Student Profiles

Ainul Fitria Mahmudah

Promotor	:	Prof. Himawan Tri Bayu Murti Petrus, S.T., M.E., D.Eng.
Co-Promotor 1	:	Prof. Dr. Yekti Asih Purwestri, S.Si., M.Si.
Co-Promotor 2	:	Ir. Agus Prasetya, M.Eng. Sc., Ph.D.
Dissertation Title	:	Analysis of the Effectiveness of a Bacterial Consortium from Red Mud from Tayan for the Extraction of Gallium and REEY (Rare Earth Elements and Yttrium)
Abstract	:	The Indonesian government has banned bauxite ore exports starting in June 2023. Although this will reduce the value of bauxite ore exports, it will increase exports of higher-value alumina and aluminum. PT Indonesia Chemical Alumina (ICA) has been producing Chemical Grade Alumina (CGA) from bauxite ore since 2007. High alumina production can cause the accumulation of bauxite waste (red mud) of around 150 million tons per year. The biological approach using bioleaching is the most environmentally friendly method, adds value to the country's economy, and does not cause other problems. This research will focus on exploring potential bioleaching bacteria from Red Mud by increasing bioleaching activity through bacterial consortia and bioflocculation pre-treatment. The methods that will be used include next-generation sequencing (NGS) testing, bioflocculation testing, bioleaching, non-antagonistic, metal content analysis, 16S rRNA analysis, whole-genome sequencing, biosynthesis pathway approaches (RAST and AntiSMASH), and analysis of the content of organic acids or compounds in the growth medium (GC-MS and C-NMR). The aim of this research is the publication of international journal articles and patents of the Bioleaching Bacteria Consortium, as well as basic information for genetic engineering to increase the activity of bioleaching bacteria.
Email	:	ainulfitria@mail.ugm.ac.id

Anika Prastyowati

Promotor	:	Prof. dr. Tri Wibawa, Ph.D., SpMK(K)
Co-Promotor 1	:	dr. Mohamad Saifudin Hakim, M.Sc., Ph.D.
Co-Promotor 2	:	Dr.biol.hom. Nastiti Wijayanti, S.Si., M.Si.
Dissertation Title	:	Expression of Type 2 Human Papillomavirus Protein in Lactococcus lactis Expression System as Candidate of Oral Prophylactic Vaccine
Abstract	:	Human papillomavirus (HPV) type 52 is top three threatening oncogenic types that induce cervical cancer worldwide, especially in Indonesia. Designing vaccine against HPV with expression system of Lactococcus lactis is promising strategy for the bacteria is well known as safe status and probiotic properties to be utilized as delivery carrier of oral vaccine. This research was designed to optimize codon of protein L1 HPV 52 therefore it could be expressed in L. lactis expression system and then be identified by using bioinformatics tools. The synthetic gene were constructed, cloned, expressed, and verified by using in vivo method, then be analyzed.
Keywords	:	HPV type 2, expression system, Lactococcus lactis, oral vaccine
Publications and Seminars	:	THE 5th INTERNATIONAL CONFERENCE ON BIOINFORMATICS, BIOTECHNOLOGY, AND BIOMEDICAL ENGINEERING, 6–7 September 2023
Email	:	anika.prastyowati@gmail.com

Aprilia Indra Kartika

Promotor	:	Prof. dr. Sofia Mubarika Harjana, M.Med.Sc.,Ph.D.
Co-Promotor 1	:	Dr. biol.hom. Nastiti Wijayanti, S.Si., M.Si.
Dissertation Title	:	Exosome microRNA Signature in Lung Adenocarcinoma Advance Stage as A Candidate of Diagnosis Biomarker
Email	:	apriliaindrak@mail.ugm.ac.id

Arlinda Puspita Sari

Promotor	:	Prof. Dr. Yekti Asih Purwestri, S.Si., M.Si.
Co-Promotor 1	:	Dr. Rikno Harmoko, M.Sc.
Co-Promotor 2	:	Dr. Tri Rini Nuringtyas, S. Si., M. Sc.
Dissertation Title	:	Increasing Tobacco Resistance to Drought Stress Through Modifying the Trehalose Pathway Using the CRISPR-Cas9 Genome Editing Approach
Email	:	arlindapuspitasari@mail.ugm.ac.id

Budi Setyawan

Promotor	:	Prof. Dr. Ir. Siti Subandiyah, M.Arg.Sc.
Co-Promotor 1	:	Dr. Ir. Arif Wibowo, M.Agr.Sc.
Co-Promotor 2	:	Valérie Pujade-Renaud, PhD., HDR.
Dissertation Title	:	Identification and pathogen diversity of new emerging leaf fall disease on rubber (Hevea brassiliensis muell. Arg.) in Indonesia
Abstract	:	A new emerging infectious plant disease, with a distinct symptom, is causing severe leaf fall on rubber tree, in Indonesia and other Asian countries. The disease presumably attributed to several pathogens, namely Pestalotiopsis spp., Colletotrichum spp., and Neopestalotiopsis spp. Disease distribution, pathogen characterization, pathogen variability, and interaction with the host plant, are still understudied. This study was conducted to confirm the causal agent, investigate the virulence- and genetic-based diversity among isolates, and reveal the fungal community associated to the disease in the phyllosphere of rubber. A total of 88 isolates were obtained from various regions in Indonesia, which were suspected to be Pestalotiopsis and Colletotrichum. Colony morphology and microscopic characteristics showed variations. Molecular identification is in progress. ITS amplicon sequencing showed that the Ascomycota and Basidiomycota dominated all phyllosphere in both seasons and areas at the phyla level, while Colletotrichum and Phyllosticta dominated at the genus level. Colletotrichum was the genera commonly found as the pathogen on rubber. Pestalotiopsis, Neopestalotiopsis, Corynespora, and Pestalotia were also found in small quantities which have the potential as rubber plant pathogens. Data showed that the diversity of the fungal community increased with the increase of symptom severity, as does the abundance of the fungus.
Keywords	:	Fungal diversity, Identification, ITS amplicon metagenomic, New emerging leaf fall disease, Rubber tree.
Email	:	bud1se@yahoo.com

