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HAYATI Journal of Biosciences

hayati
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Published by Institut Pertanian Bogor

ISSN : 19783019 EISSN : 20864094 DOI : -

Core Subject : Science, Agriculture,

Agriculture, Biological Sciences & Forestry Earth & Planetary Sciences

HAYATI Journal of Biosciences (HAYATI J Biosci) publishes articles and short communication in tropical bioscience fields such as development, biotechnology, biodiversity and environmental issues. HAYATI J Biosci covers wide range of all life forms topics including virus, microbes, fungi, plants, animal and human. HAYATI J Biosci has been also indexed/registered in Crossref, DOAJ, CABI, EBSCO, Agricola and ProQuest.

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Articles 1,077 Documents

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Expression Study of Banana Pathogenic Resistance Genes Fenny M. Dwivany; Rizkita Rahmi Esyanti; Aksarani 'Sa Pratiwi; Herafi Zaskia
HAYATI Journal of Biosciences Vol. 23 No. 4 (2016): October 2016
Publisher : Bogor Agricultural University, Indonesia

Banana is one of the world's most important trade commodities. However, infection of banana pathogenic fungi (Fusarium oxysporum race 4) is one of the major causes of decreasing production in Indonesia. Genetic engineering has become an alternative way to control this problem by isolating genes that involved in plant defense mechanism against pathogens. Two of the important genes are API5 and ChiI1, each gene encodes apoptosisinhibitory protein and chitinase enzymes. The purpose of this study was to study the expression of API5 and ChiI1 genes as candidate pathogenic resistance genes. The amplified fragments were then cloned, sequenced, and confirmed with in silico studies. Based on sequence analysis, it is showed that partial API5 gene has putative transactivationdomain and ChiI1 has 9 chitinase family GH19 protein motifs. Data obtained from this study will contribute in banana genetic improvement.

Microencapsulation Improved Probiotics Survival During Gastric Transit Amal Bakr Shori
HAYATI Journal of Biosciences Vol. 24 No. 1 (2017): January 2017
Publisher : Bogor Agricultural University, Indonesia

Several studies have demonstrated differences among strains of probiotic bacteria with regard to their survival in acid environment. Probiotics must survive in gastric acids to reach the small intestine and colonize the host for appropriate prevention and management of several gastrointestinal diseases. To improve the survival rates of probiotic microorganisms during gastric transit, microencapsulation is considered to be a promising process. A variety of polymers are commonly used for microencapsulation. Thus, there is a widespread interest in the improvement of the physical and mechanical stability of the polymers use in probiotics encapsulation. In addition, there is a developing trend toward the use of milk proteins as encapsulation device. To fulfill many demands of a successful probiotics encapsulation, different techniques have been applied to increase the resistance of these sensitive microorganisms against gastric conditions. Therefore, the objective of this study is to review the effect of microencapsulation on survival of probiotics in an in vitro model simulating gastric transit.

Metagenomic Survey of Potential Symbiotic Bacteria and Polyketide Synthase Genes in an Indonesian Marine Sponge Nia M. Kurnia; Agustinus R. Uria; Yudi Kusnadi; Lidia Dinawati; Dewi S. Zilda; Tri A. Hadi; Siswa Setyahadi; Feliatra Felix
HAYATI Journal of Biosciences Vol. 24 No. 1 (2017): January 2017
Publisher : Bogor Agricultural University, Indonesia

There has been emerging evidence that the bacteria associated with marine sponges are the key producers of many complex bioactive compounds. The as-yet uncultured candidate bacterial genus “Candidatus Entotheonella” of the marine sponge Theonella swinhoei from Japan have recently been recognized as the source of numerous pharmacologically relevant polyketides and modified peptides, as previously reported by the Piel group (Wilson et al. 2014). This work reported the presence of “Candidatus Entotheonella sp.” in the highly complex microbiome of an Indonesian marine sponge from Kapoposang Island, SouthSulawesi. We further identified the Kapoposang sponge specimen used in this work as Rhabdastrella sp. based on the integrated morphological, histological, and cytochrome oxidase subunit I (COI) gene analyses. To detect the polyketide biosynthetic machinery called type I polyketide synthase (PKS) in this Indonesian Rhabdastrella sp., we amplified and cloned the ketosynthase-encoding DNA regions of approximately 700 bp from the uncultured sponge's microbiome. Further sequencing and analysis of several randomly chosen clones indicated that all of them are mostly likely involved in the biosynthesis of methyl-branched fatty acids. However, employing a PKS-targeting primer designed in this work led to the isolation of four positive clones. BlastX search and subsequent phylogenetic analysis showed that one of the positive clones, designed as RGK32, displayed high homology with ketosynthase domains of many type I PKS systems and may belong to the subclass cis-AT PKS group.

