Informatics

Oncotarget

The cover for issue 36 of Oncotarget features Figure 7, "Knockdown of APOBEC3B is associated with a lower tumor growth in an adrenocortical carcinoma xenograft mouse model," by Gara, et al. which reported that the role of APOBEC3B in adrenocortical carcinoma and the mechanisms through which its expression is regulated in cancer are not fully understood.

Here, the authors report that APOBEC3B is overexpressed in ACC and it regulates cell proliferation by inducing S phase arrest. They show high APOBEC3B expression is associated with a higher copy number gain/loss at chromosome 4 and 8 and TP53 mutation rate in ACC.

GATA3 was identified as a positive regulator of APOBEC3B expression and directly binds the APOBEC3B promoter region.

Both GATA3 and APOBEC3B expression levels were associated with patient survival.

This Oncotarget study provides novel insights into the function and regulation of APOBEC3B expression in addition to its known mutagenic ability.

Dr. Electron Kebebew from Stanford University said, "Adrenocortical carcinoma (ACC) is a rare and aggressive endocrine malignancy."

The distinct pattern of DNA base alterations has been characterized in the cancer genome using high throughput deep sequencing technologies, that reflect the underlying mutational process.

Whole-genome and exome mutation analysis of The Cancer Genome Atlas data on multiple cancers has revealed that this pattern is consistent with the deaminase activity of the AID/APOBEC family of enzymes, therefore, implying its significance as an endogenous mutator and a crucial contributor to somatic mutations and genomic instability.

APOBEC3B is overexpressed in ovarian cancer cell lines and high-grade primary ovarian cancers.

In addition, APOBEC3B expression is positively correlated with the total mutation load, as well as, elevated levels of transversion mutations.

Given there are no well-established exogenous factors associated with ACC, the Oncotarget authors postulated whether APOBEC3B could be an endogenous mechanism of genomic instability/mutations in ACC and investigated its function in vitro and in vivo.

The Kebebew Research Team concluded in their Oncotarget Research Paper, "APOBEC3B overexpressed in ACC, and is associated with DNA damage, S phase arrest, higher copy number alterations and TP53 mutations in ACC. For the first time, we demonstrated that GATA3 directly regulates the expression of APOBEC3B and that both are prognostic markers in ACC."

DOI - https://doi.org/10.18632/oncotarget.27703

Full text - https://www.oncotarget.com/article/27703/text/

Correspondence to - Electron Kebebew - kebebew@stanford.edu

Keywords - adrenocortical carcinoma, APOBEC3B, GATA3, prognosis, DNA damage

About Oncotarget

Oncotarget is a bi-weekly, peer-reviewed, open access biomedical journal covering research on all aspects of oncology. 

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

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

Oncotarget is published by Impact Journals, LLC. Please visit https://www.impactjournals.com/ or connect with @ImpactJrnls

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18009220957

Author Testimonial: Dr. Monica Varun Tyagi - Stanford University

Aging (Aging-US)

The researchers recruited healthy older participants to two groups according to their history of tea drinking frequency and investigated both functional and structural networks to reveal the role of tea drinking on brain organization.

The suppression of hemispheric asymmetry in the structural connectivity network was observed as a result of tea drinking.

The authors did not observe any significant effects of tea drinking on the hemispheric asymmetry of the functional connectivity network.

Dr. Junhua Li and Dr. Lei Feng said, "Tea has been a popular beverage since antiquity, with records referring to consumption dating back to the dynasty of Shen Nong (approximately 2700 BC) in China."

Tea is consumed in diverse ways, with brewed tea and products with a tea ingredient extremely prevalent in Asia, especially in China and Japan.

Although individual constituents of tea have been related to the roles of maintaining cognitive abilities and preventing cognitive decline, a study with behavioural and neurophysiological measures showed that there was a degraded effect or no effect when a constituent was administered alone and a significant effect was observed only when constituents were combined.

The superior effect of the constituent combination was also demonstrated in a comparative experiment that suggested that tea itself should be administered instead of tea extracts; a review of tea effects on the prevention of Alzheimers disease, found that the neuroprotective role of herbal tea was apparent in eight out of nine studies.

It is worth noting that the majority of studies thus far have evaluated tea effects from the perspective of neurocognitive and neuropsychological measures, with direct measurement of brain structure or function less-well represented in the extant literature.

These studies focusing on brain regional alterations did not ascertain tea effects on interregional interactions at the level of the entire brain.

The Li/Feng Research team concluded, "In summary, our study comprehensively investigated the effects of tea drinking on brain connectivity at both global and regional scales using multi-modal imaging data and provided the first compelling evidence that tea drinking positively contributes to brain structure making network organization more efficient."

