bluuebunny/crossref_metadata_2025 huggingface dataset:
Nuclear factor I/A coordinates the timing of oligodendrocyte differentiation/maturation via Olig1 promoter methylation
Authors: Semi Katsunori , Sanosaka Tsukasa , Namihira Masakazu , Nakashima Kinichi
Published: August 2021

Transcription factors (TFs) and epigenetic modifications function cooperatively to regulate various biological processes such as cell proliferation, differentiation, maturation, and metabolism. TF binding to regulatory regions of target genes controls their transcriptional activity through alteration of the epigenetic status around the binding regions, leading to transcription network formation regulating cell fates. Although nuclear factor I/A (Nfia) is a well-known TF that induces demethylation of astrocytic genes to confer astrocytic differentiation potential on neural stem/precursor cells (NS/PCs), the epigenetic role of NFIA in oligodendrocytic lineage progression remains unclear. Here, we show that oligodendrocyte differentiation/maturation is delayed in the brains of Nfia-knockout (KO) mice, and that NFIA-regulated DNA demethylation in NS/PCs plays an important role in determining the timing of their differentiation. We further demonstrate that the promoter activity of the oligodendrocyte transcription factor 1 (Olig1) gene, involved in oligodendrocyte differentiation/maturation, is suppressed by DNA methylation, which is in turn regulated by Nfia expression. Our results suggest that NFIA controls the timing of oligodendrocytic differentiation/maturation via demethylation of cell-type-specific gene promoters.
Growth Performance of Black Soldier Fly Larvae (Hermetia illucens) Fed on Some Plant Based Organic Wastes
Authors: Kinasih Ida , Putra Ramadhani Eka , Permana Agus Dana , Gusmara Finsa Firlana , Nurhadi Muhammad Yusuf , Anitasari Ramadini Aini
Published: August 2021

Insect larvae, such as black soldier fly larvae (BSFL: Hermetia illucens) are currently being considered as an alternative source of protein for poultry and aquaculture industry while in the same time apply as agent to manage organic wastes. In order to achieve both roles it is necessary to develop an appropriate farming methodology and understand the impact of different feeding source for the insect production. The study explored the effect of three local plant based organic wastes as feedstocks to growth of the black soldier fly larvae. Separate feeding trials on horse manure (HM), vegetable wastes (VW), and tofu dreg (TD) was done and their effect on BSF larvae growth rate, larvae weight and total prepupal yield in grams content analysed. The efficiency of the BSF larvae to consume and ability to reduce the waste load of the different substrates was also evaluated. The result showed all materials suitable as feeding material for black soldier fly. Difference on physical properties and chemical content affected the development time, harvested biomass, efficiency of digestivity, and efficiency of biomass production which is unique for each type of waste. This study provide base line information for future development of plant based organic waste management.
Bacterial Communities in Aquatic Sediment from Bukit Duabelas Raintforest and Oil Palm Plantation at Sumatra Indonesia
Authors: Wijayanti Marini , Wahyudi Aris Tri , Yuhana Munti , Engelhaupt Martin , Meryandini Anja
Published: August 2021

The diversity of bacterial communities in aquatic sediment of rainforest and oil palm plantation at Sumatra was studied using pyrosequencing of 16S rRNA gene and common biodiversity indices.  Phylogenetic approach was used for revealing the community shift of bacterial phyla and genera in both areas.  Ecological approach used soil pH, total Carbon (TC), total Nitrogen (TN), available Phosphorus (AP) measurement and bacterial diversity with Shanon and Simpson indices, and bacterial richness with Chao1-ACE indices and OTUs.  Bacterial diversity and richness in aquatic sediment of forest area was higher than that ones in oil palm plantation area, although their pH, TC, and TN in both areas were not different significantly. The majority of sequences related to Proteobacteria (34.85%), Acidobacteria (32.67%), Nitrospirae (6.86%), Chloroflexi (4.31%), and Actinobacteria (4.02%) were from forest; whereas those related to Acidobacteria (46.10%), Proteobacteria (25.86%), Nitrospirae (9.20%), Chloroflexi (4.99%), and Actinobacteria (2.34%) invented from oil palm plantation. The genera of Alphaproteobacteria and Betaproteobacteria dominated in genera phylotype of bacterial 16S rRNA phylogenetic revealed both aquatic sediment of forest and oil palm plantation. The most genera in the phylogenetic tree from aquatic sediment of both areas was Burkholderia.  The bacterial community shift in aquatic sediment of forest transformation indicated higher bacterial diversity index, richness index, some of phyla and genera in aquatic sediment from forest than from oil palm plantation.
Population Growth Models of Forest Trees for Conservation Management: Case of Teak (Tectona Grandis) Forest in Begal, East Java, Indonesia
Authors: Sumarti Novriana , Wardana Mharta A. , Nuraini Nuning
Published: August 2021

Based on 2010 FAO report, teak forest and plantation in Indonesia covers 1,269 million hectares or 7 per mill of total area of Indonesia. It can be found dominantly in Central and East Java. PT Perhutani, Indonesia has responsible for management of the government owned forests in the islands of Java and Madura. Based on 2007 data, the teak wood production is 517,627 m3 and the highest percentage, which is 37% of total production, is coming from East Java. In this paper, we develop growth population models using Leslie Matrix and Markov Chain in order to predict the future condition based on the current condition. The models are implemented into data from Teak Forest in Begal, East Java, that covers 2,052.8 hectares and consists of 114 sites. The result from the first model using Leslie Matrix shows that it needs 16 years from year 2011 that the sustainable condition of the forest can be achieved. The result from the implementation of the second model using Markov Chain into the existing data shows that the condition of the teak forest can be classified as quite critical because the good condition part based on its density of the early age group (0 - 4 years) has potential to become the worst condition before its harvest time.
DNA Barcode of Seven Indonesian Hornbills Species (Aves: Bucerotidae) Based on Mitochondrial DNA Cytochrome Oxidase Subunit I
Authors: Jarulis Jarulis , Solihin Dedy Duryadi , Mardiastuti Ani , Prasetyo Lilik Budi
Published: August 2021

