Journal of Tropical Biodiversity and Biotechnology
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Genetic Variation Within Four Captive Chital (Axis axis) Populations in Indonesia
Get PDFChital is a native animal from South Asia. Chital had been introduced to many countries, including Indonesia. Chital was first introduced to Indonesia in 1811 at Bogor Palace and since had been kept captive around Indonesia. Currently, no research had been done concerning the genetic variation of Indonesian chital. Therefore, the purpose of this research was to analyze genetic variation and phylogenetic relationship of chital from Pusat Inovasi Agroteknologi Universitas Gadjah Mada (PIAT UGM), Prambanan Temple, Gembira Loka Zoo, and Bogor Palace, based on mitochondrial D-loop fragment. This study used a Polymerase Chain Reaction (PCR) method. DNA was extracted from faecal samples and amplified with L15995 and H16498 primers. The analysis used for this research were genetic variations, haplotype networking, and phylogenetic relationships between populations. This study detected 5 haplotypes out of 20 sequences with 10 polymorphic sites and 2 indels. The haplotype diversity and the nucleotide diversity were 0.443 and 0.002 respectively, and the genetic distance was between 0 and 2.03% (average 0.55%). This research also showed one main haplotype, labelled as haplotype 1, which consisted of all individuals from PIAT and Prambanan Temple, four individuals from Bogor Palace, and one individual from Gembira Loka. This grouping proves that the majority of chital population in Indonesia came from Bogor Palace. One individual from Gembira Loka has a considerable genetic divergence from the rest of the samples, which might indicate it originated from a different source population.
The Diversity and Uniqueness of Avifauna in Erek-Erek Geoforest at Ijen Geopark, East Java, Indonesia
Get PDFErek-Erek Geoforest (EEG) is one of the Biosites of Ijen Geopark located at the eastern slope of Mount Ijen. This location has unique topography of highland forests restricted by mountain ridges. This topography creates dense vegetation and humid ecosystem supporting microhabitats for endemic birds. This study aims to investigate the diversity and uniqueness of avifauna in EEG based on the existing value of birds. The method used is a point count at three potential station for the presence of birds. The data collected are the bird species, individual number of species, and species existence based on conservation status, distribution, and protection status. Data analysis includes the Shannon Wiener diversity index (H’), Evenness index (E), and existence factor (Ef) of bird community. The results show there are 57 species of birds belonging to 46 genera and 31 families. The diversity of birds in EEG Biosite has a high value (H'=3.40) and also a high evenness value (E=0.84). The Ef value of birds in this area is 51.35, which means the uniqueness value is a medium category. There are three bird species that have the highest Ef value, i.e Arborophila orientalis (Ef=80.00), Pycnonotus bimaculatus (Ef=73.33) and Locustella montis (Ef=73.33). The three species are endemic to Indonesia, especially A. orientalis whose distribution is limited to the highlands of East Java. Based on the composition, diversity, and uniqueness of avifauna in the EEG, it becomes valuable information for the government, Ijen Geopark Manager, and local communities to manage EEG Biosite conservatively by maintaining the existence of avifauna and their habitats.
Cobalamin and Thiamine Effect on Microalgae Biomass Production in the Glagah Consortium
Get PDFThe Glagah consortium is a mixed culture of various microalgae and bacteria isolated from Glagah Beach, Yogyakarta. Cobalamin and thiamine, which are given by symbiotic bacteria, are assumed will increase biomass. This study aimed to determine the effect of cobalamin and thiamine on microalgae biomass production in the Glagah consortium. The microalgae of Glagah consortium were cultivated for 10 days with vancomycin and gentamicin antibiotic as treatment and without antibiotics as a control. The parameters measured included the number of bacterial colonies, cobalamin and thiamine levels measured by LC-MS, chlorophyll a and b levels, cell density of microalgae and dry biomass. The highest level of cobalamin and thiamine was in the Glagah consortium without antibiotics. Cobalamin and thiamine increased in the exponential phase along with the increasing Staphylococcus sp. colonies. The Quantity of Staphylococcus sp. colonies in the exponential phase was 62.105 (cfu/mL). The level of cobalamin in the exponential phase was 2.33 µg/L and the level of thiamine in the exponential phase was 49.71 µg/L. The highest productivity dried weight biomass was 0.0134 g/L/day in the day-6th on the Glagah consortium without antibiotics. This result showed that microalgae and bacterial interaction was mutualism symbiosis involving cobalamin and thiamine that increased in the exponential phase along with the increasing Staphylococcus sp. colonies. This interaction was able to increase biomass microalgae
In silico Screening of Potential Antidiabetic Phenolic Compounds from Banana (Musa spp.) Peel Against PTP1B Protein
Get PDFType 2 diabetes mellitus (T2DM) is a global problem with increasing prevalence. The current treatments have made an immense progress with some side effects, such as drug resistance, acute kidney toxicity, and increased risk of heart attack. Banana (Musa spp.) peel comprises 40% of banana fruit contains high phenolic compounds whilst some studies have suggested a correlation between phenolic compounds and antidiabetic activity. One of the novel protein targets that has been identified as a potential anti-diabetic treatment is PTP1B (PDB ID:2NT7). Therefore, this study aimed to screen the potential PTP1B inhibitor for antidiabetic treatment from phenolic compounds in banana peel. QSAR, molecular docking, ADME-Tox, and molecular dynamics analysis were deployed to examine forty-three phenolic compounds in banana peel. Eighteen ligands were screened by QSAR analysis and eight of them had a lower binding energy than the standard (ertiprotafib) in molecular docking, with urolithin A and chrysin were the lowest. Both passed Lipinski’s rule of five, had a good intestinal absorption, and no blood-brain barrier penetration, however, their mutagenicity, carcinogenicity, and irritation to the skin and eyes were still in questions. Molecular dynamics analysis found both of them were in a stable conformation with PTP1B. This study suggested a potential of urolithin A and chrysin as PTP1B inhibitor for antidiabetic treatment. Additionally, further experimentation is required to validate this finding.
