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KRISTIANTO NUGROHO, KRISTIANTO
Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumber Daya Genetik Pertanian, Jl. Tentara Pelajar 3A, Bogor 16111 Indonesia Telp. (0251) 8337975
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemistry Earth & Planetary Sciences Economics, Econometrics & Finance Environmental Science Immunology & microbiology Medicine & Pharmacology Nursing Veterinary

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KARAKTERISASI KERAGAMAN GENETIK 27 GENOTIPE CABAI BERDASARKAN MARKA SSR (SIMPLE SEQUENCE REPEAT) Terryana, Rerenstradika Tizar; Nugroho, Kristianto; Rijzaani, Habib; Lestari, Puji
BERITA BIOLOGI Vol 17, No 2 (2018)
Publisher : Research Center for Biology-Indonesian Institute of Sciences

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/beritabiologi.v17i2.3313

Abstract

Chili pepper (Capsicum annuum) is one of the high economical horticultural comodity in Indonesia and its genetic diversity contributes to the success of breeding programs. Simple sequence repeat (SSR) markers can be used to analyze genetic diversity among chili pepper genotypes. The aim of this research was to analyze the genetic diversity of twenty-seven genotypes of chili pepper by using 24 SSR markers. The collected data was analyzed using cluster analysis and principle coordinate analysis (PCoA). The result showed that high allele variation (4–17 alleles) was observed among chili pepper genotypes tested, with an average allele number and Polymorphism Information Content (PIC) value was 7.708 and 0.758 (0.598–0.920) respectively. All of SSR markers showed PIC value >0.5 which indicated that these markers were suitable for chili pepper diversity studies with a high differentiation and with the average value of genetic diversity was 0.78. The clustering and principle coordinate analysis showed that twenty-seven genotypes of chili pepper were divided into two groups (coefficient of similarity 0.74 in cluster analysis) indicating a high genetic variability among them. Genetic diversity analysis in this study will be useful as an initial basis of selection for appropriate parents with desired traits to assist the breeding program of chili pepper in Indonesia.
METODE EKSTRAKSI DNA TANAMAN TANPA PRESIPITASI ETANOL UNTUK KEGIATAN POLYMERASE CHAIN REACTION (PCR) Nugroho, Kristianto; Terryana, Rerenstradika Tizar; Reflinur, .; Lestari, Puji
Jurnal Bioteknologi & Biosains Indonesia (JBBI) Vol 6, No 1 (2019): June 2019
Publisher : Badan Pengkajian dan Penerapan Teknologi (BPPT)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (196.537 KB) | DOI: 10.29122/jbbi.v6i1.3082

Abstract

A Simplified Plant DNA Extraction Protocol without Ethanol Precipitation for Polymerase Chain Reaction (PCR) Activities ABSTRACTMolecular-based research in agriculture includes DNA extraction stage involving DNA precipitation using ethanol or isopropanol which tends to take a long time. The purpose of this study was to obtain a plant DNA extraction method for Polymerase Chain Reaction (PCR) activities without going through the ethanol precipitation stage. Five important agricultural commodity crops, namely rice, corn, soybeans, chilies, and shallots were extracted by DNA using the modified Doyle and Doyle method. After the extraction phase using chloroform and isoamil alcohol solvents, the supernatant obtained was not precipitated using ethanol but was directly diluted and used as a template in PCR activities using two pairs of Simple Sequence Repeat (SSR) markers. The results showed that all samples could be well amplified, and amplicon tape visualized in both 1% agarose gel and 6% polyacrylamide gel were clearly visible. This method could save time and material, and reduce the dependence on liquid nitrogen. But this method is still limited to PCR requirements only, and cannot be used for activities that require high quality and quantity of DNA such as Next Generation Sequencing (NGS), digestion, and hybridization.Keywords: DNA extraction, ethanol precipitation, liquid nitrogen, PCR, SSR,  ABSTRAKPenelitian berbasis molekuler pada bidang pertanian mencakup tahapan ekstraksi DNA yang melibatkan presipitasi DNA menggunakan etanol atau isopropanol yang cenderung memakan waktu lama. Tujuan penelitian ini adalah untuk memperoleh metode ekstraksi DNA tanaman untuk kegiatan Polymerase Chain Reaction (PCR) tanpa melalui tahapan presipitasi etanol. Lima tanaman komoditas pertanian penting yaitu padi, jagung, kedelai, cabai, dan bawang merah diekstraksi DNA-nya menggunakan metode Doyle and Doyle yang dimodifikasi. Setelah tahap ekstraksi menggunakan pelarut kloroform dan isoamil alkohol, supernatan yang terbentuk tidak dipresipistasi menggunakan etanol melainkan langsung diencerkan dan digunakan sebagai template dalam kegiatan PCR menggunakan dua pasang marka Simple Sequence Repeat (SSR). Hasil menunjukkan bahwa seluruh sampel dapat teramplifikasi dengan baik serta pita hasil amplikon yang tervisualisasi baik pada gel agarosa 1% maupun gel poliakrilamid 6% terlihat jelas. Metode ini dapat menghemat waktu dan bahan serta mengurangi ketergantungan pemakaian nitrogen cair. Tetapi metode ini masih terbatas hanya untuk kebutuhan PCR saja dan tidak dapat digunakan untuk kegiatan yang membutuhkan DNA dengan kualitas serta kuantitas tinggi seperti Next Generation Sequencing (NGS), digesti, maupun hibridisasi.Kata Kunci: ekstraksi DNA, nitrogen cair, PCR, presipitasi etanol, SSR
METODE EKSTRAKSI DNA TANAMAN TANPA PRESIPITASI ETANOL UNTUK KEGIATAN POLYMERASE CHAIN REACTION (PCR) Nugroho, Kristianto; Terryana, Rerenstradika Tizar; Reflinur, .; Lestari, Puji
Jurnal Bioteknologi & Biosains Indonesia (JBBI) Vol. 6 No. 1 (2019): June 2019
Publisher : Balai Bioteknologi, Badan Pengkajian dan Penerapan Teknologi (BPPT)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (196.537 KB) | DOI: 10.29122/jbbi.v6i1.3082