Full Text - https://www.aging-us.com/article/102023/text

Correspondence to: Junhua Li email: junhua.li@essex.ac.uk and Lei Feng email: pcmfl@nus.edu.sg

Keywords: tea drinking, brain efficiency, fMRI, DTI, default mode network, hemispheric asymmetry

About Aging-US

Launched in 2009, Aging-US publishes papers of general interest and biological significance in all fields of aging research as well as topics beyond traditional gerontology, including, but not limited to, cellular and molecular biology, human age-related diseases, pathology in model organisms, cancer, 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 or connect with us on:

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/agingus​
LinkedIn - https://www.linkedin.com/company/aging/
Pinterest - https://www.pinterest.com/AgingUS/

Aging-US is published by Impact Journals, LLC please visit http://www.ImpactJournals.com or connect with @ImpactJrnls

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Author Insight: Habitual Tea Drinking Modulates Brain Efficiency

The cover for issue 36 of Oncotarget features Figure 7, "Knockdown of APOBEC3B is associated with a lower tumor growth in an adrenocortical carcinoma xenograft mouse model," by Gara, et al. which reported that the role of APOBEC3B in adrenocortical carcinoma and the mechanisms through which its expression is regulated in cancer are not fully understood.

Here, the authors report that APOBEC3B is overexpressed in ACC and it regulates cell proliferation by inducing S phase arrest. They show high APOBEC3B expression is associated with a higher copy number gain/loss at chromosome 4 and 8 and TP53 mutation rate in ACC.

GATA3 was identified as a positive regulator of APOBEC3B expression and directly binds the APOBEC3B promoter region.

Both GATA3 and APOBEC3B expression levels were associated with patient survival.

This Oncotarget study provides novel insights into the function and regulation of APOBEC3B expression in addition to its known mutagenic ability.

Dr. Electron Kebebew from Stanford University said, "Adrenocortical carcinoma (ACC) is a rare and aggressive endocrine malignancy."

The distinct pattern of DNA base alterations has been characterized in the cancer genome using high throughput deep sequencing technologies, that reflect the underlying mutational process.

Whole-genome and exome mutation analysis of The Cancer Genome Atlas data on multiple cancers has revealed that this pattern is consistent with the deaminase activity of the AID/APOBEC family of enzymes, therefore, implying its significance as an endogenous mutator and a crucial contributor to somatic mutations and genomic instability.

APOBEC3B is overexpressed in ovarian cancer cell lines and high-grade primary ovarian cancers.

In addition, APOBEC3B expression is positively correlated with the total mutation load, as well as, elevated levels of transversion mutations.

Given there are no well-established exogenous factors associated with ACC, the Oncotarget authors postulated whether APOBEC3B could be an endogenous mechanism of genomic instability/mutations in ACC and investigated its function in vitro and in vivo.

The Kebebew Research Team concluded in their Oncotarget Research Paper, "APOBEC3B overexpressed in ACC, and is associated with DNA damage, S phase arrest, higher copy number alterations and TP53 mutations in ACC. For the first time, we demonstrated that GATA3 directly regulates the expression of APOBEC3B and that both are prognostic markers in ACC."

DOI - https://doi.org/10.18632/oncotarget.27703

Full text - https://www.oncotarget.com/article/27703/text/

Correspondence to - Electron Kebebew - kebebew@stanford.edu

Keywords - adrenocortical carcinoma, APOBEC3B, GATA3, prognosis, DNA damage

About Oncotarget

Oncotarget is a bi-weekly, peer-reviewed, open access biomedical journal covering research on all aspects of oncology.

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

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

Oncotarget is published by Impact Journals, LLC please visit https://www.ImpactJournals.com or connect with @ImpactJrnls

Media Contact
MEDIA@IMPACTJOURNALS.COM
18009220957

Author Insight: GATA3 and APOBEC3B are Prognostic Markers in Adrenocortical Carcinoma

Teach Me in 10

In this Teach Me in 10, we are joined by Ed George, Senior Application Specialist at Thermo Fisher Scientific. Ed will provide an overview of dwell time settings on triple quadrupole mass spectrometers and the importance of this, as well as the impact and challenges with setting dwell times. 

We will also explore the overall benefits and advanced features in the new Thermo Scientific TSQ Plus MS Systems for complex multi-residue methods and the importance of optimizing SRM dwell times for large-scale targeted compound lists.

For more information, be sure to check out the following resources:

[url][link]https://www.thermofisher.com/uk/en/home/industrial/food-beverage/food-analytical-testing/pesticide-residues-analysis.htmll[/link][name] -Thermo Scientific TSQ Plus Mass Spectrometers Portfolio[/name][/url]

[url][link]https://www.thermofisher.com/uk/en/home/industrial/food-beverage/food-analytical-testing/pesticide-residues-analysis.html [/link][name] -Thermo Scientific Pesticides Residue Analysis [/name][/url]

[url][link]https://assets.thermofisher.com/TFS-Assets/CMD/Application-Notes/an-64971-lc-ms-pesticides-food-matrices-an64971-en.pdf [/link][name] - Thermo Scientific Application Note:  Robustness, reproducibility reliability with best-in-class sensitivity:  increased confidence in targeted quantitation of pesticides in food matrices [/name][/url]

[url][link] https://www.thermofisher.com/uk/en/home/industrial/food-beverage/food-analytical-testing/veterinary-drug-residues-analysis.html [/link][name] - Thermo Scientific VetDrug Residue Analysis  [/name][/url]

