| 1. |
- Casaite, Vida, et al.
(författare)
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Expression and purification of active recombinant equine lysozyme in Escherichia coli
- 2009
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Ingår i: Protein Engineering Design & Selection. - : Oxford University Press (OUP). - 1741-0126 .- 1741-0134. ; 22:11, s. 649-654
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Tidskriftsartikel (refereegranskat)abstract
- Equine lysozyme (EL) is a calcium (Ca)-binding lysozyme and is an intermediary link between non-Ca-binding C-type lysozyme and alpha-lactalbumin. The feature of lysozymes to assemble into the fibrils has recently gained considerable attention for the investigation of the functional properties of these proteins. To study the structural and functional properties of EL, a synthetic gene was cloned and EL was overexpressed in Escherichia coli as a fused protein. The His-tagged recombinant EL was accumulated as inclusion bodies. Up to 50 mg/l of the recombinant EL could be achieved after purification by Ni(2+) affinity chromatography, refolding in the presence of arginine, CM-Sepharose column purification following TEV protease cleavage. The purified protein was functionally active, as determined by the lysozyme activity, proving the proper folding of protein. The purified lysozyme was used for the oligomerisation studies. The protein formed amyloid fibrils during incubation in acidic pH and elevated temperature. The recombinant EL forms two types of fibrils: ring shaped and linear, similar to the native EL.
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| 2. |
- Dagys, Marius, et al.
(författare)
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Comparison of bioelectrocatalysis at Trichaptum abietinum and Trametes hirsuta laccase modified electrodes
- 2014
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Ingår i: Electrochimica Acta. - : Elsevier. - 0013-4686 .- 1873-3859. ; 130, s. 141-147
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Tidskriftsartikel (refereegranskat)abstract
- Bioelectrocatalytic reduction of oxygen to water at electrodes modified with gold nanoparticles and a new laccase from Trichaptum abietinum (TaLc) was studied. The bioelectrocatalytic current was found to be much higher at TaLc modified electrodes than at similarly prepared electrodes modified with a broadly used laccase from Trametes hirsuta (ThLc). To explain this difference the bioelectrocatalysis was described in terms of kinetic rate constants based on simultaneous cyclic voltammetry and quartz crystal microbalance measurements. From analysis of the rate constants both laccases appeared to possess similar rates (k(0)) of direct electron transfer. However, the enzyme turnover (k(cat)) was about three-fold higher for gold nanoparticle bound TaLc than for ThLc, calculated using surface concentration of enzyme established by QCM-D. Near reversible potential-induced reorientation of adsorbed proteins was observed by surface enhanced Raman spectroscopy. (C) 2014 Elsevier Ltd. All rights reserved.
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| 3. |
- Dagys, Marius, et al.
(författare)
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Oxygen electroreduction catalysed by laccase wired to gold nanoparticles via the trinuclear copper cluster
- 2017
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Ingår i: Energy & Environmental Science. - : Royal Society of Chemistry. - 1754-5692 .- 1754-5706. ; 10:2, s. 498-502
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Tidskriftsartikel (refereegranskat)abstract
- Specific wiring of biocatalysts par excellence, viz. redox enzymes, to an electrode can be exploited in the fabrication of high-performance bioelectronic devices. Here we report oxygen electroreduction catalysed by Didymocrea sp. J6 laccase wired to gold nanoparticles via the trinuclear copper cluster. Bypassing the intramolecular electron transfer, which under certain conditions is the rate-limiting step of oxygen bioelectroreduction, has resulted in the fabrication of a high current density biocathode based on high-redox-potential laccase, which is able to operate in electrolytes with a broad pH range in the presence of high fluoride concentrations.
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| 4. |
- Krikstolaityte, Vida, et al.
