STUDI KERAGAMAN GENETIK Tarsius sp. ASAL KALIMANTAN, SUMATERA, DAN SULAWESI BERDASARKAN SEKUEN GEN NADH DEHIDROGENASE SUB-UNIT 4L (ND4L)

Widayanti, Rini; Susmiati, Trini

doi:10.21157/j.ked.hewan.v6i2.339

Cited by 3 publications

(3 citation statements)

References 8 publications

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“…Outgroups are chosen based on the relationship of the sample being analyzed [21]. Tarsius is a type of primate known for being small, nocturnal, and having large eyes [22]. Tarsius can be separated into different clades of Homo sapiens, which makes it a suitable outgroup for constructing a phylogenetic tree [23].…”

Section: Construction Analysis Of Phylogenetic Treesmentioning

confidence: 99%

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Isolation of Genes Encoding for Human Epidermal Growth Factor (hEGF) from Human Blood: In Vitro and In Silico Study

2023

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The 6.12 kDa human epidermal growth factor (hEGF) protein is expressed in the body and plays a role in cell proliferation and differentiation. This research aims to isolate the hEGF genes, determine the phylogenetic relationship between organisms based on the hEGF gene, construct the 3D structure of the hEGF protein, and identify the precise binding position between the hEGF protein and the tested Myosin-9. DNA was isolated from blood of healthy individuals followed by amplification using specified primers. DNA sequencing was utilized to identify the amplification results before generating the phylogenetic trees. The retrieved sequences were then modeled using the Swiss model and docking proteins in silico. In three samples, DNA was successfully amplified to 700 bp and the phylogenetic analysis revealed that the three hEGF gene samples belonged to the same clades. With a 30 % identity seq, aligned result sequences modeled using the Swiss model created proteins which were not homologous. The outcomes of this modeling were compared to the hEGF protein from the database, which had a sequence identity of greater than 90 %. The i-RMSD value of the target protein (5.4 +/- 0.4), the Van der Waals energy (-29.3 +/- 1.7), and the Z-score were determined by simulation (-1.7). These results indicate a potential interaction between the isolated EGF protein and the myosin-9 tested. HIGHLIGHTS Human Epidermal Growth Factor (hEGF) protein is a potential protein expressed in the body and plays a role in cell proliferation and differentiation Isolation of the EGF gene through human blood can be carried out to get data on protein size, phylogenetic analysis, and protein structure The results of in vitro study were modeled in silico to obtain the three-dimensional structure as well as intermolecular interactions of the protein Information beginning this study is used in follow-up research to predict EGF communications with other molecules GRAPHICAL ABSTRACT

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Section: Construction Analysis Of Phylogenetic Treesmentioning

confidence: 99%

“…Tarsius is a type of primate known for being small, nocturnal, and having large eyes [22]. Tarsius can be separated into different clades of Homo sapiens, which makes it a suitable outgroup for constructing a phylogenetic tree [23]. The results of the tree construction can be seen in Figure 4.…”

Section: Construction Analysis Of Phylogenetic Treesmentioning

confidence: 99%

Isolation of Genes Encoding for Human Epidermal Growth Factor (hEGF) from Human Blood: In Vitro and In Silico Study

2023

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“…Molecular studies at the species level have never been carried out. According to the previous studies, the NADH dehydrogenase subunit 3 (ND3) gene sequence, the 4L NADH dehydrogenase subunit (ND4L) gene, and 12 rRNA gene can be used as genetic markers of Tarsius bancanus from Sumatra, Kalimantan with Tarsius from Sulawesi [16][17][18].…”

Section: Introductionmentioning

confidence: 99%

Genetic characterization and phylogenetic study of Indonesian cuscuses from Maluku and Papua Island based on 16S rRNA gene

2020

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Background and Aim: Indonesian cuscuses are now becoming scarce because of the reduction of habitat and poaching. Further, molecular characterization of Indonesian cuscuses is still very lacking. This study aimed to determine genetic markers and phylogenetic relationships of Indonesian cuscuses based on 16S rRNA gene sequences. Materials and Methods: This study used 21 cuscuses caught from two provinces and 16 islands: 13 from Maluku and eight from Papua. Cuscus samples were taken by biopsy following ethics guidelines for animals. The genome isolation was done using gSYNC DNA Mini Kit (Geneaid Biotech Ltd., Taiwan). The 16S rRNA gene was amplified by primers (16SKUSAF and 16SKUSAR), and the polymerase chain reaction product obtained was 1875 base pair (bp). The analysis of genetic characterization and the phylogenetic relationship was performed using MEGA version X software (https://www. megasoftware.net/). Results: 16S rRNA gene sequencing attained 1598 bp for all samples. Based on the 16S rRNA nucleotide sequences, cuscuses from Papua and Maluku belong to the genus Phalanger and Spilocuscus. Phalanger spp. and Spilocuscus spp. from Papua can be distinguished from Phalanger and Spilocuscus from Maluku, except Spilocuscus from Ternate has a very close relationship with cuscus from Sentani, Papua. Conclusion: Indonesian cuscuses were derived into two clades based on 16S rRNA gene sequence, one group to genus Phalanger and another group to Spilocuscus.

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Validation of NADH Dehydrogenase 4L (ND4L) Primers Gene for Porcine Detection Using A SYBR Green Real-Time PCR Analysis on Commercial Processed Meat Products

Volkandari,

Jenie,

Rohman

et al. 2024

Preprint

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Porcine contamination in halal products is known to be found in commercial food markets in Indonesia. Detection methods are needed, one of which is Real-Time PCR with robust biomarkers in various types of processed food. In this study, we focused on designing a novel primer from NADH Dehydrogenase 4L (ND4L) gene that has never been explored as a porcine detection. Primers were assembled using GenBank NCBI (MK251046 Sus scrofa), and their efficacy (repeatability, sensitivity, and specificity) was evaluated. The capability primer performance was also compared with a commercial kit. Results showed that primer effectively amplified porcine DNA with a melting curve (Tm) of 78.17 ± 0.05oC and a Cq value of 11.95 ± 0.48 at a 20 ng/µL DNA concentration. CV values of Cq and Tm repeatability were 4,01 and 0.09%, respectively. The limit of detection primer reached 5 pg/µL DNA and 0.001% w/w binary meat mixture of pork-beef. This primer is highly specific to pig and wild boar species (against 30 species (non-pig). A comparative study on the ND4L primer with a commercial porcine detection kit (FAM label) revealed similar results in detecting porcine DNA in food products. ND4L primer successfully detected porcine DNA in 20 of 52 commercial meat products with various types of processing (according to their claims). Primer performed satisfactorily in all validation parameters with high sensitivity and specificity. Hence, this finding of the specific primers on the ND4L gene could be promising for detecting porcine DNA in food products.

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STUDI KERAGAMAN GENETIK Tarsius sp. ASAL KALIMANTAN, SUMATERA, DAN SULAWESI BERDASARKAN SEKUEN GEN NADH DEHIDROGENASE SUB-UNIT 4L (ND4L)

Cited by 3 publications

References 8 publications

Isolation of Genes Encoding for Human Epidermal Growth Factor (hEGF) from Human Blood: In Vitro and In Silico Study

Isolation of Genes Encoding for Human Epidermal Growth Factor (hEGF) from Human Blood: In Vitro and In Silico Study

Genetic characterization and phylogenetic study of Indonesian cuscuses from Maluku and Papua Island based on 16S rRNA gene

Validation of NADH Dehydrogenase 4L (ND4L) Primers Gene for Porcine Detection Using A SYBR Green Real-Time PCR Analysis on Commercial Processed Meat Products

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