SwePub - search: WFRF:(Rahimi Shadi 1982)

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1.	Rahimi, Shadi, 1982, et al. (author) Automated Prediction of Bacterial Exclusion Areas on SEM Images of Graphene–Polymer Composites 2023 In: Nanomaterials. - 2079-4991. ; 13:10 Journal article (peer-reviewed)abstract To counter the rising threat of bacterial infections in the post-antibiotic age, intensive efforts are invested in engineering new materials with antibacterial properties. The key bottleneck in this initiative is the speed of evaluation of the antibacterial potential of new materials. To overcome this, we developed an automated pipeline for the prediction of antibacterial potential based on scanning electron microscopy images of engineered surfaces. We developed polymer composites containing graphite-oriented nanoplatelets (GNPs). The key property that the algorithm needs to consider is the density of sharp exposed edges of GNPs that kill bacteria on contact. The surface area of these sharp exposed edges of GNPs, accessible to bacteria, needs to be inferior to the diameter of a typical bacterial cell. To test this assumption, we prepared several composites with variable distribution of exposed edges of GNP. For each of them, the percentage of bacterial exclusion area was predicted by our algorithm and validated experimentally by measuring the loss of viability of the opportunistic pathogen Staphylococcus epidermidis. We observed a remarkable linear correlation between predicted bacterial exclusion area and measured loss of viability (R2 = 0.95). The algorithm parameters we used are not generally applicable to any antibacterial surface. For each surface, key mechanistic parameters must be defined for successful prediction.
2.	Abid, Suleman, et al. (author) Synthesis and characterization of glycol chitosan coated selenium nanoparticles acts synergistically to alleviate oxidative stress and increase ginsenoside content in Panax ginseng 2021 In: Carbohydrate Polymers. - : Elsevier BV. - 0144-8617. ; 267 Journal article (peer-reviewed)abstract The objective of the present study is synthesis of glycol chitosan coated selenium nanoparticles (GC-Se NPs) and evaluation of oxidative stress and ginsenoside accumulation in P. ginseng C. A. Meyer. We synthesized (Se NPs and GC-Se NPs) and characterized using various spectroscopic analyses. The highest concentration (20 mg L−1) of GC-Se NPs induced moderate ROS (O2[rad]− and H2O2) accumulation and upregulation of PgSOD and PgCAT showing good biocompatibility and less toxicity at the highest concentration. Furthermore, ginsenoside biosynthetic pathway genes (PgHMGR, PgSS, PgSE, PgDDS) also showed significant upregulation upon 20 mg L−1 GC-Se NPs treatment. At 20 mg L−1 GC-Se NPs treatment, ginsenoside accumulated upto 217.47 mg/mL and 169.86 mg/mL mainly due to the increased proportion of Rb1 and Re ginsenosides. Altogether, our results suggested that ecofriendly conjugation of GC with Se NPs could be used as a bio fortifier to enhance the ginsenoside profile and to increase the quality of ginseng roots.
3.	Abujubara, Helal, et al. (author) Substrate-derived Sortase A inhibitors: targeting an essential virulence factor of Gram-positive pathogenic bacteria 2023 In: Chemical Science. - 2041-6520 .- 2041-6539. ; 14:25, s. 6975-6985 Journal article (peer-reviewed)abstract The bacterial transpeptidase Sortase A (SrtA) is a surface enzyme of Gram-positive pathogenic bacteria. It has been shown to be an essential virulence factor for the establishment of various bacterial infections, including septic arthritis. However, the development of potent Sortase A inhibitors remains an unmet challenge. Sortase A relies on a five amino acid sorting signal (LPXTG), by which it recognizes its natural target. We report the synthesis of a series of peptidomimetic inhibitors of Sortase A based on the sorting signal, supported by computational binding analysis. By employing a FRET-compatible substrate, our inhibitors were assayed in vitro. Among our panel, we identified several promising inhibitors with IC50 values below 200 mu M, with our strongest inhibitor - LPRDSar - having an IC50 of 18.9 mu M. Furthermore, it was discovered that three of our compounds show an effect on growth and biofilm inhibition of pathogenic Staphylococcus aureus, with the inclusion of a phenyl ring seemingly key to this effect. The most promising compound in our panel, BzLPRDSar, could inhibit biofilm formation at concentrations as low as 32 mu g mL(-1), manifesting it as a potential future drug lead. This could lead to treatments for MRSA infections in clinics and diseases such as septic arthritis, which has been directly linked with SrtA.
4.	Aminian-Dehkordi, Javad, et al. (author) Synthetic biology tools for environmental protection 2023 In: Biotechnology Advances. - 0734-9750. ; 68 Research review (peer-reviewed)abstract Synthetic biology transforms the way we perceive biological systems. Emerging technologies in this field affect many disciplines of science and engineering. Traditionally, synthetic biology approaches were commonly aimed at developing cost-effective microbial cell factories to produce chemicals from renewable sources. Based on this, the immediate beneficial impact of synthetic biology on the environment came from reducing our oil dependency. However, synthetic biology is starting to play a more direct role in environmental protection. Toxic chemicals released by industries and agriculture endanger the environment, disrupting ecosystem balance and biodiversity loss. This review highlights synthetic biology approaches that can help environmental protection by providing remediation systems capable of sensing and responding to specific pollutants. Remediation strategies based on genetically engineered microbes and plants are discussed. Further, an overview of computational approaches that facilitate the design and application of synthetic biology tools in environmental protection is presented.