Habitat Use of Migratory Shorebirds on the Coastline of Deli Serdang Regency, North Sumatra Province Chairunas Adha Putra; Dyah Perwitasari-Farajallah; Yeni Aryati Mulyani
HAYATI Journal of Biosciences Vol. 24 No. 1 (2017): January 2017
Publisher : Bogor Agricultural University, Indonesia

Mangrove forests an intertidal mudflat in the eastern coastal region of Deli Serdang are important habitats for migratory shorebirds. Land-use change and forest conversion threaten this important stopover point for migrating species. The lack of data and information of shorebirds habitats in this area limits conservation efforts and further threatens the survival of these species. The objective of this study is to investigate trends in habitat use by migratory shorebirds. Field work was conducted during migration season starting from October 2014 until April 2015. The presence of migratory shorebirds was assessed using binoculars and a monocular. Scan sampling was used to describe habitat use by shorebirds. The difference in behaviour among habitat was analyzed using analysis of variance. There were 30 species of shorebirds distributed across seven different habitat types in our study area. The most widely used habitat by shorebirds was mudflats, followed by marshes and plantations. This study revealed that mudflat habitat has high potential in supporting the existence of migratory shorebirds in this area.

Prevalence and Genotypic Distribution of Hepatitis C Virus in Peshawar KPK, Pakistan Tanweer Kumar; Nazir Ahmad; Mian Khizar Hayat; Bo-Xuan Gao; Shah Faisal; Nikhat Ilahi; Barkat Ali; Sahib Zada; Wasim Sajjad
HAYATI Journal of Biosciences Vol. 24 No. 1 (2017): January 2017
Publisher : Bogor Agricultural University, Indonesia

This present study was planned to obtain an up-to-date picture of Hepatitis C virus (HCV) infection and its genotypes distribution in Peshawar, Khyber Pakhtunkhwa, Pakistan, as well as of the relationship between HCV genotypes and demographic and clinical parameters, and the risk factors in patients with an HCV subtype. Samples (blood) from 1978 individuals were collected and were tested using a strip-based method called the immunochromatographic test (ICT) for the existence of antibodies against HCV. It was observed that 158 of the 1978 individuals (7.9%) harbored antibodies in their blood against HCV, among which the female percentage (53.2%) was higher than that of the male (46.8%). Among the different age groups, the highest number of incidences of HCV antibodies was found in the age group of 31–40 years (26.6%). ICT positive samples were further screened by polymerase chain reaction (PCR) to determine the existence of active HCV-RNA, and it was found that 6.21% (123) of the total population (1978) tested, was positive, among which the female rate (56.91%) was observed to be higher than that of the male (43.09%). The highest incidence recorded was in the age group of 41–50 years (33.3%). HCV RNA positive individuals were genotyped: genotype 3a (45.5%) was dominant among the other detected genotypes, followed by 1a (11.4%), 3b (4.9%), and 2a (4.1%). It was concluded that the highest prevalence of HCV was found in females, and that the dominant genotype of the screened individuals was 3a genotype.

Morphological and Molecular Diversity of Aspergillus From Corn Grain Used as Livestock Feed Noor Atiqah Zulkifli; Latiffah Zakaria
HAYATI Journal of Biosciences Vol. 24 No. 1 (2017): January 2017
Publisher : Bogor Agricultural University, Indonesia

The study of Aspergillus from corn grains used as livestock feed is important to ensure the safety of the grains as the occurrence of Aspergillus in the corn grain can give an indication of mycotoxin being produced. Morphological and molecular identifications were applied to identify Aspergillus isolated from corn grains used as livestock feed. Morphologically, six species were tentatively identified, namely Aspergillus niger (Groups I and II), Aspergillus flavus, Aspergillus oryzae, Aspergillus fumigatus, Aspergillus clavatus and Aspergillus terreus. Isolates of A. niger was divided into two groups based on slight differences of their colony appearances. Molecular identification using internal transcribed spacer and β-tubulin sequences supported morphological identification except isolates for A. niger Group II isolates, which were molecularly identified as Aspergillus tubingensis. Neighbour-joining phylogenetic tree showed that isolates from the same species were grouped in the same clade. The present study showed that diverse species of Aspergillus are prevalent in corn grain used as livestock feed. It is also necessary to correctly identify the Aspergillus species to employ correct treatment of contaminated corn grains. The occurrence of well-known toxigenic species such as A. niger, A. flavus and A. fumigatus suggested the possible risk of mycotoxin contamination of the corn grain.

Diversity of Protease-Producing Bacillus spp. From Fresh Indonesian Tempeh Based on 16S rRNA Gene Sequence Tati Barus; Linda Wati; . Melani; Antonius Suwanto; . Yogiara
HAYATI Journal of Biosciences Vol. 24 No. 1 (2017): January 2017
Publisher : Bogor Agricultural University, Indonesia

Tempeh is a type of traditional fermented food in Indonesia. The fermentation can be performed by Rhizopus microsporus as a main microorganism. However, Bacillus spp. is found in abundance in tempeh production. Nevertheless, information regarding the diversity of Bacillus spp. in tempeh production has not been reported yet. Therefore, the aim of this investigation was to study the genetic diversity of Bacillus spp. in tempeh production based on the 16S ribosomal RNA sequence. In this study, about 22 of 24 fresh tempeh from Jakarta, Bogor, and Tangerang were used. A total of 52 protease-producing Bacillus spp. isolates were obtained. Based on 16S ribosomal RNA results, all 52 isolates were identified to be similar to B. pumilus, B. subtilis, B. megaterium, B. licheniformis, B. cereus, B. thuringiensis, B. amyloliquefaciens, Brevibacillus brevis, and Bacillus sp. All the identified isolates were divided into two large clusters: 1) a cluster of B. cereus, B. thuringiensis, Bacillus sp., and B. brevis and 2) a cluster of B. pumilus, B. subtilis, B. megaterium, B. licheniformis, and B. amyloliquefaciens. Information about the Bacillus spp. role in determining the quality of tempeh has not been reported and this is a preliminary study of Bacillus spp. from tempeh.

