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Article ; Online: Protein aggregation and glycation in Escherichia coli exposed to desiccation-rehydration stress.

Łupkowska, Adrianna / Monem, Soroosh / Dębski, Janusz / Stojowska-Swędrzyńska, Karolina / Kuczyńska-Wiśnik, Dorota / Laskowska, Ewa

Microbiological research

2023 Volume 270, Page(s) 127335

Abstract: In natural environments, bacteria often enter a state of anhydrobiosis due to water loss. Multiple studies have demonstrated that desiccation may lead to protein aggregation and glycation both in vivo and in vitro. However, the exact effects of water- ... ...

Abstract	In natural environments, bacteria often enter a state of anhydrobiosis due to water loss. Multiple studies have demonstrated that desiccation may lead to protein aggregation and glycation both in vivo and in vitro. However, the exact effects of water-loss-induced proteotoxic stress and the interplay between protein glycation and aggregation in bacteria remain elusive. Our studies revealed that protein aggregates formation in Escherichia coli started during desiccation and continued during the rehydration stage. The aggregates were enriched in proteins prone to liquid-liquid phase separation. Although it is known that glycation may induce protein aggregation in vitro, the aggregates formed in E. coli contained low levels of glycation products compared to the soluble protein fraction. Carnosine, glycine betaine and trehalose diminished the formation of protein aggregates and glycation products, resulting in increased E. coli viability. Notably, although high concentrations of glycine-betaine and trehalose significantly enhanced protein aggregation, glycation was still inhibited and E. coli cells survived desiccation better than bacteria grown without osmolytes. Taken together, our results suggest that the aggregates might play protective functions during early desiccation-rehydration stress. Moreover, it seems glycation rather than protein aggregation is the main cause of E. coli death upon desiccation-rehydration stress.
MeSH term(s)	Escherichia coli/metabolism ; Protein Aggregates ; Desiccation ; Maillard Reaction ; Trehalose/metabolism ; Water ; Fluid Therapy ; Bacteria/metabolism
Chemical Substances	Protein Aggregates ; Trehalose (B8WCK70T7I) ; Water (059QF0KO0R)
Language	English
Publishing date	2023-02-16
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1189614-0
ISSN	1618-0623 ; 0944-5013
ISSN (online)	1618-0623
ISSN	0944-5013
DOI	10.1016/j.micres.2023.127335
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Article ; Online: Secreting oviduct epithelial cells of Coturnix coturnix japonica (QOEC) and changes to their proteome after nonviral transfection.

Stadnicka, Katarzyna / Dębowska, Michalina / Dębski, Janusz / Bajek, Anna

Journal of cellular biochemistry

2019 Volume 120, Issue 8, Page(s) 12724–12739

Abstract: The quail oviduct (Coturnix c. japonica) is a natural candidate avian bioreactor, while the secretive quail oviduct epithelial cells (QOECs) are potential in vitro producers of recombinant proteins and vaccines. In view of the need for highly performing ... ...

