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Biodiversitas Journal of Biological Diversity
Published by Universitas Sebelas Maret
ISSN : 1412033X     EISSN : 20854722     DOI : https://doi.org/10.13057/biodiv/d230231
Core Subject : Science, Agriculture,
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology
The Biodiversitas Journal was first published in 2000 by the Department of Biology, FMNS, Universitas Sebelas Maret, Surakarta, Indonesia, then in 2006 it was co-published by the Society for Indonesian Biodiversity and that department; since 2017 it was also hosted by Smujo. From 2003-2012 it was accredited by DGHE, Ministry of Education, R.I., since 2014 was indexed by Scopus, where DOAJ and Google Scholar was indexed first.
Arjuna Subject : Biokimia, Genetika dan Biologi Molekuler - Biokimia, Genetika dan Biologi Molekuler (Lain-Lain)
Articles 6,259 Documents
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Short Communication: Fish diversity of the Batang Toru River System, South Tapanuli, North Sumatra DEWI IMELDA ROESMA; ADA CHORNELIA; AHMAD MURSYID; MISTAR KAMSI
Biodiversitas Journal of Biological Diversity Vol. 17 No. 2 (2016)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d170235

Abstract

Roesma DI, Chornelia A, Mursyd A, Kamsi M. 2016. Short Communication: Fish diversity of the Batang Toru River System, South Tapanuli, North Sumatra. Biodiversitas 17: 628-634. A rapid survey on fish diversity was carried in the Batang Toru river system. The survey was carried out in the wet season between 8-14 February 2015 and 15-21 of March 2015 along various tributaries on the east (10) and west (1) side of the main Batang Toru river system. We obtained 427 individuals fish samples consisting of 24 species, from 10 families. These consist of Cyprinidae (11 species), Balitoridae (2), Channidae (2), Gobiidae (2), Nemacheilidae (2), Aplocheilidae (1), Bagridae (1), Cichlidae (1), Mastacembelidae (1), and Sisoridae (1). Four Sumatra fish species were encountered during the surveys, namely Neolissochilus sumatranus, Nemacheilus pfeifferae, Homaloptera gymnogaster and H. heterolepis. N. sumatranus and Puntius binotatus were the most frequently found in all of sampling sites.
Freshwater fish diversity in an oil palm concession area in Mimika, Papua HENDERITE L. OHEE
Biodiversitas Journal of Biological Diversity Vol. 17 No. 2 (2016)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d170240

Abstract

Ohee HL. 2016. Freshwater fish diversity in an oil palm concession area in Mimika, Papua. Biodiversitas 17: 665-672. New Guinea’s freshwater fish diversity may reach 400 species, twice the number of fish recorded in Australia. However, New Guinea’s freshwater fishes are facing rapid and poorly-planned social and economic developments, which have accelerated both habitat loss and degradation, impacting its unique biodiversity and threatening natural ecosystems. This study documents freshwater fish diversity and threats due to habitat conservation from oil palm development in the Timika Region, Papua. Fishes were sampled in canals, creeks, streams and rivers in the concession area of Pusaka Agro Lestari Company (PT. PAL) using seine and hand nets and a spear gun. Twenty two freshwater fish species in 15 families and 15 genera were recorded from the area. One of them is an endemic species ofTimika (Glossamia timika), one rainbowfish species with a restricted Southern New Guinea distribution, and 12 other native fishes. Land clearing leads to increase water turbidity and sedimentation, water temperature, and pollution which are potential threats to native fishes and their habitats. The fact that PAL’s concession is part of distribution area of known distribution of G. timika in Timika vicinity, habitat conversion to palm oil elevates the threat to this species. Hopefully, PT. PAL will adopt necessary conservation measures to mitigate the potential impact during the land clearing, especially, if they leave riparian buffer regions intact to protect aquatic habitats when clearing land.
Short Communication: Using ITS as a molecular marker for Mangifera species identification in Central Sumatra FITMAWATI FITMAWATI; IBNA HAYATI; NERY SOFIYANTI
Biodiversitas Journal of Biological Diversity Vol. 17 No. 2 (2016)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d170238

