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In-silico study of single-strand DNA aptamers against cortisol as a potential biomarker receptor in therapeutics and diagnostics

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Materials Today: Proceedings 2020年 31卷 A90-A97页

作者： Mohamad Zulkeflee Sabri Azzmer Azzar Abdul Hamid Sharifah Mariam Sayed Hitam Mohd. Zulkhairi Abdul Rahim Bioengineering Section Universiti Kuala Lumpur Malaysian Institute of Chemical and Bioengineering Technology (UniKL MICET) Lot 1988 Bandar Vendor Taboh Naning 78000 Alor Gajah Melaka Malaysia Department of Biotechnology Kulliyyah of Science International Islamic University Malaysia (IIUM) Malaysia Jalan Sultan Ahmad Shah Bandar Indera Mahkota 25200 Kuantan Pahang Malaysia Technical Foundation Section Universiti Kuala Lumpur Malaysian Institute of Chemical and Bioengineering Technology (UniKL MICET) Malaysia

Stress hormone is the number one adversary to the general health in human all over the world. In the presence of stress, cortisol, a glucocorticoid hormone synthesized by the stimulation of adrenal cortex will be secreted. Cortisol has immunosuppressive and anti-inflammatory effects, increases heart rate and blood pressure, and represses growth, and digestive and reproductive activities. Aptamers are synthetically derived nucleic acids has been long studied as a substitute of antibodies for therapeutics and diagnostics purposes. Current study focuses on in-silico approach of molecular docking and molecular dynamics simulation to study the interactions between single-strand DNA aptamers and cortisol in comparisons with the glucocorticoid receptor. In silico study were known to solve a plethora of biological related target study including the latest on COVID19 polymerase which is the inhibitors target protein. In current study, the tertiary conformational structures of ten single-strand DNA aptamers which experimentally derived were designed and docked against cortisol and compared with the binding of glucocorticoid receptor (PDB:4P6X). Binding affinity, number of hydrogen bonds and hydrophobic interactions were analyzed. The aptamer-cortisol complex with the lowest binding energy value was selected for 50 ns (ns) molecular dynamics simulation. Docking result shows that although number of intra-molecular hydrogen bond formed affecting the binding energy value of aptamer-cortisol complexes, hydrophobic interaction surrounding the cortisol is more important in determining the affinity of cortisol towards its receptor. Aptamer-1 shows the lowest binding energy value formed against cortisol (-10.1 kcal/mol) in comparison with other aptamers. Molecular dynamics simulation of Aptamer-1-cortisol complex shows that RMSD of glucocorticoid receptor-cortisol is lower in comparison with Aptamer 1-cortisol, with higher number of intra-molecular hydrogen bonds. Although the stabili

关键词： Aptamer Non-SELEX In-silico Computational chemistry Design and interaction

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Individual Alpha Frequency tACS modifies the detection of space-time optical illusion

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Brain Stimulation 2025年第1期18卷 360-360页

作者： Scoccia, Adriano Neri, Francesco Catrambone, Vincenzo Cinti, Alessandra Benelli, Alberto Romanella, Sara Grabot, Laetitia Valenza, Gaetano Smeralda, Carmelo Luca Santarnecchi, Emiliano van Wassenhove, Virginie Rossi, Simone Siena Brain Investigation and Neuromodulation Lab (Si-BIN Lab) Department of Medicine Surgery and Neuroscience Neurology and Clinical Neurophysiology Section University of Siena Italy Oto-Neuro-Tech Conjoined Lab Policlinico Le Scotte University of Siena Italy Department of Information Engineering University of Pisa Bioengineering & Robotics Research Center “E. Piaggio” Pisa Italy Precision Neuroscience & Neuromodulation Program Massachusetts General Hospital Harvard Medical School Boston MA USA Cognitive Neuroimaging Unit CEA DRF/Joliot NeuroSpin INSERM Université Paris-Saclay 91191 Gif-sur-Yvette France Department for Cognitive Neuroscience Faculty of Biology & Cognitive Interaction Technology Center of Excellence Bielefeld University Bielefeld Germany

