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Search results for: RECOMBINANT VP3 PROTEIN
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Biomolecular influenza virus detection based on the electrochemical impedance spectroscopy using the nanocrystalline boron-doped diamond electrodes with covalently bound antibodies
PublicationNew rapid pathogen detection methods with improved cost-effectiveness and efficiency are currently in the focus of the scientists from all over the world. Based on the experiences from the rapid spread of the influenza virus pandemic in 2009 it is clear that the development of the system for early diagnosis of this infection is essential. The crucial stage of the treatment is the detection of the viral infection during its initial...
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Effect of urea and glycine betaine on the hydration sphere of model molecules for the surface features of proteins
PublicationWater properties may significantly affect protein stability. Osmolytes are compounds that intrinsically affect water in many different ways and thus can influence proteins with this type of indirect mechanism. In this study, we characterize water properties in ternary solutions: model–water–osmolyte, with two model molecules: N-methylacetamide (NMA) and dimethyl sulfoxide (DMSO) and two osmolytes: glycine betaine (TMG)and urea....
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Anticancer imidazoacridinone C-1311 inhibits hypoxia-inducible factor-1α (HIF-1α), vascular endothelial growth factor (VEGF) and angiogenesis
PublicationAntitumor imidazoacridinone C-1311 is a DNA-reactive topoisomerase II and FLT3 receptor tyrosine kinase inhibitor. Here, we demonstrate the mechanism of C-1311 inhibitory action on novel targets: hypoxia-inducible factor-1α (HIF-1α), vascular-endothelial growth factor (VEGF), and angiogenesis. In a cell-free system, C-1311 prevented HIF-1α binding to an oligonucleotide encompassing a canonical hypoxia-responsive element (HRE),...
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L1 Cell Adhesion Molecule Overexpression Down Regulates Phosphacan and Up Regulates Structural Plasticity-Related Genes Rostral and Caudal to the Complete Spinal Cord Transection
PublicationL1 cell adhesion molecule (L1CAM) supports spinal cord cellular milieu after contusion and compression lesions, contributing to neuroprotection, promoting axonal outgrowth, and reducing outgrowth-inhibitory molecules in lesion proximity. We extended investigations into L1CAM molecular targets and explored long-distance effects of L1CAM rostral and caudal to complete spinal cord transection (SCT) in...
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A novel cold-active beta-D-galactosidase from the Paracoccus sp. 32d - gene cloning, purification and characterization
PublicationBeta-D-galactosidase (EC 3.2.1.23) catalyze the hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides. Cold-active beta-D-galactosidases have recently become a focus of attention of researchers and dairy product manufactures owing to theirs ability to: (I) eliminate of lactose from refrigerated milk for people afflicted with lactose intolerance, (II) convert lactose to glucose and galactose which...
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A rapid-response ultrasensitive biosensor for influenza virus detection using antibody modified boron-doped diamond
PublicationAccording to the World Health Organization (WHO), almost 2 billion people each year are infected worldwide with flu-like pathogens including influenza. This is a contagious disease caused by viruses belonging to the family Orthomyxoviridae. Employee absenteeism caused by flu infection costs hundreds of millions of dollars every year. To successfully treat influenza virus infections, detection of the virus during the initial development...
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An optimal designed experiment for the alkaline hydrolysis of feather keratin
PublicationFeathers, burdensome waste from the poultry industry, can be a cheap source of keratin, a protein with excellent physico- chemical, biological, and mechanical properties. Acid and alkaline hydrolyses are usually adopted for isolation of keratin from its natural resources. This study aimed at assessing the statistically significant effect of input variables in the alkaline hydrolysis of keratin from chicken feathers on the process...
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Expression of Deinococcus geothermalis Trehalose Synthase Gene in Escherichia coli and Its Enzymatic Properties
PublicationA novel trehalose synthase gene from Deinococcus geothermalis (DSMZ 11300) containing 1,692 bp reading-frame encoding 564 amino acids was amplified using PCR. The gene was ligated into pET30Ek/LIC vector and expressed after isopropyl alfa-D-thiogalactopyranoside induction in Escherichia coli BL21(DE3)pLysS. The recombinant trehalose synthase (DgeoTreS) containing a His6 tag at the C-terminus was purified by metal affinity chromatography...