In silico Determination of Host-Viral Interaction of Apoptotic Mimicry Pathway Proteins During Hepatitis B Viral Pathogenesis
Get PDFViruses are the opportunistic pathogens that have developed several elegant strategies to deploy their host systems for a pathogenic invasion. Viral apoptotic mimicry is characterized by the exposure of host cell phospholipid, the phosphatidylserine which marks the host cell for apoptotic activation. The Hepatitis b virus, an enveloped virus has recently been found to interact with Phosphatidylserine (Ptdser) on the host through its large surface protein experimentally. Nonetheless, the employment of apoptotic mimicry during the pathogenesis of HBV has not been determined. Therefore, in the present study, we attempt the in-silico exploration of the interaction of the apoptosis initiating receptors activated by Phosphatidylserine Receptors such as TIM3, AXL, MERTK and GAS6 by Hepatitis B Virus L protein. Molecular Docking of Phosphatidylserine Receptor were studied to observe protein – protein interaction against Surface L Protein of Hepatitis B Virus by using online protein interaction software. It was found from the in-silico studies that Phosphatidylserine Receptors i.e. TIM3 (PDB: 5F71), AXL (PDB: 5U6B), MERTK (PDB: 2POC) and Gas6 (Growth Arrest Specific protein 6) (PDB: 2C5D) have shown effective binding efficacy against Surface L Protein of Hepatitis B Virus, whereas TIM3 (PDB: F71) and Gas6 (PDB: 2C5D) has shown maximum binding energy with respect to both the software used to analyse the protein-protein docking. This interaction study can form the basis of the experimental attempt in understanding the viral-host protein interaction pattern during hepatitis b viral infection
Herbaceous Diversity in the Gumuk Ecosystem in Ledokombo District-Jember Regency with Varied Land Use Type
Get PDFGumuk is a unique landscape in Jember Regency resulting from the eruption of Mount Raung that can provide ecosystem services through its ecological functions. Increased mining activity in Gumuk and land-use changes can lead to a decline in biodiversity and affect ecosystem services. This study aims to determine the diversity of herbaceous in the Gumuk ecosystem. Conducted in January - March 2021 in Ledokombo District, Jember Regency. The spatial distribution of Gumuk was carried out using GIS. Herbaceous sampling was carried out using 2x2 plots on three types of Gumuk utilisation, namely mixed gardens, sand mining, and stone mining. The results showed that there were 136 Gumuk in Ledokombo District. One hundred twenty herbaceous species (49 families) were found in all types of Gumuk. Mixed gardens have the highest species diversity (109 species, 49 families) compared to other types. Digitaria sanguinalis (L.) Scop. has high dominance in all types. Species dominance showed a moderate category for all types of Gumuk (D = 0.07). Community complexity in all types was in the high class (D' = 0.90) and species diversity was in the high class (H’ = 3.25). Evenness index € was different in the three types of Gumuk; in mixed gardens, the evenness of species was lower (0.23) than the other two types.
Orang-utans’ (Pongo pygmaeus wurmbii) Activity Pattern in Camp Release and Feeding Site of Lamandau Wildlife Sanctuary, Central Borneo, Indonesia
Get PDFThe Bornean orang-utan (Pongo pygmaeus wurmbii) release process at Lamandau Wildlife Reserve applies the soft-release method. In this method, there is still provisioning additional food on the feeding site by human. The existence of camp release and feeding sites in the vicinity of release forests is assumed to have an impact on orang-utans’ activity patterns. This assumption is related to the principle of releasing them into their natural forest habitat, namely by reducing direct interaction between humans and orang-utans. The aims of this research were: (i) to measure the intensities of orang-utan presence on camp and feeding site, (ii) to analyze the correlation between phenology and orang-utan’s presence on camp and feeding site, and (iii) to assess orang-utan’s activity budgets, diet composition, and vertical used on camp, feeding site, and forest. Activity budgets of five group orang-utans with different categories based on age and sex were compared using the focal animal sampling method and instantaneous records. The analysis showed no correlation between the intensities of orang-utan presence and phenology. However, there were significant differences in activity patterns between adult and adolescent orang-utans. The findings revealed that adult orang-utans activity pattern tended to be high in resting at all observation locations while adolescents spending more their activity for feeding. Orang-utans at 0-10 m of height classes tend to do more activity. Almost all orang-utans feed on a non-forest diet (45-67%) in the camp release, feeding site, and surrounding. We assumed that the existence of a camp release and feeding site near the release point are affecting factors in a successful reintroduction of ex-rehabilitate orang-utans.
