Scientific Journals of Bogor Agricultural University
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Genome-Scale Screening, Characterization, and Expression Analysis of Grain Amaranth Small Auxin-Up RNA Gene Family in Response to Drought Stress
Full text linkThe Small Auxin-Up RNA (SAUR) gene family represents a class of early auxin-responsive genes that are widely involved in regulating plant cell elongation, tissue differentiation, and environmental adaptation. In this study, we performed a genome-wide analysis of the SAUR gene family in grain amaranth (Amaranthus hypochondriacus), a nutrient-rich pseudocereal. A total of 80 SAUR genes were identified based on the conserved PF02519 domain and were systematically characterized in terms of protein properties, gene structure, and phylogenetic relationships. Most SAUR genes in grain amaranth encode small, basic, and hydrophilic proteins, and gene structure analysis revealed that the majority are intronless. Phylogenetic analysis grouped AhSAURs into ten clades alongside Arabidopsis SAURs. Transcriptomic profiling across seven tissues and drought-treated samples showed that although many SAUR genes had low or no expression, several genes, including AhSAUR76, AhSAUR71, AhSAUR65, AhSAUR54, and AhSAUR73, were highly expressed in a tissue-preferential manner and showed responsiveness to drought. These findings highlight the potential regulatory roles of selected SAUR genes in growth and stress adaptation, offering a valuable resource for future genetic and functional studies aimed at enhancing agronomic traits in grain amaranth
A Comparative Study of Penicillin G Acylase Expression in Two Escherichia coli Strains: BL21 (DE3) and Arctic Express
Full text linkThe growing demand for semisynthetic beta-lactams has directed attention towards enzymes, specifically Penicillin G Acylases (PGAs), for their potential in synthesizing these antibiotics. This study delves into the expression of Achromobacter xylosoxidans PGA (AxPGA) in Escherichia coli, with a focus on enhancing the yield of active PGA, often constrained by a complex maturation process. The optimization of PGA expression included variations in IPTG concentration and the addition of CaCl2. Furthermore, the study compared PGA expression in E. coli BL21 (DE3) with that in E. coli Arctic Express (DE3), capable of co-expressing chaperones (chaperonin Cpn60 and Cpn10). Induction with 0.5 mM IPTG resulted in the highest hydrolytic activity in both strains, with Arctic Express (AE) exhibiting significantly higher activity due to improved folding facilitated by cold-adapted chaperonins. Alongside optimal IPTG induction, the addition of 10 mM CaCl2 in the culture media significantly increased PGA activity in both strains, highlighting that Ca2+ supplementation is an effective strategy to enhance the yield of functional PGA. Subcellular fractionation demonstrates that the periplasmic fraction yielded higher volumetric and specific activities compared to the cytoplasmic fractions in both E. coli strains, highlighting the importance of periplasmic processing for PGA maturation. This suggests that extracting the periplasmic fraction is an effective strategy for recovering active PGA while avoiding or reducing contamination either from co-expressed cytoplasmic chaperones or other intracellular proteins. These findings emphasize that induction strategy, ionic stabilization, and host strain selection play synergistic roles in increasing active recombinant PGA expression
Sustainable Urban Farming Rack Design Using Eco Friendly Materials with Variety Load
Full text linkVertical farming requires a structurally sound and environmentally sustainable racking system; however, existing research largely neglects the evaluation of the structural safety of eco-friendly racking materials under various operational loads. This gap necessitates further rigorous mechanical performance assessments to ensure the long-term reliability of the system. This study aims to develop a vertical farming racking design with an adequate safety factor by examining its structural response to various load scenarios. A design-construction methodology supported by SolidWorks simulations was used to evaluate stress distribution, strain behavior, and deformation patterns. Simulation results using SolidWorks software indicate that the maximum compressive stress at the loaded joint surface is 13.734 MPa, while the minimum stress is 1.149 MPa. The highest load occurs at the fourth (bottom) joint level due to pump-induced water pressure. The maximum strain recorded is 0.00491, with a minimum of 0.00041. The top shelf level exhibits a maximum displacement of 48.165 mm, while the minimum displacement is 0 mm. This shows that the material and shape of the frame that has been made are in the safe category with a safety factor (sf) of 2.4. These findings