ACHMAD FARAJALLAH
Department of Biology, Faculty of Mathematics and Natural Science, Bogor Agricultural University

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Skin Histology and Microtopography of Papuan White Snake (Micropechis ikaheka) in Relation to Their Zoogeographical Distribution KREY, KREY; FARAJALLAH, ACHMAD
HAYATI Journal of Biosciences Vol 20, No 1 (2013): March 2013
Publisher : Bogor Agricultural University, Indonesia

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Abstract

Papuan white snake (Micropechis ikaheka) is endemic to New Guinea (the region of the Papua and Papua New Guinea). Internal histology of skin layer and the microtopography structure on the surface scales of M. ikaheka were the aims of the study. This study also related to zoogeographical of the snake in Papua. Geographical skin color variation of M. ikaheka can be described in three groups, i.e. brown, yellow and black group. The three groups of the snake have specific zoogeography in the mainland of Papua and satellite islands to Papua New Guinea. Paraffin method used in this work showed approximately five layers i.e. oberhautchen, the beta (b)-layer, the mesos layer, the alpha (a)-layer, and the dermis in the snake skin. Although the paraffin method cannot explain the arrangement of pigment cells, however, the dark color on the dermis might contain melanophores that might cause dark color of the snake body. Overlapping scales formed the hinge region were flexible to assist the snakes when they moved across substrate. Scanning electron microscopy (SEM) of the oberhautchen of all of M. ikaheka revealed no microornamentation. However, dorsal and ventral scales showed many follicles on the entire surface of the boundary scales.
Basic Level of Categorization in Macaca fascicularis WIDAYATI, KANTHI ARUM; SURYOBROTO, BAMBANG; FARAJALLAH, ACHMAD; MIKAMI, AKICHIKA
HAYATI Journal of Biosciences Vol 18, No 4 (2011): December 2011
Publisher : Bogor Agricultural University, Indonesia

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Abstract

Human brain posseses the ability to create a concept to assist the process of grouping individual object or events into different classes or categories. We call this grouping process as categorization. In addition to humans, the ability to categorize has also been proposed for animals. Being able to identify, visually or otherwise, a new object as a member of a category is an advantage for animals. Present experiment aims to test the categorization ability in discriminating species by Macaca fascicularis. Using match-to-sample task with photographs of monkeys and human as stimuli, we tested whether monkeys able to categorize monkey individuals as a class against human individuals as another class. We found that monkeys categorized humans differently from monkeys. The monkeys used physical characteristic such as shape and colors from the photographs to create different concepts of human and monkeys.
Keragaman Gen K-Kasein dan Hubungannya dengan Produksi dan Kualitas Susu pada Domba di Unit Pendidikan dan Penelitian Peternakan (UP3) Jonggol Sumantri, Cece; Andreas, Eryk; Farajallah, Achmad; Jarmuji, Jarmuji
Jurnal Ilmu Pertanian Indonesia Vol 13, No 1 (2008): Jurnal Ilmu Pertanian Indonesia
Publisher : Institut Pertanian Bogor

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Abstract

The objectives of this study were to identify polymorphisms in ovine K-casein gene exon 4 and its association with milk yield, percentage of protein and milk fat in sheep under extcnsif management at JASTRU (Jonggol Animal Studies Teaching and Research Unit) farm, Fact. of Anim Sci, Bogor Agric. University. The 83 blood sample from ewes which have record of milk production were used to determined polymorphism by using PCR-SSCP (Polymerase Chain Reaction-Single Strand Conformation Polymorphism) methode. The research activities were carried out through blood collection, DNA isolation, and fragment DNA amplification by PCR and separation in electrophoresis with silver staining. Electrophoretic pattern (PCR-SSCP) revealed th rce types of K-casein gene were dcsignitcd A, Band C type. The highest proportion was A type 69.57% and followed hy B 28.99% and the lowest C 1.45%. The were no significant effect of types of of K-casein gene on milk production and milk quality (percentage of protein and fat) in local sheep from Jonggol.   Keywords: .Jonggol sheep, K-cascin gcn, PCR-SSCP, polymorphism
Microsatellite DNA Analysis on the Polyandry of Green Sea Turtle Cheloniamydas PURNAMA, DEWI; ZAMANI, NEVIATY PUTRI; FARAJALLAH, ACHMAD
HAYATI Journal of Biosciences Vol 20, No 4 (2013): December 2013
Publisher : Bogor Agricultural University, Indonesia