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Analysis of a gene expression model
PublicationWe study a mathematical model of gene transcription and protein synthesis with negative feedback. We consider a system of equations taking into account the number of active binding sites, the way in which dimers bind to DNA and time delay in translation process. For a simplified model that consist of three ordinary differential equations with time delay we derive conditions for stability of the positive steady state and for the...
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Implementing fermentation technology for comprehensive valorisation of seafood processing by-products: A critical review on recovering valuable nutrients and enhancing utilisation
PublicationFermentation technology is a biorefining tool that has been used in various industrial processes to recover valuable nutrients from different side streams. One promising application of this technique is in the reclamation of nutritional components from seafood side streams. Seafood processing generates significant amounts of waste, including heads, shells, and other side streams. These side streams contain high quantities of valued...
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Synthesis of Trehalose by the Erythritol-Producing Yeast Yarrowia lipolytica Co-Displaying Maltooligosyltrehalose Synthase and Maltooligosyltrehalose Trehalohydrolase
PublicationIndustrial trehalose production faces economic challenges with costly enzyme preparations, prompting the exploration of eco-friendly alternatives. Here, we established a coupled functional sugar production line leveraging erythritolproducing cells as an innovative enzyme preparation for trehalose synthesis. The erythritol-producing Yarrowia lipolytica was modified to express a fusion protein consisting of maltooligosyltrehalose synthase...
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Crystal structures of the DsbG disulfide isomerase reveal an unstable disulfide
PublicationDsb proteins control the formation and rearrangement of disulfide bonds during the folding of secreted and membrane proteins in bacteria. DsbG, a member of this family, has disulfide bond isomerase and chaperone activity. Here, we present two crystal structures of DsbG at 1.7- and 2.0-Angstrom resolution that are meant to represent the reduced and oxidized forms, respectively. The oxidized structure, however, reveals a mixture...
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The bile salt content of human bile impacts on simulated intestinal proteolysis of β-lactoglobulin
PublicationThe gastrointestinal hydrolysis of food proteins has been portrayed in scientific literature to predominantly depend on the activity and specificity of proteolytic enzymes. Human bile has not been considered to facilitate proteolysis in the small intestine, but rather to assist in intestinal lipolysis. However, human bile can potentially influence proteins that are largely resistant to gastric digestion, and which are mainly hydrolysed...
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In vitro affinity of Deinococcus radiodurans MutS towards mismatched DNA exceeds that of its orthologues from Escherichia coli and Thermus thermophilus
PublicationThe mismatch binding protein MutS is responsible for the recognition of mispaired and unpaired bases, which is the initial step in DNA repair. Among the MutS proteins most extensively studied in vitro are those derived from Thermus thermophilus, Thermus aquaticus and Escherichia coli. Here, we present the first report on the in vitro examination of DNA mismatch binding activity of MutS protein from Deinococcus radiodurans and confront...
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Meiothermus ruber cells as β-galactosidase activity biocatalyst
PublicationThe current study allowed to establish the possibility of using whole cells of thermophilic bacteria Meiothermus ruber as a biocatalyst with β-galactosidase activity. β-galactosidases are used for hydrolysis of lactose as well as for oligosaccharides synthesis. The advantages of using whole bacterial cells catalysis is not only elimination of tedious, expensive protein isolation and/or purification but also stabilization of enzymes...
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The possibility of use keratin products in various branches of industry
PublicationBird's feather, the main by-product of the poultry industry, are not enough utilized and negatively influencing the environment. They contain large amount of keratin, the protein with high cystine content. The aim of our work was to obtain hydrolysates and isolates of keratin, which can be used in various areas of food, cosmetics, pharmaceutical industry and as animal feed. Keratin can be hydrolyzed and extracted from feather after...
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Keep It Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS
PublicationWe describe a versatile method to enforce the rotation of subsets of atoms, e.g., a protein subunit, in molecular dynamics (MD) simulations. In particular, we introduce a “flexible axis” technique that allows realistic flexible adaptions of both the rotary subunit as well as the local rotation axis during the simulation. A variety of useful rotation potentials were implemented for the GROMACS 4.5 MD package. Application to the...
