scholarly journals Accurate RNA consensus sequencing for high-fidelity detection of transcriptional mutagenesis-induced epimutations

2017 ◽  
Vol 114 (35) ◽  
pp. 9415-9420 ◽  
Author(s):  
Kate S. Reid-Bayliss ◽  
Lawrence A. Loeb
Keyword(s):  
Single Molecule ◽  
High Fidelity ◽  
Causal Association ◽  
Cdna Synthesis ◽  
Rna Transcription ◽  
Sequencing Method ◽  
Transcriptional Mutagenesis ◽  
Polymerase Mutants ◽  
And Oxidative Stress

Transcriptional mutagenesis (TM) due to misincorporation during RNA transcription can result in mutant RNAs, or epimutations, that generate proteins with altered properties. TM has long been hypothesized to play a role in aging, cancer, and viral and bacterial evolution. However, inadequate methodologies have limited progress in elucidating a causal association. We present a high-throughput, highly accurate RNA sequencing method to measure epimutations with single-molecule sensitivity. Accurate RNA consensus sequencing (ARC-seq) uniquely combines RNA barcoding and generation of multiple cDNA copies per RNA molecule to eliminate errors introduced during cDNA synthesis, PCR, and sequencing. The stringency of ARC-seq can be scaled to accommodate the quality of input RNAs. We apply ARC-seq to directly assess transcriptome-wide epimutations resulting from RNA polymerase mutants and oxidative stress.

Mass-Casualty Training Exercise Using High-Fidelity Computerized Simulators and Involving Time and Resource Limitation

2021 ◽  
Vol 36 (3) ◽  
pp. 313-320
Author(s):  
Phillip A. Jacobson ◽  
Paul N. Severin ◽  
Dino P. Rumoro ◽  
Shital Shah
Keyword(s):  
Health Care ◽  
Resource Limitation ◽  
Mass Casualty ◽  
Health Care Personnel ◽  
High Fidelity ◽  
Medical Team ◽  
Training Exercise ◽  
The Mean ◽  
Medical Teams

AbstractPurpose:Training emergency department (ED) personnel in the care of victims of mass-casualty incidents (MCIs) is a highly challenging task requiring unique and innovative approaches. The purpose of this study was to retrospectively explore the value of high-fidelity simulators in an exercise that incorporates time and resource limitation as an optimal method of training health care personnel in mass-casualty care.Methods:Mass-casualty injury patterns from an explosive blast event were simulated for 12 victims using high-fidelity computerized simulators (HFCS). Programmed outcomes, based on the nature of injuries and conduct of participants, ranged from successful resuscitation and survival to death. The training exercise was conducted five times with different teams of health care personnel (n = 42). The exercise involved limited time and resources such as blood, ventilators, and imaging capability. Medical team performance was observed and recorded. Following the exercise, participants completed a survey regarding their training satisfaction, quality of the exercise, and their prior experiences with MCI simulations. The Likert scale responses from the survey were evaluated using mean with 95% confidence interval, as well as median and inter-quartile range. For the categorical responses, the frequency, proportions, and associated 95% confidence interval were calculated.Results:The mean rating on the quality of experiences related trainee survey questions (n = 42) was between 4.1 and 4.6 on a scale of 5.0. The mean ratings on a scale of 10.0 for quality, usefulness, and pertinence of the program were 9.2, 9.5, and 9.5, respectfully. One hundred percent of respondents believed that this type of exercise should be required for MCI training and would recommend this exercise to colleagues. The five medical team (n = 5) performances resulted in the number of deaths ranging from two (including the expectant victims) to six. Eighty percent of medical teams attempted to resuscitate the “expectant” infant and exhausted the O- blood supply. Sixty percent of medical teams depleted the supply of ventilators. Forty percent of medical teams treated “delayed” victims too early.Conclusion:A training exercise using HFCS for mass casualties and employing limited time and resources is described. This exercise is a preferred method of training among participating health care personnel.

scholarly journals Methodologies to Assess the Bioactivity of an Herbal Extract on Immunity, Health, Welfare and Production Performance in the Chicken: The Case of Melissa officinalis L. Extract

2021 ◽  
Vol 8 ◽  
Author(s):  
Angélique Travel ◽  
Angélique Petit ◽  
Perrine Barat ◽  
Anne Collin ◽  
Camille Bourrier-Clairat ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Blood Cells ◽  
Ex Vivo ◽  
Redox Balance ◽  
Herbal Extracts ◽  
Melissa Officinalis ◽  
Starting Conditions ◽  
Anti Inflammatory ◽  
And Oxidative Stress

