In this workshop, students learned about DNA, genes, proteins, and bacteria through a series of experiments. First, each student isolated their own DNA from saliva samples, which varied in size between students. Next, students used PCR and electrophoresis to copy and study a specific gene. Then, SDS-PAGE electrophoresis was used to separate different sized proteins on a gel. Finally, macrophages were observed consuming GFP-infected E. coli bacteria under a microscope using UV and Lux light to view the fluorescence. The overall workshop covered the process from DNA to proteins and how bacteria function.
Field-based, real-time metagenomics and phylogenomics for responsive pathogen...Joe Parker
Talk presented at the UK-India Joint Bioinformatics Workshop, Pirbright Institute, 09 Feb 2018
Abstract:
In a globalised world of increasing trade, novel threats to animal and plant health, as well as human diseases, can cross political and geographical borders spontaneously and rapidly. One such example is the rise of Acute Oak Decline (AOD) in the UK, a multifactorial decline syndrome with uncertain aetiology, vectors, and host risk factors first reported in the UK a decade ago. Affected oaks display significant morbidity and mortality, with symptoms including vascular interruption, crown loss and characteristic striking bark lesions breaching cambium and filled with a viscous, aromatic, dark-brown/black exudate, which may sometimes be released under considerable pressure. Although multiple bacterial species have been associated to lesion sites in affected oaks, and a putative insect vector identified, the basic risk factors, transmission, progression and treatment of the syndrome remain unclear.
This dispiriting state of affairs presents an ideal opportunity to exploit recent developments in nanopore sequencing to develop and test field-based methods of real-time phylogenomics and metagenomics to establish baseline data for healthy oaks, and contrast these with affected / dying oaks to shed light on syndrome causes and management. WGS metagenomic sampling was carried out on leaf and bark tissue from 37 affected, asymptomatic, and recovering individuals (nine Quercus species) at three field sites over a year. Extraction and DNA sequencing were performed in the field for a subset of samples with MinION nanopore rapid sequencing kits, and also using MinION and paired-end Illumina sequencing under laboratory conditions. Metagenomic analyses to determine microbial community composition were carried out, and real-time phylogenomic methods were also developed and applied. Early results from these analyses and lessons for future work are presented.
Metagenomic datasets can be rapidly generated in the field with minimal equipment using nanopore sequencing, providing a responsive capability for emerging disease threats and reducing transmission risks associated with transporting quantities of potentially infectious samples from outbreaks of novel diseases. Furthermore, real-time data analysis can provide rapid feedback to field teams, both to inform management decisions and also to allow for adaptive experimental protocols that dynamically target data collection to extract maximum information per unit effort.
Field-based, real-time metagenomics and phylogenomics for responsive pathogen...Joe Parker
Talk presented at the UK-India Joint Bioinformatics Workshop, Pirbright Institute, 09 Feb 2018
Abstract:
In a globalised world of increasing trade, novel threats to animal and plant health, as well as human diseases, can cross political and geographical borders spontaneously and rapidly. One such example is the rise of Acute Oak Decline (AOD) in the UK, a multifactorial decline syndrome with uncertain aetiology, vectors, and host risk factors first reported in the UK a decade ago. Affected oaks display significant morbidity and mortality, with symptoms including vascular interruption, crown loss and characteristic striking bark lesions breaching cambium and filled with a viscous, aromatic, dark-brown/black exudate, which may sometimes be released under considerable pressure. Although multiple bacterial species have been associated to lesion sites in affected oaks, and a putative insect vector identified, the basic risk factors, transmission, progression and treatment of the syndrome remain unclear.
This dispiriting state of affairs presents an ideal opportunity to exploit recent developments in nanopore sequencing to develop and test field-based methods of real-time phylogenomics and metagenomics to establish baseline data for healthy oaks, and contrast these with affected / dying oaks to shed light on syndrome causes and management. WGS metagenomic sampling was carried out on leaf and bark tissue from 37 affected, asymptomatic, and recovering individuals (nine Quercus species) at three field sites over a year. Extraction and DNA sequencing were performed in the field for a subset of samples with MinION nanopore rapid sequencing kits, and also using MinION and paired-end Illumina sequencing under laboratory conditions. Metagenomic analyses to determine microbial community composition were carried out, and real-time phylogenomic methods were also developed and applied. Early results from these analyses and lessons for future work are presented.
Metagenomic datasets can be rapidly generated in the field with minimal equipment using nanopore sequencing, providing a responsive capability for emerging disease threats and reducing transmission risks associated with transporting quantities of potentially infectious samples from outbreaks of novel diseases. Furthermore, real-time data analysis can provide rapid feedback to field teams, both to inform management decisions and also to allow for adaptive experimental protocols that dynamically target data collection to extract maximum information per unit effort.
DNA barcoding is a standardized approach to identifying plants and animals by minimal sequences of DNA, called DNA barcodes.
DNA barcode - short gene sequences taken from a standardized portion of the genome that is used to identify species
and this presentation gives much introducing about DNA barcodes developed for Prokaryotes and Eukaryotes.
