1.Decreasingα-synuclein aggregation by methanolic extract of Centella asiatica in zebraifsh Parkinson’s model
Khotimah Husnul ; Ali Mulyohadi ; Sumitro Bambang Sutiman ; Widodo Aris Mochamad
Asian Pacific Journal of Tropical Biomedicine 2015;(11):898-904
Objective:To observe the effects of Centella asiatica (C. asiatica) methanolic extract onα-synuclein aggregation and its expression in rotenone-exposed zebrafish.
Methods: Zebrafish (Danio rerio) were exposed to 5 μg/L rotenone for 28 days and co-incubated with 2.5, 5.0 and 10.0 μg/mL of C. asiatica methanolic extract. The medium was changed every 48 h for maintain the concentration of rotenone and extract. After 28 days zebrafish were sacrificed on the ice block and protein was isolated from zebrafish brain for ELISA of dopamine and Western blotting of α-synuclein. Immunohistochemistry was conducted to observe the α-synuclein expressions from histopathological preparation of zebrafish brain. The head were soaked in 10%formaline for less than 24 h and embedded onto paraffin block, then sliced for immunohistochemistry using antiα-synuclein antibody. We also measured zebrafish motility for 5 min in each week.
Results:C. asiatica has important bioactive compounds such as asiaticoside that has anti-inflammatory and antioxidant properties. It may inhibit cascade reaction due to oxidative stress induced by rotenone. Decreasing reactive oxygen species proposed probability of radical attack toα-synuclein protein that caused aggregation and increase of its expression. The motility of zebrafish was also maintained in C. asiatica groups due to the increasing dopamine level in rotenone-induced zebrafish. High level of reactive oxygen species inactivated enzyme for dopamine synthesis such as tyrosine hydroxylase, and oxidized dopamine itself. Oxidized dopamine increasedα-synuclein aggregation. Thus, the dopamine level decreased in rotenone-induced zebrafish, but C. asiatica increased dopamine level.
Conclusions: C. asiatica has a potential to be developed as an anti-Parkinson's disease treatment due to its capability for minimized the sign of Parkinson’s such asα-synuclein aggregation and expression, increasing motility and dopamine as well.
2.Plasma CRH Level Difference Between Wistar Rats Exposed To Acute Stress Due To Predator And To The Psychological Stress Device
B Handoko Daeng ; Analis Wisnu Wardhana ; Aris Widodo ; Hidayat Sujuti ; Karyono Mintaroem ; Edi Widjajanto
ASEAN Journal of Psychiatry 2015;16(2):1-10
Objective: Stress triggers and causes psychiatric disorders. This study compared
stress generated by different stressors: a cat as the predator of rats and a
Psychological Stress Device (PSD) which was developed and modified by the
researchers based on the model by Xu and Rocher. Methods: Twenty-eight
Wistar rats were simple randomly divided into one control group and six
treatment groups, each consisting of 4 rats. Each treatment group was
individually exposed to stressor for 30, 60, and 90 minutes. The first three
treatment groups were treated using the PSD while the other three treatment
groups were treated exposed to the cat. Plasma CRH level was measured using
the ELISA (Cusabio) method. Result: Plasma CRH levels in the rat exposed to
stressor using the PSD ranged from 9.89 to 50.22 ng/mL, higher than plasma
CRH level in the groups exposed to cat ranged from 0.22 to 23.44 ng/mL with
significance level (p<0,05). The average of plasma CRH level in the rats exposed
to the PSD for 30, 60, and 90 minutes were 14.83, 28.19, and 36 respectively. 14
ng/mL while in the groups exposed to cats were 11.53, 7.81, and 4.97 ng/mL
respectively. The increase of plasma CRH level had positive correlation with the
length of exposure to stressor in the group treated with the PSD (r=0.895, p of
<0.05) while plasma CRH level in the group exposed to cat did not correlate with
the length of exposure (r=-0.043, p>0.05). Conclusion: Plasma CRH level of the
rats exposed to stressor using the PSD was higher and positively correlate with
the length of exposure compared to those exposed to cat.