The potential of herbal extracts containing bioactive compounds to strengthen immunity could contribute to reducing antimicrobial use in poultry. This study aimed at developing a reliable and robust methodological pipeline to assess the ability of herbal extracts to strengthen chicken innate defenses, especially concerning inflammation and oxidative stress. This methodology was applied to Melissa officinalis L. (MEL) extract, recognized for its biological activities including antioxidant and anti-inflammatory properties. Different methods were used to (1). guarantee the quality of MEL extract and its capacity to stimulate the innate immune system; (2). evaluate the relevance of an ex vivo model to mimic inflammatory and oxidative stress challenges to replace LPS injection in chickens; (3). analyse the effects of feed supplemented with MEL extract on inflammation and oxidative stress induced ex vivo; (4). assess the effects of MEL extract on the redox balance, health, welfare and performance in broilers exposed to suboptimal starting conditions through a large-scale approach. The quality of MEL extract preparations, through phytochemical quantification of rosmarinic acid (RA), revealed varying concentrations of RA in the different MEL extracts. RA concentrations remained stable for at least 9 months and in feed three months after incorporating MEL extract. When incubated with chicken cell lines MEL extract showed potential metabolic activation and ability to stimulate immune functions but induced cytotoxicity at high concentrations. The original ex vivo model of inflammation developed on chicken blood cells enabled inflammation and oxidative stress biomarkers to be expressed and revealed antioxidative and anti-inflammatory properties of blood cells from chickens fed MEL extract. The experimental model of chicken suboptimal starting conditions validated beneficial effects of MEL extract on the redox balance and also evidenced improved performance during the growth phase, a tendency for fewer muscle defects but a higher severity of pododermatitis lesions without affecting other welfare indicators. This study grouped methods and tools that could be combined according to the plant extract, the needs of professionals working in poultry production systems and staff responsible for animal health, welfare and feeding.

Maintaining Effective Microsurgery Training with Reduced Utilisation of Live Rats

2020 ◽  
Vol 25 (02) ◽  
pp. 206-213 ◽  
Author(s):  
Amitabha Lahiri ◽  
Sandeep Sebastin Muttath ◽  
Siti Khadijah Yusoff ◽  
Alphonsus KS. Chong
Keyword(s):  
Skill Acquisition ◽  
Ex Vivo ◽  
High Fidelity ◽  
Training Time ◽  
Training Models ◽  
Ethical Concerns ◽  
Utilisation Rate ◽  
Group A ◽  
Group B

Background: Microvascular surgery is now an integral part of many surgical disciplines, and the success of these procedures relies on the technical skills of the surgeon. Although numerous training models and simulations have been developed, the living rat model is favoured for its high fidelity to clinical microsurgery. However, there are serious ethical concerns over the use of live models for training. The aim of this study was to demonstrate if effective skill acquisition was possible with a reduction in the number of live rats. Methods: Two course structures were designed, that were implemented. Total training hours remained the same in both the courses, but the number of rats used was reduced from conventional five rats per participant to four in group A and to three in group B while increasing the training time spent on synthetic and ex-vivo models. We assessed the effectiveness of the courses by comparing the patency rates, the time taken per anastomosis and efficiency of the utilisation rate of rats. Results: There were 30 participants in Group A and 28 participants in group B. We observed that group B was able to perform anastomosis in a significantly shorter time and with patency rates similar to group A in spite of a lesser number of rats used in the training. Conclusions: we were able to conclusively demonstrate that it was possible to reduce live rat usage in microsurgical training without compromising on the quality of training.

scholarly journals High-Fidelity Depth Upsampling Using the Self-Learning Framework

Sensors ◽  
2018 ◽  
Vol 19 (1) ◽  
pp. 81
Author(s):  
Inwook Shim ◽  
Tae-Hyun Oh ◽  
In Kweon
Keyword(s):  
Stereo Matching ◽  
Depth Map ◽  
The Self ◽  
Sensor Data ◽  
High Fidelity ◽  
Learning Framework ◽  
Depth Maps ◽  
Potential Applications ◽  
Self Learning

