Proteomics and Metabolomics

Teach Me in 10

In this episode of Teach Me in 10, we are joined by Matt Hammond who is an applications and collaborations manager of protein quantitation at Bio-Rad Laboratories. 
Matt teaches us about the strengths of using a total protein signal as the reference signal in a western lot experiment, as well as how to use Bio-Rad’s Stain Free technology to provide this signal easily and reliably.

Total Protein Normalization in the Western Blotting Workflow

Creative Proteomics videos

Glycan microarray has become a sensitive and versatile approach for the analysis of glycosylation changes in complex biological samples. It can not only investigate glycan-GBPs binding but also provide kinetic analysis of glycan–protein interactions. Nowadays, this application has rapidly expanded and now achieves successful discrimination of selective interactions between glycans and, not only proteins, but also viruses, bacteria and eukaryotic cells, and most recently even live cell responses to immobilized glycans. Glycan microarray can be used to discover functional glycans, characterize glycan-processing enzymes, and detect pathogens for diagnosis. It is also suitable for monitoring multiple molecular interactions with biomolecules where glycans are involved, offering a large variety of bioassay options.

As one of the leading companies in the omics field with over years of experience in omics study, Creative Proteomics provides Glycan Microarray Assay customized to your needs. https://www.creative-proteomics.com/services/glycan-microarray-assay.htm

Glycan Microarray Assay

Proteomics is a large-scale comprehensive study of a specific proteome, including information on protein abundances, the variations and modifications, as well as their interacting partners and networks. In discovery proteomics, proteome analysis can be performed in two different strategies, bottom-up and top-down approaches, respectively. In the bottom-up approach, a crude protein mixture undergoes protease digestion first, and then separation by liquid chromatography, followed by MS analysis. In the top-down method, proteins are characterized by MS without prior proteolysis. This type of approach has the advantage of providing greater sequence coverage, resolution of sequence ambiguities and preservation of PTMs. https://www.creative-proteomics.com/services/proteomics-service.htm

Protein Sequencing

Proteins are the critical players in molecular recognition at the core of all biological processes. They can interact with the other components of cells, such as small-molecule metabolites, nucleic acids, membranes, and other proteins to build supramolecular assemblies and elaborate molecular machines that perform all sorts of functions, from chemical catalysis and mechanical work to signaling and regulation. As one of the most important interactions, Protein-Protein Interactions have been studied widely. So far large scale protein-protein interactions have been identified, and all the generated data collected together in specialized databases, enables the creation of large protein interaction networks. https://www.creative-proteomics.com/services/protein-protein-interactions-analysis-service.htm

Techniques for Protein-Protein Interaction

Equipped with advanced tandem mass spectrometry for determination of lipid composition, powerful bioinformatic analytic systems, and a panel of experienced scientists and technicians, Creative Proteomics provide customer-tailored service with rapid analysis procedures and easy to read report, to speed up your scientific research.
https://www.creative-proteomics.com/services/targeted-lipidomics.htm

Mass Spectrometry Based Lipidomics

Oncotarget

Oncotarget published this research paper in Volume 13, entitled, “Essential amino acids as diagnostic biomarkers of hepatocellular carcinoma based on metabolic analysis" by researchers from Department of Surgery, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan; Department of Clinical Nutrition and Food Management, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan; Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan; Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-0882, Japan; Department of Gastroenterology and Hepatology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan.

