| 1. |
- Borsa, Baris Ata, et al.
(author)
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Antibiotic administration in targeted nanoparticles protects the faecal microbiota of mice
- 2021
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In: RSC MEDICINAL CHEMISTRY. - : ROYAL SOC CHEMISTRY. - 2632-8682. ; 12:3, s. 380-383
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Journal article (peer-reviewed)abstract
- Antibiotic therapy comes with disturbances on human microbiota, resulting in changes of bacterial communities and thus leading to well-established health problems. In this study, we demonstrated that targeted teicoplanin administration maintains the faecal microbiota composition undisturbed in a mouse model while reaching therapeutic improvements for S. aureus infection.
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| 2. |
- Balian, Alien, et al.
(author)
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Kinetic Screening of Nuclease Activity using Nucleic Acid Probes
- 2019
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In: Journal of Visualized Experiments. - United States : JOURNAL OF VISUALIZED EXPERIMENTS. - 1940-087X. ; :153
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Journal article (peer-reviewed)abstract
- Nucleases are a class of enzymes that break down nucleic acids by catalyzing the hydrolysis of the phosphodiester bonds that link the ribose sugars. Nucleases display a variety of vital physiological roles in prokaryotic and eukaryotic organisms, ranging from maintaining genome stability to providing protection against pathogens. Altered nuclease activity has been associated with several pathological conditions including bacterial infections and cancer. To this end, nuclease activity has shown great potential to be exploited as a specific biomarker. However, a robust and reproducible screening method based on this activity remains highly desirable. Herein, we introduce a method that enables screening for nuclease activity using nucleic acid probes as substrates, with the scope of differentiating between pathological and healthy conditions. This method offers the possibility of designing new probe libraries, with increasing specificity, in an iterative manner. Thus, multiple rounds of screening are necessary to refine the probes design with enhanced features, taking advantage of the availability of chemically modified nucleic acids. The considerable potential of the proposed technology lies in its flexibility, high reproducibility, and versatility for the screening of nuclease activity associated with disease conditions. It is expected that this technology will allow the development of promising diagnostic tools with a great potential in the clinic.
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| 3. |
- Balian, Alien, 1988-
(author)
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Nuclease Activity as a Biomarker in Cancer Detection
- 2023
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Doctoral thesis (other academic/artistic)abstract
- Nucleases are a group of enzymes that cleave the phosphodiester bonds in nucleic acids. As such, nucleases act as biological scissors that exhibit a plethora of fundamental roles, in prokaryotes and eukaryotes, dependent or non-dependent on their catalytic capability. Thus, differential status of nucleases between healthy and disease conditions might not be surprising, and can be deployed in disease detection. Specifically, there is growing body of research demonstrating the potential of nucleases as diagnostic biomarkers in several types of cancer. Biomarkers for early diagnosis are an immense need in the diagnostic landscape of cancer. In this sense, nucleases are promising biomolecules, and they possess a unique feature of catalytic activity that could be deployed for diagnosis and future therapeutic strategies. In this thesis we aim to demonstrate the use of nucleases as biomarkers associated to cancer, and the capability of oligonucleotide substrates for targeting a specific nuclease. The thesis work begins with comprehensive review of nucleases as promising biomarkers in cancer diagnosis (paper I). Then, we provide a methodological study in paper II, in which we propose a flexible approach for detection of disease associated nuclease activity using oligonucleotides as substrates. The probes utilized here are flanked with fluorophore at the 5’-end and a quencher at the 3’-end. Upon cleavage by nucleases, the fluorescent signal is increased in a proportional fashion to nuclease activity. This platform is suitable to implement in detection of any disease in which nuclease activity is altered. We have applied this method in paper III, by using 75 probes as substrates to screen breast cancer cells, along with controls, for nuclease activity. We have identified a probe (DNA PolyAT) that discriminates between BT-474 breast cancer cells and healthy cells based on nuclease activity profile associated with cell membrane. Next, we screened tissue samples from breast tumors for nuclease activity, and we have identified a set of probes with the capability to discriminate breast tumor and healthy tissues in 89% of the cases (paper IV). To achieve a step forward towards non-invasive diagnosis, we have developed an activatable magnetic resonance imaging (MRI)-probe (paper V). The MRI-probe is oligonucleotide-based that works like a contrast agent, and it is activated only in presence of a specific nuclease. MRI-probes provide advantages over fluorescent probes, such as high spatial resolution and unlimited tissue penetration. In conclusion, our findings suggest the utility of nuclease activity as a biomarker in cancer detection. Moreover, we demonstrate the applicability of nuclease activity-based approaches in imaging modalities, such as MRI. Our future aim is to translate our findings into non-invasive detection of breast cancer by utilizing breast cancer activatable MRI-probes.
