EVOLUTIONARY ANALYSIS OF POLLINARIA MORPHOLOGY OF SUBTRIBE AERIDINAE (ORCHIDACEAE)

HIDAYAT, TOPIK; YUKAWA, TOMOHISA; ITO, MOTOMI. 2006. Evolutionary analysis of pollinaria morphology of subtribe Aeridinae (Orchidaceae). Reinwardtia 12(3): 223–235.–– Pollinarium is one of the distinct synapomorphies of Orchidaceae. With using characters derived from the pollinarium, phylogenetic relationships among genera of subtribe Aeridinae was examined. Cladistic analysis showed that (1) Subtribe Aeridinae is monophyletic group. (2) Five of six groups constructed in the analysis are consistent with the groups recognized in previous molecular phylogenetic analyses.(3)The genera Cleisostoma and Phalaenopsis are non-monophyletic group.(4) Pollinarium morphology endorses monophyly Trichoglottis and Phalaenopsis alliances. (5) Although transformation of the stipe and viscidium shapes in the subtribe is subjected to parallelism, the results showed that these characters are much useful in determining relationships in the subtribe than those of pollinium

Single Strand Conformation Polymorphism Method for Initial Detection DNA Sequences Homogeneity

In molecular phylogenetic study, homogeneity of DNA sequences is a prerequisite before putting it into practice. Internal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA) has been common in phylogenetic study, but a homogenous sequence is often difficult to obtain. Here we use single-stranded conformation polymorphism (SSCP) method to detect homogeneity for nine pooled amplified products of ITS region. Our results suggested that SSCP method has been applicable in detection homogeneity of ITS region prior to using it in sequencing processes

ULASAN Kajian Filogenetika Molekuler dan Peranannya dalam Menyediakan Informasi Dasar untuk Meningkatkan Kualitas Sumber Genetik Anggrek

Early informationresulted from molecular phylogenetic studies of many importantornamental crops is often less attention to manygrowers and farmers. Phylogenetics is one of the most preferablemethod in systematics to reconstruct evolutionaryrelationships of groups of biological organisms in order tounderstand their biodiversities. This has been revolutionizedby DNA sequences data. In this method, a group of organismsthat shares many identical characteristics are consideredto be closely related; deriving from a commonancestor and is assumed to have similar genetic patternsand biochemical properties. By these basic principles,molecular phylogenetics plays important roles in revealing abasic knowledge on pattern of relationships to whichgenetic resources can be improved. Over the past decade,botanists have done several thousand phylogenetic analysesbased on molecular data of economically and horticulturallyimportant crops. Orchids are the best example for this.There is no doubt that most orchid plants had played roles inhorticulture and hybridization. At present, many infragenericand intergeneric hybrids are available commercially. Successfulhybridization can be achieved if two or more individualplants understudy are closely related in respect to theirgenetics and evolution

KONSTRUKSI POHON FILOGENETIK SECARA IN-SILICO JAMUR BERKERABAT DEKAT Trametes versicolor SEBAGAI TERAPI LUPUS BERDASARKAN MARKER 18s rRNA

