27/11/2017

HSP70

HSP70s are monomeric proteins that reside in the cytosol of prokaryotes and the cytosol, nuclei, ER, mitochondria and chloroplasts of eukaryotes 8. In addition to their intracellular location, HSP70s have been found in the plasma membrane of malignantly transformed cells, on virally / bacterially infected cells and in the extracellular space. Extracellular Hsp70 exists in a free soluble form, complexed to antigenic peptides, or in exosomes 12,13,14,15. Noteworthy, Hsp70-1 as the most prominent member of the HSP70 family can be detected in the plasma membrane of a large proportion of different tumor entities, but not in the plasma membrane of normal cells/tissues 16,17,18. Several observations have led to the hypothesis that in tumor cells Hsp70-1 is an integral membrane protein associated with certain membrane lipid components 15, 16.

Fig 1: Ribbon and tube representation of the tertiary Hsp70-1 structure in the presence of ADP.

Heat shock proteins (HSPs) were originally described in the early 1960s by the pioneering work of Ferruccio Ritossa on the fruit fly Drosophila melanogaster 5,6,7. Expression of HSPs was found as being induced after exposure to different kinds of stress such as heat shock and could be demonstrated subsequently in any cellular organism 8. Nevertheless, other stress conditions, including heavy metals, hypoxia, nutrient deprivation and irradiation as well as oxidative and toxic stress, infections and exposure to inflammatory cytokines are also able to induce HSP expression 8, 9. Members of the HSP70 family were identified for the first time as being upregulated in bacteria in response to cellular stress 10. The painstaking analysis of the limited number of proteins firstly identified by heat shock induction in D. melanogaster and in E. coli led to the finding that DnaK, DnaJ and GrpE were also members of the heat shock class of proteins. In 1984, Bardwell and Craig demonstrated that the E. coli DnaK and the Drosophila 70 kDa heat shock proteins were highly conserved at the sequence level 11. Moreover, hybridization between the DNA of the archaebacterium Methanosarcina barkeri and the HSP70 genes of D. melanogaster, Saccharomyces cerevisiae, and E. coli has been detected, suggesting the existence of Hsp70-related genes in the three “primary kingdoms”: eukaryotes, eubacteria, and archaebacteria11.

The HSP70 Family

The HSP70 family represents the most conserved and best characterized group of HSPs comprising polypeptides whose molecular weights range from 66 – 78 kDa and that are encoded by a multigene family encompassing up to 17 genes and 30 pseudogenes in humans 19. Functional genes encoding HSP70 proteins map to human chromosomes 6, 14, 21, and at least one other chromosome 20. The most studied genes are HSPA1A and HSPA1B encoding proteins that only differ by two amino acids and are believed as being completely interchangeable proteins. The genes are clustered in the major histocompatibility complex class III region on chromosome 6p21.3.

The HSP70 family constitutes one of the most conserved protein families in evolution. Their members are present in all organisms and subcellular compartments and can be found from archaebacteria and plants to humans. In archaea and eubacteria Hsp70 is referred to as DnaK. In yeasts they are called Ssa, in mammals including humans they are referred to as HspA.

More information is available on the HSP70 website
and antibodies and related products are available by searching on the Newmarket Scientific website.

References:
1. Gribaldo,S. et al. Discontinuous occurrence of the hsp70 (dnaK) gene among Archaea and sequence features of HSP70 suggest a novel outlook on phylogenies inferred from this protein. J. Bacteriol.181, 434-443 (1999). [PubMed]

2. Sharma,D. & Masison,D.C. Hsp70 structure, function, regulation and influence on yeast prions. Protein Pept. Lett.16, 571-581 (2009). [PubMed]

3. Sharma,D. et al. Function of SSA subfamily of Hsp70 within and across species varies widely in complementing Saccharomyces cerevisiae cell growth and prion propagation. PLoS. ONE.4, e6644 (2009). [PubMed]

4. Kampinga,H.H. & Craig,E.A. The HSP70 chaperone machinery: J proteins as drivers of functional specificity. Nat. Rev. Mol. Cell Biol.11, 579-592 (2010). [PubMed]