5.	Balusamy, Sri Renukadevi, et al. (author) A comprehensive and systemic review of ginseng-based nanomaterials: Synthesis, targeted delivery, and biomedical applications 2023 In: Medicinal Research Reviews. - : Wiley. - 0198-6325 .- 1098-1128. ; 43:5, s. 1374-1410 Research review (peer-reviewed)abstract Among 17 Panax species identified across the world, Panax ginseng (Korean ginseng), Panax quinquefolius (American ginseng), and Panax notoginseng (Chinese ginseng) are highly recognized for the presence of bioactive compound, ginsenosides and their pharmacological effects. P. ginseng is widely used for synthesis of different types of nanoparticles compared to P. quinquefolius and P. notoginseng. The use of nano-ginseng could increase the oral bioavailability, membrane permeability, and thus provide effective delivery of ginsenosides to the target sites through transport system. In this review, we explore the synthesis of ginseng nanoparticles using plant extracts from various organs, microbes, and polymers, as well as their biomedical applications. Furthermore, we highlight transporters involved in transport of ginsenoside nanoparticles to the target sites. Size, zeta potential, temperature, and pH are also discussed as the critical parameters affecting the quality of ginseng nanoparticles synthesis.
6.	Balusamy, Sri Renukadevi, et al. (author) Chitosan, chitosan nanoparticles and modified chitosan biomaterials, a potential tool to combat salinity stress in plants 2022 In: Carbohydrate Polymers. - : Elsevier BV. - 0144-8617. ; 284 Research review (peer-reviewed)abstract Chitosan being non-toxic, biocompatible, and biodegradable gained considerable interest among agriculturists. Our research review discusses about the role of Cs, chitosan nanoparticles (CsNPs), and modified chitosan biomaterials (CsBMs) under salt stress to improve growth parameters such as plant height, weight, stem width, fruit yield, pigments such as chlorophyll a, b, total chlorophyll, and carotenoid contents, as well as antioxidant and non-antioxidative enzymes. Upon Cs treatment and salt stress, total aminoacids (TAA), glutamic acids, and gamma-aminobutyric acid (GABA) were increased. Furthermore, Cs activated SOS1 pathway and increased various gene transcripts involved in sodium compartmentalization, proton motive force, energy production, and phenol metabolism. On the other hand, CsNPs and modified CsBMs treated plants under salinity stress increased indole terpene alkaloid metabolism, defense related genes, decreased ROS production by enhancing JA signaling, increased essential oil, anthocyanins, membrane stability, alkaloids, and diterpene glycosides. This is the first review that specifically brings insights about the physiological and biochemical parameters of the plants by comparing Cs/CsNPs/modified CsBMs treatment options under salt stress and encourages the use of CsNPs and modified CsBMs compared to Cs for better plant function under salinity stress.
7.	Chen, Yanyan, 1990, et al. (author) Graphene nanospikes exert bactericidal effect through mechanical damage and oxidative stress 2024 In: Carbon. - 0008-6223. ; 218 Journal article (peer-reviewed)abstract Microbial contamination of biomedical surfaces is an important clinical challenge, driving the development of new antibacterial materials. Nanoprotrusions on the wing surface of some insects have intrinsic antibacterial and antifouling properties, which inspires fabrication of biomimetic nanopatterns on medical devices. Herein, we report a broad-spectrum bactericidal surface consisting of graphene nanospikes synthesized by plasma-enhanced chemical vapor deposition. Similar coatings have been reported before, but the killing mechanism and main parameters for efficiency of such coatings have not been clarified. We investigated the correlation of anti-biofilm efficiency of graphene nanospikes to their major physicochemical parameters. While height and thickness of nanospikes did not directly correlate with bactericidal effects, edge/defect density showed linear correlation with lethality for both Gram-negative and Gram-positive bacteria. We further demonstrated that the killing mechanism is synergistic, depending on physical rupture of bacterial membranes as well as considerable oxidative damage to the cells. Of note, for the first time, we quantify the level of oxidative stress induced by graphene nanospikes in two bacterial species using genetically encoded biosensors. Our work provides a fundamental understanding of the impact of various parameters of graphene nanostructures on the bactericidal efficiency, enabling rational design of graphene-based bactericidal surfaces.