Various barcoding genes which are evolutionary conserved.
techniques to develop a DNA bar-code and its future perspectives
Current technologies and future technologies of DNA barcoding. Applications regarding environment awareness. it also contains 2-3 case studies
This lecture covers key findings to the development of genomics as a field. This first part covers briefly Mendel to knowing that DNA is the genetic material by Hershey and Chase
A systematic approach to Genotype-Phenotype correlationsfisherp
It is increasingly common to combine Microarray and Quantitative Trait Loci data to aid the search for candidate genes responsible for phenotypic variation. Workflows provide a means of systematically processing these large datasets and also represent a framework for the re-use and the explicit declaration of experimental methods. Here we highlight the issues facing the manual analysis of microarray and QTL data for the discovery of candidate genes underlying complex phenotypes. We show how automated approaches provide a systematic means to investigate genotype-phenotype correlations. This methodology was applied to a use case of resistance to African trypanosomiasis in the mouse. Pathways represented in the results identified Daxx as one of the candidate genes within the Tir1 QTL region.
DNA Barcoding: A simple way of identifying species by DNAmarkstoeckle
DNA barcoding makes it easier for experts and non- experts to identify species including from bits and pieces, immature forms, and those with many close look-alikes. Applications include health, environment, and education. High school students are using DNA barcoding to explore the world around them and make scientific discoveries. Like a giant Wikipedia entry, the multitude of researchers depositing DNA barcodes in GenBank are creating the first large-scale maps of the genetic structure of biodiversity.
DNA barcoding is a technique in which species identification is performed by using DNA sequences from a small fragment of the genome, with the aim of contributing to a wide range of ecological and conservation studies in which traditional taxonomic identification is not practical.
DNA barcoding is a standardized approach to identifying plants and animals by minimal sequences of DNA, called DNA barcodes.
DNA barcode - short gene sequences taken from a standardized portion of the genome that is used to identify species
and this presentation gives much introducing about DNA barcodes developed for Prokaryotes and Eukaryotes.
Various barcoding genes which are evolutionary conserved.
techniques to develop a DNA bar-code and its future perspectives
Current technologies and future technologies of DNA barcoding. Applications regarding environment awareness. it also contains 2-3 case studies
This lecture covers key findings to the development of genomics as a field. This first part covers briefly Mendel to knowing that DNA is the genetic material by Hershey and Chase
A systematic approach to Genotype-Phenotype correlationsfisherp
It is increasingly common to combine Microarray and Quantitative Trait Loci data to aid the search for candidate genes responsible for phenotypic variation. Workflows provide a means of systematically processing these large datasets and also represent a framework for the re-use and the explicit declaration of experimental methods. Here we highlight the issues facing the manual analysis of microarray and QTL data for the discovery of candidate genes underlying complex phenotypes. We show how automated approaches provide a systematic means to investigate genotype-phenotype correlations. This methodology was applied to a use case of resistance to African trypanosomiasis in the mouse. Pathways represented in the results identified Daxx as one of the candidate genes within the Tir1 QTL region.
DNA Barcoding: A simple way of identifying species by DNAmarkstoeckle
DNA barcoding makes it easier for experts and non- experts to identify species including from bits and pieces, immature forms, and those with many close look-alikes. Applications include health, environment, and education. High school students are using DNA barcoding to explore the world around them and make scientific discoveries. Like a giant Wikipedia entry, the multitude of researchers depositing DNA barcodes in GenBank are creating the first large-scale maps of the genetic structure of biodiversity.
DNA barcoding is a technique in which species identification is performed by using DNA sequences from a small fragment of the genome, with the aim of contributing to a wide range of ecological and conservation studies in which traditional taxonomic identification is not practical.
The term DNA Finger printing is also known as DNA Typing, Genetic Profiling or Genotyping, it is a process in which the DNA characteristics of a person is determined by isolating and identifying variable elements in the base-pair sequence of DNA.
By developing this method in 1984 the British geneticist Alec Jeffery found that some sequence area unit extremely variable Deoxyribonucleic acid called as minisatellites. These minisatellites do not have contribution in functioning of DNA and are repeated in the genes. Geneticist found that in every person there is a unique pattern of these minisatellites except the identical twins.
1. University of Puerto Rico<br />Cayey Campus<br />Jessica Díaz Rivera<br />Prof. Elena Gonzalez<br />RISE Program<br />Laboratory #4: Gene to Protein Workshop<br /> In this workshop given by Patricia Casbas, Rodrigo González, Sean Bailey, and Daniel Dominguez we discussed some information about DNA. In the first experiment, each student isolated their own DNA using cells from their mouth. The DNA that each student obtained had different sizes because of the variation in the source of DNA, the quantity of saliva the person used to see their own DNA, or the force that the person used to swirl clear Gatorade in their mouth. In the second experiment based on Separation and Detection, we did a PCR (Polymerase Chain Reaction) to allow specific fragments of DNA to be copied and amplified. Later we did an electrophoresis to study a single gene out of over 21,000 using a specific protein called Green Fluorescence Protein (GFP). The third experiment was about Proteins and Methods for Detection. We used SDS-PAGE Electrophoresis to separate different sized proteins in polyacrylamide gel. With SDS-PAGE stained with coomassie, we only separated proteins on a polyacrylamide gel. We did not use antibodies to detect a specific protein of interest. When we separated the proteins in the electrophoresis we able to study the weight. The last workshop was about Macrophage infection with green fluorescent protein bacteria to see how macrophages eat foreign particles, including pathogens. Here we studied E. coli that was infected by GFP. We also observed in the stereomicroscope the cells of the macrophages and the macrophages with the E. coli. We also used UV light and Lux to see the E. coli. To conclude all the workshop was about how DNA, genes, bacterias, and proteins function. <br />