How Genetics and Caffeine Shape Cognitive Performance: Insights from a New Study

How Genetics and Caffeine Shape Cognitive Performance: Insights from a New Study

Check out this hot-off-the-press publication by Kapellou et al. from St Mary’s University in London, where questionnaires, cognitive tests, and genotyping were used to investigate the interactions between genetics and habitual caffeine consumption on cognitive performance.

Healthy participants completed questionnaires on sociodemographic, health, and lifestyle factors and caffeine and alcohol intake.

They were then subjected to cognitive tests to assess social and emotional cognition, memory, attention, and executive function.

Finally, DNA was collected remotely from participants using an Isohelix RapiDri™ Swab kit. DNA was extracted and samples were genotyped at loci associated with caffeine metabolism and response, using TaqMan® SNP genotyping assays.

The findings suggest an association between genetic caffeine metabolism, habitual caffeine intake, and cognitive function in terms of social cognition and executive function.

Participants were grouped into ‘fast’ and ‘slow’ metabolizers:

  • ‘Fast’ metabolizers consumed significantly more caffeine than ‘slow’ metabolizers.
  • ‘Slow’ metabolizers performed better than ‘fast’ metabolizers in emotion recognition among high-caffeine consumers.
  • “Fast’ metabolizers performed better than ‘slow’ metabolizers in the executive function domain, but only within moderate caffeine consumers.

The study confirms that the association between caffeine and cognition is domain-specific, with social and emotional cognition and executive linked to habitual intake. It also replicates previous findings that ‘fast’ metabolizers consume more caffeine. More research in natural environments using larger cohorts is needed to confirm these findings and understand how habitual caffeine may influence cognitive function based on individual genotypes.

Rapidly extract DNA for sensitive applications with Buccalyse Direct-to-PCR kits

We are always thrilled to see our products cited in peer-reviewed publications.

This month, we would like to share some publications in which our popular Buccalyse Direct-to-PCR (BEK) kits (sometimes referred to as Buccalyse DNA Release kits) have been used to rapidly extract DNA for applications such as PCR and microarray analysis:

“Advancing human genotyping: The Infinium HTS iSelect Custom microarray panel (Rita) development study” Matute et al (2024)

The objective of this research was to assess the sensitivity, repeatability, reproducibility, accuracy, and precision of an HTS iSelect Custom panel called ‘Rita’, a custom SNP microarray panel developed using Illumina Infinium HTS technology. Designed for high-throughput genotyping, the panel efficiently facilitates the analysis of over 4000 markers associated with health, lifestyle, and forensic factors.

Studies revealed consistent panel performance across different batches and operators, with no significant deviations in call rates or genotyping results. The evaluation confirmed the Rita microarray as a robust, high-throughput genotyping tool, underscoring its potential in genetic research and forensic applications.

Samples for the study were extracted from buccal swabs using the Buccalyse DNA Release Kit. The sensitivity study showed that it is possible to obtain more than a 99 % call rate when working with as little as 0.78 ng of DNA.

The ability to a lower DNA input increases the assay’s utility in forensic laboratories, where casework samples may sometimes contain small amounts of genetic material.

Genes Involved in Susceptibility to Obesity and Emotional Eating Behavior in a Romanian Population Vranceanu et al, (2024)

This study examined the relationship between six obesity-related genes (CLOCK, FTO, GHRL, LEP, LEPR, MC4R) and their impact on measures of obesity and emotional eating behavior in 220 Romanian adults.

Buccal cells were collected from the lateral wall of the oral vestibule and sent for processing in a UK laboratory using the Rapidri Swab kit. DNA was then extracted from the buccal cells using Buccalyse, and genotype analysis was performed using the ABI7900 real-time thermocycler system.

The analysis revealed significant variability in obesity-related phenotypes and emotional eating behaviors across different genotypes. The study provides a foundation for targeted interventions to prevent and reduce obesity and suggests potential strategies for gene expression modulation to mitigate the effects of emotional eating.

“Systemic immunity shapes the oral microbiome and susceptibility to bisphosphonate-associated osteonecrosis of the jaw.” Kaylan et al (2015)

Osteonecrosis of the jaw (ONJ) is a rare but serious adverse drug effect linked to long-term and/or high-dose exposure to nitrogen-bisphosphonates (N-BP). The objective of this investigation was to assess the relationship linking immune function, N-BP exposure, the oral microbiome, and ONJ susceptibility.