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A new B-D-galactosidase with a low temperature optimum isolated from the Antarctic Arthrobacter sp. 20B: gene cloning, purification and characterization.
PublicationA psychrotrophic bacterium producing a coldadaptedB-galactosidase upon growth at low temperatureswas classiWed as Arthrobacter sp. 20B. A genomic DNAlibrary of strain 20B introduced into Escherichia coliTOP10F' and screening on X-Gal (5-bromo-4-chloro-3-indolyl-B-D-galactopyranoside)-containing agar plates ledto the isolation of B-galactosidase gene. The B-galactosidasegene (bgaS) encoding a protein of 1,053 amino acids,with a...
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Enzyme Conjugation - A Promising Tool for Bio-catalytic and Biotransformation Applications – A Review
PublicationEnzymes have revolutionized conventional industrial catalysts as more efficient, eco-friendly, and sustainable substitutes that can be used in different biotechnological processes, food, and pharmaceutical industries. Yet, the enzymes from nature are engineered to make them adapt and enhance their durability in the industrial environment. One promising approach involves the combined use of multiple enzymes that catalyze highly...
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Unraveling the Interplay between DNA and Proteins: A Computational Exploration of Sequence and Structure-Specific Recognition Mechanisms
PublicationMy PhD dissertation focused on DNA-protein interactions and the recognition of specific DNA sequences and structures. I discovered that acidic amino acid residues (Asp/Glu) play a crucial role by exhibiting a preference for cytosine. Their contribution to binding affinity depends on nearby cytosines, balancing electrostatic repulsion with specific interactions. Acidic residues act as negative selectors, discouraging non-cytosine...
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Enhancing colloidal stability of nanodiamond via surface modification with dendritic molecules for optical sensing in physiological environments
PublicationPre-treatment of diamond surface in low-temperature plasma for oxygenation and in acids for carboxylation was hypothesized to promote the branching density of the hyperbranched glycidol polymer. This was expected to increase the homogeneity of the branching level and suppress interactions with proteins. As a result, composite nanodiamonds with reduced hydrodynamic diameters that are maintained in physiological environments were...
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Molecular mechanism and energetics of coupling between substrate binding and product release in the F 1 -ATPase catalytic cycle
PublicationF1-ATPase is a motor protein that couples the rotation of its rotary γ subunit with ATP synthesis or hydrolysis. Single-molecule experiments indicate that nucleotide binding and release events occur almost simultaneously during the synthesis cycle, allowing the energy gain due to spontaneous binding of ADP to one catalytic β subunit to be directly harnessed for driving the release of ATP from another rather than being dissipated...
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IFI16 Impacts Metabolic Reprogramming during Human Cytomegalovirus Infection
PublicationCellular lipid metabolism plays a pivotal role in human cytomegalovirus (HCMV) infection, as increased lipogenesis in HCMV-infected cells favors the envelopment of newly synthesized viral particles. As all cells are equipped with restriction factors (RFs) able to exert a protective effect against invading pathogens, we asked whether a similar defense mechanism would also be in place to preserve the metabolic compartment from HCMV...
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Multicopy Suppressor Analysis of Strains Lacking Cytoplasmic Peptidyl-Prolyl cis/trans Isomerases Identifies Three New PPIase Activities in Escherichia coli That Includes the DksA Transcription Factor
PublicationConsistent with a role in catalyzing rate-limiting step of protein folding, removal of genes encoding cytoplasmic protein folding catalysts belonging to the family of peptidyl-prolyl cis/trans isomerases (PPIs) in Escherichia coli confers conditional lethality. To address the molecular basis of the essentiality of PPIs, a multicopy suppressor approach revealed that overexpression of genes encoding chaperones (DnaK/J and GroL/S),...
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A vector-enzymatic DNA fragment amplification-expression technology for construction of artificial, concatemeric DNA, RNA and proteins for novel biomaterials, biomedical and industrial applications
PublicationA DNA fragment amplification/expression technology for the production of new generation biomaterials for scientific, industrial and biomedical applications is described. The technology enables the formation of artificial Open Reading Frames (ORFs) encoding concatemeric RNAs and proteins. It recruits the Type IIS SapI restriction endonuclease (REase) for an assembling of DNA fragments in an ordered head-to-tail-orientation. The...
