This document discusses microfluidic devices for DNA analysis. It summarizes that:
1) Microfabricated electrophoresis devices allow for faster DNA analysis and sequencing - in under 2 minutes for short-tandem-repeat genotyping assays and under 15 minutes for single-stranded DNA sequencing.
2) The microdevice format is a natural extension of improvements to electrophoresis over 100 years, operating in an almost perfect way limited only by the sieving medium.
3) Procedures for making the microfluidic devices are simple using current semiconductor fabrication technology, requiring one or two lithography steps at low resolution.
An accurate distance_to_the_nearest_galaxySérgio Sacani
This document summarizes recent research that more accurately measured the distance to the Large Magellanic Cloud (LMC) galaxy. A team called the Araucaria Project measured the distances to eight eclipsing binary stars in the LMC to determine a distance of 49.3 ± 0.5 kiloparsecs, which is accurate to 2.2%. This more precise measurement of the distance to the LMC will help astronomers better determine distances to more distant galaxies and improve our understanding of properties like dark energy. The new measurement is consistent with but more accurate than previous estimates, addressing issues with prior discrepancies in LMC distance measurements.
Using a new experimental technique, scientists have unraveled part of a 15-year mystery about how DNA is able to suddenly extend to almost twice its normal length when exposed to a certain amount of force. The technique involves attaching one end of a DNA molecule to a microbead and stapling the other end to a surface, then applying laser-measured force to the bead. They discovered that DNA stretches in this way when exposed to 65 piconewtons of force, absorbing energy as it extends. This finding helps explain DNA's elasticity under tiny forces and could support standardization work and studies of drug binding.
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
Dna knots and dna supercoilin cell cycle 2011Nikitas_5
1) Type II DNA topoisomerases play an important role in DNA transactions by allowing the passage of one DNA strand through another, but these passages can sometimes lead to the formation of knots that impede processes like transcription and replication.
2) Previous studies showed that type IIA DNA topoisomerases can reduce knot formation on relaxed DNA in vitro, but this ability decreases with increasing DNA length.
3) The authors propose that on supercoiled DNA, knots adopt a tighter form that increases their curvature compared to other DNA regions. This allows type IIA topoisomerases to preferentially bind and act on knotted regions due to their affinity for bent DNA, providing an efficient means of recognizing and
The document summarizes the classic experiment conducted by Matthew Meselson and Frank Stahl in 1958 that determined the mechanism of DNA replication. They grew bacteria in a culture containing the heavy isotope nitrogen-15 to produce "heavy" DNA. When these bacteria were then grown in a culture with regular nitrogen-14, the resulting DNA had an intermediate density, indicating that DNA replicates semiconservatively, with each parent strand serving as a template to produce two daughter double helices. Subsequent experiments showed that after a second generation, the DNA was half heavy and half light, confirming the semiconservative model. This elegant experiment provided the first direct evidence that DNA replicates in this manner.
The document discusses molecular medicine and various diagnostic techniques. It covers diagnostics for infectious diseases, which has shifted from examining microbial phenotypes to using nucleic acid techniques like PCR and probes. These DNA-based methods allow detection without culturing and can identify sub-species and drug resistance genes. The document also discusses diagnostics for genetic diseases using techniques like linkage analysis and pedigree analysis to find disease-causing genes. Finally, it outlines gene therapy techniques like germline and somatic cell therapy which aim to cure inherited diseases by providing a correct copy of defective genes.
The study of Gregor Mandel put the basis for the advancement in science. Then discovery of nucleic acid allowed researchers to see things in different perspective. Later Kary Mullis provided with the major break through by inventing PCR.
Recombinant DNA (rDNA) molecules are DNA molecules formed by laboratory methods of genetic recombination (such as molecular cloning) to bring together genetic material from multiple sources, creating sequences that would not otherwise be found in the genome.
An accurate distance_to_the_nearest_galaxySérgio Sacani
This document summarizes recent research that more accurately measured the distance to the Large Magellanic Cloud (LMC) galaxy. A team called the Araucaria Project measured the distances to eight eclipsing binary stars in the LMC to determine a distance of 49.3 ± 0.5 kiloparsecs, which is accurate to 2.2%. This more precise measurement of the distance to the LMC will help astronomers better determine distances to more distant galaxies and improve our understanding of properties like dark energy. The new measurement is consistent with but more accurate than previous estimates, addressing issues with prior discrepancies in LMC distance measurements.
Using a new experimental technique, scientists have unraveled part of a 15-year mystery about how DNA is able to suddenly extend to almost twice its normal length when exposed to a certain amount of force. The technique involves attaching one end of a DNA molecule to a microbead and stapling the other end to a surface, then applying laser-measured force to the bead. They discovered that DNA stretches in this way when exposed to 65 piconewtons of force, absorbing energy as it extends. This finding helps explain DNA's elasticity under tiny forces and could support standardization work and studies of drug binding.
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
Dna knots and dna supercoilin cell cycle 2011Nikitas_5
1) Type II DNA topoisomerases play an important role in DNA transactions by allowing the passage of one DNA strand through another, but these passages can sometimes lead to the formation of knots that impede processes like transcription and replication.
2) Previous studies showed that type IIA DNA topoisomerases can reduce knot formation on relaxed DNA in vitro, but this ability decreases with increasing DNA length.
3) The authors propose that on supercoiled DNA, knots adopt a tighter form that increases their curvature compared to other DNA regions. This allows type IIA topoisomerases to preferentially bind and act on knotted regions due to their affinity for bent DNA, providing an efficient means of recognizing and
The document summarizes the classic experiment conducted by Matthew Meselson and Frank Stahl in 1958 that determined the mechanism of DNA replication. They grew bacteria in a culture containing the heavy isotope nitrogen-15 to produce "heavy" DNA. When these bacteria were then grown in a culture with regular nitrogen-14, the resulting DNA had an intermediate density, indicating that DNA replicates semiconservatively, with each parent strand serving as a template to produce two daughter double helices. Subsequent experiments showed that after a second generation, the DNA was half heavy and half light, confirming the semiconservative model. This elegant experiment provided the first direct evidence that DNA replicates in this manner.