Dewi Marbawati

Promotor	:	Prof. Tri Joko Raharjo, S.Si, M.Si., Ph.D.
Co-Promotor 1	:	Dr. Tri Rini Nuringtyas, S.Si, M.Sc.
Co-Promotor 2	:	Dr.rer.nat. Niko Prasetyo, S.Si, M.Sc.
Dissertation Title	:	Identification of Anti Leptospira from Phyllanthus niruri Using Metabolomics Approach
Abstract	:	Leptospirosis is a re-emerging disease that threatens the world. Data from the International Leptospirosis Society (ILS) states that Indonesia declared a country with a high incidence of leptospirosis and was ranked 3rd in the world for mortality. Leptospirosis was also often missed, under diagnosed and under reported. The Phyllanthus niruri plant was known have potential as an anti-bacterial against Leptospira in vitro. This aims of this research was describe the anti-leptospira potential of Phyllanthus niruri. This is an experimental research, with stages of extraction, fractionation and column chromatography of Phyllanthus niruri, a metabolomics approach carried out using mass spectrophotometry, confirmation of active compounds carried out in silico (molecular docking) and the inhibition mechanism of Leptospira will be explained using molecular examination.
Keywords	:	Leptospira, Leptospirosis, Phyllanthus niruri, anti bacterial, metabolomics
Email	:	dewimarbawati@mail.ugm.ac.id

Dewi Retnaningati

Promotor	:	Prof. Dr. Yekti Asih Purwestri, S.Si., M.Si.
Co-Promotor 1	:	Respati Tri Swasono, S.Si, M.Phil., Ph.D.
Co-Promotor 2	:	Dr. Tri Rini Nuringtyas, S.Si, M.Sc.
Dissertation Title	:	Transcriptomic Analysis and Genome Editing Related to Anthocyanin Biosynthesis in Cempo Ireng Black Rice Plants using CRISPR/Cas9
Abstract	:	Black rice contains higher anthocyanins than other rice and has higher mineral content, ash content, raw fiber, protein, oil and hydrolyzable carbohydrates than white rice. The anthocyanin content has the potential to be an antioxidant, anti-diabetic, anti-cancer, anti-inflammatory, anti-microbial, anti-obesity, and can prevent cardiovascular disease. Black rice “Cempo Ireng” is one of Yogyakarta's local genetic resources with high nutritional content, lower calorie content than other types of rice, and rich in anthocyanins. Studies related to genes that play a role in anthocyanin biosynthesis and efforts to increase the anthocyanin content in black rice to increase its nutritional value are important. In this dissertation research plan, transcriptomic analysis will be carried out to study genes related to anthocyanin biosynthesis and genome editing related to anthocyanin biosynthesis in Cempo Ireng black rice plants using the CRISPR/Cas9 method.
Keywords	:	Genetic Engineering, CRISPR/Cas9, Transcriptopic Analysis, Anthocyanin, Black Rice, Cempo Ireng
Email	:	dewi.retnaningati@mail.ugm.ac.id

Diana Indrasanti

Promotor	:	Prof. Dr. drh. Wayan Tunas Artama
Co-Promotor 1	:	Dr.rer.nat. Ir. Sena Adi Subrata, S.Hut., M.Sc., IPU.
Dissertation Title	:	Analysis of Zoonotic Bacteria and Gastrointestinal Parasites in Timor Deer (Cervus timorensis) and Beef Caws in The Interface Area of Baluran National Park Using A One Health Approach
Abstract	:	Contact between wild animals and livestock can cause two-way disease transfer, especially zoonotic diseases, and can even cause disease outbreaks. In the Baluran National Park (TN), East Java, in the northern coastal area there is an area bordering residential areas who make their living as livestock breeders, where as many as ±3800 beef cattle are grazed every day in the Baluran National Park area. This disrupts the sustainability of wildlife, especially Timor deer (Cervus timorensis) because they compete for food and grazing places. The interaction between the two ruminants has the potential for disease transmission, especially bacteria, between deer and beef cattle, which is feared to lead to transmission to humans. The aim of this research is to show evidence of potential transmission, by analyzing zoonotic gastrointestinal bacteria and parasites including Streptococcus agalactiae, Clostridium tetani, Escherichia coli and Bacillus anthracis as well as the parasites Giardia lamblia and Cryptosporidium parvum in deer and beef cattle. Social survey data was taken from residents regarding risk factors for raising livestock. The results of the research were used to develop recommendations for breeders, the Situbondo Livestock Service and Baluran National Park regarding good livestock rearing practices in the interface area of Baluran National Park using a One Health approach, so that Timor deer are preserved and ASUH (safe, healthy, whole and halal) livestock products are produced. The research used a purposive sampling survey method. The research took place in the interface area (9 places) in Baluran National Park. Samples consisted of deer feces, beef cattle and questionnaires. The sample size for deer feces was 30 samples in each area, and a total of 363 samples of beef cattle feces. Interviews with 30% of the population, namely heads of households, livestock breeders and shepherds. PCR molecular detection method with specific primers to identify environmental DNA (e-DNA) bacterial species and zoonotic gastrointestinal parasites from deer and beef cattle feces. The data obtained are the prevalence of parasites and bacteria in deer and cutting fires, risk factors for raising livestock in the interface area of Baluran National Park and the formulation of recommendations for raising livestock using the One Health concept. Data were analyzed using descriptive and logistic regression.
Keywords	:	zoonotik, rusa Timor, sapi potong, Taman Nasional Baluran, One Health
Email	:	diana.indrasanti@mail.ugm.ac.id