DNA barcoding based on mitochondrial DNA COI gene is very useful in identifying of Indonesian hornbill. We sequenced the DNA barcode of seven hornbill species using the mitochondrial DNA COI gene to explore their genetic variation, identity, distance, and phylogenetic. Thirty-one blood samples from seven hornbill species were isolated and analyzed. Slight variation was observed within the nucleotide of the hornbill species. In contrary, fairly significant difference was shown within the genus and family level. COI gene sequences generated from this study, showed unmatched result with BoLD System database. These seven Indonesian hornbill species were then divided into two groups, namely Group I consisting of Aceros cassidix, Rhyticeros plicatus, R. undulatus, Buceros rhinoceros, and B. bicornis, while Group II occupied by Anthracoceros albirostris and A. malayanus; both groups with genetic distance 5.90%. Overall in-group had 9.40% distances to the hornbill used as the out group. COI sequence gene from these seven hornbill species are novel for identifying Indonesian hornbills. We encourage its use as quick species identification, applied to prevent illegal poaching conservation management.
Metagenomic Analysis of Bacteria Phylum Firmicutes and Bacteroidetes in Women with Type 2 Diabetes
Authors: Zulhaerati Zulhaerati , Budiarti Sri , Astuti Rika Indri
Published: August 2021

Diabetes mellitus (DM) is a serious health problem in Indonesia. Type 2 diabetes is a metabolic disease which primarily caused by obesity-linked insulin resistance. There is a link between insulin resistance and bacterial populations in the gut. Therefore, the aims of this study was to analyze composition of bacteria belong to the phylum Firmicutes and Bacteroidetes in women with type 2 diabetes and non-diabetic persons as control. The study included five female adults type 2 diabetes patients and five healthy controls. The bacteria composition was analyzed for abundance by denaturing gradient gel electrophoresis (DGGE). Metagenomic analysis based on 16S rRNA gene was represented by 12 DGGE bands. The twelve respective bands showed the similarity ranging from 77 up to 98%. Diversity of microbial composition in women type 2 diabetes was represented by five DGGE bands are Bacteroides fragilis, Bacteroides vulgatus, uncultured Bacteroides sp. clone Lb4eF4, uncultured bacterium clone 16sms90-5g05, and uncultured bacterium clone Malaga 1F14. Four DGGE bands in women healthy controls are closely related to uncultured bacterium isolate DGGE gel band Eub42, uncultured bacterium isolate DGGE gel band K115, uncultured bacterium clone HFV04255, and Enterococcus sp. the finding shows bacterial species belong to the phylum Bacteroidetes was mostly found in women diabetic group, while those belong to the phylum Firmicutes was mostly found in healthy controls.
Isolation and Characterization of C-C Chemokine Ligand 7 (CCL7) in Cynomolgus Macaques
Authors: Mariya Sela S. , Dewi Fitriya N. , Villiandra Villiandra , Paramastri Yasmina A. , Iskandriati Diah , Saepuloh Uus , Hayes Eric , Pamungkas Joko , Sajuthi Dondin
Published: August 2021

Cynomolgus macaques (Macaca fascicularis) are an established animal model of asthma, which exhibit different responses to allergen exposure that are clinically relevant. The chemokine ligand gene (CCL7) encodes Monocyte Chemotactic Protein-3, which has an important role in asthma pathogenesis. While CCL7 polymorphism in humans is associated with asthma phenotype, very little is known about CCL7 in nonhuman primate models of respiratory disease. The objective of this study was to isolate and characterize CCL7 gene in cynomolgus macaques of Indonesian origin. In this study, we used sequencing and bioinformatics technique for gene isolation, characterization, and protein 3D structure prediction. We isolated a 2253 base-pair (bp) sequence of CCL7 in cynomolgus macaques, which exhibited 95% similarity in coding sequence to human CCL7. The amino acid sequence was more closely clustered with human CCL7 than with that of rodents. Importantly, the predictive protein structure of CCL7 was similar to that in humans. These similarities in CCL7 suggests the potential of cynomolgus macaque as a translational model to study asthma, particularly in the context of genetics and role of chemokines such as CCL7.
Propagation of Dendrobium antennatum Lindl via Seed Culture In Vitro Using Simple Medium: Fertilizer and Complex Organic Based Medium
Authors: Nugroho Julius Dwi , Arobaya Agustina Yohana Setyarini , Tanur Evelyn Anggelina
Published: August 2021

