Indonesian Journal of Biotechnology
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Genetic diversity of local rice varieties (Oryza sativa L.) in Vietnam’s Mekong Delta based on SSR markers and morphological characteristics
No full textBased on target traits, use of the genetic diversity of rice is beneficial for crop improvement. In this study, 41 rice varieties local to Vietnam’s Mekong Delta were evaluated on the basis of 11 quantitative morphological traits, along with the assessment of genetic diversity according to 50 SSR markers. The actual yield had a significance level of 0.05, while plant height and panicles per square meter had a high significance level of 0.001. Cluster analysis based on 11 quantitative traits also revealed that two were the optimal number of clusters used in this study. The highest polymorphic information content (PIC) value obtained was for RM286 (0.49), with a range of 0.00 to 0.49 and an average PIC of 0.14. Both structure and phylogenetic tree analyses as inferred from 50 SSR markers by the unweighted pair‐group method with arithmetic mean (UPGMA) also indicated that the 41 local rice varieties could be divided into two major groups. This study provides a useful information for Mot bui do cao CM, and Mot bui five varieties for improvements in the yield and intermediate amylose content of local rice‐breeding programs in future, especially for the Mekong Delta region
Identification of gene expression location of angiotensin‐converting enzyme‐2 SNPs as a receptor for SARS‐CoV‐2 in different populations by using various databases
No full textThe World Health Organization (WHO) has announced that Severe Acute Respiratory Syndrome Coronavirus‐2 (SARS‐CoV‐2) and Coronavirus disease (COVID‐19) is considered a worldwide pandemic. Rapidly rising numbers of patients have been reported in almost every country, along with the growing mortality rates. Uncontrolled growth in patient numbers may be due to reasons such as treatment options and vaccine availabilities and unidentified targets of SARS‐CoV‐2. Previous study has revealed that the molecular target of SARS‐CoV‐2 is analogous to SARS (2003), i.e. angiotensin‐converting enzyme‐2 (ACE‐2). Therefore, the determination of ACE‐2 may enrich existing information and facilitate development of drugs targeted toward SARS‐CoV‐2. This study aims to screen the expression of ACE‐2 genes and their relationship to the types of SNP variants in SARS‐CoV‐2. We explored a series of observations using powerful databases, e.g. GTEx portal, HaploReg, 1000 Genome and Ensembl, to identify the gene variant of ACE‐2. We showed that ACE‐2 is highly expressed in the testes and small intestine, while its lowest level is observed in lymphocytes. Subsequently, we observed 17 gene variants containing a missense mutation potentially damaging protein level. Among these genes, single nucleotide polymorphism (SNP) rs370187012 shows the highest damage‐level score, while the lowest effect is in SNP rs4646116. The highest frequency of the C allele was observed in European populations (1%). In addition to showing that ACE‐2 is expressed in several organs, we concluded that the ACE‐2 gene variation can be found in African, American, Southeast and East Asian, and European populations. The polymorphisms of ACE‐2 impact on the ACE2 protein structure and the binding capacity of the ACE‐2 receptor with the S‐Protein of SARS‐CoV‐2
Spatial learning and memory of young and aging rats following injection with human Wharton’s jelly‐mesenchymal stem cells
No full textHuman Wharton’s jelly‐mesenchymal stem cells (hWJ‐MSC) are an emerging potential source of stem cells derived from the umbilical cord. Previous studies have shown their potential as treatment for traumatic brain injury and Parkinson’s disease. However, no study has yet investigated the effect of hWJ‐MSC injections in countering spatial learning and memory impairment in aging rats. The effect of hWJ‐MSC injection on young rats is also unknown. The objective of this research was to analyze the effect of an hWJ‐MSC injection on spatial learning, memory, density of putative neural progenitor cells (pNPC), and neuronal apoptosis in the dentate gyrus (DG) of young and aging rats. Injection of hWJ‐MSC did not change spatial learning and memory in young rats until two months post‐injection. This might be due to retained pNPC density and neuronal apoptosis in the DG of young rats after injection of hWJ‐MSC. In contrast, injection of hWJ‐MSC promoted both spatial learning and memory in aging rats, a finding that might be attributable to the increased pNPC density and attenuated neuronal apoptosis in DG of aging rats during the two months post‐injection. Our study suggests that a single injection of hWJ‐MSC might be sufficient to promote improvement in long‐term learning and memory in aging rats
Molecular bird sexing of sulphur‐crested cockatoo (Cacatua galerita) by polymerase chain reaction method