DOI - https://doi.org/10.18632/oncotarget.28306

Correspondence to - Yuji Morine - ymorine@tokushima-u.ac.jp 

Abstract

Metabolomics, defined as the comprehensive identification of all small metabolites in a biological sample, has the power to shed light on phenotypic changes associated with various diseases, including cancer. To discover potential metabolomic biomarkers of hepatocellular carcinoma (HCC), we investigated the metabolomes of tumor and non-tumor tissue in 20 patients with primary HCC using capillary electrophoresis–time-of-flight mass spectrometry. We also analyzed blood samples taken immediately before and 14 days after hepatectomy to identify associated changes in the serum metabolome. Marked changes were detected in the different quantity of 61 metabolites that could discriminate between HCC tumor and paired non-tumor tissue and additionally between HCC primary tumors and colorectal liver metastases. Among the 30 metabolites significantly upregulated in HCC tumors compared with non-tumor tissues, 10 were amino acids, and 7 were essential amino acids (leucine, valine, tryptophan, isoleucine, methionine, lysine, and phenylalanine). Similarly, the serum metabolomes of HCC patients before hepatectomy revealed a significant increase in 16 metabolites, including leucine, valine, and tryptophan. Our results reveal striking differences in the metabolomes of HCC tumor tissue compared with non-tumor tissue, and identify the essential amino acids leucine, valine, and tryptophan as potential metabolic biomarkers for HCC.

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Keywords - metabolomics, essential amino acid, hepatocellular carcinoma, diagnostic biomarker

About Oncotarget

Oncotarget is a primarily oncology-focused, peer-reviewed, open access journal. Papers are published continuously within yearly volumes in their final and complete form, and then quickly released to Pubmed. On September 15, 2022, Oncotarget was accepted again for indexing by MEDLINE. Oncotarget is now indexed by Medline/PubMed and PMC/PubMed.

To learn more about Oncotarget, please visit https://www.oncotarget.com and connect with us:

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Essential Amino Acids as Diagnostic Biomarkers of Hepatocellular Carcinoma

Aging (Aging-US)

Aging (Aging-US) published this trending research paper in Volume 14, Issue 21, entitled, “The deubiquitylase USP7 is a novel cyclin F-interacting protein and regulates cyclin F protein stability” by researchers from the Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, India; Sri Shankara Cancer Hospital and Research Centre, Bengaluru, India; Department of Surgery, University of Utah Health, Huntsman Cancer Institute, Salt Lake City, UT.

DOI - https://doi.org/10.18632/aging.204372

Corresponding author - Savitha S. Sharma - savitha.sharma@ssnccpr.org

ABSTRACT

Cyclin F, unlike canonical and transcriptional cyclins, does not bind or activate any cyclin-dependent kinases. Instead, it harbors an F-box motif and primarily functions as the substrate recognition subunit of the Skp1-Cul1-F-box E3 ubiquitin ligase complex, SCFCyclin F. By targeting specific proteins for ubiquitin-mediated proteasomal degradation, cyclin F plays a critical role in the regulation of centrosomal duplication, DNA replication and repair, and maintenance of genomic stability. Cyclin F abundance and activity are tightly regulated throughout the cell cycle. However, the molecular mechanisms regulating cyclin F are scantily understood. Here, we identify the deubiquitylase USP7 as a novel cyclin F-interacting protein. We observe that USP7 stabilizes cyclin F protein and that this function is independent of the deubiquitylase activity of USP7. Additionally, our data suggest that USP7 is also involved in the regulation of cyclin F mRNA. Pharmacological inhibition of the deubiquitylase activity of USP7 resulted in downregulation of cyclin F mRNA.

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Keywords - cyclin F, atypical cyclins, USP7, cell cycle, genomic integrity

About Aging-US

Launched in 2009, Aging-US publishes papers of general interest and biological significance in all fields of aging research and age-related diseases, including cancer—and now, with a special focus on COVID-19 vulnerability as an age-dependent syndrome. Topics in Aging-US go beyond traditional gerontology, including, but not limited to, cellular and molecular biology, human age-related diseases, pathology in model organisms, signal transduction pathways (e.g., p53, sirtuins, and PI-3K/AKT/mTOR, among others), and approaches to modulating these signaling pathways.