A New Guinea Orchid, Dendrobium antennatum Lindl urgently needs to conserve. The availability of in vitro germination technique for this orchids is significantly important to present the useful tool for conservation effort. This study aimed to find a simple media that consists of Growmore 10-55-10, a foliar fertilizer and complex organic i.e. coconut water, banana pulp, onion spring extract, and carrot juice. Five in vitro medium for seed germination and four in vitro sub-culture medium for planlet growth were formulated and used in this study. Our findings revealed that seed germination in vitro of Dendrobium antennatum well occured on the medium of Growmore 10-55-10 supplemented with 10% coconut water (GCw) and of Growmore 10-55-10 supplemented with 50 g/l extract spring onion. The seed germination process from sowing the seed to plantlet production ready to transfer to sub-culture medium for further growth took time 140 days. The embryo became pale green at the day 11 on the germination media. It could be used as a tool for detection of viability of the seeds. Both seed germination medium could be used also as sub-culture medium for enhancing the growth of the plantlets but not for multiplication of shoots.
Protective Effect of Green Algae Ulva reticulata Against Pseudomonas aeruginosa in Drosophila Infection Model
Authors: Nainu Firzan , Asri Rangga Meidianto , Djide M. Natsir , Ahsan Muhammad , Arfiansyah Rudi , Sartini Sartini , Alam Gemini
Published: August 2021

The emergence of antibiotic-resistant Pseudomonas aeruginosa is one of main health issues in global communities. To overcome such threat, the discovery of novel antibacterial agents is indispensable. This study aimed to evaluate the in vivo antipseudomonal activity of Ulva reticulata extract in Drosophila model of infection. Ethanolic extract of Ulva reticulata was prepared using maceration method and the extract was subsequently assessed for its in vivo antibacterial effect against P. aeruginosa using survival assay, bacterial load enumeration, and gene expression analysis in the wildtype Drosophila. Survival and bacterial load analysis were further performed in a similar fashion on the mutant flies devoid of component responsible in the activation of immune responses against P. aeruginosa. Decline in the survival of infected host accompanied by augmentation of bacterial proliferation was documented in the wildtype Drosophila upon infection with P. aeruginosa. These phenotypic events were further amplified in immune-deficient mutant Drosophila. Nevertheless, improvement of host survivorship and reduction of bacterial burden were demonstrated in both wildtype or immune-deficient mutant flies upon treatment with Ulva reticulata extract after bacterial challenge. Our data demonstrated in vivo antipseudomonal activity of Ulva reticulata extract and thus provide a valuable information about its future potential for health promotion.
Oil Palm Phytochrome-Interacting Factor4 (PIF4) Gene is Conserved and Highly Expressed During Somatic Embryogenesis
Authors: Suksirt Mantira , Khianchaikhan Kamolwan , Thuzar Mya , Vuttipongchaikij Supachai , Jantasuriyarat Chatchawan
Published: August 2021

Oil palm is used in food, fuel and cosmetic industries. Tissue culture is the best way to propagate oil palm; unfortunately the somatic embryogenesis during tissue culture takes long time. The molecular mechanism of somatic embryogenesis in oil palm remains unknown. Recent research reported that auxin plays an important role in early and post-embryogenic plant. PHYTOCHROME-INTERACTING FACTOR4 (PIF4) regulates levels of auxin and the expression of key auxin biosynthesis genes. Our research aims to characterize oil palm PIF4 gene. Thus, we cloned EgPIF4, analyzed the domain using bioinformatic and examined the expression of EgPIF4 during somatic embryogenesis at different tissue including callus and somatic embryo stages; globular, torpedo, cotyledon, and plantlet stage using real-time PCR method. The result showed that EgPIF4 gene comprised 1,737 bp with 9 exons, which encode 578 amino acid residuals. It contains a conserved domain called basic helix-loop-helix domain. EgPIF4 has high level of expression at somatic embryogenetic stage specifically globular and torpedo stage suggested that EgPIF4 plays an important role during somatic embryogenesis. The future characterization of EgPIF4 function in oil palm will help to understand somatic embryogenesis process and facilitate the improvement of the oil palm tissue culture.
3D Landscape Recording and Modeling of Individual Trees
Authors: Trisyanti Shafarina Wahyu , Suwardhi Deni , Harto Agung Budi
Published: August 2021

The 3D city/landscape model is digital representation of real environment that can be used for planner or landscape architecture in urban development planning. That model’s more focused on building, whereas vegetation model’s also needed for urban planning simulation. This research purposes are to map existing vegetation and to generate individual trees model in some level of details. The research area is campus of ITB Jatinangor and the used data are orthophoto and DSM from UAV-Photogrammetry technology. Manual segmentation, classification, and NDSM generation process can provide tree information (position, crown diameter, species, height)-as 3D vegetation modeling input. It’s also necessary to provide classification, information, detail level, and visualization of vegetation model according to landscape architecture analysis needs. This research results are 3D vegetation models in LoD 1-3 with differents information based on appearance, geometry, semantic, and topology aspects of CityGML. Models then tested qualitatively based on visualization and sun shadow analysis. For visualization, the used data only able to generate LoD 1 and 2 vegetation model and the minimum LoD required for sun shadow analysis is LoD 2. Terrestrial data, which provide the real form and size of each tree part, is needed to generate LoD 3 vegetation model.
Soil Moisture Mapping at Paddy Field in Indramayu Residence Using Landsat 8 OLI/TIRS
Authors: Ghazali Mochamad Firman , Susantoro Tri Muji , Wikantika Ketut , Harto Agung Budi , Nurtyawan Rian
Published: August 2021