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| 4. |
- Borsa, Baris Ata, First Research Engineer, et al.
(author)
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Therapeutic-oligonucleotides activated by nucleases (TOUCAN) : A nanocarrier system for the specific delivery of clinical nucleoside analogues.
- 2023
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In: Journal of Controlled Release. - : ELSEVIER. - 0168-3659 .- 1873-4995. ; 361, s. 260-269
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Journal article (peer-reviewed)abstract
- Nucleoside analogues have been in clinical use since 1960s and they are still used as the first therapeutic option for several cancers and viral infections, due to their high therapeutic efficacy. However, their wide clinical acceptance has been limited due to their high toxicity and severe side effects to patients. Herein, we report on a nanocarrier system that delivers nucleosides analogues in a target-specific manner, making nucleoside-based therapeutics safer and with the possibility to be used in other human conditions. This system, named, Therapeutic OligonUCleotides Activated by Nucleases" (TOUCAN) combines: i) the recognition power of oligonucleotides as substrates, ii) the use of nucleases as enzymatic biomarkers and iii) the clinical efficacy of nucleoside analogues, in a single approach. As a proof-of-concept, we report on a TOUCAN that is activated by a specific nuclease produced by bacteria and releases a therapeutic nucleoside, floxuridine. We demonstrate, for the first time, that, by incorporating a therapeutic nucleoside analogue into oligonucleotide probes, we can specifically inhibit bacterial growth in cultures. In this study, Staphylococcus aureus was selected as the targeted bacteria and the TOUCAN strategy successfully inhibited its growth with minimal inhibitory concentration (MIC) values ranging from 0.62 to 40 mg/L across all tested strains. Moreover, our results indicate that the intravenous administration of TOUCANs at a dose of 20 mg/kg over a 24-h period is a highly effective method for treating bacterial infections in a mouse model of pyomyositis. Importantly, no signs of toxicity were observed in our in vitro and in vivo studies. This work can significantly impact the current management of bacterial infections, laying the grounds for the development of a different class of antibiotics. Furthermore, it can provide a safer delivery platform for clinical nucleoside therapeutics in any human conditions, such as cancer and viral infection, where specific nuclease activity has been reported.
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| 5. |
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| 6. |
- Dursun, Ali D., et al.
(author)
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Surface plasmon resonance aptasensor for Brucella detection in milk
- 2022
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In: Talanta. - Amsterdam, Netherlands : Elsevier. - 0039-9140 .- 1873-3573. ; 239
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Journal article (peer-reviewed)abstract
- A Surface Plasmon Resonance (SPR) aptasensor was developed for the detection of Brucella melitensis (B. melitensis) in milk samples. Brucellosis is a bacterial zoonotic disease with global distribution caused mostly by contaminated milk or their products. Aptamers recognizing B. melitensis were selected following a whole bacteria-SELEX procedure. Two aptamers were chosen for high affinity and high specificity. The high affinity aptamer (B70 aptamer) was immobilized on the surface of magnetic silica core-shell nanoparticles for initial purification of the target bacteria cells from milk matrix. Another aptamer, highly specific for B. melitensis cells (B46 aptamer), was used to prepare SPR sensor chips for sensitive determination of Brucella in eluted samples from magnetic purification since direct injection of milk samples to SPR sensor chips is known for a high background unspecific signal. Thus, we integrated a quick and efficient magnetic isolation step for subsequent instant detection of B. melitensis contamination in one ml of milk sample by SPR with a LOD value as low as 27 ± 11 cells.
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| 7. |
- Goikoetxea, Garazi, et al.
(author)
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Fluorescent and electrochemical detection of nuclease activity associated with Streptococcus pneumoniae using specific oligonucleotide probes
- 2024
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In: The Analyst. - : ROYAL SOC CHEMISTRY. - 0003-2654 .- 1364-5528.