indicate that the proposed rack design maintains structural integrity within safe limits and is suitable for application in vertical farming systems.Vertical farming requires a structurally sound and environmentally sustainable racking system; however, existing research largely neglects the evaluation of the structural safety of eco-friendly racking materials under various operational loads. This gap necessitates further rigorous mechanical performance assessments to ensure the long-term reliability of the system. This study aims to develop a vertical farming racking design with an adequate safety factor by examining its structural response to various load scenarios. A design-construction methodology supported by SolidWorks simulations was used to evaluate stress distribution, strain behavior, and deformation patterns. Simulation results using SolidWorks software indicate that the maximum compressive stress at the loaded joint surface is 13.734 MPa, while the minimum stress is 1.149 MPa. The highest load occurs at the fourth (bottom) joint level due to pump-induced water pressure. The maximum strain recorded is 0.00491, with a minimum of 0.00041. The top shelf level exhibits a maximum displacement of 48.165 mm, while the minimum displacement is 0 mm. This shows that the material and shape of the frame that has been made are in the safe category with a safety factor (sf) of 2.4. These findings indicate that the proposed rack design maintains structural integrity within safe limits and is suitable for application in vertical farming systems
Vannamei shrimp Litopenaeus vannamei mortality correlation with water quality dynamics and blue-green algae in earthen pond
Full text linkMortality represents a significant challenge in enhancing productivity in intensive vannamei shrimp (Litopenaeus vannamei) farming systems. In ponds with soil bottoms, shrimp mortality is often caused by poor water quality, influenced by fluctuations in physicochemical parameters and changes in phytoplankton communities. This study aims to analyze the correlation between water quality, phytoplankton succession, and shrimp mortality. Pond water samples (E9, E10, F9, F10, and F11) were collected periodically to measure key physicochemical parameters, such as temperature, pH, dissolved oxygen (DO), ammonia (NH3), total ammonia nitrogen (TAN), and nitrite (NO2), as well as the abundance and dominance of phytoplankton. The results showed that shrimp mortality positively correlated with plankton abundance (0.57) and the presence of Blue-green Algae (0.43) in the water. Further, descriptively, shrimp mortality followed a similar pattern across several observation ponds, with deaths occurring after the decline or disappearance of Blue-green algae from previous observations. The water quality parameters that correlated with plankton abundance and blue-green algae dominance included TAN, BOD, and turbidity. The transformation in phytoplankton dominance to Blue-green algae can increase BOD levels and produce toxic compounds upon lysis, which may disrupt physiology and lead to shrimp mortality. These results underscore the importance of water quality management and phytoplankton monitoring to reduce vannamei shrimp mortality.
Keywords: Blue-green algae, correlation, earthen pond, Vaname shrimp, water quality
Abstrak
Kematian merupakan tantangan dalam meningkatkan produktivitas pada kegiatan budidaya udang vaname (Litopenaeus vannamei) dengan sistem intensif. Pada kolam budidaya dengan dasar kolam tanah sering kali kematian udang disebabkan oleh kualitas air yang buruk, yang dipengaruhi oleh fluktuasi parameter fisikokimia dan perubahan komunitas fitoplankton. Penelitian ini bertujuan untuk menganalisis korelasi antara kualitas air, suksesi fitoplankton, dan mortalitas Litopenaeus vannamei. Sampel air kolam budidaya (E9, E10, F9, F10 dan F11) diambil secara berkala untuk mengukur parameter fisikokimia utama, seperti suhu, pH, DO, amonia (NH3), TAN dan nitrit (NO2), serta kelimpahan dan dominansi fitoplankton. Hasil penelitian menunjukkan mortalitas udang memiliki nilai korelasi positif dengan kelimpahan pankton (0,57) dan Blue-green Algae (0,43) yang ada pada perairan. Selain itu secara deskriptif kematian udang memiliki pola yang sama pada beberapa kolam pengamatan dimana kematian terjadi setelah terjadinya kematian atau berkurangnya kelimpahan Blue-green Algae dari pengamatan sebelumnya. parameter kualitas air yang memiliki nilai korelasi terhadap kelimpahan plankton dan dominasi Blue-green Algae yaitu TAN, BOD dan Kecerahan. Pergeseran dominansi fitoplankton ke Blue-green algae dapat meningkatkan BOD dan menghasilkan senyawa toksik ketika lisis yang dapat mengganggu fisiologi hingga menyebabkan kematian udang. Temuan ini menekankan pentingnya pengelolaan kualitas air dan pemantauan fitoplankton untuk mengurangi mortalitas udang vaname.
