This document introduces the nullarbor bioinformatics tool. It provides instructions on running nullarbor using test Campylobacter dataset isolates. The summary shows that nullarbor performs analysis including assembly, annotation, variant calling and phylogenetic trees on microbial sequencing data from multiple isolates. It finds one of the four test isolates was contaminated and another was passaged through a chicken based on differences observed in the nullarbor output.
WGS in public health microbiology - MDU/VIDRL Seminar - wed 17 jun 2015Torsten Seemann
How genomics is changing the practice of public health microbiology. The role of whole genome sequencing as the "one true assay". Another powerful tool for the epidemiologist.
Engineering plant immunity using crispr cas9 to generate virus resistanceSheikh Mansoor
Targeted genome editing by use of artificial nucleases has the plausible potential to speed basic research as well as plant breeding by providing the means to modify genomes quickly in a specific and predictable manner but advanced CRISPR-Cas9 based technologies first confirmed in mammalian cell systems are quickly being fitted for use in plants. These new technologies increase CRISPR-Cas9’s utility and effectiveness by diversifying cellular capabilities through expression construct system evolution and enzyme orthogonality, as well as enhanced efficiency through delivery and expression mechanisms. RNA-guided genome editing using Streptococcus pyogenes CRISPR-Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats) has renewed the concept of genome editing in plants. CRISPR-associated surveillance complexes are easily programmable molecular sleds that can target any sequence of choice. These complexes offer new opportunities for implementation in biotechnology. Recent studies have used CRISPR/Cas9 to engineer virus resistance in plants, either by directly targeting and cleaving the viral genome, or by modifying the host plant genome to introduce viral immunity. The CRISPR/Cas9 platform could also be used for targeted mutagenesis to identify host factors that control plant resistance and susceptibility to viral infection. Thus, CRISPR/Cas9 technology offers a promising approach for under- standing and engineering resistance to single and multiple viral infections in plants.
A peek inside the bioinformatics black box - DCAMG Symposium - mon 20 july 2015Torsten Seemann
An introduction to basic genomics bioinformatics concepts in 20 minutes for an audience of clinicians, epidemiologists and other public health officials.
CRISPR is easily the best gene editing tool to date. For decades, scientists have been looking for a way to to perform precise changes to genetic sequences. In the past several years, researchers were able to exploit the immune systems of bacteria to edit the genome of other living cells. CRISPR is reported to have higher targeting efficiencies when compared to TALENs and Zinc Fingers. It is efficient, easy to use and cheap; making it a scalable genetic engineering tool that is highly desirable in various industry-wide applications.
Microbiome Profiling with the Microbial Genomics Pro SuiteQIAGEN
In this slide deck, we introduce the scientist-friendly Microbial Genomics Pro Suite offering workflows optimized for microbiome profiling, microbial typing and outbreak analysis. The workflows and tools for microbial genomics introduced with this software package are further extending the comprehensive set of genomics, transcriptomics and epigenomics analysis solutions that researchers know from CLC Genomics Workbench.
WGS in public health microbiology - MDU/VIDRL Seminar - wed 17 jun 2015Torsten Seemann
How genomics is changing the practice of public health microbiology. The role of whole genome sequencing as the "one true assay". Another powerful tool for the epidemiologist.
Engineering plant immunity using crispr cas9 to generate virus resistanceSheikh Mansoor
Targeted genome editing by use of artificial nucleases has the plausible potential to speed basic research as well as plant breeding by providing the means to modify genomes quickly in a specific and predictable manner but advanced CRISPR-Cas9 based technologies first confirmed in mammalian cell systems are quickly being fitted for use in plants. These new technologies increase CRISPR-Cas9’s utility and effectiveness by diversifying cellular capabilities through expression construct system evolution and enzyme orthogonality, as well as enhanced efficiency through delivery and expression mechanisms. RNA-guided genome editing using Streptococcus pyogenes CRISPR-Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats) has renewed the concept of genome editing in plants. CRISPR-associated surveillance complexes are easily programmable molecular sleds that can target any sequence of choice. These complexes offer new opportunities for implementation in biotechnology. Recent studies have used CRISPR/Cas9 to engineer virus resistance in plants, either by directly targeting and cleaving the viral genome, or by modifying the host plant genome to introduce viral immunity. The CRISPR/Cas9 platform could also be used for targeted mutagenesis to identify host factors that control plant resistance and susceptibility to viral infection. Thus, CRISPR/Cas9 technology offers a promising approach for under- standing and engineering resistance to single and multiple viral infections in plants.
