Journal of Tropical Biodiversity and Biotechnology
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Plukenetia volubilis L.: A New Record of a Cultivated Alien Species in Java
Full text linkPlukenetia volubilis L. has been documented as a new record for the first time in Java, Indonesia. The species is easily distinguished from the native species, P. corniculata Sm., by its exstipellate basilaminar-glands, long cylindrical column, and wingless fruit-lobes. Plukenetia volubilis is cultivated mainly in South America for its beneficial values as food and medicine and was recently introduced to Asia. However, its occurrence in Java has not been reported. We collected specimens from West Java (Depok City, Bandung Barat and Sumedang Regency) and East Java (Malang Regency). Morphological description, identification key, and photographs of the species are provided
Identifying Single Nucleotide Polymorphisms (SNPs) in OsFER1 and OsFER2 Genes Linked to Iron accumulation in Pigmented Indonesian Rice (Oryza sativa L.)
Full text linkIron (Fe) is an essential micronutrient for the well-being of plants, animals, and bacteria. In plants, iron plays a pivotal role in a myriad of metabolic processes, encompassing redox reaction, photosynthesis, respiration, chlorophyll synthesis, and nitrogen fixation. For humans, iron is indespensable for several metabolic functions, particularly in the synthesis of haemoglobin. Iron deficiency can lead to health issues on a global scale, therefore identifying key crops, such as rice for providing sufficient iron in diet intake is very important. In rice, the maintenance of iron homeostasis is orchestrated by various genes, with OsFER1 and OsFER2 acting as iron accumulator genes in leaves, stems, flowers, and grains. The primary objective of this study was to ascertain the single nucleotide polymorphisms (SNP) in the OsFER1 and OsFER2 and to assess the iron content in Indonesian local rice cultivars. To achieve this, we examined partial sequences of OsFER1 and OsFER2 to identify SNPs in the Indonesian rice cultivars used (Cempo Ireng, Pari Ireng, Hitam Kalsel, Merah Pari Eja, and Ciherang). Concurrently, the iron content in the seeds was quantified using Atomic Absorption Spectrophotometry (AAS). The analysis revealed that the OsFER1 gene sequence, specifically exon 5, exhibited a SNP in the form of a transition. In contrast, the OsFER2 gene sequences, specifically in intron 2 displayed SNPs in the form of insertions. Notably, the iron content in the seeds was highest in Cempo Ireng (black rice), while it was lowest in Merah Pari Eja (red rice) and Ciherang (non-pigmented rice). Importantly, the identified SNPs in these partial gene sequences did not exert any discernible influence on iron levels or the formation of ferritin protein.
Mangosteen (Garcinia mangostana L.) Peel Decoction Effect on Embryological Development of Wader Pari Fish Rasbora lateristriata (Bleeker, 1854)
Full text linkMangosteen (Garcinia mangostana L.) is a tropical fruit that has become a sought-after commodity by enthusiasts from various countries, including Indonesia. The active components found in mangosteen peel primarily consist of active xanthone compounds, such as mangostenol, mangostin, mangostino A, mangostino B, tvophylin B, trapezifolixanthone, alpha mangostin, beta mangostin, garcinon B, mangostano, as well as flavonoids epicatechin and gartanin. These compounds exhibit a range of beneficial properties, including anti-inflammatory, antibacterial, antifungal, antihistamine, antidiabetic, anticancer, and more. Consequently, there is significant potential in developing mangosteen peel extract as a valuable ingredient in herbal medicine. However, there is currently no available data on the effects of exposure to mangosteen peel decoction on fish animal models. Therefore, it is essential to investigate the impact of mangosteen peel decoction on wader pari fish (Rasbora lateristriata) embryos. In this study, wader pari embryos were subjected to various concentrations of mangosteen peel decoction (0.5, 1, 5, and 25 µg/mL). The effects on egg hatchability, survival rate (SR), heart rate frequency, and heart morphology of the larvae were meticulously examined using a Leica microscope. The data obtained were subjected to statistical analysis using one-way ANOVA. The findings demonstrated that exposure to mangosteen peel decoction resulted in lower hatching rates and embryonic survival, alongside an increased heart rate frequency. Additionally, the exposed embryos displayed cardiac edema and cardiac bending, particularly at the concentration of 25 µg/mL. In conclusion, the exposure of wader pari fish embryos to mangosteen peel decoction at the concentrations of 25 µg/mL and higher significantly affected the hatching rate, survival rate, and heart rate of R. lateristriata fish larvae.
