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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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Dietary Variation of Long Tailed Macaques (Macaca fascicularis) in Telaga Warna, Bogor, West Java SARAH NILA; BAMBANG SURYOBROTO; KANTHI ARUM WIDAYATI
HAYATI Journal of Biosciences Vol. 21 No. 1 (2014): March 2014
Publisher : Bogor Agricultural University, Indonesia

The genus Macaca, member of sub-family Cercopithecinae, is the most widely distributed non-human primates in Asian countries. The habitats are strongly influence the dietary variation of the populations. The dietary variation of the macaques reflect ecological plasticity in coping with differences both in availability and abundance of food. The macaques are plastic in taking any kind of food that available in their home range and adjust their behaviour according to its abundance. Here, we present the dietary variation of long-tailed macaques (Macaca fascicularis) in the high altitude rain forest of Telaga Warna, West Java, Indonesia. The proportion of their food from natural sources is greater than those from visitors. The natural food consisted of plants, small animals (insects and earthworm), fungi and water from lake. The plant food comprised of 29 species plus a few mosses. The frequency of eating artificial food was influenced by visitors who come for picnic. In this site, the macaques learned that the visiting of tourists is identical with food.

Identification of New Lactone Derivatives Isolated from Trichoderma sp., An Endophytic Fungus of Brotowali (Tinaspora crispa) . ELFITA; . MUNAWAR; . MUHARNI; MASTUR ADHY SUDRAJAT
HAYATI Journal of Biosciences Vol. 21 No. 1 (2014): March 2014
Publisher : Bogor Agricultural University, Indonesia

Endophytic fungi is a rich source of novel organic compounds with interesting biological activities and a high level of structural diversity. As a part of our systematic search for new bioactive lead structures and specific profiles from endophytic fungi, an endophytic fungus was isolated from roots of brotowali (Tinaspora crispa), an important medicinal plant. Colonial morphological trait and microscopic observation revealed that the endophytic fungus was Trichoderma sp. The pure fungal strain was cultivated on 7 L Potatos Dextose Broth (PDB) medium under room temperature (no shaking) for 8 weeks. The ethyl acetate were added to cultur medium and left overnight to stop cell growth. The culture filtrates were collected and extracted with EtOAc and then taken to evaporation. Two new lactone derivatives, 5-hydroxy-4-hydroxymethyl-2H-pyran-2-one (1) and (5-hydroxy-2-oxo-2H pyran-4-yl) methyl acetate (2) were obtained from the EtOAc extracts of Trichoderma sp. Their structures were determined on the basic of spectroscopic methods including UV, IR, 1H-NMR, 13C-NMR, HMQC, and HMBC.

Independent Effects of Temperature, Salinity, Ammonium Concentration and pH on Nitrification Rate of the Ariake Seawater Above Mud Sediment ALIM ISNANSETYO; SAI GETSU; MASAHIRO SEGUCHI; MASUMI KORIYAMA
HAYATI Journal of Biosciences Vol. 21 No. 1 (2014): March 2014
Publisher : Bogor Agricultural University, Indonesia

The Ariake Sea located in the west parts of Kyushu Island is a semi-closed and macro-tidal shallow sea, and has the largest tidal flat in Japan. A large mud tidal flat with a productive ecosystem found along the western shoreline of the sea makes this area ideal as a major production site of nori (Porphyra yezoensis) in Japan. We determined the independent effect of temperature, salinity, ammonium concentration and pH on nitrification rates (NR) in the Ariake seawater above the mud sediment. The NR was determined by measuring accumulation of NO2-N production after adding sodium chlorate, an inhibitor of NO2-N to NO3-N oxidation. NRs were relatively high at 20-35 oC (optimum at 29.5 oC), but the rates were very low at 5, 10, and 40 oC. NRs increased sharply when increasing the salinity from 13 to 20 ppt, but it decreased drastically at salinity levels more than 35 ppt (optimum at 19 ppt). The relationship between ammonium concentration and NR showed a typical kinetic curve of enzymatic reaction with the maximum NR (Vmax) of 0.029 mM N.h-1 at 200 mM NH4-N (the half saturation constant (Ks) = 35 mM NH4-N). High NRs were determined at pH 7.5-8.0 (optimum pH 7.8). This is the first report on the independent effects of temperature, pH, salinity and NH4-N concentration on the NR of seawater, specifically the Ariake seawater.