Dini Achnafani

Promotor	:	Muhammad Saifur Rohman, S.P., M.Si., M.Eng, Ph.D.
Co-Promotor 1	:	Prof. dr. Sofia Mubarika Harjana, M.Med.Sc., Ph.D.
Co-Promotor 2	:	Dr. Harto Widodo, S.P., M.Biotech.
Dissertation Title	:	Actinomycetes Utilization as L-Asparaginase Enzyme Producer for Anticancer Drug Therapy Candidates
Email	:	diniachnafani@ugm.ac.id

Dyah Ayu Widyastuti

Promotor	:	Prof. Dr. Abdul Rohman, S. F., M. Si., Apt.
Co-Promotor 1	:	Dr. Tri Rini Nuringtyas, S. Si., M. Sc.
Co-Promotor 2	:	Dr. Djoko Santosa, S. Si., M. Si.
Dissertation Title	:	In Vitro Culture of Red Ginger (Zingiber officinalle var. rubrum) with Fusarium oxysporum's elicitation as Anti-Salmonella sp.
Abstract	:	The potential of red ginger as a herbal medicine is supported by the content of secondary metabolite compounds which have been proven to be important in the health sector. The high demand for red ginger in society leads to the need of an appropriate cultivation methods to produce red ginger with optimal secondary metabolite content. Red ginger can be cultured in laboratory using explants in the form of shoots from the rhizome. Increasing the production of secondary metabolite compounds through in vitro culture can be optimized by adding elicitors. Elicitation of in vitro cultures is carried out to increase the production of secondary metabolite compounds by induction of stress through abiotic and biotic factors. One of the endogenous fungi of red ginger in nature is Fusarium oxysporum, so this type has the potential to be used as an elicitor in in vitro cultures. This study aims to identify differences in metabolites produced using a metabolomics approach and genes expressed using a transcriptomics approach in red ginger resulting from in vitro culture with and without elicitors and how their activity is as an anti-Salmonella sp. so that its potential as a herbal medicine can be optimized.
Keywords	:	elicitor, Fusarium oxysporum; metabolomic; transcriptomic; Zingiber officinale
Publications and Seminars	:	The 6th International Seminar on Agribusiness, Semarang, July 26th 2023
Publications and Seminars	:	Dyah Ayu Widyastuti, Tri Rini Nuringtyas, Djoko Santosa, Abdul Rohman. A perspective on the in vitro tissue culture of red ginger and its impact on antioxidant activity. Food Research (Accepted) and Dyah Ayu Widyastuti, Djoko Santosa, Tri Rini Nuringtyas, Siti Fatimah, Abdul Rohman. Total phenolic and flavonoid contents and antioxidant activity of red ginger (Zingiber officinale var. rubrum)’s rhizomes from seven different regions in the island of Java Indonesia. Food Research (Under Review)
Email	:	dyah.ayu.widyastuti@mail.ugm.ac.id

Fatimah

Promotor	:	Prof. Dr.drh. Asmarani Kusumawati, M.P.
Co-Promotor 1	:	Prof. Dr. Rarastoeti Pratiwi, M. Sc
Co-Promotor 2	:	Dr. Dini Wahyu Kartika Sari, S.Pi., M. Si.
Dissertation Title	:	Design of Multiepitope Vaccine for Jembrana Disease Virus
Abstract	:	Jembrana disease is an acute viral disease that can attack Bali cattle and their cross breeds. This disease is known to have a mortality rate of up to 30% in the acute phase and an abortion rate of up to 49%, thus causing economic losses for cattle breeders. Efforts to control the spread of Jembrana disease are important to reduce economic losses caused by high livestock mortality rates. One way to control the spread of disease in livestock can be done by developing vaccines. In this research, a multiepitope vaccine will be developed to reduce the spread of Jembrana disease. In this research, in designing a multiepitope vaccine, the immunogenic proteins TM and CA of the Jembrana virus were selected. The process of designing a multiepitope vaccine begins with mapping the epitopes of B cells and T cells, which is followed by analysis of antigenicity, allergenicity and toxicity. Then the vaccine construction design is carried out. The vaccine was then subjected to physiochemical, solubility, toxicity, allergenicity, secondary structure analysis, 3D structure modeling was carried out and the quality of vaccine construction was analyzed using Ramachandran plot analysis. Next, the vaccine was analyzed for its interaction ability with TLR4 as a receptor using molecular docking. The results of the docking were analyzed by interacting residues of the docking complex with molecular dynamics analysis to determine the flexibility of the vaccine. Then the vaccine construction sequence was subjected to codon optimization and in silico sequence cloning. The vaccine is then subjected to in silico simulation analysis of the immune response to determine the vaccine's ability to induce an immune response. The next stage after in silico analysis, in vitro analysis is carried out which begins with construct design, continues with vaccine protein expression and finally protein purification. In this study, the pET-28b+ expression vector was used, and it was expressed in the prokaryotic host E.coli BL-21. The purified protein is formulated with Incomplete Freud's Adjuvant (IFA) and then injected into female BABL/C mice, which will then be analyzed for the immune response that appears after vaccine injection using ELISA.
Keywords	:	Jembrana Disease Virus, In Silico, Multiepitope Vaccine, BALB/C Mice, ELISA
Email	:	fatimahbiotech@mail.ugm.ac.id