Abstract

Fitmawati, Hayati I, Sofiyanti N. 2016. Using ITS as a molecular marker for Mangifera species identification in Central Sumatra. Biodiversitas 17: 653-656. The relationship among Mangifera species in Central Sumatra is currently unclear. Previous molecular studies on these taxa using cpDNA were unable to produce well-resolved phylogenetic trees. In this study, we explored the potential of the ITS sequences as molecular markers for Mangifera species to better resolve the phylogenetic analysis. Parsimony analysis revealed that the common ancestor M. quadrifida as the first species appeared in Central Sumatra. Mangifera sp. which assumed as new species had the longest genetic distance among species examined and may assumed as the most primitive species of Mangifera in Neighbor-Joining analysis. M. sumatrana and M. torquenda were closely related as well as M. foetida and M. odorata. Also, M. indica was closely related to M. kemanga. This finding and the other marker of cpDNA such as trnL-F and rbcL gene may suggest a possibility to revision in the latest Mangifera classification based on morphological character. Our results also revealed and support the genus Mangifera is a monophyletic group.
Antidiabetic screening of some Indonesian marine cyanobacteria collection SRI PRIATNI; THELMA A. BUDIWATI; DIAH RATNANINGRUM; WAWAN KOSASIH; RINA ANDRYANI; HANI SUSANTI; DWI SUSILANINGSIH
Biodiversitas Journal of Biological Diversity Vol. 17 No. 2 (2016)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d170236

Abstract

Priatni S, Budiwati TA, Ratnaningrum D, Kosasih W, Andryani R, Susanti H, Susilaningsih D. 2016. Antidiabetic screening of some Indonesian marine cyanobacteria collection. Biodiversitas 17: 642-646. Cyanobacteria have been known as a potential extracellular-polysaccharide (EPS) producer. The objective of this study was to screen the marine cyanobacteria as potential antidiabetic agents. The present investigation was designed to determine the antidiabetic activity of EPS, intracellular-polysaccharide (IPS) and biomass extracts from marine cyanobacteria isolates. 10 cyanobacteria isolates were cultivated in IMK medium, at 25oC for 21 days. The morphology of cells was identified by a light microscope. EPS and IPS were separated by ethanol precipitation method and their antidiabetic activity was analyzed by the inhibition of α-glucosidase activity method. Results of morphology identification of 10 cyanobacteria isolates consist of Oscillatoria limnetica, Oscillatoria sp., Leptolyngbya sp., Pseudanabaena sp., Lyngbya sp. and Phormidium sp., Coelastrella sp., Aphanothece sp. and Synechococcus sp., and Chroococcus sp. Almost all of EPS from marine cyanobacteria isolates were potential as inhibitor of α-glucosidase, except for Oscillatoria limnetica and Phormidium sp. isolates. The highest activity in α-glucosidase inhibition was detected in Pseudanabaena sp. (14.02%) and Chroococcus sp. (13.0%) isolates.
The water quality parameters controlling diatoms assemblage in Rawapening Lake, Indonesia T. R. SOEPROBOWATI; S. D. TANDJUNG; SUTIKNO SUTIKNO; S. HADISUSANTO; P. GELL; HADIYANTO HADIYANTO; S. W.A. SUEDY
Biodiversitas Journal of Biological Diversity Vol. 17 No. 2 (2016)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d170239

Abstract

Soeprobowati TR, Tandjung SD, Sutikno, Hadisusanto S, Gell P, Hadiyanto. 2016. The water quality parameters controlling diatoms assemblage in Rawapening Lake, Indonesia. Biodiversitas 17: 657-664. Diatoms are microalgae that have an important role in aquatic ecosystem. The silicious diatoms fossil had been used for paleolimnological analysis. However, data set diatoms of Indonesia does not develop yet. The aims of this research were to assess water quality parameters controlling diatoms assemblage of RawapeningLake, to assess transfer function, to develop diatoms data set of Rawapening, and to compare Rawapening diatoms data set with European diatoms data set for the reconstruction of total phosphorous and pH. Water samples were taken from 3 sites of Rawapening Lake for water quality analysis. Sediment samples had been taken from 3 sites in Rawapening Lake using hand auger, and were sliced every 0.5 cm for diatoms analysis. Diatoms slides were prepared from about 5 g of dry sediment using 10% of chloride acid followed by 10% of peroxide to remove organic matters and carbonates, respectively.300 diatom valves were calculated on the entire samples, calculation the number of valve’s diatom aims to identify the lowest level of taxonomy. Phosphate, temperature, and calcium were theenvironmental parameters that influence the diatoms assemblage of Rawapening Lake. Phosphate was contributed 50% on diatoms assemblage. Internal based transfer function of diatoms provides more suitable diatoms data set rather than European diatom data set. The Rawapening diatoms data set of total phosphorous is the initial Indonesian diatoms data set for past trophic status, therefore, research has to be continued spatially for other Indonesian lakes and temporary on specific Indonesian lake to develop Indonesia diatoms data set.
The abundance of phytoplankton and its relationship to the N/P ratio in Jakarta Bay, Indonesia TUMPAK SIDABUTAR; DIETRIECH G. BENGEN; SAM WOUTHUYZEN; TRI PARTONO
Biodiversitas Journal of Biological Diversity Vol. 17 No. 2 (2016)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d170241