No full textSex identification of endangered and protected birds in captivity is very important for conservation programs. Half of the world’s bird species are monomorphic, where male and female are difficult to distinguished morphologically, including cockatoos. Sex identification using molecular bird sexing is more accurate and applicable because it directly targets the sex chromosomes. The purpose of this study was to determine the sex of Sulphur‐crested cockatoo (Cacatua galerita) by detecting differences in the intron size of the chromodomain helicase DNA‐binding 1 (CHD1) gene on the Z and W chromosomes by polymerase chain reaction (PCR) method and to compare of plucked feathers and blood samples as DNA sources for molecular bird sexing. DNA was extracted from feather and blood samples from four C. galerita. Extracted DNA was amplified on the CHD1 gene by PCR method with P2, MP, and NP primers, which were visualized using agarose gel 1.5% under UV transilluminator with a wavelength of 280 nm. The resulting PCR product was detected at 392 bp for the CHD1 Z gene segment and 297 bp for CHD1 W gene segments, where males showed a single DNA band (ZZ) and females showed a double DNA band (ZW). Four C. galerita were 100% successfully determined, consisting of one female and three males. Electrophoresis results showed DNA bands from blood samples were thicker and brighter than DNA bands from feather samples
A recombinant DNA‐satellite associated with Pepper yellow leaf curl Indonesia virus in highland area
No full textYellow curl disease caused by begomovirus is a major threat for horticulture in Indonesia. Control mea‐ sures for the disease face several constraints, one of which is the association between begomovirus and DNA satellites which can affect the severity of symptoms. In this study, we detected the presence of a DNA satellite associated with begomovirus in a highland area. The sample was obtained from Ketep, Magelang, located approximately 1400 meters above sea level. Begomovirus was detected using primers PAL1V1978/PAR1C715 that resulted in an amplicon of ap‐ proximately 1600bp. The presence of this satellite was detected using primers CLB36F/CLB37R, resulting in full‐length satellite genome of approximately 1300bp. Sequence analysis showed the sample was infected by Pepper yellow leaf curl Indonesia virus (PepYLCIV) and a non‐coding satellite which resembled some characteristics of common betasatellites with imperfect putative ORF βC1. SimPlot analysis revealed the recombination event between betasatellites and DNA‐B of PepYLCIV. The satellite found in this study is thought to be the result of recombination due to multiple infections in plants
Spatial analysis of toxoplasmosis through EcoHealth approaches using GRA-1 recombinant: case in Sleman, Yogyakarta
No full textToxoplasmosis is an obligate intracellular zoonotic parasite caused by Toxoplasma gondii that can infect all warm-blooded animals including humans. Prevalence of toxoplasmosis varies depending on climate, geography, and the presence of cats in an area. This study aimed to identify the prevalence and distribution of toxoplasmosis in Sleman, Yogyakarta through EcoHealth approaches. A total of 385 blood samples were collected from residents in the district of Sleman. Seven people from 55 villages were selected for blood sampling using a cluster method. The collected serums were tested by ELISA using recombinant Granule 1 protein (GRA-1) as coated antigen. Data on altitude and coordinates of sampling sites were collected using GPS. instruments, soil surface temperature in Sleman was obtained by satellite imagery, and cat population in residential areas was determined by questionnaire. The prevalence of toxoplasmosis in Sleman was 58%, of which distributed around rivers and in cattle pens. Based on altitude and temperature, toxoplasmosis cases were found the highest at 0-150 m (66.3%) and at temperatures of 26-30°C (66.4%). Areas with large numbers of cats had toxoplasmosis prevalence of 75.8% while areas with moderate and few cats were 56.5% and 49.0%, respectively. Thus, differences in the prevalence of toxoplasmosis at settlement were found based on altitude, soil surface temperature, and cat populations
CRISPR/Cas9‐mediated knockout of an oil palm defense‐related gene to the pathogenic fungus Ganoderma boninense
No full textOil palm plantation in Indonesia is significantly affected by basal stem rot disease caused by the pathogenic fungus Ganoderma boninense. Tolerant oil palm cultivars toward G. boninense have been developed through a breeding program accelerated by the implementation of the CRISPR/Cas9 technology. This study was conducted to perform a gene knockout (KO) of oil palm that confers a putative defense‐related trait toward G. boninense. A plasmid pCRISPR_EMLP containing modules, i.e., 35S‐CaMV‐promoter‐driven CRISPR/Cas9, U6‐promoter‐driven sgRNA to the target EgEMLP gene (EL695076), and hygromycin resistance gene as the selectable marker, was established for Agrobacterium‐mediated delivery into oil palm calli (OPC). The transformed OPCs were regenerated and screened in DF (de Fossard) media containing hygromycin. The working concentration of hygromycin was successfully optimized for selection at 20 ppm. Through PCR‐based selection using HYG primers, we succeeded in discerning positive transformed OPC clones. The sequenced PCR products