Identification of mercury‐resistant Streptomyces isolated from Cyperus rotundus L. rhizosphere and molecular cloning of mercury (II) reductase gene

Streptomyces is one of mercury‐resistant bacteria which can convert Hg2+ into nontoxic Hg0 . This study aimed to identify mercury‐resistant Streptomyces present in the Cyperus rotundus rhizosphere from artisanal small‐scale gold mining (ASGM) area and clone merA gene to the cloning and expression vectors. Molecular identification was conducted using 16s rRNA gene with the maximum likelihood algorithms. Results revealed that the AS1 and AS2 strains were a group of Streptomyces ardesiacus and the BR28 strain was closed to Brevibacillus agri. The AS2 merA gene was cloned to pMD20 cloning vectors, pGEX‐5x‐1 and pET‐28c expression vectors. The transformation was successfully performed in BL21 and DH5α competent cells. The full length of the merA gene was confirmed to be 1,425 bp. This study is the first research on identifying mercury‐resistant Streptomyces and cloning the full‐length merA gene in Indonesia

PENGEMBANGAN MAGGOT SEBAGAI PAKAN ALTERNATIF BUDIDAYA NILA PADA KAWASAN AGROWISATA MINAPADI

Abstrak: Budidaya ikan nila di sawah (minapadi) merupakan potensi utama yang diangkat oleh desa wisata Kebonagung. Akan tetapi, tingginya harga pakan ikan menjadi kendala utama yang dihadapi oleh warga dalam pengembangan wisata minapadi. Pakan berbasis maggot merupakan alternatif pakan yang murah dengan kualitas nutrisi yang tinggi. Program pengabdian ini bertujuan untuk memberikan pemahaman dan keterampilan pembuatan pakan alternatif dari maggot untuk minapadi. Program pengabdian ini dilaksanakan bersama dengan Karang Taruna Tani Rukun Santoso dan Kelompok Wanita Tani (KWT) Sekar Arum, di Kebonagung, Imogiri, Bantul, Yogyakarta. Metode pelaksanaan kegiatan meliputi sosialisasi dan pelatihan budidaya maggot, sosialisasi budikamber, pemijahan ikan wader pari, program One Health Education, dan evaluasi. Berdasarkan hasil pengabdian ini, masyarakat menjadi paham dan terampil dalam budidaya maggot. Saran yang diberikan untuk kegiatan selanjutnya adalah pengembangan maggot skala masal dan peningkatan branding kawasan wisata minapadi.Abstract: Fish cultivation in rice fields (minapadi) is the main aspect of tourism developed by the Kebonagung tourism village. However, the high price of fish feed is the main obstacle faced by residents in developing minapadi tourism. Maggot-based feed is an inexpensive alternative to feed with high nutritional quality. Our program aimed to provide skills in making alternative feed from maggot for minapadi. The programs were carried out in collaboration with the Rukun Santoso Farmer Youth Organization and the Sekar Arum Women's Farmer Group, in Kebonagung, Imogiri, Bantul, Yogyakarta. The method of implementing the activities included socialization and training on maggot cultivation, socialization of budikamber, One Health Education program, and evaluation. Based on the results of this program, the community becomes aware and skilled in maggot cultivation. The suggestions for the next programs are the development of mass scale maggots and the improvement of the branding of the minapadi tourism

ISOLASI DAN KLONING GEN PENGKODE ENZIM MERKURI REDUKTASE (merA) PADA ISOLAT Streptomycetes

merA is a gene that encodes mercuric reductase enzyme, an enzyme that plays a role in the reduction of Hg2+ into Hg0 that is less toxic. The gene is a part of operon system called the mer operon which contained on chromosomal and plasmid DNA. This study aims to isolate merA gene and clone this gene into cloning and expression vector. This research was carried out by testing the ability of resistance to mercury with Paper disk method. Linear plasmid and chromosomal DNA was isolated from Streptomycetes used alkaline lysis method. merA gene obtained then cloned into Blunt-TOPO and pMD20 vector. Transformation was done using competent cells of E. coli DH5α. The results showed that isolate AS1, AS2 and BR28 still have the ability to reduce mercury. They form clear zones less than 10 mm with the addition of 1 mM HgCl2 2 μL. Because plasmid DNA isolation using the alkaline lysis method was not successful, then the isolation of chromosomal DNA using Spooling with a Glass Rod methods was done. Chomosomal DNA was used as a template to amplify the merA gene. In this study, the gene merA obtained on the size of 1456 bp. Cloning and transformation performed on E. coli DH5α. Br28�s merA gene was not isolated yet. Cloning of merA gene from AS1 and AS2 into pET-28c succesfully done with the correct of open reading frame. merA gene of AS2 succesfully expressed using pGEX-5x-1 vector. merA gene sequences of AS2 is closed to merA gene of Streptomyces lividans TK24 and AS1 closed to Streptomyces sp. CHR28 plasmid