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Photocatalytic degradation of anthracene by biochar-based graphitic carbon nitride

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IOP Conference Series: Materials Science and Engineering 2021年第1期1195卷

作者： S N Q Syed Abd Halim N A M Nazri N A H M Nordin Section of Chemical Engineering Universiti Kuala Lumpur Kampus Malaysian Institute of Chemical and Bioengineering Technology (UniKL MICET) Lot 1988 Kawasan Perindustrian Bandar Vendor Taboh Naning 78000 Alor Gajah Malacca Malaysia Chemical Engineering Department Universiti Teknologi Petronas Seri Iskandar 32610 Perak Malaysia

Polycyclic aromatic hydrocarbons (PAHs) are persistent and toxic to living organisms, that can be classified as carcinogenic, mutagenic and teratogenic pollutants. In this study, a green photocatalyst of biochar-based graphitic carbon nitride (BC/g-C3N4-M) is derived from sugarcane bagasse (SB) and melamine were developed as a potential material for the degradation of PAHs. BC(SB)/g-C3N4-M prepared with varied ratios of melamine to SB and different synthesis temperature were characterized by FTIR, BET and UV-DRS. The efficiency of the catalyst for the degradation of anthracene were investigated further in terms of its efficiency at various pH mediums, catalyst dosage and anthracene initial concentration. Experimental results revealed that g-C3N4 showed better degradation efficiency to anthracene than BC(SB)/g-C3N4-M. Additionally, the best degradation efficiency of anthracene by g-C3N4 and BC/g-C3N4-M75% composites were found at pH 3 with 1.0 g/L dosage at 2 ppm and 1 ppm initial concentration, respectively. The catalysts were also discovered to be reusable for 5 cycles with a slight decrease in photocatalytic degradation. The use of agricultural biomass waste in this study could provide a promising approach to water and wastewater treatment.

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Effect of curing on hydrolytic degradation of montmorillonite nanoclays filled biobased polyesters

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Polymers from Renewable Resources 2017年第2期8卷 43-60页

作者： Islam, M.R. Isa, N. Yahaya, A.N. Section of Chemical Engineering Technology Malaysian Institute of Chemical and Bioengineering Technology Universiti Kuala Lumpur Alor Gajah Melaka78000 Malaysia

Palm oil based polyester (POPE) reinforced with montmorillonite nano clays (MNCs) were investigated for curing kinetics and hydrolytic degradation analysis. Alcoholises and esterification process were followed to produce POPE. The prepared resins were cured thermally by using methyl ethyl ketone peroxide (MEKP), styrene and cobalt-naphthenate at 120°C. The curing kinetics was analysed by differential scanning calorimetry (DSC). The rate of reaction, activation energy and degree of conversion were measured by this analysis. The activation energy and reaction order were found to be decreased due to increase of heating rate of the curing process. Alkali solution was used for the hydrolytic degradation for different samples prepared at different curing conditions such as low period-high temperature (LPHT) and high period-low temperature (HPLT). The properties were affected due to the variation of curing process as confirmed by degradation behaviours in terms of tensile strength, melting point and surface morphology. The degradation of the composites were influential and faster at LPHT condition compared to HPLT condition. ©Smithers Information Ltd, 2017.

关键词： Palm oil

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Epithelial cells provide immunocompetence to the early embryo for bacterial clearance