Abstract

A Simplified Plant DNA Extraction Protocol without Ethanol Precipitation for Polymerase Chain Reaction (PCR) Activities ABSTRACTMolecular-based research in agriculture includes DNA extraction stage involving DNA precipitation using ethanol or isopropanol which tends to take a long time. The purpose of this study was to obtain a plant DNA extraction method for Polymerase Chain Reaction (PCR) activities without going through the ethanol precipitation stage. Five important agricultural commodity crops, namely rice, corn, soybeans, chilies, and shallots were extracted by DNA using the modified Doyle and Doyle method. After the extraction phase using chloroform and isoamil alcohol solvents, the supernatant obtained was not precipitated using ethanol but was directly diluted and used as a template in PCR activities using two pairs of Simple Sequence Repeat (SSR) markers. The results showed that all samples could be well amplified, and amplicon tape visualized in both 1% agarose gel and 6% polyacrylamide gel were clearly visible. This method could save time and material, and reduce the dependence on liquid nitrogen. But this method is still limited to PCR requirements only, and cannot be used for activities that require high quality and quantity of DNA such as Next Generation Sequencing (NGS), digestion, and hybridization.Keywords: DNA extraction, ethanol precipitation, liquid nitrogen, PCR, SSR,  ABSTRAKPenelitian berbasis molekuler pada bidang pertanian mencakup tahapan ekstraksi DNA yang melibatkan presipitasi DNA menggunakan etanol atau isopropanol yang cenderung memakan waktu lama. Tujuan penelitian ini adalah untuk memperoleh metode ekstraksi DNA tanaman untuk kegiatan Polymerase Chain Reaction (PCR) tanpa melalui tahapan presipitasi etanol. Lima tanaman komoditas pertanian penting yaitu padi, jagung, kedelai, cabai, dan bawang merah diekstraksi DNA-nya menggunakan metode Doyle and Doyle yang dimodifikasi. Setelah tahap ekstraksi menggunakan pelarut kloroform dan isoamil alkohol, supernatan yang terbentuk tidak dipresipistasi menggunakan etanol melainkan langsung diencerkan dan digunakan sebagai template dalam kegiatan PCR menggunakan dua pasang marka Simple Sequence Repeat (SSR). Hasil menunjukkan bahwa seluruh sampel dapat teramplifikasi dengan baik serta pita hasil amplikon yang tervisualisasi baik pada gel agarosa 1% maupun gel poliakrilamid 6% terlihat jelas. Metode ini dapat menghemat waktu dan bahan serta mengurangi ketergantungan pemakaian nitrogen cair. Tetapi metode ini masih terbatas hanya untuk kebutuhan PCR saja dan tidak dapat digunakan untuk kegiatan yang membutuhkan DNA dengan kualitas serta kuantitas tinggi seperti Next Generation Sequencing (NGS), digesti, maupun hibridisasi.Kata Kunci: ekstraksi DNA, nitrogen cair, PCR, presipitasi etanol, SSR
Pemanfaatan Teknologi Droplet Digital PCR (ddPCR) dalam Kegiatan Analisis Molekuler Tanaman Nugroho, Kristianto; Widyajayantie, Dwi; Ishthifaiyyah, Sayyidah Afridatul; Apriliani, Elisa
JURNAL BIOS LOGOS Vol 11, No 1 (2021): JURNAL BIOS LOGOS
Publisher : Universitas Sam Ratulangi