Freini Dessi Effendi

Promotor	:	Prof. Dr. Ir. Endang Sutriswati Rahayu, M.S.
Co-Promotor 1	:	Prof. Ir. Donny Widianto, Ph.D.
Co-Promotor 2	:	Prof. Dr. Ir. Tyas Utami, M.Sc.
Dissertation Title	:	Isolation, Identification, and Characterization of Potential Probiotic Lactic Acid Bacteria Producing Folate from Fermented Mustard Greens
Email	:	freinidessieffendi@mail.ugm.ac.id

Hasna Fadlilatul Bidayah

Promotor	:	Prof. Dr. Rarastoeti Pratiwi, M.Sc.
Co-Promotor 1	:	Prof. Dr. Abdul Salam Sofro
Co-Promotor 2	:	Dr. dr. Teguh Triyono, M.Kes, Sp.PK (K)
Dissertation Title	:	Molecular Basic of ABO Blood Group System in Indonesia
Abstract	:	Among the 45 human blood group systems reported so far, the ABO system was the most important. In the field of transfusion and transplant medicine, the accuracy of ABO blood group typing was clinically important. To characterize ABO blood group status, the gold standard remains serological testing. As an alternative and/or complementary approach to the standard blood group serological typing, genotyping has emerged in immunohematology laboratories for years. To this aim, the molecular determinants driving phenotype variability must be reported on a population-specific basis, to guarantee an optimal identification of the variations by molecular typing. Although widely studied in the Caucasian and East-Asian populations, but the was no molecular data have been generated in Indonesia. The purpose of this research was to study the ABO system blood group polymorphisms in the Indonesian population, especially related to the molecular study of the ABO gene. The study begins with standart serological identification to find unusual variants. These sample then be identified by PCR-ASP and PCR-sequencing techniques. Correlation between phenotypes and genotypes were analyzed by functional genetic studies. Allele and genotype frequencies were also estimated. Then new novel population-specific variants/clusters could be determined.
Keywords	:	ABO Blood Group, ABO Distribution, Genotyping, Indonesia
Publications and Seminars	:	myHAM UMY, 11th May 2024 (The 1st International Conference Muhammadiyah Yogyakarta – Hospital & Healthcare Management)
Publications and Seminars	:	ICOPH-TCD UNDIP, 30th-31st July 2024 (International Conference on Public Health for Tropical and Coastal Development)
		Distribution of ABO and Rhesus D antigen expression in Yogyakarta, Java Island: a pioneer large-scale study in Indonesia. BMC RESEARCH NOTE (peer review)
Email	:	hasnafadlilatul@gmail.com

Iffan Alif

Promotor	:	Prof. Dr. apt. Edy Meiyanto, M.Si.
Co-Promotor 1	:	Dr. apt. Muthi' Ikawati, M.Sc.
Co-Promotor 2	:	Prof. Dr. dr. Agung Putra, M.Si. Med.
Dissertation Title	:	The Potency of Pentagamavunon-1 and Chemoprevention-Curcumin Analog 1.1 as Effector Cytotoxic T Cell Co-Immunotherapy Agents against Breast Cancer Stem Cells
Abstract	:	Breast cancer stem cells (bCSCs) possess aggressive self-renewal characteristics responsible for cancer heterogeneity. Efforts to reduce breast cancer mortality have been not optimal due to the presence of bCSCs clones resistant to conventional therapies, necessitating alternative therapies targeting bCSCs. Effector cytotoxic T cells (CTL) can recognize and induce apoptosis in cancer, but bCSCs can avoid these mechanisms through immune checkpoint mediators, such as programmed death ligand-1 (PD-L1) and cluster of differentiation 80 (CD80). Pentagamavunon-1 (PGV-1) and Chemoprevention Curcumin Analog-1.1 (CCA-1.1) are anti-cancer curcumin analogs and believed to inhibit the immune checkpoint mechanism of bCSCs. This study aims to develop potential of PGV-1 and CCA-1.1 as co-immunotherapy agents for CTL against bCSCs. CTL were reactivated in vitro using CD3/CD28 activator and interleukin-2 (IL-2), then viability and differentiation ability after PGV-1 or CCA-1.1 treatments were analyzed using CCK-8 and flow cytometry targeting CD3, CD8, CD45RO and CCR7. The cytotoxicity and apoptosis ability of PGV-1 and CCA-1.1 on bCSCs were analyzed by MTT and flow cytometry using annexin-V/Propidium iodide (PI). The expression of PD-L1 and CD80 on bCSCs after PGV-1 and CCA-1.1 treatment was analyzed using flow cytometry. Effector cytotoxic T cells treated with PGV-1 or CCA-1.1 were co-cultured with bCSCs and their cytotoxicity and apoptosis capabilities were analyzed using MTT and flow cytometry. Granzyme and perforin levels in co-culture medium were analyzed using ELISA, and read by ELISA reader at absorbance of 450 nm. In silico docking potential of PGV-1 or CCA-1.1 with PD-L1 or CD80 was analyzed using MOE docking.
Keywords	:	Curcumin Analog, Pentagamavunon-1. Chemoprevention-Curcumin Analog 1.1, Effector Cytotoxic T Cells, Breast Cancer Stem Cells
Email	:	iffanalif@gmail.com

