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All Journal HAYATI Journal of Biosciences MEDIA PETERNAKAN - Journal of Animal Science and Technology Jurnal Ilmu Pertanian Indonesia MEDIA KONSERVASI Jurnal Ilmu dan Teknologi Kelautan Tropis Buletin Peternakan ILMU KELAUTAN: Indonesian Journal of Marine Sciences JBIO: jurnal biosains (the journal of biosciences) BIOTROPIA - The Southeast Asian Journal of Tropical Biology Jurnal Biologi dan Pembelajarannya (JBP) Jurnal Ilmu Ternak Veteriner Journal of the Indonesian Tropical Animal Agriculture Jurnal Pengelolaan Sumberdaya Alam dan Lingkungan (Journal of Natural Resources and Environmental Management) JITRO (Jurnal Ilmiah dan Teknologi Peternakan Tropis) BioCONCETTA Journal of Tropical Biodiversity and Biotechnology Aceh Journal of Animal Science JURNAL BIOLOGI INDONESIA ZOO INDONESIA Jurnal Biologi Tropis ANNALES BOGORIENSES Majalah Ilmiah Biologi BIOSFERA: A Scientific Journal Bioma : Jurnal Biologi Indonesia AL-HAYAT: Journal of Biology and Applied Biology Zoo Indonesia
ACHMAD FARAJALLAH
Departemen Biologi, Fakultas Matematika Dan Ilmu Pengetahuan Alam, Institut Pertanian Bogor, Kampus IPB Dramaga Bogor, 16680, Indonesia
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Decision Sciences, Operations Research & Management Earth & Planetary Sciences Education Environmental Science Health Professions Immunology & microbiology Library & Information Science Medicine & Pharmacology Veterinary Other

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DISTRIBUTION OF Charybdis (Archias) padangensis Leene & Buitendijk, 1952 (CRUSTACEA: DECAPODA: BRACHYURA) IN THE WATERS OF SUMATRA AND JAVA Hanim, Nisfa; Farajallah, Achmad; Widayat, Kanthi Arum i; Mashar, Ali
JURNAL BIOSAINS Vol. 10 No. 3 (2024): JBIO : JURNAL BIOSAINS (THE JOURNAL OF BIOSCIENCES)
Publisher : Universitas Negeri Medan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24114/jbio.v10i3.61142

Abstract

Until this decade, Charybdis (Archias) padangensis was only from Padang, West Sumatra. It was reported first and the only one in 1952. We obtained several crab samples based on the by-catch from daily fishermen in several locations. Based on morphological identification, we obtained several Charybdis (Archias) padangensis individuals from two locations in Sumatra and one location in Java. The results of this research add to data on the distribution of the species, which was previously only known from the locality type.
Polymorphism of Cyt-b Gene in Several Indonesian Cattle Using PCR-RFLP Method Agung, Paskah Partogi; Perwitasari, Dyah; Farajallah, Achmad; Said, Syahruddin; Kaiin, Ekayanti Mulyawati; Saputra, Ferdy; Hermansyah, Alfandy; Kuswati, Kuswati; Susilorini, Tri Eko; Zein, Moch. Syamsul Arifin
Buletin Peternakan Vol 48, No 2 (2024): BULETIN PETERNAKAN VOL. 48 (2) MAY 2024
Publisher : Faculty of Animal Science, Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21059/buletinpeternak.v48i2.87484