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.35799/jbl.11.1.2021.31101

Abstract

(Article History: Received 23 October 2020; Revised 9 January 2021; Accepted 18 January 2021) ABSTRAKSelama beberapa dekade terakhir, teknik PCR memberikan manfaat yang begitu besar dalam kegiatan penelitian di bidang biologi molekuler. Digital droplet PCR (ddPCR) merupakan salah satu teknologi PCR terbaru yang diklaim memiliki keunggulan dibanding teknik qPCR. Prinsip kerja teknik ini yaitu membagi sampel menjadi molekul-molekul kecil yang dipisahkan oleh emulsi minyak, air, dan senyawa penstabil sehingga membentuk droplets. Teknik ini memiliki kelebihan mampu melakukan kuantifikasi absolut maupun relatif pada DNA dengan konsentrasi sangat rendah, tidak memerlukan kurva standar, serta tidak sensitif terhadap kehadiran senyawa inhibitor. Teknik ini telah diaplikasikan pada kegiatan analisis molekuler tanaman di antaranya kegiatan pengukuran konsentrasi DNA dengan sangat akurat, deteksi kehadiran patogen pada jaringan tanaman, dan estimasi jumlah salinan T-DNA pada proses transformasi genetik.Kata kunci: PCR; droplet digital PCR; DNA; biologi molekuler; alat deteksi ABSTRACTOver the past decades, PCR technique has provided enormous benefits in molecular biology research activities. Digital droplet PCR (ddPCR) is one of the latest PCR technologies that is claimed to have advantages over the qPCR technique. The working principle of this technique is to divide the sample into small molecules, which separated by emulsions of oil, water, and stabilizing compounds to form droplets. This technique has the advantage of being able to perform absolute and relative quantification with very low DNA concentrations, does not require a standard curve, and less sensitive to the presence of inhibitor compounds. This technique has been applied to a number of plant molecular analysis, such as for measuring DNA concentrations very accurately, detecting the presence of pathogens in plant tissue, and estimating the copy number of T-DNA in the genetic transformation process.Keywords: PCR; droplet digital PCR; DNA; molecular biology; diagnostic tool.
The Use of Molecular Markers to Analyze the Genetic Diversity of Indonesian Pepper (Capsicum spp.) Varieties Based on Anthracnose Resistance Nugroho, Kristianto; Terryana, Rerenstradika T.; Manzila, Ifa; Priyatno, Tri Puji; Lestari, Puji
Makara Journal of Science Vol. 23, No. 3
Publisher : UI Scholars Hub

Show Abstract | Download Original | Original Source | Check in Google Scholar

Abstract

Anthracnose is an important disease affecting the pepper plant and can lead to significant decreases in harvest yield. In this study, the genetic diversity of Indonesian pepper varieties was analyzed based on anthracnose resistance using molecular markers. DNA collected from 15 pepper varieties belonging to two species—Capsicum annuum L. and C. frutescens L.—was amplified using 14 molecular markers. The fungal isolate Colletotrichum capsici was inoculated into ripe harvested pepper fruits to observe their resistance to anthracnose as indicated by lesion size. Phylogenetic analysis revealed that the 15 pepper varieties could be classified into two major clusters with a genetic similarity coefficient of 0.63, and the pepper varieties exhibited varying degrees of resistance to anthracnose based on lesion size. Using the molecular markers, we were able to differentiate the species of pepper varieties, but not their resistance to anthracnose. All markers used in this study were confirmed to be highly informative (PIC > 0.5), suggesting their potential use in genetic studies on peppers. The marker GPMS29 was found to be significantly associated (P < 0.05) with anthracnose resistance. This information about the genetic diversity of peppers—along with the molecular markers used in our study—could prove to be useful in the further development of breeding programs of pepper plants in terms of anthracnose resistance in Indonesia.
Optimization of PCR Analysis Based on Start Codon Targeted Markers (SCoT Markers) for Identification of Genetic Variation of Seaweed from Central Sulawesi Santoso, Tri Joko; Husni, Ali; Nugroho, Kristianto; Ya’la, Zakirah Raihani; Dewi, Triyani; Marhawati, Marhawati; Maemunah, Maemunah; Rosyida, Eka; Ndobe, Samliok
Journal La Lifesci Vol. 5 No. 1 (2024): Journal La Lifesci
Publisher : Newinera Publisher