8.	Chen, Yanyan, 1990, et al. (author) Interactions Between Graphene-Based Materials and Biological Surfaces: A Review of Underlying Molecular Mechanisms 2021 In: Advanced Materials Interfaces. - : Wiley. - 2196-7350. ; 8:24 Research review (peer-reviewed)abstract Understanding the underlying molecular mechanism of how graphene materials (GMs) interact with biological surfaces is the key to develop safe and effective biomedical applications of GMs. Here, a systematic and comprehensive mechanistic perspective of interactions between pristine GMs and biological membranes is provided. To this end, first the known mechanisms of interaction between GMs and membrane components are summarized and classified, with a focus on phospholipids, cholesterol, and membrane proteins. Both experimental observations and computational simulations are included. Detailed experimental conditions and physiochemical properties of GMs are listed for each cited application. At the end of this review, current challenges and conflicts that limit biomedical applications of GMs are discussed. Based on reported mechanisms, guidelines for future studies to address the remaining challenges are proposed, specifically with respect to modulating the intrinsic properties of GMs for more efficient and safer therapeutic applications.
9.	Eswaran, Muthusankar, 1988, et al. (author) A flexible multifunctional electrode based on conducting PANI/Pd composite for non-enzymatic glucose sensor and direct alcohol fuel cell applications 2023 In: Fuel. - : Elsevier BV. - 0016-2361. ; 345 Journal article (peer-reviewed)abstract In this work, we fabricated a flexible, multifunctional polyimide (PI)/Au-polyaniline (PAN)/Pd nanocomposite electrode with excellent electrochemical properties. Structural geometry, morphological views, and functional group analyses indicated that the physicochemical and electrochemical performance of the electrode is based on the strong and synergistic metal-polymer interaction between the conducting PAN and Pd, which ensured high conductivity, rapid response, and high electron transfer rate through more electroactive spots available in the nanocomposite. Here, we demonstrated that the fabricated PI/Au-PAN/Pd electrodes can be successfully used for biomedical sensing of glucose, as well as for energy conversion application, using the oxidation of alcohols such as methanol and ethanol in fuel cells. The electrochemical analysis shows that the flexible sensor (PI/Au-PAN/Pd) has ultra-high sensitivity of 2140 μA/μM.cm2 with a low detection limit of 0.3 μM for glucose. Also, the interference analysis, reproducibility, and stability studies reveal its excellent capability for glucose sensing. Furthermore, the electrode also demonstrates prominent electrocatalytic behavior to the electrooxidation of methanol and ethanol in an alkaline medium with a current density of 3 mA/cm2 and 0.96 mA/cm2 along with good cyclic stability. Thus, this efficient flexible electrocatalyst with good stability, practicability, and reproducibility claims its potential applications in flexible/wearable healthcare diagnostics systems as well as in alternative energy conversion devices.
10.	Eswaran, Muthusankar, 1988, et al. (author) A Road Map toward Field-Effect Transistor Biosensor Technology for Early Stage Cancer Detection 2022 In: Small Methods. - : Wiley. - 2366-9608. ; 6 Research review (peer-reviewed)abstract Field effect transistor (FET)-based nanoelectronic biosensor devices provide a viable route for specific and sensitive detection of cancer biomarkers, which can be used for early stage cancer detection, monitoring the progress of the disease, and evaluating the effectiveness of therapies. On the road to implementation of FET-based devices in cancer diagnostics, several key issues need to be addressed: sensitivity, selectivity, operational conditions, anti-interference, reusability, reproducibility, disposability, large-scale production, and economic viability. To address these well-known issues, significant research efforts have been made recently. An overview of these efforts is provided here, highlighting the approaches and strategies presently engaged at each developmental stage, from the design and fabrication of devices to performance evaluation and data analysis. Specifically, this review discusses the multistep fabrication of FETs, choice of bioreceptors for relevant biomarkers, operational conditions, measurement configuration, and outlines strategies to improve the sensing performance and reach the level required for clinical applications. Finally, this review outlines the expected progress to the future generation of FET-based diagnostic devices and discusses their potential for detection of cancer biomarkers as well as biomarkers of other noncommunicable and communicable diseases.
11.	Jiang, Shan, et al. (author) Editorial: Efficient Treatment of Industrial Wastewater With Microbiome and Synthetic Biology 2022 In: Frontiers in Environmental Science. - : Frontiers Media SA. - 2296-665X. ; 10 Journal article (other academic/artistic)
12.	Koushki, Mehdi, et al. (author) Screening the critical protein subnetwork to delineate potential mechanisms and protective agents associated with arsenic-induced cutaneous squamous cell carcinoma: A toxicogenomic study 2024 In: Food and Chemical Toxicology. - 1873-6351 .- 0278-6915. ; 185 Journal article (peer-reviewed)abstract Recent studies show that complex mechanisms are involved in arsenic-induced malignant transformation of cells. This study aimed to decipher molecular mechanisms associated with arsenic-induced cutaneous squamous cell carcinoma (cSCC) and suggest potential protective factors. RNA-seq-based differentially expressed genes between arsenic-exposed human keratinocytes (HaCaT) and controls were used to construct a protein-protein interaction (PPI) network and discover critical subnetwork-based mechanisms. Protective compounds against arsenic toxicity were determined and their target interactions in the core sub-network were identified by the comparative toxicogenomic database (CTD). The binding affinity between the effective factor and target was calculated by molecular docking. A total of 15 key proteins were screened out as critical arsenic-responsive subnetwork (FN1, IL-1A, CCN2, PECAM1, FGF5, EDN1, FGF1, PXDN, DNAJB9, XBP1, ERN1, PDIA4, DNAJB11, FOS, PDIA6) and 7 effective protective agents were identified (folic acid, quercetin, zinc, acetylcysteine, methionine, catechin, selenium). The GeneMANIA predicted detailed interactions of the subnetwork and revealed terms related to unfolded protein response as the main processes. FN1, IL1A and CCN2, as top significant genes, had good docking affinity with folic acid and quercetin, as selected key compounds. Integration of gene expression and protein-protein interaction related to arsenic exposure in cSCC explored the potential mechanisms and protective agents.
