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"Perairan Laboratorium Alam di Fakultas MIPA kampus Universitas Indonesia telah lama diketahui memiliki jenis-jenis desmid. Desmid merupakan kelompok mikroalga dari bangsa Desmidiales yang bersel tunggal atau berfilamen, dan terdiri atas 2 semi sel. Penentuan 4 lokasi pengambilan sampel desmid dilakukan dengan metode purposive sampling pada bulan Maret-April 2008 dengan frekuensi 1 kali setiap bulannya. Pada setiap stasiun, dilakukan pengambilan sampel epifitik dan sampel planktonik. Jenisjenis desmid diperoleh dari 4 sampel epifitik dengan 563 individu dan 4 sampel planktonik dengan 179 individu, dan diidentifikasi berdasarkan karakter morfologi sel vegetatif dan kloroplas. Berdasarkan hasil penelitian, di perairan Laboratorium Alam ditemukan 17 jenis desmid yang termasuk dalam 6 marga, yaitu Closterium (1 jenis), Cosmarium (8 jenis), Euastrum (3 jenis), Micrasterias (2 jenis), Pleurotaenium (1 jenis), dan Staurastrum (2 jenis). Jenis-jenis tersebut lebih bersifat epifitik daripada planktonik, dan marga Cosmarium memiliki jumlah jenis terbanyak dibandingkan margamarga lainnya. Sepuluh jenis desmid yang berhasil diidentifikasi dan dideskripsikan, yaitu Closterium littorale Gay, Cosmarium circulare Reinsch, Cosmarium granatum Brébisson in Ralfs, Cosmarium lundellii Delponte, Cosmarium trilobulatum Reinsch, Cosmarium quadrum Lundell, Euastrum ansatum Ralfs, Euastrum spinulosum Delponte, Euastrum turgidum Formae, dan Micrasterias pinnatifida Kützing ex Ralfs. Tujuh jenis desmid yang telah diidentifikasi dan dideskripsikan tetapi belum diketahui penunjuk jenisnya, yaitu Cosmarium sp.1, Cosmarium sp.2, Cosmarium sp.3, Micrasterias sp., Pleurotaenium sp., Staurastrum sp.1, dan Staurastrum sp.2."

"Penelitian mengenai struktur komunitas diatom di Pulau Penjaliran Timur dan Teluk Jakarta telah dilakukan masing-masing pada bulan Juni 2007 dan Maret 2008. Sampel diambil secara horizontal dari 10 stasiun di sekeliling perairan Pulau Penjaliran Timur dan 6 muara sungai di Teluk Jakarta. Hasil identifikasi sampel fitoplankton berupa 57 jenis diatom dari perairan Pulau Penjaliran Timur dan 30 jenis dari Teluk Jakarta. Kepadatan diatom di Pulau Penjaliran Timur berkisar antara 24.232--127.079 plankter/m3 yang didominasi oleh Coscinodiscus sp. dan Rhizosolenia alata. Kepadatan diatom di perairan Teluk Jakarta berkisar antara 15.148--854.192 plankter/m3 yang didominasi oleh Skeletonema costatum. Indeks kekayaan, kemerataan, dan keanekaragaman jenis diatom di perairan Pulau Penjaliran Timur lebih tinggi dibandingkan Teluk Jakarta. Skeletonema costatum tidak terdapat pada perairan Pulau Penjaliran Timur, namun sangat mendominasi di Teluk Jakarta. Berdasarkan struktur komunitas, jenis Skeletonema costatum diduga merupakan jenis spesifik pada perairan tercemar sehingga dapat digunakan sebagai indikator kerusakan lingkungan perairan."