The document discusses molecular medicine and various diagnostic techniques. It covers diagnostics for infectious diseases, which has shifted from examining microbial phenotypes to using nucleic acid techniques like PCR and probes. These DNA-based methods allow detection without culturing and can identify sub-species and drug resistance genes. The document also discusses diagnostics for genetic diseases using techniques like linkage analysis and pedigree analysis to find disease-causing genes. Finally, it outlines gene therapy techniques like germline and somatic cell therapy which aim to cure inherited diseases by providing a correct copy of defective genes.
The study of Gregor Mandel put the basis for the advancement in science. Then discovery of nucleic acid allowed researchers to see things in different perspective. Later Kary Mullis provided with the major break through by inventing PCR.
Recombinant DNA (rDNA) molecules are DNA molecules formed by laboratory methods of genetic recombination (such as molecular cloning) to bring together genetic material from multiple sources, creating sequences that would not otherwise be found in the genome.
botanic gardens, meta-analysis, use of networks in ecology, conservation of biodiversity, species-people correlation, sudden oak death, Phytophthora ramorum, network epidemiology, geographical genetics, scale-dependence of the species-people correlation, invasion of plant pathogens, plant health and global change, sustainability,
Biotechnophysics: DNA Nanopore SequencingMelanie Swan
Biophysics (not merely bioengineering) is required to understand the fundamental mechanisms of biology in order to make technologies (bench and bioinformatic) for understanding them
This document provides an overview of nanopore sensors and their applications. It discusses biological nanopores formed by pore-forming proteins, solid state nanopores fabricated in materials like silicon nitride, and hybrid nanopores combining biological and solid state elements. The document outlines several applications of nanopore sensors including DNA sequencing, detection of DNA damage, analysis of circulating microRNAs for cancer detection, and single-molecule protein studies. It also discusses the potential of solid state nanopores integrated with nanowire field-effect transistors and hybrid nanopores for improved specificity.
This lecture covers some nice stories about the origins of the words "genome" and the derived word "genomics". the lecture also introduces viral, bacterial, and eukaryotic genomes.
UC Davis EVE161 Lecture 15 by @phylogenomicsJonathan Eisen
This document summarizes a lecture on shotgun metagenomics from a course on microbial phylogenomics. The lecture discusses how shotgun sequencing was applied to sequence microbial communities directly from environmental samples, without culturing. This allowed reconstruction of near-complete genomes from dominant species in an acid mine drainage biofilm sample. The sample was dominated by a few microbial populations, and shotgun sequencing generated enough data to assemble genomes representing Leptospirillum group II and Ferroplasma type II. Analysis of the assembled genomes provided insights into the metabolic pathways and survival strategies of these uncultivated organisms inhabiting an extreme environment.
Paper Biology 280 S Minireview Advances In Cancer Detection And TherapeuticsJoshua Mendoza-Elias
Abstract:
Nanotechnology is a field that has made significant advances in the engineering of technologies that allow earlier detection and treatment of disease – specifically cancer. In the modern era, these technologies define the emerging field of nanomedicine and seek to redefine detection and treatment with the promise of more effective, sensitive and cost effective high throughput systems. Compared to conventional treatment options, these next generation cancer therapeutics also seek to overcome the invasiveness of surgery, chemotherapy, radiotherapy, immunotherapy, and hormonal therapy. These technologies include nanoshells, quantum-dots, ultraoxide particles, DNA microarrays, liposomes, dendrimers, and fullerines. Highlighted in this paper, microwires and microcantilevers (“biofinger”) show promise in becoming multiplex platforms (“Labs on a chip”) that detect a variety of biological markers at low concentration in real time. In addition, DNA based diagnostic computer constructs (DNAdc) that release therapeutic nucleic acid sequences in a gene expression specific manner will be highlighted as well. The potential for a wide range of clinical applications to disease, including cancer, makes a basic understanding of the field of nanomedicine important to the biomedical sciences. In addition, nanomedicine will have a huge impact in developing a repertoire of nano-based therapeutics for other diseases.
Keywords: “Biofinger”-lab on a chip, DNA diagnostic computer construct (DNAdc), DNA microarrays, nanoshells, quantum-dots, ultraoxide particles, liposomes, dendrimers, fullerines, single wall carbon nanotubes (SWNT).
DNA origami involves folding a long single strand of DNA into designed shapes using short staple strands. This technique can be used to create drug delivery vehicles by incorporating drug molecules like doxorubicin into the DNA nanostructures. Doxorubicin intercalates into the double helix of DNA origami through interactions with its GC base pairs. DNA origami carriers can then selectively deliver doxorubicin into cancer cells and reduce side effects by protecting healthy cells. The technique offers stable and precise drug delivery but remains limited by cost and potential immune responses.
Professor Alan Cooper presents the sixth instalment of the Science Seminar Series. The accurate and rapid assessment of biodiversity is a critical aspect for modern science, and ranges from the measurement of environmental and climate change, to microbes in water systems or at the point of care in medical centres. Similarly, the need for the rapid and responsible economic development of primary resources, and the monitoring of invasive species and biosecurity, also place a premium on the ability to quickly assess and quantify biodiversity across a range of diverse habitats. We have combined methods developed to detect trace amounts of ancient DNA with 2nd Generation Sequencing technology to design a vertical barcoding system capable of rapidly screening the genetic and taxonomic diversity of modern, complex biological samples. In parallel with studies of taxonomically identified museum and herbaria material, this approach promises to provide the first genetic audits of diverse Australian environments.
The document describes DNA structure and replication. It begins by discussing early evidence that DNA is the genetic material, including Griffith's experiments showing bacterial transformation and Hershey and Chase's experiments tracing phage DNA and proteins during infection. Watson and Crick then developed the first accurate double-helix model of DNA structure in 1953 based on Franklin's X-ray crystallography images, with base-pairing of A-T and C-G. The document concludes by explaining that DNA replication involves unwinding the double helix and using each strand as a template to build new complementary strands based on base-pairing rules, with many proteins involved.
UC Davis EVE161 Lecture 10 by @phylogenomicsJonathan Eisen
The document summarizes key concepts from Lecture 10 of the Microbial Phylogenomics course taught by Jonathan Eisen in winter 2014. It discusses the history of genome sequencing, including the first bacterial genome sequenced. It then covers the general steps involved in genome sequencing projects, including library construction, random sequencing, closure, and annotation. Subsequent slides discuss trends in completed genomes over time, structural annotation of genes and features, functional annotation including Gene Ontology and enzyme classification, and methods for functional prediction such as membrane protein prediction and phylogeny-based approaches.