Kata kunci: blue-green algae, korelasi, kolam tanah, kualitas air, udang vanam
Hematology profile of kissing gourami Helostoma temminckii infected with Aeromonas hydrophila bacteria
Full text linkThe kissing gourami (Helostoma temminckii) is an important commodity in aquaculture, but its susceptibility to bacterial infections such as Aeromonas hydrophila can hinder production. This study aims to investigate the hematological profile of kissing gourami (Helostoma temminckii) with an average length of 8.00 ± 1.00 cm and weight of 10.00 ± 1.00 g, following intramuscular injection of Aeromonas hydrophila at a dose of 10⁶ CFU/mL.Evaluations were conducted on survival rate, hematological parameters such as total erythrocytes, total leukocytes, hemoglobin levels, and hematocrit, as well as phagocytic activity, respiratory burst, and lysozyme activity. Infection with A. hydrophila caused a decrease in erythrocytes and hemoglobin, and an increase in leukocytes, phagocytic activity, respiratory burst, and lysozyme activity. The survival rate dropped to 47.5% in the treatment group, while the control group showed 100% survival. The conclusion is, infection of Aeromonas hydrophila significantly affects the immune response of kissing gourami, characterized by an decrease in erythrocyte count and hemoglobin levels in the treatment group. However, phagocytic activity, respiratory burst, and lysozyme levels consistently decreased in infected fish.
Keywords: Aeromonas hydrophila, hematology, kissing gourami, pathogenicity
Abstrak
Ikan tambakan (Helostoma temminckii) merupakan komoditas penting dalam budidaya perikanan, namun kerentanannya terhadap infeksi bakteri seperti Aeromonas hydrophila dapat menghambat produksi. Penelitian ini bertujuan untuk mengkaji profil hematologi ikan tambakan (Helostoma temminckii) dengan panjang rata-rata 8,00 ± 1,00 cm dan bobot 10,00 ± 1,00 g setelah disuntik intramuskular Aeromonas hydrophila dengan dosis 10⁶ CFU/mL. Evaluasi dilakukan terhadap tingkat kelangsungan hidup, parameter hematologi seperti jumlah eritrosit total, leukosit total, kadar hemoglobin, dan hematokrit, serta aktivitas fagositosis, respiratory burst, dan aktivitas lisozim. Infeksi A. hydrophila menyebabkan penurunan jumlah eritrosit dan kadar hemoglobin, serta peningkatan jumlah leukosit, aktivitas fagositosis, respiratory burst, dan aktivitas lisozim. Tingkat kelangsungan hidup menurun menjadi 47,5% pada kelompok perlakuan, sedangkan kelompok kontrol menunjukkan kelangsungan hidup 100%. Kesimpulannya, infeksi Aeromonas hydrophila secara signifikan memengaruhi respons imun ikan kissing gourami, yang ditandai dengan penurunan jumlah eritrosit dan kadar hemoglobin, serta peningkatan aktivitas fagositosis, respiratory burst, dan kadar lisozim pada ikan yang terinfeksi.
Kata kunci: Aeromonas hydrophila, hematologi, ikan tambakan, patogenisita
Kebiasaan Menonton Mukbang dan Perilaku Emotional Eating serta Kaitannya dengan Status Gizi Mahasiswa Universitas PGRI Yogyakarta: Mukbang Video Exposure, Emotional Eating, and Its Relationship with Nutritional Status among University Students
Full text linkMukbang is a video show featuring someone consuming large amounts of food, and it has now become a popular phenomenon among the public, especially young adults. This show has the potential to influence food consumption behaviour and impact nutritional status. Additionally, emotional eating behaviour is known to influence energy intake and nutritional balance in individuals. This study aims to analyse the relationship between the habit of watching mukbang videos and emotional eating behaviour with nutritional status among students at PGRI University Yogyakarta. This study used a quantitative cross-sectional design with 410 active students as respondents. Data were collected using the Mukbang Addiction Scale (MAS) and Dutch Eating Behaviour Questionnaire (DEBQ) distributed. Nutritional status was determined based on body mass index (BMI), and relationship analysis was conducted using Fisher’s Exact test. The results showed that 61.0% of respondents had normal nutritional status, 32.4% were overweight, and 6.6% were underweight. Furthermore, there was a significant association between the habit of watching mukbang videos and nutritional status (p<0.05), as well as between emotional eating behaviour and nutritional status (p<0.05). These findings highlight the importance of education on the influence of food-related content and emotional management as part of efforts to maintain a balanced nutritional status.Mukbang merupakan tayangan video yang menampilkan seseorang mengonsumsi makanan dalam jumlah besar, dan kini menjadi fenomena di kalangan masyarakat, khususnya dewasa muda. Tayangan