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  • 1.
    Bungon, Theodore
    et al.
    Univ Plymouth, Wolfson Nanomat & Devices Lab, Sch Engn Comp & Math, Fac Sci & Engn, Plymouth, Devon, England..
    Haslam, Carrie
    Univ Plymouth, Wolfson Nanomat & Devices Lab, Sch Engn Comp & Math, Fac Sci & Engn, Plymouth, Devon, England..
    Damiati, Samar
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    O'Driscoll, Benjamin
    Univ Plymouth, Wolfson Nanomat & Devices Lab, Sch Engn Comp & Math, Fac Sci & Engn, Plymouth, Devon, England..
    Whitley, Toby
    Univ Plymouth, Wolfson Nanomat & Devices Lab, Sch Engn Comp & Math, Fac Sci & Engn, Plymouth, Devon, England..
    Davey, Paul
    Univ Plymouth, Wolfson Nanomat & Devices Lab, Sch Engn Comp & Math, Fac Sci & Engn, Plymouth, Devon, England..
    Siligardi, Giuliano
    Rutherford Appleton Lab, Diamond Light Source, Chilton, Oxon, England..
    Charmet, Jerome
    Univ Warwick, Inst Digital Healthcare, WMG, Coventry, W Midlands, England..
    Awan, Shakil A.
    Univ Plymouth, Wolfson Nanomat & Devices Lab, Sch Engn Comp & Math, Fac Sci & Engn, Plymouth, Devon, England..
    Graphene FET Sensors for Alzheimer's Disease Protein Biomarker Clusterin Detection2021In: Frontiers in Molecular Biosciences, E-ISSN 2296-889X, Vol. 8, article id 651232Article in journal (Refereed)
    Abstract [en]

    We report on the fabrication and characterisation of graphene field-effect transistor (GFET) biosensors for the detection of Clusterin, a prominent protein biomarker of Alzheimer's disease (AD). The GFET sensors were fabricated on Si/SiO2 substrate using photolithographic patterning and metal lift-off techniques with evaporated chromium and sputtered gold contacts. Raman Spectroscopy was performed on the devices to determine the quality of the graphene. The GFETs were annealed to improve their performance before the channels were functionalized by immobilising the graphene surface with linker molecules and anti-Clusterin antibodies. Concentration of linker molecules was also independently verified by absorption spectroscopy using the highly collimated micro-beam light of Diamond B23 beamline. The detection was achieved through the binding reaction between the antibody and varying concentrations of Clusterin antigen from 1 to 100 pg/mL, as well as specificity tests using human chorionic gonadotropin (hCG), a glycoprotein risk biomarker of certain cancers. The GFETs were characterized using direct current (DC) 4-probe electrical resistance (4-PER) measurements, which demonstrated a limit of detection of the biosensors to be similar to 300 fg/mL (4 fM). Comparison with back-gated Dirac voltage shifts with varying concentration of Clusterin show 4-PER measurements to be more accurate, at present, and point to a requirement for further optimisation of the fabrication processes for our next generation of GFET sensors. Thus, we have successfully fabricated a promising set of GFET biosensors for the detection of Clusterin protein biomarker. The developed GFET biosensors are entirely generic and also have the potential to be applied to a variety of other disease detection applications such as Parkinson's, cancer, and cardiovascular.

  • 2.
    Cadet, Frederic
    et al.
    Univ Paris City, Inserm UMR S1134, Lab Excellence LABEX GR, DSIMB, Paris, France.;Univ Reunion, Paris, France.;PEACCEL, Artificial Intelligence Dept, Paris, France..
    Saavedra, Emma
    Inst Nacl Cardiol Ignacio Chavez, Dept Biochem, Mexico City, Mexico..
    Syrén, Per-Olof
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Coating Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Gontero, Brigitte
    Aix Marseille Univ, CNRS, UMR7281 Bioenerget & Ingn Prot, Marseille, France..
    Editorial: Machine learning, epistasis, and protein engineering: From sequence-structure-function relationships to regulation of metabolic pathways2022In: Frontiers in Molecular Biosciences, E-ISSN 2296-889X, Vol. 9, article id 1098289Article in journal (Other academic)
  • 3.
    Damiati, Safa A.
    et al.
    King Abdulaziz Univ, Fac Pharm, Dept Pharmaceut, Jeddah, Saudi Arabia..
    Damiati, Samar
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab. King Abdulaziz Univ, Fac Sci, Dept Biochem, Jeddah, Saudi Arabia.
    Microfluidic Synthesis of Indomethacin-Loaded PLGA Microparticles Optimized by Machine Learning2021In: Frontiers in Molecular Biosciences, E-ISSN 2296-889X, Vol. 8, article id 677547Article in journal (Refereed)
    Abstract [en]

