scholarly journals Nanopore Sequencing in Microgravity

2015 ◽  
Author(s):  
Alexa B.R. McIntyre ◽  
Lindsay Rizzardi ◽  
Angela M Yu ◽  
Gail L. Rosen ◽  
Noah Alexander ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Point Of Care ◽  
Parabolic Flight ◽  
Space Station ◽  
Lessons Learned ◽  
Microgravity Environment ◽  
Technological Advancement ◽  
Reduced Gravity ◽  
Sequencing Technologies ◽  
Minimal Modification

The ability to perform remote,in situsequencing and diagnostics has been a long-sought goal for point-of-care medicine and portable DNA/RNA measurements. This technological advancement extends to missions beyond Earth as well, both for crew health and astrobiology applications. However, most commercially available sequencing technologies are ill-suited for space flight for a variety of reasons, including excessive volume and mass, and insufficient ruggedization for spaceflight. Portable and lightweight nanopore-based sequencers, which analyze nucleic acids electrochemically, are inherently much better suited to spaceflight, and could potentially be incorporated into future missions with only minimal modification. As a first step toward evaluating the performance of nanopore sequencers in a microgravity environment, we tested the Oxford Nanopore Technologies MinIONTMin a parabolic flight simulator to examine the effect of reduced gravity on DNA sequencing. The instrument successfully generated three reads, averaging 2,371 bases. However, the median current was shifted across all reads and the error profiles changed compared with operation of the sequencer on the ground, indicating that distinct computational methods may be needed for such data. We evaluated existing methods and propose two new methods; the first new method is based on a wave-fingerprint method similar to that of the Shazam model for matching periodicity information in music, and the second is based on entropy signal mapping. These tools provide a unique opportunity for nucleic acid sequencing in reduced gravity environments. Finally, we discuss the lessons learned from the parabolic flight as they would apply to performing DNA sequencing with the MinIONTMaboard the International Space Station.

scholarly journals The effects of real and simulated microgravity on cellular mitochondrial function

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Hong Phuong Nguyen ◽  
Phuong Hoa Tran ◽  
Kyu-Sung Kim ◽  
Su-Geun Yang
Keyword(s):  
Oxidative Stress ◽  
Respiratory Chain ◽  
Metabolic Pathways ◽  
Molecular Mechanisms ◽  
Simulated Microgravity ◽  
Space Shuttle ◽  
Parabolic Flight ◽  
Space Station ◽  
Microgravity Environment ◽  
Mitochondrial Stress

AbstractAstronauts returning from space shuttle missions or the International Space Station have been diagnosed with various health problems such as bone demineralization, muscle atrophy, cardiovascular deconditioning, and vestibular and sensory imbalance including visual acuity, altered metabolic and nutritional status, and immune system dysregulation. These health issues are associated with oxidative stress caused by a microgravity environment. Mitochondria are a source of reactive oxygen species (ROS). However, the molecular mechanisms through which mitochondria produce ROS in a microgravity environment remain unclear. Therefore, this review aimed to explore the mechanism through which microgravity induces oxidative damage in mitochondria by evaluating the expression of genes and proteins, as well as relevant metabolic pathways. In general, microgravity-induced ROS reduce mitochondrial volume by mainly affecting the efficiency of the respiratory chain and metabolic pathways. The impaired respiratory chain is thought to generate ROS through premature electron leakage in the electron transport chain. The imbalance between ROS production and antioxidant defense in mitochondria is the main cause of mitochondrial stress and damage, which leads to mitochondrial dysfunction. Moreover, we discuss the effects of antioxidants against oxidative stress caused by the microgravity environment space microgravity in together with simulated microgravity (i.e., spaceflight or ground-based spaceflight analogs: parabolic flight, centrifugal force, drop towers, etc.). Further studies should be taken to explore the effects of microgravity on mitochondrial stress-related diseases, especially for the development of new therapeutic drugs that can help increase the health of astronauts on long space missions.

scholarly journals Integration of mobile sequencers in an academic classroom

2015 ◽  
Author(s):  
Sophie Zaaijer ◽  
Yaniv Erlich
Keyword(s):  
Dna Sequencing ◽  
Rapid Development ◽  
Lessons Learned ◽  
Educational Opportunities ◽  
Educational Resources ◽  
Sequencing Technologies ◽  
Oxford Nanopore ◽  
Hands On ◽  
Academic Class ◽  
Oxford Nanopore Technologies

The rapid development of DNA sequencing technologies creates new educational opportunities for hands-on training. We report our experience in integrating handheld DNA sequencers (Oxford Nanopore Technologies MinION) as part of an academic class. This manuscript describes lessons learned to facilitate successful integration and provides educational resources for the benefit of the community.