This document outlines a lesson plan on genetic engineering that includes activities and videos. It will begin with having students pretend they have the "warrior gene" and watching a video on it. They will then learn about how cloning is used to purify DNA and isolate genes. The process of cloning a gene will be illustrated by cutting DNA with enzymes, inserting it into a vector, and transforming bacteria. Later, the class will watch several videos on topics like DNA sequencing, gene chips, using sequencing to diagnose rare diseases, and genetically modifying T-cells to cure leukemia. If time allows, the lesson will cover using biotechnology in plants through techniques like PCR and DNA markers to select for traits in plant breeding.
Fredrick Griffith discovered that heat-killed pneumonia bacteria could transform harmless bacteria into deadly disease-causing bacteria when mixed together and injected into mice. This led researchers like Oswald Avery to determine that DNA was the molecule responsible for transformation. Further experiments by Hershey and Chase showed that the genetic material of viruses that infect bacteria is DNA. Together, these findings established DNA as the genetic material that gets passed from parents to offspring and controls inheritance.
This document provides an overview of DNA fingerprinting (also called DNA profiling). It discusses the stages of DNA fingerprinting including extraction, cutting, separation, transfer and analysis. The principle of DNA fingerprinting is that restriction enzymes cut DNA at unique sites, creating variable fragment patterns between individuals. Applications include determining paternity, criminal identification using DNA from crime scenes, and personal identification. Advantages are that DNA profiling can identify individuals with certainty, while limitations include samples being easily contaminated and complex patterns. The document also discusses uses in forensics, plants, centers that perform DNA fingerprinting, and concludes with an overview.
The document discusses experiments that identified DNA as the genetic material. Frederick Griffith discovered that live bacteria could be transformed by dead bacteria, indicating transfer of some transforming factor. Avery determined this factor was DNA. Hershey and Chase found that when bacteriophage infected bacteria, only the DNA core, not the protein coating, entered the bacterial cells. Their results confirmed that DNA is the genetic material that carries inheritable traits.
This document contains a chapter on DNA testing with multiple choice questions, modified true/false statements, completion questions, short answer questions, and essay questions about DNA structure and replication. The chapter covers Griffith's experiments which showed bacterial transformation, Avery's work identifying DNA as the transforming factor, the Hershey-Chase experiment, Watson and Crick's DNA model, and differences between prokaryotic and eukaryotic DNA replication.
1) Bacterial transformation experiments and studies of bacteriophages provided evidence that DNA carries genetic information. Avery discovered DNA was the transforming factor in bacteria. Hershey and Chase found that the genetic material of bacteriophages was DNA.
2) The structure of DNA was elucidated. Chargaff found rules of base pairing in DNA. Franklin's X-ray diffraction revealed DNA's double helix structure. Watson and Crick built a DNA model explaining its structure and base pairing.
3) DNA replication copies genetic information by unwinding the double helix and synthesizing new complementary strands according to base pairing rules, ensuring each daughter cell inherits the full genome. It occurs at replication forks in prok
Next generation sequencing (NGS) refers to modern DNA sequencing technologies that allow for high-speed, low-cost sequencing of entire genomes. NGS works by massively parallel sequencing of millions of DNA fragments. The Illumina sequencing by synthesis method is the most commonly used NGS approach. It involves library preparation, cluster generation on a flow cell, sequencing via reversible dye-terminator chemistry, and computational analysis of sequenced reads. Key advantages of NGS include its scalability, unlimited dynamic range, tunable coverage levels, and ability to multiplex many samples simultaneously in a single run.
The document summarizes the identification of six hemocyte cell types in Culex quinquefasciatus by light and transmission electron microscopy:
1) Prohemocytes, the smallest hemocytes, with a large central nucleus and few organelles. They represent 9.3% of hemocytes.
2) Spherulocytes, small hemocytes with numerous spherules containing a lamellar pattern and dense core. They are 1.6% of hemocytes.
3) Adipohemocytes, rare cells with a large nucleolated nucleus, cytoplasm containing organelles and lipid inclusions. They are 0.8% of hemocytes.
4) Oenocytoids
Genome editing methods such as ZFNs, TALENs, and CRISPR/Cas9 use engineered nucleases to create targeted double-stranded breaks in DNA which are then repaired through endogenous cellular processes. These nucleases can be used to modify genomes through techniques like gene knockout, targeted mutation insertion/deletion/correction, and studying gene function. CRISPR/Cas9 uses a guide RNA and Cas9 nuclease to target specific DNA sequences for editing. The four main steps for CRISPR are: 1) selecting target sequences near a PAM site, 2) designing and cloning gRNA, 3) delivering Cas9 and gRNA into cells, and 4) DNA repair after cleavage results in gene modification
The document discusses two bioinformatics software tools: DNA Baser and Darwin. DNA Baser is a tool for manual and automatic DNA sequence assembly, analysis, editing, and more. It allows for automation of sequence assembly through functions like end trimming, vector removal, and batch assembly of thousands of sequences. Darwin is an interpreted computer language for research in bioscience that provides libraries and functions for tasks like sequence comparison, alignment, phylogenetics, and more.
botanic gardens, meta-analysis, use of networks in ecology, conservation of biodiversity, species-people correlation, sudden oak death, Phytophthora ramorum, network epidemiology, geographical genetics, scale-dependence of the species-people correlation, invasion of plant pathogens, plant health and global change, sustainability,
Biotechnophysics: DNA Nanopore SequencingMelanie Swan
Biophysics (not merely bioengineering) is required to understand the fundamental mechanisms of biology in order to make technologies (bench and bioinformatic) for understanding them
This document provides an overview of nanopore sensors and their applications. It discusses biological nanopores formed by pore-forming proteins, solid state nanopores fabricated in materials like silicon nitride, and hybrid nanopores combining biological and solid state elements. The document outlines several applications of nanopore sensors including DNA sequencing, detection of DNA damage, analysis of circulating microRNAs for cancer detection, and single-molecule protein studies. It also discusses the potential of solid state nanopores integrated with nanowire field-effect transistors and hybrid nanopores for improved specificity.
