential source of pharmacologically active metabolites. Bioactive compounds from D. hirsuta have been previously reported through in vitro metabolomic analyses using gas chromatography–mass spectrometry (GC–MS) and liquid chromatography–mass spectrometry (LC–MS). In this study, the biological activities of the GC-MS-identified metabolites were evaluated in silico using the Way2Drug PASS Online platform. The results indicated that ten metabolites from D. hirsuta exhibit medicinal potential, with Pa values greater than 0.7, suggesting a high probability of biological activity. Among these compounds, stigmasterol (Pa = 0.970) and lathosterol (Pa = 0.960) demonstrated the strongest antihypercholesterolemic potential, indicating their role as natural agents for reducing cholesterol levels. These findings highlight the pharmacological potential of D. hirsuta metabolites and warrant further validation through in vitro cholesterol-lowering assays to confirm their predicted activities.
Phylogenetic Analysis of Manihot sp. Based on matK and rbcL Markers Rosida, Wakiatil; Ulum, Fuad bahrul; Su'udi, Mukhamad
Life Science and Biotechnology Vol. 3 No. 1 (2025): May 2025
Publisher : Department of Biology, Faculty Mahematics and Natural Sciences, University of Jember

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Abstract

Cassava (Manihot sp.) is a staple crop of major economic and ethnomedicinal importance. Understanding the phylogenetic relationships within the genus Manihot is essential for clarifying its taxonomy and supporting genetic improvement programs. This study aimed to reconstruct the phylogeny of several Manihot species using two chloroplast DNA markers, matK and rbcL. Sequence data were retrieved from the GenBank database, and Ricinus communis was designated as the outgroup. Phylogenetic analyses were performed using the Neighbor-Joining (NJ) and Maximum Likelihood (ML) methods, each with 1,000 bootstrap replications to assess branch support. The resulting trees consistently clustered Manihot esculenta within a well-supported monophyletic group, indicating a close genetic relationship with other congeners. Distinct clades corresponding to genetic similarity were also observed among the analyzed species. These findings enhance current knowledge of Manihot systematics, providing molecular evidence that supports its taxonomic classification. Furthermore, the results contribute valuable insights for cassava breeding and conservation efforts through improved understanding of its evolutionary relationships.
Trichosanthes tricuspidata Lour. dari Kabupaten Jember, Jawa Timur Ulum, Fuad bahrul; Wiyono, Hidayat teguh; Setyati, Dwi
Jurnal Penelitian Sains dan Teknologi Indonesia Vol 1 No 1 (2022): Jurnal Hasil Penelitian UNIVERSITAS JEMBER
Publisher : Lembaga Penelitian dan Pengabdian Kepada Masyarakat (LP2M) Universitas Jember

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.19184/jpsti.v1i1.17

Abstract

Trichosanthes, one of the largest genera of Cucurbitaceae with in species and sub-species diversity offers a broad study for the systematic and taxonomy and also for the phytochemistry and conservation especially for the local specimen. The aims of this study were to determine the specimen and provided the information of medicinal uses and potency, also the conservation strategy. Determination was conducted by literature and confirmation to the experts, while the medicinal and conservation studied with literature review. The taxonomic investigation through the morphological of specimen collected from Jember, East Java represented Trichosanthes tricuspidata Lour. Medicinal potencies of the species were for threatment of imflamation, worm infection, migrain, and fever. Conservation action via habitat protection, species exploration, seed production, breeding activities were purposed for the flora sustainability.
Evaluasi Lokus Potensial matK dan ITS2 Untuk DNA Barcoding Anggrek Bulbophyllum lobbii Lindl. Su'udi, Mukhamad; Ulum, Fuad Bahrul; Ardiyansah, Muhammad; Fitri, Nurfajri Eka
Al-Kauniyah: Jurnal Biologi Vol. 17 No. 2 (2024): AL-KAUNIYAH JURNAL BIOLOGI
Publisher : Department of Biology, Faculty of Science and Technology, Syarif Hidayatullah State Islami