13.	Lanai, Victor, 1990, et al. (author) Differences in interaction of graphene/graphene oxide with bacterial and mammalian cell membranes 2023 In: Nanoscale. - 2040-3372 .- 2040-3364. ; 16:3, s. 1156-1166 Journal article (peer-reviewed)abstract Graphene, a single layer, hexagonally packed two-dimensional carbon sheet is an attractive candidate for diverse applications including antibacterial potential and drug delivery. One of the knowledge gaps in biomedical application of graphene is the interaction of these materials with the cells. To address this, we investigated the interaction between graphene materials (graphene and graphene oxide) and plasma membranes of cells (bacterial and mammalian cells). The interactions of four of the most abundant phospholipids in bacteria and mammalian plasma membranes with graphene materials were studied using density functional theory (DFT) at the atomic level. The calculations showed that the mammalian phospholipids have stronger bonding to each other compared to bacterial phospholipids. When the graphene/graphene oxide sheet is approaching the phospholipid pairs, the bacterial pairs exhibit less repulsive interactions, thereby a more stable system with the sheets was found. We also assembled bacterial and mammalian phospholipids into liposomes. We further observed that the bacterial liposomes and cells let the graphene flakes penetrate the membrane. The differential scanning calorimetry measurements of liposomes revealed that the bacterial liposomes have the lowest heat capacity; this strengthens the theoretical predictions of weaker interaction between the bacterial phospholipids compared to the mammalian phospholipids. We further demonstrated that graphene oxide could be internalized into the mammalian liposomes without disrupting the membrane integrity. The results suggest that the weak bonding among bacteria phospholipids and less repulsive force when graphene materials approach, result in graphene materials interacting differently with the bacteria compared to mammalian cells.
14.	Martinez Ruiz, Jose Luis, 1981, et al. (author) Biofilm formation and dispersal of Staphylococcus aureus wound isolates in microtiter plate-based 2-D wound model 2024 In: Heliyon. - 2405-8440. ; 10:13 Journal article (peer-reviewed)abstract Biofilm-associated wound infections in diabetic and immunocompromised patients are an increasing threat due to rising antibiotic resistance. Various wound models have been used to screen for efficient antiinfection treatments. However, results from in vitro models do not always match in vivo results, and this represents a bottleneck for development of new infection treatments. In this study, a static 2-D microtiter plate-based biofilm model was tested for growing clinically relevant Staphylococcus aureus wound isolates in various operating conditions, seeking to identify an optimal setup that would yield physiologically relevant results. Specifically, the tested variables included wound-mimicking growth media, precoating of surface with different proteins, multiwell plates with various surface properties, and the effect of bacterial pre-attachment step. Our results indicated that protein precoating is a key factor for supporting biofilm growth. The same wound isolate responded with significant differences in biofilm formation to different wound-mimicking media. Biofilm dispersal, as a proxy for effectiveness of antibiofilm treatments, was also investigated in response to proteinase K. The dispersal effect of proteinase K showed that the biofilm dispersal is contingent upon the specific wound isolate, with isolates CCUG 35571 and ATCC 6538 showing considerable dispersal responses. In conclusion, this study observed a higher biofilm formation in isolates when a protein precoating of collagen type I was applied but being dependent on the growth media selected. That is why we recommend to use simulated wound fluid or a wound-mimicking growth media to perform similar studies. Furthermore, proteinase K is suggested as an important factor that could affect biofilm dispersal within such models, since biofilm dispersal was induced in isolates CCUG 35571 and ATCC 6538 in simulated wound fluid on precoated collagen type I plates.
15.	Mijakovic, Ivan, 1975, et al. (author) Learning by teaching efficiently enhances learning outcomes in molecular biology of the cell course 2024 In: Biochemistry and Molecular Biology Education. - 1539-3429 .- 1470-8175. ; 52:1, s. 15-24 Journal article (peer-reviewed)abstract To evaluate the impact of active learning approaches in a basic molecular and cell biology course for undergraduate students, we assessed the effect of learning by teaching and peer review on the learning outcomes. A literature seminar activity with peer review and feedback was organized as a compulsory activity for all students, covering about 25% of the course content. The remaining 75% of the course was delivered as classical lectures. The students collaborated in groups to present the content of a review article complemented with a research article. For each group of students, an opponent group was assigned to challenge the presenting group by questions and contribute to the evaluation of the presentation together with the teacher. Based on the feedback survey, the students reacted positively to this active learning exercise, and they strongly recommended keeping it in the future editions of the course. The students' exam scores strongly indicated that the learning outcomes from the learning by teaching part of the course were consistently higher than from the classical lecture part of the course. Further optimization of the active learning part of the course is outlined based on student feedback.