This lecture covers some nice stories about the origins of the words "genome" and the derived word "genomics". the lecture also introduces viral, bacterial, and eukaryotic genomes.
UC Davis EVE161 Lecture 15 by @phylogenomicsJonathan Eisen
This document summarizes a lecture on shotgun metagenomics from a course on microbial phylogenomics. The lecture discusses how shotgun sequencing was applied to sequence microbial communities directly from environmental samples, without culturing. This allowed reconstruction of near-complete genomes from dominant species in an acid mine drainage biofilm sample. The sample was dominated by a few microbial populations, and shotgun sequencing generated enough data to assemble genomes representing Leptospirillum group II and Ferroplasma type II. Analysis of the assembled genomes provided insights into the metabolic pathways and survival strategies of these uncultivated organisms inhabiting an extreme environment.
Paper Biology 280 S Minireview Advances In Cancer Detection And TherapeuticsJoshua Mendoza-Elias
Abstract:
Nanotechnology is a field that has made significant advances in the engineering of technologies that allow earlier detection and treatment of disease – specifically cancer. In the modern era, these technologies define the emerging field of nanomedicine and seek to redefine detection and treatment with the promise of more effective, sensitive and cost effective high throughput systems. Compared to conventional treatment options, these next generation cancer therapeutics also seek to overcome the invasiveness of surgery, chemotherapy, radiotherapy, immunotherapy, and hormonal therapy. These technologies include nanoshells, quantum-dots, ultraoxide particles, DNA microarrays, liposomes, dendrimers, and fullerines. Highlighted in this paper, microwires and microcantilevers (“biofinger”) show promise in becoming multiplex platforms (“Labs on a chip”) that detect a variety of biological markers at low concentration in real time. In addition, DNA based diagnostic computer constructs (DNAdc) that release therapeutic nucleic acid sequences in a gene expression specific manner will be highlighted as well. The potential for a wide range of clinical applications to disease, including cancer, makes a basic understanding of the field of nanomedicine important to the biomedical sciences. In addition, nanomedicine will have a huge impact in developing a repertoire of nano-based therapeutics for other diseases.
Keywords: “Biofinger”-lab on a chip, DNA diagnostic computer construct (DNAdc), DNA microarrays, nanoshells, quantum-dots, ultraoxide particles, liposomes, dendrimers, fullerines, single wall carbon nanotubes (SWNT).
DNA origami involves folding a long single strand of DNA into designed shapes using short staple strands. This technique can be used to create drug delivery vehicles by incorporating drug molecules like doxorubicin into the DNA nanostructures. Doxorubicin intercalates into the double helix of DNA origami through interactions with its GC base pairs. DNA origami carriers can then selectively deliver doxorubicin into cancer cells and reduce side effects by protecting healthy cells. The technique offers stable and precise drug delivery but remains limited by cost and potential immune responses.
Professor Alan Cooper presents the sixth instalment of the Science Seminar Series. The accurate and rapid assessment of biodiversity is a critical aspect for modern science, and ranges from the measurement of environmental and climate change, to microbes in water systems or at the point of care in medical centres. Similarly, the need for the rapid and responsible economic development of primary resources, and the monitoring of invasive species and biosecurity, also place a premium on the ability to quickly assess and quantify biodiversity across a range of diverse habitats. We have combined methods developed to detect trace amounts of ancient DNA with 2nd Generation Sequencing technology to design a vertical barcoding system capable of rapidly screening the genetic and taxonomic diversity of modern, complex biological samples. In parallel with studies of taxonomically identified museum and herbaria material, this approach promises to provide the first genetic audits of diverse Australian environments.
The document describes DNA structure and replication. It begins by discussing early evidence that DNA is the genetic material, including Griffith's experiments showing bacterial transformation and Hershey and Chase's experiments tracing phage DNA and proteins during infection. Watson and Crick then developed the first accurate double-helix model of DNA structure in 1953 based on Franklin's X-ray crystallography images, with base-pairing of A-T and C-G. The document concludes by explaining that DNA replication involves unwinding the double helix and using each strand as a template to build new complementary strands based on base-pairing rules, with many proteins involved.
UC Davis EVE161 Lecture 10 by @phylogenomicsJonathan Eisen
The document summarizes key concepts from Lecture 10 of the Microbial Phylogenomics course taught by Jonathan Eisen in winter 2014. It discusses the history of genome sequencing, including the first bacterial genome sequenced. It then covers the general steps involved in genome sequencing projects, including library construction, random sequencing, closure, and annotation. Subsequent slides discuss trends in completed genomes over time, structural annotation of genes and features, functional annotation including Gene Ontology and enzyme classification, and methods for functional prediction such as membrane protein prediction and phylogeny-based approaches.
This document outlines a lesson plan on genetic engineering that includes activities and videos. It will begin with having students pretend they have the "warrior gene" and watching a video on it. They will then learn about how cloning is used to purify DNA and isolate genes. The process of cloning a gene will be illustrated by cutting DNA with enzymes, inserting it into a vector, and transforming bacteria. Later, the class will watch several videos on topics like DNA sequencing, gene chips, using sequencing to diagnose rare diseases, and genetically modifying T-cells to cure leukemia. If time allows, the lesson will cover using biotechnology in plants through techniques like PCR and DNA markers to select for traits in plant breeding.
Fredrick Griffith discovered that heat-killed pneumonia bacteria could transform harmless bacteria into deadly disease-causing bacteria when mixed together and injected into mice. This led researchers like Oswald Avery to determine that DNA was the molecule responsible for transformation. Further experiments by Hershey and Chase showed that the genetic material of viruses that infect bacteria is DNA. Together, these findings established DNA as the genetic material that gets passed from parents to offspring and controls inheritance.
This document provides an overview of DNA fingerprinting (also called DNA profiling). It discusses the stages of DNA fingerprinting including extraction, cutting, separation, transfer and analysis. The principle of DNA fingerprinting is that restriction enzymes cut DNA at unique sites, creating variable fragment patterns between individuals. Applications include determining paternity, criminal identification using DNA from crime scenes, and personal identification. Advantages are that DNA profiling can identify individuals with certainty, while limitations include samples being easily contaminated and complex patterns. The document also discusses uses in forensics, plants, centers that perform DNA fingerprinting, and concludes with an overview.