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Boron-doped carbon nanowalls for fast and direct detection of cytochrome C and ricin by matrix-free laser desorption/ionization mass spectrometry
PublicationDetecting proteins via surface assisted laser desorption/ionization mass spectrometry (SALDI-MS) method is still highly challenging, and only few examples of nanomaterials have been demonstrated to perform such detection so far. In this study, carbon nanowalls (CNWs), vertically aligned graphene sheet-based materials, presenting specific morphology, dimensions, and boron doping levels have shown improved performances for both qualitative...
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Nutrients and Bioactive Components of Human Milk After one Year of Lactation. Implication for Human Milk Banks
PublicationObjective: Specifying the nutrient content and bioactive compounds in milk from long-term lactation for the purpose of finding additional sources of donors’ milk for HMBs. Method: Human milk samples were collected from 43 mothers of term infants (term infant human milk, TIHM) (3–6 weeks of lactation) and 50 mothers who have breastfed for over a year (long-nursing human milk, LNHM). The milk collection time was 24 hours. The analyses...
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Chicken feather keratin as a source of bioactive peptides useful in prevention of metabolic disorders – in silico and in vitro hydrolysis
PublicationProtein derived bioactive peptides not only serve as nutrients but can also exert drug-like activity, e.g. antidiabetic, antihypertensive, or antimicrobial, to name a few. Most biopeptides have beneficial effects on health that make them attractive for nutraceutical applications. The majority of bioactive peptides have been obtained from food proteins, but protein-rich by-products generated by agriculture...
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Simplified AutoDock force field for hydrated binding sites
Publicationhas been extracted from the Protein Data Bank and used to test and recalibrate AutoDock force field. Since for some binding sites water molecules are crucial for bridging the receptor-ligand interactions, they have to be included in the analysis. To simplify the process of incorporating water molecules into the binding sites and make it less ambiguous, new simple water model was created. After recalibration of the force field on...
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Detection of Toxoplasma gondii Infection in Small Ruminants: Old Problems, and Current Solutions
PublicationToxoplasmosis is a parasitic zoonosis of veterinary importance, with implications for public health. Toxoplasma gondii infection causes abortion or congenital disease in small ruminants. Moreover, the consumption of infected meat, cured meat products, or unpasteurized milk and dairy products can facilitate zoonotic transmission. Serological studies conducted in various European countries have shown the high seroprevalence of specific...
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IgG Avidity Test as a Tool for Discrimination between Recent and Distant Toxoplasma gondii Infection—Current Status of Studies
PublicationToxoplasma gondii, an obligate intracellular protozoan parasite, is the causative agent of one of the most prevalent zoonoses worldwide. T. gondii infection is extremely important from a medical point of view, especially for pregnant women, newborns with congenital infections, and immunocompromised individuals. Thus, an accurate and proper diagnosis of this infection is essential. Among the available diagnostic tests, serology...
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Characterization of immobilized Escherichia coli cells transformed by β-galactosidase gene from Pyrococcus woesei
PublicationThermostable β-galactosidase from Escherichia coli transformant containing theenzyme gene from Pyrococcus woesei was immobilized on alginate gel.The benefits of using whole bacterial cells not only exclude expensive, laborious proteinisolation and purification but also stabilize enzymes by cytosol components. Increase inproductivity of enzyme can be achieved by cells permeabilization. To increase permeability ofcytoplasmic membrane...
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Detoxification of the tricyclic antidepressant opipramol and its analog – IS-noh by UGT enzymes before and after activation by phase I enzymes in rat liver microsomes
PublicationThe present studies were carried out to evaluate the simultaneous one-pot metabolism of opipramol (IS-opi) and analog (IS-noh) by phase I and phase II enzymes present in rat liver microsomes (RLM) as an alternative to separate testing with recombinant enzymes. This approach allows for more time-saving and cost-effective screening of the metabolism of newly discovered drugs. We also considered that the lack of results for phase...