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Abstract

Green turtle (Cheloniamydas; Testudines) is included in the group of polyandryanimals, which is single female mated with many male. DNA polymorphism method generally considered to have a high degree of accuracy as compared to other methods to elucidate polyandry phenomena on many animals. In this research, three microsatellite loci were used to identify the number and frequency of genotypes per locus, the number and frequency alleles per locus, and genotypes and number of alleles in the nest. The purpose of this research was to study the reproductive pattern of Cheloniamydas and compensation eggs of males from hatchling’s population in turtle conservation area of Pangumbahan Coastal Park, West Java. The result showed that from 10 nests, we could find 37 genotypes with 11 alleles for D108 locus, 21 genotypes with 9 alleles for B103 locus, and 27 genotypes with 9 alleles for C102 locus. The alleles number of each nest was more than 5 alleles for 5 nests, and more than 4 alleles for the remaining nests. Based on the probabilities of alleles contribution of each parent, the green turtle was polyandry animals.
Three Species of Ectoparasite Mites (Acari: Pterygosomatidae) Infested Geckos in Indonesia PRAWASTI, TARUNI SRI; FARAJALLAH, ACHMAD; RAFFIUDIN, RIKA
HAYATI Journal of Biosciences Vol 20, No 2 (2013): June 2013
Publisher : Bogor Agricultural University, Indonesia

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Abstract

Limited data is hitherto available on the diversity and dispersal of parasitic mites of geckos in Indonesia. Here, we collected three species of geckos, namely Cosymbotus platyurus, Hemidactylus frenatus, and H. garnotii throughout Indonesia to study the distribution and diversity of its parasitic mites. We conducted detail morphological analysis of the mites using whole mount polyvinyl lactophenol and scanning electron microscope preparation. Three species of ectoparasite mites from genus Geckobia were identified in a total of 221 individuals out of 448 geckos collected from 25 sites in Indonesia. Two species were G. glebosum and G. bataviensis, and the other one was designated as Geckobia sp 1. Based on our result, the three mites species were spread randomly and live sympatrically. The G. bataviensis mite showed the widest distribution, because it was found in almost all gecko collection sites, hence the most cosmopolitan mites. We also found that C. platyurus gecko had the lowest mite prevalence which might due to the fact that it has the least number of skin folds, an important site for mite protection. This result implies that further research on the relationship of anatomy of gecko skin with chelicera and claw structure of mites is necessary in the future.
APLIKASI TEKNIK ENVIRONMENTAL DNA(eDNA) UNTUK DETEKSI SPESIES Cheraxquadricarinatus (VON MARTENS 1868) MENGGUNAKAN SAMPEL AIR Djalil, Vella Nurazizah; Farajallah, Achmad; Wardiatno, Yusli
Jurnal Biologi Tropis Jurnal Biologi Tropis Vol.18 No.2 Juli-Desember 2018
Publisher : Program Studi Pendidikan Biologi FKIP Universitas Mataram