ABSTRAK Pengobatan herbal telah banyak dikembangkan contohnya adalah pengembangan obat tradisional pada penyakit Lupus. Diketahui bahwa Jamur Tremetes versicolor adalah jamur  yang memiliki sifat immunodulator yang berfungsi untuk mengobati penyakit autoimun yaitu Systemic Lupus Erythematosus (SLE) yang memiliki senyawa protein unik  Polysaccharide Peptide Krestin (PSK). Tetapi jamur Trametes tidak banyak dikonsumsi oleh masyarakat Indonesia. Tujuan dari penelitian ini adalah  mengetahui jamur yang berkerabat dekat dengan Trametes versicolor yang dapat juga dijadikan sebagai terapi pada penyakit autoimun dan dapat dikonsumsi di Indonesia. Studi yang digunakan adalah studi filogenetik secara in-silico dengan jamur yang berkerabat dengan jamur Trametes versicolor dengan penanda gen 18s rRNA yang diperoleh dari genbank NCBI. Data molekuler sekuen menunjukkan bahwa jamur yang berkerabat dekat dengan jamur Trametes versicolor adalah Ganoderma lucidum, Lenzites betulinus, Agaricus bisporus, Agaricus subrufescens, Auricularia polytrica, dan Auricularia auricula-judae berdasarkan penanda gen 18s rRNA. Jamur ini dapat dijadikan sebagai obat alternatif untuk terapi penyakit autoimun dan mendapatkan senyawa yang terkandung dalam jamur tersebut dengan studi in-vitro lebih lanjut. Kata Kunci: In-Silico, Trametes, Ganoderma, Lenzites, Auricularia, Agaricus, Autoimun   ABSTRACT Development of herbal treatment have been done quite frequently, for example the development of traditional medicines for Lupus.  It is known that Tremetes versicolor mushroom is a fungus that has immunodulatory properties which functions to treat autoimmune disease namely Systemic Lupus Erythematosus (SLE) which has a unique protein compound Polysaccharide Peptide Krestine (PSK). However, Trametes are not widely consumed by Indonesian people. The purpose of this study was to find out which fungi are closely related to Trametes versicolor which can also be used as a therapy for autoimmune diseases and can be available for consupmtion in Indonesia. This study used an in-sillico phylogenetic with fungi that are related to Trametes versicolor mushroom with the 18s rRNA gene marker obtained from the NCBI genbank. Sequential molecular data shows that fungi closely related to Trametes versicolor mushrooms are Ganoderma lucidum, Lenzites betulinus, Agaricus bisporus, Agaricus subrufescens, Auricularia polytrica, and Auricularia auricula-judae based on the 18s rRNA gene marker. This fungi can be used as an alternative medicine for autoimmune diseases treatment by obtaining compounds contained in these fungi with further in-vitro studies. Keywords: In-Silico, Trametes, Ganoderma, Lenzites, Auricularia, Agaricus, Autoimu

Screening Tumbuhan Alternatif Penghasil Xanthorrhizol Menggunakan Pendekatan In-Silico Berdasarkan Marker MatK

Xanthorrhizol is a compound that has many uses such as anticancer, antimicrobial, anti-inflammatory, antioxidant, antihyperglycemic, antihypertensive, etc. However, this xanthorrhizol is only found in javanese turmeric (Curcuma zanthorrhiza) where this species only grows well in Indonesia. MatK from the GeneBank NCBI is used to find plants that are closely related to Curcuma zanthorrhiza. Multiple sequence alignment was done using ClustalX 1.83, and phylogenetic analysis was done using PAUP 4.0. The results of the reconstruction of the phylogenetic tree showed that white turmeric (Curcuma zedoaria) was the closest plant related to Curcuma zanthorrhiza. Curcuma zedoaria is a plant commonly found in tropical countries, such as India, Japan and Thailand. In Indonesia Curcuma zedoaria is known as Temu Putih. It is known that the chemical content of Temu Putih rhizome consists of curcuminoids, essential oils, and polysaccharides. Curcuminoid includes: curcumin, demethoxycurcumin, bisdemetoksikurkumin and 1,7-bis (4-hydroxyphenyl) -1,4,6-heptatrien-3-on.  Curcuma zedoaria has rich essential oils: starch, curcumin, arabin, gums, etc. There is also more than ten sesquiterpene from Rhizome of Curcuma zedoaria such as furanodiene, furanodienone, zedorone, curzerenone, curzeone, germacrone, 13-hydroxy germacrone, dihydro-curdione, curcumenone and zedoaronediol. Based on that Curcuma zedoaria doesn’t produce xanthorrhizol naturally, but Curcuma zedoaria has a bioactive substance such as sesquiterpene and its closely related to Curcuma zanthorrhiza, genetic engineering can probably be used to produce xanthorrhizol

ULASAN Kajian Filogenetika Molekuler Dan Peranannya Dalam Menyediakan Informasi Dasar Untuk Meningkatkan Kualitas Sumber Genetik Anggrek