To investigate the oral microbiome, Isohelix DNA swabs were used to obtain microbial DNA by running the swab along an area of the outer gumline of subjects. DNA was extracted using the Isohelix Buccalyse DNA extraction kit and stored at −20°C until analysis.

The oral microbiome was characterized by 454 pyrosequencing of the 16S rRNA gene in 93 subjects stratified by N-BP exposure and a history of ONJ.

The oral microbiome was found to be unlikely to cause ONJ. Instead, individuals with bisphosphonate-associated ONJ lacked immune resiliency, which impaired their capacity to respond adequately to the immunological stress of N-BP.

Buccalyse offers researchers a robust, user-friendly tool that consistently delivers reliable results. Its widespread adoption in diverse studies reflects its quality and adaptability, making it an indispensable asset for advancing research in genetics, microbiome studies, and forensic science.

Summary

The above publications feature DNA extracted using the Buccalyse Direct-to-PCR kit being used in a range of molecular biology applications including (but not limited to) genotyping using SNP micorarrays and PCR methods, and 454 pyrosequencing of the 16S rRNA gene for microbiome characterization.

The Buccalyse Direct-to-PCR Kit has been specially formulated to produce high DNA yields from buccal swabs. The kit is a quick and simple one-tube alternative to existing DNA isolation methods when extracting DNA for use in PCR reactions. The yield of DNA from a single buccal swab using Buccalyse is generally around 2 to 4ug from an adult.

CLICK HERE TO FIND OUT MORE ABOUT BUCCALYSE

Meet Isohelix at ASHG 2024 in Denver!

Isohelix is delighted to be attending ASHG 2024 in Denver from November 5 to 9. Join us at Booth #775!

We can’t wait to hear about your projects and introduce you to our innovative solutions for sample collection, stabilization, and purification.

Come by to discuss how our products can enhance your research efforts. We look forward to connecting with you at the event!

GeneFix™ Saliva collection devices used in large Japanese GWAS study on dental caries

What are Genome-wide association studies (GWAS)?

GWAS studies are genomic studies that test hundreds of thousands of genetic variants across many genomes, to find those statistically associated with a specific trait. GWAS have a range of applications including understanding the underlying biology of  a phenotype, estimating the heritability of a trait, investigating genetic correlations and making clinical predictions.

Advantages and Disadvantages of GWAS

GWAS can identify associations but doesn’t typically pinpoint causal relationships, so further studies are usually required to confirm findings and explore their biological significance.

GWAS Studies to investigate dental caries and
peridontal disease

Genome wide association studies (GWAS) play a crucial role in understanding the mechanisms underlying dental caries and periodontal disease. There are large variations in genetics and lifestyles across ethnicities, and although large-scale genome-wide association studies (GWAS) on dental caries and periodontal disease have been conducted extensively, few studies focus on Asian populations.

The recent study,  “Genome-wide association meta-analysis identifies two novel loci associated with dental caries” by Nogawa et al., used genome data from 45,525 Japanese individuals to conduct a GWAS, assessing the self-reported history of dental caries and periodontal disease of study participants. A meta-analysis was then performed by integrating our results with those from a previous large-scale GWAS predominantly involving European populations.

Although no new loci associated with periodontal disease were identified, two novel loci associated with dental caries were discovered. The findings contribute to understanding the mechanisms underlying dental caries and periodontal disease.

We were delighted that this study used GeneFix Saliva collection devices to collect and stabilize DNA in saliva samples collected from participants. Genotyping was executed employing various Illumina Infinium BeadChips.

The GeneFix™ range of DNA/RNA products has been designed to maximize the yields and purity of DNA/RNA collected and stabilized from saliva. GeneFix kits are ideal for collecting samples from study participants at home or in the clinic, as they are non-toxic, simple to use, and contain a reagent that stabilizes DNA at room temperature for up to 60 months. After sample collection, kits can be mailed to the lab for DNA extraction.