"Penelitian yang bertujuan menghasilkan klona gen NS1 virus dengue pada vektor ekspresi pGEX-6P1 dalam Escherichia coli BL21 Star?(DE3) telah dilakukan di Laboratorium Biologi Molekular, LAPTIAB, BPPT, Serpong selama Januari--November 2008. Gen NS1 dengue diamplifikasi dengan primer spesifik d3-2336sbam (forward) dan d3-NS1-1056c (reverse). Produk PCR gen NS1 (1.160 pb) yang telah dipurifikasi, didigesti dengan enzim BamHI-XhoI (double digestion) kemudian diligasikan pada vektor ekspresi pGEX-6P1. Reaksi ligasi ditransformasikan ke dalam sel kompeten E. coli BL21 Star?(DE3). Sebanyak 19 koloni diisolasi secara acak dari 162 koloni yang tumbuh pada medium seleksi ampisilin. Hasil verifikasi dengan digesti dan PCR menunjukkan koloni 1b3 sebagai koloni positif rekombinan. Hasil sequencing terhadap 356 basa pertama gen NS1 menggunakan primer spesifik d3-2716c, menunjukkan bahwa plasmid rekombinan 1b3 mengandung gen NS1. Analisis BLASTN terhadap database DNA pada GenBank menunjukkan homologi 96% dengan sekuen DEN-3 strain KJ71 (accession number AY858044.2). Kloning gen NS1 dengue pada vektor pGEX-6P1 dalam E. coli BL21 Star?(DE3) berhasil dilakukan."

"Keragaman enterovirus di Indonesia belum banyak diketahui, terutama enterovirus nonpolio spesies Human enterovirus C (HEV-C) yang dapat berekombinasi dengan poliovirus galur oral poliovirus vaccine (OPV).Penelitian bertujuan mendeteksi dan mengidentifikasi enterovirus pada anakanak balita di Desa Antajaya yang memiliki fasilitas sanitasi minim. Sampel feses dikumpulkan selama bulan Februari--Juni 2008 dari 100 anak-anak balita partisipan serta dianalisis melalui metode CODEHOP VP1 RT-snPCR, sequencing parsial gen pengkode kapsid VP1, penelusuran BLAST, dan rekonstruksi pohon filogenetik. Prevalensi enterovirus paling tinggi yang terdeteksi dan teridentifikasi terdapat pada kelompok umur 12--23 bulan dengan kecenderungan penurunan prevalensi pada kelompok umur yang semakin besar. Analisis pohon filogenetik dari 65 sampel positif enterovirus memperlihatkan 14 cluster berbeda yang sesuai dengan 14 serotipe enterovirus hasil penelusuran BLAST, yaitu coxsackievirus A2 (CVA2), CVA5, CVA10 dari spesies HEV-A (16,92%); echovirus 1 (E1), E9, E14, E21, E25, coxsackievirus B3 (CVB3), CVB4 dari spesies HEV-B (38%); dan poliovirus 2 (PV2), CVA1, CVA20, CVA24 dari spesies HEV-C (24,62%). Prevalensi enterovirus nonpolio spesies HEV-C yang relatif tinggi dalam penelitian dapat menjadi salah satu dasar pertimbangan penggunaan inactivated poliovirus vaccine (IPV) di Indonesia untuk mencegah wabah poliomielitis akibat rekombinasi antara poliovirus galur OPV dan enterovirus nonpolio spesies HEV-C."