Abstract

The cytochrome b (Cyt-b) gene is one of the genes that is located in the mitochondrial DNA. Variations in the Cyt-b gene can be used to compare different animal species to investigate the origin of certain animal species. This study aimed to assess the genetic diversity of Indonesian local cattle breeds, including Bali cattle as an Indonesian native cattle breed and Banteng as the wild type of Bali cattle, using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). A total of 336 individual DNA samples from Indonesian cattle breeds were analyzed in this study. The RFLP method using three restriction enzymes, i.e., HinfI, HaeIII, or XbaI, was used to identify the variation of the Cyt-b gene. The Cyt-b gene was polymorphic based on the PCR-RFLP method. There were six alleles of the Cyt-b gene found in this study, i.e., A and B allele (HinfI), C and D allele (HaeIII), X and Y allele (XbaI). All alleles can be found in Pasundan, Madura, and PO cattle. Pesisir cattle have the highest allele frequency D. The UPGMA results showed three clusters of Indonesian native cattle in this study. Cluster 1 consists of Pasundan, Banteng, and Bali cattle. Cluster 2 consists of Madura, PO, and SO cattle. Pesisir was separated from other cattle in cluster 3. The X allele could become an indicator to distinguish Banteng and Bali cattle.
Catatan Sebaran Baru Dromidiopsis indica Gray, 1831 (Decapoda: Brachyura: Dromiidae) dari Pantai Tengor, Lampung, Indonesia Yudhistiro Muhammad Khalid; Achmad Farajallah; Windra Priawandputra
Jurnal Biologi dan Pembelajarannya (JB&P) Vol 13 No 1 (2026): APRIL 2026
Publisher : Universitas Nusantara PGRI Kediri

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29407/jbp.v13i1.27657

Abstract

Dromidiopsis is found in the waters of Asia, Australia, Oceania, Africa, and several small islands in the Indian Ocean. In Indonesia, there are two documented reports of this genus: one in the Java Sea, where Lauridromia indica was exist, and another in the Matasiri Islands of South Kalimantan, where Dromidiopsis abrolhensis, Lauridromia indica, and Dromia intermedia were found. To provide more specific distribution records, it is important to report the discovery of Dromidiopsis indica with Gray (1831) in the waters of the Southern Peninsula of Sumatra from this study. Research conducted in October 2023 using a convenience sampling method discovered Dromidiopsis indica at Tengor Beach, Tanggamus Regency, Lampung Province, Indonesia. The distribution of the species Dromidiopssis indica is not confined to specific areas, indicating a need for further exploration and research in the Southern Peninsula of Sumatra. This report marks the first discovery of Dromidiopsis indica on the Southern Peninsula of Sumatra.
Karakterisasi Ekson 4 Gen DRD4 pada Ayam Arab Tiara G15 dengan Tingkah Laku Feather Pecking Achmad Farajallah; Pristina Tuti Wijayanti; Achmad Alfiyan; Maria Ulfah
Jurnal Ilmu Pertanian Indonesia Vol. 29 No. 3 (2024): Jurnal Ilmu Pertanian Indonesia
Publisher : Institut Pertanian Bogor

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.18343/jipi.29.3.430

Abstract

Feather pecking (FP) is a potentially fatal behavioral disorder in chickens. Various factors, including genetics such as DRD4 gene, affected this behavior. The Arab TIARA G15 chicken is a laying hen breed selected based on FP behavior. However, genetic selection linked to this FP as not yet been conducted. This study aimed to characterize the 4th exon of the DRD4 gene in Arab golden red TIARA G15 chickens and confirm its potential as an FP genetic marker. The study used 30 TIARA G15 chickens that were divided into three groups: high feather pecking (HFP) (n = 10), low feather pecking (LFP) (n = 10), and control (n = 10). The DNA extraction kit extracted total genomic DNA from each blood sample. The 4th exon of the DRD4 gene was amplified using primer pairs MU140-141. Amplicons from samples within a group were pooled in a single tube and sequenced using the Sanger method. The sequencing results were analyzed for nucleotide variation using MEGA6 software. Nucleotide sequences obtained from each group were 642 bp, consisting of partial intron 3 (55 bp), full-length exon 4 (202 bp), and partial 3'UTR (385 bp). None of the three groups of Arab golden red TIARA G15 chickens were found to have any nucleotide variants in the partial intron 3, full-length exon 4, and 3'UTR regions of the DRD4 gene. Consequently, selecting the full-length exon 4 of the DRD4 gene for FP behavior was not feasible. Keywords: arab chicken, DRD4, feather pecking, golden red
RAPID DETECTION OF THE AFRICANIZED HONEY BEE: A TOOL FOR INDONESIAN ANIMAL QUARANTINE RIKA RAFFIUDIN; ANIFA BINTAR; M. CHANDRA WIDJAJA; AHMAD FARAJALLAH; BAMBANG PURWANTARA
BIOTROPIA Vol. 16 No. 1 (2009): BIOTROPIA Vol. 16 No. 1 June 2009
Publisher : SEAMEO BIOTROP