Abstract	The quail oviduct (Coturnix c. japonica) is a natural candidate avian bioreactor, while the secretive quail oviduct epithelial cells (QOECs) are potential in vitro producers of recombinant proteins and vaccines. In view of the need for highly performing and transformable cell lines, QOEC may potentially act as an alternative bioreactor platform to the existing ones, for example, to the Chinese hamster ovary. The aim of this work was to characterize QOECs and their response to nucleofection with a nonviral plasmid DNA carrying the human interferon-α 2a gene (hIFNλ2a), in vitro. Primary QOEC cultures from laying quails (10-15 weeks old) were characterized by their proliferation rate, doubling time, and multilineage differentiation. Electroporation to cell nuclei (nucleofection) was used to deliver nonviral plasmid DNA containing a reporter GFP and hIFN under the ovalbumin promoter. The posttransfection analysis included polymerase chain reaction, Western blot analysis, and liquid chromatography coupled to tandem mass spectrometry. QOEC showed a typical epithelial characteristic in a primary 2D monolayer culture system and retained secretive potential up to the first passage. QOEC showed differentiation into osteoblastic lineage after stimulation. The nucleofection mean efficiency was low (2.3%). Differences of up to 10% in the proteomic profiles between nontransfected and transfected QOEC were found, the most important of these were related to the absence of keratins and cell-adhesion proteins in the transfected QOEC. Concluding, with the practical information provided here, QOEC have the potential to serve as an avian secreting cellular platform. QOEC may be further transformed to cell lineage to meet the requirement for a stable, electrocompetent, and transfectable model. The first proteomic comparison of QOEC delivered in this study showed, in the majority, a stable proteome of the nontransfected vs transfected QOEC.
MeSH term(s)	Animals ; Bioreactors ; Cell Differentiation ; Cell Proliferation ; Cells, Cultured ; Coturnix ; Electroporation ; Epithelial Cells/cytology ; Epithelial Cells/metabolism ; Female ; Humans ; Interferon-alpha/genetics ; Interferon-alpha/metabolism ; Osteoblasts/cytology ; Osteoblasts/metabolism ; Oviducts/cytology ; Oviducts/metabolism ; Plasmids/genetics ; Primary Cell Culture/methods ; Proteomics/methods ; Transfection
Chemical Substances	IFNA2 protein, human ; Interferon-alpha
Language	English
Publishing date	2019-03-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	392402-6
ISSN	1097-4644 ; 0730-2312
ISSN (online)	1097-4644
ISSN	0730-2312
DOI	10.1002/jcb.28541
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Article ; Online: Quantitative and structural changes of blood platelet cytoskeleton proteins in multiple sclerosis (MS).

Dziedzic, Angela / Michlewska, Sylwia / Jóźwiak, Piotr / Dębski, Janusz / Karbownik, Michał Seweryn / Łaczmański, Łukasz / Kujawa, Dorota / Glińska, Sława / Miller, Elżbieta / Niwald, Marta / Kloc, Malgorzata / Balcerzak, Łucja / Saluk, Joanna

Journal of autoimmunity

2024 Volume 145, Page(s) 103204

Abstract: Epidemiological studies show that cardiovascular events related to platelet hyperactivity remain the leading causes of death among multiple sclerosis (MS) patients. Quantitative or structural changes of platelet cytoskeleton alter their morphology and ... ...

Abstract	Epidemiological studies show that cardiovascular events related to platelet hyperactivity remain the leading causes of death among multiple sclerosis (MS) patients. Quantitative or structural changes of platelet cytoskeleton alter their morphology and function. Here, we demonstrated, for the first time, the structural changes in MS platelets that may be related to their hyperactivity. MS platelets were found to form large aggregates compared to control platelets. In contrast to the control, the images of overactivated, irregularly shaped MS platelets show changes in the cytoskeleton architecture, fragmented microtubule rings. Furthermore, MS platelets have long and numerous pseudopodia rich in actin filaments. We showed that MS platelets and megakaryocytes, overexpress β1-tubulin and β-actin mRNAs and proteins and have altered post-translational modification patterns. Moreover, we identified two previously undisclosed mutations in the gene encoding β1-tubulin in MS. We propose that the demonstrated structural changes of platelet cytoskeleton enhance their ability to adhere, aggregate, and degranulate fueling the risk of adverse cardiovascular events in MS.
Language	English
Publishing date	2024-03-22
Publishing country	England
Document type	Journal Article
ZDB-ID	639452-8
ISSN	1095-9157 ; 0896-8411
ISSN (online)	1095-9157
ISSN	0896-8411
DOI	10.1016/j.jaut.2024.103204
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Article: New Candidates for Biomarkers and Drug Targets of Ischemic Stroke-A First Dynamic LC-MS Human Serum Proteomic Study.