Drought monitoring is important for the paddy planting planning. Remote sensing is one tool can be used for it. Paddy field monitoring based on the soil moisture gives much knowledge related to the water content in the soil. Soil moisture analysis in this study is using Normalized Different Water Index (NDWI), Linear Soil Moisture (LSM), and Tasseled Cap. Soil moisture change could explain based on calculation results of NDWI, Linear Soil Moisture (LSM), and Tasseled Cap Transformation (TCT). Based on the results has explained that the driest year occurs in 2015 and June 2016 has a higher soil moisture. Comparison with the radar shows that the results of soil moisture analysis with Landsat was effective can be used with results relatively close to the radar results.
Functional Analysis of an Appressorium-Specific Gene from Colletotrichum gloeosporioides
Authors: Priyatno Tri Puji , Bakar Farah Diba Abu , Redzuan Rohaiza Ahmad , Mahadi Nor Muhammad , Murad Abdul Munir Abdul
Published: August 2021

A novel gene (CAS2) specifically expressed during appressorium formation was isolated from Colletotrichum gloeosporioides using Differential Display RT-PCR. CAS2 comprises 368 deduced amino acid residues and is 50% identical to a hypothetical protein from Chaetomium globosum. ProtFun 2.2 server analysis predicted that Cas2 functions as a transport and binding protein. Based on putative transmembrane domain prediction software (HMMTOP), Cas2 protein is composed of five alpha-helical transmembrane domains with a very short external N-terminus tail and long internal C-terminus. ExPASy ScanProsite analysis showed the presence of integrin beta chain cysteine-rich domain, N-myristoylation site, EGF-like domain, 2Fe-2S ferredoxins, iron-sulfur binding region, VWFC domain, fungal hydrophobins signature, membrane lipoprotein lipid attachment site, and Janus-faced atracotoxin (J-ACTX) family signature in CAS2 protein. Mutants with deleted CAS2 were not significantly different in terms of vegetative growth, conidiation, and appressoria production compared to wild type. However, the Cas2 mutant produced multipolar germination, a feature which distinguishes it from wild type strain. Interestingly, the mutant is non-virulent to mango fruits, indicating that CAS2 may encode proteins that function as novel virulence factors in fungal pathogens.
Application of Proteomics to Identify Fertility Markers in Angus Bull Sperm
Authors: Kutchy Naseer A. , Dogan Sule , Wang Xiaojun , Topper Einko , Kaya Abdullah , Memili Erdogan
Published: August 2021

The goal of the study was to ascertain sperm proteins as fertility markers by identifying sperm proteins in Angus bull sperm using proteomics and validate the markers through comparative sperm biology between Angus and Holstein bulls for which there is reliable fertility data available. We aimed to determine proteins differentially expressed in sperm from Angus bulls with different fertility phenotypes. Two-dimensional differential gel electrophoresis with mass-spectrometry, functional gene clusters, canonical pathways and protein networks, using integrated discovery bioinformatics software and ingenuity pathway analysis were used to identify and analyze sperm proteome. We identified 80 proteins that were differentially expressed in sperm of our experimental population. Using computational biology approaches we demonstrated involvement of structural proteins such as outer dense fiber of sperm tails 2 and enzymes including kinases, and phosphatases having functions in essential pathways in glycolysis/gluconeogenesis and free scavenging. The results are significant because analyzed proteins in Angus sperm are determinants of fertility, gene-environment interactions, as well as potential biomarkers for animal breeding.
Peptides Hydrolysate Derived from Collagen of Snakehead Murrel (Channa striata) Skin Demonstrate Anti-cholesterol and Anti-oxidant activities
Authors: Sinaga Wenny Silvia L. Br. , Ismaya Wangsa T. , Retroningrum Debbie S. , Tjandrawinata Raymond R. , Suhartono Maggy T.
Published: August 2021

Anti-cholesterol and anti-oxidant play a crucial role to combat cardiovascular disease (CVD), due to formation of arterial plagues from oxidation of cholesterol. In the past decades, bioactive peptides demonstrating anti-cholesterol and anti-oxidant activities have emerged as the alternative drugs. In this study, acid soluble collagen was extracted from the skin of snakehead murrel and employed to induce secretion of collagenase by Bacillus licheniformis F11.4. The collagenases secreted were in turn used to produce peptides hydrolysate and were grouped in two distinct collagenase fractions, designated as fraction D and F. Peptides hydrolysate produced by the fraction D was found to demonstrate HMG-CoA inhibitor activity comparable to pravastatin and limited anti-oxidant activity. Meanwhile, peptides hydrolysate generated using the fraction F demonstrated anti-oxidant activity comparable to BHT (2mM), vitamin C (2mM), and vitamin E (2mM), but limited HMG-CoA activity. Combination of the fraction D and F resulted in substantial HMG-CoA inhibition and anti-oxidant activities.
Isolation, Selection and Identification of Polyaromatic Hydrocarbons (PAHs) Degrading Bacteria from Heavy Oil Waste (HOW)-Contaminated Soil
Authors: Yani Mohamad , Charlena Charlena , Mas’ud Zainal Alim , Anas Iswandi , Setiadi Yadi , Syakti Agung Dhamar
Published: August 2021

The heavy oil waste (HOW) containing polyaromatic hydrocarbon (PAHs) is a persistent organic pollutants (POPs) that difficult to degrade. The new PAH degrading consortium was investigated from HOW contaminated soil in North Sumatera of  Indonesia. The isolation, selection and identification of polyaromatic hydrocarbon degrading bacteria from soil contaminated by HOW was conducted to solve a bioremediation process. The isolation microbes from soil contaminated by HOW was performed using a minimum ONR7a media and followed on marine agar media for purification purposes. From the performed isolation results, 11 isolates were able to degrade PAHs compounds, such as phenanthrene, dibenzothiophene, or fluorene compounds. They grew at pH range of 4.8-8.2 and performed on emulsification activity in paraffin from 0.150-0.662. Three of them showed the best performance on HOW biodegradation capability and then successfully selected and identified as Salipiger sp., Bacillus altitudinis, and Ochrobactrum anthropi. using 16S rDNA. The HOW biodegradation as TPH-degradation were 38.66%, 59.60%, and 47.16%, respectively. Those isolated bacteria could potentially be as bioremediation agents to develop on bioremediation process for soils contaminated by HOW.
Molecular Characterization and Phylogenetic Relationships of Melon (Cucumis melo L. Meloni Cultivar) Based on Expression of Andromonoecious Gene
Authors: Al-Mughni Eka Wasi’ , Daryono Budi Setiadi
Published: August 2021