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Cell Host & Microbe 2025年

作者： Joan Roncero-Carol June Olaizola-Muñoa Begoña Arán Loris Sebastiano Mularoni Marta Miret Cuesta Nuria Blanco-Cabra Marc Casals Mireia Rumbo Miquel Solé Inarejos Samuel Ojosnegros Berta Alsina Eduard Torrents Anna Veiga Manuel Irimia Esteban Hoijman Regenerative Medicine Program Bellvitge Biomedical Research Institute (IDIBELL) L’Hospitalet de Llobregat Barcelona Spain Molecular Biology Institute of Barcelona (IBMB) Spanish Research Council (CSIC) Barcelona Science Park Barcelona Spain Barcelona Stem Cell Bank L’Hospitalet de Llobregat Barcelona Spain L’Hospitalet de Llobregat Barcelona Spain Department of Medicine and Life Sciences Universitat Pompeu Fabra PRBB Barcelona Spain Centre for Genomic Regulation The Barcelona Institute of Science and Technology (BIST) Barcelona Spain Institute for Bioengineering of Catalonia (IBEC) The Barcelona Institute of Science and Technology Barcelona Spain Microbiology Section Department of Genetics Microbiology and Statistics Faculty of Biology University of Barcelona Barcelona Spain Dexeus Fertility Department of Obstetrics Gynecology and Reproductive Medicine Hospital Universitari Dexeus Barcelona Spain Institució Catalana de Recerca i Estudis Avançats (ICREA) Barcelona Spain

Early embryos are exposed to environmental perturbations that may influence their development, including bacteria. Despite lacking a proper immune system, the surface epithelium of early embryos (trophectoderm in mammals) can phagocytose defective pluripotent cells. Here, we explore the dynamic interactions between early embryos and bacteria. Quantitative live imaging of infection models developed in zebrafish embryos reveals the efficient phagocytic capability of surface epithelia in detecting, ingesting, and destroying infiltrated E. coli and S. aureus . In vivo single-cell interferences uncover actin-based epithelial zippering protrusions mediating bacterial phagocytosis, safeguarding developmental robustness upon infection. Transcriptomic and inter-scale dynamic analyses of phagocyte-bacteria interactions identify specific features of this epithelial phagocytic program. Notably, live imaging of mouse and human blastocysts supports a conserved role of the trophectoderm in bacterial phagocytosis. This defensive role of the surface epithelium against bacterial infection provides immunocompetence to early embryos, with relevant implications for understanding failures in human embryogenesis.

关键词： embryonic development cell dynamics phagocytosis epithelial tissue quantitative live imaging bacterial infections host-pathogen interactions zebrafish human embryo

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Optimization of EDTA enriched phytoaccumulation of zinc by Ophiopogon japonicus: Comparison of Response Surface, Artificial Neural Network and Random Forest models

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Bioresource technology Reports 2019年 7卷

作者： K., Janani N., Sivarajasekar S., Muthusaravanan K., Ram J., Prakashmaran S., Sivamani Dhakal, Nirajan Shahnaz, Tasrin N., Selvaraju Laboratory for Bioremediation Research Unit Operations Laboratory Department of Biotechnology Kumaraguru College of Technology CoimbatoreTN641049 India Department of Food Science and Nutrition Periyar University SalemTN India Chemical Engineering Section Salalah College of Technology Salalah211 Oman Environmental Engineering and Water Technology Department IHE Delft Institute for Water Education Netherlands Department of Bioscience and Bioengineering Indian Institute of Technology Guwahati GuwahatiAssam India

Zinc (Zn) contaminated soil was remediated by EDTA enriched phytoaccumulation strategy using Ophiopogon japonicus. The main and interactive effects of three variables such as initial Zn concentration (0.5 × 10−4 M–1 × 10−4 M), EDTA concentration (0–25 mmol kg−1), and time period (1–14 days) were investigated via Box–Behnken statistical design (BBD). The optimal phytoaccumulation efficiency of 95.30% was found to be at Zn concentration: 1 × 10−4 M kg−1, EDTA concentration: 16.42 mM kg−1, and time period: 13.86 days. The same data was given as input to Multilayer Feed-Forward Networks Back-Propagation and Random Forest (RF) models to classify the data as high and low yield in order to develop a real-time monitoring system. The performance of the aforementioned models for Zn phytoaccumulation was evaluated in terms of parity plot, normal probability plot, and error functions and RF model was found suitable. © 2019 Elsevier Ltd

关键词： Decision trees

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Erratum to: Different micro/nano-scale patterns of surface materials influence osteoclastogenesis and actin structure

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Nano Research 2022年第5期15卷 4773-4773页