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Abstract

Cherax quadricarinatus merupakan spesies introduksi yang berasal dari Australia. Siklus hidup yang cepat dan toleransi yang tinggi terhadap lingkungan mengakibatkan C. quadricarinatusmudah menginvasi ekosistem perairan. Penelitian ini bertujuan untuk mengaplikasikan teknik eDNA secara cepat untuk deteksi C.quadricarinatus. Teknik ekstraksi dilakukan dengan menggunakan teknik pengendapan. Validasi keberadaan C.quadricarinatusdilakukan dengan menggunakan metode pengembangan PCR dan desain primer spesifik. Hasil menunjukkan bahwa keberadaan C.quadricarinatusterdeteksi sebanyak 60%dari keseluruhan badan perairan. Kombinasi protokol deteksi eDNA dan metode pengembangan PCR, serta primer spesifik yang didesain dapat digunakan untuk mendeteksi keberadaan C. quadricarinatus.Kata kunci :Cherax quadricarinatus, Environmental DNA, deteksi, keberadaan, PCR
Phylogenetic Analysis of the Darkfin Hind, Cephalopholis urodeta (Serranidae) Using Partial Mitochondrial CO1 Gene Sequences (Analisis Filogenetik Cephalopholis urodeta (Serranidae) Menggunakan Runutan Gen CO1 Mitokondria Parsial) Ariyanti, Yanti; Farajallah, Achmad; Arlyza, Irma Shita
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 20, No 1 (2015): Jurnal Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

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Abstract

Cephalopholis merupakan salah satu genera terbesar dalam subfamili Epinephelinae yang memiliki banyak species. Secara fenotip, C. urodeta dewasa mirip dengan juvenil C. sonnerati karena memiliki ciri mencolok yaitu garis yang menyudut pada sirip ekor. Untuk memahami hubungan genetik pada spesies ikan ini, maka dilakukan analisis molekuler menggunakan ruas gen CO1. Sejumlah spesies ikan (famili Serranidae) dikumpulkan dari wilayah Sulawesi Selatan seperti Sinjai dan Kepulauan Selayar. Karakter fenotip diidentifikasi menggunakan buku katalog spesies kerapu dunia FAO, kemudian sampel yang diduga C. urodeta secara morfologi dipisahkan. Jaringan yang digunakan sebagai sumber DNA adalah jaringan otot bagian dorsal. Berdasarkan sebagian runutan gen CO1, diyakini bahwa sampel tersebut adalah C. urodeta. Runutan basa nukleotida dari sampel dibandingkan dengan 22 runutan basa nukleotida C. urodeta dari GenBank. Berdasarkan rekonstruksi pohon filogeni, C. urodeta dari Sinjai dan Kepulauan Selayar mengelompok dengan C. urodeta dari berbagai tempat seperti Polynesia, Mariana Utara, Filipina, pulau-pulau di sekitar Madagascar (Ouest, St. Gilles, Canyon, Cimetiere, Jaune) dan Adaman, sedangkan sampel dari Laut Arab di lepas pantai India berada pada cabang yang terpisah. Penelitian ini menyatakan bahwa C. urodeta yang melibatkan beberapa tempat dari berbagai perairan seperti Samudera Pasifik bagian Selatan (Polynesia), Samudera Pasifik bagian Utara (Northern Mariana), Laut China Selatan (Filipina), Teluk Bengal (Andaman), Laut Laccadive (reunion of Ouest, St. Gilles and Cimetiere), Laut Arab dan Indo Pasifik Barat (Indonesia) memiliki perbedaan jarak genetik yang kecil. Hal ini berimplikasi pada pemahaman pola migrasi spesies tersebut dan sebagai bahan pertimbangan pengambilan kebijakan konservasi. Kata kunci: Cephalopholis urodeta, CO1, filogenetik, Serranidae, Sulawesi Selatan Cephalopholis is one of the largest genera belonging to Subfamilly Epinephelinae, which has various species. Phenotypically, an adult C. urodeta similar to a juvenile of C. sonnerati, since both of them have a striking trait, two white oblique stripes or bands on the caudal fins. This work was conducted to investigate the genetic relationships of this species using CO1 gene segment. Fish were collected from several sampling point in South Sulawesi areas such as Sinjai and Selayar Island. The phenotypic characterizations were identified using the FAO species catalogue of groupers of the world, and the species that seemed to have C. urodeta morphology then separated. Tissue samples from dorsal muscle tissue were used as the source of DNA. Using part of the CO1 gene sequence, it can be confirmed that our samples are exactly C. urodeta species. The 22 C. urodeta sequences from GeneBank compared with our sequences. Interestingly, because based on the phylogenetic tree, our sequences clustered with the other C. urodeta sequences from several part of the world except the Arabian Sea off the coast of India, which is a separate branch. The present study reveals less genetic distance in C. urodeta than some other parts of the ocean as follows; South Pacific Ocean (Polynesia), North Pacific Ocean (Northern Mariana), South China Sea (Philippines), Andaman, west coast of Réunion Island, Arabian Sea and Indo West Pacific (Indonesia). This has implications for understanding the migration pattern of the species and may affect conservation policy decisions. Keywords: Cephalopholis urodeta, CO1, phylogenetics, Serranidae, South Sulawesi
Kejadian Indel Simultan pada Intron 7 Gen Branched-Chain α-Ketoacid Dehydrogenase E1a (BCKDHA) pada Sapi Madura Febriana, Asri; Farajallah, Achmad; Perwitasari, Dyah
Jurnal Ilmu Pertanian Indonesia Vol 20, No 2 (2015): Jurnal Ilmu Pertanian Indonesia
Publisher : Institut Pertanian Bogor