Turek-Jakubowska, Aleksandra / Dębski, Janusz / Jakubowski, Maciej / Szahidewicz-Krupska, Ewa / Gawryś, Jakub / Gawryś, Karolina / Janus, Agnieszka / Trocha, Małgorzata / Doroszko, Adrian

Journal of clinical medicine

2022 Volume 11, Issue 2

Abstract: 1) Background: The aim of this dynamic-LC/MS-human-serum-proteomic-study was to identify potential proteins-candidates for biomarkers of acute ischemic stroke, their changes during acute phase of stroke and to define potential novel drug-targets. (2) ... ...

Abstract	(1) Background: The aim of this dynamic-LC/MS-human-serum-proteomic-study was to identify potential proteins-candidates for biomarkers of acute ischemic stroke, their changes during acute phase of stroke and to define potential novel drug-targets. (2) Methods: A total of 32 patients (29-80 years) with acute ischemic stroke were enrolled to the study. The control group constituted 29 demographically-matched volunteers. Subjects with stroke presented clinical symptoms lasting no longer than 24 h, confirmed by neurological-examination and/or new cerebral ischemia visualized in the CT scans (computed tomography). The analysis of plasma proteome was performed using LC-MS (liquid chromatography-mass spectrometry). (3) Results: Ten proteins with significantly different serum concentrations between groups volunteers were: complement-factor-B, apolipoprotein-A-I, fibronectin, alpha-2-HS-glycoprotein, alpha-1B-glycoprotein, heat-shock-cognate-71kDa protein/heat-shock-related-70kDa-protein-2, thymidine phosphorylase-2, cytoplasmic-tryptophan-tRNA-ligase, ficolin-2, beta-Ala-His-dipeptidase. (4) Conclusions: This is the first dynamic LC-MS study performed on a clinical model which differentiates serum proteome of patients in acute phase of ischemic stroke in time series and compares to control group. Listed proteins should be considered as risk factors, markers of ischemic stroke or potential therapeutic targets. Further clinical validation might define their exact role in differential diagnostics, monitoring the course of the ischemic stroke or specifying them as novel drug targets.
Language	English
Publishing date	2022-01-11
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662592-1
ISSN	2077-0383
ISSN	2077-0383
DOI	10.3390/jcm11020339
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Article: Platelet-Derived Drug Targets and Biomarkers of Ischemic Stroke-The First Dynamic Human LC-MS Proteomic Study.

Gawryś, Karolina / Turek-Jakubowska, Aleksandra / Gawryś, Jakub / Jakubowski, Maciej / Dębski, Janusz / Szahidewicz-Krupska, Ewa / Trocha, Małgorzata / Derkacz, Arkadiusz / Doroszko, Adrian

Journal of clinical medicine

2022 Volume 11, Issue 5

Abstract: 1) Objective: The aim of this dynamic LC-MS (liquid chromatography and mass spectrometry) human platelet proteomic study was to identify the potential proteins candidates for biomarkers of acute ischemic stroke (AIS), their changes during the acute ... ...

Abstract	(1) Objective: The aim of this dynamic LC-MS (liquid chromatography and mass spectrometry) human platelet proteomic study was to identify the potential proteins candidates for biomarkers of acute ischemic stroke (AIS), their changes during the acute phase of stroke and to define potential novel drug targets. (2) Methods: A total of 32 patients (18-80 years old) were investigated that presented symptoms of AIS lasting less than 24 h from the onset, confirmed by neurological examination and/or new cerebral ischemia visualized in the CT (computed-tomography) scans. The analysis of platelet proteome was performed using LC-MS at baseline, and then on the third and seventh day from the onset of symptoms. The control group was demographically matched without any clinical signs of acute brain injury. (3) Results: The differences between platelets, at 24 h after first symptoms of stroke subjects and the control group included: β-amyloid A4 and amyloid-like protein 2, coactosin-like protein, thymidine phosphorylase 4 (TYMP-4), interferon regulatory factor 7 (IRF7), vitamin K-dependent protein S, histone proteins (H2A type 1 and 1-A, H2A types 2B and J, H2Av, -z, and -x), and platelet basic protein. The dynamic changes in the platelet protein concentration involved thrombospondin-1, thrombospondin-2, filamin A, B, and C. (4) Conclusions: This is the first human dynamic LC-MS proteomic study that differentiates platelet proteome in the acute phase of ischemic stroke in time series and compares the results with healthy controls. Identified proteins may be considered as future markers of ischemic stroke or therapeutic drug targets. Thymidine phosphorylase 4 (TYMP-4) holds promise as an interesting drug target in the management or prevention of ischemic stroke.
Language	English
Publishing date	2022-02-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662592-1
ISSN	2077-0383
ISSN	2077-0383
DOI	10.3390/jcm11051198
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Article ; Online: Influence of Environmental and Genetic Factors on Proteomic Profiling of Outer Membrane Vesicles from

