Identification of immunoglobulins using Chou's pseudo amino acid composition with feature selection technique

2016 ◽  
Vol 12 (4) ◽  
pp. 1269-1275 ◽  
Author(s):  
Hua Tang ◽  
Wei Chen ◽  
Hao Lin
Keyword(s):  
Feature Selection ◽  
Immune System ◽  
Amino Acid ◽  
Cell Surface ◽  
Surface Proteins ◽  
Pseudo Amino Acid Composition ◽  
Feature Selection Technique ◽  
Cell Surface Proteins ◽  
Selection Technique ◽  
Foreign Substance

Immunoglobulins, also called antibodies, are a group of cell surface proteins which are produced by the immune system in response to the presence of a foreign substance (called antigen).

scholarly journals Identification and Analysis of Novel Tandem Repeats in the Cell Surface Proteins of Archaeal and Bacterial Genomes Using Computational Tools

2004 ◽  
Vol 5 (1) ◽  
pp. 2-16 ◽  
Author(s):  
S. Adindla ◽  
K. K. Inampudi ◽  
K. Guruprasad ◽  
L. Guruprasad
Keyword(s):  
Amino Acid ◽  
Cell Surface ◽  
Protein Sequence ◽  
Tandem Repeats ◽  
Surface Proteins ◽  
Sequence Motifs ◽  
Methanosarcina Acetivorans ◽  
Bacterial Genomes ◽  
Cell Surface Proteins ◽  
Conserved Sequence

We have identified four novel repeats and two domains in cell surface proteins encoded by theMethanosarcina acetivoransgenome and in some archaeal and bacterial genomes. The repeats correspond to a certain number of amino acid residues present in tandem in a protein sequence and each repeat is characterized by conserved sequence motifs. These correspond to: (a) a 42 amino acid (aa) residue RIVW repeat; (b) a 45 aa residue LGxL repeat; (c) a 42 aa residue LVIVD repeat; and (d) a 54 aa residue LGFP repeat. The domains correspond to a certain number of aa residues in a protein sequence that do not comprise internal repeats. These correspond to: (a) a 200 aa residue DNRLRE domain; and (b) a 70 aa residue PEGA domain. We discuss the occurrence of these repeats and domains in the different proteins and genomes analysed in this work.

scholarly journals Cell Surface Profiling of Retinal Müller Glial Cells Reveals Association to Immune Pathways after LPS Stimulation

Cells ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 711
Author(s):  
Lea Lorenz ◽  
Sieglinde Hirmer ◽  
Adrian Schmalen ◽  
Stefanie M. Hauck ◽  
Cornelia A. Deeg
Keyword(s):  
Immune System ◽  
Cell Surface ◽  
Glial Cells ◽  
Decisive Role ◽  
Retinal Disease ◽  
Surface Proteins ◽  
Spectrometric Analysis ◽  
Cell Surface Proteins ◽  
Müller Glial Cells ◽  
Surface Profiling

Retinal Müller glial cells (RMG) are involved in virtually every retinal disease; however, the role of these glial cells in neuroinflammation is still poorly understood. Since cell surface proteins play a decisive role in immune system signaling pathways, this study aimed at characterizing the changes of the cell surface proteome of RMG after incubation with prototype immune system stimulant lipopolysaccharide (LPS). While mass spectrometric analysis of the human Müller glia cell line MIO-M1 revealed 507 cell surface proteins in total, with 18 proteins significantly more abundant after stimulation (ratio ≥ 2), the surfaceome of primary RMG comprised 1425 proteins, among them 79 proteins with significantly higher abundance in the stimulated state. Pathway analysis revealed notable association with immune system pathways such as “antigen presentation”, “immunoregulatory interactions between a lymphoid and a non-lymphoid cell” and “cell migration”. We could demonstrate a higher abundance of proteins that are usually ascribed to antigen-presenting cells (APCs) and function to interact with T-cells, suggesting that activated RMG might act as atypical APCs in the course of ocular neuroinflammation. Our data provide a detailed description of the unstimulated and stimulated RMG surfaceome and offer fundamental insights regarding the capacity of RMG to actively participate in neuroinflammation in the retina.

scholarly journals An exploration of immunohistochemistry-based prognostic markers in patients undergoing curative resections for colon cancer