(författare)
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Impact of molecular linker size on physicochemical properties of assembled gold nanoparticle mono-/multi-layers and their applicability for functional binding of biomolecules
- 2019
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Ingår i: Journal of Colloid and Interface Science. - : Elsevier. - 0021-9797 .- 1095-7103. ; 543, s. 307-316
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Tidskriftsartikel (refereegranskat)abstract
- In this work the impact of molecular inter-linker size on gold nanoparticle (AuNP) mono-/multilayer structural properties, density and homogeneity has been investigated. These characteristics are of great importance for functional binding of biomolecules. Positively charged high or low molecular weight inter-linkers, poly-L-lysine (PLL) or N-(6-mercapto)hexylpyridinium (MHP), were used to attach negatively charged AuNPs on a planar gold surface as well as to further interlink into a multilayer structure via layer-by-layer deposition. The inter-particle interaction within the assembled AuNP films was adjusted by the ionic strength in the AuNPs dispersions The AuNP layer density and structural/viscoelastic properties were evaluated by the quartz crystal microbalance with dissipation (QCM-D) technique. The validity of the commercial Voigt model, specifically developed for quantitative QCM-D data analysis of homogeneous viscoelastic films, was evaluated by a model independent analysis when comparing the assembled AuNP films with a homogeneous layer of a mucin from bovine submaxillary glands. Both AuNP mono- and multilayers, attached/interlinked via long flexible PLL molecules assembled to denser and more soft/viscous structures compared to those interlinked by short MHP compounds. Thus, PLL-interlinked AuNP mono-/multilayer structures were further investigated as a platform for laccase enzyme functional adsorption via qualitative assessment of bioelectrochemical characteristics of the enzyme. (C) 2019 Elsevier Inc. All rights reserved.
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| 5. |
- Malisauskas, Mantas, et al.
(författare)
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Ultrathin silver nanowires produced by amyloid biotemplating
- 2008
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Ingår i: Biotechnology progress (Print). - : Wiley. - 8756-7938 .- 1520-6033. ; 24:5, s. 1166-1170
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Tidskriftsartikel (refereegranskat)abstract
- By using a self-assembled amyloid from lysozyme as biotemplate we produced an ultrathin silver wire of 1 nm diameter and up to 2 μm in length, which is at the limit attainable in nanobiotechnological manufacturing. We showed that 2,2,2-trifluoroethanol produces a dual effect: it reduces ionic silver to colloidal nanoparticles with a regular size, depending on the length of incubation, and induces fibrillar assembly into the amyloid scaffold, forming the hollow channel filled with silver.
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| 6. |
- Misiunas, Audrius, et al.
(författare)
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Horse heart cytochrome c entrapped into the hydrated liquid-crystalline phases of phytantriol: X-ray diffraction and Raman spectroscopic characterization
- 2012
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Ingår i: Journal of Colloid and Interface Science. - : Elsevier BV. - 1095-7103 .- 0021-9797. ; 378, s. 232-240
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Tidskriftsartikel (refereegranskat)abstract
- Small angle X-ray diffraction (SAXD), resonance Raman (RR) spectroscopy with 413 nm excitation, and non-resonance Raman technique with 785 nm excitation were used to probe the influence of entrapped cytochrome c (Cyt c) on the structure of hydrated phytantriol (Phyt) liquid-crystalline phases as well as conformational changes of heme group and secondary structure of the protein. SAXD measurements indicated that incorporation of Cyt c affects both nanostructure dimensions and type of liquid-crystalline phases of hydrated Phyt. The unit cell dimensions decrease with increasing Cyt c concentration for all phases. In addition, protein perturbs the nanostructure of Q(230) and Q(224) liquid-crystalline phases of hydrated Phyt to such an extent that they transform into the Q(229) phase with the Im3m space group. RR data revealed that entrapment of oxidized Cyt c into the Q(230) phase at 1 wt.% content results in near complete reduction of central iron ion of the heme group, while its low-spin state and six-ligand coordination configuration are preserved. Based on the analysis of heme out-of-plane folding vibration near 568 cm(-1) (gamma(21)) and nu(48) mode at 633 cm(-1), it was demonstrated that the protein matrix tension on the heme group is relaxed upon incorporation of protein into Q(230) phase. Non-resonant Raman bands of difference spectra showed the preservation of alpha-helix secondary structure of Cyt c in the liquid-crystalline phase at relatively high (5 wt.%) content. The Cyt c induced spectroscopic changes of Phyt bands were found to be similar as decrease in temperature. (C) 2012 Elsevier Inc. All rights reserved.