GeneFix Saliva Collection Products Used for Ground-Breaking Breast Cancer Research

Between 1993 and 2018[1] breast cancer rates in women increased by 24%, and in the UK in 2022, breast cancer was the most common cause of death for women between 35-49 and 50-64 years of age.[2]

We are delighted to see Isohelix products used for Breast Cancer research, with two recent UK-based studies using GeneFix Saliva collection devices to collect and stabilize DNA in saliva samples collected from study participants:

  • BRCA Direct: A Digital Pathway for BRCA-Testing in Breast Cancer
  • Breast Cancer Risk Assessment in Younger Women (BCAN-RAY) study

GeneFix Saliva Collection Products

The GeneFix™ range of DNA/RNA products has been designed to maximize the yields and purity of DNA/RNA collected and stabilized from saliva. GeneFix kits are ideal for collecting samples from study participants at home or in the clinic, as they are non-toxic, simple to use, and contain a reagent that stabilizes DNA at room temperature for up to 60 months. After sample collection, kits can be mailed to the lab for DNA extraction.
Read on to learn about recent studies using GeneFix products for Breast Cancer Research.

BRCA-Direct: A Digital Pathway for BRCA-Testing in Breast Cancer

The BRCA-DIRECT study was funded by Cancer Research UK and affiliated with the Institute of Cancer Research, SHORE-C,  Manchester University Foundation Trust, and The Royal Marsden Foundation Trust. The study aimed to provide an easy way for patients with breast cancer to access genetic testing within the NHS.

The BRCA1, BRCA2, and PALB2 genes are associated with hereditary breast cancer, so Identification of a pathogenic variant in one of these genes can have health implications for patients and their relatives. This study examined the feasibility, safety, and acceptability of a digital information model.

Participants provided a saliva or blood sample and accessed a digital platform using a device connected to the internet.  Family history details were collected, and information was gathered about the general knowledge of BRCA testing. Participants were asked about their anxiety levels at different points in the process. Half of all those who took part saw digital information, and half booked a standard appointment with genetic counselors.

Participants were then randomized to receive their results digitally or by booking a telephone appointment with a genetic counselor. Everyone who had a positive result was then referred to their local clinical genetics team. If the digital pathway is successful, the concept could be expanded to other cancers and hospitals.

​We are looking forward to seeing the results of the study that has led to further funding for a pilot across North Thames GLH, funding by SBRI Healthcare/NHS England Cancer Programme: SBRI Healthcare – NHS Cancer Programme awards £12.1 million to accelerate new front-line innovations that detect and diagnose cancer earlier

The BCAN-RAY study

The Breast Cancer Risk Assessment in Younger Women (BCAN-RAY) study began in May 2023. BCAN-RAY is one of the first research studies in the world to identify new ways to predict the risk of younger women getting breast cancer. The study aims to evaluate a comprehensive breast cancer risk assessment strategy among a diverse ethnic and socioeconomic population of women aged 30–39 years without a strong family history of breast cancer.

Two hundred fifty women previously diagnosed with breast cancer without a strong family history of the disease will be studied alongside 750 women (control participants) in the same age group who have not had breast cancer and who also have no strong family history of the disease. 

Control participants will complete questionnaires about breast cancer risk factors, undergo low-dose mammograms, and donate a saliva sample, which is collected using Isohelix GeneFix Saliva Collection Kits. Saliva samples will be used to analyze the genetic makeup of participants and identify those at higher risk using a tool called a polygenic risk score, which is a powerful predictor of breast cancer risk.

Cancer tissue biopsy

The BCAN-RAY study should complete recruitment in May 2025, and we look forward to seeing the results.

The study is funded by Cancer Research UK via the International Alliance for Cancer Early Detection (ACED), The Christie Charity, and The Shine Bright Foundation. It is led by Manchester University NHS Foundation Trust, and delivered at The Nightingale Centre at Wythenshawe Hospital and breast oncology centers across Greater Manchester and Cheshire.