3.In silico molecular analysis of novel L-specific dehalogenase from Rhizobium sp. RC1
Azza Hanif Harisna ; Mohamed Faraj Edbeib ; Aliyu Adamu ; Azzmer Azzar Abdul Hamid ; Roswanira Abdul Wahab ; Widodo ; Fahrul Huyop
Malaysian Journal of Microbiology 2017;13(1):xx-xx
Aims: This study presents the first structural model and proposed the identity of four important key amino acid residues,
Asp13, Arg51, Ser131 and Asp207 for the stereospecific haloalkanoic acid dehalogenase from Rhizobium sp. RC1.
Methodology and results: The enzyme was built using a homology modeling technique; the structure of crystallized LDEX
YL from Pseudomonas sp. strain YL as a template. Model validation was performed using PROCHECK to generate
the Ramachandran plot. The results showed 80.4% of its residues were located in the most favoured regions suggested
that the model is acceptable. Molecular dynamics simulation of the model protein was performed in water for 10
nanoseconds in which Na+ was added to neutralize the negative charge and achieved energy minimization. The energy
value and RMSD fluctuation of Cα backbone of the model were computed and confirmed the stability of the model
protein.
Conclusion, significance and impact of study: In silico or computationally based function prediction is important to
complement with future empirical approaches. L-haloacid dehalogenase (DehL), previously isolated from Rhizobium sp.
RC1 was known to degrade halogenated environmental pollutants. However, its structure and functions are still
unknown. This structural information of DehL provides insights for future work in the rational design of stereospecific
haloalkanoic acid dehalogenases.
4.Frey’s Procedure for Chronic Pancreatitis in an Adolescent with Recurrent Upper Gastrointestinal Bleeding: A Case Report
Adianto NUGROHO ; Ariani Dewi WIDODO ; Indah JAMTANI ; Asri Dwi RACHMAWATI
Korean Journal of Pancreas and Biliary Tract 2022;27(4):164-167
Chronic fibroinflammatory pancreatitis causes irreparable damage to the pancreatic parenchyma. This frequently results in food restrictions, painkiller addiction, and serious quality of life impairment in children. We observed a 13-year-old girl who had previously been hospitalized multiple times and had undergone acute pancreatitis arrived with excruciating abdominal pain and recurrent hematemesis. A chronic intra-pseudocyst bleed and an ampulla of Vater hemorrhage were discovered during an upper gastrointestinal endoscopy. A 3×2×1 cm pancreatic head pseudocyst was discovered on the magnetic resonance cholangiopancreatography, however the computed tomography scan revealed a pancreatic head pseudocyst, pancreatic duct stones, and substantial peripancreatic inflammation. The multidisciplinary team determined that Frey’s surgery was the most efficient method to minimize her suffering. No complications occurred during the healing phase following surgery, and two years later, neither recurrence bleeding nor abdominal pain appeared. In summary, Frey’s method is a secure and efficient intervention when applied by a multidisciplinary team.
5.Pseudomonas aeruginosa in Chronic Suppurative Otitis Media
Artono ARTONO ; Nyilo PURNAMI ; Edi HANDOKO ; Agung Dwi Wahyu WIDODO ; Juniastuti JUNIASTUTI
Infection and Chemotherapy 2025;57(1):63-71
Background:
Chronic suppurative otitis media (CSOM) has caused many hearing disorder cases in developing countries.Inappropriate antibiotic use resulted in a shift of bacterial resistance. The biofilm-forming bacteria, like Pseudomonas aeruginosa, was a common germ detected in CSOM that contributed to a poor prognosis. This study aimed to investigate the bacterial pattern from samples taken from CSOM patients regarding its antibiotic susceptibility and the antibiofilm activity of acetic acid against P. aeruginosa.