    Several attempts have been made to encapsulate indomethacin (IND), to control its sustained release and reduce its side effects. To develop a successful formulation, drug release from a polymeric matrix and subsequent biodegradation need to be achieved. In this study, we focus on combining microfluidic and artificial intelligence (AI) technologies, alongside using biomaterials, to generate drug-loaded polymeric microparticles (MPs). Our strategy is based on using Poly (D,L-lactide-co-glycolide) (PLGA) as a biodegradable polymer for the generation of a controlled drug delivery vehicle, with IND as an example of a poorly soluble drug, a 3D flow focusing microfluidic chip as a simple device synthesis particle, and machine learning using artificial neural networks (ANNs) as an in silico tool to generate and predict size-tunable PLGA MPs. The influence of different polymer concentrations and the flow rates of dispersed and continuous phases on PLGA droplet size prediction in a microfluidic platform were assessed. Subsequently, the developed ANN model was utilized as a quick guide to generate PLGA MPs at a desired size. After conditions optimization, IND-loaded PLGA MPs were produced, and showed larger droplet sizes than blank MPs. Further, the proposed microfluidic system is capable of producing monodisperse particles with a well-controllable shape and size. IND-loaded-PLGA MPs exhibited acceptable drug loading and encapsulation efficiency (7.79 and 62.35%, respectively) and showed sustained release, reaching approximately 80% within 9 days. Hence, combining modern technologies of machine learning and microfluidics with biomaterials can be applied to many pharmaceutical applications, as a quick, low cost, and reproducible strategy.

  • 4.
    Edwards, Steven J.
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Carannante, Valentina
    Karolinska Inst, Sci Life Lab, Dept Microbiol Tumor & Cell Biol, Stockholm, Sweden..
    Kuhnigk, Kyra
    Karolinska Inst, Dept Med Huddinge, Ctr Hematol & Regenerat Med, Stockholm, Sweden..
    Ring, Henrik
    Uppsala Univ, BMC, Dept Neurosci, Uppsala, Sweden..
    Tararuk, Tatsiana
    Uppsala Univ, BMC, Dept Neurosci, Uppsala, Sweden..
    Hallböök, Finn
    Uppsala Univ, BMC, Dept Neurosci, Uppsala, Sweden..
    Blom, Hans
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Önfelt, Björn
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Brismar, Hjalmar
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    High-Resolution Imaging of Tumor Spheroids and Organoids Enabled by Expansion Microscopy2020In: Frontiers in Molecular Biosciences, E-ISSN 2296-889X, Vol. 7, article id 208Article in journal (Refereed)
    Abstract [en]

    Three-dimensional cell cultures are able to better mimic the physiology and cellular environments found in tissuesin vivocompared to cells grown in two dimensions. In order to study the structure and function of cells in 3-D cultures, light microscopy is frequently used. The preparation of 3-D cell cultures for light microscopy is often destructive, including physical sectioning of the samples, which can result in the loss of 3-D information. In order to probe the structure of 3-D cell cultures at high resolution, we have explored the use of expansion microscopy and compared it to a simple immersion clearing protocol. We provide a practical method for the study of spheroids, organoids and tumor-infiltrating immune cells at high resolution without the loss of spatial organization. Expanded samples are highly transparent, enabling high-resolution imaging over extended volumes by significantly reducing light scatter and absorption. In addition, the hydrogel-like nature of expanded samples enables homogenous antibody labeling of dense epitopes throughout the sample volume. The improved labeling and image quality achieved in expanded samples revealed details in the center of the organoid which were previously only observable following serial sectioning. In comparison to chemically cleared spheroids, the improved signal-to-background ratio of expanded samples greatly improved subsequent methods for image segmentation and analysis.

