Analytical Techniques

Teach Me in 10

In today's laboratory settings, one of the most significant challenges we face is effectively managing the immense volume of data both describing and generated by our operations. In this Teach Me in 10 session, we will delve into the realm of best practices for harnessing this data. Our goal is to empower you with the ability to identify anomalies and take proactive measures to enhance the overall efficiency and operation of your laboratory.

Traversing the Flood of Data in Today’s Digital Labs

Oncotarget

Oncotarget published this trending research paper on September 15, 2023 in Volume 14, entitled, “Real time ex vivo chemosensitivity assay for pancreatic adenocarcinoma" by researchers from the Department of Gastrointestinal Oncology, Moffitt Cancer Center, Tampa, FL; Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL.

DOI - https://doi.org/10.18632/oncotarget.28508

Correspondence to - Jason B. Fleming - jason.fleming@moffitt.org

Abstract

Background: Patient-derived organoids (PDOs) and xenografts (PDXs) have been extensively studied for drug-screening. However, their usage is limited due to lengthy establishment time, high engraftment failure rates and different tumor microenvironment from original tumors. To overcome the limitations, we developed real time-live tissue sensitivity assay (RT-LTSA) using fresh tumor samples.

Methods: Tissue slices from resected pancreatic cancer samples were placed in 96-well plates, and the slices were treated with chemotherapeutic agents. The correlation between the chemo-sensitivity of tissue slices and each patient’s clinical outcome was analyzed.

Results: The viability and tumor microenvironment of the tissue slices are well-preserved over 5 days. The drug sensitivity assay results are available within 5 days after tissue collection. While all 4 patients who received RT-LTSA sensitive adjuvant regimens did not develop recurrence, 7 of 8 patients who received resistant adjuvant regimens developed recurrence. We observed significantly improved disease-free survival in the patients who received RT-LTSA sensitive adjuvant regimens (median: not reached versus 10.6 months, P = 0.02) compared with the patient who received resistant regimens. A significant negative correlation between RT-LTSA value and relapse-free survival was observed (Somer’s D: −0.58; P = 0.016).

Conclusions: RT-LTSA which maintains the tumor microenvironment and architecture as found in patients may reflect clinical outcome and could be used as a personalized strategy for pancreatic adenocarcinoma. Further, studies are warranted to verify the findings.

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Keywords - cancer, pancreatic cancer, sensitivity assay, chemotherapy

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.

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Real Time Ex Vivo Chemosensitivity Assay for Pancreatic Adenocarcinoma | Oncotarget

Organomation

Nitrogen Blowdown vs Rotary Evaporation

Laboratories often need to use evaporation techniques to further concentrate their test samples prior to analysis. Concentration occurs when excess solvent is converted into a vapor, leaving behind either a solid or liquid solute. There are countless evaporation methods available, so how do you know which one is best for your application?

This video will explain both nitrogen blowdown and rotary evaporation – two widely used evaporation methods. We will explain how each method accelerates the concentration process, and when each is recommended.

Let’s begin with nitrogen blowdown evaporation.

If we look at a sample under ambient conditions with no external forces, we’ll notice that the solvent molecules move around very slowly. Because of this, only some are able to be vaporized and separated from the sample. The high pressure right above the surface of the sample also causes many of these molecules to return back to the sample. These factors lead to a very slow evaporation rate.

The nitrogen blowdown method decreases the vapor pressure above the sample by applying a steady stream of nitrogen gas on the solvent’s surface.

The nitrogen gas can also cool the sample slightly, which decreases the energy of the molecules, slowing down their movement and ability to vaporize.

To counteract this, a form of heat is added to the sample which causes the molecules to re-energize and speed back up. The heat can be in the form of a water bath, or a dry block.

The sample is now in an optimal environment for concentration. The combination of heat and nitrogen blowdown allows the molecules to quickly vaporize and be whisked away from the sample.

Now, let’s compare that to rotary evaporation.