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Abstract

Madura cattle is one of the Indonesian local cattle breeds derived from crossing between Zebu cattle (Bos indicus) and banteng (Bos javanicus). Branched-chain α-ketoacid dehydrogenase (BCKDH) is one of the main enzyme complexes in the inner mitochondrial membrane that metabolizes branched chain amino acid (BCAA), ie valine, leucine, and isoleucine. The diversity of the nucleotide sequences of the genes largely determine the efficiency of enzyme encoded. This paper aimed to determine the nucleotide variation contained in section  intron 7, exon 8, and intron 8 genes BCKDHA on Madura cattle. This study was conducted on three Madura cattle that used as bull race (karapan), beauty contest (sonok), and beef cattle. The analysis showed that the variation in intron higher than occurred in the exon. Simultaneous indel found at base position 34 and 68 in sonok cattle. In addition, the C266T variant found in beef cattle. These variants do not cause significant changes in amino acids. There was no specific mutation in intron 7, exon 8, and intron 8 were found in Madura cattle designation. This indicated the absence of differentiation Madura cattle designation of selection pressure of BCKDHA gene.
Keragaman Gen K-Kasein dan Hubungannya dengan Produksi dan Kualitas Susu pada Domba di Unit Pendidikan dan Penelitian Peternakan (UP3) Jonggol Sumantri, Cece; Andreas, Eryk; Farajallah, Achmad; Jarmuji, Jarmuji
Jurnal Ilmu Pertanian Indonesia Vol 13, No 1 (2008): Jurnal Ilmu Pertanian Indonesia
Publisher : Institut Pertanian Bogor

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Abstract

The objectives of this study were to identify polymorphisms in ovine K-casein gene exon 4 and its association with milk yield, percentage of protein and milk fat in sheep under extcnsif management at JASTRU (Jonggol Animal Studies Teaching and Research Unit) farm, Fact. of Anim Sci, Bogor Agric. University. The 83 blood sample from ewes which have record of milk production were used to determined polymorphism by using PCR-SSCP (Polymerase Chain Reaction-Single Strand Conformation Polymorphism) methode. The research activities were carried out through blood collection, DNA isolation, and fragment DNA amplification by PCR and separation in electrophoresis with silver staining. Electrophoretic pattern (PCR-SSCP) revealed th rce types of K-casein gene were dcsignitcd A, Band C type. The highest proportion was A type 69.57% and followed hy B 28.99% and the lowest C 1.45%. The were no significant effect of types of of K-casein gene on milk production and milk quality (percentage of protein and fat) in local sheep from Jonggol.   Keywords: .Jonggol sheep, K-cascin gcn, PCR-SSCP, polymorphism
Diversity and Abundance of Sand Crabs on the South Coast of Central Java (Diversitas dan Kelimpahan Kepiting Pasir di Pantai Selatan Jawa Tengah) Mashar, Ali; Wardiatno, Yusli; Boer, Mennofatria; Butet, Nurlisa A.; Farajallah, Achmad
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 19, No 4 (2014): Jurnal Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