Gas Evolution in Rotating Electrochemical Cells Under Reduced and Normal Gravity Conditions

2003 ◽  
Vol 19 (3) ◽  
pp. 349-355
Author(s):  
Fang-Bor Weng ◽  
Ay Su ◽  
Yasuhiro Kamotani ◽  
Simon Ostrach
Keyword(s):  
Mass Transfer ◽  
Rotation Rate ◽  
Life Support ◽  
Parabolic Flight ◽  
Advanced Life Support ◽  
Water Electrolysis ◽  
Microgravity Environment ◽  
Reduced Gravity ◽  
Bubble Behavior ◽  
Bubble Generation

AbstractElectrochemical experiments in microgravity are essential for the optimum design of advanced life support systems and power storage systems in space. In the absence of gravity, the evolved gas bubbles will clog the electrode and slow the reaction. Here, a rotating cell concept is introduced as a plan for improving mass transfer and bubble removal in a microgravity environment. A primary experimental study of bubble behavior in rotating water electrolysis cells has been done in reduced gravity through KC-135 parabolic flight. The results show that the cell resistance decreases with increasing rotation rate. Without rotation, the bubbles stick on the electrode surface during reduced gravity period, thus, the cell efficiency degrades. Mass transfer enhanced by bubble generation is investigated in ground-based work at high rotation rate of test cells, so that gravitational effects are minimized.

scholarly journals From Genetics to Genomics of Epilepsy

2012 ◽  
Vol 2012 ◽  
pp. 1-18 ◽  
Author(s):  
Silvio Garofalo ◽  
Marisa Cornacchione ◽  
Alfonso Di Costanzo
Keyword(s):  
Dna Sequencing ◽  
Dna Microarrays ◽  
Molecular Cytogenetics ◽  
Entire Genome ◽  
Sequencing Technologies ◽  
Genomic Approach ◽  
Molecular Karyotype ◽  
High Throughput Dna Sequencing ◽  
Laboratory Technology ◽  
Near Future

The introduction of DNA microarrays and DNA sequencing technologies in medical genetics and diagnostics has been a challenge that has significantly transformed medical practice and patient management. Because of the great advancements in molecular genetics and the development of simple laboratory technology to identify the mutations in the causative genes, also the diagnostic approach to epilepsy has significantly changed. However, the clinical use of molecular cytogenetics and high-throughput DNA sequencing technologies, which are able to test an entire genome for genetic variants that are associated with the disease, is preparing a further revolution in the near future. Molecular Karyotype and Next-Generation Sequencing have the potential to identify causative genes or loci also in sporadic or non-familial epilepsy cases and may well represent the transition from a genetic to a genomic approach to epilepsy.

scholarly journals Modernizing the Toolkit for Arthropod Bloodmeal Identification

Insects ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 37
Author(s):  
Erin M. Borland ◽  
Rebekah C. Kading
Keyword(s):  
Nuclear Dna ◽  
Point Of Care ◽  
Isotope Analysis ◽  
Digital Pcr ◽  
Lessons Learned ◽  
Molecular Techniques ◽  
Melting Analysis ◽  
Field Deployment ◽  
Blood Meal Identification ◽  
Bloodmeal Identification

Understanding vertebrate–vector interactions is vitally important for understanding the transmission dynamics of arthropod-vectored pathogens and depends on the ability to accurately identify the vertebrate source of blood-engorged arthropods in field collections using molecular methods. A decade ago, molecular techniques being applied to arthropod blood meal identification were thoroughly reviewed, but there have been significant advancements in the techniques and technologies available since that time. This review highlights the available diagnostic markers in mitochondrial and nuclear DNA and discusses their benefits and shortcomings for use in molecular identification assays. Advances in real-time PCR, high resolution melting analysis, digital PCR, next generation sequencing, microsphere assays, mass spectrometry, and stable isotope analysis each offer novel approaches and advantages to bloodmeal analysis that have gained traction in the field. New, field-forward technologies and platforms have also come into use that offer promising solutions for point-of-care and remote field deployment for rapid bloodmeal source identification. Some of the lessons learned over the last decade, particularly in the fields of DNA barcoding and sequence analysis, are discussed. Though many advancements have been made, technical challenges remain concerning the prevention of sample degradation both by the arthropod before the sample has been obtained and during storage. This review provides a roadmap and guide for those considering modern techniques for arthropod bloodmeal identification and reviews how advances in molecular technology over the past decade have been applied in this unique biomedical context.