Field Adaptation of Some Introduced Wheat (Triticum aestivum L.) Genotypes in Two Altitudes of Tropical Agro-Ecosystem Environment of Indonesia ADEEL ABDUL KARIM ALTUHAISH; . MIFTAHUDIN; . TRIKOESOEMANINGTYAS; SUDIRMAN YAHYA
HAYATI Journal of Biosciences Vol. 21 No. 1 (2014): March 2014
Publisher : Bogor Agricultural University, Indonesia

Heat stress is a major environmental factor limiting wheat productivity in tropical regions such as Indonesia. The objective of this study was to investigate the adaptability of introduced wheat genotypes in tropical agro-ecosystems. Sixteen spring wheat genotypes were grown at two different altitudes i.e. low altitude (176 m asl) with an average temperature of 29.8 oC located at Leuwikopo Field Experimental Station, Bogor Agricultural University, Darmaga Bogor and high altitude (1100 m asl) with an average temperature of 20.6 oC at Cipanas Field Experimental Station (Ornamental Crop Research Station), Cianjur, West Java, Indonesia from July to November 2012. Plant height, number of tillers, flag leaf area, leaf angle, days to flowering, spike number per plant, empty spikelet number, grain weight per plant and 100 grain weight were observed following the standard methods. Heat susceptibility index was calculated based on grain weight per plant. The results showed that cultivation at a low altitude, hotter environment remarkably affected wheat growth and yield, as reflected in overall reduction of plant height, reduced number of tillers and leaf area, and ultimately reduced yield and yield components for most genotypes compared to the same measures taken at high altitude in lower temperatures. Plant growth before heading was similar in both locations, but the days to flowering was longer in high altitude than that in low altitude. High temperature stress in low altitude reduced the spike number/plant, grain weight/plant, 100 grain weight and increase number of empty spikelet/spike. Based on our results for heat susceptibility index, six genotypes, namely Sbr, Ymh, Astreb/Cbrd, Astreb/Ningma, H-20 and Nias, were characterized as heat tolerant genotypes.

Genetic Diversity of Musa balbisiana Colla in Indonesia Based on AFLP Marker FAJARUDIN AHMAD; RITA MEGIA; YUYU SURYASARI POERBA
HAYATI Journal of Biosciences Vol. 21 No. 1 (2014): March 2014
Publisher : Bogor Agricultural University, Indonesia

Musa balbisiana Colla, known as Pisang Klutuk/Pisang Batu, is important for banana breeding program due to its B genome and often considered to be resistant to pest, disease and drought. Banana is a big and tall herb up to 7-9 m in height.The study was conducted to assess genetic diversity of 21 accessions of M. balbisiana cultivars/varieties from Indonesia based on Amplified Fragment Length Polymorphism (AFLP) markers in order to provide basic information to support banana breeding program. Analyses of similarity index of Nei and Li and clustering based on UPGMA was conducted using NTSYS program. Principal Component Analysis (PCA) was conducted by MINITAB 14. Twenty two primer pairs of AFLP markers produced 485 AFLP bands varying from 51-3206 bp in size and 46.18% of the AFLP bands were polymorphic. Genetic diversity among the 21 accessions of M. balbisiana was 13.8%. The genetic diversity of wild M. balbisiana was 12.9%, higher than the genetic diversity of cultivated M. balbisiana which was 11.5%. Cluster analysis based on UPGMA suggested that wild M. balbisiana and cultivated M. balbisiana could not be separated into different clusters. Both cluster analysis and PCA produced the same three groups of the accessions. The PCA analyses showed that 17 AFLP bands were responsible for the grouping.