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Abstract

Kepiting pasir atau undur-undur laut merupakan biota bentik yang hidup di pantai berpasir yang mempunyai nilai ekologi dan nilai ekonomi cukup penting. Adanya tekanan penangkapan mengharuskan adanya pengelolaan yang bijak yang disesuaikan dengan karakteristik populasi kepiting pasir. Informasi tentang jenis dan kelimpahan kepiting pasir penting untuk diketahui terlebih dahulu sebagai langkah awal upaya pengelolaan lestari kepiting pasir. Penelitian ini bertujuan untuk mengetahui komposisi jenis dan kelimpahan setiap jenis kepiting pasir yang terdapat di dua lokasi penelitian, yaitu pantai Bocor, Kabupaten Kebumen, dan pantai Bunton, Kabupaten Cilacap. Hasil penelitian menunjukkan bahwa di kedua lokasi penelitian ditemukan tiga jenis kepiting pasir, yaitu Emerita emeritus, Hippa adactyla, dan Albunea symmysta. Kepiting pasir E. emerita ditemukan dengan persentase komposisi paling besar, 70,5%-75,3%; disusul H. adactyla 22,5%-24,7%; dan A. symmysta 2,2%-4,8%. Kepiting pasir betina dijumpai dengan persentase komposisi paling tinggi, yaitu 78,2% hingga 92,8%. Kepiting pasir E. emeritus juga ditemukan dengan kelimpahan rata-rata paling tinggi di kedua lokasi penelitian, yaitu 5 dan 34 ekor/100m2. Kepiting pasir E. emeritus dan H. adactyla yang ditemukan di pantai Bunton, Cilacap mempunyai kelimpahan lebih tinggi dari yang ditemukan di pantai Bocor, Kebumen, adapun kelimpahan rata-rata Albunea symmysta relatif sama di kedua lokasi penelitian, yaitu sekitar 1 ekor/100m2. Implikasi dari hasil penelitian ini adalah diversitas kepiting pasir di pesisir selatan Jawa Tengah relatif tinggi dengan kelimpahan yang berbeda-beda yang dipengaruhi oleh intensitas aktivitas manusia di wilayah pantai berpasir. Kata kunci: Albunea symmysta, Emerita emeritus, Hippa adactyla, kelimpahan, kepiting pasir, komposisi jenis  Sand crabs or mole crabs are benthic fauna that live in the sandy beaches. They have ecological and economic value. Because of fishing pressure to this organism, it requires wise management based on the characteristics of the sand crab population. Information on the type and abundance of sand crabs is important as an initial step in sustainable management of sand crabs. This study aims to determine the species composition and abundance of each species of sand crabs. Sand crab specimens were collected from two study sites, namely Bocor beach, Kebumen, and Bunton beach, Cilacap. The results showed that in both sites found three species of sand crabs, namely Emerita emeritus, Hippa adactyla, and Albunea symmysta. E. emerita found in greatest composition percentage, 70.5% -75.3%; followed by H. adactyla 22.5% -24.7%; and A. symmysta 2.2% -4.8%. Females sand crab found in highest composition percentage, which is 78.2% to 92.8%. E. emeritus were also found in highest abundance average in both sites, 5 and 34 ind.100m-2. E. emeritus and H. adactyla were found on Bunton beach, Cilacap have abundance higher than that found on Bocor beach, Kebumen, while average abundance ofAlbunea symmysta relatively similar in both study sites, which is about 1 ind.100m-2. Implication of this research is high diversity of sand crabs relatively on the southern coast of Central Java with varying abundance that affected by intensity of human activities in the sandy beach area. Keywords: abundance, Albunea symmysta, Emerita emeritus, Hippa adactyla, sand crab, species composition