Melon (Cucumis melo L.) is one of horticultural commodities with good economic prospect for melon farmers because of several advantages. 'Meloni' is result of crossing between ‘Sun Lady-3’ and ‘PI 371795’ by Genetics and Breeding Laboratory, Faculty of Biology, UGM. The 'Meloni' plant produces females flowers that expressed by CmACS-7 gene and it can be expected that melon plants 'Meloni' included in the primitive cultivars, while 'Meloni' is a cultivation cultivar. The aim of this research is to study the relation of 'Meloni' kinship to primitive and modern cultivars. Characterization of the CmACS-7 gene is begun by a total isolation process of RNA from a sample of melon plant flowers and detection using a specific primer. The cDNA bands obtained are sequenced and then phylogenetic analysis is performed based on CmACS-7 gene expression using MEGA 7.0. Result of this study show that the presence of the CmACS-7 gene in female and hermaphrodite flowers of ‘Meloni’, ‘PI 371795’, ‘Sun Lady-3’, and ‘Hikapel’. Phylogenetic tree analyze show that ‘Meloni’ from female plant, ‘PI 371795’ and ‘Sun Lady-3’ have closely relation, while 'Hikapel' separated from other cultivars.
Flight Activities and Pollen Load of Lepidotrigona terminata Smith (Apidae: Meliponinae)
Authors: Wicaksono Anggun , Atmowidi Tri , Priawandiputra Windra
Published: August 2021

Worker bees actively forage to supply colony necessity i.e., pollens, nectar, and resin. Flight activities of the worker bees are influenced by food availability and environmental conditions. This study aimed to measure flight activities of Lepidotrigona terminata in terms of leaving and returning to the nest (including carrying of pollen and pollen type) and their relation to environmental conditions. The observation of flight activities of L. terminata were conducted from August to December 2016, at 07.00-17.00 for 1 minute with 1 hour interval. Pollen load and pollen types were analyzed by the acetolysis method. Flight activities of leaving and returning to the nest were lower at 07.00-08.00 (1 individual/min) and at 16.00-17.00 (2 individuals/min). However, the peak activities occurred at 10.00 until 13.00 (8 and 6 individuals/min for leaving and returning to the nest, respectively). Temperature and light intensity were positively correlated with flight activities of bees that carried nectar and resin, as well as leaving the nest without garbage. The returned workers averagely carried 32,696 pollen grains from four pollen types. Based on selection index values, this stingless bee species mostly preferred Araceae (ⱳi=1.522) plant family for pollen resources to others, Anacardiaceae, Aceraceae, and Acanthaceae (x2=39.32, p<0.01).
Ecological Diversity of Microbial Consortium Feces of Beef Cattle and Lignite Coal
Authors: Puteri Gina Chynthia Kamarudin , Ridwan Roni , Harlia Ellin
Published: August 2021

Increasing energy demand is not alongside the availability of limited fossil fuels. Alternative and renewable energy sources are not only an option to overcome energy problems but also essential to minimize global warming. Another critical and promising renewable energy source is biomass-derived from livestock feces. Beef cattle feces contain a microorganism consortium that can be used as a starter with coal media to form biogas. Indonesia recently developed coal waste processing into renewable energy, such as biogas. This study aimed to overview the ecological diversity of microbial consortium of beef cattle feces, lignite coal waste, and a combination of livestock and lignite coal waste under mesophilic conditions. This research is an explorative method, the data obtained were analyzed descriptively. The process of formation was carried out anaerobically on a bottle containing the rumen fluid medium. The fermentation process lasted 42 days at 39℃ of temperature. After that, the sample was electrophoresis, followed by next-generation sequencing (NGS) method. NGS data is processed with the MG-Rast website. This study demonstrates the ecological diversity of microbial consortium of beef cattle, lignite coal waste, and a combined consortium. The results showed ecological diversity in the form of taxonomy dominated by bacteria, eukaryotes, and archaea.
Identification of Follower Status Based on Male Proximity Score in Crested Macaque
Authors: Pasetha Andre , Danish Lisa Michelle , Perwitasari-Farajallah Dyah , Agil Muhammad , Engelhardt Antje
Published: August 2021

Crested macaque live in multimale-multifemale social groups where temporary association (consortship) typically occurs. Current theory and these limited qualitative observations suggest the hypothesis that behavior functions as a means for males to gain access to fertile females. The aim of this study was to investigate follower status based on quantitative method. Males were classified as either “consort males,” “followers,” and “non-followers” based on proximity maintanance every 15 minute uses scan sampling. Tactics used by followers were classified into 1) individual challenge, 2) coalitionary challenge, 3) abandoned takeover, and 4) opportunistic takeover. The proportion of successful takeovers by followers was calculated by dividing the number of takeovers by followers by the total number of observed takeovers. The proportion of followers is higher than average on D-5 and earlier, D-4, and D-3. Only two of the four consort takeover tactics were used by followers. For abandoned which made up 40% and for individual tactic was made up to 11.5% of consort takeovers tactic used. This study contribute to our understanding of alternative mating strategy in primate and provide the first quantitative data demonstrating that following is an alternative mating strategy in crested macaque (Macaca nigra).
Integration Stability of sHBsAg-Multi Expression Cassettes in Pichia pastoris GS115 during Methanol Induction
Authors: Naully Patricia Gita , Nurainy Neni , Restiawaty Elvi , Natalia Dessy , Retnoningrum Debbie Soefie , Niloperbowo Wardono , Giri-Rachman Ernawati Arifin
Published: August 2021