Please visit our website at http://www.Aging-US.com​​ and connect with us:

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Aging-US is published by Impact Journals, LLC: http://www.ImpactJournals.com​​

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USP7 Regulates Cyclin F Protein Stability

Scientific Imagers

Camera

Featuring a 24 megapixel coloured digital camera with a superfast autofocus lens inside a dust resistant enclosure, which can be controlled from a PC or a touchscreen. Live view images and capture times of less than a few seconds provides efficient imaging. Gel image acquisition and control software has full function control panel which allows user to adjust camera and lens settings like exposure time settings, focus and aperture (iris). Histogram display on the screen shows image saturation.

Low Noise CMOS imaging sensor
8-bit and 14-bit options
24 megapixel camera
Sharp Zoom lens
Motorized auto-focus
Motorized aperture setting
Manual zoom range 3x
Exposure from 0.00025s onwards
Single/Dual 312nm/365nm/254nm UV
RGB LEDs and convertor screens
Operate camera via PC
Timer for auto-off of UV
Advanced Gel Analysis Software
 

Darkroom Cabinet

The epoxy coated, chemical & corrosion resistant light-tight cabinet has filter holder (1, 3 or 7 filter holder), a UV safety switch and a roll-out transilluminator. The safety switch switches off UV lights as soon as the door is opened. Options for front viewing window with two side windows on the cabinet for excision of bands are also available.

 

Illumination

Standard lighting systems are UV transillumination in 302-312nm* and Epi-white light
Gel filter illumination area is 20x20cm, with 21x26cm option for larger gels. For extra large gels, we also offer a 26x26cm filter.
Gels up to a maximum of 26x26cm can be observed, captured and analysed
Sample size area is 38x30cm
We also offer UV transillumination in dual wavelength (312+365nm being most common)
For rare applications UV transillumination in triple wavelength (254+312+365nm) can also be given
Multi broad band wavelengths can also be offered 254nm, 312nm and 365nm UV trans lights
Intensity control for low and high trans-illumination - low for preparative work and high for quantitative
White light tables are optional to use gel doc for protein gels documentation
For special stains, blue light tables can also be given
Multi-wavelength epi-illumination LEDs are also available for Red, Green, Blue lights for special stains
* Please note that 300nm, 302nm, 306nm and 312nm are in the same range of wavelengths called UV-B (also known as mid-range). Some manufacturers quote 302nm but it is the same as 312nm..

 

Transillumination

Ultraviolet transillumination can be provided in 302-312nm, 365nm or 254nm individual ranges or as Dual or Triple options. Filter size of transilluminator is 20x20 cm, optionally 21x26cm can be provided too. Low & high intensity of 70% & 100% on the transilluminator provides an easy switch between preparative & final imaging. A timer is attached to the transilluminator, which auto switches off UV light in case the user forgets to turn it off. This increases the life of the UV lamps. Trans White & Trans Blue light tables are also available.

 

Epillumination

Epi-white light illumination through dual LED tubes from above is standard. Ultraviolet epi-illumination in a variety of wavelengths can also be provided. For specific stains, epi-light in blue, green or red LEDs can be provided. A combination of all these illumination modes in the same system can be provided.

 

Filter Holder

Standard is manual single position filter holder
Advanced models with 3, 4 and 7-position manual and motorized filter holder are also available
Orange 590 EtBr and clear are standard

Filters

Orange 590: Ethidium Bromide (EtBr), SYPRO Ruby, ProQ Diamond, Deep Purple, etc
Green 520: SYBR Green I, Green II, SYBR Gold, GFP, Fluorescein, FITC
Orange 560: SYBR Safe, Rhodamine, Cy3, etc
Red 630: SYPRO Red, Texas Red, etc
Blue 480: Hoechst, Coumarin, etc
Clear: Coomassie Blue, Silver etc
 

How the Gel Documentation & Imaging Analysis System works

A transilluminator is mounted on roll-out rails inside a light-tight cabinet. To place the gel, the door is opened and transilluminator pulled out. Push it in, close the door and switch on the UV light and camera. The camera is mounted on top of the cabinet along with zoom lens and wavelenght filter (nominally 590nm filter suitable for Ethidium Bromide EtBr gels is provided).