Please follow the link to the Sarah Harding Breast Cancer Appeal: A letter from Girls Aloud (christie.nhs.uk) 

Read our blog article about genomic analysis using saliva instead of blood: https://isohelix.com/saliva-instead-of-blood/

Find out how to simplify Saliva and Buccal Swab sample collection and processing: https://isohelix.com/how-to-simplify-saliva-and-buccal-swab-sample-collection-and-processing/

Click here to find out more about our GeneFix Saliva Collection Products: https://isohelix.com/genefix-saliva-dna-rna-collection/


References

[1] Facts and figures | Breast Cancer UK

[2] Office for National Statistics. Deaths registered in England and Wales: 2022-2023

Introducing Long Read Sequencing

Long read sequencing was described as the “method of the year[i]” In an article published in Nature Methods at the start of 2023. The development of long read sequencing has significantly expanded the possibilities for genomic analysis.

Despite challenges such as the cost and the complexity of data analysis, the technology continues to improve, with increased accuracy, affordability, and accessibility.

This article introduces long read sequencing, highlights some of the key advantages compared with short read sequencing, and gives some key applications for long read sequencing.

Key points:

  • Long read sequencing length
  • Long read sequencing methods
  • Advantages of long read sequencing vs short read sequencing
  • Challenges with long read sequencing
  • Long read sequencing technology platforms
  • DNA extraction for long read sequencing
  • Should I use short read or long read sequencing?

Long Read Sequencing Length

Long-read sequencing, sometimes called “third generation sequencing,”  is a DNA sequencing technique that enables the sequencing of much longer stretches of DNA, typically ranging from thousands to over a million base pairs. By comparison, traditional short read sequencing typically captures sequences of 100-500 base pairs.

Long Read Sequencing Methods

Long read sequencing can be either “true long read” sequencing, or ‘synthetic long read sequencing.”

“True long read” sequencing directly reads longer fragments of DNA, typically ranging from thousands to over a million base pairs. This method is employed by companies such as Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), enabling the sequencing of long DNA strands in a single continuous process.

“Synthetic” long read sequencing uses short read sequencing data to reconstruct longer stretches of DNA. This method is employed by companies such as, Element Biosciences and Illumina (primarily known for short read sequencing). In synthetic short read sequencing, short DNA fragments are barcoded and sequenced using standard short read technology platforms, and computational methods are then used to assemble the short reads into longer sequences based on barcodes and overlaps, effectively creating a “synthetic” long read. This approach provides some of the benefits of “true” long read sequencing, like the better assembly of repetitive regions or complex genomic structures, without needing specialized long read sequencing equipment.

Both long-read and short-read sequencing have pros and cons. A “hybrid” DNA sequencing approach combines different DNA sequencing technologies to leverage each other’s strengths while compensating for their weaknesses. This approach typically involves using both long-read and short-read sequencing technologies together.

Advantages of Long-Read Sequencing vs Short Read Sequencing

The development of long read sequencing has been driven by the search for more complete and accurate genomic information.

The key limitation of short read sequencing is the inability to sequence long stretches of DNA. If the sequence of a large region of DNA is required, e.g. for a genome assembly, then the DNA has to be first fragmented, then amplified and sequenced. Bioinformatics tools are used to assemble these short sequences to give the full length sequence. However, if there is insufficient overlap between these shorter DNA fragments, there will be gaps or errors in the final sequence. Also amplification steps can introduce sequencing errors, particularly in repetitive regions of the genome.

The key limitation of short read sequencing is the inability to sequence long stretches of DNA. If the sequence of a large region of DNA is required, e.g. for a genome assembly, then the DNA has to be first fragmented, then amplified and sequenced. Bioinformatics tools are used to assemble these short sequences to give the full length sequence. However, if there is insufficient overlap between these shorter DNA fragments, there will be gaps or errors in the final sequence. Also amplification steps can introduce sequencing errors, particularly in repetitive regions of the genome.

Long read sequencing can provide a more comprehensive view of a genome than short read sequencing, enabling better identification of structural variants and repetitive regions that are often challenging to resolve with short reads, because it is difficult to reassemble sequencing data over long stretches of DNA.

Long reads can be particularly useful when:

  1. Resolving Complex Genomic Regions: Long reads are particularly advantageous when sequencing regions with repetitive elements, structural variants, and complex rearrangements, which are often challenging for short-read technologies.
  2. Assembling Genomes: Long-read sequencing provides more contiguous and accurate genome assemblies. This is especially important for de novo sequencing, where a reference genome is not available.
  3. Detecting Structural Variants: Long-read sequencing is useful for detecting large structural variants such as insertions, deletions, inversions, and translocations, which play significant roles in genetic diversity and disease.
  4. Phasing and Haplotyping: Long reads can span entire genes or large genomic regions, allowing for the accurate phasing of alleles and haplotype reconstruction.