"Gen DefH9-iaaM merupakan gen pengkode senyawa prekursor pembentukan auksin. Kandungan auksin yang tinggi menginduksi pembentukan buah partenokarpi, tanpa melalui polinasi dan fertilisasi. Tiga galur tanaman tomat transgenik yang membawa insersi dan mengekspresikan gen DefH9-iaaM, yaitu OvR1#14-4, OvM2#10-1, dan OvM2#6-2, telah dihasilkan melalui transformasi genetik dengan Agrobacterium oleh kelompok peneliti di BB-BIOGEN. Penelitian bertujuan menguji stabilitas insersi dan mengetahui ekspresi gen DefH9-iaaM pada tanaman T3 dari ketiga galur tersebut. Uji stabilitas gen dilakukan dengan metode PCR menggunakan primer spesifik IAAM 5 dan IAAM 3. Kedua primer tersebut menghasilkan fragmen gen iaaM sebesar ± 148 pb. Fragmen DNA produk PCR divisualisasikan menggunakan gel elektroforesis. Hasil uji molekuler dianalisis menggunakan uji chi-square dengan level of significant 0,05. Galur OvR1#14-4 memiliki insersi gen yang telah stabil dengan perbandingan filial transgenik dan non transgenik yang memenuhi perbandingan penyilangan monohibrid Mendel yaitu 3:1. Tanaman dengan hasil uji molekuler positif kemudian ditanam di lapang untuk uji ekspresi fenotipik dan evaluasi daya hasil. Hasil uji fenotipik dianalisis dengan uji ANOVA level of significant 0,05. Ekspresi gen partenokarpi DefH9-iaaM pada tanaman tomat transgenik meningkatkan jumlah tandan sebesar 191--227%, jumlah bunga sebesar 191--310%, dan jumlah buah sebesar 331--426% dibandingkan dengan kontrol Opal, serta menyebabkan terbentuknya buah tomat berbiji sedikit dan tanpa biji. Galur OvR1#14-4 menghasilkan jumlah tandan, jumlah bunga, dan jumlah buah paling tinggi dibandingkan dua galur lain."

"Telah dilakukan penelitian yang bertujuan untuk melakukan transformasi gen Osdep1-Tc ke kalus padi cv. Taipei 309 menggunakan Agrobacterium tumefaciens. Transformasi gen Osdep1-Tc dilakukan menggunakan A. tumefaciens strain LBA4404 yang membawa plasmid rekombinan pCAMBIA1301-Osdep1-Tc, mengandung gen reporter (gus), gen nptII dan hptI. Gen Osdep1-Tc yang telah dikloning ke vektor pengklonaan pGEM-T Easy pada penelitian sebelumnya digunakan sebagai sampel untuk kemudian isubkloning ke pCAMBIA 1301 dan ditransformasikan ke dalam Escherichia coli DH5α sehingga dihasilkan vektor rekombinan pCAMBIA-Osdep1-Tc. Vektor rekombinan kemudian dielektroporasi ke A. tumefaciens dan ditransformasi ke kalus embriogenik padi. Aktivitas GUS pada kalus berhasil dideteksi 3 hari setelah infeksi dengan A. tumefaciens. Analisis PCR kalus transforman menunjukkan bahwa gen hptI berhasil terintegrasi dengan stabil pada kelima kalus uji.

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Research about transformation of Osdep1-Tc gene into rice calli cv. Taipei 309 using Agrobacterium tumefaciens had been done. Transformation of Osdep1-Tc was carried out using A. tumefaciens strain LBA4404, harbored recombinant plasmid pCAMBIA1301-Osdep1-Tc, which contained a reporter gene (gus), hptI and nptII gene. Osdep1-Tc gene had been cloned previously into the pGEM-T Easy cloning vector. The gene was being subcloned into pCAMBIA 1301 and transformed into Escherichia coli DH5α in order to obtain recombinant vectors pCAMBIA-Osdep1-Tc. Furthermore, the recombinant vectors was electroporated into A. tumefaciens and transformed into rice embryogenic calli. GUS activity in rice calli was detected 3 days after infection with A. tumefaciens. PCR analysis of the transformant calli revealed that all five calli tested showed a succeeded stable integration of hptI gene."