  • 5.
    Lopez-Guajardo, Ana
    et al.
    Univ Sheffield, Med Sch, Dept Oncol & Metab, Sheffield, England..
    Zafar, Azeer
    Univ Sheffield, Med Sch, Dept Oncol & Metab, Sheffield, England..
    Al Hennawi, Khairat
    Univ Sheffield, Med Sch, Dept Oncol & Metab, Sheffield, England..
    Rossi, Valentina
    IOV IRCCS, Veneto Inst Oncol, Immunol & Mol Oncol Diagnost, Padua, Italy..
    Alrwaili, Abdulaziz
    Univ Sheffield, Med Sch, Dept Oncol & Metab, Sheffield, England..
    Medcalf, Jessica D.
    Univ Sheffield, Med Sch, Dept Oncol & Metab, Sheffield, England..
    Dunning, Mark
    Univ Sheffield, Med Sch, Bioinformat Core, Sheffield, England..
    Nordgren, Niklas
    RISE Res Inst Sweden, Div Bioecon & Hlth, Stockholm, Sweden..
    Pettersson, Torbjörn
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Fibre Technology.
    Estabrook, Ian D.
    Univ Sheffield, Dept Phys & Astron, Sheffield, England.;Tech Univ Dresden, Ctr Adv Elect Dresden, Dresden, Germany..
    Hawkins, Rhoda J.
    Univ Sheffield, Dept Phys & Astron, Sheffield, England.;African Inst Math Sci, Accra, Ghana..
    Gad, Annica K. B.
    Univ Sheffield, Med Sch, Dept Oncol & Metab, Sheffield, England.;Univ Madeira, Madeira Chem Res Ctr, Funchal, Portugal.;Karolinska Inst, Dept Oncol Pathol, Stockholm, Sweden..
    Regulation of cellular contractile force, shape and migration of fibroblasts by oncogenes and Histone deacetylase 62023In: Frontiers in Molecular Biosciences, E-ISSN 2296-889X, Vol. 10, article id 1197814Article in journal (Refereed)
    Abstract [en]

    The capacity of cells to adhere to, exert forces upon and migrate through their surrounding environment governs tissue regeneration and cancer metastasis. The role of the physical contractile forces that cells exert in this process, and the underlying molecular mechanisms are not fully understood. We, therefore, aimed to clarify if the extracellular forces that cells exert on their environment and/or the intracellular forces that deform the cell nucleus, and the link between these forces, are defective in transformed and invasive fibroblasts, and to indicate the underlying molecular mechanism of control. Confocal, Epifluorescence and Traction force microscopy, followed by computational analysis, showed an increased maximum contractile force that cells apply on their environment and a decreased intracellular force on the cell nucleus in the invasive fibroblasts, as compared to normal control cells. Loss of HDAC6 activity by tubacin-treatment and siRNA-mediated HDAC6 knockdown also reversed the reduced size and more circular shape and defective migration of the transformed and invasive cells to normal. However, only tubacin-mediated, and not siRNA knockdown reversed the increased force of the invasive cells on their surrounding environment to normal, with no effects on nuclear forces. We observed that the forces on the environment and the nucleus were weakly positively correlated, with the exception of HDAC6 siRNA-treated cells, in which the correlation was weakly negative. The transformed and invasive fibroblasts showed an increased number and smaller cell-matrix adhesions than control, and neither tubacin-treatment, nor HDAC6 knockdown reversed this phenotype to normal, but instead increased it further. This highlights the possibility that the control of contractile force requires separate functions of HDAC6, than the control of cell adhesions, spreading and shape. These data are consistent with the possibility that defective force-transduction from the extracellular environment to the nucleus contributes to metastasis, via a mechanism that depends upon HDAC6. To our knowledge, our findings present the first correlation between the cellular forces that deforms the surrounding environment and the nucleus in fibroblasts, and it expands our understanding of how cells generate contractile forces that contribute to cell invasion and metastasis.

  • 6.
    Oliveira, Daniel V.
    et al.
    Karolinska Inst, Dept Neurobiol Care Sci & Soc, Stockholm, Sweden..
    Svensson, Julia
    Karolinska Inst, Dept Neurobiol Care Sci & Soc, Stockholm, Sweden..
    Zhong, Xueying
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Biomedical Engineering and Health Systems, Structural Biotechnology.
    Biverstal, Henrik
    Karolinska Inst, Dept Biosci & Nutr, Huddinge, Sweden..
    Chen, Gefei
    Karolinska Inst, Dept Biosci & Nutr, Huddinge, Sweden..
    Karlstrom, Helena
    Karolinska Inst, Dept Neurobiol Care Sci & Soc, Stockholm, Sweden..
    Molecular Chaperone BRICHOS Inhibits CADASIL-Mutated NOTCH3 Aggregation In Vitro2022In: Frontiers in Molecular Biosciences, E-ISSN 2296-889X, Vol. 9, article id 812808Article in journal (Refereed)
    Abstract [en]