Haemozoin Detection in Mouse Liver Histology Using Simple Polarized Light Microscope DWI RAMADHANI; SITI NURHAYATI; TUR RAHARDJO
HAYATI Journal of Biosciences Vol. 21 No. 1 (2014): March 2014
Publisher : Bogor Agricultural University, Indonesia

The presence of malarial pigment (haemozoin) due to Plasmodium infection is a common histopathological effect in mouse liver. Previous research showed that by using a polarized light microscope, researchers were better able to detect haemozoin in mouse liver histology section. Thus, the aim of this research was to compare the haemozoin area observed by a conventional vs. simple polarized light microscope by using image processing analysis. A total of 40 images produced from both conventional light microscope and simple polarized light microscope were collected. All images were analyzed using ImageJ 1.47 software to measure the haemozoin areas. Our results showed that non birefringent haemozoin and birefringent haemozoin area was significantly different. This was because when using conventional light microscope the brown area that contained images of non birefringent haemozoin images also contained Kupffer cells which appeared as the same brown color as haemozoin. In contrast, haemozoin gave bright effect and can be easily differentiated with Kupffer cells in the birefringent haemozoin images. This study concluded that haemozoin detection in mouse liver histology using a simple polarized light microscope was more accurate compared to that of conventional light microscope.

Characterization of α-Nitrile Hydratase and Amidase of Rhodococcus aff. qingshengii from Indonesia AERMA HASTUTY; WIBOWO MANGUNWARDOYO; BAMBANG SUNARKO
HAYATI Journal of Biosciences Vol. 21 No. 2 (2014): June 2014
Publisher : Bogor Agricultural University, Indonesia

A study on biotransformation of acetonitrile using Gram-positive bacteria has been conducted. Two isolates of nitrile-degrading bacteria (strain 100A and 100D) were screened from sediments of a contaminated river in Cibinong, West Java. The bacterial isolates were identified as Rhodococcus aff. qingshengii based on molecular phylogenetic analyses of 16S rRNA sequence. These bacteria were capable to grow on medium containing 100 mM acetonitrile, but unable to grow on medium amended with 25 mM benzonitrile. Analyses using Gas Chromatography (GC) indicated that R. aff. qingshengii strain 100A and 100D has the ability to produce nitrile hidratase and amidase. The highest enzyme activity on mineral medium with the addition of 100 mM acetonitrile was 73.49 mmol/min/mL by strain 100A, and 70.52 mmol/min/mL by strain 100D. In addition, the ammonia concentration produced by strain 100A and 100D were 180.20 and 54.10 mM, respectively. These results were supported by molecular characterization using specific primers, where strain 100A and 100D positively contain genes encoding α-nitrile hydratase (α-NHase) and amidase. There was a difference at the first position of amino acid composition of the gene encoding α-NHase between strain 100A (Methionine1) and strain 100D (Glycine1), but the amino acids composition of amidase of both strain were identical. This is the first report of R. aff. qingshengii as nitrile-degrading bacterium in Indonesia.

Molecular Sex Determination of Captive Komodo Dragons (Varanus komodoensis) at Gembira Loka Zoo, Surabaya Zoo, and Ragunan Zoo, Indonesia SRI SULANDARI; MOCH SAMSUL ARIFIN ZEIN; EVY AYU ARIDA; AMIR HAMIDY
HAYATI Journal of Biosciences Vol. 21 No. 2 (2014): June 2014
Publisher : Bogor Agricultural University, Indonesia