A peek inside the bioinformatics black box - DCAMG Symposium - mon 20 july 2015Torsten Seemann
An introduction to basic genomics bioinformatics concepts in 20 minutes for an audience of clinicians, epidemiologists and other public health officials.
CRISPR is easily the best gene editing tool to date. For decades, scientists have been looking for a way to to perform precise changes to genetic sequences. In the past several years, researchers were able to exploit the immune systems of bacteria to edit the genome of other living cells. CRISPR is reported to have higher targeting efficiencies when compared to TALENs and Zinc Fingers. It is efficient, easy to use and cheap; making it a scalable genetic engineering tool that is highly desirable in various industry-wide applications.
Microbiome Profiling with the Microbial Genomics Pro SuiteQIAGEN
In this slide deck, we introduce the scientist-friendly Microbial Genomics Pro Suite offering workflows optimized for microbiome profiling, microbial typing and outbreak analysis. The workflows and tools for microbial genomics introduced with this software package are further extending the comprehensive set of genomics, transcriptomics and epigenomics analysis solutions that researchers know from CLC Genomics Workbench.
Baculovirus-Insect cell expression system is one of the most popular eukaryotic expression systems for research and industrial applications. There are several advantages of using the baculovirus-Insect cell expression system, such as improved solubility, ability to incorporate post-translational modifications, and higher yield of secreted proteins.
Crispr-Cas9 system works on the concept of bacterial defence mechanism. The idea of which was replicated in eukaryotic cell in in- vitro condition by the researchers.
VS-CNV Annotations from the User's PerspectiveGolden Helix
Next-generation sequencing has enabled clinicians and researchers alike to identify novel genetic variants associated with rare Mendelian Diseases across the human genome. To help enable researchers and clinicians understand the role of CNVs in human health and disease, Golden Helix has a fully integrated CNV annotations to provide clinicians and researchers with more effective methods to identify pathogenic CNVs for heritable diseases. In this webcast, we will present our comprehensive clinical workflows that integrates the annotating and reporting of high-quality CNV alongside their existing NGS variants.
CRISPR system is very simple, consisted of a Cas9 protein and a single guided RNA. With the guidance of sgRNA, Cas9 could cause a double stranded breaks in the target site.
With the excellent CRISPR/Cas9 platform and experienced scientists, our well-trained staff successfully finishes scores of custom gene editing projects every year.
https://www.creative-biogene.com/crispr-cas9/
Creative Biolabs-CAMouse™-Fully Human Antibody Generation PlatformCreative-Biolabs
Creative Biolabs is highly specialized in therapeutic antibody discovery, and we have extensive experience in multifunctional antibody discovery methods.
This slide introduces CAMouse™, a new transgenic mouse strain from Creative Biolabs, and establishes a complete human antibody generation platform.
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.
CRISPR : CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT
It is a prokaryotic immune system that confers resistance to foreign genetic elements such as those present within plasmids and phages that provides a form of acquired immunity.
It forms the basis of a genome editing technology known as CRISPR-Cas9 that allows permanent modifications of genes within organisms.
CRISPR-Cas system consist of two key molecules that introduce a change into the DNA sequence 1. Cas 9 - act as molecular scissors 2. gRNA – guides Cas9 to the right part of the genome gRNA = crispr rRNA + tracrRNA
Prezi Link: https://prezi.com/q8lkxnmwk25-/untitled-prezi/?utm_campaign=share&utm_medium=copy
Metagenomics is the study of metagenomes, genetic material recovered directly from environmental samples. The broad field was referred to as environmental genomics, ecogenomics or community genomics. Recent studies use "shotgun" Sanger sequencing or next generation sequencing (NGS) to get largely unbiased samples of all genes from all the members of the sampled communities.
dkNET Webinar: Addgene, The Nonprofit Plasmid Repository 04/24/2020dkNET
Abstract
Addgene’s mission is to accelerate research and discovery by improving access to useful research materials and information. We facilitate the sharing of high-quality scientific materials, research reproducibility, and open science by archiving and distributing DNA-based research reagents and associated data to scientists worldwide. Our repository contains over 84,000 plasmids, including special collections on CRISPR and fluorescent proteins, and more than 450 ready-to-use AAV and lentiviral preparations. There is no cost for scientists to deposit plasmids, which saves time and money associated with shipping plasmids themselves. All plasmids in Addgene’s repository were deposited by your scientific colleagues from around the world. All plasmids are fully sequenced for validation and sequencing data is openly available. Furthermore, we offer free educational resources about molecular biology topics including the AAV Data Hub, our blog, eBooks, and written and video protocols.