of genomic DNA as the template amplified using EMLP1 primers showed a point mutation, causing a frameshift in the edited EgEMLP and premature stop codon. Furthermore, in silico modeling demonstrated that the mutation resulted in a change in the C‐terminal region, affecting the tertiary protein structure. Moreover, electrophoresis analysis of PCR products of cDNA as the template from transformed OPC clones showed several samples with faint or undetected bands. This indicated that the CRISPR/Cas9 module induced a mutation that could destabilize the transcribed mRNA, e.g., premature degradation. Altogether, this study has successfully implemented CRISPR/Cas9 gene editing in oil palm in a model gene that is responsible for putative defense‐related traits toward the pathogenic fungus G. boninense
The structural insight of class III of polyhydroxyalkanoate synthase from Bacillus sp. PSA10 as revealed by in silico analysis
No full textPhaC synthase is an enzyme responsible for PHA polymerization. In this work, the catalytic mechanism class III of PhaC synthase from Bacillus sp. PSA10 (BacPhaCSynt) was reported through in silico modelling approach based on the primary sequence of the PhaC synthase. The open reading frame BacPhaCSynt has been successfully isolated, cloned and overexpressed the recombinant protein in Escherichia coli BL21(DE3). To know the global architecture and catalytic mechanism, the structural prediction of BacPhaCSynt has been carried out by using MODELLER. The recombinant BacPhaCSynt exhibited monomeric molecular weight (MW) of 43.6 kDa, when it was analyzed on 12% SDS‐PAGE gel. Based on the structural prediction, BacPhaCSynt exhibited global architecture of α/β hydrolase fold, with the root mean square deviation (r.m.s.d) value of 0.94Å. The catalytic residues composition of BacPhaCSynt consists of C151, D307, and H336, but the H336 and D307 residues of the model have been distorted 62.8o and 175.2o from the corresponding residues of the template. Since the D307 is quite a distance from the H336, it might act as a general base for the activation of ‐OH group of the substrate. The results strongly suggested that the mode of action of BacPhaCSynt obeyed the covalent catalysis mechanism
Enhanced astaxanthin production by oxidative stress using methyl viologen as a reactive oxygen species (ROS) reagent in green microalgae Coelastrum sp.
No full textMicroalgae are known to be a potential resource of high-value metabolites that can be used in the growing field of biotechnology. These metabolites constitute valuable compounds with a wide range of applications that strongly enhance a bio-based economy. Among these metabolites, astaxanthin is considered the most important secondary metabolite, having superior antioxidant properties. For commercial feasibility, microalgae with enhanced astaxanthin production need to be developed. In this study, the tropical green microalgae strain, Coelastrum sp., isolated from the environment in Malaysia, was incubated with methyl viologen, a reactive oxygen species (ROS) reagent that generates superoxide anion radicals (O2-) as an enhancer to improve the accumulation of astaxanthin. The effect of different concentrations of methyl viologen on astaxanthin accumulation was investigated. The results suggested that the supplementation of methyl viologen at low concentration (0.001 mM) was successfully used as a ROS reagent in facilitating and thereby increasing the production of astaxanthin in Coelastrum sp. at a rate 1.3 times higher than in the control
Differentiation ability of rat‐mesenchymal stem cells from bone marrow and adipose tissue to neurons and glial cells
No full textMesenchymal stem cells (MSCs) are multipotent cells and can differentiate into neurons and glial cells. In vitro differentiation would be done by the addition of various factors. There remains no comparison for the differentiation of MSCs from rat bone marrow (rBMMSCs) and adipose tissue (rATMSCS) into neurons and glial cells with basic fibroblast growth factor (bFGF), epidermal growth factor (EGF), and brain‐derived neurotrophic factor (BDNF). The aims of this study were to investigate the effect of bFGF, EGF, and BDNF supplementation on the differentiation ability of rBMMSCs and rATMSCs into neurons and glial cells. MSCs were cultured with bFGF and EGF for 4 days and then BDNF was added until day 8. Characterization of MSCs before and after induction was carried out by observing the cell morphology and several cell markers. Flowcytometry analysis was performed for MSCs markers (CD90, CD29) and neurons and glial cell markers (A2B5, Beta‐III‐tubulin, PSAN‐CAM); while MAP‐2, a neuron marker, was analyzed by immunocytochemistry. Induction of both types of MSCs showed MAP‐2‐positive cells, decreased MSCs markers, and in rBMMSCs showed increased neuron markers. The number of neuron marker positive cells in rBMMSCS was higher than rATMSCs. This study showed that the addition of bFGF, EGF, and BDNF to the medium induced rBMMSCs into neurons and glial cells, but the conditions were not optimal for rATMSC as judged by the expression of neural markers (A2B5, Beta‐III‐tubulin, PSAN‐CAM, and MAP‐2)