Genomics

Aging (Aging-US)

Aging-US published this priority research paper as the cover for Volume 15, Issue 20, entitled, "Proteomic quantification of native and ECM-enriched mouse ovaries reveals an age-dependent fibro-inflammatory signature" by researchers from the Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL; Buck Institute for Research on Aging, Novato, CA; Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL.

DOI - https://doi.org/10.18632/aging.205190

Corresponding authors - Francesca E. Duncan - f-duncan@northwestern.edu, and Birgit Schilling - bschilling@buckinstitute.org

Abstract

The ovarian microenvironment becomes fibrotic and stiff with age, in part due to increased collagen and decreased hyaluronan. However, the extracellular matrix (ECM) is a complex network of hundreds of proteins, glycoproteins, and glycans which are highly tissue specific and undergo pronounced changes with age. To obtain an unbiased and comprehensive profile of age-associated alterations to the murine ovarian proteome and ECM, we used a label-free quantitative proteomic methodology. We validated conditions to enrich for the ECM prior to proteomic analysis. Following analysis by data-independent acquisition (DIA) and quantitative data processing, we observed that both native and ECM-enriched ovaries clustered separately based on age, indicating distinct age-dependent proteomic signatures. We identified a total of 4,721 proteins from both native and ECM-enriched ovaries, of which 383 proteins were significantly altered with advanced age, including 58 ECM proteins. Several ECM proteins upregulated with age have been associated with fibrosis in other organs, but to date their roles in ovarian fibrosis are unknown. Pathways regulating DNA metabolism and translation were downregulated with age, whereas pathways involved in ECM remodeling and immune response were upregulated. Interestingly, immune-related pathways were upregulated with age even in ECM-enriched ovaries, suggesting a novel interplay between the ECM and the immune system. Moreover, we identified putative markers of unique immune cell populations present in the ovary with age. These findings provide evidence from a proteomic perspective that the aging ovary provides a fibroinflammatory milieu, and our study suggests target proteins which may drive these age-associated phenotypes for future investigation.

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Keywords - aging, reproductive aging, ovary, proteomics, extracellular matrix, data-independent acquisition

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 https://www.Aging-US.com​​ and connect with us:

SoundCloud - https://soundcloud.com/Aging-Us
Facebook - https://www.facebook.com/AgingUS/
Twitter - https://twitter.com/AgingJrnl
Instagram - https://www.instagram.com/agingjrnl/
YouTube - https://www.youtube.com/@AgingJournal
LinkedIn - https://www.linkedin.com/company/aging/
Pinterest - https://www.pinterest.com/AgingUS/

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Age-Dependent Fibro-Inflammatory Signature in Mouse Ovaries | Aging-US

Hamilton Company (Robotics)

Are you interested in automating your DMPK assays? Learn how Vertex Pharmaceutical is leveraging the flexibility of Hamilton Liquid handlers to automate multiple workflows on the same deck. 

This video is part of our Webinar on " Automating Workflows for DMPK Studies - Vertex Pharmaceuticals’ Experience." Watch the full Webinar here: https://hubs.li/Q026SCwX0 

If you are interested in more field-focused content describing the latest trends in automation within specific scientific areas, visit Hamilton Robotics' Scientific Content Hub here: https://hubs.ly/Q018Prtz0 


Automating Workflows for DMPK Studies - Vertex Pharmaceuticals’ Experience 

Aging-US published this trending research paper on October 9, 2023, in Volume 15, Issue 19, entitled, “Live while the DNA lasts. The role of autophagy in DNA loss and survival of diploid yeast cells during chronological aging" by researchers from the Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland; Institute of Medical Sciences, Rzeszów University, Rzeszów 35-959, Poland; Institute of Biology, Rzeszów University, Rzeszów 35-601, Poland.

DOI - https://doi.org/10.18632/aging.205102

Corresponding author - Adrianna Skoneczna - ada@ibb.waw.pl

Abstract

Aging is inevitable and affects all cell types, thus yeast cells are often used as a model in aging studies. There are two approaches to studying aging in yeast: replicative aging, which describes the proliferative potential of cells, and chronological aging, which is used for studying post-mitotic cells. While analyzing the chronological lifespan (CLS) of diploid Saccharomyces cerevisiae cells, we discovered a remarkable phenomenon: ploidy reduction during aging progression. To uncover the mechanism behind this unusual process we used yeast strains undergoing a CLS assay, looking for various aging parameters. Cell mortality, regrowth ability, autophagy induction and cellular DNA content measurements indicated that during the CLS assay, dying cells lost their DNA, and only diploids survived. We demonstrated that autophagy was responsible for the gradual loss of DNA. The nucleophagy marker activation at the start of the CLS experiment correlated with the significant drop in cell viability. The activation of piecemeal microautophagy of nucleus (PMN) markers appeared to accompany the chronological aging process until the end. Our findings emphasize the significance of maintaining at least one intact copy of the genome for the survival of post-mitotic diploid cells. During chronological aging, cellular components, including DNA, are exposed to increasing stress, leading to DNA damage and fragmentation in aging cells. We propose that PMN-dependent clearance of damaged DNA from the nucleus helps prevent genome rearrangements. However, as long as one copy of the genome can be rebuilt, cells can still survive.