Challenges with Long Read Sequencing

Despite its advantages, long-read sequencing historically faced several challenges, including higher costs and error rates compared to short-read sequencing. However, ongoing technological advancements are rapidly addressing these issues.

  1. Error Rates: Long read sequencing historically had higher error rates compared to short reads, affecting data accuracy. However, read accuracy is improving.
  2. Cost: The initial cost of long read sequencing technologies and associated data analysis can be higher than short read sequencing.
  3. Bioinformatics: Analyzing long read data may require specialized bioinformatics tools and computational resources, due to the unique characteristics of long reads. Data processing can take longer than with short read sequencing.

Long-Read Sequencing Technology Platforms

There are several platforms that facilitate long-read sequencing, with the two most well known being Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT).

Pacific Biosciences (PacBio): PacBio’s Single Molecule Real-Time (SMRT) sequencing technology can generate reads averaging 10,000-15,000 bp. The technology utilizes real-time observation of DNA synthesis, where fluorescently labelled nucleotides are incorporated by DNA polymerase, allowing for the continuous reading of the sequence.

Oxford Nanopore Technologies (ONT): ONT’s nanopore sequencing passes a DNA molecules through a nanopore embedded in a membrane. As the DNA translocates through the pore, changes in ionic current are measured and translated into sequence data. ONT platforms can produce ultra-long reads offering unparalleled length and flexibility.

DNA Extraction for Long Read Sequencing

Short read sequencing generally requires DNA fragments between 100 and 600 base pairs in length, and therefore, it can tolerate somewhat degraded DNA since the required fragment size is smaller. DNA is often fragmented mechanically (using sonication) or enzymatically during sample preparation.

Short read sequencing generally requires DNA fragments between 100 and 600 base pairs in length, and therefore, it can tolerate somewhat degraded DNA since the required fragment size is smaller. DNA is often fragmented mechanically (using sonication) or enzymatically during sample preparation.

Long-read sequencing requires high-quality, high-molecular-weight DNA, typically upwards of 10,000 base pairs. Any nicks or breaks in DNA strands can significantly impact the ability to generate long reads. The main limiting factor for ONT read lengths is the DNA extraction; Jain et al (2018) found that read lengths produced by the MinION [iii] nano pore sequencer were dependent on the input fragment length[ii]. This often necessitates more careful handling and extraction procedures, and there are several extraction methods and commercially available kits for preparing DNA for long read sequencing.

Should I use Short Read or Long Read Sequencing?

The choice between long-read and short-read sequencing methods will depend on the specific requirements of the research question including the characteristics of the region to be amplified, sample type, cost, and accuracy.

Recent improvements in error correction algorithms, cost reduction strategies, and hybrid sequencing approaches that combine long-read and short-read data are paving the way for broader adoption.


[i] Marx, V. Method of the year: long-read sequencing. Nat Methods 20, 6–11 (2023). https://doi.org/10.1038/s41592-022-01730-w

[ii] Jain M et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat.  Biotechnol 36, 338–345 (2018).

[iii] MinION is a trademark of Oxford Nanopore

How to Simplify Saliva and Buccal Swab Sample Collection and Processing

This article explains how to optimize and streamline sample collection and processing for nucleic acid analysis, to ensure consistent and reliable results while minimizing sample collection, processing, and shipping costs.

Key things to consider are:

  • Sample collection protocols
  • Nucleic acid stabilization
  • Sample transport
  • Streamlined sample processing
  • Sample tracking

Use Simple Saliva Sample Collection Protocols

Buccal swabs and saliva samples can be collected non-invasively, which encourages more people to participate in studies. This is especially important for large-scale population studies, where broad participation is crucial for the validity of the results.

Allowing donors to collect samples at home removes the need to travel to a clinic or laboratory, which is particularly beneficial for individuals with mobility issues, busy schedules, or living in remote areas. Collecting samples at home can significantly reduce costs associated with sample collection by eliminating the need for dedicated space and staff to handle sample collection in a clinical setting.

