Herjuno Ari Nugroho | Indonesian Institute of Sciences (original) (raw)

Papers by Herjuno Ari Nugroho

Veterinary World, Mar 24, 2021

Background and Aim: Baung fish is an essential commodity in Indonesia; however, few studies have ... more Background and Aim: Baung fish is an essential commodity in Indonesia; however, few studies have explored the genetic diversity of Indonesian catfish. Thus, this study aimed to analyze the genetic variation and phylogenetic relationships among Indonesian catfish based on the mitochondrial 12S ribosomal RNA (rRNA) gene. Materials and Methods: In total, 28 catfish were collected from nine rivers in seven provinces and from the Indian Ocean. Catfish genomes were obtained from epaxial and hepaxial muscle samples. The mitochondrial 12S rRNA gene was amplified by polymerase chain reaction using a pair of primers (Baung12SF and Baung12SR). The 12S rRNA sequences were analyzed using MEGA X to determine genetic variation and phylogenetic relationships. Results: In total, 178 variation sites in the 12S rRNA gene were substituted among Indonesian catfish. The genetic distance between all Indonesian catfish samples was 0.1-16.0%. The closest genetic distance was between MP and PM catfish, whereas the farthest genetic distances were between BF and EM and PD and EM. For the entire population, based on mean diversity calculations, the number of base substitutions per site was 0.08. Conclusion: Indonesian catfish were divided into four clades based on the 12S rRNA gene. The catfish MP, KR, PM, MS, BB, and KS were grouped with Hemibagrus nemurus, the catfish EM was grouped with Mystus vittatus, the catfish BSBJ was grouped with Pangasius pangasius, and the catfish PD and BF were grouped with Netuma thalassina.

Open veterinary journal, 2023

Background: Fasciolosis is a parasitic disease affecting the hepatobiliary system of livestock wo... more Background: Fasciolosis is a parasitic disease affecting the hepatobiliary system of livestock worldwide. The control of the fluke is important to be performed in endemic regions. Aim: This study aims to evaluate the effect of Etlingera elatior ethanolic extract on egg and adult stadia of Fasciola gigantica. Methods: F. gigantica in different stages were incubated with Etlingera elatior ethanolic extract in different concentrations and time points. Results: The number of developed eggs with different concentrations of 1.25%, 2.5%, and 5% was significantly decreased by 36.67, 56.67%, and 56.67% on day 11 post-incubation, which showed an ovicidal effect of the herb. The developed eggs on day 14, which was represented by hatched larvae, were also decreased by 70%, 50%, and 13.33%, respectively. Significant flukicidal effects were observed in the incubation time of 80 minutes for the concentration of 20% (P= 0.007) and 640 minutes for 10% concentration (P= 0.003). Surface microscopy of adult F. gigantica showed damaged skin and spina with the erosion of the inner membrane and detached syncytium from the tegument. Conclusion: Overall, the results indicate that E. elatior has a promising anthelmintic property against F. gigantica in both ova and adult stages.

Veterinary World

Background and Aim: Fasciolosis due to Fasciola gigantica is endemic to tropical countries and Fa... more Background and Aim: Fasciolosis due to Fasciola gigantica is endemic to tropical countries and Fasciola hepatica in temperate climates, highly detrimental to livestock and known as foodborne zoonotic diseases. The strategic control of the disease is mainly the use of chemical anthelmintic. This study aimed to evaluate the anthelmintic properties of Artemisia vulgaris extract on the ova and adult stages of F. gigantica. Materials and Methods: Samples were collected from the Ampel Abbatoir, Boyolali District, Central Java, Indonesia. The ova from 20-gallbladders of cattle which were naturally infected with F. gigantica and 270 living F. gigantica worms were used in this study. The ovicidal assay was performed by incubating the ova with A. vulgaris in different concentrations, that is, 5%, 2.5%, and 1.25% for 5, 9, 11, 14, and 16 days. The efficacies were evaluated by quantification of ova degeneration during developmental stages in different time points and egg-hatch assay. The flukic...