作者： Tsukasa Akasaka Miho Tamai Yoshitaka Yoshimura Natsumi Ushijima Shinichiro Numamoto Atsuro Yokoyama Hirofumi Miyaji Ryo Takata Shuichi Yamagata Yoshiaki Sato Ko Nakanishi Yasuhiro Yoshida Department of Biomaterials and Bioengineering Faculty of Dental MedicineHokkaido UniversitySapporo 060-8586Japan Immune Signal Unit Okinawa Institute of Science and Technology Graduate UniversityOkinawa 904-0495Japan Department of Pharmacology Faculty of Dental Medicine and Graduate School of Dental MedicineHokkaido UniversitySapporo 060-8586Japan Support Section for Education and Research Faculty of Dental MedicineHokkaido UniversitySapporo 060-8586Japan Oral Functional Prosthodontics Division of Oral Functional ScienceFaculty of Dental MedicineHokkaido UniversitySapporo 060-8586Japan Department of Periodontology and Endodontology Faculty of Dental MedicineHokkaido UniversitySapporo 060-8586Japan Department of Orthodontics Faculty of Dental Medicine and Graduate School of Dental MedicineHokkaido UniversitySapporo 060-8586Japan

The article“Different micro/nano-scale patterns of surface materials influence osteoclastogenesis and actin structure”,written by Tsukasa Akasaka,Miho Tamai,Yoshitaka Yoshimura,Natsumi Ushijima,Shinichiro Numamoto,Atsuro Yokoyama,Hirofumi Miyaji,Ryo Takata,Shuichi Yamagata,Yoshiaki Sato,Ko Nakanishi,and Yasuhiro Yoshida,was originally published electronically on the publisher’s internet portal on January 17,2022 without open access.

关键词： internet portal Nat

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The CONSIDER study: assessing the risk of catheter-associated bloodstream infections beyond the intensive care setting

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American journal of infection control 2025年

作者： Fabio Borgonovo Marta Colaneri Federico Fassio Giovanni Scaglione Lucia Galli Martina Offer Camilla Genovese Rebecca Fattore Monica Schiavini Giovanni De Capitani Maria Calloni Arianna Bartoli Francesco Casella Alba Taino Antonio Gidaro Chiara Cogliati Valentina Breschi Jessica Leoni Andrea Gori Antonella Foschi Department of Infectious Diseases Unit II L. Sacco Hospital ASST Fatebenefratelli Sacco Milan Italy. Department of Infectious Diseases Unit II L. Sacco Hospital ASST Fatebenefratelli Sacco Milan Italy Department of Biomedical and Clinical Sciences University of Milan Milan Italy. Electronic address: marta.colaneri@unimi.it. Department of Public Health Experimental and Forensic Medicine Section of Biostatistics and Clinical Epidemiology University of Pavia Pavia Italy. Department of Biomedical and Clinical Sciences University of Milan Milan Italy. Division of Internal Medicine Luigi Sacco Hospital University of Milan Milan Italy. Department of Electrical Engineering University of Technology Eindhoven Netherlands. Department of Electronics Information and Bioengineering (DEIB) Politecnico di Milano Milan Italy.

BACKGROUND:Catheter-associated and related bloodstream infection (CABSI and CRBSI) are major causes of hospital- acquired infections. However, their incidence and risk factors in non-ICU patients with vascular access devices (VADs) are scarce. METHODS:This retrospective study conducted at a large university Hospital of Northern Italy (2021-2024) evaluated CABSI and CRBSI incidence and risk factors in non-ICU hospitalized adults with VADs. Hazard ratios (HR) were estimated with gamma frailty models and random survival forest analysis with sensitivity tests. Key variables were identified and validated in multivariable models. RESULTS:Among 2,326 VAD insertions (corresponding to 1,892 patients), 153 with CRBSI or CABSI were identified. The incidence was 1.80 per 1,000 catheter-days for CABSI, 1.24 per 1,000 catheter-days for CRBSI, and the overall incidence of around 2.97 per 1,000 catheter-days. Coagulase-negative staphylococci were the most isolated pathogens (43.9%). Infections were associated to factors such as parenteral nutrition (PN) (HR = 4.12) and multi-lumen catheters (HR = 2.56). Random Survival Forest models identified PN, intravenous drug use (IVDU), and in-patient regimen as top variables. Specifically, CRBSI showed stronger associations with PN (HR = 7.42), while CABSI was linked to IVDU (HR = 7.20). CONCLUSION:Our study showed a significantly high incidence of CABSI and CRBSI in non-ICU adult patients. By identifying the risk factors of these infections, it suggests the settings in which stringent infection prevention strategies are needed.