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.37899/journallalifesci.v5i1.1062

Abstract

Seaweed is a fishery commodity that has high economic value because it contains carrageenan which can be used in the pharmaceutical, food, cosmetics, and industrial fields. Central Sulawesi Province is the second largest seaweed producer in Indonesia after South Sulawesi Province. The genetic diversity of seaweed in Central Sulawesi has not been studied much. Therefore, molecular-based characterization activities to identify the genetic variation of seaweed in the province are urgently needed. The purpose of the study was to optimize PCR techniques based on targeted start codon markers (SCoT markers) to identify the genetic diversity of seaweed accessions from Central Sulawesi Province. The results showed that the parameters for seaweed PCR amplification have been optimized. Of the fifteen SCoT primers, 10 of them can work to amplify seaweed DNA collected from several regions in Central Sulawesi. This is shown by the production of PCR result amplicons. PCR results also indicate polymorphism from the seaweed samples tested, although some seaweed samples have not been successfully amplified. The parameters of the PCR technique still need to be improved, especially the concentration of DNA prints, so that valid PCR results will be obtained for use in identifying seaweed genetic diversity.
Molecular diversity of citrus genotypes using callose synthase 7 gene markers linked to Huanglongbing resistance Nugroho, Kristianto; Purwito, Agus; Sukma, Dewi; Kosmiatin, Mia; Santoso, Tri Joko; Husni, Ali; Martasari, Chaireni; Lestari, Puji
Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) Vol. 53 No. 2 (2025): Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy)
Publisher : Indonesia Society of Agronomy (PERAGI) and Department of Agronomy and Horticulture, Faculty of Agriculture, IPB University, Bogor, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24831/jai.v53i2.64952

Abstract

Huanglongbing (HLB), caused by Candidatus Liberibacter asiaticus, is a notable disease affecting citrus plantations globally. Several studies showed that the callose synthase 7 gene is crucial for the citrus defense system against this pathogen. The study aimed to analyze the nucleotide variations and genetic diversity among several citrus genotypes using specific gene primers designed from the callose synthase 7 gene sequence. Genomic DNA from eleven citrus genotypes was amplified using the specific primers, and Sanger sequencing was employed to identify the nucleotide sequence of the PCR products. The results revealed a total of 66 single-nucleotide polymorphisms (SNPs), 10 insertions, and 11 deletions were detected in callose synthase 7 gene fragment sequences. Of these, one out of five noteworthy SNPs identified at a position of 200 bp downstream of the START codon showed distinguishing features between susceptible and resistant/tolerant genotypes. Phylogenetic analysis clearly discriminated the eleven citrus genotypes into two clusters at a dissimilarity coefficient of 0.05, with all genotypes grouped in the first cluster, except for the Chinese box orange and orange jasmine. The identification of notable SNPs in this study can aid in developing new markers for the rapid selection of genotypes with enhanced HLB resistance in citrus breeding programs.   Keywords: Candidatus Liberibacter asiaticus; nucleotide variations; Sanger sequencing; phylogenetic analysis; SNP
Nucleotide variations of WRKY70 gene sequence related to Huanglongbing resistance in citrus Nugroho, Kristianto; Purwito, Agus; Sukma, Dewi; Kosmiatin, Mia; Santoso, Tri Joko; Reflinur, Reflinur; Mastur, Mastur
Jurnal Biologi Tropis Vol. 25 No. 4 (2025): Oktober-Desember
Publisher : Biology Education Study Program, Faculty of Teacher Training and Education, University of Mataram, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29303/jbt.v25i4.10092