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (194.086 KB) | DOI: 10.11598/btb.2009.16.1.65

Abstract

Molecular detection methods were used to determine if Africanized Honey Bees (AHBs) are present in populations of imported Apis mellifera in Indonesia. The cytochrome b (cyt b gene) was amplified from mitochondrial DNA and digested with the BglII restriction enzyme (cytb/BglII). Two types of animal DNA extraction kits were used and found suitable for rapid preparation of DNA from A. mellifera by the Animal Quarantine facility. Results showed that all 94 colony samples from beekeepers in Java produced a 485 bp PCR product from the amplification of this gene. Two DNA fragments of 194 and 291 bp from all samples were produced after digestion with BglII. This cytb/BglII result together with the DNA sequence of cyt b showed that all collected samples of A. mellifera were the non-AHB type. Hence, this study did not detect AHB in Indonesia.Key words :  Apis mellifera, molecular detection methods, DNA, cytochrome b, mitochondrial genetics
TESTING RELIABILITY OF SERUM SAMPLES AS A DNA SOURCE ON CAPTIVE BREEDING LONG-TAILED MACAQUES (Macaca fascicularis) Dyah Perwitasari-Farajallah; Achmad Farajallah
BIOTROPIA Vol. 21 No. 2 (2014): BIOTROPIA Vol. 21 No. 2 December 2014
Publisher : SEAMEO BIOTROP

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (126.976 KB) | DOI: 10.11598/btb.2014.21.2.306

Abstract

The serum realibility was tested in captive breeding conditions on the long-tailed macaques (Macaca fascicularis). Serum and buffy coat were applied to standard protocol of DNA extration following the amplification of microsatellite DNA locus of D2S1777 by PCR and visualized PCR products by means of PAGE with silver staining.  The amount of genomic DNA extracted from serum was sufficient for genotyping individuals at DNA microsatellite locus of D2S1777 with the allele size is approximately 160 bp.  We show that serum can provide a reliable alternative for obtaining DNA where taking blood using anticoagulant is impracticable
Reanalysis of Mitochondrial and Nuclear Markers (COI, 16S, 28S) in Coenobitidae, Diogenidae, and Paguridae for Species Delimitation Tazkiah Auliaputri; Tyani Fitrian; Achmad Alfiyan; Intan Ratu Pratiwi; Vendi Eko Susilo; Ali Mashar; Achmad Farajallah
Jurnal Ilmu dan Teknologi Kelautan Tropis Vol 18 No 1 (2026): Jurnal Ilmu dan Teknologi Kelautan Tropis
Publisher : Department of Marine Science and Technology, Faculty of Fisheries and Marine Science, IPB University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29244/jitkt.18.1.69987