ini berpotensi memengaruhi perilaku konsumsi makanan dan berdampak pada status gizi. Selain itu, perilaku emotional eating juga diketahui dapat memengaruhi asupan energi dan keseimbangan gizi individu. Penelitian ini bertujuan untuk menganalisis hubungan antara kebiasaan menonton video mukbang dan perilaku emotional eating dengan status gizi pada mahasiswa Universitas PGRI Yogyakarta. Penelitian ini menggunakan desain kuantitatif cross-sectional dengan jumlah responden sebanyak 410 mahasiswa aktif. Data dikumpulkan menggunakan kuesioner Mukbang Addiction Scale (MAS) dan Dutch Eating Behavior Questionnaire (DEBQ) yang disebarkan secara online. Status gizi ditentukan berdasarkan indeks massa tubuh (IMT), dan analisis hubungan dilakukan menggunakan uji Fisher’s Exact. Hasil penelitian menunjukkan bahwa 61,0% responden memiliki status gizi normal, 32,4% berstatus gizi lebih, dan 6,6% berstatus gizi kurang. Terdapat hubungan yang signifikan antara kebiasaan menonton video mukbang dengan status gizi (p<0,05), serta antara perilaku emotional eating dengan status gizi (p<0,05). Temuan ini menunjukkan pentingnya edukasi mengenai pengaruh tayangan makanan dan pengelolaan emosi sebagai bagian dari upaya menjaga status gizi yang seimbang
Detection of quinolone antibiotic resistance genes in Escherichia coli isolated from dairy cattle feces
Full text linkBackground Livestock raised in densely populated areas can serve as reservoirs for bacteria such as Escherichia coli, which may harbor antibiotic resistance genes that threaten both animal and human health.
Objective This study aimed to identify and characterize quinolone resistance genes in E. coli isolated from dairy cattle feces.
Methods Fifteen E. coli isolates were obtained from 15 dairy farms located in Kebon Pedes, Bogor, West Java. Genotypic detection of quinolone resistance genes was conducted using DNA sequencing on the MinION platform.
Results All E. coli isolates (100%) carried at least one quinolone resistance gene. Of these, ten isolates (67%) contained a single resistance gene, while five isolates (33%) possessed two genes. The qnrS1_1 gene was identified in all isolates and represented the predominant genotype, whereas the qnrVC4_1 gene was found in five isolates (33%), mostly co-occurring with qnrS1_1. Both genes are plasmid-mediated and categorized as plasmid-mediated quinolone resistance (PMQR) genes.
Conclusion The detection of qnrS1_1 and qnrVC4_1 genes in E. coli isolated from dairy cattle feces indicates that livestock manure may act as a reservoir for quinolone resistance genes, contributing to their persistence and potential spread within farm environments
Hubungan Frekuensi Kemoterapi dan Kecemasan dengan Asupan Energi-Protein Pasien Kanker Payudara di RS Onkologi Surabaya: The Relationship between Chemotherapy Frequency and Anxiety with Energy-Protein Intake among Breast Cancer Patients at Surabaya Oncology Hospital
Full text linkKemoterapi menjadi salah satu pengobatan bagi pasien kanker. Frekuensi kemoterapi yang tinggi cenderung disertai dengan efek samping yang berat pada pasien kanker, salah satunya penurunan nafsu makan. Kanker dan pengobatannya juga memberikan dampak psikis, salah satunya kecemasan, yang dapat menurunkan nafsu makan pasien kanker. Penelitian ini bermaksud untuk mengetahui gambaran frekuensi kemoterapi, tingkat kecemasan, tingkat asupan energi dan protein, serta menganalisis hubungan frekuensi kemoterapi dan tingkat kecemasan dengan tingkat asupan energi dan protein pada pasien kanker payudara di Rumah Sakit Onkologi Surabaya. Jenis penelitian ini ialah cross-sectional study dengan desain studi observasional analitik. Total sampel berjumlah 52 pasien yang diambil menggunakan metode accidental sampling. Instrumen yang dijadikan alat ukur yaitu kuisioner Generalized Anxiety Disorder 7 dan Semi Quantitative Food Frequency Questionnaires, serta menggunakan data sekunder yakni rekam medis. Penelitian ini menggunakan uji statistik uji Kendall Tau. Temuan penelitian menyatakan sebanyak 63,5% subjek menjalani kemoterapi dengan frekuensi yang tergolong rendah (≤4 siklus), 19,2 % subjek berada dalam kategori cemas (ringan dan sedang), 46,2% subjek memiliki tingkat asupan energi berlebih dan 36,5% subjek memiliki tingkat asupan protein berlebih. Tidak terdapat hubungan antara frekuensi kemoterapi dengan tingkat asupan energi (p=0,409). Tidak terdapat hubungan antara frekuensi kemoterapi dengan tingkat asupan protein (p=0,840). Terdapat hubungan antara tingkat kecemasan dengan tingkat asupan energi (p=0,014, τ=0,255). Tidak terdapat hubungan antara tingkat kecemasan dengan tingkat asupan protein (p=0,242).Chemotherapy is among the treatments for cancer patients. High