Materials and Methods:
Sterile swabs of forty-five patients with CSOM were collected, followed by isolation of bacterial pathogens, identification, and evaluation of antibiotic sensitivity using modified Kirby Bauer disc diffusion protocol. In vitro testing was done by adding acetic acid to P. aeruginosa culture to gauge the minimum concentration of biofilm inhibition and eradication. They were conducted using the microtiter plate assay method and quantified with an ELISA reader. The data were analyzed statistically using One-Way ANOVA and Tukey Honestly Significant Difference post hoc test.
Results:
The samples obtained from 31 of 45 CSOM patients showed positive microbial growth; 26 (57.78%) had a monomicrobial pattern, and 5 (11.11%) had a polymicrobial pattern. The researcher ascertained that 24 isolates, representing 66.67%, were gram-negative bacteria, with P.-aeruginosa identified as the predominant species.P. aeruginosa isolates were sensitive to several antibiotics, including meropenem, amikacin, piperacillin-tazobactam, ceftazidime, and cefoperazone-sulbactam with a rate of 93.33%. The minimum concentration of acetic acid required to qualify as the minimum biofilm inhibitory concentration (MBIC) was determined to be 0.16%, yielding an inhibition rate of 26.79%. A concentration of 0.31% was identified as the minimum biofilm eradication concentration (MBEC), achieving an eradication rate of 77.27%.
Conclusion
P. aeruginosa, the most common bacteria found in CSOM samples, was sensitive to imipenem, amikacin, piperacillin-tazobactam, ceftazidime, and cefoperazone-sulbactam. Acetic acid suppresses P. aeruginosa bacterial biofilm formation at MBIC of 0.16% and MBEC of 0.31%.
6.Pseudomonas aeruginosa in Chronic Suppurative Otitis Media
Artono ARTONO ; Nyilo PURNAMI ; Edi HANDOKO ; Agung Dwi Wahyu WIDODO ; Juniastuti JUNIASTUTI
Infection and Chemotherapy 2025;57(1):63-71
Background:
Chronic suppurative otitis media (CSOM) has caused many hearing disorder cases in developing countries.Inappropriate antibiotic use resulted in a shift of bacterial resistance. The biofilm-forming bacteria, like Pseudomonas aeruginosa, was a common germ detected in CSOM that contributed to a poor prognosis. This study aimed to investigate the bacterial pattern from samples taken from CSOM patients regarding its antibiotic susceptibility and the antibiofilm activity of acetic acid against P. aeruginosa.
Materials and Methods:
Sterile swabs of forty-five patients with CSOM were collected, followed by isolation of bacterial pathogens, identification, and evaluation of antibiotic sensitivity using modified Kirby Bauer disc diffusion protocol. In vitro testing was done by adding acetic acid to P. aeruginosa culture to gauge the minimum concentration of biofilm inhibition and eradication. They were conducted using the microtiter plate assay method and quantified with an ELISA reader. The data were analyzed statistically using One-Way ANOVA and Tukey Honestly Significant Difference post hoc test.
Results:
The samples obtained from 31 of 45 CSOM patients showed positive microbial growth; 26 (57.78%) had a monomicrobial pattern, and 5 (11.11%) had a polymicrobial pattern. The researcher ascertained that 24 isolates, representing 66.67%, were gram-negative bacteria, with P.-aeruginosa identified as the predominant species.P. aeruginosa isolates were sensitive to several antibiotics, including meropenem, amikacin, piperacillin-tazobactam, ceftazidime, and cefoperazone-sulbactam with a rate of 93.33%. The minimum concentration of acetic acid required to qualify as the minimum biofilm inhibitory concentration (MBIC) was determined to be 0.16%, yielding an inhibition rate of 26.79%. A concentration of 0.31% was identified as the minimum biofilm eradication concentration (MBEC), achieving an eradication rate of 77.27%.
Conclusion
P. aeruginosa, the most common bacteria found in CSOM samples, was sensitive to imipenem, amikacin, piperacillin-tazobactam, ceftazidime, and cefoperazone-sulbactam. Acetic acid suppresses P. aeruginosa bacterial biofilm formation at MBIC of 0.16% and MBEC of 0.31%.