Biodiversitas Journal of Biological Diversity

Detecting fish product adulteration is crucial to ensure food safety since pleco meat was already... more Detecting fish product adulteration is crucial to ensure food safety since pleco meat was already reported to carry several heavy metals that might harm human health. Pleco is invasive species in the Ciliwung River and is commonly used as adulteration material for fish-based products. Adulteration in mackerel-based food products may alter the nutritional value and carry heavy metal contamination from the bottomfeeder fish's meat (pleco). Therefore, using the DNA barcoding technique, a molecular approach has been used to authenticate mackerel fish products (including dumplings and otak-otak). This study aimed to develop a specific multiplex PCR method for simultaneously detecting processed products from mackerel and pleco. The sample consists of 21 processed food items initially made from mackerel. The samples were taken in the selected area around the Ciliwung River. All the samples can be amplified successfully, and amplification lengths were 108, 171, and 300 bp, respectively. Analysis from various claimed mackerel products showed that five samples were positive for pleco adulteration, and 11 products contained chicken meat addition. The phylogenetic tree was constructed from selected sequences from our samples and showed that the amplicons were clustered in three clades, mackerel (Scomberomorus), pleco (Pterygoplichthys), and chicken (Gallus gallus Linnaeus, 1758). The findings of this study revealed that 23.80% (5/21) products contained pleco, and 52.38% (11/21) contained chicken meat addition. The addition of an unusual component to food composition may alter nutritional value as well as may affect food hygiene and safety.

PeerJ, 2022

Background Indonesia is one of the Southeast Asian countries with high case numbers of COVID-19 w... more Background Indonesia is one of the Southeast Asian countries with high case numbers of COVID-19 with up to 4.2 million confirmed cases by 29 October 2021. Understanding the genome of SARS-CoV-2 is crucial for delivering public health intervention as certain variants may have different attributes that can potentially affect their transmissibility, as well as the performance of diagnostics, vaccines, and therapeutics. Objectives We aimed to investigate the dynamics of circulating SARS-CoV-2 variants over a 15-month period in Bogor and its surrounding areas in correlation with the first and second wave of COVID-19 in Indonesia. Methods Nasopharyngeal and oropharyngeal swab samples collected from suspected patients from Bogor, Jakarta and Tangerang were confirmed for SARS-CoV-2 infection with RT-PCR. RNA samples of those confirmed patients were subjected to whole genome sequencing using the ARTIC Network protocol and sequencer platform from Oxford Nanopore Technologies (ONT). Results We...

Zoo Indonesia, Jun 8, 2016

Penentuan jenis kelamin pada burung monomorfik seperti Nuri Kepala Hitam (Lorius lory) kadang sul... more Penentuan jenis kelamin pada burung monomorfik seperti Nuri Kepala Hitam (Lorius lory) kadang sulit dilakukan, meskipun hal itu penting dalam program penangkaran. Tujuan dari studi ini untuk mengevaluasi reliabilitas dan efektifitas metode penentuan jenis kelamin untuk Nuri Kepala Hitam berdasarkan pengukuran karakter morfologi (morfometri) dan identifikasi molekuler menggunakan gen CHD1 dari kromosom seks. Analisis diskriminan diterapkan pada ukuran panjang tubuh dan culmen dari 9 spesimen museum. Fungsi yang terbentuk diaplikasikan pada 6 ekor burung hidup dan mampu mengklasifikasikan dengan benar 83,33% individu (5/6). Amplifikasi gen CHD1 mampu menentukan 100% sampel (6/6) dengan jantan menunjukkan pita DNA tunggal (ZZ) dan betina menunjukkan pita DNA ganda (ZW). Berdasarkan evaluasi kedua metode, metode molekular lebih akurat dan aplikatif digunakan untuk determinasi seksual Nuri Kepala Hitam dengan jumlah sampel kecil dibandingkan dengan metode morfometri, akan tetapi melalui metode morfometri akan diperoleh karakter morfologi pembeda antara kedua jenis kelamin. Penelitian ini menganjurkan bahwa teknik molekuler dapat digunakan dalam determinasi kelamin burung monomorfik.