We’ll start with a large liquid sample in a round flask which will be hooked up to a rotary evaporator unit.

This flask will sit in a heated water bath causing the solvent molecules to speed up, and vaporize at an accelerated rate.

The flask will also rotate while in the water bath, increasing the surface area of the solvent, and allowing more solvent molecules to escape.

The vaporized solvent molecules will travel up towards a chilled condenser, where they’ll begin to condense and drip down into a receiving flask. This is where all the excess solvent will collect, leaving behind a concentrated sample in the rotating flask.

Some rotary evaporators also include a vacuum pump which can be connected to the condenser. This vacuum pump is meant to decrease the pressure inside the rotating flask, causing the solvent to evaporate at a lower-than-normal temperature. The combination of heat, rotation, and decreased pressure creates an ideal environment for efficient evaporation.

So when are each of these methods recommended for use?

Nitrogen blowdown is ideal when evaporating a high number of samples. Some nitrogen evaporators can accommodate batches of up to 100 samples.

This method is also meant for small volume samples. Samples larger than 100 mL will have a prolonged evaporation time.

The precision of nitrogen blowdown also makes it a great option for those who are looking to evaporate to complete dryness, or would like to stop it at a specific endpoint.

Rotary evaporation is ideal when working with a very small number of samples. Since these units can only handle one sample at a time, they would not be an ideal choice for evaporating large batches.

This method is also meant to handle large volume samples. Most rotary evaporators can handle sample volumes up to 2 L.

Lastly, rotary evaporation is great for evaporating solvents with high boiling points. The use of a vacuum pump for reduced pressure lowers the boiling point of the solvent, allowing them to be evaporated with minimal heat.

Each concentration method is designed for different applications, so it’s important to know which one will best meet your needs. If you have any questions on either of these methods, or need help identifying which is right for you, feel free to contact us at sales@organomation.com.

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Nitrogen Blowdown vs Rotary Evaporation

Harvesting involves the separation of the cell culture from the growth medium. There are several cell harvesting methods available, and the choice depends on the specific context of the work. In this Teach Me in 10 session, we will delve into these options, which include centrifugation, filtration, and separation techniques with Hilary Sherman a Senior Scientist, Corning Life Sciences.

Harvesting Cell Methods

CloudLIMS

CloudLIMS, a SOC 2 compliant and ISO 9001:2015 certified informatics company, hosted a complimentary webinar to provide insights into the key elements of the ISO 15189 standard and how a healthcare LIMS software can help laboratories achieve and maintain the standard to elevate the quality and reliability of diagnostic processes. 

#LIMS #clinicaldiagnostics #ISO15189 #laboratories #ondemandwebinar #laboratorysoftware #compliance

On-Demand Webinar: Exploring the Benefits of LIMS & ISO 15189 Integration for Diagnostic Labs

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:

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

Aging (Aging-US)

Aging-US published this trending research paper on August 28, 2023, in Volume 15, Issue 16, entitled, “Copy number variation as a tool for implementing pregnancy as an aging model" by researchers from the Department of Human Biology, University of Haifa, Haifa 3498838, Israel; Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel.

DOI - https://doi.org/10.18632/aging.204936

Corresponding author - Gil Atzmon - gatzmon@univ.haifa.ac.il

Abstract

Copy number variations (CNV) are a major contributor to genome variability and have been linked to aging and other degradable phenotypes such as pregnancy physiology. To demonstrate how pregnancy can be used as a model of aging, we used CNVs from pregnant mice. Candidate CNVs were selected by applying case-control analysis in human centenarians compared with control groups. These CNVs were aligned with the mouse genome and their copy variation was assessed using qRT-PCR in liver and blood tissue samples from pregnant mice throughout pregnancy (baseline; first, second, and third trimester; post-partum). Eight of the ten selected CNVs demonstrated a significant decline/increase trend throughout the pregnancy followed by opposite direction soon after delivery in the liver and blood of the mouse tissues. Furthermore, significant differential expression was detected among the candidate CNVs’ close vicinity genes (APA2A, LSS, RBDHF1, PLAAT1, and SCL17A2), but not in the WSCD2 gene. Establishing a genetic link between longevity and pregnancy is a significant step toward implementing the pregnancy process as a model for aging. These results in pregnant mice highlight the mechanism and similarities between pregnancy and aging. Investigating the mechanisms that cause such rejuvenation after labor could change our aging treatment paradigm.