The top 3 key questions that Addgene repository can answer:
1. How can I find relevant DNA-based reagents for studying my disease model of interest?
2. Which molecular biology tools and techniques are appropriate for my experiments?
3. What are the benefits of sharing my plasmids and how do I deposit plasmids into the repository?
Presenter: Dr. Angela Abitua, Outreach Scientist at Addgene, the nonprofit plasmid repository
dkNET Webinar Information: https://dknet.org/about/webinar
QIAseq Technologies for Metagenomics and Microbiome NGS Library PrepQIAGEN
In this slide deck, learn about the innovative technologies that form the basis of QIAGEN’s portfolio of QIAseq library prep solutions for metagenomics and microbiome sequencing. Whether your research starts from single microbial cells, 16s rRNA PCR amplicons, or gDNA for whole genome analysis, QIAseq technologies offer tips and tricks for capturing the genomic diversity of your samples in the most unbiased, streamlined way possible.
Baculovirus-Insect cell expression system is one of the most popular eukaryotic expression systems for research and industrial applications. There are several advantages of using the baculovirus-Insect cell expression system, such as improved solubility, ability to incorporate post-translational modifications, and higher yield of secreted proteins.
Crispr-Cas9 system works on the concept of bacterial defence mechanism. The idea of which was replicated in eukaryotic cell in in- vitro condition by the researchers.
VS-CNV Annotations from the User's PerspectiveGolden Helix
Next-generation sequencing has enabled clinicians and researchers alike to identify novel genetic variants associated with rare Mendelian Diseases across the human genome. To help enable researchers and clinicians understand the role of CNVs in human health and disease, Golden Helix has a fully integrated CNV annotations to provide clinicians and researchers with more effective methods to identify pathogenic CNVs for heritable diseases. In this webcast, we will present our comprehensive clinical workflows that integrates the annotating and reporting of high-quality CNV alongside their existing NGS variants.
CRISPR system is very simple, consisted of a Cas9 protein and a single guided RNA. With the guidance of sgRNA, Cas9 could cause a double stranded breaks in the target site.
With the excellent CRISPR/Cas9 platform and experienced scientists, our well-trained staff successfully finishes scores of custom gene editing projects every year.
https://www.creative-biogene.com/crispr-cas9/
Creative Biolabs-CAMouse™-Fully Human Antibody Generation PlatformCreative-Biolabs
Creative Biolabs is highly specialized in therapeutic antibody discovery, and we have extensive experience in multifunctional antibody discovery methods.
This slide introduces CAMouse™, a new transgenic mouse strain from Creative Biolabs, and establishes a complete human antibody generation platform.
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.
CRISPR : CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT
It is a prokaryotic immune system that confers resistance to foreign genetic elements such as those present within plasmids and phages that provides a form of acquired immunity.
It forms the basis of a genome editing technology known as CRISPR-Cas9 that allows permanent modifications of genes within organisms.
CRISPR-Cas system consist of two key molecules that introduce a change into the DNA sequence 1. Cas 9 - act as molecular scissors 2. gRNA – guides Cas9 to the right part of the genome gRNA = crispr rRNA + tracrRNA
Prezi Link: https://prezi.com/q8lkxnmwk25-/untitled-prezi/?utm_campaign=share&utm_medium=copy
Metagenomics is the study of metagenomes, genetic material recovered directly from environmental samples. The broad field was referred to as environmental genomics, ecogenomics or community genomics. Recent studies use "shotgun" Sanger sequencing or next generation sequencing (NGS) to get largely unbiased samples of all genes from all the members of the sampled communities.
dkNET Webinar: Addgene, The Nonprofit Plasmid Repository 04/24/2020dkNET
Abstract
Addgene’s mission is to accelerate research and discovery by improving access to useful research materials and information. We facilitate the sharing of high-quality scientific materials, research reproducibility, and open science by archiving and distributing DNA-based research reagents and associated data to scientists worldwide. Our repository contains over 84,000 plasmids, including special collections on CRISPR and fluorescent proteins, and more than 450 ready-to-use AAV and lentiviral preparations. There is no cost for scientists to deposit plasmids, which saves time and money associated with shipping plasmids themselves. All plasmids in Addgene’s repository were deposited by your scientific colleagues from around the world. All plasmids are fully sequenced for validation and sequencing data is openly available. Furthermore, we offer free educational resources about molecular biology topics including the AAV Data Hub, our blog, eBooks, and written and video protocols.