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15408/kauniyah.v17i2.33897

Abstract

AbstrakBulbophyllum lobbii Lindl. merupakan anggrek dari famili Orchidaceae yang berpotensi sebagai bahan baku obat herbal. Identikasi morfologi anggrek B. lobii memiliki keterbatasan karena kemiripan spesies dengan anggrek lain. Alternatif identifikasi secara molekuler menggunakan sekuen matK dan ITS2 sebagai barcode dalam DNA barcoding diharapkan menjadi salah satu lokus pembeda spesies anggrek B. lobbii secara akurat dan efisien. Penelitian ini bertujuan untuk mengidentifikasi sekuen matK dan ITS2 sebagai penanda molekuler yang efektif untuk anggrek B. lobbii. DNA genom B. lobbii diisolasi dengan metode Cethyl Trimethyl Ammonium Bromide (CTAB) dan amplifikasi DNA dengan PCR. Hasil penelitian menunjukkan sekuen matK dari B. lobbii memiliki tingkat homologi tinggi dengan dua spesies B. lobbii (KY966747.1 dan KY966691.1) dari China dengan nilai Per. Ident sebesar 99,20%, sedangkan sekuen ITS2 memiliki homologi tertinggi dengan nilai Per. Ident sebesar 99,76% pada spesies B. lobbii (MG253848.1) dari Polandia. Hasil analisis menunjukkan sekuen ITS2 dapat mengidentifikasi spesies dari tingkatan subspesies atau diatasnya (ordo atau genus) dan juga meningkatkan resolusi filogenetik yang baik pada hasil BLAST, sedangkan sekuen matK memberikan sedikit kontribusi dalam pengelompokkan hubungan kekerabatan antara spesies B. lobbii dengan spesies pembanding lainnya. Sekuen ITS2 dapat direkomendasikan sebagai penanda molekuler yang paling baik untuk identifikasi sampel anggrek Bulbophyllum, khususnya Bulbophyllum lobbii.AbstractBulbophyllum lobbii Lindl. is an orchid from the Orchidaceae family which has potential as a raw material for herbal medicine. Morphological identification of the B. lobii orchid has limitations due to the species' similarity to other orchids. The alternative molecular identification using matK and ITS2 sequences as barcodes in DNA barcoding is expected to be one of the loci for distinguishing the B. lobbii orchid species accurately and efficiently. This study aims to identify matK and ITS2 sequences as effective molecular markers for the orchid B. lobbii. Bulbophyllum lobbii genomic DNA was isolated using the Cethyl Trimethyl Ammonium Bromide (CTAB) method and DNA amplification by PCR. The results showed that the matK sequence from B. lobbii has a high level of homology with two B. lobbii species (KY966747.1 and KY966691.1) from China with a value of Per. Ident is 99.20%, while the ITS2 sequence has the highest homology with a Per. Ident value of 99.76% with the species B. lobbii (MG253848.1) from Poland. The results of the analysis show that the ITS2 sequence can identify species from the subspecies level or above (ordo or genus) and also improves good phylogenetic resolution in BLAST results, while the matK sequence makes little contribution in grouping the relationship between the B. lobbii species and other comparison species. The ITS2 sequence can be recommended as the best molecular marker for identifying Bulbophyllum orchid samples, especially Bulbophyllum lobbii. 
Liparis condylobulbon Reichb. f. from Gumitir, Indonesia: Morphology, Molecular, and Phytochemical Profile Ulum, Fuad Bahrul; Arum, Asyifa Yasmin; Sa’adah, Kurnia; Setyati, Dwi; Dwinianti, Edia Fitria; Rajamani, Ranjithkumar; Nugraha, Ari Satia; Su’udi, Mukhamad
Makara Journal of Science Vol. 30, No. 1
Publisher : UI Scholars Hub

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Abstract

Liparis condylobulbon Rchb.f. is an epiphytic orchid across South and Southeast Asia, which holds notable ethnomedicinal and pharmacological significance. This study aims to characterize Indonesian Liparis condylobulbon using integrated morphological, molecular (matK, rbcL, ITS2), and phytochemical (LC-MS, DPPH) analyses of specimens from Mount Gumitir, providing the first comprehensive taxonomic and pharmacological profile to support species authentication and future bioprospecting. The L. condylobulbon specimen displays diagnostic epiphytic morpho-logy, including fusiform pseudobulbs, two elongate leaves, and an erect inflorescence bearing ~123 flowers. Molecular barcoding using matK, rbcL, and ITS2 confirmed its identity, with phylogenetic analyses consistently clustering it with L. condylobulbon, supporting taxonomic placement despite minor ITS2-based variation. Metabolomic analysis revealed 58 distinct secondary metabolites, including 30 flavonoids, 22 terpenoids, and 6 phenolic compounds, with key bioactives such as diosmin, picrasinoside B, and 6-gingerol exhibiting known anti-inflammatory, antioxidant, and anticancer properties. Although the crude extract showed relatively low antioxidant capacity (IC₅₀ = 650 µg/mL), the chemical diversity and presence of pharmacologically active constituents underscore the species' potential for future phytotherapeutic applications.
Community Structure of Avifauna in The Rehabilitation Zone at Wonoasri Resort, Meru Betiri National Park Arif Mohammad Siddiq; Hari Sulistiyowati; Munaa Aqidatul Ulaa; Fuad Bahrul Ulum; Firda Fadri
Jurnal Biodjati Vol 9 No 1 (2024): May
Publisher : UIN Sunan Gunung Djati Bandung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15575/biodjati.v9i1.30033