Connect the camera to the PC using the USB cable and gel capture software, to get a real-time live view image of the gel. Adjust camera settings (like shutter speed, aperture, focus) till the optimum image is obtained. Click your images and save them on the PC. A white light epi-illuminations source is also provided, that illuminates objects from top.

With the optional 1D gel analysis software, you can analyse the gels.

 

Package Includes

Dark room cabinet with safety switch
Roll out variable intensity 312nm transilluminator
Epi-white light illumination
24 megapixel camera
Gel capture software
590nm filter, suitable for EtBr stained gels
Power cords, USB cable, instruction manual, warranty card

Gel Documentation Systems

Oncotarget published this trending research paper in Volume 13, entitled, "Mutation analysis performed on tumor biopsies from patients with newly-diagnosed germinal center aggressive B cell lymphomas" by researchers from the Department of Medicine University of Pennsylvania, Philadelphia, PA.
#openaccess #research #germinalcancer #lymphoma #cancer #oncologyresearch #peerreview #openscience #chemotherapy

DOI - https://doi.org/10.18632/oncotarget.28309

Correspondence to - Daniel J. Landsburg - daniel.landsburg@pennmedicine.upenn.edu 

Abstract

Comprehensive genomic analyses of tumor biopsies from patients with newly-diagnosed germinal center B cell (GCB) diffuse large B cell/high grade B cell lymphoma (DLBCL/HGBL) have identified molecular subtypes predictive of inferior survival, which are characterized by somatic mutations that can be detected through clinical laboratory mutation analysis (CLMA). To determine the frequency and predictive value of individual genetic mutations associated with these experimentally-defined poor-risk subgroups, we reviewed the findings from CLMA performed on tumors from patients with newly-diagnosed GCB DLBCL/HGBL who were previously treated at our institution. CLMA was successfully performed on 58/59 patient tumor biopsies with a median turnaround time of 16 days, and 51 on which CLMA was routinely performed with adequate clinical follow-up were analyzed. Patients whose tumors demonstrated CREBBP mutation experienced a lower estimated rate of 2-year disease free survival (DFS) as compared to those whose tumors did not (45% [95% CI 18–68%] vs. 67% [95% CI 44–83%], P = 0.045). CREBBP mutations may be frequent and predict for inferior DFS in patients with newly-diagnosed GCB DLBCL/HGBL. Furthermore, CLMA may be practically-applied to translate experimental findings into those with more direct application to risk stratification and clinical trial design in subsets of patients with DLBCL/HGBL.

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Press release - https://www.oncotarget.com/news/pr/oncotarget-mutation-analysis-performed-on-tumor-biopsies-from-patients-with-newly-diagnosed-germinal-center-aggressive-b-cell-lymphomas/

Keywords - diffuse large B cell lymphoma, high grade B cell lymphoma, mutation analysis, next generation sequencing, chemotherapy

About Oncotarget

Oncotarget is a primarily oncology-focused, peer-reviewed, open access journal. Papers are published continuously within yearly volumes in their final and complete form, and then quickly released to Pubmed. On September 15, 2022, Oncotarget was accepted again for indexing by MEDLINE. Oncotarget is now indexed by Medline/PubMed and PMC/PubMed.

To learn more about Oncotarget, please visit https://www.oncotarget.com and connect with us:

SoundCloud - https://soundcloud.com/oncotarget
Facebook - https://www.facebook.com/Oncotarget/
Twitter - https://twitter.com/oncotarget
Instagram - https://www.instagram.com/oncotargetjrnl/
YouTube - https://www.youtube.com/OncotargetYouTube
LinkedIn - https://www.linkedin.com/company/oncotarget
Pinterest - https://www.pinterest.com/oncotarget/
Reddit - https://www.reddit.com/user/Oncotarget/

Media Contact
MEDIA@IMPACTJOURNALS.COM
18009220957

Proteomics and Metabolomics

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