The top 3 key questions that Addgene repository can answer:
1. How can I find relevant DNA-based reagents for studying my disease model of interest?
2. Which molecular biology tools and techniques are appropriate for my experiments?
3. What are the benefits of sharing my plasmids and how do I deposit plasmids into the repository?
Presenter: Dr. Angela Abitua, Outreach Scientist at Addgene, the nonprofit plasmid repository
dkNET Webinar Information: https://dknet.org/about/webinar
QIAseq Technologies for Metagenomics and Microbiome NGS Library PrepQIAGEN
In this slide deck, learn about the innovative technologies that form the basis of QIAGEN’s portfolio of QIAseq library prep solutions for metagenomics and microbiome sequencing. Whether your research starts from single microbial cells, 16s rRNA PCR amplicons, or gDNA for whole genome analysis, QIAseq technologies offer tips and tricks for capturing the genomic diversity of your samples in the most unbiased, streamlined way possible.
Construcción y consolidación del estado liberal (1833-1874)Teresa Pérez
TEMA 11. CONSTRUCCIÓN Y CONSOLIDACIÓN DEL ESTADO LIBERAL (1833-1874). Organización política: monarquía, constitucionalismo y partidos políticos. Reinado de Isabel II. Sexenio Democrático (Amadeo I, I República)
Next generation Sequencing or massive parallel sequencing is a high throughput approach to sequence genetic material using the concept of massively parallel processing. It is also called second generation sequencing.This enables researchers a wide variety of applications & study biological systems.
Overview of the commonly used sequencing platforms, bioinformatic search tool...OECD Environment
24 June 2019: This OECD seminar presented and discussed the potential use of genome sequence, bioinformatic tools and databases in a regulatory decision process for microbial pesticides.
CRISPR-Cas9 is a genome editing tool that is creating a buzz in the science world. It is faster, cheaper and more accurate than previous techniques of editing DNA and has a wide range of potential applications.
The National Center for Biotechnology Information (NCBI) Pathogen Analysis Pi...ExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Real time sequencing of food borne pathogens: Pathogen Analysis Pipeline at The National Center for Biotechnology Information (NCBI). Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management -23-25 May 2016, Rome, Italy.
20150918 - F. Malvestiti - Chromosomal microarray in prenatal diagnosis Roberto Scarafia
Francesca MALVESTITI, Ph.D., ErCLG
Citogenetica Molecolare, TOMA Advanced Biomedical Assays, S.p.A.
fmalvestiti@tomalab.com
Present an historical overview of the modern molecular cytogenetics
Present the principal assays to detect submicroscopic copy number variations (CNV) on fetal samples
Describe pros and cons of targeted vs genome-wide methods
Present additional yield for pCNV by microarray analysis in anatomically normal and abnormal fetuses with normal karyotype
Setting up for successful lot release testing by Edmund AngMilliporeSigma
Is your lot release testing strategy ready for global commercialization?
In this webinar, you will learn:
• CMC testing requirements with CHO production platform for global commercialization
• Lot release testing of product intermediates and final product
• Product-specific qualification study
• Alternative rapid testing methods to advance lot release testing
CHO cells continue to serve as a key cell substrate for the manufacturing of recombinant proteins that span beyond therapeutic monoclonal antibodies and including subunit vaccines.
In this presentation, we will cover the CMC testing requirements with CHO production platform for global commercialization, Lot release testing of product intermediates and final product, product-specific qualification study and highlight the application of new testing methods and the benefits they bring to advance Lot Release Testing.
Setting up for successful lot release testing by Edmund AngMerck Life Sciences
Is your lot release testing strategy ready for global commercialization?
In this webinar, you will learn:
• CMC testing requirements with CHO production platform for global commercialization
• Lot release testing of product intermediates and final product
• Product-specific qualification study
• Alternative rapid testing methods to advance lot release testing
CHO cells continue to serve as a key cell substrate for the manufacturing of recombinant proteins that span beyond therapeutic monoclonal antibodies and including subunit vaccines.