5. Ritossa,F. Experimental activation of specific loci in polytene chromosomes of Drosophila. Exp. Cell Res.35, 601-607 (1963). DOI: 10.1016/0014-4827(64)90147-8

6. Ritossa,F. New puffs induced by temperature shock, DNP and salicilate in salivary chromosomes of D. melanogaster. Drosophila Information Service37, 122-123 (1963). [Drosophila Information Service]

7. Ritossa,F. A new puffing pattern induced by temperature shock and DNP in Drosophila. Experientia18, 571-573 (1962). DOI: 10.1007/BF02172188

8. Lindquist,S. & Craig,E.A. The heat-shock proteins. Annu. Rev. Genet.22, 631-677 (1988). [PubMed]

9. Jäättelä,M. Heat shock proteins as cellular lifeguards. Ann. Med.31, 261-271 (1999). [PubMed]

10. Craig,E.A. & Gross,C.A. Is hsp70 the cellular thermometer? Trends Biochem. Sci.16, 135-140 (1991). [PubMed]

11. Bardwell,J.C. & Craig,E.A. Major heat shock gene of Drosophila and the Escherichia coli heat-inducible dnaK gene are homologous. Proc. Natl. Acad. Sci. U. S. A81, 848-852 (1984). [PubMed]

12. Bausero,M.A., Gastpar,R., Multhoff,G., & Asea,A. Alternative mechanism by which IFN-gamma enhances tumor recognition: active release of heat shock protein 72. J. Immunol.175, 2900-2912 (2005). [PubMed]

13. Gastpar,R. et al. Heat shock protein 70 surface-positive tumor exosomes stimulate migratory and cytolytic activity of natural killer cells. Cancer Res.65, 5238-5247 (2005). [PubMed]

14. Lancaster,G.I. & Febbraio,M.A. Exosome-dependent trafficking of HSP70: a novel secretory pathway for cellular stress proteins. J. Biol. Chem.280, 23349-23355 (2005). [PubMed]

15. Vega,V.L. et al. Hsp70 translocates into the plasma membrane after stress and is released into the extracellular environment in a membrane-associated form that activates macrophages. J. Immunol.180, 4299-4307 (2008). [PubMed]

16. Gehrmann,M. et al. Tumor-specific Hsp70 plasma membrane localization is enabled by the glycosphingolipid Gb3. PLoS. ONE.3, e1925 (2008). [PubMed]

17. Schilling,D. et al. Binding of heat shock protein 70 to extracellular phosphatidylserine promotes killing of normoxic and hypoxic tumor cells. FASEB J.23, 2467-2477 (2009). [PubMed]

18. Stangl,S. et al. Targeting membrane heat-shock protein 70 (Hsp70) on tumors by cmHsp70.1 antibody. Proc. Natl. Acad. Sci. U. S. A108, 733-738 (2011). [PubMed]

19. Brocchieri,L., Conway de,M.E., & Macario,A.J. hsp70 genes in the human genome: Conservation and differentiation patterns predict a wide array of overlapping and specialized functions. BMC. Evol. Biol.8, 19 (2008). [PubMed]

20. Harrison,G.S. et al. Chromosomal location of human genes encoding major heat-shock protein HSP70. Somat. Cell Mol. Genet.13, 119-130 (1987). [PubMed]


25/10/2017

A unique kit for the detection of Dibromo-tyrosine

Dibromo-tyrosine is produced by the oxidative bromination of tyrosine residues. This reaction occurs via eosinophil peroxidase (EPO), an enzyme released by activated eosinophils. Upon activation of eosinophils, a respiratory burst occurs releasing elevated levels of O2 and H202. In the oxidation of tyrosine, EPO utilises H202 to catalyse the peroxidation of physiological levels of bromine found within plasma to generate the brominating reagent hypobromous acid (HOBr) (Ref: 1-5)


Figure 1. Bromination of tyrosine (Ref: 8)

Eosinophils play an immunomodulatory role through their recruitment to host sites of parasitic invasion. EPO levels also contribute to diseases such as asthma, cancers and allergic disorders where cellular activation is found to occur at pathological sites (Ref: 6-10)

Brominated products such as 3,5-dibromo-tyrosine serve as biological markers for in vivo eosinophil-mediated tissue damage which allows for understanding the overall roll oxidative stress has on pathways implicated in diseased states within organisms (Ref: 4) .


