A new high-resolution photo scanning system enables rapid, high-throughput analysis of C. elegans toxicology. For example, an experiment showed that phosphine resistance granted by DLD suppression is dependent on the master stress regulator DAF-16. The scanning system is capable of automatically counting tens of thousands of individual C. elegans at once, allowing for high throughput analysis of C. elegans phenotypes and genetic influences on phosphine resistance.
in this chapter covers the symptoms modulation and diseases severity increases and decreases. and role of SiRNA in diseases severity reduction. and also covers the types of SRNA..
Detection techniques of Tomato_Brown_Rugose_Fructose_VirusAasma sharma
It is based on result of detection techniques used in Department of virology at Universitat Politechnica de Valencia, Spain as a part of second semester internship.
in this chapter covers the symptoms modulation and diseases severity increases and decreases. and role of SiRNA in diseases severity reduction. and also covers the types of SRNA..
Detection techniques of Tomato_Brown_Rugose_Fructose_VirusAasma sharma
It is based on result of detection techniques used in Department of virology at Universitat Politechnica de Valencia, Spain as a part of second semester internship.
DNA-based methods for bioaerosol analysisjordanpeccia
Information for producing phylogenetic/taxonomic libraries of airborne bacteria and fungi. Includes fundamental background information, approaches for sequencing and data analysis, two case studies, and a review of sampling methods
Measuring RNA and DNA biomarkers in liquid biopsiesBiogazelle
The interest in liquid biopsies is booming, for obvious reasons: liquid biopsies allow serial follow-up of patients and result in higher patient comfort. Biogazelle offers various customized workflows to fully deploy the biomarker potential from your liquid biopsies.
Assessment of microbial population diversity in polymicrobial research sample...Thermo Fisher Scientific
Analysis of 16S sequences in microbial populations using NGS gives a rapid overview of the community diversity, and is usually performed by sequencing one or two hypervariable regions (V-regions), out of the nine present in the 16S rRNA gene. In this study we compared the community structure of fecal, oral and water microbiomes by analyzing sequences from a single variable region, or from the seven V-regions (V2, V3, V4, V6-7, V8 and V9) included into Ion 16S™ Metagenomics Kit (multi-V analysis)
Rapid 16S Next Generation Sequencing for Bacterial Identification in Polymicr...Thermo Fisher Scientific
In order to identify prokaryotic species in a sample, it is often necessary to culture the sample for hours or days to increase the abundance of bacteria to assayable levels. This often precludes the rapid identification of infectious species.
Furthermore, some species are not easily culturable. We
have developed a facile research method for identifying
bacterial species by 16S ribosomal RNA sequencing on the
Ion Torrent platform. The Ion 16S™ Metagenomics Kit is
designed to PCR amplify the hypervariable regions of the 16S
gene of bacteria. We used this kit to construct libraries from
15 retrospective samples of synovial fluid with various
bacterial species either spiked in or present at collection.
Libraries were sequenced on the Ion PGM™ system and the
data analysis performed using the Ion Reporter™ workflow
which provides an automated analysis solution. Bacteria
present in the samples were correctly identified in samples
containing a single spiked-in species, mixed-species samples,
and in infected samples. Thus, the Ion Torrent™ platform
provides a mechanism for rapidly identifying bacteria that are
present in research samples without culturing.
Until recently, the properties and compositions of the microbiota in the planet are still largely a black box. Next generation sequencing (NGS) has proven to be an invaluable tool for investigating diverse environmental and host-associated microbial communities, helping to generate enormous new data sets that can be mined for information on the composition and functional properties of vastly great numbers of microbial communities.
Recombinant Antibody Overview II - Creative BiolabsCreative-Biolabs
It is created by Creative Biolabs who is specialized in providing recombinant antibodies and engineered antibodies. The part two of recombinant antibody overview, we will explain introduction of recombinant antibody ant recombinant antibody expression.
introduction
What is virus
What is virus resistance plant
History
Gene use for develop virus resistance plant
Coat protein gene
cDNA of satellite RNA
Defective viral genome
Antisense RNA approach and
Ribozyme – mediated protection
conclusion
References
The diversity of microbial species in a metagenomic study is commonly assessed using 16S rRNA gene sequencing. With the rapid developments in genome sequencing technologies, the focus has shifted towards the sequencing of hypervariable regions of 16S rRNA gene instead of full length gene sequencing. Therefore, 16S Classifier is developed using a machine learning method, Random Forest, for faster and accurate taxonomic classification of short hypervariable regions of 16S rRNA sequence. It displayed precision values of up to 0.91 on training datasets and the precision values of up to 0.98 on the test dataset. On real metagenomic datasets, it showed up to 99.7% accuracy at the phylum level and up to 99.0% accuracy at the genus level. 16S Classifier is available freely at http://metagenomics.iiserb.ac.in/16Sclassifier and http://metabiosys.iiserb.ac.in/16Sclassifier.