Abstract

Sidabutar T, Bengen DG, Wouthuyzen S, Partono T. 2016. The abundance of phytoplankton and its relationship to the N/P ratio in Jakarta Bay, Indonesia. Biodiversitas 17: 673-678. The occurrence of phytoplankton blooms in Jakarta Bay has increased significantly, and resulted in, the mass mortality of fish and other organisms. Phytoplankton bloom events are indicated by a change in the color of the sea’s surface. Generally, phytoplankton growth is influenced by the levels of nutrients in the water, while spatial distribution is influenced by the pattern of the current. In connection with this phenomenon, research was conducted in 2010, 2011 and 2013, to determine the abundance and distribution of phytoplankton and their connection with the N/P ratio. The results showed that the abundance of phytoplankton ranged from 40x106 cells/m3 up to 1699.1x106 cells/m3, with the highest recorded data was during the east monsoon in 2010 and the lowest during the first transition period of 2011. The predominant phytoplanktons were frequently diatoms such as Skeletonema, Chaetoceros and Thalassiosira. The distribution of phytoplankton seemingly follows the nutrient concentration ratio where phosphate acted as the limiting factor and nitrogen as the triggering factor. The higher the N/P ratio, the more potentially uncontrolled growth of phytoplankton occurred. When the availability of nutrients increased an increase in total algal biomass occurred, however, the alteration in nutrient composition led to a change in composition of community.
Short Communication: RAPD fingerprinting key and phylogenetic of nine seagrass species from Sanur coastal water, Bali, Indonesia using matK sequences MADE PHARMAWATI; UUL SHOVI NURKAMILA; STEVANUS STEVANUS
Biodiversitas Journal of Biological Diversity Vol. 17 No. 2 (2016)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d170243

Abstract

Pharmawati M, Nurkamila US, Stevanus. 2016. RAPD fingerprinting key and phylogenetic of nine seagrass species from Sanur coastal water, Bali, Indonesia using matK sequence. Biodiversitas 17: 687-693. In Bali, there are nine species of seagrass identified based on morphological characteristics. Development of molecular markers assist identificaton and evolutionary studies of many species including seagrass species. This study aimed to develop a fingerprinting key of nine seagrass species found at Sanur (Sanur Beach and Sindhu Beach), Bali, based on RAPD markers and to analyse their phylogenetic relationships using the matK region. Seagrass samples were collected at low tide and DNA was extracted using CTAB buffer. Six RAPD primers were used in the study. Sequences of matK were analyzed using MEGA 5.2. The phylogenetic tree was constructed by Maximum Likelihood method with 1000 bootstrap replicates. Based on RAPD banding pattern, a DNA fingerprinting key was successfully developed using only one primer — OPB12. Phylogenetic analysis of matK sequences grouped seagrass species by genera. There were five clades identified and the tree recognised that Cymodoceaceae was paraphyletic. This result is in disagreement with a previous study using combined rbcL and matK sequences which discussed the monophyly of Cymodoceaceae. Recent published paper using ITS sequence showed that cymodoceaceae might not be monophyletic group. This result supported our finding that Cymodoceaceae is not in the monophyletic group. Combined DNA sequences of chloroplast, nuclear and published paper using ITS sequencing showed that Cymodoceaceae mitochondrial DNA will further resolve phylogeny of seagrass species.
Data provision of PIK3CA gene diversity and recombinant plasmids preparation for control DNA in developing the trastuzumab predictive response diagnostic kit DESRIANI DESRIANI; BUGI RATNO BUDIARTO; WIRSMA ARIF HARAHAP; M. ALI WARISMAN; AUDREY VANIA CLARISSA OMPUSUNGGU; DINA ATHARIAH; FARIDA MIRNAWATI; IDA YUSSRIYANI; FUAD ALAHWANI; AHMAD RIZQI KURNIAWAN
Biodiversitas Journal of Biological Diversity Vol. 17 No. 2 (2016)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d170237