Ika Rahmawati Sutejo

Promotor	:	Prof. Dr. apt. Edy Meiyanto, M. Si.
Co-Promotor 1	:	Prof. dr. Sofia Mubarika Harjana, M.Med.Sc., Ph.D.
Co-Promotor 2	:	Dr. apt. Riris Istighfari Jenie, M.Si.
Dissertation Title	:	Analysis of the Molecular Phenomena and Anti-Cancer Mechanism of Curcumin Analog Compounds in a 3D Liver Cancer Model Expressing MYCN
Email	:	ika.rahmawati.sutejo@mail.ugm.ac.id

Irwan Sudarmanto

Promotor	:	Prof. Dr. drh. Wayan Tunas Artama
Co-Promotor 1	:	Muhammad Saifur Rohman, S.P., M.Si., M.Eng, Ph.D.
Dissertation Title	:	Characterization of Recombinant Rubisco Like Protein (RLP) Enzyme from Chromohalobacter salexigen BKL 5
Abstract	:	Rubisco is a protein/enzyme that is claimed to be the most abundant in the biosphere, accounting for almost 50% (Ellis, 1981). This enzyme plays a crucial role in the process of photosynthesis to produce glucose, a basic molecule that forms the building blocks of living organisms. The main function of Rubisco is to fix CO2 and initiate the enolization process of RuBP substrates as the starting material for glucose formation (Sharkey, 1998). Rubisco is categorized into three groups based on phylogenetic analysis: Group I, II, and III. In its development, proteins were discovered that structurally resemble Rubisco and are classified as Rubisco Group IV. Rubisco Group IV, or what is known as Rubisco-like proteins (RLPs), lacks the ability to fix CO2 due to substitutions in the amino acid residues at the active site. It participates in catalyzing the enolization of RuBP analogs, a reaction similar to the enolase reaction catalyzed by Rubisco. Rahman et al. successfully isolated and expressed the Rubisco-like protein (RLP) gene from Chromohalobacter salexigen BKL 5. This bacterium was obtained from a halophilic environment and, based on its phylogenetic evolution, is believed to have originated from the anoxic era. It is suspected that this Rubisco family has an active site that does not experience competitive binding between CO2 and O2, thus having a high enolase activity. This research represents an initial step in obtaining recombinant Rubisco-like protein (RLP), a type of Rubisco enzyme family, from halophilic bacteria that can be transformed into mesophilic bacteria such as E. coli, potentially creating a new strain capable of performing enolase processes very efficiently.
Keywords	:	halofilik, Chromohalobacter salexigen BKL 5, Cloning, Bioinformatics
Publications and Seminars	:	IRWAN SUDARMANTO, LINCE SITOHANG, M. SAIFUR ROHMAN, WAYAN TUNAS ARTAMA. Cloning and Expression of Rubisco Like Protein (RLP) from halophilic bacterium Chromohalobacter salexigen BKL 5. Biodiversitas Journal (Accepted)
		Irwan Sudarmanto, Wayan Tunas Artama, Muhammad Saifur Rohman Physicochemical characterization and comparative analysis of ribulose 1,5 biphospate carboxylase-oxygenase like proteins (RLP) from halophilic Chromohalobacter salexigen BKL 5 and non halophilic counterparts using in silico approaches. JKSA Journal (Accepted)
		Irwan Sudarmanto, Muhammad Saifur Rohman, Wayan Tunas Artama EFFECT OF THE D185 MUTATION ON THE STABILITY AND FUNCTIONALITY OF RUBISCO LIKE PROTEIN (RLP) FROM CHROMOHALOBACTER SALEXIGEN BKL 5. Journal Of Chemistry (Published)
		Seminar Nasional Bioteknologi VIII, Yogyakarta, 29 Oktober 2022
		Seminar Nasional Bioteknologi IX, Yogyakarta, 21 Oktober 2023
		7th International Conference on Science, Infrastructure Technology and Regional Development (ICoSITeR) 2022
Email	:	sudarmantoirwan2016@gmail.com

Ismail

Promotor	:	Dr. Sylvia Utami Tunjung Pratiwi, S.Si., M.Si
Co-Promotor 1	:	Dr. Ema Damayanti, M. Biotech.
Co-Promotor 2	:	Ir. Jaka Widada, M.P., Ph.D.
Dissertation Title	:	Exploration of The Potential Metabolyte Compounds of Streptomyces sp. BSE7F in Inhibition of Biofilm Candida sp. Through A Multi-Omic Approach
Email	:	ismail27@mail.ugm.ac.id

Lili Sugiyarto

Promotor	:	Prof. Dr. Tutik Dwi Wahyuningsih, M.Si. Ph.D.
Co-Promotor 1	:	Ir. Jaka Widada, M.P. Ph.D.
Dissertation Title	:	Root Microbiota Composition and Metabolomics Analysis of Interactions with Maize Plants
Abstract	:	Maize growth cannot be separated from the role of microorganisms associated with all parts of the maize plant known as microbiota. The interaction is influenced by many factors, including plant genotype and soil type. Microbiota associated with roots, with chemical changes that occur can mediate changes in microbiota. Plant genotypes influence the composition of their microbiomes by secreting various chemicals to attract beneficial microbes and defend against pathogens. Secondary metabolites released from grain roots can be used as attractants to alter root-associated fungal and bacterial communities, or attract endophytic bacteria in the roots to colonize. This research aims to study and analyze the growth response of 6 maize varieties (Bisma, Srikandi, NK, Bisi 18, local madura, local red) and the root microbiome community profile of maize plants grown on 2 soil types (Co60 irradiated and non-irradiated). Observations will include the growth of the six corn varieties through plant dry weight and plant physiology measured by the Li-6400 tool. Analysis of the root bacteriome community profile will be carried out by NGS with the target 16S rRNA gene in the V3-V4 region and analysis of the endophytic fungus profile with the target ITS1 and ITS2 regions. Root metabolite analysis with LC-MS.
Keywords	:	Genotype, Irradiation soil, NGS
Email	:	lilisugiyarto@mail.ugm.ac.id