This paper presents a depth upsampling method that produces a high-fidelity dense depth map using a high-resolution RGB image and LiDAR sensor data. Our proposed method explicitly handles depth outliers and computes a depth upsampling with confidence information. Our key idea is the self-learning framework, which automatically learns to estimate the reliability of the upsampled depth map without human-labeled annotation. Thereby, our proposed method can produce a clear and high-fidelity dense depth map that preserves the shape of object structures well, which can be favored by subsequent algorithms for follow-up tasks. We qualitatively and quantitatively evaluate our proposed method by comparing other competing methods on the well-known Middlebury 2014 and KITTIbenchmark datasets. We demonstrate that our method generates accurate depth maps with smaller errors favorable against other methods while preserving a larger number of valid points, as we also show that our approach can be seamlessly applied to improve the quality of depth maps from other depth generation algorithms such as stereo matching and further discuss potential applications and limitations. Compared to previous work, our proposed method has similar depth errors on average, while retaining at least 3% more valid depth points.

scholarly journals Adaptive nanopores: A bioinspired label-free approach for protein sequencing and identification

Nano Research ◽  
2020 ◽  
Vol 14 (1) ◽  
pp. 328-333 ◽  
Author(s):  
Andrea Spitaleri ◽  
Denis Garoli ◽  
Moritz Schütte ◽  
Hans Lehrach ◽  
Walter Rocchia ◽  
...  
Keyword(s):  
Amino Acids ◽  
Single Molecule ◽  
Dynamic Range ◽  
Protein Sequencing ◽  
High Fidelity ◽  
Label Free ◽  
Therapeutic Approaches ◽  
Highly Sensitive ◽  
Dynamics Simulations ◽  
Structure Of Proteins

AbstractSingle molecule protein sequencing would tremendously impact in proteomics and human biology and it would promote the development of novel diagnostic and therapeutic approaches. However, its technological realization can only be envisioned, and huge challenges need to be overcome. Major difficulties are inherent to the structure of proteins, which are composed by several different amino-acids. Despite long standing efforts, only few complex techniques, such as Edman degradation, liquid chromatography and mass spectroscopy, make protein sequencing possible. Unfortunately, these techniques present significant limitations in terms of amount of sample required and dynamic range of measurement. It is known that proteins can distinguish closely similar molecules. Moreover, several proteins can work as biological nanopores in order to perform single molecule detection and sequencing. Unfortunately, while DNA sequencing by means of nanopores is demonstrated, very few examples of nanopores able to perform reliable protein-sequencing have been reported so far. Here, we investigate, by means of molecular dynamics simulations, how a re-engineered protein, acting as biological nanopore, can be used to recognize the sequence of a translocating peptide by sensing the “shape” of individual amino-acids. In our simulations we demonstrate that it is possible to discriminate with high fidelity, 9 different amino-acids in a short peptide translocating through the engineered construct. The method, here shown for fluorescence-based sequencing, does not require any labelling of the peptidic analyte. These results can pave the way for a new and highly sensitive method of sequencing.

scholarly journals S-allyl cysteine ameliorates the quality of sperm and provides protection from age-related sperm dysfunction and oxidative stress in rats

2014 ◽  
Vol 55 (3) ◽  
pp. 155-161 ◽  
Author(s):  
Shigekazu Takemura ◽  
Hiroshi Ichikawa ◽  
Yuji Naito ◽  
Tomohisa Takagi ◽  
Toshikazu Yoshikawa ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Age Related ◽  
Sperm Dysfunction ◽  
And Oxidative Stress

scholarly journals The Exacerbation of Aging and Oxidative Stress in the Epididymis of Sod1 Null Mice

Antioxidants ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 151 ◽  
Author(s):  
Anaīs Noblanc ◽  
Alicia Klaassen ◽  
Bernard Robaire
Keyword(s):  
Oxidative Damage ◽  
Oxygen Species ◽  
Superoxide Dismutase 1 ◽  
Free Radical Theory ◽  
Radical Theory ◽  
Theory Of Aging ◽  
Accumulation Of Damage ◽  
Effects Of Aging ◽  
And Oxidative Stress

There is growing evidence that the quality of spermatozoa decreases with age and that children of older fathers have a higher incidence of birth defects and genetic mutations. The free radical theory of aging proposes that changes with aging are due to the accumulation of damage induced by exposure to excess reactive oxygen species. We showed previously that absence of the superoxide dismutase 1 (Sod1) antioxidant gene results in impaired mechanisms of repairing DNA damage in the testis in young Sod1−/− mice. In this study, we examined the effects of aging and the Sod−/− mutation on mice epididymal histology and the expression of markers of oxidative damage. We found that both oxidative nucleic acid damage (via 8-hydroxyguanosine) and lipid peroxidation (via 4-hydroxynonenal) increased with age and in Sod1−/− mice. These findings indicate that lack of SOD1 results in an exacerbation of the oxidative damage accumulation-related aging phenotype.

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