7.Pseudomonas aeruginosa in Chronic Suppurative Otitis Media
Artono ARTONO ; Nyilo PURNAMI ; Edi HANDOKO ; Agung Dwi Wahyu WIDODO ; Juniastuti JUNIASTUTI
Infection and Chemotherapy 2025;57(1):63-71
Background:
Chronic suppurative otitis media (CSOM) has caused many hearing disorder cases in developing countries.Inappropriate antibiotic use resulted in a shift of bacterial resistance. The biofilm-forming bacteria, like Pseudomonas aeruginosa, was a common germ detected in CSOM that contributed to a poor prognosis. This study aimed to investigate the bacterial pattern from samples taken from CSOM patients regarding its antibiotic susceptibility and the antibiofilm activity of acetic acid against P. aeruginosa.
Materials and Methods:
Sterile swabs of forty-five patients with CSOM were collected, followed by isolation of bacterial pathogens, identification, and evaluation of antibiotic sensitivity using modified Kirby Bauer disc diffusion protocol. In vitro testing was done by adding acetic acid to P. aeruginosa culture to gauge the minimum concentration of biofilm inhibition and eradication. They were conducted using the microtiter plate assay method and quantified with an ELISA reader. The data were analyzed statistically using One-Way ANOVA and Tukey Honestly Significant Difference post hoc test.
Results:
The samples obtained from 31 of 45 CSOM patients showed positive microbial growth; 26 (57.78%) had a monomicrobial pattern, and 5 (11.11%) had a polymicrobial pattern. The researcher ascertained that 24 isolates, representing 66.67%, were gram-negative bacteria, with P.-aeruginosa identified as the predominant species.P. aeruginosa isolates were sensitive to several antibiotics, including meropenem, amikacin, piperacillin-tazobactam, ceftazidime, and cefoperazone-sulbactam with a rate of 93.33%. The minimum concentration of acetic acid required to qualify as the minimum biofilm inhibitory concentration (MBIC) was determined to be 0.16%, yielding an inhibition rate of 26.79%. A concentration of 0.31% was identified as the minimum biofilm eradication concentration (MBEC), achieving an eradication rate of 77.27%.
Conclusion
P. aeruginosa, the most common bacteria found in CSOM samples, was sensitive to imipenem, amikacin, piperacillin-tazobactam, ceftazidime, and cefoperazone-sulbactam. Acetic acid suppresses P. aeruginosa bacterial biofilm formation at MBIC of 0.16% and MBEC of 0.31%.
8.Platelet-Rich Fibrin Lysate Can Ameliorate Dysfunction of Chronically UVA-Irradiated Human Dermal Fibroblasts.
Yohanes Widodo WIROHADIDJOJO ; Arief BUDIYANTO ; Hardyanto SOEBONO
Yonsei Medical Journal 2016;57(5):1282-1285
To determine whether platelet-rich fibrin lysate (PRF-L) could restore the function of chronically ultraviolet-A (UVA)-irradiated human dermal fibroblasts (HDFs), we isolated and sub-cultured HDFs from six different human foreskins. HDFs were divided into two groups: those that received chronic UVA irradiation (total dosages of 10 J cm-2) and those that were not irradiated. We compared the proliferation rates, collagen deposition, and migration rates between the groups and between chronically UVA-irradiated HDFs in control and PRF-L-treated media. Our experiment showed that chronic UVA irradiation significantly decreased (p<0.05) the proliferation rates, migration rates, and collagen deposition of HDFs, compared to controls. Compared to control media, chronically UVA-irradiated HDFs in 50% PRF-L had significantly increased proliferation rates, migration rates, and collagen deposition (p<0.05), and the migration rates and collagen deposition of chronically UVA-irradiated HDFs in 50% PRF-L were equal to those of normal fibroblasts. Based on this experiment, we concluded that PRF-L is a good candidate material for treating UVA-induced photoaging of skin, although the best method for its clinical application remains to be determined.