Phytoplankton Diversity as a Bioindicator of Water Quality Mangrove Ecosystems in Clungup Mangrove Conservation, Kondang Merak and Sempu Island, Malang Regency
Get PDFLocal community groups have handled damage to the mangrove ecosystem on the coast of South Malang by carrying out restoration. The purpose of this study was to evaluate water quality in the restoration mangrove ecosystem based on phytoplankton diversity as bioindicators. A water and phytoplankton sampling was repeated three times with a depth of about 10-15 cm (below the surface water) at each location consisting of 4 restored mangrove ecosystems in Clungup Mangrove Conservation (CMC) and Kondang Merak as well as one natural mangrove ecosystem in Teluk Semut, Sempu Island, Malang Regency. Water quality parameters include water temperature, air temperature, conductivity, pH, Dissolved Oxygen (DO), Biochemical Oxygen Demand (BOD), nitrate, and orthophosphate content. The biotic index includes the Trophic Diatom Index (TDI) as an indicator of water nutrient content and Percentage Pollution Tolerance Value (%PTV) as an indicator of organic pollution. The water quality in the five mangrove ecosystems of CMC, Kondang Merak, and Teluk Semut has met the water quality standard for marine biota except for DO, nitrate, and orthophosphate content in several locations. Water quality in five mangrove ecosystems CMC, Kondang Merak, and Teluk Semut based on phytoplankton indicators did not show any contamination with toxic materials (H’). Based on TDI, it is categorized as eutrophic – hypereutrophic, except at the reference site of Teluk Semut mangrove; based on PTV polluted with moderate to high organic matter except at the reference site locations, namely Teluk Semut, and CMC 2. Thus, a location that has good phytoplankton bioindicators is Teluk Semut.
Bioremediation of Mercury- Polluted Water in Free Water Surface-Constructed Wetland System by Euglena sp. and Echinodorus palifolius (Nees & Mart.) J.F. Macbr.
Get PDFMercury accumulation in the aquatic environment can be highly harmful. The body takes mercury vapor through the lungs, then absorbs mercury metal through the digestive system, and then the blood carries the metal to the brain. Bioremediation is the process of breaking down or converting harmful compounds into non-toxic forms, which can be accomplished through phytoremediation or phycoremediation. The goal of this study was to examine the growth and anatomy of Euglena sp. after being cultured in the mercury-containing FWS-CW waste treatment system. The ability of Euglena sp. and Echinodorus palifolius to bioremediate mercury at different concentration as well as association and non-association treatments. This study was carried out in a bioreactor known as FSW-CW (Free Water Surface-Constructed Wetlands). Plant growth (plant height and number of leaves), chlorophyll content, diameter of root and petiole, metaxylem diameter of root, petiole, and leaves, cortical thickness of root and leaves, and petiole anatomy were all measured. Water temperature, pH, salinity, and light intensity were all measured as environmental parameters. Mercury treatment reduced Euglena density (183.5 cells. mL-1103 in control and 12.6 cells. mL-1103 in 100 ppm mercury treatment) and number of E. palifolius leaves, but not plant height and chlorophyll. Root and petiole diameters were affected by the mercury treatment, petiole diameter decreased unless the concentration was 100 ppm, whereas root diameter actually increased. The diameter of the root metaxylem increased, but the petioles and leaves, as well as the thickness of the root cortex, did not provide a significant response. The growth of E. palifolius was still optimal in the presence of Euglena in mercury-containing medium.
Extremophilic Cellulases: A Comprehensive Review
Get PDFMicrobial cellulases are an important industrial enzyme having diverse applications in biotechnology, environmental challenges, industrial products and processes. Extremophiles like thermophillic bacteria are a good source of industrially important cellulases as these can withstand industrially rigorous procedures like paper deinking, fabric material softening, bio stoning, paper and pulp, biopolishing cloth material, animal feed and juice. Identification of novel cellulases or improving them through biotechnological interventions has remained a challenge for researchers. Genetic manipulation of thermophilic bacteria for increased cellulase production or synthetic biology approaches for cellulase gene/gene cluster extraction from thermophilic bacteria and expression in appropriate hosts for improved cellulase synthesis. The classic and high-throughput technologies like genomics, metagenomics and bioinformatics could be exploited to isolate cellulase genes from a variety of thermophilic bacteria and further processing. Keeping in view the ultimate requirement of extremophilic cellulases in industries, present study is a compilation of various aspects related to extremophilic cellulases their sources, production, biotechnological interventions and challenges.