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Keywords - aging, pregnancy, copy number variation, gene expression

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:

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Copy Number Variation as Tool for Implementing Pregnancy as Aging Model | Aging-US

Aging-US published this research paper on August 29, 2023 in Volume 15, Issue 16, entitled, “Reorganization of pancreas circadian transcriptome with aging" by researchers from the Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL; Division of Allergy and Immunology, Department of Internal Medicine, Rush University Medical Center, Chicago, IL; University of Wisconsin-Parkside, Department: Biological Sciences, Kenosha, WI; Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL; Department of Anatomy and Cell Biology, Rush University Medical Center, Chicago, IL.

DOI - https://doi.org/10.18632/aging.204929

Corresponding author - Faraz Bishehsari - Faraz_Bishehsari@rush.edu

Abstract

The evolutionarily conserved circadian system allows organisms to synchronize internal processes with 24-h cycling environmental timing cues, ensuring optimal adaptation. Like other organs, the pancreas function is under circadian control. Recent evidence suggests that aging by itself is associated with altered circadian homeostasis in different tissues which could affect the organ’s resiliency to aging-related pathologies. Pancreas pathologies of either endocrine or exocrine components are age-related. Whether pancreas circadian transcriptome output is affected by age is still unknown. To address this, here we profiled the impact of age on the pancreatic transcriptome over a full circadian cycle and elucidated a circadian transcriptome reorganization of pancreas by aging. Our study highlights gain of rhythms in the extrinsic cellular pathways in the aged pancreas and extends a potential role to fibroblast-associated mechanisms.

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Keywords - aging, circadian rhythms, RNA transcriptomics, pancreas

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
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LinkedIn - https://www.linkedin.com/company/aging/
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Reorganization of Pancreas Circadian Transcriptome with Aging | Aging-US

Oncotarget published this research paper on August 30, 2023 in Volume 14, entitled, “Analytic validation of NeXT Dx™, a comprehensive genomic profiling assay" by researchers from Personalis, Inc., Fremont, CA.

DOI - https://doi.org/10.18632/oncotarget.28490

Correspondence to - Richard Chen - richard.chen@Personalis.com

Abstract

We describe the analytic validation of NeXT Dx, a comprehensive genomic profiling assay to aid therapy and clinical trial selection for patients diagnosed with solid tumor cancers. Proprietary methods were utilized to perform whole exome and whole transcriptome sequencing for detection of single nucleotide variants (SNVs), insertions/deletions (indels), copy number alterations (CNAs), and gene fusions, and determination of tumor mutation burden and microsatellite instability. Variant calling is enhanced by sequencing a patient-specific normal sample from, for example, a blood specimen. This provides highly accurate somatic variant calls as well as the incidental reporting of pathogenic and likely pathogenic germline alterations. Fusion detection via RNA sequencing provides more extensive and accurate fusion calling compared to DNA-based tests. NeXT Dx features the proprietary Accuracy and Content Enhanced technology, developed to optimize sequencing and provide more uniform coverage across the exome. The exome was validated at a median sequencing depth of >500x. While variants from 401 cancer-associated genes are currently reported from the assay, the exome/transcriptome assay is broadly validated to enable reporting of additional variants as they become clinically relevant. NeXT Dx demonstrated analytic sensitivities as follows: SNVs (99.4%), indels (98.2%), CNAs (98.0%), and fusions (95.8%). The overall analytic specificity was >99.0%.

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Keywords - cancer, comprehensive genomic profiling, whole exome sequencing, whole transcriptome sequencing, tumor-normal, precision medicine

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.

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