The document discusses experiments that identified DNA as the genetic material. Frederick Griffith discovered that live bacteria could be transformed by dead bacteria, indicating transfer of some transforming factor. Avery determined this factor was DNA. Hershey and Chase found that when bacteriophage infected bacteria, only the DNA core, not the protein coating, entered the bacterial cells. Their results confirmed that DNA is the genetic material that carries inheritable traits.
This document contains a chapter on DNA testing with multiple choice questions, modified true/false statements, completion questions, short answer questions, and essay questions about DNA structure and replication. The chapter covers Griffith's experiments which showed bacterial transformation, Avery's work identifying DNA as the transforming factor, the Hershey-Chase experiment, Watson and Crick's DNA model, and differences between prokaryotic and eukaryotic DNA replication.
1) Bacterial transformation experiments and studies of bacteriophages provided evidence that DNA carries genetic information. Avery discovered DNA was the transforming factor in bacteria. Hershey and Chase found that the genetic material of bacteriophages was DNA.
2) The structure of DNA was elucidated. Chargaff found rules of base pairing in DNA. Franklin's X-ray diffraction revealed DNA's double helix structure. Watson and Crick built a DNA model explaining its structure and base pairing.
3) DNA replication copies genetic information by unwinding the double helix and synthesizing new complementary strands according to base pairing rules, ensuring each daughter cell inherits the full genome. It occurs at replication forks in prok
Next generation sequencing (NGS) refers to modern DNA sequencing technologies that allow for high-speed, low-cost sequencing of entire genomes. NGS works by massively parallel sequencing of millions of DNA fragments. The Illumina sequencing by synthesis method is the most commonly used NGS approach. It involves library preparation, cluster generation on a flow cell, sequencing via reversible dye-terminator chemistry, and computational analysis of sequenced reads. Key advantages of NGS include its scalability, unlimited dynamic range, tunable coverage levels, and ability to multiplex many samples simultaneously in a single run.
The document summarizes the identification of six hemocyte cell types in Culex quinquefasciatus by light and transmission electron microscopy:
1) Prohemocytes, the smallest hemocytes, with a large central nucleus and few organelles. They represent 9.3% of hemocytes.
2) Spherulocytes, small hemocytes with numerous spherules containing a lamellar pattern and dense core. They are 1.6% of hemocytes.
3) Adipohemocytes, rare cells with a large nucleolated nucleus, cytoplasm containing organelles and lipid inclusions. They are 0.8% of hemocytes.
4) Oenocytoids
Genome editing methods such as ZFNs, TALENs, and CRISPR/Cas9 use engineered nucleases to create targeted double-stranded breaks in DNA which are then repaired through endogenous cellular processes. These nucleases can be used to modify genomes through techniques like gene knockout, targeted mutation insertion/deletion/correction, and studying gene function. CRISPR/Cas9 uses a guide RNA and Cas9 nuclease to target specific DNA sequences for editing. The four main steps for CRISPR are: 1) selecting target sequences near a PAM site, 2) designing and cloning gRNA, 3) delivering Cas9 and gRNA into cells, and 4) DNA repair after cleavage results in gene modification
The document discusses two bioinformatics software tools: DNA Baser and Darwin. DNA Baser is a tool for manual and automatic DNA sequence assembly, analysis, editing, and more. It allows for automation of sequence assembly through functions like end trimming, vector removal, and batch assembly of thousands of sequences. Darwin is an interpreted computer language for research in bioscience that provides libraries and functions for tasks like sequence comparison, alignment, phylogenetics, and more.
The document discusses DNA sequencing software. It describes a fast and accurate DNA sequencing assembly software for Windows that can assemble DNA sequences into contigs and directly compare trace data to nucleotide data. It handles over 100,000 samples from various sequence and file formats and accelerates proofreading and comparing nucleotides to trace peaks. Several other related DNA sequencing software are also mentioned such as DNA DYNAMO, DNA MASTER, and Mesto DNA program starter.
The document discusses interval position analysis (IPA), a method for analyzing DNA and RNA sequences. IPA calculates characteristics such as V, G, and g values based on the distances between similar elements in a sequence. The values of IPA characteristics are sensitive to the order of elements in a sequence. IPA can be used to construct phylogenetic trees and analyze local profiles of RNA sequences. Heap's law and rank distribution models are also discussed in relation to evaluating DNA segmentation.
this is the project regarding the detection and analysis of DNA sequences,it provide the fascility to find the repets from the hudge data set.we can find tha all repeats which is occured in human body.
Genome assembly: then and now (with notes) — v1.2Keith Bradnam
This was a talk given on 2014-09-17 for the Genome Center’s Bioinformatics Core as part of a 1 week workshop. It concerns the Assemblathon projects as well as other aspects relating to genome assembly.
A version of this talk is also available on Slideshare without notes.
Note, this is an evolving talk. There are older and newer versions of the talk also available on slideshare.
DNA testing has become the "gold standard" of forensics, but linking an item of evidence to a person of interest isn't always clear cut. New open source tools allow DNA analysts to give statistical weight to evidentiary profiles that were previously unusable, letting juries weigh the evidence for themselves. This talk will discuss the Lab Retriever software package for probabilistic genotyping.
Genome and Proteome data integration in RDFNadia Anwar
The document summarizes integrating genome and proteome data from Francisella tularensis in RDF. It discusses integrating data from multiple sources, including genome annotations, proteomics experiments, and transcriptomics data. Semantic data integration across "omes" data silos is demonstrated using RDF and the open source Sesame framework. Reifying biological statements, such as identified peptides and abundances, allows more complex queries across the integrated data.
The document discusses analysis of DNA microarray data using various techniques including gene-based, gene set, and functional group approaches. It describes preprocessing methods, platforms like Affymetrix, and tools for analysis including LIMMA and GSEA. Applications mentioned include biomarker discovery, clinical outcomes, and regulatory network analysis.