"ABSTRAKOrangutan is the Asian representative of the great apes. Its present range is confined to dwindling areas on the islands of Sumatera (Pongo abelii) and Borneo (Pongo pygmaeus) (Rijksen & Meijaard, 1999). Orangutans are arboreal (Rijksen, 1978; Galdikas, 1978), frugivorous (MacKinnon, 1974) and live semi-solitary in fission- fusion societies (Delgado & van Schaik, 2000). Ketambe, one of the major orangutan sites, supports a population density of 3-5 ind/km2 . Ketambe Research Center, which is based in Gunung Leuser Ecosystem, was run since early 1970. There are at least six families of orangutans living in the research areal of 450 ha, including the offspring of the ex rehabilitation orangutans. Orangutans in this area have been studied since 1971, where many behavioral and ecological studies have been conducted.. One of the most important studies identified matrilines within Ketambe based on genetic analysis (Atmoko, 2000) Female orangutans in Ketambe tend to be philopatric which means that they remain in their natal or birth groups. This condition is the result of intense competition among individual orangutans over food patchs because they often form dominance relations when meeting in the same food patch. Dominan ranking of ex-rehabilitation orangutans, based on a liniear index of responses in the context of displacement at a food patch, tends to be lower than those of wild orangutans. Orangutans travel and forage to find food patches within their habitat. By using software GIS Arc View 3.3, Day Journey Length (DHL) adult females including ex-rehabilitation female orangutan ex-rehabilitant is known to be 37-2.106 meters with an average between 437-795 meter. The matrilinial relationship between individuals influence each other in foraging and competition to form home ranges, especially for females. Orangutans matrilines tend to have overlapping home ranges between 46,66% - 97,07%)."

"Palm Kernel Meal is solid waste from Palm Oil extraction (Ng, 2003). Akubuo & Eje (2002) reported that mechanical extraction produced Palm Kernel Oil (PKO) dan Palm Kernel Meal (PKM). Perez (1997) mentioned that Palm Kernel Meal contains rich arginin, leusin, and sistein matters. Hem et al., (2008), utilizing Palm Kernel Meal pass through bioconversion process for developing larvae Hermetia illucens L. as alternative natural feedstuff in aquaculture industry. Macromolecule composition of Palm Kernel Meal like cellulose, hemicellulose and lignin can be degrade to be simply compound and can be used by another organism like larvae Hermetia illucens L. in bioconversion process. Bioconversion Palm Kernel Meal for feedstuff nutrition consist with microorganism assistance. Suharyanto et al., (2006) define bioconversion as a certain biological process which involving microorganism or enzyme that can change organic matters. Slime molds have great play role in process reduction macromolecule composition of Palm Kernel Meal. Molds have enzyme which can reduce cellulose, hemicellulose and lignin become more simple compound. Study about fermentation fungi already been done through isolation, identification, and fungi screening. However, only a few study about fungi related consist in process bioconversion Palm Kernel Meal reported in Indonesia. This study consist of two part. First part describes the isolation, identification, and growth screening fungi from bioconversion Palm Kernel Meal. Second part of this study describes the fermentation Palm Kernel Meal by selected indigenous fungi. The selected indigenous fungi obtained from result of the first part. The fermentation result included ash matters, crude fiber, crude protein and dry matters experiment. The study was carried out at the Institut de Recherche pour le Developpement (IRD) Laboratory, Depok and the Laboratory of Microbiology, Departement of Biology, UI, Depok during April?Oktober 2009. The isolation of fungi was conducted with spread methods on Potato Dectrose Agar (PDA). Identification of the isolates was carried out on Potato Dectrose Agar (PDA), Czapeck Dox Agar (CDA), and Malt Extract Agar (MEA) based on macroscopic and microscopic morphological observation of the colonies. The Mimura agar (MA) was used for growth fungi screening. The isolation resulted in 15 representative