Determining an individual sex is often difficult in monomorphic birds like Black Caped Lory (Lori... more Determining an individual sex is often difficult in monomorphic birds like Black Caped Lory (Lorius lory), even though it is important for captive breeding program. The objective of this study was to evaluate the reliability and effectivity of sex identification method for Black Caped Lory based on morphological measurement (morphometric) and molecular identification using CHD1 genes of sex chromosomes. Discriminant analysis was performed on total body length and culmen measurements from 9 museum specimens. The created function was applied for 6 live birds and showed correctly classified 83,33% individuals (5/6). The amplification of CHD1 genes determined 100% samples (6/6) with male showed a single DNA band (ZZ) and female showed double DNA bands (ZW). Based on comparison and evaluation between two methods, molecular method was more accurate and applicable to determine the sex of Black Caped Lory with small sample size compared with morphometric method, but from morphometric method...

Veterinary World, 2019

Background and Aim: Many avian species are considered sexually monomorphic. In monomorphic bird s... more Background and Aim: Many avian species are considered sexually monomorphic. In monomorphic bird species, especially in young birds, sex is difficult to identify based on an analysis of their external morphology. Accurate sex identification is essential for avian captive breeding and evolutionary studies. Methods with varying degrees of invasiveness such as vent sexing, laparoscopic surgery, steroid sexing, and chromosome inspection (karyotyping) are used for sex identification in monomorphic birds. This study aimed to assess the utility of a non-invasive molecular marker for gender identification in a variety of captive monomorphic birds, as a strategy for conservation. Materials and Methods: DNA was isolated from feather samples from 52 individuals representing 16 species of 11 families indigenous to both Indonesia and elsewhere. We amplified the chromodomain helicase DNA-binding (CHD) gene using polymerase chain reaction with MP, NP, and PF primers to amplify introns with lengths ...

Journal of Coastal Life Medicine, 2016

Parasitic nematodes of amphibians from Lombok Island, Indonesia with description of Camallanus se... more Parasitic nematodes of amphibians from Lombok Island, Indonesia with description of Camallanus senaruensis sp. nov. and Meteterakis lombokensis sp. nov.

Pemeriksaan parasit dilakukan secara berkala di fasilitas konservasi eksitu seperti penangkaran u... more Pemeriksaan parasit dilakukan secara berkala di fasilitas konservasi eksitu seperti penangkaran untuk mengetahui keragaman parasit, angka kejadian penyakit dan derajat infeksinya. Informasi tersebut dapat digunakan sebagai referensi dalam penentuan kebijakan medik seperti pencegahan dan penanggulangan penyakit pada satwa penangkaran. Pemeriksaan parasit gastrointestinal dilakukan di fasilitas penangkaran mamalia Pusat Penelitian Biologi LIPI, Cibinong, Jawa Barat dengan menggunakan sampel feses dari 26 ekor landak jawa (Hystrix javanica), 4 ekor kukang jawa (Nycticebus javanicus), 4 ekor kukang sumatera (Nycticebus coucang), 2 ekor jelarang (Ratufa bicolor) dan satu ekor bajing tiga warna (Callosciurrus prevostii). Pemeriksaan feses dilakukan dengan metode natif dengan tiga kali pengulangan. Bedah bangkai dilakukan pada dua ekor kukang sumatera yang telah mati sebelumnya untuk menyidik sebab kematian dan koleksi parasit internal. Parasit yang ditemukan selanjutnya diidentifikasi. Hasil pemeriksaan feses menunjukkan bahwa landak jawa terinfeksi Gireterakis girardi dengan prevalensi 19,23% (5/26) dan Trichuris landak dengan prevalensi 3,85% (1/26). Sementara pada hewan lain tidak ditemukan telur maupun larva pada feses. Pada bedah bangkai kedua kukang sumatera, ditemukan adanya infeksi Pterygodermatites nycticebii di organ intestinum tenue dan intestinum crassum. Berdasarkan hasil pemeriksaan, parasit yang ditemukan berasal dari alam liar sehingga perlu dilakukan tindakan karantina sebelum hewan masuk fasilitas dan terapi deworming untuk nematoda

Jurnal Saintifika Gadjah …, 2011

Summary/Kata Kunci: Tarsius merupakan jenis primata Indonesia yang terancam akan kepunahan. Upaya... more Summary/Kata Kunci: Tarsius merupakan jenis primata Indonesia yang terancam akan kepunahan. Upaya konservasi secara insitu dan exsitu pada satwa ini akan lebih terarah dan berhasil guna apabila keragaman genetiknya diketahui secara pasti. Tujuan ...

