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The Impact of Storage Times of Museum Insect Specimens on PCR Success: Case Study on Moth Collections in Indonesia

HAYATI Journal of Biosciences Vol 19, No 2 (2012): June 2012
Publisher : Bogor Agricultural University, Indonesia

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Abstract

Museum specimens are vast repositories of genetic information of interests to biological researchers. Since a new method in DNA extraction, a non destructive method, has been reported to be successful in extracting DNA of museum specimens even fossils without any morphological damages, using museum specimens as resources of genetic information for molecular studies is becoming popular recently. However, the PCR success depends on the quality of the specimens. To evaluate the impact of the storage times of museum specimens on PCR success, we conducted DNA extraction of 14 dry museum specimens of the moths collected from 1992 to 2010 by using a non destructive method. The results showed that the DNA specimens museum were fragmented into various sizes (100-1000 bp) depend on the storage times. On the other hand, fresh specimens which were preserved within absolute ethanol were almost not fragmented. The specimens of < 6 years old (2005-2010) succeed to amplify in 650 bp amplicon but for some specimens of 7 years old (2 of 3 specimens) resulted in a very weak amplification. These specimens, however, were able to amplify strongly in 300 bp amplicon. The results also showed that specimens of 1-19 years old were success to amplify in 100 bp amplicon.

Molecular Phylogeny of Indonesian Armyworm Mythimna Guenée (Lepidoptera: Noctuidae: Hadeninae) Based on CO I Gene Sequences

HAYATI Journal of Biosciences Vol 19, No 2 (2012): June 2012
Publisher : Bogor Agricultural University, Indonesia

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Abstract

Armyworm Mythimna Guenée is one of the most important pests on graminaceous crops and pastures in South East Asia (i.e. M. separata Walker is well known to cause serious damages on rice in Indonesia). Like of most other genera of moths, the systematic of this genus is still in dispute, especially on the taxonomy and classification within this genus due to their morphological characters that are very difficult to distinguish from one to others. Molecular approaches such as using CO I gene sequence to differentiate among species has been recommended since this gene has ability to reveal the character identity at the specific level.  In order to populate the genetic characters of Indonesian Mythimna, to clarify the clasification within the genus Mythimna and to reveal the phylogenetic relationship among them, we analyzed 14 species of Mythimna and two species outgroups (Spodoptera litura dan S. exigua) based on nucleotide sequence variation across a 649 bp region in the CO I gene.  Over entire 649 bp region 72% of the nucleotide positions were constant, 10.6% were uninformtive (i.e. any variants were found in a single sequence) and 16.9% were parsimony informative. The informative site constituted in the 3rd codon position was the highest, whereas in 2nd codon position was the lowest. The results also showed that the base composition of this region was low A + T biased. The results showed that the monophyly of Mytimna was supported by 95% bootstrap test at any tree building methods. The three subgenera based on morphology were recovered but M. (Mythimna) shown to be a paraphyletic group in term of M. (Hyphilare), and M. (Pseudalteia); M. (Mythimna) was branched off first then followed by M. (Pseudaletia) and M. (Hyphilare).  However, all internal nodes were least support except for the monophyly of subgenus M. (Hyphilare). It indicates that the relationships among internal nodes proposed here were least valid due to the number of species included in the analysis which may not be enough to represent the real number of species in the nature. More investigation was needed by including more species and other genes.

The Impact of Human Activities to Dynamic of Insect Communities: a Case Study in Gunung Salak, West Java

HAYATI Journal of Biosciences Vol 17, No 4 (2010): December 2010
Publisher : Bogor Agricultural University, Indonesia

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Abstract

Huge areas of diverse tropical forest are lost or degraded every year with dramatic consequences for biodiversity. Human activities such as deforestation, fragmentation, over-exploitation, and monoculture practices are the main drivers of tropical forest biodiversity loss.  Investigating of these threats with focusses on changes in species richness or species diversity will be able to minimize any impact of human activities at the early stage in a certain region. Therefore, to know the impact of human activities to dynamic of insect communities in Gunung Salak, West Java, we measured moth diversity and their structure within communities by comparing the index diversity, species richness and species composition across five different habitat types. The results showed that the habitat changes due to human activities had changed not only to the moth diversity but also to their structure within communities. The number of moth species decreased significantly as well as the number of lower taxa (family) in the disturbed forest (secondary forest, Agathis forest, and transition area) within ranges: 20-50 and 10-20%.  The composition of the two main families, Geometridae and Noctuidae also showed a major change, family Geometridae decreased within ranges 10-50% in the disturbed area but Noctuidae increased up to 50% in those areas. Indeed, habitat lost due to human activities such as illegal logging, change of land use and land clearing is the main threats to decrease on macro-moth diversity and change their structures within communities.