16.	Neissi, Alireza, 1985, et al. (author) Cold-Resistant Heterotrophic Ammonium and Nitrite-Removing Bacteria Improve Aquaculture Conditions of Rainbow Trout (Oncorhynchus mykiss) 2020 In: Microbial Ecology. - : Springer Science and Business Media LLC. - 0095-3628 .- 1432-184X. ; 80:2, s. 266-277 Journal article (peer-reviewed)abstract The aim of this study was isolation and characterization of heterotrophic bacteria capable of ammonium and nitrite removal at 15 °C (optimal temperature for growing rainbow trout Oncorhynchus mykiss). Environmental isolates were grown in liquid media containing ammonium or nitrite, and best strains in terms of growth and ammonium or nitrite removal were identified via 16S rRNA sequencing. Dyadobacter sp. (no. 68) and Janthinobacterium sp. (no. 100) were selected for optimal adaptation to growth at 15 °C and best ammonium and nitrite removal (P < 0.05), respectively. A heterotrophic ammonium and nitrite removal (HAN) microbial complex, containing selected strains, was prepared and applied in a trout culture system. After 10 days, the effect of microbial HAN complex was investigated in terms of ammonium and nitrite removal, as well as stress and immune indices present in the plasma of cultivated trout. Compared to a standard cultivation setup, addition of the HAN complex had a clear beneficial effect on keeping the un-ionized ammonia and nitrite level below prescribed standards (P < 0.05). This resulted in reduction of stress and immune reactions of cultivated fish (P < 0.05), leading to an augmentation of final weight and survival. Application of the selected microbial complex resulted in a significant improvement of the aquaculture ecosystem.
17.	Neissi, Alireza, 1985, et al. (author) Enriched microbial communities for ammonium and nitrite removal from recirculating aquaculture systems 2022 In: Chemosphere. - : Elsevier BV. - 0045-6535 .- 1879-1298. ; 295 Journal article (peer-reviewed)abstract The aim of this study was the enrichment of high-performance microbial communities in biofilters for removal of ammonium and nitrite from aquaculture water. Ammonium oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) were enriched from different environmental water samples. The microbial communities with higher ammonium and nitrite removal activity were selected and adapted to different temperatures [9 °C, 15 °C, room temperature (25 °C), and 30 °C]. The expression of genes involved in nitrification including ammonia monooxygenase (AMO) and nitrite oxidoreductase (NXR) were measured in temperature-adapted AOB and NOB microbiomes. The microbial species present in the selected microbiomes were identified via 16s rRNA sequencing. The microbial communities containing Nitrosomonas oligotropha and Nitrobacter winogradskyi showed the highest ammonium and nitrite removal activity at all temperatures used for adaptation. Furthermore, the microbial communities do not contain any pathogenic bacteria. They also exhibited the highest expression of AMO and NXR genes. Using the enriched microbial communities, we achieved a 288% and 181% improvement in ammonium and nitrite removal over the commonly used communities in biofilters at 9 °C, respectively. These results suggest that the selected microbiomes allowed for a significant improvement of water quality in a recirculating aquaculture system (RAS).
18.	Pandit, Santosh, 1987, et al. (author) Graphene-based sensor for detection of bacterial pathogens 2021 In: Sensors. - : MDPI AG. - 1424-8220. ; 21:23 Journal article (peer-reviewed)abstract Microbial colonization to biomedical surfaces and biofilm formation is one of the key challenges in the medical field. Recalcitrant biofilms on such surfaces cause serious infections which are difficult to treat using antimicrobial agents, due to their complex structure. Early detection of microbial colonization and monitoring of biofilm growth could turn the tide by providing timely guidance for treatment or replacement of biomedical devices. Hence, there is a need for sensors, which could generate rapid signals upon bacterial colonization. In this study, we developed a simple prototype sensor based on pristine, non-functionalized graphene. The detection principle is a change in electrical resistance of graphene upon exposure to bacterial cells. Without functionalization with specific receptors, such sensors cannot be expected to be selective to certain bacteria. However, we demonstrated that two different bacterial species can be detected and differentiated by our sensor due to their different growth dynamics, adherence pattern, density of adhered bacteria and microcolonies formation. These distinct behaviors of tested bacteria depicted distinguishable pattern of resistance change, resistance versus gate voltage plot and hysteresis effect. This sensor is simple to fabricate, can easily be miniaturized, and can be effective in cases when precise identification of species is not needed.