Abstract

The rehabilitation zone of Meru Betiri National Park (MBNP) needs to be measured in relation to the success of ecosystem restoration. It can be used as a bioindicator, such as the bird community structure, hence their sensitivity to environmental changes. Therefore, the aims of this study are to determine the community structure of avifauna in the rehabilitation zone at Wonoasri Resort, MBNP including bird diversity, richness, dominance, feeding guilds, and their correlation with forest cover. The research was conducted in January 2023 in the Bonangan Block at three observation points, namely low vegetation cover, medium vegetation cover, and high vegetation cover. The ecological data, such as species and abundance, were collected using the point count method, while additional information related to conservation statuses were collected by web browsing on the IUCN Red List, the CITES appendix, and Indonesian government regulation (LHK No.106/2018). Data analysis used the dominance index, species diversity index (Shannon Wiener), and evaluated for statistical data using a Kruskal-Wallis (KW) test in R version 3.2.1. We recorded 38 bird species belonging to 31 genera and 21 families during this study. Among the feeding guilds, the insectivorous birds (14 species) were recorded as the higher species richness, followed by omnivorous (eight species), frugivorous (five species), granivorous (five species), carnivorous (four species), and nectarivorous (two species). The Kruskal-Wallis test shows there is a significant correlation among the feeding guilds (value of 11.644, with p-value = 0.040). Furthermore, referring to species richness, high vegetation cover areas have the highest species richness (30 species) compared to medium vegetation cover areas (27 species) and low vegetation cover areas (26 species). The dominance of avifauna species at this location falls into the low category (C = 0.07). According to the diversity index, avifauna in Bonangan Block is classified as a high category (H'=3.01).
Effect of Colchicine and Bio-catharantin on the DNA Relative Content and Stomatal Structure of Black Rice (Oryza sativa L. var. Jeliteng) Dwi Setyati; Mukhamad Su’udi; Dyah Retno Wulandari; Tri Handoyo; Fuad Bahrul Ulum
Caraka Tani: Journal of Sustainable Agriculture Vol 39, No 2 (2024): October
Publisher : Universitas Sebelas Maret

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20961/carakatani.v39i2.88279

Abstract

Black rice (Oryza sativa L. var. Jeliteng), known for its health benefits compared to white rice, faces challenges in productivity. Among varieties, this black rice is popular in Indonesia but shows low yield. Research on improving black rice through genetic manipulation with antimitotic substances is limited. Therefore, this study aims to compare the effects of colchicine and Bio-catharantin on the germination rate, DNA relative content, and stomatal structure of O. sativa L. var. Jeliteng. Seeds were treated with colchicine (0.1%, 0.2%, and 0.3%) and Bio-catharantin (0.1%, 0.2%, 0.3%, 0.4%, and 0.5%) at soaking durations of 12, 24, and 48 hours. Germination was assayed, ploidy was determined using flow cytometry, and stomatal traits, including size and density, were examined microscopically. The results showed that Bio-catharantin did not exhibit any toxic effects on germination rates, whereas colchicine reduced germination starting at 0.2% concentration. Both chemical agents modified the DNA relative content of Jeliteng black rice. Colchicine generally increased stomatal length and width while decreasing stomatal density, with significant changes at 0.3% concentration for 24 hours. Bio-catharantin also altered stomatal traits, enhancing length and width in most cases but significantly reducing density under certain conditions. Bio-catharantin emerged as a promising alternative to colchicine for inducing chromosomal mutations in plants, offering benefits in altered stomatal structures without the toxic effects on germination, compared to colchicine.
Antimicrobial and Phytochemistry study of Liparis resupinata Ridl. from Mount Gumitir, East Java, Indonesia Fuad Bahrul Ulum; Dwi Setyati; Moh. Ikmal Alfi Rizqoni; Mukhamad Su'udi
JPSCR: Journal of Pharmaceutical Science and Clinical Research Vol 8, No 3 (2023)
Publisher : Universitas Sebelas Maret