Abstract

Desriani, Budiarto BR, Harahap WA, Warisman MA,Ompusunggu AVC, Athariah D, Mirnawati F, Sriyani IY, Alahwani F, Kurniawan AR. 2016. Data provision of PIK3CA gene diversity and recombinant plasmids preparation for control DNA in developing the trastuzumab predictive response diagnostic kit. Biodiversitas 17: 647-652. HER-2 overexpression is well known as a poor prognostic factor for breast cancer patients. Targeted therapy can be carried out using monoclonal antibody named trastuzumab. Some reports have higlighted the core problem of HER2 positive-breast cancer resitance on trastuzumab due to incorrect in selecting HER2 status patient who will reciept the drug and the emergence of PIK3CA mutations especially in exon 9 and 20 which is the downstream of HER-2 pathway. In this study, data provision of PIK3CA gene and preparation of plasmid to support developing the trastuzumab predictive response diagnostic kits will be reported. Based on direct DNA sequencing result, two samples of 68 breast cancer patients exhibited mutation at exon 20 H1047R, while another three samples showed silent mutation (T1025T) at the same exon. On the other hand, careful strategy should be considered for exon 9 analysis, since we found that almost 68 samples sequenced none of them were exon 9 positive (pesudogene). Two prepared plasmids, pGEMT-easy PIK3CA exon 9 and 20 will be applied as control PIK3CA gene for qPCR SYBR green I-based PIK3CA genotyping, while pGEMT easy HER-2 will be applied as a reference gene for scoring HER-2 status. The standard curve equation of plasmid-cloned HER2 gene amplification was Y=-3,0472x + 46,465, R2= 0,99 with qPCR efficiency was 115%, respectively. Inconclusion, data provision and control DNA preparation of predicted factors for breast cancer patients who positively respond to trastuzumab are very fundamental important aspects for the development of trastuzumab response diagnostic kit which is based on Indonesian population genetics profile.
Biological characteristics on three demersal fish landed in Tegal, north coast of Central Java, Indonesia DUTO NUGROHO; MUFTI P. PATRIA; JATNA SUPRIATNA; LUKY ADRIANTO
Biodiversitas Journal of Biological Diversity Vol. 17 No. 2 (2016)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d170242

Abstract

Nugroho D, Patria MP, Supriatna J, Andrianto L. 2016. Biological characteristics on three demersal fish landed in Tegal, north coast of Central Java, Indonesia. Biodiversitas 17: 679-686. Java Sea has a potential marine biodiversity that has been harvested since years. Demersal fish resources is one of the targeted species by Danish seine fisheries operated in North coast of Java. To support on developing conservation and management measures, an observation on species composition, length frequencies and maturity stages were carried out during August 2014 to July 2015. Sampling took place in landing place of Tegalsari fishing port central Java. A total 129 fish species identified, among them 91 species were targeted as edible fish. Sampling on three dominant species i.e., Purple-spotted bigeye Priacanthus tayenus (Richardson, 1846), Lattice monocle bream Scolopsis taenioptera (Cuvier, 1830) and goatfish Upeneus sulphureus (Cuvier, 1829) were measured regarding length, weight and their maturity stages. The results shows that length-weight relationship for each species were P. tayenus W = 0.0324 L 2.7321, S. taenioptera W = 0.0366 L2.7262 and U. sulphureus W = 0.038 L2.7312.Monthly average GSI of P. tayenus and S. taenioptera indicated that the highest index occurred during SE monsoon while U. sulphureus on NW monsoon. Maturity stage analysis indicated that estimated of length at first maturity (Lm) were at 12.9 cmFL (U. sulphureus), 16.8 cmFL (S. taenioptera) and 19.4 cmFL (P. tayenus). Size frequency distribution shows that most of the fish were caught at immature cohorts. The diversity or evenness indices of ichtyofauna is also described as descriptors of community structure and be complemented with information on biological characteristics of those dominant species.Keywords: Demersal fish, dominant species, biological characteristics, north coast, Java
The diversity of secondary metabolites in Indonesian soybean genotypes ERIYANTO YUSNAWAN
Biodiversitas Journal of Biological Diversity Vol. 17 No. 2 (2016)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d170245

Abstract

Yusnawan E. 2016. The diversity of secondary metabolites in Indonesian soybean genotypes. Biodiversitas 17: 704-710. Soybean secondary metabolites protect the crop from pathogen infection. These secondary metabolites especially phenolic compounds also have functional properties.This study aimed to determine total phenolic and flavonoid contents as well as antioxidant activity of Indonesian soybean genotypes. A total of 63 soybean genotypes with four different seed coat colors (green yellow, light yellow, yellow, and black) and different seed sizes (small, medium and large) was used in this study. Total phenolic content was measured using Folin- Ciocalteu’s reagent and antioxidant activity was determined with 2,2-diphenyl-1-picrylhydrazyl. All six genotypes with black seed coat color had higher total phenolic and flavonoid contents as well as antioxidant activity than those in other colors’ genotypes. Total phenolic contents of those six black soybeans ranged from 7.19 to 14.72 mg gallic acid equivalent per gram and total flavonoid contents varied from 1.91 to 5.30 mg catechin equivalent per gram. Antioxidant activities of these genotypes ranged from 10.99 to 20.38 μmol trolox equivalent per gram. An estimation of the total phenolic contents as well as antioxidant activities particularly in black soybeans was valuable and important for seeking soybeans with high antioxidant properties.

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