    CADASIL (cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy) is the most common familial form of stroke, which is caused by mutations located in the epidermal growth factor (EGF)-like repeats of the NOTCH3 gene. Mutations cause the NOTCH3 (N3) protein to misfold and aggregate. These aggregates will be a component of granular osmiophilic material, which when accumulated around the arteries and arterioles is believed to cause the degradation of vascular smooth muscle cells (VSMC). VSMC degradation affects blood flow regulation and leads to white matter and neuronal death. Currently, there is no treatment for CADASIL. The dementia-relevant BRICHOS domain is a small multitalented protein with functions that include ATP-independent chaperone-like properties. BRICHOS has been shown to prevent the aggregation of both fibrillar and non-fibrillar structures. Therefore, the objective of this study is to investigate whether BRICHOS exhibits anti-aggregating properties on a recombinant CADASIL-mutated N3 protein consisting of the first five repeats of EGF (EGF(1-5)), harboring a cysteine instead of an arginine in the position 133, (R133C). We found that the N3 EGF(1-5) R133C mutant is more prone to aggregate, while the wildtype is more stable. Recombinant human Bri2 BRICHOS is able to interact and stabilize the R133C-mutated N3 protein in a dose-dependent manner. These results suggest an anti-aggregating impact of BRICHOS on the N3 EGF(1-5) R133C protein, which could be a potential treatment for CADASIL.

  • 7.
    Pasquadibisceglie, Andrea
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Bonaccorsi Di Patti, Maria Carmela
    Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, Rome, Italy.
    Miniero, Daniela Valeria
    Department of Biosciences, Biotechnologies and Environment, University “Aldo Moro” of Bari, Bari, Italy.
    Musci, Giovanni
    Department of Biosciences and Territory, University of Molise, Pesche, Italy.
    Polticelli, Fabio
    Department of Sciences, University Roma Tre, Rome, Italy; National Institute of Nuclear Physics, Roma Tre Section, Rome, Italy.
    Editorial: Understanding membrane transporters: from structure to function2023In: Frontiers in Molecular Biosciences, E-ISSN 2296-889X, Vol. 10, article id 1323824Article in journal (Other academic)
  • 8.
    Saeedimasine, Marzieh
    et al.
    Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
    Montanino, Annaclaudia
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Biomedical Engineering and Health Systems, Neuronic Engineering.
    Kleiven, Svein
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Biomedical Engineering and Health Systems, Neuronic Engineering.
    Villa, Alessandra
    KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.
    Elucidating axonal injuries through molecular modelling of myelin sheaths and nodes of Ranvier2021In: Frontiers in Molecular Biosciences, E-ISSN 2296-889X, Vol. 8Article in journal (Refereed)
  • 9.
    Wei, Yongjun
    et al.
    Zhengzhou Univ, Sch Pharmaceut Sci Lab Synthet Biol, Zhengzhou, Peoples R China..
    Zhang, Cheng
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. Zhengzhou Univ, Sch Pharmaceut Sci Lab Synthet Biol, Zhengzhou, Peoples R China..
    Mardinoglu, Adil
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. Kings Coll London, Fac Dent Oral & Craniofacial Sci, Ctr Host Microbiome Interact, London, England..
    Zhang, Peng
    Capital Med Univ, Beijing Childrens Hosp, Natl Ctr Childrens Hlth, Beijing Pediat Res Inst, Beijing, Peoples R China..
    Editorial: Application of systems biology in molecular characterization and diagnosis of cancer, Volume II2022In: Frontiers in Molecular Biosciences, E-ISSN 2296-889X, Vol. 9, article id 1089463Article in journal (Other academic)
  • 10.
    Zhang, Cheng
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. Zhengzhou Univ, Sch Pharmaceut Sci, Zhengzhou, Peoples R China.;Zhengzhou Univ, Key Lab Adv Drug Preparat Technol, Minist Educ, Zhengzhou, Peoples R China..
    Wei, Yongjun
    Zhengzhou Univ, Sch Pharmaceut Sci, Zhengzhou, Peoples R China.;Zhengzhou Univ, Key Lab Adv Drug Preparat Technol, Minist Educ, Zhengzhou, Peoples R China..
    Mardinoglu, Adil
    Zhengzhou Univ, Sch Pharmaceut Sci, Zhengzhou, Peoples R China.;Zhengzhou Univ, Key Lab Adv Drug Preparat Technol, Minist Educ, Zhengzhou, Peoples R China.;Kings Coll London, Fac Dent Oral & Craniofacial Sci, Ctr Host Microbiome Interact, London, England..
    Zhang, Peng
    Univ Maryland, Sch Med, Dept Surg, College Pk, MD 20742 USA..
    Editorial: Application of Systems Biology in Molecular Characterization and Diagnosis of Cancer2021In: Frontiers in Molecular Biosciences, E-ISSN 2296-889X, Vol. 8, article id 668146Article in journal (Other academic)
1 - 10 of 10
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