isolates consisting of 4 group of fungi (Aspergillus, Mucor, Penicillium, and Geotrichum). Based on 7 days periods of fermentation processing, Mucor groups had the highest frequency distribution and Geotrichum had the highest quantity. After the growth fungi screening, 4 isolates (P3, P4, P10, P15) was selected for futher study in part II. Microscopic identification showed P3 (Penicillium chrysogenum), P4 (Mucor racemosus), P10 (Aspergillus flavus), and P15 (Geotrichum candidum). Mucor racemosus was the most wide diameter colony on Mimura agar?MA (9 cm) comparing to other isolates. These selected fungi was used for fermentation of Palm Kernel Meal as inoculant. After process bioconversion which fermented was done, proximate analysis were carried out to examine crude protein, crude fiber, ash matters, and dry matters. Ng (2003) methods was used for this Palm Kernel Meal fermentation and Hart & Fisher (1971) was used for proximate analysis. The results after 7 days fermentation showed that the increased nutrition of crude protein composition of Palm Kernel Meal fermented by fungus Aspergillus flavus (1,33%), Geotrichum candidum (5,90%), Mucor racemosus (0,29%), and Penicillium chrysogenum (12,09%). The increased crude fiber contains fermented by Aspergillus flavus (3,03%), Geotrichum candidum (1,93%), Mucor racemosus (4,32%), and Penicillium chrysogenum (14,11%). Chemical cellulose structure and fungi species influence the difference percentage of crude protein and crude fiber. Chemical cellulose structure which amorf shape was more easy to degrade better than crystal shape. Fungi species have difference complexity enzymes (cellulose, hemicellulose, ligninase) and optimum growth level. High oil that can blocked the optimum growth of fungi and raising temperature matter that have involved in aeration and water activity alteration were another influence factor that have made difference percentage of crude protein and crude fiber."

"ABSTRAKEfficiency of water usage is needed for sustainable agriculture. The aim of this research is to investigate the hydroponic (NFT, DFT, Aeroponic) efficiency on water use using Amaranthus viridis L. as the planted material. Efficiency on water use was measured by comparing the water use on hydroponic with the control during the plant growing period. The result shows that the three type of hydroponics are able to increase efficiency of water use. NFT is the most efficient technique with efficiency on water use 20.43%. While DFTand Aeroponic, has the efficiency on water use 12.29% and 3.57%, respectively. Enhancing efficiency of water use on hydroponic was caused by the clossing and circulating irrigation technique on hydroponic are able to minimize the evaporation . "

"Microbial communities usually have mixed populations, only in uniqueenvironmental situations do microorganisms live entirely alone. Thus many types of interactions are possible among the members of an ecosystem?s community. In general, the constant association of different organisms in an ecosystem is referred to as symbiosis, with the associates being called symbionts. One type of a symbiosis is antagonism. Antagonism is a symbiotic relationship in whichone population of microorganisms has a harmful effect on the growth of another microbial population (Batzing 2002: 696). A number of microorganisms (bacteria, yeasts, fungi) which effectivelycontrol postharvest pathogens have been identified as antagonists (Mari and Guizzardi 1998:60). A variety of microbial antagonists were reported to control several different pathogens on various fruits. The organism that suppresses the pest or pathogen is referred to as the biological control agent (BCA) (Pal & Mcspadden Gardener 2006: 1). Biological control may in simple terms be defined as the use of one living organism to control another (Druvefors 2004: 4).Often antagonists are isolated on the surface of plants; this natural presence makes them more likely to succeed because of their colonization ability and environmental adaptation (Mari and Guizzardi 1998:60). The use of yeasts as antagonists appears to be quite promising, although the mechanism has not yet been fully elucidated. Some antagonist yeasts have been reported as biocontrol agent of fungal pathogen on fruits. Zhao et al. (2008: 