Moth Diversity at Gunung Halimun-Salak National Park, West Java

HAYATI Journal of Biosciences Vol 15, No 3 (2008): September 2008
Publisher : Bogor Agricultural University, Indonesia

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Abstract

A study on moth fauna with focus on macro-moths was conducted at Gunung Halimun-Salak National Park from January to December 2007. The aims of the study were to acquire information of macro-moth diversity and to access the composition of the species at this area. Another objective of the research was to explore undescribed species of moths that inhabit this park. The result showed that a year collecting time with four sampling sites recorded only about 86% of estimated value in this park (846 of 983 species). Index diversity based on Fisheries ? is high. In addition, the number of families recorded from this park is also high, 29 families, or about half of the moth families that occur in Indo-Malayan region. Citiis site was the highest among other sites in term of the diversity index, while Gunung Botol is the lowest. These two sites have a few species in common. In general, Geometridae, Noctuidae, and Pyralidae dominate across all sites. The other significant finding of the research is that Dudgeonidae that has never been recorded from Indonesia was found at Citiis site. Key words: diversity, macro-moths, similarity

Molecular Phylogeny of Agrioglypta Meyrick and Talanga Moore (Lepidoptera: Crambidae; Spilomelinae) Inferred from Nuclear EF-1a Gene

HAYATI Journal of Biosciences Vol 12, No 2 (2005): June 2005
Publisher : Bogor Agricultural University, Indonesia

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Abstract

The phylogeny of the two closely- related genera, Agrioglypta Meyrick and Talanga Moore, was inferred from nucleotide sequence variation across a 973-bp region in the nuclear elongation factor-1 (EF-1) gene. Seven species representing the two genera and two outgroup species (Feltia jaculifera Guene and Metallarcha aureodiscalis Meyrick) were analyzed. The results showed the averages of the p-distances in the comparisons between species within genus and between species belonging to other different genera were 3.5% and 4.9%, respectively. EF-1 gene had almost reached saturation at the level of the divergence of these two genera. The phylogenetic analysis using MP and NJ methods showed that each genus was found to be a monophyletic group and the species relationships within each genus were almost consistent as well. A. eurytusalis is the basal species in the genus Agrioglypta. In the genus Talanga, T. sabacusalis lied in the basal node and T. tolumnialis was found to be sister group of T. sexpunctalis.

Moth Diversity at Sebangau Peat Swamp and Busang River Secondary Rain Forest, Central Kalimantan

HAYATI Journal of Biosciences Vol 12, No 3 (2005): September 2005
Publisher : Bogor Agricultural University, Indonesia

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Abstract

A study on the diversity of moths was conducted from July to Augustus 2004 at the peat swamp forest Setya Alam research station, Sebangau, Central Kalimantan. The result showed that diversity of moths at this area was lower (100 species of 12 families; H = 6.643, E = 0.794) than that in secondary rain forest Busang River (278 species of 19 families; H = 8.139, E = 0.831). The result also showed that the similarity index (Cj) of the two areas was very low (0.05). Geometridae, Noctuidae, and Pyralidae were dominant in both areas. There might be more species that have not been found during eight night sampling as indicated by the species numbers in both areas has not reach a plateau.

Evolution of a Wingless Gene and its Utility for Inferring the Relationships within Glyphodes Moths

HAYATI Journal of Biosciences Vol 13, No 4 (2006): December 2006
Publisher : Bogor Agricultural University, Indonesia

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Abstract

The evolution of a nuclear Wingless gene was investigated and its utility for inferring the phylogenetic relationship within Glyphodes moths was assessed by comparing with other three genes namely, COI, COII, and EF-1?. The results show that the bias of base compositions in Wingless (C: 0.19) is the lowest among those in COI, COII, and EF-1?. The averages of nucleotide sequence divergences for comparison between groups based on the Wingless were the highest. While substitutions in Wingless and EF-1? genes were not saturated at the divergence of the species groups, COI and COII genes attained saturation at those levels. The phylogenetic analysis based on Wingless solely show that this gene was very useful to resolve the relationships between groups but gave a poor resolution at the specific level, i.e. the relationships within group 1 was not resolved. Combination of all data supports the phylogenetic hypothesis based on morphological data. Glyphodes falls into three species groups: group 2 branched off first then followed by groups 1 and 3. Key words: COI, COII, EF-1?, genes, Glyphodes, mitochondria, moth, phylogeny, relationships, Wingless