Hepatitis B is the major health problem worldwide including in Indonesia. Vaccination is the best prevention strategy for the disease. For the purpose of vaccine development and to decrease drug import, production of Hepatitis B Virus (HBV) small surface antigen (sHBsAg) from Indonesian HBV subtype is needed. The recombinant protein production can be conducted by integrating multi expression cassettes of sHBsAg gene in Pichia pastoris chromosome using gene replacement method. Such integration method turns out to allow loss of foreign gene from chromosome by excisional recombination-mediated looping out. This research was aimed to determine integration stability of four copies of sHBsAg expression cassette in P. pastoris GS115 chromosome inducted with 2% methanol in FM22 medium. The methanol induction was conducted twice at 63-h and 75-h. Integration stability determination was conducted qualitatively using PCR and quantitatively using qPCR absolute quantification. A band of 208 bp with similar intensity was observed after amplification of genomic DNA. All samples generated the same Ct value of around 22 with four copies of sHBsAg gene per genome. The result from this experiment shows that integration of four copies of sHBsAg expression cassette in P. pastoris GS115 chromosome is stable during methanol induction.
Cysteamine in Maturation Medium Enhances Nuclear Maturation and Fertilization Rate of Sheep Oocytes In Vitro
Authors: Gulo Feni Dwi Kartika , Karja Ni Wayan Kurniani , Setiadi Mohamad Agus
Published: August 2021

Low nuclear maturation and fertilization rate is one obstacle in the in vitro embryo production which decrease embryo yield. This problem is presumable related with high production of reactive oxygen species (ROS) during maturation process. Glutathione (GSH) as an antioxidant is well known to overcome effect of ROS production. GSH synthesis in the cytosol part of the oocyte cytoplasm is influenced by cysteine availability. It is therefore, this research was conducted to evaluate the ability of cysteamine to provide cysteine availability as GSH precursor on the nuclear maturation and fertilization rate of sheep oocytes. Results of this experiment revealed additional cysteamine at 150 µm and 200 µm could significantly improve nuclear maturation rate. On the other side, although additional of cysteamine at 50 µm could not improve nuclear maturation rate, however 50 µm cysteamine in the maturation medium could significantly improve the fertilization rate. Based on those experiment results, it seems that the additional cysteamine might be improve not only GSH availability but also the oocyte quality which characterized the ability of pronuclear formation. This finding strongly suggested that additional cysteamine in the maturation medium could improve nuclear maturation and fertilization rate of sheep oocytes.
Differentiation of Cardiomyocytes and Identification of Cardiac Conduction System Connexins Derived from Bone Marrow Mesenchymal Stem Cells of Macaca nemestrina
Authors: Harsoyo Agus , Suparto Irma Herawati , Yuniadi Yoga , Boediono Arief , Sajuthi Dondin
Published: August 2021

Bone marrow mesenchymal stem cells have been widely used, because plasticity, specific surface markers, self-renewal to transform into various lineages including cardiomyocytes. Information about the connexin (Cx) cardiac conduction systems of the pigtail macaque (Macaca nemestrina) is limited. This study aimed to evaluate cardiomyocyte differentiation from bone marrow mesenchymal stem cells of pigtail macaques and to clarify the Cx cardiac conduction system. Bone marrow aspirates were obtained from the proximal humerus of four adult male pigtail macaques, collected into heparinized tubes, then centrifuged to obtain mononuclear cells that were isolated and cultured in an incubator. After these cells reached 70–80% monolayer confluency as homogeneous fibroblast-like cells, they were subcultured. On the second subculture passage, the cells were pelleted to extract the mRNA, which was analysed by reverse transcription–polymerase chain reaction, and then cultured for a third passage. Cells were positive for CD73 and CD105 and the reference gene glyceraldehyde-3-phosphate dehydrogenase, and negative for CD34 and CD45. Osteogenic, chondrogenic, adipogenic, and cardiomyocyte differentiation was confirmed based on specific staining. The pigtail macaque bone marrow mesenchymal stem cells can be isolated and subcultured. The transcription of genes and translation of proteins of the connexin cardiac conduction systems was successfully identified.
GC-MS Analysis of Active and Applicable Compounds in Methanol Extract of Sweet Star Fruit (Averrhoa carambola L.) Leaves
Authors: Astiti Ni Putu Adriani , Ramona Yan
Published: August 2021