Polymerase chain reaction (PCR) is a method widely used to rapidly make millions to billions of copies of a specific DNA sample, allowing scientists to take a very small sample of DNA and amplify it to a large enough amount to study in detail. PCR was invented in 1984 by the American biochemist Kary Mullis at Cetus Corporation. It is fundamental to much of genetic testing including analysis of ancient samples of DNA and identification of infectious agents. Using PCR, copies of very small amounts of DNA sequences are exponentially amplified in a series of cycles of temperature changes. PCR is now a common and often indispensable technique used in medical laboratory and clinical laboratory research for a broad variety of applications including biomedical research and criminal forensics.
neoplex pcr test kit [genematrix advantages of neo_plex covid-19 Rapid Test K...HK HuZef
This Presentation Briefly Explains All About Neoplex Pcr Test Kit, for Corona Virus Detection. Pcr Covid-19 Rapid test Kits Have Advantages Over Other Manufacturers.
Molecular Basis for Genetic Resistance of Fusarium virguliforme, the Causal A...Chloe Siegel
This poster was presented at the Undergraduate Research Symposium at the University of Illinois at Urbana-Champaign. It summarizes a semester-long research project I participated in through the Department of Natural Resources and Environmental Sciences.
Research investigating the use a genome-informed approach to develop diagnostic tools, for the detection of exotic phytopathogenic bacteria that pose a threat to Australian agriculture.
The aim of this research project is to establish Australian developed seed testing protocols as an international standard for the detection of viroids and cucumber green mottle mosaic virus (CGMMV) in seed, and to reduce the risks of contaminated traded seed.
DNA-based methods for bioaerosol analysisjordanpeccia
Information for producing phylogenetic/taxonomic libraries of airborne bacteria and fungi. Includes fundamental background information, approaches for sequencing and data analysis, two case studies, and a review of sampling methods
Measuring RNA and DNA biomarkers in liquid biopsiesBiogazelle
The interest in liquid biopsies is booming, for obvious reasons: liquid biopsies allow serial follow-up of patients and result in higher patient comfort. Biogazelle offers various customized workflows to fully deploy the biomarker potential from your liquid biopsies.
Assessment of microbial population diversity in polymicrobial research sample...Thermo Fisher Scientific
Analysis of 16S sequences in microbial populations using NGS gives a rapid overview of the community diversity, and is usually performed by sequencing one or two hypervariable regions (V-regions), out of the nine present in the 16S rRNA gene. In this study we compared the community structure of fecal, oral and water microbiomes by analyzing sequences from a single variable region, or from the seven V-regions (V2, V3, V4, V6-7, V8 and V9) included into Ion 16S™ Metagenomics Kit (multi-V analysis)
Rapid 16S Next Generation Sequencing for Bacterial Identification in Polymicr...Thermo Fisher Scientific
In order to identify prokaryotic species in a sample, it is often necessary to culture the sample for hours or days to increase the abundance of bacteria to assayable levels. This often precludes the rapid identification of infectious species.
Furthermore, some species are not easily culturable. We
have developed a facile research method for identifying
bacterial species by 16S ribosomal RNA sequencing on the
Ion Torrent platform. The Ion 16S™ Metagenomics Kit is
designed to PCR amplify the hypervariable regions of the 16S
gene of bacteria. We used this kit to construct libraries from
15 retrospective samples of synovial fluid with various
bacterial species either spiked in or present at collection.
Libraries were sequenced on the Ion PGM™ system and the
data analysis performed using the Ion Reporter™ workflow
which provides an automated analysis solution. Bacteria
present in the samples were correctly identified in samples
containing a single spiked-in species, mixed-species samples,
and in infected samples. Thus, the Ion Torrent™ platform
provides a mechanism for rapidly identifying bacteria that are
present in research samples without culturing.
Until recently, the properties and compositions of the microbiota in the planet are still largely a black box. Next generation sequencing (NGS) has proven to be an invaluable tool for investigating diverse environmental and host-associated microbial communities, helping to generate enormous new data sets that can be mined for information on the composition and functional properties of vastly great numbers of microbial communities.