Maythesya Oktavioni

Promotor	:	Dewi Kartikawati Paramita, S.Si., M.Si., Ph.D.
Co-Promotor 1	:	Dr. Tri Rini Nuringtyas, S.Si., M.Sc.
Dissertation Title	:	Discovery of Colorectal Cancer (CCR) Specific Biomarker through Glycoprotein and Lectin Interaction
Email	:	maythesyaoktavioni@mail.ugm.ac.id

Medhina Magdalena

Promotor	:	Ir. Donny Widianto, Ph.D.
Co-Promotor 1	:	Prof. Ir. Irfan Dwidya Prijambada, Ph.D.
Dissertation Title	:	Exploration of Fructophilic Yeast and Its Utilization to Improve Ethanol Fermentation Efficiency from Sweet Sorghum Juice
Abstract	:	In biofuel production, using raw materials that do not conflict with the food supply and are easy to cultivate, is expected to be a solution to the provision of sustainable raw materials and can reduce production prices. Sweet sorghum can meet feedstock requirements for bioethanol production as it contains relatively high glucose and fructose content. During ethanol fermentation, yeast tends to use glucose first, compared to fructose. As a result, when other nutrients are depleted, fructose residues remain at the end of fermentation. This condition causes fermentation to get sluggish and stuck. Fructophilic yeast was required to solve the fermentation problem. The fructophilic tendency is linked to hexose transporters that transport glucose and fructose into cells. This study aimed to isolate and characterize fructophilic yeasts, investigate the correlation between the Hxt1, Hxt3, and Fsy1 transporters and their fructophilic behavior, and evaluate the capacity of these yeasts to enhance the fermentation efficiency of sweet sorghum juice into ethanol.
Keywords	:	Yeast, fructophilic, sweet sorghum, bioethanol
Publications and Seminars	:	International Conference for Green Science and Technology, (provided online by Shizuoka University ), 21- 22 September 2021
Publications and Seminars	:	11th International Seminar of Indonesian Society for Microbiology (11th ISISM), (online, 16-17 November, 2021)
		Medhina Magdalena, Candra Rahmani Priyambada, Donny Widianto, Sri Wedhastri, Irfan Dwidya Prijambada. Yeast Diversity in Honey Produced by Wild Honeybees at Different Elevations. Baghdad Science Journal (Accepted)
Email	:	medhinamagdalena2018@mail.ugm.ac.id

Nurhening Yuni Ekowati

Promotor	:	Prof. Dr. Yekti Asih Purwestri, S.Si., M.Si.
Co-Promotor 1	:	Dr. Fatimah
Co-Promotor 2	:	Dr. Tri Rini Nuringtyas, S.Si., M.Sc.
Dissertation Title	:	Genome Editing using CRISPR/Cas9 Targeting the GAD (Glutamic Acid Decarboxylase) Gene to Increase Gamma-Aminobutyric Acid (GABA) Content in Rice (Oryza sativa L.).
Email	:	nurhening2@gmail.com

Putu Cri Devischa Gallantiswara

Promotor	:	Prof. Dr. Ir. Siti Subandyah, M.Agr.Sc
Co-Promotor 1	:	Prof. Dr. drh. Wayan Tunas Artama
Co-Promotor 2	:	Dr. Windi Muziasari
Dissertation Title	:	Antibiotic Resistance Gene Monitoring in the Agricultural Environment in Java, Indonesia
Abstract	:	The use of antimicrobial agent in livestock farm has been a common strategy for several purposes including bacterial, protozoal, and fungal infection treatment, and growth promotor. Antibiotics, the most common antimicrobial agent use in livestock, are commonly mixed with the feeds for bacterial infection treatment or as a growth promotor. This accelerates the emerging of antibiotic resistant bacteria in the animal’s gut microbiomes. When the animal manures are applied to the soil, it is not only antibiotic compounds, but also considerable numbers of antibiotic-resistant bacteria, antibiotic resistance genes (ARGs), and associated mobile genetic elements (MGEs) are introduced to soil. Several kinds of antimicrobial agents also used for managing the plant health including fungicides, bactericides (antibacterials), insecticides, and pesticides. This phenomenon can drive those antimicrobial residues from animal and plant to agriculture sector. This study is designed to characterize the presence and the abundance of targeted ARGs and MGEs, monitor the gene distribution, and study the gene’s prevalence in agricultural environment using culture independent and molecular microbiology technology including conventional PCR, qPCR, a high throughput qPCR (HTqPCR), and the SmartChip qPCR system. Three kinds of samples including animal feces, animal manure, and plant cultivating soil are collected from several agricultural farms in Yogyakarta, consisting of chili, shallot, and rice field. The study will be divided into three stages: (1) profile of the ARGs and MGEs in Integrated Farming Agrotechnology Innovation Center, Universitas Gadjah Mada, Yogyakarta and Java, Indonesia (2) design a primer set to target the important ARGs and MGEs according to the first stage result through an in silico analysis and (3) study the prevalence of ARGs and MGEs in Yogyakarta agricultural environment based on designed and controlled farming systems in Bantul district, Yogyakarta.
Keywords	:	antibiotic resistance gene, mobile genetics element, feces, manure, soil
Publications and Seminars	:	World Microbe Forum, 20-24 June 2021, Online Worldwide
Publications and Seminars	:	The 6th International Symposium Association of Japan-Indonesia Veterinary Education 2022 (11 Febtuary 2022)
Email	:	putu.cri.d@ugm.ac.id