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New PCR test for detection of Candida glabrata based on the molecular target chosen by the RAPD technique
PublicationRapid, reliable diagnosis is a necessary condition for the successful treatment of infections. Such diagnostic assays are continually being developed. #e paper presents a method for selecting the molecular target for PCR-based diagnostics based on the comparison of RAPD patterns. A sequence encoding Candida glabrata CBS138 hypothetical protein was selected. The limit of detection for PCR and real-time PCR reactions with DNA extracted...
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Dehydration converts DsbG crystal diffraction from low to high resolution
PublicationDiffraction quality crystals are essential for crystallographic studies of protein structure, and the production of poorly diffracting crystals is often regarded as a dead end in the process. Here we show a dramatic improvement of poorly diffracting DsbG crystals allowing high-resolution diffraction data measurement. Before dehydration, the crystals are fragile and the diffraction pattern is streaky, extending to 10 Å resolution....
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Coarse-grained simulation - an efficient approach for studying motions of large proteins
PublicationOne of the most important challenges in performing Molecular Dynamics (MD) simulations of large protein complexes is to accommodate the model accuracy and the simulation timescale. Hitherto, for the most relevant dynamics of protein aggregates in an explicit aqueous environment, the timescale reachable for the all-atoms simulations is of hundreds of nanoseconds. This range is four to six orders of magnitude smaller than processes...
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Alphitobius diaperinus larvae (lesser mealworm) as human food – An approval of the European Commission – A critical review
PublicationDue to the increasing threat of climate change and the need for sustainable food sources, human consumption of edible insects or entomophagy has gained considerable attention globally. The larvae of Alphitobius diaperinus Panzer (Coleoptera: Tenebrionidae), also known as the lesser mealworm, have been identified as a promising candidate for mass-rearing as a food source based the on evaluation on several aspects such as the production...
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Edible Lepidoptera as human foods – a comprehensive review
PublicationAs the global population continues to grow, traditional protein sources like meat and fish are becoming increasingly unsustainable due to their environmental impact. Edible insects, on the other hand, are highly nutritious, require minimal resources to produce, and emit significantly fewer greenhouse gases than traditional livestock. Lepidoptera, one of the most diverse insect orders, contains some popular edible species that have...
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Density functional theory calculations on entire proteins for free energies of binding: Application to a model polar binding site
PublicationIn drug optimization calculations, the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method can be used to compute free energies of binding of ligands to proteins. The method involves the evaluation of the energy of configurations in an implicit solvent model. One source of errors is the force field used, which can potentially lead to large errors due to the restrictions in accuracy imposed by its empirical nature....
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CYP3A4 overexpression enhances apoptosis induced by anticancer agent imidazoacridinone C-1311, but does not change the metabolism of C-1311 in CHO cells
PublicationWe examine whether CYP3A4 overexpression influences the rate and pattern of antitumor imidazoacridinone C-1311 metabolism, in relation to the impact of this overexpression on cell cycle progression and final cellular response of CHO cells following C-1311 treatment. Methods: Three CHO cell lines: CHO-WT, wild type, CHO-HR, overexpressing cytochrome P450 reductase (CPR) and CHO-HR-3A4, coexpressing CPR and CYP3A4 were applied....
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Identification of antigen Ag43 in uropathogenic Escherichia coli Dr+ strains and defining its role in the pathogenesis of urinary tract infections
PublicationUrinary tract infections (UTIs) caused by uropathogenic Escherichia coli (UPEC) are among the most common bacterial infectious diseases in the developed world. The urovirulence of UPEC is mainly associated with the surface-exposed fimbrial adhesins and adhesins of the autotransporter (AT) family. The best studied of theses proteins is antigen 43 (Ag43) mediating cell aggregation, adhesion and biofilm development as the causes of...
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Two bacterial small heat shock proteins, IbpA and IbpB, form a functional heterodimer
PublicationSmall heat shock proteins (sHsps) are a conserved class of ATP-independent chaperones which in stress conditions bind to unfolded protein substrates and prevent their irreversible aggregation. Substrates trapped in sHsps-containing aggregates are efficiently refolded into native structures by ATP-dependent Hsp70 and Hsp100 chaperones. Most γ-proteobacteria possess a single sHsp (IbpA), while in a subset of Enterobacterales, as...