Isohelix sample collection kits include several features that simplify sample collection:

  • All kits include clear instructions for use that can be followed by donors at home
  • Isohelix GeneFix saliva collection kits have a unique funnel design that prevents spillages or buffer flow back.
  • GeneFix™ collection tubes have clear, legible markings to indicate the correct volume of saliva to be collected
  • Buccal Swabs are provided in easy-to-handle formats

Nucleic Acid Stabilization

Isohelix offers several options for nucleic acid stabilization that remove the need for a cold chain during sample shipment, significantly reducing the costs and logistical challenges associated with sample storage and transport.

Stabilization Reagents

Including collection tubes prefilled with a nucleic acid stabilization reagent is a simple method of immediately stabilizing samples at the point of collection, with minimal handling steps and cross-contamination risk.

For swabs and saliva collection, Isohelix collection tubes are pre-filled with BuccalFix or GeneFix stabilizing buffers that completely inhibit all enzymatic and microbial activity following sampling. As a result, DNA is fully stabilized, and the structure and integrity of the DNA are maintained. DNA can be stored in BuccalFix at room temperature for over 2 years and in GeneFix for up to 5 years.

Nucleic Acid Stabilization via sample desiccation

For shorter-term storage, RapiDri™ Swab kits (RD-01) include a microporous moisture-wicking pouch that rapidly dries the swab, stabilizing the DNA on the swab matrix, where it is protected from degradation. DNA can be stabilized for 3 months at ambient temperature, allowing safe and easy sample transport and storage.

Alternatively, Isohelix Dri-Capsules are silica gel capsules that offer an easy-to-use alternative to chemical stabilization for the long-term stability of buccal DNA on a swab head before isolation. DNA stabilized using Dri-Capsules is stable for 3 years at ambient temperature. 

Streamline Sample Transport

If collection tubes and sample packaging are sufficiently robust, stabilized samples can be sent to the laboratory for processing using regular mail, a straightforward and cost-effective method of sample transport.

There are a range of products available from Isohelix to simplify shipping:

  • Isohelix collection tubes comply with UN3373 on leak-proof sample transport that specify that collection tubes must withstand defined physical pressures of 95KPA. 
  • Mailing boxes are suitable for GeneFix Saliva collectors and have space to fit a transport pack underneath. They are designed to fit through most letterboxes and are certified to UN3373. They include a security sealing strip.
  • Transport packs are suitable for saliva and swab samples and include an absorbent pad to contain leakages, a separate document pocket, and are tested to resist 95kPa.
  • Saliva transport packs are specifically designed for saliva samples, featuring a slimmer profile for easier postage

Medium and High-Throughput Sample Processing

For large numbers of samples, automated systems reduce handling errors, save hands-on time, and increase processing throughput. Genefix High Throughput tubes (GFXH) for saliva collection have a key-fitting cap and locking base designed to fit automated de-capping machines. For buccal swabs, SwabCatcher tubes include a unique cap design that automatically removes swabs and is suitable for automated and high-throughput systems.

Isohelix also offers magnetic bead-based nucleic extraction kits, Buccal-Mag, and Saliva-Mag. These kits can be used manually or with most openly programmable automated DNA isolation and liquid handling systems fitted with magnetic racks and heat blocks.

Alternatively, for saliva collection, Isohelix has adapted the Saliva-Prep2 kit for use with 1.2ml or 2.0ml 96 – Deep Well Plates. This gives a manual method for isolating 96 samples per plate, requiring only low-cost, widely available benchtop laboratory equipment.

Sample Tracking

Easy and accurate sample tracking is a key component of sample collection and isolation. All GeneFix Saliva Collection tubes include a unique 10-digit, alphanumeric 1D barcode on the side of the tube which allows for full traceability of the sample from production to distribution and testing. Tubes can be specified with a 2D barcode on the base of the tube that corresponds with the 1D barcode on the side. Having a 2D barcode available on the base of the tube allows automation systems to scan the barcodes while in racking to maintain traceability when using high-throughput methods. Barcodes printed in triplicate on cryogenic labels are also available for attaching to tubes or paper. All barcodes are scannable on common readers, including those widely available on mobile phones, so that even patients at home can scan their devices to provide additional traceability.