Recombinant Antibody Overview II - Creative BiolabsCreative-Biolabs
It is created by Creative Biolabs who is specialized in providing recombinant antibodies and engineered antibodies. The part two of recombinant antibody overview, we will explain introduction of recombinant antibody ant recombinant antibody expression.
introduction
What is virus
What is virus resistance plant
History
Gene use for develop virus resistance plant
Coat protein gene
cDNA of satellite RNA
Defective viral genome
Antisense RNA approach and
Ribozyme – mediated protection
conclusion
References
The diversity of microbial species in a metagenomic study is commonly assessed using 16S rRNA gene sequencing. With the rapid developments in genome sequencing technologies, the focus has shifted towards the sequencing of hypervariable regions of 16S rRNA gene instead of full length gene sequencing. Therefore, 16S Classifier is developed using a machine learning method, Random Forest, for faster and accurate taxonomic classification of short hypervariable regions of 16S rRNA sequence. It displayed precision values of up to 0.91 on training datasets and the precision values of up to 0.98 on the test dataset. On real metagenomic datasets, it showed up to 99.7% accuracy at the phylum level and up to 99.0% accuracy at the genus level. 16S Classifier is available freely at http://metagenomics.iiserb.ac.in/16Sclassifier and http://metabiosys.iiserb.ac.in/16Sclassifier.
Polymerase chain reaction (PCR) is a method widely used to rapidly make millions to billions of copies of a specific DNA sample, allowing scientists to take a very small sample of DNA and amplify it to a large enough amount to study in detail. PCR was invented in 1984 by the American biochemist Kary Mullis at Cetus Corporation. It is fundamental to much of genetic testing including analysis of ancient samples of DNA and identification of infectious agents. Using PCR, copies of very small amounts of DNA sequences are exponentially amplified in a series of cycles of temperature changes. PCR is now a common and often indispensable technique used in medical laboratory and clinical laboratory research for a broad variety of applications including biomedical research and criminal forensics.
neoplex pcr test kit [genematrix advantages of neo_plex covid-19 Rapid Test K...HK HuZef
This Presentation Briefly Explains All About Neoplex Pcr Test Kit, for Corona Virus Detection. Pcr Covid-19 Rapid test Kits Have Advantages Over Other Manufacturers.
Molecular Basis for Genetic Resistance of Fusarium virguliforme, the Causal A...Chloe Siegel
This poster was presented at the Undergraduate Research Symposium at the University of Illinois at Urbana-Champaign. It summarizes a semester-long research project I participated in through the Department of Natural Resources and Environmental Sciences.
Research investigating the use a genome-informed approach to develop diagnostic tools, for the detection of exotic phytopathogenic bacteria that pose a threat to Australian agriculture.
The aim of this research project is to establish Australian developed seed testing protocols as an international standard for the detection of viroids and cucumber green mottle mosaic virus (CGMMV) in seed, and to reduce the risks of contaminated traded seed.
The diagnosis of viral pathogens is a crucial component of plant biosecurity surveillance and preventing the introduction of exotic plant viruses and viroids at the border. Existing quarantine procedures can be time-consuming and require detailed knowledge of potential infecting viral pathogens. Currently, imported plants can spend as long as two years in quarantine, with associated costs.
To simplify the post-entry quarantine process researchers have developed a plant diagnostic toolkit for plant viruses and viroids. The toolkit takes advantage of the natural antiviral system of plants, using small RNA next generation sequencing (sRNA-seq) technology to detect nearly all known viruses and viroids in a single test. The new test, and associated toolkit, will reduce the time imported plant material spends in Australia’s quarantine system while improving accuracy of detection in a single sRNA-seq experiment.
This research has developed recommendations for stakeholders involved in area-wide management of fruit fly, including social and institutional requirements.
This project aims to build the ability of indigenous communities (Maori and Aboriginal), regulatory authorities and industries to better manage the impact of biosecurity threats. Models have been developed for Indigenous engagement.
This social biosecurity project, aims to improve plant biosecurity management by developing the capacity of regional and remote communities to engage in biosecurity surveillance activities.
Surveillance systems are an essential component of biosecurity. Design of biosecurity surveillance systems may include designs of grids of static traps, plans for field sampling, or deployment of potentially "game-changing" mobile trap technology. The aim of these systems is to achieve defined detection objectives, (e.g. early detection, supporting area-freedom status) at minimum cost. This project will develop and apply statistically-based surveillance systems that account for organism biology, trap behaviour and landscape characteristics.
Ships arriving in Australia may have visited multiple ports along the way. These complex pathways present opportunities for pest species, such as the Asian Gypsy Moth, to arrive into Australia from indirect routes. Understanding those pathways that link Australia directly or indirectly to countries in which a pest or disease occurs is necessary to identify arriving ships with the highest likelihood of carrying hitchhiker species. This project proposes to address three important questions:
1. What general shipping pathways pose the greatest risk?
2. How to make decisions regarding what ships to search?
3. How much inspection to conduct?
This research project is collecting data on past pest invasions in both Australia and New Zealand, in order to identify common patterns in plant biosecurity pests.
Long distance natural (wind-assisted) dispersal of exotic plant pests and pathogens into Australia, is a very real and underestimated, biosecurity risk.
This research will investigate technologies to enable the development of spore traps capable of in-field detection, and identification, of specific biosecurity threats.