Early informationresulted from molecular phylogenetic studies of many importantornamental crops is often less attention to manygrowers and farmers. Phylogenetics is one of the most preferablemethod in systematics to reconstruct evolutionaryrelationships of groups of biological organisms in order tounderstand their biodiversities. This has been revolutionizedby DNA sequences data. In this method, a group of organismsthat shares many identical characteristics are consideredto be closely related; deriving from a commonancestor and is assumed to have similar genetic patternsand biochemical properties. By these basic principles,molecular phylogenetics plays important roles in revealing abasic knowledge on pattern of relationships to whichgenetic resources can be improved. Over the past decade,botanists have done several thousand phylogenetic analysesbased on molecular data of economically and horticulturallyimportant crops. Orchids are the best example for this.There is no doubt that most orchid plants had played roles inhorticulture and hybridization. At present, many infragenericand intergeneric hybrids are available commercially. Successfulhybridization can be achieved if two or more individualplants understudy are closely related in respect to theirgenetics and evolution

THE PHYLOGENETIC POSITION OF THE PAPUASIAN GENUS SARCOCHILUS R.BR. (ORCHIDACEAE: AERIDINAE): EVIDENCE FROM MOLECULAR DATA

HIDAYAT,T.; ITO, M.; YUKAWA, T. 2008. The phylogenetic position of thePapuasian genus Sarcochilus R.Br.(Orchidaceae: Aeridinae): evidence from molecular data. Reinwardtia 12(4).281 – 284. –– The taxonomic status of the Papuasian orchid genus Sarcochilus R.Br. remains unresolved. Represented by Sarcochilus chrysanthus Schltr.,a phylogenetic analysis to evaluate relationships between the Papuasian species and those from Australia was conducted using molecular characters.Parsimony analysis using DNA sequences of the internal transcribed spacer (ITS) region showed that this Papuasian species, is in a distant position from the so-called the true Sarcochilus sensu stricto.These results provide additional evidence for the establishment of a new genus Monantochilus

Pengembangan Primer Diagnostik Menggunakan Penanda mat-K Secara In Silico untuk Mendeteksi Kelangkaan Jenis Tumbuhan Di Indonesia

Indonesia merupakan negara dengan kekayaan biodiversitas tertinggi di dunia. Terdapat sekitar 40.000 jenis tumbuhan yang tumbuh di Indonesia dan sebagian besar tumbuhan sudah menunjukkan kelangkaan. Penentuan kelangkaan suatu jenis tumbuhan dapat diketahui berdasarkan distribusi populasinya, namun membutuhkan waktu yang cukup lama. Ketidakstabilan genom akan terjadi pada jenis tumbuhan langka, karena tidak mampu beradaptasi pada ekosistem. Banyaknya tumbuhan yang terancam punah dan habitat asli yang rusak, maka mengharuskan para peneliti untuk mengetahui keberadaan dan melakukan pendataan terhadap keragaman jenis tumbuhan di Indonesia secara cepat. DNA barcoding merupakan teknik yang dikembangkan untuk mempercepat dan mempermudah proses identifikasi organisme dengan menggunakan potongan DNA tertentu. Tujuan dari penelitian ini adalah mencari primer spesifik untuk mendeteksi status kelangkaan pada tumbuhan menggunakan penanda mat-K secara in silico. Gen mat-K merupakan penanda umum yang direkomendasikan untuk analisis pada tumbuhan. Metode yang digunakan yaitu dengan pendekatan secara in silico karena waktu yang diperlukan relatif lebih singkat dan murah. Penelitian ini berhasil mendapatkan sepasang primer forward 1:F_1635–1657 dan primer reverse 1:R_2093–2113 dengan persentase keberhasilan amplifikasi yang dicapai sebesar 66%. Kedepannya, primer ini dapat digunakan untuk mengidentifikasi status kelangkaan pada tumbuhan.AbstractIndonesia is a country with the highest biodiversity wealth in the world. There are around 40,000 types of plants that grow in Indonesia and most of the plants are rare. Determining the rarity of a plant type can be determined based on its population distribution, but it takes quite a long time. Genome instability will occur in rare plant species, because they are unable to adapt to the ecosystem. The large number of plants that are threatened with extinction and their natural habitats are damaged requires researchers to quickly identify the existence and collect data on the diversity of plant species in Indonesia. DNA barcoding is a technique developed to speed up and simplify the process of identifying organisms using certain pieces of DNA. The aim of this research is to look for specific primers to detect rarity status in plants using mat-K markers in silico. The mat-K gene is a general marker recommended for analysis in plants. The method used is an in silico approach because the time required is relatively shorter and cheaper. This research succeeded in obtaining a pair of forward primers 1:F_1635–1657 and reverse primers 1:R_2093–2113 with a successful amplification percentage of 66%. In the future, this primer can be used to identify rarity status in plants