A I Macan Markar & Co is a chartered accountancy firm founded in 1946 in Sri Lanka. It has 4 partners and provides auditing, taxation, management consulting, and IT services to clients across various industries. The firm also has associated companies that offer secretarial services, management consulting, and legal advice.
ubio is starting a series of biology tutorials aimed at introducing biology, biotechnology and bioinformatics to computer engineers. The first part of the presentation is essentially a biochemistry tutorial that introduces molecular biochemistry.
Application of Marker Assisted Selection (MAS) for the improvement of Bean Co...CIAT
The document summarizes efforts to develop common bean varieties in Rwanda resistant to Bean Common Mosaic Necrotic Virus (BCMNV) using Marker Assisted Selection (MAS). Researchers screened 219 bean varieties and identified genes conferring resistance. They developed 86 breeding lines by crossing donor lines containing resistance genes with local varieties. These lines were selected using linked markers and for resistance to BCMNV and other diseases. Participatory plant breeding involved farmers in selection. The integration of conventional breeding and MAS was successful in pyramiding resistance genes and developing lines adapted to Rwanda.
- DNA molecules are very long and consist of millions of base pairs. To study their structure, restriction enzymes are used to cut the DNA molecules into smaller, easier to analyze fragments at specific recognition sites.
- The fragments produced can be separated by gel electrophoresis based on their size, with shorter fragments traveling farther through the gel. This produces a pattern called a genetic fingerprint that can be used for applications like genetic profiling in criminal cases.
- The human genome project aimed to map all human genes by determining the full DNA sequence. While about 3% of human DNA codes for proteins, other non-coding "junk DNA" may have undiscovered functions and contains regions of repeated sequences that vary between individuals.
The document summarizes several recent biotechnology innovations, including using oil-eating bacteria to clean up oil spills, using a protein called GDF 11 to improve aging brains and muscles in mice, developing advanced biofuels from cellulosic biomass, using 3D x-ray filming to study insect movements, discovering anti-psychotic drugs that kill brain cancer, developing affordable genome sequencing technology, engineering immune cells to attack cancer, creating RNA detection probes without harming cells, and assessing monoclonal antibody therapies using ADCC reporter assays.
Now days Biotech Era, What is application of biotechnology in Agriculture, Plantation and fertilizer. If we want to Improve qualitative and quantitative of Agri & Plantation then we definitely need of applying Biotechnological application.
Back to Basics: Fundamental Concepts and Special Considerations in gDNA Isola...QIAGEN
This document provides an overview of genomic DNA (gDNA) isolation. It discusses key considerations for gDNA isolation including sample stabilization, disruption, and storage. Common isolation technologies like silica membrane and magnetic bead kits are described. The document reviews measuring gDNA concentration and quality via UV spectroscopy and gel electrophoresis. It also provides guidance on selecting appropriate QIAGEN gDNA isolation kits based on sample type.
Analysis and Interpretation of Cell-free DNAQIAGEN
Identification and monitoring of cancer mutations from cell free DNA-Seq data is a key application in liquid biopsy. In this part of the webinar we will show how mutations can be best identified from this type of data and how they can be interpreted. Furthermore, potential challenges when analyzing this type of data will be discussed together with relevant strategies.
Statistical approaches for the interpretation of DNA evidencehindahaned
This document discusses different statistical approaches for interpreting DNA evidence, including allele-centric and genotype-centric approaches. It describes probability of exclusion/inclusion, random match probability, and likelihood ratios. Likelihood ratios are considered the preferred approach as they make use of more information, provide a better estimation of evidence strength, and can model uncertainties in DNA sample composition. International consensus now recommends probabilistic and likelihood ratio approaches over classical methods for DNA evidence interpretation.
Superconducting qubits for quantum information an outlookGabriel O'Brien
The document discusses the progress and future directions of quantum information processing using superconducting qubits. It describes the stages needed to build a functional quantum computer, from controlling individual qubits to implementing error correction. Superconducting qubits are well-suited for this task as their Hamiltonians can be designed using circuit elements like inductors and Josephson junctions. While full fault-tolerant quantum computing has yet to be achieved, the performance of superconducting qubits has improved dramatically in recent years, suggesting the goals may be within reach this century.
Edri And Regev 2009 “Shaken, Not Stable”: Dispersion Mechanism and Dynami...edrier
This study examines the dispersion dynamics of single-walled carbon nanotubes (SWNTs) stabilized by bovine serum albumin (BSA) protein. The researchers investigated how BSA properties like charge and conformation affect SWNT exfoliation during sonication and subsequent recovery after centrifugation. They found that bulkier BSA conformations led to faster exfoliation and higher SWNT recovery, while higher BSA-to-SWNT ratios resulted in slower exfoliation dynamics and lower recoveries. The study links the unstable state during sonication to the stable state achieved after centrifugation removal of bundles and impurities.
Single Molecule Sequence Detection Via Microfluidic Planar Extensional FlowUniv of Cincinnati
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In this deck from the Blue Waters Symposium, Dr. Rommie E. Amaro from UC San Diego presents: Computational Biophysics in the Petascale Computing Era.
"Advances in structural, chemical, and biophysical data acquisition (e.g., protein structures via X-ray crystallography and near atomic cryoEM, isothermal calorimetry, etc.), coupled with the continued exponential growth in computing power and advances in the underlying algorithms are opening a new era for the simulation of biological systems at the molecular level, and at scales never before reached. In this talk I will discuss how the BlueWaters Petascale computing architecture forever altered the landscape and potential of computational biophysics. In particular, new and emerging capabilities for multiscale dynamic simulations that cross spatial scales from the molecular (angstrom) to cellular ultrastructure (near micron), and temporal scales from the picoseconds of macromolecular dynamics to the physiologically important time scales of organelles and cells (milliseconds to seconds) are now possible. These efforts are driven by the outstanding and persistent advances in peta- and exascale computing and availability of multimodal biological datasets, as well as by gaps in current abilities to connect across scales where it is already clear that new approaches will result in novel fundamental understanding of biological phenomena or open new therapeutic avenues."
Watch the video: https://wp.me/p3RLHQ-j1u
Learn more: https://bluewaters.ncsa.illinois.edu/blue-waters-symposium-2018
Sign up for our insideHPC Newsletter: http://insidehpc.com/newsletter
This document discusses recent findings that some bacterial and viral DNA sequences can induce low-frequency electromagnetic waves in high aqueous dilutions. Specifically:
1) Electromagnetic signals were detected in certain high dilutions of filtrates from cultures of microorganisms or plasma from infected humans. The signals could also be induced from extracted DNA.