115--116) reported that tomato fruit treated with Pichia guillermondii had an infection rate of 25% which was caused by Rhizopus nigricans, which wassignificantly lower than the control (41.67%). Kalogiannis et al. (2006: 72) reported that Rhodotorula glutinis Y-44 significantly reduced disease incidence caused by Botrytis cinerea on tomato by 52%, compared to the untreated control. Zhang et al. (2004: 84) reported that the application of Cryptococcus laurentii resulted in low average decay incidence caused by B. cinerea in fruit by 7.1%, compared with 40% in the water-treated control fruit. University of Indonesia Culture Collection (UICC) collected epiphytic yeasts from plant samples of Cibodas Botanical Garden, and moulds from decayed tomatoes and infected plants. The ability of the epiphytic yeasts as biocontrol agents against tomato spoilage-causing moulds has not beenreported. This study consists of two parts. Part 1 is The Antagonistic Ability of Epiphytic Yeasts of Cibodas Botanical Garden on Tomato Plant Infected-Causing Moulds. Part 2 is The Potential of Candida sp. UICC Y-328 as a Biocontrol Agent of Aspergillus ochraceus on Postharvest Tomatoes.The purposes of this study were to investigate the ability of six species of epiphytic yeasts in inhibiting the growth of tomato plant infected-causing moulds, and the potential of Candida sp. UICC Y-328 as a biocontrol agent in reducing postharvest tomato spoilage caused by Asp. ochraceus. The media used for growing the yeasts was Yeast Malt Agar (YMA), and maintenance for fungi was Potato Dextose Agar (PDA). The media used for antagonistic test were PDA and Potato Dextrose Broth (PDB). Antagonistic test by strip method was carried out by using the concentrations of yeast cells at (0.7--4.45) x 108 CFU/ml, and Asp. ochraceus at (7.0--8.1) x 107 CFU/ml, Asp. terreus Thom at (7.7--8.6) x 107 CFU/ml andDrechslera sp. at (0.45--3.5) x 105 CFU/ml. The yeast cells were inoculated 4 hours earlier before inoculation of mould spores on PDA in Petri dishes. Results showed that Candida sp. UICC Y-328 has highest percentage of colony reduction of Asp. ochraceus (56.45%), followed by Metschnikowia reukaufii UICC Y-351 on reducing colonies of Asp. terreus and Drechslera sp. (25.42% and 51.28%, respectively) during 6-day incubation. Antagonistic test by co-culture method was carried out by using the concentrations of yeast cells at (0.7--4.45) x 108 CFU/ml, and Asp. ochraceus at (6.0--8.6) x 107 CFU/ml, Asp. terreus at (4.6--9.5) x 107 CFU/ml. The yeast cells were inoculated 8 hours earlier before inoculation of mould spores on PDB. Results showed that Candida sp. UICC Y-328 reduced the size of conidial heads(5.52%) and hyphae (8.29%) of Asp. ochraceus, at 3-day incubation.Cryptococcus laurentii UICC Y-379 reduced the size of conidial heads and hyphae of Asp. ochraceus (15.07% and 11.60% respectively) and Asp.terreus (12.35% and 24.47% respectively) at 3-day incubation. Antagonistic test by slide culture method showed that the yeast cells of four strains (Candida rancensis UICC Y-326, Cr. laurentii UICC Y-319, Cr. laurentii UICC Y-379,and M. reukaufii UICC Y-351) attached to hyphae of Drechslera sp. after 3- and 4-day incubation.Cells of Candida sp. UICC Y-328 attached to hyphae of Drechslera sp. after 4-day incubation. Cells of Cr. laurentii UICC Y-385 was not able to attach to hyphae of Drechslera sp. Candida sp. UICC Y-328 was potential in reducing the growth of Asp. ochraceus, and was investigated further for its potential as a biocontrol agent. Wounds on postharvest tomatoes were inoculated with 25 µl of yeast cellsuspension and 25 µl of mould spore suspension. The yeast cells wereinoculated 24 hours earlier before inoculation of mould spores on wounds of tomatoes. Biocontrol study showed that incidence of spoilage in postharvest tomatoes which were wounded and inoculated with Candida sp. UICC Y-328 and Asp. ochraceus, were reduced by 20% after 15-day incubation at room temperature. All postharvest tomatoes which were wounded and inoculated with Asp. ochraceus as control, were spoiled (100%). Synthetic fungicide Dithane M-45 at a concentration of 0.08% reduced spoilage incidence by 70%. Candida sp.UICC Y-328 was not effective as biofungicide in reducing spoilage incidence."