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20961/jpscr.v8i3.70856

Abstract

Liparis resupinata Ridl. is one of the abundant epiphytic orchids in the Mount Gumitir, Jember Regency with potency for phytopharmacy study. Our study focused on the observation of the species for their antimicrobial and metabolite profiles. This study used Gram-positive and Gram-negative bacteria, i.e., S. aureus, S. typhi, and E. coli with an agar diffusion method for antibacterial activity test. The metabolite profile was generated through GC-MS. The methanolic extract of the leaves of L. resupinata showed positive antibacterial activity. The GC-MS data analysis suggested the presence of antimicrobial substances e.g., (-)-loliolide, nonanoic acid, 1,2-ethanediamine, and hydroxy dimethyl furanone.
Co-Authors ABDILLAH MAULANA FARHAN AFIATRI PUTRIKA Afiatri Putrika AFIATRI PUTRIKA, AFIATRI Afidah, Yusfi Andiana, Jocelin Angraeni, Devi Silvia Ardiyansah, Muhammad Ari Satia Nugraha Arif Mohammad Siddiq Arsetyo Rahardianto Arum, Asyifa Yasmin Asa Hanifatul Hayyinah ‘Ain, Salsabila Qurrotu BAMBANG SUGIHARTO DIAN APRIANI DIAN APRIANI DWI INDAHNING ROHMAH Dwi Setyati Dwinianti, Edia Fitri Dwinianti, Edia Fitria Dyah Retno Wulandari Eny Yuniati ERLIN NOVITA SARI FADZILAH AG FADZILAH AG. KANAK FADZILAH AG. KANAK, FADZILAH AG. Farhan, Abdillah Maulana Firda Fadri Fitri, Edia Fitri, Nurfajri Eka Gilani, Noor Azizah Hidayat Teguh Wiyono Hidayatullah, Alhabsy Ika Oktavianawati INDAH WAHYUNI Indah Wahyuni KAHAR MUZAKHAR KAHAR MUZAKHAR KANAK KANJANA WONGKUNA KANJANA WONGKUNA KANJANA WONGKUNA, KANJANA Khoirunnisa, Gita Ayu Kurniawan, Ludfi Laili, Alvina Nur LESLEY C. LUBOS LESLEY C. LUBOS LESLEY C. LUBOS, LESLEY C. LUONG THIEN TAM LUONG THIEN TAM LUONG THIEN TAM, LUONG THIEN M. Akbar, Salahuddin Miatin Alvin Septianasari Mika Rizki Puspaningrum MIKA RIZKI PUSPANINGRUM MIKA RIZKI PUSPANINGRUM, MIKA RIZKI MOH. IKMAL ALFI RIZQONI Moh. Ikmal Alfi Rizqoni MOHD RAWIYANI PG. HJ. SERUDIN MOHD RAWIYANI PG. HJ. SERUDIN MOHD RAWIYANI PG. HJ. SERUDIN, MOHD RAWIYANI PG. MONICA SULEIMAN MONICA SULEIMAN MONICA SULEIMAN, MONICA Mudinillah, Adam Muhammad Ardiyansah MUKHAMAD SU’UDI MUKHAMAD SU’UDI Mukhamad Su'udi Mukhamad Su'udi Mukhamad Su'udi Mukhamad Su'udi MUKHAMAD SU’UDI Mukhamad Su’udi Munaa Aqidatul Ulaa Musyarofah Zuhri Musyarofah Zuhri MUSYAROFAH ZUHRI NG AIK MIN NG AIK MIN NG AIK MIN, NG AIK Nurfajri Eka Fitri NURLISMA JUNITA NURLISMA JUNITA NURLISMA JUNITA, NURLISMA Nursahara Pasaribu Nursahara Pasaribu NURSAHARA PASARIBU Rajamani, Ranjithkumar RANJITHKUMAR RAJAMANI Rendy Setiawan Rizqoni, Moh Ikmal Alfi ROBBERT GRADSTEIN ROBBERT GRADSTEIN ROBBERT GRADSTEIN, ROBBERT Robi’atul Adawiyah Rosida, Waki'atil Rosida, Wakiatil Rosyadi, Achmad SATRIYAS ILYAS Sattya Arimurti Sa’adah, Kurnia SOONTHREE KORNOCHALERT SOONTHREE KORNOCHALERT SOONTHREE KORNOCHALERT, SOONTHREE Su'udi, M. Su'udi, Mukhamad Sudarmadji, S. Sulistiyowati, Hari Sutoyo Su’udi, Mukhamad Tri Handoyo Tri Ratnasari Tri Ratnasari Veren Yuliana Saputri Wulandari, Dyah Retno YONG KIEN–THAI, YONG YONG KIEN–THAI YONG KIEN–THAI YUSI ANANDA PUTRI YUSRINA RISKY AMALINI