The leaves of star fruit plants (Averrhoa carambola) have been traditionally used to cure many diseases, such as hypertension and fever. Besides, the leaves of this plant have also widely been used as the main raw material in lawar (a Balinese traditional food) making. In this research, the methanol extract of this plant leaves was analyzed and identified for active compound contents. The main objective of this research was to investigate types of possible active and applicable compounds contained in such leaves, previously extracted/macerated in methanol solution. Analysis was conducted by applying GC-MS instrumentation using methanol solution. The results showed that 10 possible active and applicable compounds (Butane, 1,1-diethoxy-3 methyl-(CAS)1.1-DII, Dodecanoic acid, methyk ester(CAS) methyl, Dodecanoic acid, methyl ester (CAS) Ethyl Laun, Pentadecanoic acid ethyl ester, Hexadecanoic acid methyl ester (CAS) Methyl pa, OCTADECA 9.12 DIENOIC ACID METHYL, 9-Octadecenoic acid methyl ester (E)-(CAS), Octadecanoic acid methyl ester, and (E) 9-Octadecanoic acid ethyl ester) were identified in methanol extract of such leaves. Among those compounds, Butane, 1,1-diethoxy-3-methyl and Hexadecanoic acid, methyl ester was two most abundance constituents with percentage of peak areas of 35.67% and 26.93%, respectively.
Characteristics of The Three Cultivar Physiological Growth of Jatropha curcass L. in Two Different Locations Based on Topography
Authors: Indriana Kovertina Rakhmi , Suherman Cucu , Rosniawaty Santi , Sumadi Sumadi , Sukmayana Dodi
Published: August 2021

The purpose of this study was to reveal the sensitivity of cross-location based on topography by giving different FMA consortiums to physiological growth characteristics in three Jatropha curcass L. cultivars. Based on these objectives, the nature of this research is verification. Experiments were carried out in two different places based on topography. The trial time starts from November 2017 to May 2018. Experiments A simple randomized block design (RBD) pattern consisting of fifteen treatment combinations is repeated twice. The experimental results showed that the dose of 10 gr FMA consortium (glomus sp., Acaulospora sp., Gigaspora sp.). With the same spore density gave the best performance of Jatropha plant growth in two different locations based on topography. Observation of chlorophyll content in leaves (age 21, 63, 21 DAP in two locations), plant height (age 21, 63, 21 DAP in two locations), stem diameter (age 21, 63, 21 DAP in two locations) and number of branches secondary (age 21 DAP in two locations) there was a significant effect on the single factor of giving the FMA consortium but there was no interaction between location and treatment.
First Phylogenetic Treatment of Apple Cucumber (Family Cucurbitaceae) from Indonesia Utilizing DNA Variation of Internal Transcibed Spacer Region
Authors: Hidayat Topik , Saputro Nurcahyo Widyodaru , Khamid Miftakhul Bakhrir Rozaq , Bayfurqon Fawzy Muhammad
Published: August 2021

Cucurbitaceae is one of the largest family in Angiosperm in which the most member of this family is important fruit crops in Indonesia such as Cucumber, Melon, Watermelon, and Apple Cucumber. In particular, Apple Cucumber, currently attracts attention to many researchers due to its phylogeneticand taxonomic problem. In term of its appearance, the fruit looks like an apple but the taste is melon. The purpose of this study was to elucidatephylogenetic relationship between Apple Cucumber and other species of Cucurbitaceae based on variation of DNA sequences derived from internal transcribed spacer (ITS) region. As many as six individuals of Apple Cucumber collected from Karawang, Jember, and Aceh were examined. The ITS sequences of some species of family Cucurbitaceae were retrieved from GenBank, and put them in the analysis. Phylogenetic analysis based on parsimony method with using Begoniaas outgroup reveals that Apple Cucumber are nested in the same clade as Melon (Cucumis melo) with high bootstrap value (100%), suggesting that Apple Cucumber is under the same species as Melon. However, on the basis of morphological characters of fruit, apple cucumber is different with that of Melon. This considerably first phylogenetics treatment provides fundamental knowledge for establishing a subspecies of Melon.
Inflammation-mediated Phenoconversion: A Potential Threat to COVID-19 Pharmacotherapy
Authors: Bahar Muh. Akbar , Wilffert Bob , Harapan Harapan , Nainu Firzan
Published: August 2021

One of the important hallmarks of coronavirus disease 2019 (COVID-19) is the existence of severe inflammatory responses. Many reports indicated that inflammatory mediators might suppress the biological functions of some drug metabolizing enzymes and transporters, and therefore result in a transient mismatch between their genotype and phenotype expressions, a phenomenon which is called phenoconversion. The incidence might be clinically relevant to the COVID-19 patients with comorbidities. The patients are treated with multiple drugs that are prone to be altered pharmacokinetically by inflammation-mediated phenoconversion, leading to the modification of their effectiveness and safety. In this review, we discuss the regulation of inflammatory responses during COVID-19 infection and the evidence as well as potential mechanisms of inflammation-mediated phenoconversion. We also provide possible clinical implications of such phenoconversion events as a potential threat in the management of COVID-19 patients.
Gold Mine Wastewater Induced Morpho-physiological Alteration of Four Biodiesel Producing Species
Authors: Hamim Hamim , Lutfiani Lutfiani , Saprudin Deden , Hutagalung Putri Nur Azizah , Hadisunarso Hadisunarso , Setyaningsih Luluk , Putra Hirmas Fuady
Published: August 2021