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Journal article (peer-reviewed)abstract
- Streptococcus pneumoniae (S. pneumoniae) represents a significant pathogenic threat, often responsible for community-acquired pneumonia with potentially life-threatening consequences if left untreated. This underscores the pressing clinical need for rapid and accurate detection of this harmful bacteria. In this study, we report the screening and discovery of a novel biomarker for S. pneumoniae detection. We used S. pneumoniae nucleases as biomarker and we have identified a specific oligonucleotide that works as substrate. This biomarker relies on a specific nuclease activity found on the bacterial membrane, forming the basis for the development of both fluorescence and electrochemical biosensors. We observed an exceptionally high sensitivity in the performance of the electrochemical biosensor, detecting as low as 10(2) CFU mL(-1), whereas the fluorescence sensor demonstrated comparatively lower efficiency, with a detection limit of 10(6) CFU mL(-1). Moreover, the specificity studies have demonstrated the biosensors' remarkable capacity to identify S. pneumoniae from other pathogenic bacteria. Significantly, both biosensors have demonstrated the ability to identify S. pneumoniae cultured from clinical samples, providing compelling evidence of the potential clinical utility of this innovative detection system.
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| 8. |
- Meng, Lingyin, et al.
(author)
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A conducting polymer-based array with multiplex sensing and drug delivery capabilities for smart bandages
- 2024
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In: COMMUNICATIONS MATERIALS. - : SPRINGERNATURE. - 2662-4443. ; 5:1
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Journal article (peer-reviewed)abstract
- Effective individual wound management, particularly in cases of prolonged healing and increased infection vulnerability, has prompted the development of wound theranostics, combining real-time diagnostic assessment and on-demand treatment. Here, we present a multifunctional conducting polymer-based smart theranostic bandage that integrates pH sensing, pH-compensated uric acid (UA) biosensing, and on-demand antibiotic release using different conducting polymers, each leveraging their advantageous intrinsic properties. Specifically, the polyaniline-based pH sensor operates reversibly across a pH range of 4-10, while the functionalized poly(3,4-ethylenedioxythiophene)-based UA biosensor exhibits a linear response up to 0.9 mM UA. Simultaneous detection of pH and UA allows accurate UA determination via pH compensation. Upon detecting abnormal pH/UA levels, the polypyrrole-based drug carrier releases ciprofloxacin via 0.6 V electrical stimulation, successfully inhibiting bacterial growth in vitro. The array is assembled as a 3D patch, connected to a flexible printed circuit board, and embedded in a wound bandage, offering potential for remote wound monitoring, targeted treatment, and wireless wound management. Smart devices for wound management combine biosensing with drug release. Here, a smart theranostic bandage is reported that can detect pH and uric acid levels and release antibiotics as necessary, all of which can be done remotely.
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| 9. |
- Ucak, Samet, et al.
(author)
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Inhibitory effects of aptamer targeted teicoplanin encapsulated PLGA nanoparticles for Staphylococcus aureus strains
- 2020
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In: World Journal of Microbiology & Biotechnology. - : SPRINGER. - 0959-3993 .- 1573-0972. ; 36:5
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Journal article (peer-reviewed)abstract
- Emergence of resistance to traditional antibiotic treatments necessitates alternative delivery systems. Teicoplanin is a glycopeptide antibiotic used in the treatments of serious infections caused by Gram-positive bacteria, including Methicillin Resistant Staphylococcus aureus (MRSA). One strategy to keep up with antibiotic resistance development is to limit dose and amount during treatments. Targeted delivery systems of antibiotics have been suggested as a mechanism to slow-down the evolution of resistance and to increase efficiency of the antimicrobials on already resistant pathogens. In this study, we report teicoplanin delivery nanoparticles of Poly Lactic-co-Glycolic Acid (PLGA), which are functionalized with S. aureus specific aptamers. A 32-fold decrease in minimum inhibitory concentration (MIC) values of teicoplanin for S. aureus was demonstrated for susceptible strains and about 64-fold decline in MIC value was achieved for moderately resistant clinical isolates of MRSA upon teicoplanin treatment with aptamer-PLGA nanoparticles. Although teicoplanin delivery in PLGA nanoparticles without targeting demonstrated eightfold decrease in MIC of susceptible strains of S. aureus and S. epidermidis and twofold in MIC of resistant strains, the aptamer targeting specifically decreased MIC for S. aureus, but not for S. epidermidis. Therefore, aptamer-targeted PLGA delivery of antibiotic can be an attractive alternative to combat with some of the multi-drug resistant bacterial pathogens.
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