Hewan peliharaan eksotik seperti baning cokelat (Manouria emys) dan baning Sulawesi (Indotestudo ... more Hewan peliharaan eksotik seperti baning cokelat (Manouria emys) dan baning Sulawesi (Indotestudo forstenii) tidak lepas dari ancaman penyakit infeksi nematoda parasit gastrointestinal. Tujuan dari kajian ini adalah untuk mendeskripsikan nematoda beserta sifat patogenitas parasit yang ditemukan pada pemeriksaan bangkai M. emys dan I. forstenii. Bangkai kura-kura dinekropsi dan perubahan patologis yang ditemukan didokumentasikan. Nematoda dikoleksi dan dipreservasi dalam alkohol 70%. Nematoda diamati dengan mikroskop cahaya dan mikroskop elektron. Organ yang diduga mengalami perubahan patologis (sekum) dilakukan pengambilan dua sampel untuk proses pembuatan preparat histopatologi guna melihat struktur mikro jaringan terinfeksi dan mikroskop elektron guna melihat struktur ultra jaringan terinfeksi. Berdasarkan hasil pemeriksaan parasit, ditemukan nematoda Cissophyllus sp. sebanyak 318 individu dan Tonaudia sp. sebanyak enam individu pada sekum M. emys. Pada I. forstenii, empat individu Spironoura sp. dikoleksi dari organ intestinum. Berdasarkan hasil pemeriksaan histopatologi serta pemeriksaan mikroskop elektron pada organ sekum M. emys ditemukan adanya potongan cacing dan peradangan pada tunika submukosa dan muskularis. Morfologi kompleks mulut Cissophyllus sp. dan Tonaudia sp. diduga berkontribusi pada perubahan patologis dan menyebabkan peradangan pada sekum M. emys. Perubahan patologis yang ditemukan menunjukkan bahwa nematoda parasit Cissophyllus dan Tonaudia sp. memiliki sifat patogenitas untuk hospes M. emys. Kajian lebih lanjut perlu dilakukan untuk melihat patogenesis infeksi jenis-jenis nematoda tersebut.

Journal of Venomous Animals and Toxins including Tropical Diseases

Background: Several studies have been published on the characterization of Trimeresurus venoms. H... more Background: Several studies have been published on the characterization of Trimeresurus venoms. However, there is still limited information concerning the venom composition of Trimeresurus species distributed throughout Indonesia, which contributes to significant snakebite envenomation cases. The present study describes a comparative on the composition of T. albolabris, T. insularis, T. puniceus, and T. purpureomaculatus venoms originated from Indonesia. Methods: Protein content in the venom of four Trimeresurus species was determined using Bradford assay, and the venom proteome was elucidated using one-dimension SDS PAGE nano-ESI-LCMS/MS shotgun proteomics. Results: The venom of T. albolabris contained the highest protein content of 11.1 mg/mL, followed by T. puniceus, T. insularis and T. purpureomaculatus venom with 10.7 mg/mL, 8.9 mg/mL and 5.54 mg/mL protein, respectively. In total, our venomic analysis identified 65 proteins belonging to 16 protein families in T. purpureomaculatus; 64 proteins belonging to 18 protein families in T. albolabris; 58 different proteins belonging to 14 protein families in T. puniceus; and 48 different proteins belonging to 14 protein families in T. insularis. Four major proteins identified in all venoms belonged to snake venom metalloproteinase, C-type lectin, snake venom serine protease, and phospholipase A2. There were 11 common proteins in all venoms, and T. puniceus venom has the highest number of unique proteins compared to the other three venoms. Cluster analysis of the proteins and venoms showed that T. puniceus venom has the most distinct venom composition. Conclusion: Overall, the results highlighted venom compositional variation of four Trimeresurus spp. from Indonesia. The venoms appear to be highly similar, comprising at least four protein families that correlate with venom's toxin properties and function. This study adds more information on venom variability among Trimeresurus species within the close geographic origin and may contribute to the development of optimum heterologous antivenom.

