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Immunogenic proteins in the somatic proteome of the adult cestode Hymenolepis diminuta - a proteomic approach

100%

Mlocicki D., Bien J., Salamatin R., Sulima A.

Annals of Parasitology

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2016

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tom 62

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nr Suppl.

2

Mass spectrometry approaches in proteomic and metabolomic studies

86%

Rodziewicz P., Swarcewicz B., Chmielewska K.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2014

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tom 95

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nr 3

3

Use of zwitterionic type of detergent in isolation of Escherichia coli O56 outer membrane proteins improves their two-dimensional electrophoresis [2-DE]

86%

Bugla-Ploskonska G., Futoma-Koloch B., Skwara A., Doroszkiewicz W.

Polish Journal of Microbiology

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2009

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tom 58

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nr 3

205-209

Escherichia coli O56 were originally isolated from infected humans. Here it is reported that using the zwitterionic detergent (Zwittergent Z 3-14®) to isolate outer membrane proteins (OMPs) from Escherichia coli O56 is suitable for their separation by two-dimensional electrophoresis (2-DE) using pH 3-10 immobilized pH gradient IPG strips (BIO-RAD).

4

Sperm mitochondrial dysfunction and oxidative stress as possible reasons for isolated asthenozoospermia

86%

Nowicka-Bauer K., Lepczynski A., Ozgo M., Kamieniczna M., Fraczek M., Stanski L., Olszewska M., Malcher A., Skrzypczak W., Kurpisz M. K.

Journal of Physiology and Pharmacology

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2018

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tom 69

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nr 3

5

Plasma proteomic profiling of African catfish (Clarias gariepinus)

86%

Herosimczyk A., Ozgo M., Lepczynski A., Ciechanowicz A., Colussi A., Seniuta P., Skrzypczak W. F.

Medycyna Weterynaryjna

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2013

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tom 69

|

nr 10

This study was aimed at profiling plasma proteins of healthy 8-month-old African catfish. Plasma proteins within the isoelectric point ranging from 3.0 to 10.0 were separated by high resolution two-dimensional electrophoresis (2-DE). In total, 8 different gene products were identified with a matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometer. These included carrier proteins (fatty acid-binding protein 1, metallothionein, mitoferrin-2), a structural protein (vimentin), proteins involved in the regulation of transcription (thyroid hormone receptor alpha A, endothelial differentiation-related factor 1 homolog), and others (B-cell lymphoma 6 protein homolog, FGFR1 oncogene partner 2 homolog). This is the first study attempting to map the plasma proteome of Clarias gariepinus. Owing to the lack of information concerning catfish protein sequences in the relevant databases, protein spots were identified by matching peptide data to interspecies homology. The results of this preliminary study may encourage other authors to undertake further research on the plasma proteome of the African catfish.

6

Proteomics of anther and pollen development in tomato and Arabidopsis

86%

Sawhney V. K., Sheoran I. S., Sproule K.

Acta Biologica Cracoviensia. Series Botanica. Supplement

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2005

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tom 47

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nr 1

7

To predict human Biomarker for the obesity using mouse homologous expression data at different theiler stages

86%

Kumar A., Puri R., Gupta K., Pal A.

International Letters of Natural Sciences

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2015

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tom 45

There are numerous genetic factors like MC4R (Melanocortin-4 receptor), POMC (Proopiomelanocortin), SIM1 (Single Minded Gene) etc. important in obesity, which can be used as biomarker. But more reliable diagnostic markers are the need for today, along with new therapeutic strategies that target specific molecules in the disease pathways. As in mouse and human genes, where mutations in one or both species are associated with some phenotypic characteristics as observed in human disease. In molecular mechanisms of development, differentiation, and disease gene expression data provide crucial insights. Up-regulation and down-regulation of selective genes can have major effects on diet-induced obesity, but there is little or no effect when animals are fed a low-fat diet. In present study we have studied the gene expression data of mouse at different theiler stages using GXD BioMart. The interacting partners and pathway of the genes that are already used as biomarker in mouse as well as in humans have been studied. A gene NPY1R (Neuropeptide Y1 receptor) was taken as common after STRING and KEGG results on the basis of biochemical pathways and interactions similar to MC4R. Our present work focuses on comparative genomics and proteomics analysis of NPY1R, which has led to identification of biomarker by comparing it with already known MC4R human and mouse biomarker. It has been concluded that both the proteins are structurally and functionally similar.

8

ESH Euroconference on Translational Research in Transplantation: immunogenetics, pharmacogenomics, proteomics, and immunobiology

86%

Basak G. W., Gronkowska A.

Archivum Immunologiae et Therapiae Experimentalis

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2006

|

tom 54

|

nr 6

9

Corpora amylacea from multiple sclerosis brain tissue consists of aggregated neuronal cells

86%

Selmaj K., Pawlowska Z., Walczak A., Koziolkiewicz W., Raine C. S., Cierniewski C. S.