About This Assay

This unique kit is part of the StressMarq range. It is a is a competitive ELISA assay that can be used for the quantification of 3,5-dibromo-tyrosine in urine, plasma, and other sample matrices. The assay utilises a dibromo-tyrosine-coated plate and an biotin-conjugated antibody for detection which provides an assay range of 0.078 - 5 μg/mL, with a sensitivity of 0.04 μg/mL. Additional kit highlights are quick incubation times, stable reagents, and an easy to use protocol.

It is important to note that the dibromo-tyrosine antibody used in this assay recognises both free dibromo-tyrosine and brominated residues within a protein. Since complex samples such as plasma, are comprised of mixtures of protein fragments and free 3,5-dibromo-tyrosine, concentrations of 3,5-dibromo-tyrosine reported by ELISA methodology may not coincide with literature values where the free residue is typically measured. This should be kept in mind when analysing and interpreting experimental results.



Assay Overview



Figure 2. Schematic of the dibromo-tyrosine competitive ELISA

    Further details for this kit are available here:
    Dibromo-tyrosine ELISA Kit Details and Pricing

    References:
    1. MacPherson, J.C., Comhair, S. A. A., Erzurum, S.C., et al. Eosinophils are a major source of nitric oxide-derived oxidants in severe asthma: characterization of pathways available to eosinophils for generating reactive nitrogen species. J. Immun. 166, 5763-577 (2001).
    2. Mayeno, A. N., Curran, A. J., Roberts, R. L., et al. Eosinophils Preferentially Use Bromide to Generate Halogenating Agents. J. Biol. Chem. 264, 5660-5668 (1989).
    3. Babior, B. M. Oxygen-dependent microbial killing by phagocytes. N. Engl. J. Med. 298, 659-668 (1978).
    4. Wu W., Chen, Y., d’Avignon, A. et al. 3-Bromotyrosine and 3,5-dibromotyrosine are major products of protein oxidation by eosinophil peroxidase: potential markers for eosinophil-dependent tissue injury in vivo. Biochem. 38, 3538-3548 (1999)
    5. Kambayashi, Y., Ogino, K., Takemoto, K. et al. Preparation and characterization of a polyclonal antibody against brominated protein. J. Clin. Biochem. Nutr. 44, 95-103 2009
    6. Wang J., Slungaard A. Role of eosinophil peroxidase in host defense and disease pathology. Arch. Biochem. Biophys. 445, 256–260 (2006).
    7. Kazura, J. W., Fanning, M. M., Blumer, J. L. Mahmoud, A. A. Role of cellgenerated hydrogen peroxide in granulocyte-mediated killing of schistosomula of Schistosoma mansoni in vitro. J. Clin. Invest. 67, 93 (1981).
    8. Klebanoff, S. J., Locksley, R. M., Jong, E. C., Rosen, H. Oxidative response of phagocytes to parasite invasion. CIBA Found. Symp. 99: 92 (1983)
    9. Gleich, G. J., Ottesen, E. A., Leiferman, K. M., Ackerman, S. J. Eosinophils and human disease. Int. Arc. Allergy Appl. Immunol. 88: 59 (1989).
    10. Wardlaw, A. J., Eosinophils in the 1990s: new perspectives on their role in health and disease. Postgrad. Med. J. 70: 536 (1994).

    25/09/2017

    EXO-DNAc-PS: Isolation of circulating and EV-associated DNA

    Circulating DNA is emerging as a novel non-invasive tool for patient’s stratification and disease monitoring.

    While most of the research has focused on circulating cell-free (cfDNA) or circulating-tumorcell-(CTC)-derived DNA, extracellular vesicle-(EVs)-associated DNA (EV-DNA) is emerging as a third valuable “liquid biopsy” platform.

    Genomic single or double-stranded DNA and mitocondrial DNA have been detected in extracellular vesicles. In particular the majority of double-stranded DNA in extracellular vesicles seems to be associated with tumor derived exosomes (Thakur BK et al. 2014; Kalhert et al. 2014 ) where it represents the entire genome of the cancerous tumor from which exosomes were derived.