Universitas Gadjah Mada, 2019

Journal of Biomedical Informatics, Jul 24, 2019

Zoo Indonesia, Mar 9, 2018

Penelitian ini bertujuan untuk mempelajari khasiat afrodisiak ekstrak etanol dari daging ekor lan... more Penelitian ini bertujuan untuk mempelajari khasiat afrodisiak ekstrak etanol dari daging ekor landak (Hystrix javanica F. Cuvier, 1823) yang oleh masyarakat di Jawa (Indonesia) diyakini dapat meningkatkan vitalitas dan kinerja seksual pria. Satu jam setelah pemberian ekstrak dan bahan kontrol, dua puluh mencit jantan yang belum berpengalaman secara seksualdibagi secara acak ke dalam empat kelompok dan dipasangkan dengan mencit betina. Mencit jantan diberikan ekstrak etanol dalam dua dosis; 150 dan 750 mg/kg BB (p.o). Sebagai kontrol positif digunakan sildenafil citrate 5 mg/kg dan 5% Tween 80 sebagai control negatif. Selama pengamatan terlihat adanya parameter perilaku seksual seperti mounting dan intromisi. Mencit jantan yang diberi ekstrak etanol pada dosis 750 mg/kg menunjukkan frekuensi mounting dan intromission yang lebih tinggi dibandingkan ekstrak etanol 150 mg/kg dan setelah 2 jam kelompok ini menunjukkan frekuensi yang tertinggi. Namun, ekstrak etanol pada kedua dosis tersebut belum dapat menurunkan waktu latensi mounting dan intromission serendah Kontrol positif.Temuan ini merupakan bukti awal mengenai khasiat afrodisiak ekstrak etanol daging ekor landak.

Biodiversitas Journal of Biological Diversity, 2022

BIO Web of Conferences, 2021

The Androgen Receptor (AR) Gene’s expression is essential during puberty and testes maturation, w... more The Androgen Receptor (AR) Gene’s expression is essential during puberty and testes maturation, which is also used as a reference for Turkey’s breeding program. Therefore, this study aims to develop and optimize two primer sets for studying relative expression using qPCR technology. The primers were designed to amplify specific regions in the AR gene as the main target, and the β-actin gene as an internal control. They were tested using in-silico and amplicon sequencing, as well as efficiency calculation with a constructed standard curve from serially diluted reactions. Based on the sequencing methods, the primers amplified the corresponding regions of the respective targets. The primer for AR gene had an efficiency of 98.03%, a slope of -3.37, and an R2 of 0.995, while that of the β-actin gene had an efficiency of 98.01%, a slope of -3.371, and an R2 of 0.999. The two efficiencies exceeded the standard (93 -103%) value and the melting curve analysis showed that no non-specific ampl...

In order to nutritional needs of the sugar glider ( Petaurus breviceps ) in captivity, it has bee... more In order to nutritional needs of the sugar glider ( Petaurus breviceps ) in captivity, it has been given a Leadbeater modified feed and insects (superworm and crickets) as a natural food. The average feed intake of Leadbeater and fruits juice was 27.5 grams per head and superworm/crickets were 4 pieces per head per week. The nutritional content of feed modification Leadbeater 19% protein; 8.8% fat; 3.5% Ca; and 0.5% P. Each pairs of sugar glider placed in wire cages (60 cm x 40 cm x 40 cm) in order to facilitate the monitoring of reproduction. The mean increase in young birth of sugar gliders from March to October 2015 was 4.75 head per month. The bonding process is done since young sugar glider aged 2 months, in order to obtain young sugar glider as a product of pet animals

Journal of Biogeography, 2017

The aims of the research was to analyze nutrient requirements, performance, and feed efficiency o... more The aims of the research was to analyze nutrient requirements, performance, and feed efficiency of porridge formulation on sugar gliders (Petaurus breviceps) based on daily feed intake and digestibility. The research was conducted at the Small Mammal Captivity of Zoology Division, Research Center for Biology, Indonesian Institute of Sciences (LIPI) Cibinong, Bogor. Descriptive method was used in this experiment, with 14 days of preliminary period and 70 days (10 weeks) of data collection. The research materials were 16 sugar gliders aged about 3-5 months and randomly divided into 2 treatments ie. 8 heads were given porridge formulation I (P0 - control treatment) and 8 heads were given porridge formulation II (PI) plus superworm 2 times a week. Estimation of feed digestibility done in vivo with the method of the feces total collection. Variables of this experiment are daily feed intake, nutrient requirement, total digestible nutrients (TDN), daily weight gain, and feed efficiency. Th...