Acta Biochimica Polonica

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2008

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tom 55

|

nr 1

In this report, we describe proteomic analysis of corpora amylacea collected by postmortem laser microdissection from multiple sclerosis (MS) brain lesions. Using low level protein loads (about 30 µg), a combination of two-dimensional electrophoresis with matrix-assisted laser desorption/ionization-time of flight mass spectrometry and database interrogations we identified 24 proteins of suspected neuronal origin. In addition to major cytoskeletal proteins like actin, tubulin, and vimentin, we identified a variety of proteins implicated specifically in cellular motility and plasticity (F-actin capping protein), regulation of apoptosis and senescence (tumor rejection antigen-1, heat shock proteins, valosin-containing protein, and ubiquitin-activating enzyme E1), and enzymatic pathways (glyceraldehyde-3-dehydrogenase, protein disulfide isomerase, protein disulfide isomerase related protein 5, lactate dehydrogenase). Samples taken from regions in the vicinity of corpora amylacea showed only traces of cellular proteins suggesting that these bodies may represent remnants of neuronal aggregates with highly polymerized cytoskeletal material. Our data provide evidence supporting the concept that biogenesis of corpora amylacea involves degeneration and aggregation of cells of neuronal origin.

10

Protein profiling of sickle cell versus control RBC core membrane skeletons by ICAT technology and tandem mass spectrometry

86%

Chou J., Choudhary P. K., Goodman S. R.

Cellular and Molecular Biology Letters

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2006

|

tom 11

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nr 3

A proteomic approach using a cleavable ICAT reagent and nano-LC ESI tandem mass spectrometry was used to perform protein profiling of core RBC membrane skeleton proteins between sickle cell patients (SS) and controls (AA), and determine the efficacy of this technology. The data was validated through Peptide/Protein Prophet and protein ratios were calculated through ASAPratio. Through an ANOVA test, it was determined that there is no significant difference in the mean ratios from control populations (AA1/AA2) and sickle cell versus control populations (AA/SS). The mean ratios were not significantly different from 1.0 in either comparison for the core skeleton proteins (α spectrin, β spectrin, band 4.1 and actin). On the natural-log scale, the variation (standard deviation) of the method was determined to be 14.1% and the variation contributed by the samples was 13.8% which together give a total variation of 19.7% in the ratios.

11

Mass spectrometry analysis of the excretory-secretory (E-S) products of the model cestode Hymenolepis diminuta reveals their immunogenic properties and the presence of new E-S proteins in cestodes

72%

Bien J., Salamatin R., Sulima A., Savijoki K., Conn D. B., Nareaho A., Mlocicki D.

Acta Parasitologica

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2016

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tom 61

|

nr 2

12

Forest tree research in post genomic era. Introduction to systems biology of broadleaves

72%

Staszak A. M., Pawlowski T. A.

Dendrobiology

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2012

|

tom 68

Trees are long living organisms, rarely used in molecular experiments because of large size of the genome and long time of reproduction cycle. Sequencing data from Populus trichocarpa genome allowed for the development of research on the processes associated with tree biology such as secondary wood formation, long-term perennial growth, seasonal changes, biotic interactions, evolution etc. Reference data enable the investigation of non-model trees such as Quercus or Fagus, having ecological and economic significance. During projects scientists use genomic, transcriptomic, proteomic and metabolomic approaches which contribute to better understanding of the physiological processes regulating tree biology. Data collected from these multiple studies need to be integrated. The integration of data is the subject of the newly established field of science called systems biology. This review presents progress in tree research after finishing the sequencing project of Populus. It concentrates on modern trends in 'omics' and systems biology study of temperate broadleave trees during the last 10 years of studies.

13

Where are we in genomics?

72%

Hocquette J.-F.

Journal of Physiology and Pharmacology. Supplement

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2005

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tom 56

|

nr 3

37-70

Genomic studies provide scientists with methods to quickly analyse genes and their products en masse. The first high-throughput techniques to be developed were sequencing methods. A great number of genomes from different organisms have thus been sequenced. Genomics is now shifting to the study of gene expression and function. In the past 5-10 years genomics, proteomics and high-throughput microarray technologies have fundamentally changed our ability to study the molecular basis of cells and tissues in health and diseases, giving a new comprehensive view. For example, in cancer research we have seen new diagnostic opportunities for tumour classification, and prognostication. A new exciting development is metabolomics and lab-on-a-chip techniques (which combine miniaturisation and automation) for metabolic studies. However, to interpret the large amount of data, extensive computational development is required. In the coming years, we will see the study of biological networks dominating the scene in Physiology. The great accumulation of genomics information will be used in computer programs to simulate biologic processes. Originally developed for genome analysis, bioinformatics now encompasses a wide range of fields in biology from gene studies to integrated biology (i.e. combination of different data sets from genes to metabolites). This is systems biology which aims to study biological organisms as a whole. In medicine, scientific results and applied biotechnologies arising from genomics will be used for effective prediction of diseases and risk associated with drugs. Preventive medicine and medical therapy will be personalised. Widespread applications of genomics for personalised medicine will require associations of gene expression pattern with diagnoses, treatment and clinical data. This will help in the discovery and development of drugs. In agriculture and animal science, the outcomes of genomics will include improvement in food safety, in crop yield, in traceability and in quality of animal products (dairy products and meat) through increased efficiency in breeding and better knowledge of animal physiology. Genomics and integrated biology are huge tasks and no single lab can pursue this alone. We are probably at the end of the beginning rather than at the beginning of the end because Genomics will probably change Biology to a greater extent than previously forecasted. In addition, there is a great need for more information and better understanding of genomics before complete public acceptance.