Notes on Some Biological Aspects of Arctornis riguata Snellen (Lepidoptera: Lymantriidae)

HAYATI Journal of Biosciences Vol 20, No 1 (2013): March 2013
Publisher : Bogor Agricultural University, Indonesia

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Abstract

Arctornis riguata Snellen is one of lymantriids which attacked a vast range of mango trees in Probolinggo at the beginning of 2011. About 1.2% mango trees from nine sub-districts have been defoliated by the larvae of this species. The larvae of this genus have been reported to forage at Anacardiacea as well; however, they have never been reported to forage at cultivated mango trees in Indonesia. Since there is no biological information of this species, thus, a study on some biological aspects of this species is needed. This study was conducted in the field as well as in the laboratory during 4 months (March-July 2011). The diagnostic characters of this species are black scale at dorsal antenna on both male and female and slightly setae particularly at the costal angle of valve on the male genitalia. Life span of this species is in the range of 30-37 days. This study also found four natural enemies of A. riguata i.e.: Bleparipa sp. (Diptera: Tachinidae), Euagathis sp. (Hymenoptera: Brachonidae), Theronia sp. (Hymenoptera: Ichneumonidae), and Brachymeria lasus (Hymenoptera: Chalcididae). Moreover, a single fungal pathogen of this species also was identified, i.e. Isaria fumosorosea Wize. Having these results, we considered that to control A. riguata, one need to conserve the native natural enemies by manipulating their environment.  

An Application of Digital Chemistry Telling (DCT) in the Basic Inorganic Chemistry Course to Improve Students’ Listening and Speaking Skills

JOURNAL OF EDUCATION Vol 4, No 01: November 2011
Publisher : JOURNAL OF EDUCATION

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Abstract

This study aims to design implementation strategies of DCT in the Basic Inorganic Chemistry course, develop an appropriate course to increase students’ active participation, and develop an evaluation system capable of providing an integrated assessment (both the learning process and outcomes) in the course. This study was conducted in two cycles for one semester during the academic year of 2008/2009. The implementation applied the principles of classroom action research consisting of four stages, i.e. planning, action implementation, observation, and reflection. The data were analyzed by grouping them into categories. The findings were as follows. Qualitatively, the classroom obser­vations showed an increasing active participation of students, both in making the DCT and in conducting discussions in English. Quantitatively, the results of the observations on the learning activities showed an average value of 4 (scale 1-5) for several aspects of DCT.

TRANSISI FASA TITATNIUM OKSIDA MELALUI KONDENSASI EX-SITU HIDROGEN TITANAT TIPE STRUKTUR LEPIDOKSROSIT

Jurnal Penelitian Saintek Vol 15, No 1 (2010): April 2010
Publisher : Jurnal Penelitian Saintek

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Abstract

The objectives of the research are to study of the structure type of titanium dioxide (TiO2) obtained form the ex-situ condensation of hydrated hydrogen titanates with the structure type of lepidocrocite. Hydrated hydrogen titanates were obtained by ion exchabge of H+ for Cs+ in cesium titanates by 1 M HCl solution by Chimie Douce method. The results show that TiO2 (B), anatase, and anatase-rutile mixture were obtained heat treatment of hydrated hydrogen titanate at 100, 200, 300, 500, and 600oc respectively. The powders were characterized by X-rays diffractometer (XRD), High Resolution Scanning Electron Microscopy (HRSEM) and High Resolution Transmission Electron Microscopy (HRTEM). The research indicated that the protonic titanate, H0.54 Ti1.865 0.135O4 0.5H2O ( =vacancy), lost the interlayer water by being heated up to 200oC to produce a dehydrated phase, H0.54 Ti1.865 0.135O4. Above 300oC, the dehydrated phase completely transformed to TiO2(B) and anatase was obtained as pure phase at 600oC. The phase transformed as the following process: H0.54Ti1.865 0.135O4 0.5H2O à H0.54Ti1.865 0.135O4 0.25H2Oà H0.54Ti1.865 0.135O4 à TiO2(B) à TiO2-anatase.