Functional 3D Structure Analysis of Quasispecies Variants of Hepatitis B Virus Surface and Core Protein in Advanced Liver Disease and Chronic HBV Infection Patients in Indonesia: In Silico

Hepatitis B Virus (HBV) is an endemic virus and belongs to Hepadnaviridae family. This virus can result in variations of quasispecies due to its high rate of mutation. A quasispecies variant is a small population and develops as a result of mutation and can become a wild-type population. This research aims to study and carry out 3D modeling on 12 in-house full sequence HBV genome isolates from Indonesia and obtain predictive visualization data to become a reference for further research leading to the production of anti-virals and natural treatments for HBV. 12 in-house full HBV genome sequences obtained from previous research were used to carry out 3D modeling and structural analysis of the surface protein, core protein, and polymerase protein. Analysis was carried out in silico using programs available online. Phylogenetic analysis was carried out using MEGA11, translation of nucleotides into protein sequences using the ExPAsy Translate portal, physiochemical analysis using ProtParam portal, and functional domain testing using the MOTIF tool from GenomeNet. Then 3D modelling using Phyre2 and SWISS-MODEL. The major mutation of the S protein occurs in L21S and mutations in the C protein mainly occur in P79Q and S87G. The model for S Protein from homology structure prediction is not reliable thus it still needs more templates from experimental techniques. While C Protein structure prediction can provide information for further research in alternative natural antiviral treatment.Virus Hepatitis B (HBV) adalah virus endemik dan termasuk dalam keluarga Hepadnaviridae. Virus ini dapat menyebabkan variasi quasispecies karena tingkat mutasinya yang tinggi. Variasi quasispecies adalah populasi kecil yang berkembang sebagai hasil mutasi dan dapat menjadi populasi tipe liar. Penelitian ini bertujuan untuk mempelajari dan melakukan pemodelan 3D pada 12 isolat genom lengkap HBV dari Indonesia dan memperoleh data visualisasi prediktif sebagai referensi untuk penelitian lebih lanjut yang dapat mengarah pada produksi antiviral dan pengobatan alami untuk HBV. Dua belas urutan genom HBV lengkap yang diperoleh dari penelitian sebelumnya digunakan untuk melakukan pemodelan 3D dan analisis struktural protein permukaan, protein inti, dan protein polimerase. Analisis dilakukan secara in silico menggunakan program yang tersedia secara online. Analisis filogenetik dilakukan menggunakan MEGA11, translasi nukleotida menjadi urutan protein menggunakan portal ExPAsy Translate, analisis fisikokimia menggunakan portal ProtParam, dan pengujian domain fungsional menggunakan alat MOTIF dari GenomeNet. Kemudian pemodelan 3D menggunakan Phyre2 dan SWISS-MODEL. Mutasi utama pada protein S terjadi pada L21S dan mutasi pada protein C terutama terjadi pada P79Q dan S87G. Model untuk Protein S dari prediksi struktur homologi tidak dapat diandalkan sehingga masih memerlukan lebih banyak templat dari teknik eksperimental. Sementara prediksi struktur Protein C dapat memberikan informasi untuk penelitian lebih lanjut dalam alternatif pengobatan antiviral alami

Genetic Transformation in Prokaryotic and Eukaryotic Cells

Improving the quality and quantity of an organism and its products can be approached by molecular characters enhancement through the insertion of a gene of interest into cells of the desired organism. Genetic transformation of an organism involves isolation, identification, cloning a gene of interest into a vector, and transferring the gene to the target organism. This chapter reviews the process of genetic transformation into the organism’s cell from bacterial (Escherichia coli), yeast, plant (Onion, Tobacco, and Orchids), and mammalian. The discussion will be focused on the introduction of DNA molecules into plant cells and protoplast mediated by polyethylene glycol (PEG), electroporation, and gene gun using particle bombardment. Further discussion on the transient protein expression system of plant-based on protoplast, onion cell, and tobacco will also be covered in this chapter as well. The systems have been proven as a powerful tool for determining subcellular protein localization, protein-protein interactions, identifying gene function, and regulation. Finally, it can be clearly seen, the differences and similarities in the mechanism of genetic transformation both in prokaryotic and eukaryotic systems