    This discovery indicates the potential of exosomes as a possible diagnostic tool. Exosomes can easily be obtained from a simple blood sample, so combined with an equally simple method of isolation, they may provide an important diagnostic method in the future.


    Get genomic DNA from exosomes with the EXO-DNAc Kit.

    This kit combines the ability of our DNA-Prep reagent to co-isolate EVs and circulating DNA from biofluids or culture supernatants with a user friendly system for DNA purification. Isolated vesicles are simply lysed with the appropriate lysis buffer and DNA is purified by spin columns and optimised buffers with a fast turnaround time (approximatively 30 minutes).

    Then finally, EXO-DNAc provides a DNA concentrator for concentrating the yield (4 fold concentration) and increasing the purity of the DNA to the levels required for digital PCR analysis.

    Click here for further information on the Exo-DNAc Kits 




    29/08/2017

    WHITE PAPER: Increasing Ligation Efficiency and Discovery of miRNAs for Small RNA NGS Sequencing Library Prep with Plant Samples.

    MicroRNAs (miRNAs) are 18-22 nucleotide long non-coding small RNAs that regulate protein expression and are involved in various cellular process such as development, growth, and physiology. Many studies have shown that miRNA expression in plants is altered by stress-response and environmental changes. Thus, the analysis of miRNA profiles using next generation sequencing can be beneficial to our understanding of stress tolerance of crops and other plants.

    Although miRNAs in plants and animals share many similarities, most mature miRNAs in plants contain 2’-O-methylation at the 3’ end. Typically, ligation of a 3’ adapter via the 3’ OH of the miRNA molecule is the first step in small RNA next-generation sequencing (NGS) sequencing library construction. 2’-O-methylation of plant miRNAs reduces ligation efficiency of the 3’ OH, making plant miRNA libraries difficult to generate.

    Here, we show that miRNA profiling from bean, wheat, corn, and rice using total RNA inputs can be successfully achieved using the NEXTflex® Small RNA Sequencing Kit v3, without library purification from PAGE gels, and that extending the ligation incubation step increases library yield. Importantly, many putative novel miRNAs were discovered with the NEXTflex® Small RNA Sequencing Kit v3 that were not discovered using other methods. Thus, this protocol allows generation of reduced-bias small RNA libraries from plant total RNA without the tedious step of gel-based size selection, enabling researchers to discover and profile more small RNAs from more samples than with traditional methods.


     

    The full white paper is available here:
    https://www.newmarketscientific.com/datasheets/Increasing-Ligation-Efficiency-and-Discovery-of-miRNAs-for-Small-RNA-NGS-Sequencing-Library-Prep-with-Plant-Samples.pdf
     

    References:
    1. Trends in Plant Science, Vol. 17, Issue 4, p196–203, J Cell Physiol. 2016 Feb;231(2):303-13, Curr Opin Plant Biol. 2016 Dec;34:68-76
    2. RNA Biology 9:10, 1218–1223; October 2012, The Plant Cell, Vol. 25: 2383–2399, July 2013 3. Nucleic Acids Res, 2011. 39(21): p. e141., RNA, 2011. 17(12): p. 225662., Silence, 2012.
    3(1): p. 4., Genome Biol, 2013. 14(10): p. R109.
    4. BMC Bioinformatics. 2014; 15(1): 275.

    31/07/2017

    Anti-Human (Cell Membrane Bound) HSP70 Monoclonal

    HSP70 is a highly conserved protein that is ubiquitously expressed. It can be found in chloroplasts, eukaryotic cytosol, endoplasmic reticulum, and mitochondria, but also embedded in the cell membrane and in the extracellular space (1,2,3,4). Even though HSP70 is one of the most studied heat shock proteins, the export mechanism and method of membrane insertion are not fully understood. Most proteins in the heat shock family lack a consensus signal for secretion via the ER-Golgi pathway (5).

    Researchers have found that HSP70 may be released from cells via exosomes or secretory vesicles (6). Although HSP70 is ubiquitously expressed, there is not much information about its presence on cell surface.

    The finding that HSP70 is localized on the cell surface of cancer cells but not normal cells suggests a conformational change of HSP70 in the lower pH environment characteristic of cancer cells (7). The presence of cell membrane embedded HSP70 has been found to increase the stability of cancer cells, thereby protecting tumors from environmental stress (8, 9).