In this presentation, we will cover the CMC testing requirements with CHO production platform for global commercialization, Lot release testing of product intermediates and final product, product-specific qualification study and highlight the application of new testing methods and the benefits they bring to advance Lot Release Testing.
Next Generation Sequencing for Identification and Subtyping of Foodborne Pat...Nathan Olson
"Next Generation Sequencing for Identification and Subtyping of Foodborne Pathogens" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by the National Institute for Standards and Technology October 2014 by Rebecca Lindsey, PhD from Enteric Diseases Laboratory Branch of the CDC.
Title:
Local Genes, for Local Bacteria: Global spread of Campylobacter lineages and emergence of novel regional sequence types
Abstract.
Campylobacter remains the most common cause of bacterial diarrhoeal disease worldwide, with particularly high incidence in low- and middle-income countries (LMICs). Population genomics studies have identified common lineages (sequence types) responsible for human disease and Infection source reservoirs have been identified and analysed in developed countries (e.g., poultry), however little is known about the risk factors and transmission routes in LMICs. Risk factors such as household crowding, poor sanitation, consumption of contaminated water and cohabitation with animals, all constitute potential transmission risks, but their relative importance is unknown. Signatures of adaptation can be detected in Campylobacter genomes and by using sequence data from human clinical isolates and putative source reservoirs we are able to probabilistically attribute the source of infection to model transmission networks. Recent studies in Egypt, Vietnam, and Peru provide evidence of recent acquisition and spread between hosts and identify novel lineages with high levels of antimicrobial resistance. Genomic variation of isolates from humans, animals, and food in LMICs may indicate differences in source, survival, transmission, or virulence (compared to the high income countries). By using a global outlook, differences in the core and accessory genome may explain some of the differences we observe in the global epidemiology of campylobacteriosis.
Background: Diarrhoeal disease remains a major cause of child morbidity, growth faltering and mortality in low and middle income countries (LMICs), with Campylobacter among the most common causes. Previous work has identified source reservoirs in developed countries (e.g. contaminated poultry or unpasteurised milk), however little is known about the risk factors and transmission routes in LMICs, where incidence is extremely high (up to 85% of children infected before 1yr). Risk factors such as household crowding, poor sanitation, consumption of contaminated water and cohabitation with animals, all constitute potential transmission risks but their relative importance is unknown.
Methods: We compare core and accessory genome content within and between infection and source populations by host and region. Signatures of adaptation can be detected in Campylobacter jejuni and C. coli genomes as they recombine and adapt quickly to new hosts. Using sequence data from human clinical isolates and potential source reservoirs we are able to probabilistically attribute sources of infection and model complex transmission networks. Comparative genomics techniques are used to characterise core and accessory genome content within populations and bacterial genome-wide association studies (GWAS) are used to identify disease-severity associated genes and genetic elements.
Results: Pilot genomics studies of isolates from humans, animals and food in LMICs have identified genomic variation in strains that may indicate differences in source, survival, transmission or virulence (compared to the UK). Dissemination of homologous accessory genes across Campylobacter lineages in Egypt suggest recent acquisition and spread between hosts. Disease-severity associated genetic elements are identified through a GWAS of isolates from symptomatic and asymptomatic children in the Peruvian Amazon. We also identify novel lineages in isolates from Burkina Faso and high levels of antimicrobial resistance in isolates from Vietnam.
Conclusions: Using a global outlook, we have identified differences in the core and accessory genomes of Campylobacter populations that may explain some of the differences we observe in the global epidemiology of campylobacteriosis. As we begin to understand the relationship between the infecting isolate and disease severity, we are able to model transmission networks for appropriate intervention strategies.
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.
This pdf is about the Schizophrenia.
For more details visit on YouTube; @SELF-EXPLANATORY;
https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos
Thanks...!
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
The ASGCT Annual Meeting was packed with exciting progress in the field advan...