2) The signals are an "all or none" phenomenon, occurring only in some dilutions ranging from 10-9 to 10-18, and do not correlate linearly with initial bacterial cell numbers.
3) Even short DNA sequences, like from a single gene or 104 bp HIV fragment, were able to induce the signals, suggesting nanostructures made of water are involved.
This document discusses recent findings that some bacterial and viral DNA sequences can induce low-frequency electromagnetic waves in high aqueous dilutions. Specifically:
1) Electromagnetic signals were detected in certain high dilutions of filtrates from cultures of microorganisms or plasma from infected humans. The signals could also be induced from extracted DNA.
2) The signals are an "all or none" phenomenon, occurring in some dilutions but not linearly correlated with initial bacterial concentrations.
3) A proposed mechanism is that DNA nanostructures formed in water could transmit genetic information through electromagnetic waves.
This document discusses recent findings that some bacterial and viral DNA sequences can induce low-frequency electromagnetic waves in high aqueous dilutions. When excited by an extremely low frequency electromagnetic background, these DNA sequences form nanostructures in water that can transmit genetic information. Specifically:
1) Electromagnetic signals were detected in dilutions of bacteria/virus cultures and DNA extracts.
2) DNA sequences as short as 100 base pairs were sufficient to induce signals.
3) Signals could be transmitted into pure water, and the original DNA sequence was faithfully replicated from the water using PCR.
4) A theoretical framework based on quantum field theory is proposed to explain how DNA nanostructures formed in water can oscillate coherently
This document presents a technique called K-factor image deshadowing that can improve the localization accuracy of single fluorescent particles in stochastic super-resolution fluorescence microscopy. K-factor decomposes an image into a nonlinear set of contrast-ordered images whose product reassembles the original. Applying K-factor to raw fluorescence data prior to localization can improve localization precision by up to 85% compared to single fitting, enabling the localization of overlapping particles and faster data collection. Implementing this on experimental cellular data yielded a 37% improvement in resolution for the same acquisition time, or a 42% decrease in time needed for the same resolution.
UC Davis EVE161 Lecture 17 by @phylogenomicsJonathan Eisen
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This is Best Search Engine Better Than Google (ABSOLUTELY FREE) ATUSIUBATOCHUKWU1
This letter discusses a controversy in the field of membrane mechanics regarding how cholesterol affects the bending modulus of DOPC bilayers. While previous studies using techniques like tube pulling and X-ray scattering found no increase in bending modulus, a recent study using neutron spin echo and NMR relaxation claimed a threefold increase. However, the letter argues this controversy is unnecessary because the different techniques actually measure different properties - relaxation versus mean-square fluctuations. Specifically, the letter contends neutron spin echo is sensitive to viscosity effects rather than directly measuring the Helfrich bending modulus. The letter concludes insisting a single theory applies to all systems prevents a deeper understanding of membrane mechanics.
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06.02.13
Talk to UCSD's Sixth College
Honor's Course on Kurzweil's The Singularity is Near
Title: The Singularity: Toward a Post-Human Reality
La Jolla, CA
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This document reviews Michael Alley's book "The Craft of Scientific Writing". It summarizes key points about writing clearly and effectively in science. Specifically, it discusses avoiding needless complexity in language, using punctuation correctly, being concise with introductions and structure, and ending with analysis rather than new evidence.
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تتميز هذهِ الملزمة بعِدة مُميزات :
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3- دقة الكتابة والصور عالية جداً جداً جداً
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5- الملزمة تشرح نفسها ب نفسها بس تكلك تعال اقراني
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واخيراً هذهِ الملزمة حلالٌ عليكم وإتمنى منكم إن تدعولي بالخير والصحة والعافية فقط
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2. NANOTECHNOLOGY
The procedures for making these devices are simple
Cathode reservoir using current technology for semiconductor devices9,12;
Sample waste typically, they require one or two lithography steps at
low (~10 m) resolution. The channels are semicircular
in cross section with an etched depth of 40–100 m.
After fabrication, DNA separations require a rigorous,
stable neutralization of the intrinsic negative charge that
resides on ambient SiO2 surfaces. This method was
originally described by Hjerten13 to produce a co-
valently bonded layer of polyacylimide on internal sur-
Sample faces. Following coating, the devices are injected with
Separation load the polyacrylamide (PAA) sieving solutions.
channel In a DNA assay, samples are pipetted into reservoirs
connected to the input ends of the injector channels.
Eight separation channels A voltage is applied to electrophorese the DNA past
(sample moves to bottom of page) the channel-intersection points. An orthogonal bias
trends in Biotechnology
(along the separation channel) is then applied to run
Anode reservoir the sample from the channel intersection (typically only
several hundred picoliters) down the separation channel,
where it undergoes electrophoretic separation followed
by detection via laser-induced fluorescence.
1 cm Most of this protocol is taken directly from well-
established techniques in capillary electrophoresis (CE),
Figure 1 with the exception of sample injection. Microma-
A typical eight-lane microelectrophoresis genotyping device. The channels are micro- chined devices offer unmatched control of the injection
machined between two 15-cm-diameter fused-silica wafers, which are then diced into volume and uniform delivery of the sample compo-
six to eight individual devices. The network at the broad end of the device is matched nents. In CE devices, injection volumes are difficult to
to a four-tip pipette, used for sample and buffer loading. DNA is detected by laser control and the separations show undesired bias towards
fluorescence at the narrow end of the device. During operation, the device is housed low molecular weights. A second new aspect is the
in a ceramic cassette with integrated electrodes and microfluidic reservoirs. practicality of short, 2–15 cm, devices, which are dif-
ficult to implement other than in microdevice formats.