Godlewska, Renata / Klim, Joanna / Dębski, Janusz / Wyszyńska, Agnieszka / Łasica, Anna

Polish journal of microbiology

2019 Volume 68, Issue 2, Page(s) 255–261

Abstract: The proteomes of outer membrane vesicles (OMVs) secreted by : The proteomes of outer membrane vesicles (OMVs) secreted ... ...

Abstract	The proteomes of outer membrane vesicles (OMVs) secreted by The proteomes of outer membrane vesicles (OMVs) secreted by
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/analysis ; Campylobacter jejuni/chemistry ; Campylobacter jejuni/drug effects ; Campylobacter jejuni/genetics ; Extracellular Vesicles/chemistry ; Gene Deletion ; Heat-Shock Proteins/deficiency ; Oxidoreductases/deficiency ; Oxygen/toxicity ; Proteome/analysis ; Stress, Physiological
Chemical Substances	Anti-Bacterial Agents ; Bacterial Proteins ; Heat-Shock Proteins ; Proteome ; Oxidoreductases (EC 1.-) ; Oxygen (S88TT14065)
Language	English
Publishing date	2019-06-12
Publishing country	Poland
Document type	Journal Article
ZDB-ID	2234080-4
ISSN	2544-4646 ; 1733-1331
ISSN (online)	2544-4646
ISSN	1733-1331
DOI	10.33073/pjm-2019-027
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Article: Isolation of Proteins from Potato Tubers

Murawska, Zofia / Dębski, Janusz / Lebecka, Renata / Szajko, Katarzyna

Hodowla roślin aklimtyzacja i nasiennictwo. 2017 June 01, v. 75, no. 1

2017

Abstract: Here we optimized an efficient and reproducible method for proteins isolation from potato tubers for quantitative proteomic analysis, aimed at detection of differentially expressed proteins upon various experimental conditions. ...

Abstract	Here we optimized an efficient and reproducible method for proteins isolation from potato tubers for quantitative proteomic analysis, aimed at detection of differentially expressed proteins upon various experimental conditions.
Keywords	gene expression regulation ; potatoes ; protein synthesis ; proteins ; proteomics ; Solanum tuberosum ; tubers
Language	English
Dates of publication	2017-0601
Size	p. 23-27.
Publishing place	Sciendo
Document type	Article
ZDB-ID	2594296-7
ISSN	2083-599X ; 1429-3862 ; 0018-3040
ISSN (online)	2083-599X ; 1429-3862
ISSN	0018-3040
DOI	10.1515/plass-2017-0005
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Article: Quantitative proteomic analysis of differentially expressed proteins in tubers of potato plants differing in resistance to Dickeya solani

Lebecka, Renata / Dębski, Janusz / Kistowski, Michał / Marczewski, Waldemar / Murawska, Zofia / Szajko, Katarzyna

Plant and soil. 2019 Aug., v. 441, no. 1-2

2019

Abstract: AIMS: This study aims the detection of proteins associated with increased resistance of tubers to necrotrophic bacteria Dickeya solani in tetraploid and diploid potato plants. METHODS: Comparative analysis of differently expressed proteins in tuber ... ...

