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All Journal HAYATI Journal of Biosciences Jurnal Ilmu Pertanian Indonesia Jurnal Sumberdaya Hayati Makara Journal of Science
ALFIYAN, ACHMAD
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Earth & Planetary Sciences Immunology & microbiology

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Characterization of Exon and Intron of Defensin 1 Gene in Apis cerana and Apis dorsata Alfiyan, Achmad; Raffiudin, Rika; Astuti, Rika Indri
Makara Journal of Science Vol. 23, No. 3
Publisher : UI Scholars Hub

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Abstract

Honey bee defensin 1 gene belongs to the class of immunity genes in this social insect. The peptide acts as a defensive mechanism against infections caused by Gram-positive bacteria. The aim of this study was to characterize exon 2, intron 2, and exon 3 of defensin 1 gene in both the Indonesian honey bees Apis cerana and A. dorsata. First, defensin 1 genes of A. cerana and A. dorsata were sequenced, after which a bioinformatic analysis was conducted. The amplified length of these defensin 1 genes of A. cerana and A. dorsata were 479 and 458 bp, respectively, and their putative amino acid sequences comprised 66 and 65 amino acids, respectively, with 6 cysteine residues. The cysteine residues formed a disulfide bond and then linked the three domains in the defensin peptide with each other, thereby allowing the lysis of the bacterial membrane through pore formation. Intron 2 of the defensin gene demonstrated nucleotide variations between A. cerana from Indonesia and that from Korea and between A. dorsata from Indonesia and that from Malaysia; the latter species also demonstrated variations in exon 3. Phylogenetic tree topology of the bee, which was constructed based on defensin 1 gene, was compatible with a previous study showing that A. cerana and A. dorsata are more closely related to A. mellifera than to A. florea.
Characterization of CDS Region of Exons 1 and 2 of SOX9 Gene as Potential Gene in Construction of Syrinx Structure in Junglefowl (Gallus sp.) Alfiyan, Achmad; Farajallah, Achmad; Maria, Ulfah; Perwitasari-Farajallah, Dyah; Muladno, Muladno
HAYATI Journal of Biosciences Vol. 31 No. 6 (2024): November 2024
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.31.6.1130-1143

Abstract

The crowing of male Gallus exhibits diverse sound patterns. This is believed to be related to the phenotypic diversity of vocal organs, one of which is influenced by the nucleotide diversity of the associated genes. The SOX9 gene, involved in cartilaginous tissue growth and development, is reported to contribute e in the development of larynx and syrinx. This study aimed to characterize the CDS regions of exons 1 and 2 of the SOX9 gene in junglefowl to assess its diversity. Genomic DNA was extracted from ten individuals of G. varius from Lombok and Sumbawa. The CDS regions of SOX9 gene exons 1 and 2 were amplified using two primer pairs. Additionally, the CDS regions of SOX9 gene exons 1 and 2 from 54 junglefowl SRA data in an online repository were mapped and analyzed. The study identified all nucleotide sequences as CDS regions of SOX9 gene exons 1 and 2. Six shared, and 24 unique haplotypes were constructed. A putative amino acid sequence common to all Gallus species was also identified. The diversity observed in the CDS regions of SOX9 gene exons 1 and 2 nucleotide sequence showed a different level with the diversity observed in its amino acid sequence.
Kompleksitas Obyek dan Running-Wheel Mempengaruhi Novel Object Recognition Test pada Mencit (Mus musculus) HANIM, NISFA; WIDYASTUTI, SALMAH; ALFIYAN, ACHMAD; AKBAR, MUHAMMAD AZHARI; JULIANDI, BERRY
Jurnal Sumberdaya Hayati Vol. 4 No. 1 (2018)
Publisher : Departemen Biologi, Institut Pertanian Bogor

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29244/jsdh.4.1.7-11

Abstract

This research aimed to confirm the tendency of mice to novel object, effect of exercise (in running-wheel) toward memory of mice and to test tendency of mice in avoiding predator signal in novel object. Novel object recognition test (NORT) used to test the memory the day after acquisition phase (NORT I) and memory one week after exercise was given (running-wheel) (NORT II). The result showed that there was no tendency of mice in exploring toward novel object in both NORT I and NORT II. This might happen because the complexity of familiar object higher than novel object, so the familiar object could accommodate more activities. Exercise using running-wheel in mice had an effect on memory, it could be seen in decreasing duration of object exploration time from NORT I to NORT II. There was no tendency in avoiding predator’s signal on novel object which was attached by urine addition (odor signal).
Karakterisasi Ekson 4 Gen DRD4 pada Ayam Arab Tiara G15 dengan Tingkah Laku Feather Pecking Farajallah, Achmad; Wijayanti, Pristina Tuti; Alfiyan, Achmad; Ulfah, Maria
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
Co-Authors ACHMAD FARAJALLAH AKBAR, MUHAMMAD AZHARI Berry Juliandi DYAH PERWITASARI -FARAJALLAH HANIM, NISFA Maria Ulfah Maria Ulfah Rika Indri Astuti RIKA RAFFIUDIN WIDYASTUTI, SALMAH Wijayanti, Pristina Tuti