    Anti-HSP70 antibody, clone 1H11 (Catalog No. SMC-249) is unique from other commercially available antibodies in that it can bind to the extracellular region of the cell membrane embedded HSP70 protein, allowing researchers to differentiate between membrane bound and intracellular HSP70 across cancer cells types.



    Further details are available here:
    https://www.newmarketscientific.com/products?utf8=%E2%9C%93&simpleq=SMC-249


    References:
    1. Gribaldo, S. et al. (1999) J. Bacteriol. 181, 434-443. 2. Sharma, D. & Masison, D.C. (2009) Protein Pept. Lett. 16, 571-581. 3. Sharma, D. et al. (2009) PLoS. ONE.4, e6644. 4. Kampinga, H.H. & Craig, E.A. (2010) Nat. Rev. Mol. Cell Biol. 11, 579-592. 5. Nickel, W. & Seedorf, M. (2008) Annu. Rev. Cell Dev. Biol. 24, 287-308. 6. Multhoff, G. & Hightower, L.E. (1996) Cell Stress. Chaperones. 1, 167-176. 7. De Maio, A. (2011) Cell Stress. Chaperones. 16, 235-249. 8. Horvath, I. & Vigh, L. (2010) Nature. 463, 436-438. 9. Horvath, I., Multhoff, G., Sonnleitner, A., & Vigh, L. (2008) Biochim. Biophys. Acta 1778, 1653-1664.

    19/06/2017

    Glucagon-like Protein Receptor (GLP2R) Antibody

    https://www.newmarketscientific.com/GLP2R

    An effective anti-glucagon like peptide-2 receptor (GLP2R) antibody (Cat No: 24200).

    GLP-2 is an emerging neurotransmitter involved in feeding control in the hypothalamus and brain stem, and has also been shown to regulate satiety through the endocrine system. Additionally, GLP2R agonists have been effective in the treatment of digestive diseases as well as diabetes.

    To further understand GLP-2 activity, use of ImmunoStar's GLP2R antibody allows for highly specific staining of neurons in the hypothalamus, brain stem, pancreatic α-cells, enteroendocrine cells in the intestine, as well as enteric neurons, and vagal sensory neurons.

    The rabbit antibody for Glucagon-like Protein Receptor is generated for acetyl 65-88 amide sequence targeting rat and human proteins, but not mouse.

    Produced by Dr. Mark Brownfield, the peptide sequence encoding the rat GLP2R was retrieved from the NCBI protein database and evaluated using GeneRunner software to generate antigen candidates for antibody production. 

    This antibody demonstrates significant labeling of enteroendocrine cells in the intestinal epithelium, as well as cell bodies of vagal afferents in nodose ganglia of the parasympathetic nervous system.

    Immunolabelling of Western blot reveals a band of approximately 66 kDa in human and rat tissue.


    Further product details are available here:
    https://www.newmarketscientific.com/GLP2R


    24/04/2017

    Small RNA Next Generation Sequencing without the bias


    Selected Report:
    https://www.newmarketscientific.com/datasheets/Randomized%20Adapters%20for%20Reducing%20Bias%20in%20Small%20RNA-Seq%20LibrariesV2.pdf

    Small RNA NGS without the bias


    SUMMARY

    The past decade has seen an explosion of interest in the small RNA repertoires of animal and plant species, and in understanding the biological function of all types of small RNAs.

    Next generation sequencing (NGS) is the most practical method for large-scale small RNA studies that aim to identify and enumerate small RNAs as with qPCR-based approaches, imperfectly matched small RNAs may still be able to hybridise to PCR primers. The same is also true for immobilised probes in microarrays. However NGS for small RNA analysis is also not without its challenges.

    Small RNA libraries prepared for sRNA-Seq have been found to contain biases, resulting in libraries that inaccurately represent relative levels of the different small RNAs present in the starting RNA sample. This bias is caused by the T4-phage RNA ligases used during the ligation steps of small RNA library preparation. Ideally, the RNA ligases would show no preference for attaching adapters to small RNAs of different sequences, but in reality this is simply not the case.