Abstract	AIMS: This study aims the detection of proteins associated with increased resistance of tubers to necrotrophic bacteria Dickeya solani in tetraploid and diploid potato plants. METHODS: Comparative analysis of differently expressed proteins in tuber tissue of potato cultivars and diploid interspecific hybrids of Solanum, differing in resistance to Dickeya solani, was performed using nano-liquid chromatography coupled with tandem mass spectrometry (LC-MS-MS/MS). Two highly resistant (Bea and Humalda) and three susceptible (Irys, Katahdin, Ulster Supreme) potato cultivars, and the highly resistant (DG 00–270) and the susceptible (DG 08–305) diploid clones, were studied. Proteins were extracted from wounded potato tubers inoculated with bacteria at an early symptomatic phase of infection and from controls, i.e., intact tubers and wounded mock-inoculated tubers. Data are available via ProteomeXchange with identifier PXD013009. RESULTS: Eight constitutive differentially expressed proteins with fold changes ≥1.9 and q-value ≤0.1 between the resistant and susceptible cultivar groups after D. solani infection were selected. Probable inactive patatin-03-Kuras 1 and the proteinase inhibitor PTI exhibited significantly increased protein abundances after bacterial inoculation in both resistant cultivars compared to the susceptible cultivars. In the diploid clones, only metallocarboxypeptidase and metallocarboxypeptidase-like inhibitors exhibited much higher fold changes following pathogenic invasion (274.4- and 368.6-fold, respectively) than after mock inoculation (165.5- and 130.7-fold, respectively). CONCLUSIONS: These results show that different proteins indicating significant fold changes between the resistant and susceptible potato cultivars and diploid clones are induced at an early phase of symptomatic D. solani infection.
Keywords	bacteria ; clones ; cultivars ; Dickeya solani ; diploidy ; enzymes ; gene expression regulation ; hybrids ; interspecific hybridization ; liquid chromatography ; potatoes ; protein synthesis ; proteinase inhibitors ; proteins ; proteomics ; Solanum tuberosum ; tandem mass spectrometry ; tetraploidy ; tubers
Language	English
Dates of publication	2019-08
Size	p. 317-329.
Publishing place	Springer International Publishing
Document type	Article
ZDB-ID	208908-7
ISSN	1573-5036 ; 0032-079X
ISSN (online)	1573-5036
ISSN	0032-079X
DOI	10.1007/s11104-019-04125-7
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Article ; Online: Multi-omic signatures of atherogenic dyslipidaemia: pre-clinical target identification and validation in humans.

Olkowicz, Mariola / Czyzynska-Cichon, Izabela / Szupryczynska, Natalia / Kostogrys, Renata B / Kochan, Zdzislaw / Debski, Janusz / Dadlez, Michal / Chlopicki, Stefan / Smolenski, Ryszard T

Journal of translational medicine

2021 Volume 19, Issue 1, Page(s) 6

Abstract: Background: Dyslipidaemia is a major risk factor for atherosclerosis and cardiovascular diseases. The molecular mechanisms that translate dyslipidaemia into atherogenesis and reliable markers of its progression are yet to be fully elucidated. To address ...