Abstract

Huanglongbing, inflicted by Candidatus Liberibacter asiaticus in Asia region, is a destructive disease affecting citrus productions worlwide. Several studies have identified resistance genes that play essential roles in the citrus defense system against this pathogen. The goals of this study were to design the specific gene primers from the WRKY70 gene sequence and analyze the nucleotide variations and genetic diversity among several citrus genotypes. Genomic DNA from nine citrus genotypes were amplified using WRKY70-specific gene primers and the products of PCR were sent to Sanger sequencing, while the sequences of the other 12 genotypes were collected from Citrus Genome Database. The results revealed a total of 282 nucleotide variations which consisted of 157 SNPs, 28 insertions, and 97 deletions, were identified in the WRKY70 gene fragment sequence. There were three notable SNPs detected, with only one SNP [C/T] in first intron area at the position of 524 bp downstream from START codon that showed its ability to distinguish between susceptible and tolerant/resistant citrus genotypes. The phylogenetic analysis also revealed the clearly separation among citrus genotypes in two main clusters. The discovery of this SNP is useful for designing a functional marker as a screening tool in citrus breeding program in the future.
Relationship between Nurses' Therapeutic Communication and Family Anxiety Level of Patients Experiencing Emergency Conditions Nugroho, Kristianto; Auliya, Novisa Ismi
Babali Nursing Research Vol. 5 No. 2 (2024): April
Publisher : Babali Publisher

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.37363/bnr.2024.52303

Abstract

Introduction: One of the nursing actions to overcome anxiety problems is to carry out therapeutic communication. With the existence of therapeutic communication, nurses can help clients and families understand better through verbal and non-verbal communication. However, there is often a gap between good communication theory and communication practice, leading to gaps in the field. The study wanted to determine the relationship between the nurse's therapeutic communication and the anxiety level of the patient's family experiencing emergency conditions.Methods: This study employed a cross-sectional and descriptive correlational research design with a sample size of 50 respondents using purposive sampling.Results: The results showed a relationship between nurses' therapeutic communication and the anxiety level of patients' families experiencing emergency conditions, with a p-value of 0.003. The results of this study indicated that most of the nurses' therapeutic communication was good (96%), and the patient's family anxiety level was mild (88%).Conclusion: Good therapeutic communication by nurses can reduce family anxiety.
The Descriptions of Parents with Children Suffering from Cancer during Encountering Emergency Situation: A Qualitative Descriptive Study Putri, Fitria Mahardika; Nugroho, Kristianto; Victoria, Arlies Zenitha
Babali Nursing Research Vol. 5 No. 2 (2024): April
Publisher : Babali Publisher

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.37363/bnr.2024.52305

Abstract

Introduction: Cancer is a chronic disease caused by abnormal cell growth in the body and can affect all ages, including children. Children with cancer are very vulnerable because they experience growth and development, so they need special attention, especially in emergencies, to avoid death and complications. This study aimed to describe parents' perceptions of having children with cancer when the child is in a crisis. Methods: This research design used a qualitative descriptive approach. This study's population was parents with cancer children with sampling using purposive sampling. Data collection through in-depth interview techniques (in-depth interview) using a recorder, field notes, and interview guidelines. Research data in conversation transcripts were analyzed using Colaizzi's method.Result: Five themes developed, including 1) the participant's understanding of the emergency in pediatric cancer, 2) efforts made by participants in caring for children with cancer, 3) participants' experience in managing and treating children with cancer, 4) challenges in treatment, and 5) participants' expectations in the treatment carried out by their children. The experience obtained by participants is a feeling of fear of worsening the situation and negative thoughts that arise & impact the participants' psychology. In addition, the challenges experienced by participants are the cost of traveling the distance between health facilities and residence. Behind it all, participants hope their children will recover from cancer.Conclusion: There is a lack of understanding of parents regarding emergencies in cancer; behind that, there are efforts made, such as efforts to treat children with cancer, struggles to care for children with cancer, and spiritual aspects.
Co-Authors . REFLINUR Agus Purwito Ali Husni Apriliani, Elisa Arlies Zenitha Victoria Auliya, Novisa Ismi Chaireni Martasari Dewi Sukma Dwi Widyajayantie Eka Rosyida HABIB RIJZAANI Ifa Manzila Ishthifaiyyah, Sayyidah Afridatul Maemunah Maemunah Mastur Mastur Mia Kosmiatin Muhamad Syukur PUJI LESTARI PUJI LESTARI Putri, Fitria Mahardika Raden Mohamad Herdian Bhakti REFLINUR REFLINUR RERENSTRADIKA T. TERRYANA, RERENSTRADIKA T. Rerenstradika Tizar Terryana, Rerenstradika Tizar Samliok Ndobe TRI JOKO SANTOSO Tri Puji Priyatno Trikoesoemaningtyas Triyani Dewi Zakirah Raihani Ya’la