Genetic Divergence and Phylogenetic Relationships Among Indonesian Species of Monitor Lizards of the Genus Varanus Based on Cytochrome Oxidase I Sequences Evy Arida
HAYATI Journal of Biosciences Vol. 24 No. 1 (2017): January 2017
Publisher : Bogor Agricultural University, Indonesia

The application of cytochrome oxidase subunit I for genetic divergence and phylogenetic analyses in monitor lizards seems to be limited, despite the practicality and relevance to use the short sequence of this region known as the DNA barcode. Some Indonesian species of monitor lizards are morphologically similar, some of which are legally exported as pet animal commodities and some others being protected by Indonesian national law. Thus, a practical molecular tool that can be useful to help clarify their species identity is essential, especially for closely related species. This study used the DNA barcode to test the application of this mitochondrial DNA region as a molecular tool to identify some species of Indonesian monitor lizards for the first time. Results showed that the Barcodes can facilitate molecular speciesidentification based on their relative amount of genetic divergence and phylogenetic relationships. Closely related species can be distinguished based on the short sequences, as well as a likelihood of species misidentification among samples in this study. Further study should be performed in the future using more species, especially those belong to groups of species complex from the eastern Indonesia and species protected by the Indonesian national law.

Endophytic Fungi Associated With Turmeric (Curcuma longa L.) Can Inhibit Histamine-Forming Bacteria in Fish Eris Septiana; Nampiah Sukarno; . Sukarno; Partomuan Simanjuntak
HAYATI Journal of Biosciences Vol. 24 No. 1 (2017): January 2017
Publisher : Bogor Agricultural University, Indonesia

Turmeric (Curcuma longa L.) is a medicinal plant that is commonly used as spice and preservative. Many types of endophytic fungi have been reported as being associated with medicinal plants and able to synthesize secondary metabolites. In this study, endophytic fungi were isolated from all plant parts of turmeric plants. Identification of the endophytic fungi was done using morphological characteristics and sequencing of the internal transcribed spacer (ITS) region of ribosomal DNA. The dual culture method was used for screening antibacterial activity of the endophytic fungi against Morganella morganii, a common histamine-producing bacteria. The disc diffusion method was used to test the ability of water fractions of selected endophytic fungi to inhibit M. morganii growth. Two-dimensional thin layer chromatography was used to determine the fungal extract inhibition activity on histamine formation. In total, 11 endophytic fungi were successfully isolated and identified as Arthrobotrys foliicola, Cochliobolus kusanoi, Daldinia eschscholzii, Fusariumoxysporum, Fusarium proliferatum, Fusarium solani, Fusarium verticillioides, Phanerochaete chrysosporium, and Phaeosphaeria ammophilae. Five isolates showed inhibition activity against M. morganii in the dual culture tests. Based on the disc diffusion assay, A. foliicola and F. verticillioides inhibited the growth of M. morganii as a histamine-producing bacteria, and inhibiting histamine formation in fish. The best effects in inhibiting growth of the histamine-producing bacteria and histamine formation inhibition in fish were produced with F. verticillioides water fraction at 0°C incubation.

Emerging Developments on Pathogenicity, Molecular Virulence, Epidemiology and Clinical Symptoms of Current Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Subbaram, Kannan; Kannan, Hemalatha; Gatasheh, Mansour Khalil
HAYATI Journal of Biosciences Vol. 24 No. 2 (2017): April 2017
Publisher : Bogor Agricultural University, Indonesia

Middle East respiratory syndrome coronavirus (MERS-CoV) is a recently reported virus that is associated with severe, life threatening and rapidly spreading primarily respiratory illness called the Middle East respiratory syndrome. MERS-CoV possesses a unique positive-sense single-stranded RNA and can undergo rapid mutation in the viral genome. This results in antigenic switching and genetic variation, finally leading to the emergence of novel and new MERS-CoV subtypes which are uncontrollable by vaccines. Researchers are also finding difficulties to sort out therapeutic intervention strategies for MERS-CoV. This virus can spread from human to human, but transmission from dromedary camels to humans plays a crucial epidemiological significance. Dromedary camel acts as “gene mixing vessels” for MERS-CoV and these virus particles undergo rapid change in them. Viral receptors called dipeptidyl peptidase-4 are important receptors for attachment and spread of MERS-CoV in humans. The current method of laboratory confirmation is through real-time polymerase chain reaction on bronchoalveolar lavage, sputum and tracheal aspirates. Unfortunately, till today there are no definite anti-viral drugs available for MERS-CoV.

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