Test genetici e consenso informato

2012 ◽  
pp. 68-95
Author(s):  
Marco Seri ◽  
Claudio Graziano ◽  
Daniela Turchetti ◽  
Juri Monducci
Keyword(s):  
Dna Sequencing ◽  
Human Genetics ◽  
Ethical Issues ◽  
Clinical Care ◽  
Genomic Medicine ◽  
Genome Project ◽  
Ethical Challenges ◽  
Sequencing Technologies ◽  
The Human Genome Project

The pace of discovery in the field of human genetics has increased exponentially in the last 30 years. We have witnessed the completion of the Human Genome Project, the identification of hundreds of disease-causing genes, and the dawn of genomic medicine (clinical care based on genomic information). Reduction of DNA sequencing costs, thanks to the so-called "next generation sequencing" technologies, is driving a shift towards the era of "personal genomes", but scientific as well as ethical challenges ahead are countless. We provide an overview on the classification of genetic tests, on informed consent procedures in the context of genetic counseling, and on specific ethical issues raised by the implementation of new DNA sequencing technologies.

JAK inhibition in the myeloproliferative neoplasms: lessons learned from the bench and bedside

Hematology ◽  
2013 ◽  
Vol 2013 (1) ◽  
pp. 529-537 ◽  
Author(s):  
Jason Gotlib
Keyword(s):  
Myeloproliferative Neoplasms ◽  
Symptom Burden ◽  
Jak2 V617f ◽  
Lessons Learned ◽  
Jak Inhibitors ◽  
Jak2 Inhibitor ◽  
Sequencing Technologies ◽  
Cell Growth And Differentiation ◽  
Scientific Context ◽  
Generation Sequencing

AbstractThe discovery of the JAK2 V617F mutation in the classic BCR-ABL1–negative myeloproliferative neoplasms in 2005 catalyzed a burst of research efforts that have culminated in substantial dividends for patients. Beyond JAK2 V617F, a more detailed picture of the pathobiologic basis for activated JAK-STAT signaling has emerged. In some patients with myelofibrosis (MF), next-generation sequencing technologies have revealed a complex clonal architecture affecting both genetic and epigenetic regulators of cell growth and differentiation. Although these bench-top findings have informed the clinical development of JAK inhibitors in MF, they have also provided scientific context for some of their limitations. The JAK1/JAK2 inhibitor ruxolitinib is approved for treatment of MF in North America and Europe and other lead JAK inhibitors discussed herein (fedratinib [SAR302503], momelotinib [CYT387], and pacritinib [SB1518]), have entered advanced phases of trial investigation. Uniformly, these agents share the ability to reduce spleen size and symptom burden. A major challenge for practitioners is how to optimize dosing of these agents to secure clinically relevant and durable benefits while minimizing myelosuppression. Suboptimal responses have spurred a “return to the bench” to characterize the basis for disease persistence and to inform new avenues of drug therapy.

scholarly journals Splicing Express: a software suite for alternative splicing analysis using next-generation sequencing data

PeerJ ◽  
2015 ◽  
Vol 3 ◽  
pp. e1419 ◽  
Author(s):  
Jose E. Kroll ◽  
Jihoon Kim ◽  
Lucila Ohno-Machado ◽  
Sandro J. de Souza
Keyword(s):  
Alternative Splicing ◽  
Dna Sequencing ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Software Suite ◽  
Next Generation Dna Sequencing ◽  
Sequencing Technologies ◽  
Body Map ◽  
Sequencing Platforms

Motivation.Alternative splicing events (ASEs) are prevalent in the transcriptome of eukaryotic species and are known to influence many biological phenomena. The identification and quantification of these events are crucial for a better understanding of biological processes. Next-generation DNA sequencing technologies have allowed deep characterization of transcriptomes and made it possible to address these issues. ASEs analysis, however, represents a challenging task especially when many different samples need to be compared. Some popular tools for the analysis of ASEs are known to report thousands of events without annotations and/or graphical representations. A new tool for the identification and visualization of ASEs is here described, which can be used by biologists without a solid bioinformatics background.Results.A software suite namedSplicing Expresswas created to perform ASEs analysis from transcriptome sequencing data derived from next-generation DNA sequencing platforms. Its major goal is to serve the needs of biomedical researchers who do not have bioinformatics skills.Splicing Expressperforms automatic annotation of transcriptome data (GTF files) using gene coordinates available from the UCSC genome browser and allows the analysis of data from all available species. The identification of ASEs is done by a known algorithm previously implemented in another tool namedSplooce. As a final result,Splicing Expresscreates a set of HTML files composed of graphics and tables designed to describe the expression profile of ASEs among all analyzed samples. By using RNA-Seq data from the Illumina Human Body Map and the Rat Body Map, we show thatSplicing Expressis able to perform all tasks in a straightforward way, identifying well-known specific events.Availability and Implementation.Splicing Expressis written in Perl and is suitable to run only in UNIX-like systems. More details can be found at:http://www.bioinformatics-brazil.org/splicingexpress.

Sign in / Sign up

Export Citation Format

Share Document