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| 7. |
- Repecka, Donatas, et al.
(författare)
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Expanding functional protein sequence spaces using generative adversarial networks
- 2021
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Ingår i: Nature Machine Intelligence. - : Springer Science and Business Media LLC. - 2522-5839. ; 3:4, s. 324-333
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Tidskriftsartikel (refereegranskat)abstract
- De novo protein design for catalysis of any desired chemical reaction is a long-standing goal in protein engineering because of the broad spectrum of technological, scientific and medical applications. However, mapping protein sequence to protein function is currently neither computationally nor experimentally tangible. Here, we develop ProteinGAN, a self-attention-based variant of the generative adversarial network that is able to ‘learn’ natural protein sequence diversity and enables the generation of functional protein sequences. ProteinGAN learns the evolutionary relationships of protein sequences directly from the complex multidimensional amino-acid sequence space and creates new, highly diverse sequence variants with natural-like physical properties. Using malate dehydrogenase (MDH) as a template enzyme, we show that 24% (13 out of 55 tested) of the ProteinGAN-generated and experimentally tested sequences are soluble and display MDH catalytic activity in the tested conditions in vitro, including a highly mutated variant of 106 amino-acid substitutions. ProteinGAN therefore demonstrates the potential of artificial intelligence to rapidly generate highly diverse functional proteins within the allowed biological constraints of the sequence space.
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| 8. |
- Rzhepishevska, Olena I, et al.
(författare)
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Regulation of a novel Acidithiobacillus caldus gene cluster involved in metabolism of reduced inorganic sulfur compounds.
- 2007
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Ingår i: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 73:22, s. 7367-7372
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Tidskriftsartikel (refereegranskat)abstract
- Acidithiobacillus caldus has been proposed to play a role in the oxidation of reduced inorganic sulfur compounds (RISCs) produced in industrial biomining of sulfidic minerals. Here, we describe the regulation of a new cluster containing the gene encoding tetrathionate hydrolase (tetH), a key enzyme in the RISC metabolism of this bacterium. The cluster contains five cotranscribed genes, ISac1, rsrR, rsrS, tetH, and doxD, coding for a transposase, a two-component response regulator (RsrR and RsrS), tetrathionate hydrolase, and DoxD, respectively. As shown by quantitative PCR, rsrR, tetH, and doxD are upregulated to different degrees in the presence of tetrathionate. Western blot analysis also indicates upregulation of TetH in the presence of tetrathionate, thiosulfate, and pyrite. The tetH cluster is predicted to have two promoters, both of which are functional in Escherichia coli and one of which was mapped by primer extension. A pyrrolo-quinoline quinone binding domain in TetH was predicted by bioinformatic analysis, and the presence of an o-quinone moiety was experimentally verified, suggesting a mechanism for tetrathionate oxidation.
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| 9. |
- Shafaat, Atefeh, et al.