14

Gender dimorphism in the exercise-naive murine skeletal muscle proteome

72%

Metskas L. A., Kulp M., Scordilis S. P.

Cellular and Molecular Biology Letters

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2010

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tom 15

|

nr 3

507-516

Skeletal muscle is a plastic tissue with known gender dimorphism, especially at the metabolic level. A proteomic comparison of male and female murine biceps brachii was undertaken, resolving an average of 600 protein spots of MW 15–150 kDa and pI 5–8. Twenty-six unique full-length proteins spanning 11 KOG groups demonstrated statistically significant (p<0.05) abundance differences between genders; the majority of these proteins have metabolic functions. Identified glycolytic enzymes demonstrated decreased abundance in females, while abundance differences in identified oxidative phosphorylation enzymes were specific to the proteins rather than to the functional group as a whole. Certain cytoskeletal and stress proteins showed specific expression differences, and all three phosphorylation states of creatine kinase showed significant decreased abundance in females. Expression differences were significant but many were subtle (≤ 2-fold), and known hormonally-regulated proteins were not identified. We conclude that while gender dimorphism is present in non-exercised murine skeletal muscle, the proteome comparison of male and female biceps brachii in exercise-naive mice indicates subtle differences rather than a large or obviously hormonal dimorphism.

15

Transcriptome and proteome changes accompanying increased vigor of osmoprimed rape (Brassica napus L.) seeds

72%

Kubala S., Lechowska K., Wojtyla L., Kosmala A., Quinet M., Lutts S., Garnczarska M.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2013

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tom 94

|

nr 3

16

New proteases of the chloroplast envelope – what do they do there?

72%

Adam Z.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2013

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tom 94

|

nr 3

17

Extracellular vesicles in follicular fluid of sexually mature gilts’ ovarian antral follicles - identification and proteomic analysis

72%

Grzesiak M., Popiolek K., Knapczyk-Stwora K.

Journal of Physiology and Pharmacology

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2020

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tom 71

|

nr 1

18

A novel approach for identifying DNA repair pathways proteins using an evolutionary approach: Plasmodium falciparum case study

72%

Milanowska K., Wojtczak J.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2016

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tom 97

|

nr 4

19

Redox-mediated regulation of wheat seed dormancy revealed through modification-specific proteomics

72%

Bykova N., Hoehn B., Rampitsch C., Hu J., Fan T.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2013

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tom 94

|

nr 2

20

Plasma fibrin clots of pulmonary embolism patients present increased amounts of factor XIII and alpha2-antiplasmin at 3 months’ anticoagulation since the acute phase

72%

Zabczyk M., Natorska J., Bagoly Z., Sarkady F., Barath B., Katona E., Bryk A., Zettl K., Wisniewski J. R., Undas A.

Journal of Physiology and Pharmacology

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2020

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tom 71

|

nr 4

Ograniczanie wyników

Immunogenic proteins in the somatic proteome of the adult cestode Hymenolepis diminuta - a proteomic approach

Mass spectrometry approaches in proteomic and metabolomic studies

Use of zwitterionic type of detergent in isolation of Escherichia coli O56 outer membrane proteins improves their two-dimensional electrophoresis [2-DE]

Sperm mitochondrial dysfunction and oxidative stress as possible reasons for isolated asthenozoospermia

Plasma proteomic profiling of African catfish (Clarias gariepinus)

Proteomics of anther and pollen development in tomato and Arabidopsis

To predict human Biomarker for the obesity using mouse homologous expression data at different theiler stages

ESH Euroconference on Translational Research in Transplantation: immunogenetics, pharmacogenomics, proteomics, and immunobiology

Corpora amylacea from multiple sclerosis brain tissue consists of aggregated neuronal cells

Protein profiling of sickle cell versus control RBC core membrane skeletons by ICAT technology and tandem mass spectrometry

Mass spectrometry analysis of the excretory-secretory (E-S) products of the model cestode Hymenolepis diminuta reveals their immunogenic properties and the presence of new E-S proteins in cestodes

Forest tree research in post genomic era. Introduction to systems biology of broadleaves

Where are we in genomics?