Abstract	Background: Dyslipidaemia is a major risk factor for atherosclerosis and cardiovascular diseases. The molecular mechanisms that translate dyslipidaemia into atherogenesis and reliable markers of its progression are yet to be fully elucidated. To address this issue, we conducted a comprehensive metabolomic and proteomic analysis in an experimental model of dyslipidaemia and in patients with familial hypercholesterolemia (FH). Methods: Liquid chromatography/mass spectrometry (LC/MS) and immunoassays were used to find out blood alterations at metabolite and protein levels in dyslipidaemic ApoE Results: We identified 15 metabolites (inhibitors and substrates of nitric oxide synthase (NOS), low-molecular-weight antioxidants (glutamine, taurine), homocysteine, methionine, 1-methylnicotinamide, alanine and hydroxyproline) and 9 proteins (C-reactive protein, proprotein convertase subtilisin/kexin type 9, apolipoprotein C-III, soluble intercellular adhesion molecule-1, angiotensinogen, paraoxonase-1, fetuin-B, vitamin K-dependent protein S and biglycan) that differentiated FH patients from healthy controls. Most of these changes were consistently found in dyslipidaemic mice and were further amplified if mice were fed an atherogenic (Western or low-carbohydrate, high-protein) diet. Conclusions: The alterations highlighted the involvement of an immune-inflammatory response system, oxidative stress, hyper-coagulation and impairment in the vascular function/regenerative capacity in response to dyslipidaemia that may also be directly engaged in development of atherosclerosis. Our study further identified potential biomarkers for an increased risk of atherosclerosis that may aid in clinical diagnosis or in the personalized treatment.
MeSH term(s)	Animals ; Atherosclerosis/complications ; Dyslipidemias/complications ; Humans ; Hyperlipoproteinemia Type II ; Mice ; Proprotein Convertase 9 ; Proteomics ; Receptors, LDL
Chemical Substances	Receptors, LDL ; Proprotein Convertase 9 (EC 3.4.21.-)
Language	English
Publishing date	2021-01-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1479-5876
ISSN (online)	1479-5876
DOI	10.1186/s12967-020-02663-8
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Article ; Online: Keratinous waste decomposition and peptide production by keratinase from Geobacillus stearothermophilus AD-11.

Gegeckas, Audrius / Gudiukaitė, Renata / Debski, Janusz / Citavicius, Donaldas

International journal of biological macromolecules

2015 Volume 75, Page(s) 158–165

Abstract: A keratinolytic proteinase was cloned from thermophilic bacterium Geobacillus stearothermophilus AD-11 and was expressed in Escherichia coli BL21(DE3). Recombinant keratinolytic proteinase (RecGEOker) with an estimated molecular weight of 57 kDa was ... ...

Abstract	A keratinolytic proteinase was cloned from thermophilic bacterium Geobacillus stearothermophilus AD-11 and was expressed in Escherichia coli BL21(DE3). Recombinant keratinolytic proteinase (RecGEOker) with an estimated molecular weight of 57 kDa was purified and keratinase activity was measured. RecGEOker showed optimal activity at pH 9 and 60 °C. Recombinant keratinolytic proteinase showed the highest substrate specificity toward keratin from wool > collagen > sodium caseinate > gelatin > and BSA in descending order. RecGEOker is applicable for efficient keratin waste biodegradation and can replace conventional non-biological hydrolysis processes. High-value small peptides obtained from enzymatic biodegradation by RecGEOker are suitable for industrial application in white and/or green biotechnology for use as major additives in various products.
MeSH term(s)	Animals ; Cloning, Molecular ; Computational Biology ; Electrophoresis, Polyacrylamide Gel ; Enzyme Inhibitors/pharmacology ; Enzyme Stability/drug effects ; Escherichia coli ; Genes, Bacterial ; Geobacillus stearothermophilus/enzymology ; Geobacillus stearothermophilus/genetics ; Hydrolysis ; Ions ; Keratins/metabolism ; Metals/pharmacology ; Molecular Sequence Data ; Peptide Hydrolases/isolation & purification ; Peptide Hydrolases/metabolism ; Peptides/metabolism ; Sheep ; Solubility ; Solvents ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Substrate Specificity/drug effects ; Waste Products
Chemical Substances	Enzyme Inhibitors ; Ions ; Metals ; Peptides ; Solvents ; Waste Products ; Keratins (68238-35-7) ; Peptide Hydrolases (EC 3.4.-) ; keratinase (EC 3.4.-)
Language	English
Publishing date	2015-04
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2015.01.031
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