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In vitro studies of polyphenols, antioxidants and other dietary indices in kiwifruit (Actinidia deliciosa)
PublicationOpisano wyniki badań poziomu protein oraz potencjału przeciwutleniającego w próbkach owoców kiwi, przechowywanych i dojrzewających w atmosferze etylenu ( w ciągu pierwszych 10 dni). Próbki owoców kiwi podzielono (w sposób przypadkowy) na dwie grupy:-próbki nie poddawane obróbce,-próbki poddawane obróbce (dojrzewanie w atmosferze etylenu).W próbkach oznaczano między innymi: wolne cukry, proteiny, polifenole oraz zdolność przeciwutleniającą....
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A novel cold-active β-D-galactosidase with transglycosylation activity from the Antarctic Arthrobacter sp. 32cB - gene cloning, purification and characterization
PublicationA gene encoding a novel β-D-galactosidase from the psychrotolerant Antarctic bacterium Arthrobacter sp. 32cB was isolated, cloned and expressed in Escherichia coli. The active form of recombinant β-D-galactosidase consists of two subunits with a combined molecular weight of approximately 257 kDa. The enzyme's maximum activity towards o-nitrophenyl-β-D-galactopyranoside was determined as occurring at 28 °C and pH 8.0. However, it...
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Saccharides
PublicationSaccharides are widely distributed in nature as the major component of fruits and vegetables (primarily monosaccharides), milk and malt (mainly disaccharides), and grains (mostly polysaccharides). They are an important source of energy, structural material, as well as flavor and taste factors. Molecules of this class of compounds contain mainly carbon, hydrogen, and oxygen atoms; however, most natural saccha- rides do not have...
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Extremophile Deinococcus geothermalis as potential source of proteolytic enzymes
PublicationAmong many extremozymes, thermophilic enzymes have attracted most attention during the past four decades. Such enzymes are of considerable industrial and biotechnological interest due to the fact that the enzymes are better suited for harsh industrial processes. There are many advantages of conducting industrial processes at high temperature, such as the increased solubility of many polymeric substrates, resulting in decreased...
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In silico design of telomerase inhibitors.
PublicationTelomerase is a reverse transcriptase enzyme involved in DNA synthesis at the end of linear chromosomes. Unlike in most other cells, telomerase is reactivated most cancerous cells and, therefore, has become a promising new anticancer target. Despite extensive research, direct telomerase inhibitors have yet not been introduced to the clinics because of the complexity of this enzyme. Structures of this protein from simple organisms...
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Amino Acid Based Antimicrobial Agents – Synthesis and Properties
PublicationStructures of several dozen of known antibacterial, antifungal or antiprotozoal agents are based on the amino acid scaffold. In most of them, the amino acid skeleton is of a crucial importance for their antimicrobial activity, since very often they are structural analogs of amino acid intermediates of different microbial biosynthetic pathways. Particularly, some aminophosphonate or aminoboronate analogs of protein amino acids are...
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Molecular Recognition in Complexes of TRF Proteins with Telomeric DNA
PublicationTelomeres are specialized nucleoprotein assemblies that protect the ends of linear chromosomes. In humans and many other species, telomeres consist of tandem TTAGGG repeats bound by a protein complex known as shelterin that remodels telomeric DNA into a protective loop structure and regulates telomere homeostasis. Shelterin recognizes telomeric repeats through its two major components known as Telomere Repeat-Binding Factors, TRF1...
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c-Myc inhibition and p21 modulation contribute to unsymmetrical bisacridines-induced apoptosis and senescence in pancreatic cancer cells
PublicationBackground Pancreatic cancer (PC) is one of the most aggressive cancers and is the seventh leading cause of cancer-related death worldwide. PC is characterized by rapid progression and resistance to conventional treatments. Mutations in KRAS, CDKN2A, TP53, SMAD4/DPC4, and MYC are major genetic alterations associated with poor treatment outcomes in patients with PC. Therefore, optimizing PC therapy is a tremendous challenge. Unsymmetrical...