[url][link] https://assets.thermofisher.com/TFS-Assets/CMD/Application-Notes/an-66000-lc-ms-vet-drugs-quechers-uspe-an66000-en.pdf [/link][name] - Thermo Scientific Application Note Multi-class veterinary drug analyses of QuEChERS extracts using an automated online µSPE cleanup coupled to LC-MS/MS [/name][/url]


The Importance of Optimizing SRM Dwell Times for Large-Scale Targeted Compound Lists With Ed George

Scared of coding? Fear not, we've got the solution for you. In this installment of Teach Me in 10, we're joined by James Blackshaw, scientific data engineer at the EMBL-EBI. Blackshaw explains how a little coding can save a bench scientist a whole lot of time, and provides some useful tips and tricks to get you started.

Coding for Bench Scientists With James Blackshaw

Wyss Institute for Biologically Inspired Engineering at Harvard University

Using Human Organ Chips, researchers at the Wyss Institute were able to generate the mucus layer of the colon in vitro, which has never been done before. In the colon, the mucus layer protects intestinal epithelial cells against inflammatory stimuli such as pathogens, damaged cells, or irritants. The ability to support mucus-producing cells is one step towards modeling inflammatory bowel diseases in vitro.
 
For more information, please visit: https://wyss.harvard.edu/news/investigating-the-human-intestinal-mucus-barrier-up-close-and-personal/
 
Credit: Wyss Institute at Harvard University

Mucus Layer In Vitro on Human Colon Chip

For this installment of Teach Me in 10, we are joined by Gareth Walkom, the founder of withVR.  Gareth develops virtual reality tools for speech disorders, speech and language pathologists and researchers. Since 2015 he has been researching how virtual reality can be used within stuttering, exploring how virtual reality speaking situations can be used as a powerful tool. 

In this Teach Me in 10 video, Gareth explains more about speech disorders, how virtual reality is helping and the applications of such work.

Virtual Reality and Speech Disorders With Gareth Walkom

Aging published this research paper on March 14, 2021, entitled, “Deep longitudinal phenotyping of wearable sensor data reveals independent markers of longevity, stress, and resilience,” by researchers from Gero PTE. LTD., Singapore 409051, Singapore and Moscow Institute of Physics and Technology, Moscow Region 141700, Russia.

Abstract:
Biological age acceleration (BAA) models based on blood tests or DNA methylation emerge as a de facto standard for quantitative characterizations of the aging process. We demonstrate that deep neural networks trained to predict morbidity risk from wearable sensor data can provide a high-quality and cheap alternative for BAA determination. The GeroSense BAA model was trained and validated using steps per minute recordings from 103,830 one-week long and 2,599 of up to 2 years-long longitudinal samples and exhibited a superior association with life-expectancy over the average number of steps per day in, e.g., groups stratified by professional occupations. The association between the BAA and effects of lifestyles, the prevalence of future incidence of diseases was comparable to that of BAA from models based on blood test results. Wearable sensors let sampling of BAA fluctuations at time scales corresponding to days and weeks and revealed the divergence of organism state recovery time (resilience) as a function of chronological age. The number of individuals suffering from the lack of resilience increased exponentially with age at a rate compatible with Gompertz mortality law. We speculate that due to the stochastic character of BAA fluctuations, its mean and auto-correlation properties together comprise the minimum set of biomarkers of aging in humans.

To date, this study has generated an Altmetric Attention Score of 43. The Altmetric Attention Score provides an at-a-glance indication of the volume and type of online attention the research has received. 

Top Aging publications rated by Altmetric Attention Score -  https://www.aging-us.com/news_room/altmetric

Sign up for free Altmetric alerts about this article - https://oncotarget.altmetric.com/details/email_updates?id=10.18632%2Foncotarget.202816

DOI - https://doi.org/10.18632/aging.202816

Full text - https://www.aging-us.com/article/202816/text

Correspondence to: Timothy V. Pyrkov email: tim.pyrkov@gero.ai and Peter O. Fedichev email: peter.fedichev@gero.ai

Keywords: biological age acceleration (BAA), public health, personalized interventions, Gompertz law, resilience, aging

About Aging

Launched in 2009, Aging 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 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​​ or connect with us on:

Twitter - https://twitter.com/AgingJrnl​
Facebook - https://www.facebook.com/AgingUS/​
SoundCloud - https://soundcloud.com/aging-us​
YouTube - https://www.youtube.com/agingus​
LinkedIn -  https://www.linkedin.com/company/aging​

Aging is published by Impact Journals, LLC please visit http://www.ImpactJournals.com​​ or connect with @ImpactJrnls

Media Contact
18009220957
MEDIA@IMPACTJOURNALS.COM

Top-Performer: Wearable Sensors Reveal Biological Markers of Longevity, Stress, Resilience

Bruker Mass Spectrometry

Watch the video on PaSER 2022, Beyond “Run & Done” with Dr. Chris Adams, Business Development Director Global Bioinformatics at Bruker Daltonics during their eXceed Symposia on "Expanding the Horizons of Single Cell Research"

Informatics

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