frequency chemotherapy tends to be followed by severe side effects in cancer patients, one of which is a decrease in appetite. Cancer and its treatment also have a psychological impact, one of which is anxiety, which can reduce the appetite of cancer patients. This research aimed to examine the frequency of chemotherapy, anxiety levels, energy and protein intake levels, and to analyze the relationship between chemotherapy frequency and anxiety levels with energy and protein intake levels in breast cancer patients at Surabaya Oncology Hospital. This research used a cross-sectional study with an analytic observational study design. The total sample amounted to 52 patients selected using accidental sampling method. The instruments used as assessment tools were the Generalized Anxiety Disorder 7 questionnaire and Semi-Quantitative Food Frequency Questionnaires, and secondary data from medical records. The statistical analysis used was Kendall Tau test. The results showed that 63,5% of subject underwent chemotherapy with a low frequency (≤4 cycles), 19,2% of subjects were categorized as anxious (mild and moderate), 46,2% of subjects had excessive energy intake, and 36.5% of subjects had excessive protein intake. There was no relationship between chemotherapy frequency and energy intake level (p=0.409). There was no relationship between the frequency of chemotherapy and protein intake level (p=0.840). There was a relationship between anxiety level and energy intake level (p=0.014, τ=0.255). There was no relationship between anxiety level and protein intake level (p=0.242)
In Vitro Culture of The Natural Orchid Dendrobium spectabile (Blume) Miq. and The Characteristics of its Fragment 700 bp of the HOMEOBOX Homologous Gene
Full text linkD. spectabile is an orchid species endemic to Papua, which has the characteristic of sepals, petals, and a curly labellum, which is very attractive, so it needs to be preserved. Propagation of this plant with in vitro culture techniques promises plant propagation in large quantities and uniformly in a short time. In plants, the HOMEOBOX gene is recognized as a key regulator of gene transcription, playing a crucial role in plant organogenesis, particularly in the shoot apical meristem. This study aims to identify the optimal in vitro culture media for D. spectabile and to conduct molecular analysis of the HOMEOBOX gene. The methods used are: subculture, amplification, motif location analysis, physicochemical characterization, phylogenetic construction, and 2D protein sequence modeling. The results of the study showed that the subculture of D. spectabile on KC+IAA 20 µM media (20.67±1.76) significantly increased shoot growth. PCR with POH1 primer successfully amplified a 700 bp HOMEOBOX fragment containing 2 motifs: ELK, involved in protein-to-protein interactions, and Homeobox-KN, a transcriptional regulator. Phylogenetic analysis showed a close evolutionary relationship between D. spectabile and D. catenatum. Further studies are needed to obtain the complete sequence for functional validation in D. spectabile.
The Effect of Stevia (Stevia rebaudiana Bertoni) Leaf Extract Cream on Transforming Growth Factor-β1 Levels and Collagen Amount in the Skin of Male Wistar Rats (Rattus norvegicus) Exposed to Ultraviolet B
Full text linkUltraviolet B (UVB) exposure is a major cause of skin aging, leading to collagen degradation and wrinkles due to free radical damage. Stevia (Stevia rebaudiana Bertoni) has antioxidant properties that may counteract this by preserving Transforming Growth Factor-β1 (TGF-β1), essential for collagen synthesis. This study evaluated the effects of stevia leaf extract cream on TGF-β1 and collagen levels in male Wistar rats. Thirty rats were divided into five groups: K0 (no UVB, no cream), K1 (base cream), P1 (2.5% stevia cream), P2 (5% stevia cream), and P3 (10% stevia cream). Groups K1, P1, P2, and P3 were exposed to a cumulative UVB exposure of 840 mJ/cm2 over four weeks. However, TGF-β1 levels measured by ELISA did not differ significantly among groups (p>0.05). However, collagen levels, assessed using Picro Sirius Red staining, varied significantly (p<0.05). The K1 exhibited significantly lower collagen compared to K0 (p=0.003), whereas the P2 group effectively prevented collagen degradation compared to K1 (K1: 65.87% vs. P2: 77.92%; p = 0.005). While stevia leaf extract cream did not prevent TGF-β1 reduction, it demonstrated a clear protective effect against UVB-induced collagen loss. Among the tested concentrations, 5% stevia leaf extract cream was the most effective in preserving dermal Collagen, highlighting its potential as a topical agent for preventing photoaging and maintaining skin structural integrity