(författare)
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Glucose-to-Resistor Transduction Integrated into a Radio-Frequency Antenna for Chip-less and Battery-less Wireless Sensing
- 2022
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Ingår i: ACS Sensors. - : American Chemical Society (ACS). - 2379-3694. ; 7:4, s. 1222-1234
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Tidskriftsartikel (refereegranskat)abstract
- To maximize the potential of 5G infrastructure in healthcare, simple integration of biosensors with wireless tag antennas would be beneficial. This work introduces novel glucose-to-resistor transduction, which enables simple, wireless biosensor design. The biosensor was realized on a near-field communication tag antenna, where a sensing bioanode generated electrical current and electroreduced a nonconducting antenna material into an excellent conductor. For this, a part of the antenna was replaced by a Ag nanoparticle layer oxidized to high-resistance AgCl. The bioanode was based on Au nanoparticle-wired glucose dehydrogenase (GDH). The exposure of the cathode-bioanode to glucose solution resulted in GDH-catalyzed oxidation of glucose at the bioanode with a concomitant reduction of AgCl to highly conducting Ag on the cathode. The AgCl-to-Ag conversion strongly affected the impedance of the antenna circuit, allowing wireless detection of glucose. Mimicking the final application, the proposed wireless biosensor was ultimately evaluated through the measurement of glucose in whole blood, showing good agreement with the values obtained with a commercially available glucometer. This work, for the first time, demonstrates that making a part of the antenna from the AgCl layer allows achieving simple, chip-less, and battery-less wireless sensing of enzyme-catalyzed reduction reaction.
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| 10. |
- Sulcius, Sigitas, et al.
(författare)
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Genomic Characterization of Cyanophage vB_AphaS-CL131 Infecting Filamentous Diazotrophic Cyanobacterium Aphanizomenon flos-aquae Reveals Novel Insights into Virus-Bacterium Interactions
- 2019
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Ingår i: Applied and Environmental Microbiology. - : American Society of Microbiology. - 0099-2240 .- 1098-5336. ; 85:1
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Tidskriftsartikel (refereegranskat)abstract
- While filamentous cyanobacteria play a crucial role in food web dynamics and biogeochemical cycling of many aquatic ecosystems around the globe, the knowledge regarding the phages infecting them is limited. Here, we describe the complete genome of the virulent cyanophage vB_AphaS-CL131 (here, CL 131), a Siphoviridae phage that infects the filamentous diazotrophic bloom-forming cyanobacterium Aphanizomenon flos-aquae in the brackish Baltic Sea. CL 131 features a 112,793-bp double-stranded DNA (dsDNA) genome encompassing 149 putative open reading frames (ORFs), of which the majority (86%) lack sequence homology to genes with known functions in other bacteriophages or bacteria. Phylogenetic analysis revealed that CL 131 possibly represents a new evolutionary lineage within the group of cyanophages infecting filamentous cyanobacteria, which form a separate cluster from phages infecting unicellular cyanobacteria. CL 131 encodes a putative type V-U2 CRISPR-Cas system with one spacer (out of 10) targeting a DNA primase pseudogene in a cyanobacterium and a putative type II toxin-antitoxin system, consisting of a GNAT family N-acetyltransferase and a protein of unknown function containing the PRK09726 domain (characteristic of HipB antitoxins). Comparison of CL 131 proteins to reads from Baltic Sea and other available fresh- and brackish-water metagenomes and analysis of CRISPR-Cas arrays in publicly available A. flos-aquae genomes demonstrated that phages similar to CL 131 are present and dynamic in the Baltic Sea and share a common history with their hosts dating back at least several decades. In addition, different CRISPR-Cas systems within individual A. flos-aquae genomes targeted several sequences in the CL 131 genome, including genes related to virion structure and morphogenesis. Altogether, these findings revealed new genomic information for exploring viral diversity and provide a model system for investigation of virus-host interactions in filamentous cyanobacteria. IMPORTANCE The genomic characterization of novel cyanophage vB_AphaS-CL131 and the analysis of its genomic features in the context of other viruses, metagenomic data, and host CRISPR-Cas systems contribute toward a better understanding of aquatic viral diversity and distribution in general and of brackish-water cyanophages infecting filamentous diazotrophic cyanobacteria in the Baltic Sea in particular. The results of this study revealed previously undescribed features of cyanophage genomes (e.g., self-excising intein-containing putative dCTP deaminase and putative cyanophage-encoded CRISPR-Cas and toxin-antitoxin systems) and can therefore be used to predict potential interactions between bloom-forming cyanobacteria and their cyanophages.