关键词： CABSI CRBSI Infection prevention Risk factors VAD-related infections non-ICU Patients

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Simulating tribological characteristics of Palm Methyl Ester (PME) lubricated contact

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IOP Conference Series: Materials Science and Engineering 2020年第1期834卷

作者： S H Hamdan W W F Chong Section of Bioengineering Technology University Kuala Lumpur Malaysia Institute of Chemical & Bioengineering Technology Taboh Naning 78000 Alor Gajah Melaka Malaysia School of Mechanical Engineering Faculty of Engineering Universiti Teknologi Malaysia 81310 Johor Bahru Johor Malaysia UTM Centre for Low Carbon Transport in Cooperation with Imperial College London Universiti Teknologi Malaysia (UTM) Johor Bahru Johor Malaysia

The study simulates the lubricant Stribeck curve for Palm Methyl Ester (PME) by coupling modified Reynolds solution with Greenwood and Tripp's rough surface contact model. The predicted lubricant Stribeck curves for PME is validated with measured data from a pin-on-disc tribometer. The Reynolds equation is modified to accommodate for the lubricant properties of PME (e.g. viscosity and density), which is mathematically described using Gibbs energy additivity approach. Solving the modified Reynolds equation would then provide the fluid film formation behaviour of PME, such as the contact pressure and film thickness. These fluid film parameters are then used as the input to determine the boundary and viscous friction of the investigated lubricated contact using Greenwood and Tripp's rough surface contact model. The proposed mathematical solution correlates well with experimental data and is shown to be capable of predicting lubricant Stribeck, capturing the frictional behavior for the whole range of lubrication regimes. The findings of the present study prepare for a mathematical foundation to further explore the use of biodiesel as an alternative biodegradable lubricant to mineral-based ones.

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Utilisation of calcined Asian green mussel (Perna viridis) shells as partial cement replacement in concrete

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International Journal of Environmental Engineering 2018年第3-4期9卷 282-300页

作者： Razali, Nadia Aris, Raja Nur Farhana Raja Razali, Nadlene Pa'Ee, Khairul Faizal Section of Environmental Engineering Technology Universiti Kuala Lumpur Malaysian Institute of Chemical and Bioengineering Technology Alor Gajah Melaka78000 Malaysia Universiti Kuala Lumpur Malaysian Institute of Chemical and Bioengineering Technology Alor Gajah Melaka78000 Malaysia Faculty of Mechanical Engineering Universiti Teknikal Malaysia Melaka Melaka Durian Tunggal76100 Malaysia Section of Food Engineering Technology Universiti Kuala Lumpur Malaysian Institute of Chemical and Bioengineering Technology Alor Gajah Melaka78000 Malaysia

The aim of this study is to produce an eco-concrete mix by replacing the binder calcined mussel shells (Perna viridis) without compromising the durability of the concrete. Specimen cubes (40 mm × 40 mm × 40 mm) with various replacement percentages by volume were produced. Primary concrete parameters such as pH, carbonation depth, compressive strength and sorptivity were studied for 56 days. From the investigation, all modified concrete formulations performed better in carbonation depth, compression strength and sorptivity than control specimens on all testing days. It has been observed that the higher the replacement percentage, the better carbonation depth and sorptivity values. However, the opposing trend was detected in compressive strength;in which the higher the replacement percentage, the less strength the concrete possessed. It is believed that the aragonite polymorphs of the mussel shells contribute a low strength development due to its different symmetry and crystal shapes to calcite (from limestone) thus leading to poor bonding properties of the concrete matrix. Copyright © 2018 Inderscience Enterprises Ltd.

关键词： Compressive strength

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