The Reasoning Ability of Senior High School Students in the Study of Plant Classification with and Without Virtual Practice

Penelitian ini pertujuan untuk membandingkan kemampuan penalaran dua kelas siswa SMA pada pembelajaran klasifikasi tumbuhan. Pada kelas pertama pembelajaran dilakukan melalui praktikum yang dilaksanakan secara konvensional (kelas konvensional), sedangkan pada kelas kedua kegiatan praktikum dilakukan secara virtual (kelas virtual). Subjek penelitian adalah 67 siswa kelas X salah satu SMANegeri di Kabupaten Purwakarta yang dibagi menjadi 32 siswa di kelas konvensional dan 35 siswa dikelas eksperimen. Kemampuan penalaran siswa diukurdengan test tulis yang dikembangkan berdasarkan indikator standar berfikir kompleks, sedangkan kemampuan siswa dalam memproses informasi diukur dengan menggunakan instrumen yang dikembangkan berdasarkan standar pemrosesan informasi. Data yang diperoleh dianalis secara statistik menggunakan uji beda dua rata-rata dan uji korelasi. Secara umum siswa dari kelas virtual memiliki kemampuan penalaran yang lebih tinggi dibandingkan siswa dari kelas konvensional. Tingginya kemampuan penalaran pada kelas virtual ini berkorelasi positif dengan kemampuan siswa dalam memproses informasi selama pembelajaran berlangsung. 6 dari 7 aspek kemampuan penalaran pada kelas virtual menunjukkan rerata yang lebih tinggi danberbeda signifikan dari kelas kontrol, kecuali pada aspek analisis kesalahan. Hasil ini menggambarkan bahwa praktikum virtual dapat melatihkan 6 aspek penalaran yang diukur (constructing support, classifying, induction, deduction, abstraction, dan comparing), tetapi tidak dapat melatih penalaranan pada aspek analisis kesalahan (error analysis)

Practical Plants Classification Using Framing to Reduce Cognivite Load of High School Students

This study was conducted to reduce the cognitive load of high school students in a classification plant laboratory. The subjects were students of class X IPA one of private high school Favorite in Bandung, divided into experimental class (36 students) and control class (36 students). The experimental class used Framing for practical activities providing dikotomous key scheme, while the control class practical activities carried out in accordance used worksheet conventionally . Cognitive load was measured by looking at differences in the students' ability to receive and process information (information processing), mental effort and learning outcomes in the form of reasoning ability of students in the classification of plants. Data ability to receive and process information captured by task complexity combined worksheet on the worksheet students. Data captured by the mental effort of subjective rating scale questionnaire Likert scale-based, while the data captured using the reasoning ability of students to write test questions based on indicators describing complex thinking. Data were analyzed by using a different test and the average correlation between the three components of cognitive load. The analysis showed both the experimental class and the control class relationship between the ability to accept the reasoning ability showed a positive correlation, while the relationship between mental effort with reasoning abilities showed a negative correlation. These results illustrate the cognitive load balancing character students in practical activities in both classes of plant classification research. However, students in the experimental class has the ability to receive and process information that is higher and significantly different than the control class. Instead the experimental class mental effort value lower than the control class, showed that the cognitive load of students in the experimental class lower than the cognitive load control class. In other words, the use of framing the practical activities of classification of plants in the experimental class has been able to decrease the cognitive load of students