Ratih Restiani

Promotor	:	Prof. Dr. Yekti Asih Purwestri, S.Si., M.Si.
Co-Promotor 1	:	Prof. Jose Gutierrez-Marcos
Co-Promotor 2	:	Dr. Tri Rini Nuriningtyas, S.Si., M.Sc.
Dissertation Title	:	Transcriptomic Analysis of Indonesian Local Black Rice Cultivars and Genome Editing of Black Rice var. Cempo Ireng Using CRISPR/Cas9 Targeting the OsLCYE Gene for Carotenoid Biofortification
Abstract	:	Black rice (Oryza sativa L.) is a pigmented rice that is rich in anthocyanins and beta carotene in its aleurone layer. It is becoming popular to be developed as a functional food and has the potential to ensure food security and nutrition. Indonesia has various local cultivars of black rice in each province, such as Cempo Ireng, Toraja Black Rice, and South Lampung Black Rice. Based on preliminary studies, these local cultivars contain high levels of lutein and beta-carotene, which are useful as sources of beta-carotene but have not been studied extensively. The study of carotenoid profiling and integrated transcriptomic analysis can provide a deeper understanding of key genes and their regulation in carotenoid biosynthesis of Indonesian black rice. In addition, genome editing via CRISPR/Cas9, which targets the OsLyce gene knockout, may improve beta-carotene biosynthesis from black rice. Therefore, the integration of transcriptomic analysis and genome editing through CRISPR/Cas9 is expected to provide more in-depth knowledge of the molecular system, gene function, and carotenoid biofortification in Indonesian local cultivar black rice.
Keywords	:	Black Rice, carotenoid, Cempo Ireng, CRISPR/Cas9, transcriptomic analysis
Email	:	ratihrestiani@mail.ugm.ac.id

Rhytia Ayu Christianty Putri

Promotor	:	Prof. Dr. Ir. Eni Harmayani, M.Sc.
Co-Promotor 1	:	Ir. Jaka Widada, M.P., Ph.D.
Co-Promotor 2	:	Prof. Dr. Ir. Nurliyani, MS., IPM.
Dissertation Title	:	White Saffron (Curcuma mangga Val) Rhizomes as Prebiotic Candidates and Its Effects on Gut Microbiota Diversity and Immunomodulatory Properties
Email	:	rhytiaayuchristiantyputri@mail.ugm.ac.id

Ria Suryani

Promotor	:	Prof. Widodo, S.P., M.Sc., Ph.D.
Co-Promotor 1	:	Dr. Tri Rini Nuringtyas, S. Si., M. Sc.
Dissertation Title	:	Development of Kefir as a Functional Antihypertensive Drink
Email	:	ria.suryani@mail.ugm.ac.id

Sista Werdyani

Promotor	:	Prof. dr. Sofia Mubarika Harjana, M.Med.Sc., Ph.D.
Co-Promotor 1	:	Prof. Teruna J. Siahaan, Ph.D.
Co-Promotor 2	:	Dewi Kartikawati Paramita, S.Si., M.Si., Ph.D.
Dissertation Title	:	Methotrexate-cIBR Conjugate and Its Derivatives for Enhancing Anticancer Selectivity: In Silico and In Vitro Studies
Email	:	sista.werdyani@mail.ugm.ac.id

Siti Fatimah

Promotor	:	Prof. Abdul Rohman, SF, Apt, M.Si.
Co-Promotor 1	:	Respati Tri Swasono, S.Si, M.Phil., Ph.D.
Co-Promotor 2	:	Dr. Tri Rini Nurintyas, S.Si, M.Sc.
Dissertation Title	:	The Characterization of Red Ginger (Zingiber officinale var. Rubrum) Based on Variations in Growth Altitude: Metabolomics, Antioxidant Activity, and Antibacterial Activity
Abstract	:	Currently, traditional medicine is widely used by the public. One of these is red ginger. Red ginger contains antioxidants that are beneficial for the body, but the level of antioxidants can be influenced by the altitude at which the plant grows. The purpose of this study is to determine the characterization of red ginger based on variations in growth altitude in terms of metabolomics, antioxidant activity, and antibacterial activity. The research will be conducted using an experimental method with 4 different growth altitudes. Metabolomic profiles will be measured using FTIR, NMR, and LC-HRMS. Antioxidant activity will be measured using a UV-Vis spectrophotometer. Antibacterial and antibiofilm activities will be assessed using the microdilution method.
Keywords	:	Red Ginger, Metabolomics, Antioxidant Activity, Antibacterial Activity
Email	:	sitifatimah1977@mail.ugm.ac.id

Sri Fatmah Sari

Promotor	:	Prof. Tri Joko Raharjo, S.Si., M.Si., Ph.D.
Co-Promotor 1	:	Prof. Dr. Ir. Alim Isnansetyo, M.Sc.
Co-Promotor 2	:	Dr. Tri Rini Nuringtyas, S. Si., M. Sc.
Dissertation Title	:	Abalone Haliotis asinine Peptide as Anti inflammation Agent
Email	:	srifatmahsari1988@mail.ugm.ac.id