    A novel solution to overcome ligation bias in sRNA-seq libraries has been developed by Bioo Scientific (Austin TX USA), using a pool of adapters with randomised sequences at the ligation site, where each adapter sequence is present in vast molar excess over any given small RNA in the sample.

    To demonstrate the reduced bias when using a randomised adapter strategy, small RNA sequencing libraries were prepared in triplicate from an equimolar mixture of 23 synthetic miRNAs, using either standard or randomised adapters in the ligation steps. Further details and the results are discussed in the link in this blog post.

    Figure 1. Standard small RNA sequencing compared to NEXT flex Small RNA Sequencing Kit with randomised adapters.
    Libraries were prepared from an equimolar mix of 23 synthetic miRNAs. Each slice in the pie graph represents one miRNA.

    https://www.newmarketscientific.com/datasheets/Randomized%20Adapters%20for%20Reducing%20Bias%20in%20Small%20RNA-Seq%20LibrariesV2.pdf

    20/03/2017

    Anti-ERK1/2 Best antibody validated by Antibody Resource

    Selected Report:
    http://www.stressmarq.com/wp-content/uploads/ERK1-Antibody-Cat-No.-SPC-120-Comparison-Report-Antibody-Resource.pdf

    Stressmarq:Anti-ERK1/2 antibody validated by Antibody Resource


    SUMMARY

    Anti-ERK1/2 polyclonal antibody (Catalog No. SPC-120, referenced as P132 in the report) was independently validated by Antibody Resource for use in western blot on human breast adenocarcinoma (MCF7 cell line) whole cell lysate and mouse embryonic fibroblast (NIH3T3 cell line) whole cell lysate at a dilution of 1:5000, with bands detected at the expected molecular weight of 38-43 kDa. Can also be used in Immunohistochemistry, Immunocytochemistry/Immunofluorescence and flow cytometry.

    Immunohistochemistry analysis using Rabbit Anti-ERK1 Polyclonal Antibody (SPC-120). Tissue: backskin. Species: Mouse. Fixation: Bouin’s Fixative Solution. Primary Antibody: Rabbit Anti-ERK1 Polyclonal Antibody (SPC-120) at 1:100 for 1 hour at RT. Secondary Antibody: FITC Goat Anti-Rabbit (green) at 1:50 for 1 hour at RT. Localization: Cytoplasm.

    Immunohistochemistry analysis using Rabbit Anti-ERK1 Polyclonal Antibody (SPC-120). Tissue: Inflamed colon. Species: Mouse. Fixation: Formalin. Primary Antibody: Rabbit Anti-ERK1 Polyclonal Antibody (SPC-120) at 1:25000 for 12 hours at 4°C. Secondary Antibody: Biotin Goat Anti-Rabbit at 1:2000 for 1 hour at RT. Counterstain: Methyl Green at 200uL for 2 min at RT.
    https://www.newmarketscientific.com/stressmarq

    20/02/2017

    Tips and tricks for antibody production

    https://www.newmarketscientific.com/agrisera

    Antibody production and the validation process - How to obtain good results


    POSTER: The three crucial components for successful antibody production: Antigen, Host and Testing


    Contact us for a copy of this poster

    20/01/2017

    Highlighting NGS Disease panels

    https://www.newmarketscientific.com/ngs

    Illumina compatible disease panels


    Amplicon sequencing is based on ultra-deep sequencing of PCR products for analysing genetic variations and differences in gene expression. This approach allows researchers to focus interrogation on key regions of genomic interest using a simple workflow.

    Amplicon panels allow researchers to sequence large numbers of targeted gene regions from selected samples for analysis of mutational hot spots within a subset of genes or detection of copy number variations (CNVs), well-defined gene fusions, SNPs or Indels. RNA panels are also possible to look at differences in RNA levels of genes of interest.

    Using amplicon panels is an easily scalable, simple to use, fast, cost-effective approach which can be applied to a broad range of organisms and/or genes.

    The NEXTflex Amplicon Panels include primers flanking the regions of interest, library prep reagents, and barcodes needed for construction of libraries compatible with Illumina sequencing platforms.

    Illumina compatible disease panel sequencing kits
    BRCA1 and BRCA2 amplicon panels (FFPE & non FFPE)