Identification of mercury-resistant Streptomyces isolated from Cyperus rotundus L. rhizosphere and molecular cloning of mercury (II) reductase gene

Streptomyces is one of mercury-resistant bacteria which can convert Hg2+ into nontoxic Hg0. This study aimed to identify mercury-resistant Streptomyces present in the Cyperus rotundus rhizosphere from artisanal small-scale gold mining (ASGM) area and clone merA gene to the cloning and expression vectors. Molecular identification was conducted using 16s rRNA gene with the maximum likelihood algorithms. Results revealed that the AS1 and AS2 strains were a group of Streptomyces ardesiacus and the BR28 strain was closed to Brevibacillus agri. The AS2 merA gene was cloned to pMD20 cloning vectors, pGEX-5x-1 and pET-28c expression vectors. The transformation was successfully performed in BL21 and DH5α competent cells. The full length of the merA gene was confirmed to be 1,425 bp. This study is the first research on identifying mercury-resistant Streptomyces and cloning the full-length merA gene in Indonesia. © 2021 Universitas Gadjah Mada, Research Center for Biotechnology. All rights reserved

Genetic polymorphisms of HLA-DP and isolated anti-HBc are important subsets of occult hepatitis B infection in Indonesian blood donors: a case-control study

Abstract Background Occult hepatitis B infection (OBI) is defined as the presence of hepatitis B virus (HBV) DNA in the serum and/or liver in HBsAg-negative individuals. OBI is associated with the risk of viral transmission, especially in developing countries, and with progressive liver disease and reactivation in immunosuppressive patients. The objective of this study was to evaluate the relation of OBI to HLA-DP single nucleotide polymorphisms (SNPs) encoding antigen-binding sites for the immune response to HBV infection. As HLA-DP variants affect the mRNA expression of HLA-DPA1 and HLA-DPB1 in the liver, we hypothesised that high levels of HLA-DPA1 and HLA-DPB1 expression favour OBI development. Methods The study enrolled 456 Indonesian healthy blood donors (HBsAg negative). OBI was defined as the presence of HBV-DNA in at least two of four open reading frames (ORFs) of the HBV genome detected by nested PCR. SNPs in HLA-DPA1 (rs3077) and HLA-DPB1 (rs3135021, rs9277535, and rs2281388) were genotyped using real-time Taqman® genotyping assays. Results Of 122 samples positive for anti-HBs and/or anti-HBc, 17 were determined as OBI. The minor allele in rs3077 was significantly correlated with OBI [odds ratio (OR) = 3.87, 95% confidence interval (CI) = 1.58–9.49, p = 0.0015]. The prevalence of the minor allele (T) was significantly higher in subjects with OBI than in those without (59% and 33%, respectively). The combination of haplotype markers (TGA for rs3077–rs3135021–rs9277535) was associated with increased risk of OBI (OR = 4.90, 95%CI = 1.12–21.52 p = 0.038). The prevalence of OBI was highest in the isolated anti-HBc group among the three seropositive categories: anti-HBs <500 mIU/ml, anti-HBs ≥500 mIU/ml, and isolated anti-HBc (29.41%, p = 0.014). Conclusion Genetic variants of HLA-DP and the presence of anti-HBc are important predictors of OBI in Indonesian blood donors. Trial registration Ref: KE/FK/194/EC; registered 01 March 2013. Continuing approval Ref: KE/FK/536/EC; registered 12 May 2014

Bibliometric Analysis of Literature in Snake Venom-Related Research Worldwide (1933&ndash;2022)

Snake envenomation is a severe economic and health concern affecting countries worldwide. Snake venom carries a wide variety of small peptides and proteins with various immunological and pharmacological properties. A few key research areas related to snake venom, including its applications in treating cancer and eradicating antibiotic-resistant bacteria, have been gaining significant attention in recent years. The goal of the current study was to analyze the global profile of literature in snake venom research. This study presents a bibliometric review of snake venom-related research documents indexed in the Scopus database between 1933 and 2022. The overall number of documents published on a global scale was 2999, with an average annual production of 34 documents. Brazil produced the highest number of documents (n = 729), followed by the United States (n = 548), Australia (n = 240), and Costa Rica (n = 235). Since 1963, the number of publications has been steadily increasing globally. At a worldwide level, antivenom, proteomics, and transcriptomics are growing hot issues for research in this field. The current research provides a unique overview of snake venom research at global level from 1933 through 2022, and it may be beneficial in guiding future research