Summary

By implementing simple standardized collection methods, and optimizing processing and shipping, the integrity and reliability of saliva and buccal swab samples can be preserved, ensuring the best possible nucleic acid analysis results whilst minimizing time and cost.

To find out more about how Isohelix products simplify sample collection, CLICK HERE

Out of this world sample collection: Using swabs to study the microbiomes of astronauts

We were delighted to see that two recent, high-profile studies looking at the effects of spaceflight on astronauts’ microbiomes chose Isohelix buccal swabs to collect their valuable samples.

In the Nature paper, “Longitudinal multi-omics analysis of host microbiome architecture and immune responses during short-term spaceflight,” published by Tierney et. al., (2024), the team used Isohelix swabs to collect samples from three microbial ecosystems (oral, nasal, and skin), before and after a 3-day mission to space.

Using paired metagenomics and metatranscriptomics alongside single-nuclei immune cell profiling, the team characterized microbiomes before, during and after spaceflight. The study revealed shifts in the microbiome and immune response during short term spaceflight; although most microbiome alterations were transient, longer-term shifts were observed in the astronaut’s oral microbiomes.

Another Nature paper, “Spatial multi-omics of human skin reveals KRAS and inflammatory responses to spaceflight”, Park et al (2024), also looked at the effects of short-duration spaceflight on the skin. The study applied a wide range of -omics methods, and as part of this study, Isohelix swabs were used to collect samples of astronauts’ skin microbiomes. Metagenomics and metatranscriptomics analyses were then performed on the skin swab samples. A key finding was that post-flight samples showed significant up-regulation of genes related to inflammation and KRAS signalling across all skin regions.

The results from these two important studies can help guide spacecraft design and response countermeasures for astronauts on future missions, and we are excited to see Isohelix products being used to expand our knowledge in this area.

Isohelix swabs feature a unique swab matrix and quick-release surface that maximises nucleic acid yields. Swab batches are ethylene oxide treated and routinely tested for human DNA contamination, making them ideal for capturing precious nucleic acid samples.

CLICK HERE TO FIND OUT MORE ABOUT ISOHELIX BUCCAL SWABS FOR NUCLEIC ACID COLLECTION OF ORAL AND SKIN MICROBIOME SAMPLES

Isohelix also offer stabilization reagents for buccal swabs that offer long term sample stability prior to isolation

Link : Isohelix™ DNA Buccal Swab Stabilization – Isohelix

Research Spotlight : Exploring the legacy of African and Indigenous Caribbean admixture in Puerto Rico

The body of research using Isohelix products is growing all the time. One that caught our attention recently was, “Exploring the legacy of African and Indigenous Caribbean admixture in Puerto Rico” by Taiye Winful et al. (2023).

The goal of this study was to assess the biogeographic origins of African descendant Puerto Ricans and to investigate the potential for Indigenous ancestry within this community.

2ml saliva samples were collected from self-identified African descendant Puerto Ricans residing in Puerto Rico using Isohelix Genefix™ collection kits. GeneFix kits are ideal for collecting samples from study participants in remote communities as they are non-toxic, simple to use, and contain a reagent that stabilizes DNA at room temperature for up to 60 months. After sample collection, kits can be mailed to the lab for DNA extraction.

When the samples reached the lab, DNA was extracted using the Isohelix Genefix Saliva-Prep 2 DNA kit, which uses a precipitation method to isolate high yields of pure DNA. The mitochondrial genomes of these individuals were sequenced, and Y chromosome haplogroups were genotyped for samples donated from males. Summary statistics, comparative analyses, and network analysis were used to assess diversity and variation in haplogroup distribution between the samples and comparative populations.

Results from the mitochondrial haplogroups showed that 66% had African, 5% had European, and 29% had Indigenous American matrilines. The Y chromosome analysis showed that 52% had African, 28% had Western European, 16% had Eurasian, and 4% had Indigenous American patrilines.

This study successfully used Isohelix GeneFix and Saliva-Prep kits to collect and extract DNA from saliva samples from study participants across Puerto Rico. The genomic analysis of these saliva samples have contributed to understanding how African descendants and Indigenous American admixture have shaped present-day communities.


CONTACT US to find out how we can help with your sample collection and DNA extraction needs.