19.	Pandit, Santosh, 1987, et al. (author) Sustained release of usnic acid from graphene coatings ensures long term antibiofilm protection 2021 In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322 .- 2045-2322. ; 11:1 Journal article (peer-reviewed)abstract Protecting surfaces from bacterial colonization and biofilm development is an important challenge for the medical sector, particularly when it comes to biomedical devices and implants that spend longer periods in contact with the human body. A particularly difficult challenge is ensuring long-term protection, which is usually attempted by ensuring sustained release of antibacterial compounds loaded onto various coatings. Graphene have a considerable potential to reversibly interact water insoluble molecules, which makes them promising cargo systems for sustained release of such compounds. In this study, we developed graphene coatings that act as carriers capable of sustained release of usnic acid (UA), and hence enable long-term protection of surfaces against colonization by bacterial pathogens Staphylococcus aureus and Staphylococcus epidermidis. Our coatings exhibited several features that made them particularly effective for antibiofilm protection: (i) UA was successfully integrated with the graphene material, (ii) a steady release of UA was documented, (iii) steady UA release ensured strong inhibition of bacterial biofilm formation. Interestingly, even after the initial burst release of UA, the second phase of steady release was sufficient to block bacterial colonization. Based on these results, we propose that graphene coatings loaded with UA can serve as effective antibiofilm protection of biomedical surfaces.
20.	Perumalsamy, Haribalan, et al. (author) A comprehensive review on Moringa oleifera nanoparticles: importance of polyphenols in nanoparticle synthesis, nanoparticle efficacy and their applications 2024 In: Journal of Nanobiotechnology. - 1477-3155. ; 22:1 Research review (peer-reviewed)abstract Moringa oleifera is one of the popular functional foods that has been tremendously exploited for synthesis of a vast majority of metal nanoparticles (NPs). The diverse secondary metabolites present in this plant turn it into a green tool for synthesis of different NPs with various biological activities. In this review, we discussed different types of NPs including silver, gold, titanium oxide, iron oxide, and zinc oxide NPs produced from the extract of different parts of M. oleifera. Different parts of M. oleifera take a role as the reducing, stabilizing, capping agent, and depending on the source of extract, the color of solution changes within NP synthesis. We highlighted the role of polyphenols in the synthesis of NPs among major constituents of M. oleifera extract. The different synthesis methods that could lead to the formation of various sizes and shapes of NPs and play crucial role in biomedical application were critically discussed. We further debated the mechanism of interaction of NPs with various sizes and shapes with the cells, and further their clearance from the body. The application of NPs made from M. oleifera extract as anticancer, antimicrobial, wound healing, and water treatment agent were also discussed. Small NPs show better antimicrobial activity, while they can be easily cleared from the body through the kidney. In contrast, large NPs are taken by the mono nuclear phagocyte system (MPS) cells. In case of shape, the NPs with spherical shape penetrate into the bacteria, and show stronger antibacterial activity compared to the NPs with other shapes. Finally, this review aims to correlate the key characteristics of NPs made from M. oleifera extract, such as size and shape, to their interactions with the cells for designing and engineering them for bio-applications and especially for therapeutic purposes. Graphical Abstract: (Figure presented.)
21.	Rahimi, Shadi, 1982, et al. (author) Cellular and subcellular interactions of graphene-based materials with cancerous and non-cancerous cells 2022 In: Advanced Drug Delivery Reviews. - : Elsevier BV. - 0169-409X .- 1872-8294. ; 189 Research review (peer-reviewed)abstract Despite significant advances in early detection and personalized treatment, cancer is still among the leading causes of death globally. One of the possible anticancer approaches that is presently receiving a lot of attention is the development of nanocarriers capable of specific and efficient delivery of anticancer drugs. Graphene-based materials are promising nanocarriers in this respect, due to their high drug loading capacity and biocompatibility. In this review, we present an overview on the interactions of graphene-based materials with normal mammalian cells at the molecular level as well as cellular and subcellular levels, including plasma membrane, cytoskeleton, and membrane-bound organelles such as lysosomes, mitochondria, nucleus, endoplasmic reticulum, and peroxisome. In parallel, we assemble the knowledge about the interactions of graphene-based materials with cancerous cells, that are considered as the potential applications of these materials for cancer therapy including metastasis treatment, targeted drug delivery, and differentiation to non-cancer stem cells. We highlight the influence of key parameters, such as the size and surface chemistry of graphene-based materials that govern the efficiency of internalization and biocompatibility of these particles in vitro and in vivo. Finally, this review aims to correlate the key parameters of graphene-based nanomaterials specially graphene oxide, such as size and surface modifications, to their interactions with the cancerous and non-cancerous cells for designing and engineering them for bio-applications and especially for therapeutic purposes.