Blood Platelets/*cytology/*metabolism
;
Cell Movement/radiation effects
;
Cell Proliferation/radiation effects
;
Cells, Cultured
;
Collagen/metabolism
;
Fibrin/*metabolism
;
Fibroblasts/*cytology/metabolism/*radiation effects
;
Humans
;
Skin/*cytology
;
Time Factors
;
Ultraviolet Rays/*adverse effects
9.Feature Selection for Hypertension Risk Prediction Using XGBoost on Single Nucleotide Polymorphism Data
Lailil MUFLIKHAH ; Tirana Noor FATYANOSA ; Nashi WIDODO ; Rizal Setya PERDANA ; Solimun ; Hana RATNAWATI
Healthcare Informatics Research 2025;31(1):16-22
Objectives:
Hypertension, commonly known as high blood pressure, is a prevalent and serious condition affecting a significant portion of the adult population globally. It is a chronic medical issue that, if left unaddressed, can lead to severe health complications, including kidney problems, heart disease, and stroke. This study aims to develop a feature selection model using the XGBoost algorithm to identify specific single nucleotide polymorphisms (SNPs) as biomarkers for detecting hypertension risk.
Methods:
We propose using the high dimensionality of genetic variations (i.e., SNPs) to build a classifier model for prediction. In this study, SNPs were used as markers for hypertension in patients. We utilized the OpenSNP dataset, which includes 19,697 SNPs from 2,052 samples. Extreme gradient boosting (XGBoost) is an ensemble machine learning method employed here for feature selection, which incrementally adjusts weights in a series of steps.
Results:
The experimental results identified 292 SNPs that exhibited high performance, with an F1-score of 98.55%, precision of 98.73%, recall of 98.38%, and overall accuracy of 98%. This study provides compelling evidence that the XGBoost feature selection method outperforms other representative feature selection methods, such as genetic algorithms, analysis of variance, chi-square, and principal component analysis, in predicting hypertension risk, demonstrating its effectiveness.
Conclusions
We developed a model for predicting hypertension using the SNPs dataset. The high dimensionality of SNP data was effectively managed to identify significant features as biomarkers using the XGBoost feature selection method. The results indicate high performance in predicting the risk of hypertension.
10.Feature Selection for Hypertension Risk Prediction Using XGBoost on Single Nucleotide Polymorphism Data
Lailil MUFLIKHAH ; Tirana Noor FATYANOSA ; Nashi WIDODO ; Rizal Setya PERDANA ; Solimun ; Hana RATNAWATI
Healthcare Informatics Research 2025;31(1):16-22
Objectives:
Hypertension, commonly known as high blood pressure, is a prevalent and serious condition affecting a significant portion of the adult population globally. It is a chronic medical issue that, if left unaddressed, can lead to severe health complications, including kidney problems, heart disease, and stroke. This study aims to develop a feature selection model using the XGBoost algorithm to identify specific single nucleotide polymorphisms (SNPs) as biomarkers for detecting hypertension risk.
Methods:
We propose using the high dimensionality of genetic variations (i.e., SNPs) to build a classifier model for prediction. In this study, SNPs were used as markers for hypertension in patients. We utilized the OpenSNP dataset, which includes 19,697 SNPs from 2,052 samples. Extreme gradient boosting (XGBoost) is an ensemble machine learning method employed here for feature selection, which incrementally adjusts weights in a series of steps.
Results:
The experimental results identified 292 SNPs that exhibited high performance, with an F1-score of 98.55%, precision of 98.73%, recall of 98.38%, and overall accuracy of 98%. This study provides compelling evidence that the XGBoost feature selection method outperforms other representative feature selection methods, such as genetic algorithms, analysis of variance, chi-square, and principal component analysis, in predicting hypertension risk, demonstrating its effectiveness.
Conclusions
We developed a model for predicting hypertension using the SNPs dataset. The high dimensionality of SNP data was effectively managed to identify significant features as biomarkers using the XGBoost feature selection method. The results indicate high performance in predicting the risk of hypertension.