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Keywords - aging, genome instability, lifespan, autophagy, double-strand breaks

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 https://www.Aging-US.com​​ and connect with us:

SoundCloud - https://soundcloud.com/Aging-Us
Facebook - https://www.facebook.com/AgingUS/
X - https://twitter.com/AgingJrnl
Instagram - https://www.instagram.com/agingjrnl/
YouTube - https://www.youtube.com/@AgingJournal
LinkedIn - https://www.linkedin.com/company/aging/
Pinterest - https://www.pinterest.com/AgingUS/

Media Contact
18009220957
MEDIA@IMPACTJOURNALS.COM

Autophagy in DNA Loss & Yeast Cell Survival in Chronological Aging | Aging-US

Teach Me in 10

In this exclusive Teach Me in 10, Dr. James Goldmeyer, Associate Director at Revvity, delves into the transformative impact of functional genomic screening in the realm of drug discovery. Revvity, a leader in the field, provides comprehensive solutions spanning research, development, diagnosis, and treatment. Dr. Goldmeyer, with his extensive experience, sheds light on the potential applications and outcomes of this cutting-edge technique.

Viewers will gain an understanding of how this technique works and the tools involved, including CRISPR-based technologies and RNA interference. Dr.Goldmeyer explains how these components synergize to form a robust platform for researchers. The interview explores how this approach benefits researchers in their quest for novel therapies. Notably, functional genomic screening bridges the gap left by traditional methods, enabling the development of personalized treatments with greater precision and detail. 

The discussion further illuminates the pivotal role of functional genomic screening in various stages of drug discovery. The technique aids in target identification, elucidating drug response mechanisms, and unraveling in vivo tumor biology. Despite its numerous advantages, potential disadvantages are also examined, contributing to a well-rounded understanding of the approach. 

Revvity's specialized focus on gene modification is highlighted, with emphasis on potential applications and diseases that stand to benefit. The interview explores how functional genomic screening not only accelerates drug discovery but also lends itself to the development of innovative cell-based therapies.

Unlocking New Cures: How Functional Genomic Screening Revolutionizes Drug Discovery

Oncotarget

Oncotarget published this trending editorial on August 30, 2023 in Volume 14, entitled, “Predicting the molecular functions of regulatory genetic variants associated with cancer" by Jun S. Song and Mohith Manjunath from Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL; Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL.

DOI - https://doi.org/10.18632/oncotarget.28451

Correspondence to - Jun S. Song - songj@illinois.edu

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Keywords - cancer, genome-wide association studies, cancer risk, regulatory variants, functional genomics

About Oncotarget 

Oncotarget (a primarily oncology-focused, peer-reviewed, open access journal) aims to maximize research impact through insightful peer-review; eliminate borders between specialties by linking different fields of oncology, cancer research and biomedical sciences; and foster application of basic and clinical science.

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
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YouTube - https://www.youtube.com/@OncotargetJournal
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

Predicting Molecular Functions of Regulatory Genetic Variants Associated with Cancer | Oncotarget

Luminex Corporation

Watch the recorded presentation from the Cytokines 2022 meeting by Angela Lombardi, PhD, Assistant Professor, Department of Medicine (Endocrinology) and Department of Microbiology & Immunology, Albert Einstein College of Medicine.

Learn more about the technology used in her research: https://www.luminexcorp.com/xmap-technology/#overview

Pancreas Derived Peptide Presentation by HLA-DQ in Diabetes—Angela Lombardi, PhD at Cytokines 2022

Get to know Luminex’s xMAP® Technology all over again. For 27 years, xMAP Technology has become known as the worldwide leader in bead-based multiplexing. With the new xMAP INTELLIFLEX®, we have re-energized the xMAP platform with a modern, fast, flexible and intuitive flow-based analysis system that can deliver twice the data in a single well as compared to previous instruments.

Join us to learn about the exciting applications of the xMAP INTELLIFLEX and its new dual reporter capability. We’ll describe some recently published studies that used this system, focusing on serological analyses. xMAP Technology enabled the multiplexed analysis of antigen-specific antibodies and the xMAP INTELLIFLEX’s simultaneous measuring of two antibody isotypes within a single well.

For Research Use Only. Not for use in diagnostic procedures.

Learning Objectives:

1. Refresh your knowledge of Luminex and xMAP bead-based multiplexing technology and how it has been used in life sciences research for the past 27 years.

2. Learn about the enhanced features and the novel second reporter channel of the innovative xMAP INTELLIFLEX, Luminex's newest instrument for xMAP Technology.

3. Learn about recent work that demonstrates the dual reporter functionality of the xMAP INTELLIFLEX for multiplexed serological analysis with antibody isotyping.

Learn more: https://www.luminexcorp.com/intelliflex/#overview

Accelerate Your Research With Luminex's xMAP INTELLIFLEX – Sherry Dunbar, PhD

Introducing the Luminex MAGPIX® System. This compact, fluorescent-based detection system is the simplest, most affordable, and most compact of Luminex’s xMAP® instruments. It can perform up to 50 different analytes in a single microtiter well and reads a 96-well-plate in just 60 minutes. Instead of using flow cytometry, the MAGPIX is a fluorescent imager that can perform quantitative analysis of both protein and nucleic acids. Based on Luminex's proven xMAP® Technology, the MAGPIX System uses color-coded magnetic microspheres as the substrate on which assays are performed. This video will walk you through how the system works.

Learn more: https://www.luminexcorp.com/magpix-system/#overview

Luminex MAGPIX® System

Luminex® xMAP® Technology makes up the basis of Luminex’s core business. This flexible technology is centered on the use of Luminex xMAP Microspheres.

xMAP was originally an acronym for multi-analyte profiling, where you solve for x. The surface of the microsphere offers multiple chemical attachment sites for biological capture molecules. When these molecules attach to the microsphere, it is called coupling, and this bonding can happen with both protein and nucleic acids, which make it a versatile and easy to use chemistry.

Learn more: https://www.luminexcorp.com/xmap-technology/#overview

Genomics

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