22.	Rahimi, Shadi, 1982, et al. (author) Co-culturing Bacillus subtilis and wastewater microbial community in a bio-electrochemical system enhances denitrification and butyrate formation 2020 In: Chemical Engineering Journal. - : Elsevier BV. - 1385-8947. ; 397 Journal article (peer-reviewed)abstract Bio-augmentation could be a promising strategy to improve processes for treatment and resource recovery from wastewater. In this study, the Gram-positive bacterium Bacillus subtilis was co-cultured with the microbial communities present in wastewater samples with high concentrations of nitrate or ammonium. Glucose supplementation (1%) was used to boost biomass growth in all wastewater samples. In anaerobic conditions, the indigenous microbial community bio-augmented with B. subtilis was able to rapidly remove nitrate from wastewater. In these conditions, B. subtilis overexpressed nitrogen assimilatory and respiratory genes including nasD, nasE, narG, narH, and narI, which arguably accounted for the observed boost in denitrification. Next, we attempted to use the ammonium- and nitrate-enriched wastewater samples bio-augmented with B. subtilis in the cathodic compartment of bioelectrochemical systems (BES) operated in anaerobic condition. B. subtilis only had low relative abundance in the microbial community, but bio-augmentation promoted the growth of Clostridium butyricum and C. beijerinckii, which became the dominant species. Both bio-augmentation with B. subtilis and electrical current from the cathode in the BES promoted butyrate production during fermentation of glucose. A concentration of 3.4 g/L butyrate was reached with a combination of cathodic current and bio-augmentation in ammonium-enriched wastewater. With nitrate-enriched wastewater, the BES effectively removed nitrate reaching 3.2 mg/L after 48 h. In addition, 3.9 g/L butyrate was produced. We propose that bio-augmentation of wastewater with B. subtilis in combination with bioelectrochemical processes could both boost denitrification in nitrate-containing wastewater and enable commercial production of butyrate from carbohydrate- containing wastewater, e.g. dairy industry discharges. These results suggest that B. subtilis bio-augmentation in our BES promotes simultaneous wastewater treatment and butyrate production. © 2020 The Authors
23.	Rahimi, Shadi, 1982, et al. (author) Ginsenoside Rg3 Reduces the Toxicity of Graphene Oxide Used for pH-Responsive Delivery of Doxorubicin to Liver and Breast Cancer Cells 2023 In: Pharmaceutics. - : MDPI AG. - 1999-4923. ; 15:2 Journal article (peer-reviewed)abstract Doxorubicin (DOX) is extensively used in chemotherapy, but it has serious side effects and is inefficient against some cancers, e.g., hepatocarcinoma. To ameliorate the delivery of DOX and reduce its side effects, we designed a pH-responsive delivery system based on graphene oxide (GO) that is capable of a targeted drug release in the acidic tumor microenvironment. GO itself disrupted glutathione biosynthesis and induced reactive oxygen species (ROS) accumulation in human cells. It induced IL17-directed JAK-STAT signaling and VEGF gene expression, leading to increased cell proliferation as an unwanted effect. To counter this, GO was conjugated with the antioxidant, ginsenoside Rg3, prior to loading with DOX. The conjugation of Rg3 to GO significantly reduced the toxicity of the GO carrier by abolishing ROS production. Furthermore, treatment of cells with GO–Rg3 did not induce IL17-directed JAK-STAT signaling and VEGF gene expression—nor cell proliferation—suggesting GO–Rg3 as a promising drug carrier. The anticancer activity of GO–Rg3–DOX conjugates was investigated against Huh7 hepatocarcinoma and MDA-MB-231 breast cancer cells. GO–Rg3–DOX conjugates significantly reduced cancer cell viability, primarily via downregulation of transcription regulatory genes and upregulation of apoptosis genes. GO–Rg3 is an effective, biocompatible, and pH responsive DOX carrier with potential to improve chemotherapy—at least against liver and breast cancers.
24.	Rahimi, Shadi, 1982, et al. (author) Technologies for biological removal and recovery of nitrogen from wastewater 2020 In: Biotechnology Advances. - : Elsevier BV. - 0734-9750. ; 43 Research review (peer-reviewed)abstract Water contamination is a growing environmental issue. Several harmful effects on human health and the environment are attributed to nitrogen contamination of water sources. Consequently, many countries have strict regulations on nitrogen compound concentrations in wastewater effluents. Wastewater treatment is carried out using energy- and cost-intensive biological processes, which convert nitrogen compounds into innocuous dinitrogen gas. On the other hand, nitrogen is also an essential nutrient. Artificial fertilizers are produced by fixing dinitrogen gas from the atmosphere, in an energy-intensive chemical process. Ideally, we should be able to spend less energy and chemicals to remove nitrogen from wastewater and instead recover a fraction of it for use in fertilizers and similar applications. In this review, we present an overview of various technologies of biological nitrogen removal including nitrification, denitrification, anaerobic ammonium oxidation (anammox), as well as bioelectrochemical systems and microalgal growth for nitrogen recovery. We highlighted the nitrogen removal efficiency of these systems at different temperatures and operating conditions. The advantages, practical challenges, and potential for nitrogen recovery of different treatment methods are discussed.