Day 2: Intro to CLIMB at the MRC Unit, Gambia
1. Introduction to nullarbor
The Milner Centre for Evolution
Department of Biology & Biochemistry, University of Bath
http://www.climb.ac.uk/
http://www.sheppardlab.com/
Ben Pascoe
with Maciej Filocha (Warwick) & Mark Pallen (Warwick)
2. 1. Introduction to nullarbor
2. Setting up nullarbor with test campy dataset
3. Launching your own VM
4. (something for you try later – Shigellosis nullarbor tutorial)
5. Checking your nullarbor output
Introduction to nullarbor
4. https://github.com/tseemann/nullarbor
Nullarbor - "Reads to report" for public health and clinical microbiology
http://www.slideshare.net/torstenseemann/bioinformatics-tools-for-the-diagnostic-
laboratory-tseemann-antimicrobials-2016-melb-au-sat-27-feb-2016
5. What is nullarbor?
Per isolate
Clean /trim sequence reads (Trimmomatic)
• Remove adaptors, quality scores
Species identification (Kraken)
• K-mer analysis against KNOWN database
De novo assembly (MEGAHIT/SPAdes)
• Fast, confident genome assembly
Annotation (Prokka)
• Genome annotation
MLST calling
• From KNOWN databases
Resistome (Abricate)
• ID AMR genes from KNOWN database
Variant calling from reads compared to
reference
Per dataset
Core genome SNPs (Snippy – from reads
Phylogenetic trees (FastTree)
Accessory genome (ROARY)
Report generation
6. Workshop isolates
4 Campylobacter isolates
All LAB strains – should all be VERY similar…
Run nullarbor
How similar are the isolates?
Is there an explanation for any difference observed?
Implications
11168 widely-used as lab strain and molecular studies based on this reference strain
11. Linking phenotypes and genotypes using GWAS:
Asymptomatic isolatesVs Symptomatic isolates
Weights association
compared to relative
position on the tree
Sheppard et al, PNAS 2013; Pascoe et al, Environmental Microbiology 2015; Monteil et al, Microbial Genomics 2016, Yahara & Meric et al,
Environmental Microbiology 2017
12. Development of GWAS for use with bacteria: GWAS within clonal complex
Sheppard et al (2013) PNAS 110: (29) 11923-11927
Cattle isolates Vs Chicken isolates
Pascoe et al (2015) Environmental Microbiology
DOI: 10.1111/1462-2920.13051
Good Vs Bad Biofilm isolates
Previous studies were confined
to single clonal complex:
Bacteria are clonal – difficult
to associations biased by
lineage effects – inheritance
from common ancestor.
Accessory genome –
bacterial genomes are all
different sizes!
13. Development of GWAS for use with bacteria: pan-genome GWAS
Symptomatic
Asymptomatic
Paired isolates for pan-genome GWAS
FastML tree of 36 paired isolates (pan-genome)
Reduce false positives
Maintain statistical power
Not confined to single clonal
complex
Zero unmapped words
Mageiros & Meric et al, unpublished; Pascoe et al,
unpublished
Previous studies were confined
to single clonal complex:
Association weighted
against the clonal frame
(tree)
Paired isolates from many
CCs.
Use of reference pan-
genome instead of 1 single
reference genome.
14. Genome-wide association of Campylobacter genetic elements with disease
severity / asymptomatic carriage
Pascoe et al, unpublished
High statistical association:
glycosylation genes
Iron uptake
Motility
*scores for all genes in pan-genome from all 77
isolates – 2,996 genes
Thousands of ‘this’ in ~3,000
genes!
15. AccessVM usingVM box
Using your ip address:
gambia-1: 137.205.69.151
gambia-2: 137.205.69.153
gambia-3: 137.205.69.154
gambia-4: 137.205.69.155
gambia-5: 137.205.69.156
gambia-6: 137.205.69.157
gambia-7: 137.205.69.158
gambia-8: 137.205.69.159
gambia-9: 131.251.130.226
gambia-10: 131.251.130.227
For all:
User: ubuntu
Password: password123
16. Check we have all the files you need
What do we need?
• Input file: allinput.tab
• Reference genome: al111168.fasta
• Reads from MiSeq: *.fastq.gz
(8 files, 4 isolates)
17. Setup nullarbor
nullarbor.pl --name gambia --mlst campylobacter --ref al111168.fasta --input allinput.tab -
-outdir output --verbose
• Type command to setup nullarbor
• Nullarbor will perform checks and give you command to use to start run:
nice make -j 1 -C /home/ubuntu/gambia/output
• run
• Can also run with ‘no hangup’
nohup nice make -j 1 -C /home/ubuntu/gambia/output &