Abstract

Public sequence repositories, such as GenBank, contain an extensive collection of molecular data that are widely used for phylogenetic inference and species identification. However, inconsistent annotation and potential misidentifications can obscure true genetic patterns, particularly in groups with complex morphology such as Paguroidea. This study reanalyzed 4,871 COI, 16S, and 28S sequences belonging to the families Coenobitidae, Diogenidae, and Paguridae retrieved from GenBank. Following rigorous quality filtering, 2,450 sequences were retained for downstream analyses to quantify intra and interspecific genetic distances for each family and each molecular marker. The results reveal substantial heterogeneity in genetic divergence across families, with COI and 16S exhibiting broad ranges and frequent overlap between intra and interspecific distances, whereas 28S displayed very low variation consistent with its slower evolutionary rate. Elevated intraspecific distances in several taxa suggest potential cryptic lineages, while unusually shallow interspecific values indicate possible synonymy or recent divergence. Rather than proposing taxonomic changes, this study provides a curated reference framework that establishes empirical distance thresholds for molecular species delimitation in Paguroidea. These findings offer a practical baseline for future research employing COI, 16S, and 28S markers in species identification, validation of public sequence data, and the refinement of hermit crab systematics.
Co-Authors A Anggraeni A Anggraeni A Anggraini A Batubara A. Anggraeni A. Anggraeni Achmad Alfiyan Achmad Alfiyan Achmad, Alfiyan Agus Alim Hakim AKICHIKA MIKAMI ALFIYAN, ACHMAD Ali Mashar Ali Mashar Ali Suman AMIR HAMIDY Amir Hamidy Amir Hamidy ANIFA BINTAR Annawaty Annawaty, Annawaty Arma Aditya Kartika Aron Batubara Aron Batubara Arum Widayati, Kanthi Asri Febriana Asri Febriana, Asri B Tiesnamurti B. Tiesnamurti Baiq Farhatul Wahidah Bambang Purwantara Bambang Suryobroto Burhanuddin Burhanuddin C Sumantri C Sumantri C. SUMANTRI C. Sumantri Cece Sumantri D Perwitasari D, Nurhayati D. Herdiana D. Rahmat Daisy Wowor Daisy Wowor Daisy Wowor, Daisy Dede Setiadi Devi Sandriliana DEWI APRI ASTUTI DEWI PURNAMA Dwi Sendi Priyono Dyah Perwitasari DYAH PERWITASARI -FARAJALLAH E Andreas E. Andreas E. Andreas Eric N. Smith Eric N. Smith Erni Sulistiawati Eryk Andreas Farid Akhsani Fauzan, Muhammad Fakhri Ferdy Saputra H. Nuraini HANIM, NISFA HERA MAHESHWARI Hermansyah, Alfandy I Inounu Imas Batubara Intan Ratu Pratiwi Irma Shita Arlyza Isdoni Bustaman J F Salamena Jarmuji Jarmuji Jeane Siswitasari Mulyana Joni Setiawan Jumadin, La Kaiin, Ekayanti Mulyawati KANTHI ARUM WIDAYATI Khairiza Lubis koekoeh santoso KREY KREY Kuswati Kuswati Lora purnamasari, Lora Luthfia Nuraini Rahman M Doloksaribu M Karmita M. CHANDRA WIDJAJA M. Doloksaribu Mahendra, Arindina Maria Ulfah Mennofatria Boer Meutiya Agustina Meutiya Agustina, Meutiya Moch. Syamsul Arifin Zein, Moch. Syamsul Arifin Mufti Sudibyo N Satriani NEVIATY PUTRI ZAMANI Nirmala Fitria Firdhausi Nisfa Hanim Nisfa Hanim Novita Anggraeni Nurhayati D Nurlisa Alias Butet Nurulvadini Safrudin Paskah Partogi Agung Person Pesona Renta Pradana, Tengku Gilang Pristina Tuti Wijayanti Pudji Achmadi Putri, Vinna Windy R Diyono R Misrianti R R Noor R R Noor R.R. Noor R.R. Noor Rarah Ratih Adjie Maheswari RIKA RAFFIUDIN Rissa Herawati Ginting Riyanto, Awal Riyanto, Awal Rose Ida Ummah Rudi Alek Wahyudin Sasmita, Annissa Nuridfi Silvia Puspitasari Siti Lutvaniyah Slamet Mulyanto Smith, Eric N. Soemarno, Suprayogo Soemarno, Suprayogo Syahruddin Said Tanaka, Hiroyuki TARUNI SRI PRAWAST MIEN KAOMINI ANY ARYANI DEDY DURYADI SOLIHIN TARUNI SRI PRAWASTI Tatewaki, Takafumi Tazkiah Auliaputri Tri Eko Susilorini Tsuji, Yamato Tyani Fitrian Vella Nurazizah Djalil Vendi Eko Susilo Wahyudin Abd. Karim, Wahyudin Abd. Widayat, Kanthi Arum i Widayati, Kanthi Windra Priawandputra Yanti Ariyanti Yanti Ariyanti Yudhistiro Muhammad Khalid Yusli Wardiatno