Captive breeding of endangered species is often difficult, and may be hampered by many factors. Sexual monomorphism, in which males and females are not easily distinguishable, is one such factor and is a common problem in captive breeding of many avian and reptile species. Species-specific nuclear DNA markers, recently developed to identify portions of sex chromosomes, were employed in this study for sex determination of Komodo dragons (Varanus Komodoensis). Each animal was uniquely tagged using a passive integrated micro-transponder (TROVAN 100A type transponders of 13 mm in length and 2 mm in diameter). The sex of a total of 81 individual Komodo dragons (44 samples from Ragunan zoo, 26 samples from Surabaya zoo, and 11 samples from Gembira Loka zoo) were determined using primers Ksex 1for and Ksex 3rev. A series of preliminary PCR amplifications were conducted using DNA from individuals of known sex. During these preliminary tests, researchers varied the annealing temperatures, number of cycles, and concentrations of reagents, in order to identify the best protocol for sex determination using our sample set. We thus developed our own PCR protocol for this study, which resulted in the amplification of band A in females and band C in males. Results from band B, however, turned out to be non-determinative in our study because, for females, band B was not always visible, and for males sometimes a similar, but lighter band was also amplified, making interpretation difficult. In this study, sex determination was based mainly on the difference in size between the female-specific 812 bp fragment and the homologous, longer fragment amplified for males.

Prediction of Physicochemical Properties of Indonesian Indica Rice Using Molecular Markers PUJI LESTARI; . REFLINUR; HEE-JONG KOH
HAYATI Journal of Biosciences Vol. 21 No. 2 (2014): June 2014
Publisher : Bogor Agricultural University, Indonesia

Physicochemical properties determine the palatability and cooking quality of rice, which must be determined efficiently in order to satisfy consumer demand. To date, little information exists on the use of molecular markers to predict physicochemical properties of the “indica” rice varieties found in Indonesia. The objective of this study was to investigate physicochemical properties and genetic variation of Indonesian rice varieties, and to formulate regression equations to analyze sets of DNA markers which could predict amylose content (AC), protein content (PC) and pasting properties of the varieties. A total of 24 Indonesian indica rice varieties were chosen based on their genetic background and agricultural characteristics. We then measured selected physicochemical properties, and genotyped the varieties using 30 DNA markers. The chosen varieties showed favorable values for PC, AC, and six rapid viscosity analyzer (RVA) pasting properties, which was supported by molecular data. As demonstrated by principal component analysis (PCA), markers could provide a complementary method for differentiating rice varieties, as an alternative to measuring physicochemical properties. PCA analysis also allowed us to establish marker sets using multiple regression analysis. We formulated eight model regression equations comprising data regarding 15 to 19 markers with high coefficients (R2=0.98-0.99). The formulas provided results that consistently correlated and therefore predicted the physicochemical properties of indica rice. Further validation of these marker sets may provide rapid and efficient means for predicting the physicochemical properties of Indonesian-bred indica rice in the future.

Characterization of Trypsin-Like Protease of Lactobacillus plantarum FNCC 0270 Trismilah Margono; Wahono Sumaryono; Amarila Malik; Mohamad Sadikin
HAYATI Journal of Biosciences Vol. 21 No. 2 (2014): June 2014
Publisher : Bogor Agricultural University, Indonesia

Trypsin is an enzyme that has a unique mechanism of cutting peptide bonds specifically at the carboxyl side of lysine or arginine amino acids, with another amino acid. This study aims to analyze a trypsin-like protease (TLP) found in Lactobacillus plantarum FNCC 0270, by performing partial proteomic tests, i.e. MALDI-TOF/TOF, and standard bioinformatics tools. SDS-PAGE analysis showed 4 protein bands. Two bands of the (P1 and P2) showed molecular weights equivalent to 47.35 and 38.42 kD, each generating 8 and 11 peptide fragments respectively. According to information in www.ncbi.nlm.nih.gov/genbank/structures, the structure of serine protease HtrA (subs. plantarum L. plantarum ST–III) consists of three domains. Using Clone Manager® software by aligning two sequences we obtained eleven. The Lactobacillus produces of the trypsin-like serine protease has 40-90% similarity. Using the Clustal W2 software we passed the 11 sequences through multiple alignments, and found that the isolate L. plantarum is closely related to L. buchneri, L. brevis, and L. malefermentans on the phylogenetic tree. Alignment analysis results showed that all 8 peptide fragments of band 1 and 11 peptide fragments of band 2, of the SDS-PAGE, were located in the active domain region of the fourth trypsin-like serine protease producing Lactobacilli.

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