This experiment aimed to determine the adaptability of four biodiesel-producing plants to gold mine wastewater based on morpho-physiological properties. Four species namely jatropha (Jatropha curcas), castor bean (Ricinus communis), wild candlenut (Reutealis trisperma) and bead tree (Melia azedarach) were grown in water culture using Hoagland solution for 2 weeks and then treated with gold mining wastewater at 0% (control), 25%, 50%, and 75% (v/v) for 3 weeks. Growth, anatomical and physiological characteristics were observed during the treatment. The results showed that gold mine wastewater significantly decreased growth of the four species despite varied among the species. Wastewater had significant effect on leaves anatomy of Jatropha but not on others. It also significantly induced the increase of malondialdehyde (MDA) content in Jatropha and castor bean, but not in wild candlenut and bead-tree. Meanwhile, the treatment significantly decreased chlorophyll content of all species with the most in bead-tree plant, and leaves relative water content (RWC) particularly in castor bean and bead-tree plants. There was strong negative correlation between the increase of MDA content and the decrease of chlorophyll content and leaf RWC. Among the four species, wild candlenut (R. trisperma) was the most resistant to gold mine wastewater based on morphological and physiological properties.
Paddy Loss and Its Implication to Fertilizer Subsidy in Indonesia
Authors: Falatehan A Faroby , Syaukat Yusman , Hastuti Hastuti , Nasrullah Nizar
Published: August 2021

Indonesia is the third largest rice producer in the world, at the same time it’s a country that imports rice from various countries. The government has provided input subsidies to increase rice production and reduce imports. Modes of rice farming in Indonesia is relatively diverse, from conventional to modern, even in the post-harvest process. The objectives of this study are: to analyze the impact of post-harvest handling on food loss and to analyze the relationship between paddy or rice loss with the quantity and value of fertilizers subsidy and paddy production in Indonesia. The estimated food (rice) loss includes the stages of harvesting, threshing, drying, and milling stages and distribution. Farmers use various technologies in processing rice: serrated sickle in harvesting, power thresher in threshing, and flatbed dryer in drying; while rice milling was done using conventional rice miller. The total rice loss reached 6.91 million tons in 2014 and continued to increase to 8.14 million tons in 2018. The growth rate of fertilizer subsidy value is higher than those of subsidized fertilizer quantity and paddy or rice loss. The results indicated that growth rates of paddy production and rice loss was lower than increased of government subsidy for fertilizer.
Designing Wildlife Corridor Along Cikapundung River in Bandung Urban Area (Indonesia) based on Comparation with Kamo River in Kyoto (Japan)
Authors: Dwiyanti Evita Izza , Shibata Shozo , Nukina Ryo , Lastini Tien , Hernawan Endang
Published: August 2021

Cikapundung is a river connecting wildlife habitat in two open green space areas; there are Tahura Djuanda and Bandung Zoo. Now, these habitats are fragmented due to intervention by urban activities in the Cikapundung River boundary. One of the proposed solutions is to develop a wildlife corridor along the Cikapundung River. The purpose of this study is to identify the landcover of the Cikapundung River, analyze the potential area which can be developed into a wildlife corridor, designing the landscape of the corridor tailored to the needs of the wildlife, and comparing the condition of the Cikapundung River boundary with Kamo River in Kyoto, Japan. Primary data is landcover of Cikapundung River boundary obtained through on-screen digitizing from satellite imagery using ArcMap. Secondary data are the biodiversity list in Cikapundung River riparian area and its ecological description. Cikapundung River border has several land cover types; the highest percentage of the landcover is tree canopy 62.2%, followed by buildings 31.0%. As a result of the comparison Cikapundung River has a more significant vegetation species; however, Kamo River has a more significant number of wildlife species. In the design planning, 14 vegetation species have been selected according to 26 target wildlife species' needs.
In-Silico Design of Novel Glucagon-Like Peptide 1 Mutants as Candidate for New Peptide Agonist Drugs
Authors: Sumaryada Tony , Roslia Ajeng Widya , Afifah Alfi , Wahyudi Setyanto Tri , Kartono Agus
Published: August 2021

The binding of glucagon-like peptide 1 (GLP-1) incretin hormone and its receptor GLP-1R plays an important role in the human body. The GLP-1 acts as the insulin secretion stimulator through a GLP-1R agonist activation to avoid the type 2 diabetes mellitus problem. A recent development in computational sciences has enabled us to design a new GLP-1 mutant which has a better binding stability to GLP-1R. In this paper, we have conducted an in-depth analysis of protein-protein docking of GLP-1 and GLP-1R receptor to determine the responsible factors affecting the binding stability. The protein-protein binding stability was analyzed by performing the point mutations on the GLP-1 structure and running the molecular dynamics simulation of the docked structures. Five mutants, Lys20Arg, Lys20His, Lys20Ser, Lys20Gly, and Lys20Ala, has been created computationally and docked with GLP-1R and tested via a molecular dynamics simulation and the free energy perturbation calculation to search for the best-binding mutant. Our results have shown that the Lys20His mutant design has the best potential to be developed as a new peptide agonist drug based on its binding affinity and structural integrity as compared to other mutants and the peptide agonist drugs available in the market exenatide, and liraglutide.
Economic Valuation of Mangrove Ecosystem at Gerung District, West Lombok Regency
Authors: Patria Mufti Petala , Rosadi Siti Dian , Nisyawati Nisyawati
Published: August 2021

Research regarding economic valuation of mangrove in Gerung District, West Lombok Regency has been conducted. The purposes of this research were to calculate and analyze economic value from mangrove ecosystem at Gerung District. Research methods used observation and interviews. Direct Economic Value (DEV) were obtained from direct use of mangrove with a value IDR. 227,040,000/year. Indirect Economic Value (IEV)were calculated from mangrove ecosystem services with a value IDR. 1,405,041,200/year, Existence Value (EV) was obtained by Contingent Valuation Method (CVM) with a value IDR. 1,520,000/year. Option Value (OV) were calculated from biodiversity value with a value were IDR. 1,200,000/year. Total Economic Value (TEV) of mangrove in Gerung District were IDR. 1,634,801,200/year.