The spread of invasive species continues to provide significant challenges to those government biosecurity agencies charged with protecting a country’s borders. In an increasingly connected world, these invasive species are potentially able to spread further and more rapidly. Human mediated pathways such as ships and airlines are the most obvious ways in which invasive species can be spread. Direct routes from one port to another are currently monitored, but indirect pathways,
in which a ship picks up an invasive species and then travels to a number of different locations before arriving at the final destination, present more challenging scenarios. For the Australian Government Department of Agriculture, one particular concern is for ships arriving into Australia carrying viable eggs of the Asian gypsy moth (Lymantria dispar). We are developing a real time tool that will analyse the pathways for incoming ships and determine the likelihood the ship could be carrying viable eggs.
Planning and decision making to manage plant biosecurity risks is inherently complex, often contentious, involves unknowns and uncertainty, and needs to be adaptable to rapidly changing situations. The aim of this project is to develop a collaborative planning and shared decision making
framework that will result in better and faster decisions to respond more quickly to plant biosecurity risks, resulting in reduced impacts and costs, and more equitable and favourable outcomes for stakeholders and affected parties.
Biosecurity issues impact on key crops and environmental values across NZ and Australia. A key outcome for the project team will be the ability of indigenous communities, and relevant regulatory authorities and industries, to better manage the social, environmental and economic impacts of biosecurity threats, and to participate in biosecurity strategies through improved bicultural engagement models that build empowerment and ownership in indigenous communities and their response to those threats. The teams have developed an engagement model adapted to the indigenous peoples and their communities of each country.
The results of a baseline study on motivation and incentives involved in the decisions to control fruit fly highlight the variability of motivations within demographic groups.
More from Plant Biosecurity Cooperative Research Centre (20)
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
The increased availability of biomedical data, particularly in the public domain, offers the opportunity to better understand human health and to develop effective therapeutics for a wide range of unmet medical needs. However, data scientists remain stymied by the fact that data remain hard to find and to productively reuse because data and their metadata i) are wholly inaccessible, ii) are in non-standard or incompatible representations, iii) do not conform to community standards, and iv) have unclear or highly restricted terms and conditions that preclude legitimate reuse. These limitations require a rethink on data can be made machine and AI-ready - the key motivation behind the FAIR Guiding Principles. Concurrently, while recent efforts have explored the use of deep learning to fuse disparate data into predictive models for a wide range of biomedical applications, these models often fail even when the correct answer is already known, and fail to explain individual predictions in terms that data scientists can appreciate. These limitations suggest that new methods to produce practical artificial intelligence are still needed.
In this talk, I will discuss our work in (1) building an integrative knowledge infrastructure to prepare FAIR and "AI-ready" data and services along with (2) neurosymbolic AI methods to improve the quality of predictions and to generate plausible explanations. Attention is given to standards, platforms, and methods to wrangle knowledge into simple, but effective semantic and latent representations, and to make these available into standards-compliant and discoverable interfaces that can be used in model building, validation, and explanation. Our work, and those of others in the field, creates a baseline for building trustworthy and easy to deploy AI models in biomedicine.
Bio
Dr. Michel Dumontier is the Distinguished Professor of Data Science at Maastricht University, founder and executive director of the Institute of Data Science, and co-founder of the FAIR (Findable, Accessible, Interoperable and Reusable) data principles. His research explores socio-technological approaches for responsible discovery science, which includes collaborative multi-modal knowledge graphs, privacy-preserving distributed data mining, and AI methods for drug discovery and personalized medicine. His work is supported through the Dutch National Research Agenda, the Netherlands Organisation for Scientific Research, Horizon Europe, the European Open Science Cloud, the US National Institutes of Health, and a Marie-Curie Innovative Training Network. He is the editor-in-chief for the journal Data Science and is internationally recognized for his contributions in bioinformatics, biomedical informatics, and semantic technologies including ontologies and linked data.
Session 3: High throughput analysis of chemical and genetic factors that influence phosphine toxicity and resistance
1. biosecurity built on science
A new system using
high – resolution photo
scanners.
Enabling rapid, high–
throughput analysis of C.
elegans toxicology
For example:
Phosphine resistance granted by DLD
suppression is dependant on the master stress
regulator DAF-16
500ppm
0
10
20
30
40
50
60
70
80
90
100
Phosphine parts per million
%survivors
Daf16 mutant / DLD
suppressed
Daf16 mutant
Wild type / DLD
suppressed
Wild type
Daf16 upregulated /
DLD suppressed
Daf16 upregulated
Capable of automatically
counting tens of thousands of
individual C. elegans at once.
High throughput C. elegans phenotype analysis and genetic influences on
phosphine resistance (Timothy Puckering, University of Queensland)