Stefani Santi Widhiastuti

Promotor	:	Prof. Dr. apt. Arief Nurrochmad, M.Si., M.Sc.
Co-Promotor 1	:	Prof. dr. Madarina Julia, Sp.A(K), MPH., Ph.D.
Co-Promotor 2	:	Jajah Fachiroh, S.P., M.Si, Ph.D.
Dissertation Title	:	The Analgesic Activity of Tithonia diversifolia Extract and Its Active Compounds, and Pain-Related Gene Expression Analysis in Mice Induced with Painful Diabetic Neuropathy
Email	:	stefani.santi.w@mail.ugm.ac.id

Wiwin Kusuma Perdana Sari

Promotor	:	Prof. Ir. Donny Widianto, Ph.D.
Co-Promotor 1	:	Dr. Tri Rini Nuringtyas, S.Si., M.Sc.
Dissertation Title	:	Selection of lactic acid bacteria strains as postbiotic promoters in the development of Indonesian functional desserts based on sourdough fermentation (tentative)
Email	:	wiwinkusuma84@mail.ugm.ac.id

Yeni Indra Kumalasari

Promotor	:	Prof. Ir. Donny Widianto, Ph.D.
Co-Promotor 1	:	Prof. Dr. Yekti Asih Purwestri, S.Si., M.Si.
Dissertation Title	:	Study and Development of Endophytic Bacteria as Biocontrol Agent of Pathogenic Bacteria in Banana Plants
Email	:	yeniindrakumalasari@mail.ugm.ac.id

Yuni Sine

Promotor	:	Prof. Widodo, S.P., M.Sc., Ph.D.
Co-Promotor 1	:	Prof. Ir. Donny Widianto, Ph.D.
Co-Promotor 2	:	Prof. Dr. Yekti Asih Purwestri, S.Si., M.Si.
Dissertation Title	:	Isolation, Identification and Characterization of Probiotic Candidate Lactic Acid Bacteria from Pigeon Pea Soaked Water (Cajanus cajan L. Millps) as Pigeon Pea Yogurt Fermentation Starter for Health Food
Abstract	:	Functional food is defined as food that can have a positive impact on health. Utilization of local food sources for fermented foods that have functional properties is a very good innovation to meet the protein needs of the community. The physiological properties of functional foods are determined by the bioactive components contained in them, such as dietary fiber, inulin, fructooligosaccharides (FOS), antioxidants, polyunsaturated fatty acids (PUFA), prebiotics and probiotics. Lactic acid bacteria (LAB) is one of the key microbes in producing functional food. These bacteria are widespread in nature, associated with humans, animals and plants. In plants, LAB is an autochthonous microbial which is a representation of microbes that have the ability to increase health benefits in plants that are used as food ingredients. Legumes are also a source of LAB, one of the legumes that is widely used as a fermentation substrate is pigeon pea. Prior to the fermentation process, pigeon pea seeds are soaked. At this stage, the LAB population grows significantly, so that LAB with probiotic potential can be isolated. This study aims to isolate LAB from the water soaked with pigeon pea (Cajanus cajan L. Millps.). This study aims to isolate LAB from the water soaked by pigeon pea (C. cajan L. Millps.). The isolated LAB was then applied to pigeon pea milk as a yogurt strater. This research begins with the soaking of pigeon pea, then metagenomic microbial analysis in pigeon pea soaked water is performed, and isolation, identification and characterization of LAB probiotic potential in pigeon pea soaked water is done. After that, LAB in vitro tests will be carried out, followed by the preparation of pigeon pea milk and proximate analysis on pigeon pea milk and pigeon pea yogurt, determination of short chain fatty acids (SCFA), and in vivo tests carried out on experimental rats.
Keywords	:	Functional Food, Lactic Acid Bacteria, Pigeon Pea (Cajanus cajan L. Millps.), Yogurt.
Publications and Seminars	:	1st international conference on Agriculture (ICoFTA) 2023, Yogyakarta Indonesia October 21st 2023
Email	:	yunisine2588@mail.ugm.ac.id

Zainab

Promotor	:	Prof. Dr. Abdul Rohman, SF., M.Si., Apt.
Co-Promotor 1	:	Respati Tri Swasono, S.Si, M.Phil, Ph.D.
Co-Promotor 2	:	Sari Darmasiwi, S.Si., M.Biotech., Ph.D.
Dissertation Title	:	Secondary Metabolite Profile of The Fingerroot Rhyzome (Boesenbergia pandurata (Roxb.) Schlechter.) As Antioxidant and Antibacterial Using A Chemometric Approach
Abstract	:	The rhizome of fingerroot (Boesenbergia pandurata (Roxb.) Schlechter.) has been known to have antimicrobial, antiviral, anticancer, antioxidant, hepatoprotective activity and has long been used as a cooking spice in the community. The chemical contents contained in the fingerroot rhizome include essential oils, flavonoids, phenolic compounds and prenyl propanoids. This research was conducted with the aim of determining the secondary metabolite profile of fingerroot rhizome as an antioxidant and antibacterial using a chemometric approach. The essential oil of the fingerroot rhizome is extracted by steam and water distillation to obtain the essential oil of the fingerroot rhizome (MATK). Fingerroot rhizome powder was extracted with hexane, ethylacetate and ethanol solvents by maceration to obtain hexane extract (HTK), ethylacetate extract (EaTK) and ethanol extract (EtTK). The secondary metabolite profile of MATK was determined using the GC-MC method while the extract profile (HTK, EaTK, EtTK) used LC-MS and FTIR. Antioxidant activity was carried out using the DPPH, FRAB, ABTS methods and antibacterial tests using the microdilution method and the Kirby Bauer agar diffusion method.
Keywords	:	Fingerroot rhizome, antioxidant, antibacterial, secondary metabolite profile, chemometrics.
Email	:	zainabmsiapt@mail.ugm.ac.id

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