Intraspecific Variability and Phenetic Relationships of Centella Asiatica (L.) Urb. Accessions from Central Java Based on Morphological Characters’
Full text linkCentella asiatica (L.) Urb. is a plant species native to Java and one of the main basic materials in traditional and modern medicine. This study is the first to report the intraspecific variation and taxonomic relationships of C. asiatica accession from natural populations in Central Java. The purpose of this study was to reveal phenotypic variations of C. asiatica populations and to asses phenetic relationships based on morphological characters. Thirty-two accessions of C. asiatica were collected from natural populations from eight mountains in Central Java. Observation on vegetative organs resulted in 25 morphological characters as a basis for assessing phenetic relationships using cluster analysis and principal component analysis. Result of cluster analysis showed that the grouping of accessions was not correlated to the localities from where the samples were collected, although there was a tendency that accessions from the same localities grouped in one cluster. The results of this study confirmed the existence of intraspecies morphological variability in C. asiatica which was not affected by geographical aspects. Results of principal component analysis indicated that the grouping of accessions was mainly determined by similarities in petiole color, stolon color, leaf margin, petiole length, stolon length, and leaf color. Given that the characters contributing to the grouping of accessions were mainly qualitative characters, the results indicated a genetic basis underlying phenotypic variations of C. asiatica accession.
Composition and Conservation Status of Avifauna in Urban Non-protected Important Bird Area (IBA) Site of Western India
Full text linkKumbharwada wetland, an Important Bird Area (IBA) component in Bhavnagar, Gujarat, India, is a crucial wintering ground for migratory birds. Long-term monitoring of the avian community over a period of long time-frame is an excellent way to examine the health of this IBA site and thus provide an important ground to foster the conservation of birds in the region and management of this wetland. Given this consideration, field surveys were carried out from December 2020 to May 2023, following point count method to study the avian species richness in the study area. A total of 204 bird species belonging to 20 orders and 56 families are recorded, of which 85 species are migratory and 119 are resident. Anatidae is the most species-rich avian family (16 species). Highest number of species was recorded in the month of January (165 species in 2021 and 163 species in 2022). This wetland supports 107 (52.45%) wetland-associated species and 97 (47.55%) terrestrial species of birds. Twelve species are considered as Near Threatened, four species as Vulnerable and one species (Aquila nipalensis) as Endangered in IUCN Red List of Threatened Species. Four species (Sterna aurantia, Mycteria leucocephala, Phoeniconaias minor, and Threskiornis melanocephalus) with globally declining trend, are commonly seen in the study area, which shows that the wetland is a crucial habitat for bird species with high conservation priorities. Industrialization, encroachment, discharge of sewage water and chemical effluents, high-tension powerlines, stray dogs, and expansion of exotic vegetation remained the major threats to the habitat and avian community.
Intraspecific SSR Marker Screening for Detection of Dendrobium crumenatum Mutants Generated from In Vitro Gamma Irradiation
Full text linkDetermination of D. crumenatum mutant obtained from in vitro mutation breeding needs a long time due to its long-life cycle. SSR molecular markers can be used for early mutant detection. Specific SSR markers developed in D. crumenatum are not yet available. Alternative published SSR markers were developed from D. catenatum. The aims of this study are to screen the most informative SSR markers generated from D. catenatum tested in irradiated D. crumenatum population and to determine the gamma irradiation dose resulting the most mutants. Ten SSR markers were randomly selected and tested in 25 individuals of D. crumenatum plantlets irradiated with several doses (0, 5, 10, 15, and 20 Gy; 5 plantlets each dose). The result showed 7 of 10 primers were polymorphic and the other three were monomorphic. All seven polymorphic primers can be used to identified intraspecific variation in the D. crumenatum mutant population. Markers dnsr28 and dnsr98 were the most informative, with the highest polymorphic information content (PIC) value of 0.5. Irradiation D. crumenatum protocorms using 10-15 gray doses were detected as the highest mutant percentage obtained up to 100% in the sample tested. This resulting marker information can be used to screen wider mutant population to decrease the non-mutant individuals in the population for maintenance and cost efficiency. The 10-15 Gy can be used as reference doses for gamma irradiation in 3 months old D. crumenatum protocorm materials.