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| 11. |
- Yanamandra, Kiran, et al.
(författare)
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Alpha-Synuclein Reactive Antibodies as Diagnostic Biomarkers in Blood Sera of Parkinson's Disease Patients
- 2011
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Ingår i: PLoS One. - : Public Library of Science. - 1932-6203. ; 6:4, s. e18513-
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundAuto-antibodies with specificity to self-antigens have been implicated in a wide variety of neurological diseases, including Parkinson's (PD) and Alzheimer's diseases, being sensitive indicators of neurodegeneration and focus for disease prevention. Of particular interest are the studies focused on the auto-immune responses to amyloidogenic proteins associated with diseases and their applications in therapeutic treatments such as vaccination with amyloid antigens and antibodies in PD, Alzheimer's disease and potentially other neurodegeneration ailments.Methodology/Principal FindingsGenerated auto-antibodies towards the major amyloidogenic protein involved in PD Lewy bodies – α-synuclein and its amyloid oligomers and fibrils were measured in the blood sera of early and late PD patients and controls by using ELISA, Western blot and Biacore surface plasmon resonance. We found significantly higher antibody levels towards monomeric α-synuclein in the blood sera of PD patients compared to controls, though the responses decreased with PD progression (P<0.0001). This indicates potential protective role of autoimmunity in maintaining the body homeostasis and clearing protein species whose disbalance may lead to amyloid assembly. There were no noticeable immune responses towards amyloid oligomers, but substantially increased levels of IgGs towards α-synuclein amyloid fibrils both in PD patients and controls, which subsided with the disease progression (P<0.0001). Pooled IgGs from PD patients and controls interacted also with the amyloid fibrils of Aβ (1–40) and hen lysozyme, however the latter were recognized with lower affinity. This suggests that IgGs bind to the generic amyloid conformational epitope, displaying higher specificity towards human amyloid species associated with neurodegeneration.Conclusions/SignificanceOur findings may suggest the protective role of autoimmunity in PD and therefore immune reactions towards PD major amyloid protein – α-synuclein can be of value in the development of treatment and diagnostic strategies, especially during the early disease stages.
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| 12. |
- Zilius, Mindaugas, et al.
(författare)
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Depicting Temporal, Functional, and Phylogenetic Patterns in Estuarine Diazotrophic Communities from Environmental DNA and RNA
- 2021
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Ingår i: Microbial Ecology. - : Springer Science and Business Media LLC. - 0095-3628 .- 1432-184X. ; 81, s. 36-51
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Tidskriftsartikel (refereegranskat)abstract
- © 2020, Springer Science+Business Media, LLC, part of Springer Nature. Seasonally nitrogen-limited and phosphorus-replete temperate coastal waters generally host dense and diverse diazotrophic communities. Despite numerous studies in marine systems, little is known about diazotrophs and their functioning in oligohaline estuarine environments. Here we applied a combination of nifH transcript and metagenomic shotgun sequencing approaches to investigate temporal shifts in taxonomic composition and nifH activity of size-fractionated diazotrophic communities in a shallow and mostly freshwater coastal lagoon. Patterns in active nifH phylotypes exhibited a clear seasonal succession, which reflected their different tolerances to temperature change and nitrogen (N) availability. Thus, in spring, heterotrophic diazotrophs (Proteobacteria) dominated the nifH phylotypes, while increasing water temperature and depletion of inorganic N fostered heterocystous Cyanobacteria in summer. Metagenomic data demonstrated four main N-cycling pathways and three of them with a clear seasonal pattern: denitrification (spring) → N2 fixation (summer) → assimilative NO3− reduction (fall), with NH4+ uptake into cells occurring across all seasons. Although a substantial denitrification signal was observed in spring, it could have originated from the re-suspended benthic rather than planktonic community. Our results contribute to a better understanding of the realized genetic potential of pelagic N2 fixation and its seasonal dynamics in oligohaline estuarine ecosystems, which are natural coastal biogeochemical reactors.
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