25.	Rahimi, Shadi, 1982, et al. (author) Triterpenoid-biosynthetic UDP-glycosyltransferases from plants 2019 In: Biotechnology Advances. - : Elsevier BV. - 0734-9750. ; 37:7 Research review (peer-reviewed)abstract Triterpenoid saponins are naturally occurring structurally diverse glycosides of triterpenes that are widely distributed among plant species. Great interest has been expressed by pharmaceutical and agriculture industries for the glycosylation of triterpenes. Such modifications alter their taste and bio-absorbability, affect their intra−/extracellular transport and storage in plants, and induce novel biological activities in the human body. Uridine diphosphate (UDP)-glycosyltransferases (UGTs) catalyze glycosylation using UDP sugar donors. These enzymes belong to a multigene family and recognize diverse natural products, including triterpenes, as the acceptor molecules. For this review, we collected and analyzed all of the UGT sequences found in Arabidopsis thaliana as well as 31 other species of triterpene-producing plants. To identify potential UGTs with novel functions in triterpene glycosylation, we screened and classified those candidates based on similarity with UGTs from Panax ginseng, Glycine max, Medicago truncatula, Saponaria vaccaria, and Barbarea vulgaris that are known to function in glycosylate triterpenes. We highlight recent findings on UGT inducibility by methyl jasmonate, tissue-specific expression, and subcellular localization, while also describing their catalytic activity in terms of regioselectivity for potential key UGTs dedicated to triterpene glycosylation in plants. Discovering these new UGTs expands our capacity to manipulate the biological and physicochemical properties of such valuable molecules.
26.	Shi, Lei, 1981, et al. (author) Evolutionary Analysis of the Bacillus subtilis Genome Reveals New Genes Involved in Sporulation 2020 In: Molecular biology and evolution. - : Oxford University Press. - 0737-4038 .- 1537-1719. ; 37:6, s. 1667-1678 Journal article (peer-reviewed)abstract Bacilli can form dormant, highly resistant, and metabolically inactive spores to cope with extreme environmental challenges. In this study, we examined the evolutionary age of Bacillus subtilis sporulation genes using the approach known as genomic phylostratigraphy. We found that B. subtilis sporulation genes cluster in several groups that emerged at distant evolutionary time-points, suggesting that the sporulation process underwent several stages of expansion. Next, we asked whether such evolutionary stratification of the genome could be used to predict involvement in sporulation of presently uncharacterized genes (y-genes). We individually inactivated a representative sample of uncharacterized genes that arose during the same evolutionary periods as the known sporulation genes and tested the resulting strains for sporulation phenotypes. Sporulation was significantly affected in 16 out of 37 (43%) tested strains. In addition to expanding the knowledge base on B. subtilis sporulation, our findings suggest that evolutionary age could be used to help with genome mining.
27.	Zhang, Jian, 1989, et al. (author) Antibiotic-Loaded Boron Nitride Nanoconjugate with Strong Performance against Planktonic Bacteria and Biofilms 2023 In: ACS Applied Bio Materials. - 2576-6422. ; 6:8, s. 3131-3142 Journal article (peer-reviewed)abstract Protecting surfacesfrom biofilm formation presents a significantchallenge in the biomedical field. The utilization of antimicrobialcomponent-conjugated nanoparticles is becoming an attractive strategyagainst infectious biofilms. Boron nitride (BN) nanomaterials havea unique biomedical application value due to their excellent biocompatibility.Here, we developed antibiotic-loaded BN nanoconjugates to combat bacterialbiofilms. Antibiofilm testing included two types of pathogens, Staphylococcus aureus and Escherichiacoli. Gentamicin was loaded on polydopamine-modifiedBN nanoparticles (GPBN) to construct a nanoconjugate, which was veryeffective in killing E. coli and S. aureus planktonic cells. GPBN exhibited equallystrong capacity for biofilm destruction, tested on preformed biofilms.A 24 h treatment with the nanoconjugate reduced cell viability bymore than 90%. Our results suggest that GPBN adheres to the surfaceof the biofilm, penetrates inside the biofilm matrix, and finallydeactivates the cells. Interestingly, the GPBN coatings also stronglyinhibited the formation of bacterial biofilms. Based on these results,we suggest that GPBN could serve as an effective means for treatingbiofilm-associated infections and as coatings for biofilm prevention.
28.	Zhang, Jian, 1989, et al. (author) Polydopamine/graphene oxide coatings loaded with tetracycline and green Ag nanoparticles for effective prevention of biofilms 2023 In: Applied Surface Science. - 0169-4332. ; 626 Journal article (peer-reviewed)abstract Bacterial adhesion and biofilm formation are significant challenges for medical devices and implants. Surface modification to alter the surface properties of biomedical device surfaces to prevent the biofilm formation is an important driving force for the development of anti-biofilm coatings. Here, a simple and feasible method to fabricate antibacterial coatings that combines the adhesion properties of polydopamine (PDA) and the high drug loading capacity of graphene oxide (GO). Tetracycline and green-synthesized silver nanoparticles were successfully assembled onto the coating surface, endowing the coating an anti-biofilm effect and exhibit strong inhibitory effect on S. aureus and E. coli biofilms by a factor of more than 1000 (3 log10 units). Kirby-Bauer diffusion test, colony forming unit (CFU) counts, biofilm topography studies and live/dead staining were used to evaluate the antibacterial activity of the coatings. This study is proposed that PDA/GO coatings loaded with antibiotics or silver nanoparticles can be used as a potential approach to prevent infection associated with implantable biomedical devices.

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