Bioprospecting and Molecular Identification of Amylase and Cellulase Producing Thermophilic Bacteria from Sediment of Nglimut Hot Springs, Kendal Regency
Full text linkThe utilisation of enzymes in the industry has brought numerous benefits and advantages to production processes. Enzymes serve as biocatalysts, efficiently catalyzing reactions and hydrolysis in biochemical processes. However, there are challenges in applying enzymes in the industry, particularly concerning enzyme stability. The obstacle encountered in the production processes involving industrial enzyme applications is the low stability of enzymes when used at high temperatures. Heat-sensitive enzymes undergo damage or denaturation. Thermophilic microorganisms are chosen because they hold the potential to produce thermophilic enzymes. The thermophilic enzymes exhibit better heat stability compared to other enzymes, making them an effective alternative for future industrial production processes. This study aims to isolate thermotolerant bacteria from Nglimut Hot Spring sediment, screen for cellulase- and amylase-producing isolates, and molecularly identify the best isolate using 16S rRNA barcode. The results show that 22 bacterial isolates were found in the sediment of a hot spring; TS-14 was the best isolate in producing amylase, with the highest average amylolytic index of 2.38, whereas TS-15 had the highest cellulolytic index of 2.11. Based on 16S rRNA identification, TS-14 showed an homological identity of 79% with Bacillus amyloliquefaciens, while TS-15 had a 100% homological identity with Bacillus licheniformis. These results were important as the first step of screening bacterial potential to produce thermophilic enzymes that could be applied in the downstream processing in future industrial and biotechnology companies.
The Complete Chloroplast Genome of Medinilla tapete-magicum (Melastomataceae) from Sulawesi, Indonesia
Full text linkIn this study, the genome of an endemic Sulawesi’s plant, Medinilla tapete-magicum was sequenced using Illumina NextSeq 500 and assembled the whole chloroplast genome. Results showed that the cpGenome is 155,602 bp in size with typical quadripartite structure of a large single copy (LSC) region (85,409 bp), a short single copy (SSC) region (16,629 bp), and a pair of inverted repeats (IRs) regions (26,782 bp). The cpGenome is composed of 132 genes, which consists of 87 protein coding genes, 37 tRNAs, and 8 rRNAs. The sliding window analyses showed that psbB-psbH and ndhF-rpl32 can potentially be used as markers. Microsatellite motifs of mononucleotide A and T dominated in the cpGenome. The phylogenetic trees from the concatenated 76 shared protein coding gene sequences showed the Medinilla clade was monophyletic and M. tapete-magicum is a sister species in the SE Asian clade which contain M. magnifica and M. speciosa.
Utilisation of Snails for Wound Healing: A Review
Full text linkSnails exhibit remarkable adaptability, allowing them to flourish in diverse environmental conditions and resulting in thriving populations in specific regions. This abundance has led communities to harness snails for various purposes, including their use as animal feed, daily dietary source, and in traditional wound-healing practices with historical roots. The primary objective of this systematic review is to identify the snail species commonly employed in wound healing and evaluate the bioactivity of compounds derived from different snail species. This review was conducted using literature review method, drawing from international databases such as Scopus, and encompassed publications from 2013 to 2023. A total of 22 articles met the inclusion and exclusion criteria. Snail body parts that have been explored for wound-healing purposes include both the body and the shell, along with snail secretions, particularly their mucus. Various methods have been employed to extract mucus, involving manual stimulation of the snail's body, spraying with a saline solution (NaCl), application of electric shock, and the use of ozone gas through nebulisation. Prominent snail species found to be beneficial for wound healing include Achatina fulica, Helix aspersa, Eobania desertorum, Helix lucurus, Cornu bistrialis, Theba pisana, and Megalobulimus lopesi. These snail species demonstrate potential applications in the treatment of burns, excision wounds, incision wounds, and diabetic ulcers. Key compounds within snail secretions encompass mucopolysaccharides, polyphenols, peptides, and glycosaminoglycans. These compounds exert significant effects on haemostasis, inflammation control, cellular proliferation, and re-epithelialisation, significantly contributing to the wound healing process.
Characterization of Lactic Acid Bacteria Isolated from Soymilk and Its Growth in Soymilk By-product Medium for the Application in Soymilk Fermentation
Full text linkThe separation phase of soy-product manufacturing, especially of soymilk production, involves using the liquid portion of soy while disposing primarily of the solid portion, known as soymilk by-product (SMB). The improper disposal of SMB can contribute to environmental concerns. As SMB contains many beneficial nutrients, this could serve as a valuable culture medium for lactic acid bacteria (LAB), especially considering the expense of the standard de Man, Rogosa, and Sharpe (MRS) medium. This study aimed to isolate and identify LAB from soymilk through 16S rRNA sequencing, assess the potential of SMB as a culture medium for LAB, and ferment soymilk with LAB cultured from SMB to demonstrate the probiotic capacity. The research identified a potential LAB as Weissella confusa. Effective cultivation of LAB was demonstrated at 2% SMB concentration, although LAB cultured with MRS medium yielded a higher colony count. Furthermore, fermentation of soymilk by the LAB isolates from SMB exhibited a positive probiotic ability, reaching 5.5 × 109 CFU/mL, with a lactic acid content of 0.27%.