BMC Cancer ◽  
2022 ◽  
Vol 22 (1) ◽  
Author(s):  
Astrid Louise Bjørn Bennedsen ◽  
Luyi Cai ◽  
Rune Petring Hasselager ◽  
Aysun Avci Özcan ◽  
Khadra Bashir Mohamed ◽  
...  
Keyword(s):  
Colon Cancer ◽  
Immune System ◽  
Cell Surface ◽  
Cancer Cells ◽  
Immune Cells ◽  
Cancer Recurrence ◽  
Surface Proteins ◽  
Recurrence Rates ◽  
Cell Surface Proteins ◽  
Cdx2 Expression

Abstract Background The immune system recognizes and destroys cancer cells. However, cancer cells develop mechanisms to avoid detection by expressing cell surface proteins. Specific tumour cell surface proteins (e.g. HLA-G, PD-L1, CDX2) either alone or in combination with the relative presence of immune cells (CD3 and CD8 positive T-cells) in the tumour tissue may describe the cancer cells’ ability to escape eradication by the immune system. The aim was to investigate the prognostic value of immunohistochemical markers in patients with colon cancer. Methods We conducted a retrospective study including patients diagnosed with pT3 and pT4 colon cancers. Immunohistochemical staining with HLA-G, PD-L1, CDX2, CD3, and CD8 was performed on tissue samples with representation of the invasive margin. PD-L1 expression in tumour cells and immune cells was reported conjointly. The expression of CD3 and CD8 was reported as a merged score based on the expression of both markers in the invasive margin and the tumour centre. Subsequently, a combined marker score was established based on all of the markers. Each marker added one point to the score when unfavourable immunohistochemical features was present, and the score was categorized as low, intermediate or high depending on the number of unfavourable stains. Hazard ratios for recurrence, disease-free survival and mortality were calculated. Results We included 188 patients undergoing colon cancer resections in 2011–2012. The median follow-up was 41.7 months, during which 41 (21.8%) patients had recurrence and 74 (39.4%) died. In multivariable regression analysis positive HLA-G expression (HR = 3.37, 95%CI [1.64–6.93]) was associated with higher recurrence rates, while a preserved CDX2 expression (HR = 0.23, 95%CI [0.06–0.85]) was associated with a lower risk of recurrence. An intermediate or high combined marker score was associated with increased recurrence rates (HR = 20.53, 95%CI [2.68–157.32] and HR = 7.56, 95%CI [1.06–54.16], respectively). Neither high expression of PD-L1 nor high CD3-CD8 score was significantly associated with recurrence rates. Patients with a high CD3-CD8 score had a significantly longer DFS and OS. Conclusions In tumour cells, expression of HLA-G and loss of CDX2 expression were associated with cancer recurrence. In addition, a combination of certain tumour tissue biomarkers was associated with colorectal cancer recurrence.

What do nanometer molecular trajectories tell us about heterogeneous cell surface domaines?

1995 ◽  
Vol 53 ◽  
pp. 786-787
Author(s):  
Watt W. Webb
Keyword(s):  
Cell Surface ◽  
Lipid Membranes ◽  
Surface Proteins ◽  
Protein Diffusion ◽  
Coated Pits ◽  
Cell Surface Proteins ◽  
Membrane Heterogeneity ◽  
Fluorescence Photobleaching Recovery ◽  
Photobleaching Recovery ◽  
Plasma Membrane Heterogeneity

Plasma membrane heterogeneity is implicit in the existence of specialized cell surface organelles which are necessary for cellular function; coated pits, post and pre-synaptic terminals, microvillae, caveolae, tight junctions, focal contacts and endothelial polarization are examples. The persistence of these discrete molecular aggregates depends on localized restraint of the constituent molecules within specific domaines in the cell surface by strong intermolecular bonds and/or anchorage to extended cytoskeleton. The observed plasticity of many of organelles and the dynamical modulation of domaines induced by cellular signaling evidence evanescent intermolecular interactions even in conspicuous aggregates. There is also strong evidence that universal restraints on the mobility of cell surface proteins persist virtually everywhere in cell surfaces, not only in the discrete organelles. Diffusion of cell surface proteins is slowed by several orders of magnitude relative to corresponding protein diffusion coefficients in isolated lipid membranes as has been determined by various ensemble average methods of measurement such as fluorescence photobleaching recovery(FPR).

Sign in / Sign up

Export Citation Format

Share Document