Finally, there are also numerous system-level advantages
In the early 1990s, the concept of micromachined stemming from the fact that microfabricated devices are
devices for electrophoretic separation was proved2,3. vast planar channel structures that allow complicated
This set the stage for DNA microelectrophoresis assays intersections and other features to be fabricated easily.
to separate oligonucleotides4, restriction fragments5–7, In fact, these aspects are likely to be the most important
sequencing mixtures8,9, PCR products10, genotyping asset of the microfabricated format.
samples11 and short tandem repeats12 (STRs). We are
now at a stage where microdevices will be used at the Genotyping applications
forefront of genetic applications, some of which require Genotyping may be the first application in which the
a very high electrophoretic performance. new format outperforms the established technologies
For example, high cost, long run times, large sample in almost all practical measures. One example is the
volumes and manual operation of gel-based electro- analysis of the STR ‘CTTv’ system, which consists of
phoresis devices are among the most important the four loci CSF1PO, TPOX, THO1 and vWA. Each
factors that presently limit the pace of the Human of these loci contains STR alleles that differ in length
Genome Project. Hence, slab-gel and capillary methods by four base pairs. This assay is directly compared in
have been optimized to near their theoretical limits. As slab, capillary and microdevice formats in Fig. 2, which
a result, to be useful for such applications, any micro- shows the difference in time scales for comparable-
device must improve on the already very high perfor- quality results. In addition, the microdevice trace shows
mance standards of current methods. In the past year, a series of periodic signals, which arises from a CTTv
it has become clear that this will be achieved. This article ladder (ranging from 140 to 330 bases) that is used as
describes the current state of the art in DNA micro- an internal sizing standard for the allelic profiling. The
electrophoresis devices and some of the engineering device performance is optimized according to the
issues that limit further development of the new format. required electrophoretic resolution, R (Eqn 1),
The anatomy of a microelectrophoresis device R [(2 ln2)1/2 (t1 t2)] [(w1 w2) b] (1)
Figure 1 illustrates a typical eight-lane microelectro-
phoresis device. Micromachined into fused silica, the where t is the migration time of the fragment, w is the
heart of the structure is a series of eight pairs of inter- full width at half maximum of the peak and b is the
secting enclosed channels, each set including an injec- base-number difference between the two DNA frag-
tor channel and a separation channel. This insert is ments. The alleles of all the four loci are resolved in
made by the photolithography, etching and bonding of 2 min with resolutions (R) ranging from 1.7 for the
two fused silica or glass plates, and is housed in a vWA locus to 1.1 for the CSF1PO locus. Forensic
ceramic cassette that contains microfluidic reservoirs, applications typically require a resolution greater than
electrodes and an integrated heater. one.
316 TIBTECH AUGUST 1999 (VOL 17)
3. NANOTECHNOLOGY
Microdevices are filled with a polyacrylamide sepa-
ration matrix using a syringe inserted into the separation- a
channel exit reservoir, and the detector is placed
~26 mm from the injector. The device is then pre-
electrophoresed for 3 min at 200 V cm 1 and 50 C
across the separation channel. To load the sample,
400 V cm 1 is applied across the load and sample chan-
nels (Fig. 1). Fields of 40 V cm 1 are applied to the
cathode reservoir and separation channel to prevent the 1.3 1.6 1.9 2.2
sample from entering them. This results in a stable Time (h)
injection-plug length of 100 m and an injection b
volume of approximately 0.36 nl. The sample plug is
injected into the separation channel and the voltages
are switched to create a field strength of 200 V cm 1
in the separation channel and approximately 20 V cm 1
in the load and sample channels. This bias generates a
well-defined plug entering the separation channel, with
no excess sample leakage from the side channels.
25 30 35 40
The field strength determines the migration speed Time (min)
within the device and influences the performance of
the sieving matrix. To optimize this parameter, the field c
strength is increased stepwise from 200 V cm 1 (typical
for capillary devices) to as high as 800 V cm 1. At high
trends in Biotechnology
field strengths, the resolution suffers because of factors
including field-induced orientation of the DNA and
matrix distortions. The strongest permissible field (i.e.
the field that maintains a resolution of R 1) depends
on the specific locus (i.e. its molecular length). 70 80 90 100 110 120
For field strengths below 600 V cm 1, the device and Time (sec)
sieving matrix exhibit excellent long-term stability.
Migration times increase by approximately 10% during Figure 2
ten consecutive runs, but the original migration time A comparison of three different DNA-analysis techniques. (a) A slab-
can be restored by reinjecting the gel–buffer system. In gel allelic assay of a single individual for the four-locus CTTv short-
addition, the accuracy of the allele assignment is not tandem-repeat system (4-bp repeats), with a run time of 2.2 h.
affected by small changes in migration time because an (b) An identical assay performed on a capillary system (run time
internal standard can be used for allele identification. 40 min). (c) The same sample run on a microdevice system9. The
No other changes in separation results are observed small peaks are an internal standard achieved by spiking the sam-
even after 20 consecutive runs without replacing the ple with a CTTv ladder composed of all common alleles [not added
gel–buffer system in STR experiments. Therefore, a to (a) or (b)]; run time 2 min. The microdevice run time represents
single microdevice can be used for allelic profiling for a speed increase of 20 over the capillary system and 70 over
prolonged periods and multiple applications with the the slab gel.
need for only periodic reinjection of the gel.
laries tend to load excessive sample and distort sample
DNA sequencing concentrations, leading to a more-complicated, non-
DNA sequencing applications require longer devices ideal performance. As a result, only a few matrix-related
than those used for genotyping8,9. The trade-off in assay parameters need to be measured for a microdevice
speed against required resolution and read length has before a general model can be developed. At the limit,
still to be defined over the full range of PAA sieving when injection and diffusion are the sole contributors
materials. Figure 3 shows data from a four-color detec- to peak width, the theoretical resolution Rt achievable
tor with a total read length of ~525 bases. The signal for two adjacent DNA sequencing fragments during an
remains strong throughout the separation, with an electrophoretic separation can be described by Eqn 29,
almost uniform signal to noise ratio of 50:1. Analy-
sis of such traces indicates that single-base resolution Rt [ L (sinj2 2Dt) 1/2] 4 (2)
can be achieved for 200 bases in 8 min, for 300 bases
in 11 min, for 400 bases in only 13 min and for where is the difference in the electrophoretic
525 bases in only 20 min. The same sequencing analy- mobilities of the two DNA fragments, is their aver-
sis, when performed at 400 V cm 1 under otherwise- age electrophoretic mobility, L is the effective sepa-
identical conditions, requires only 7 min and generates ration distance, sinj2 is the variance of the injected sample
a maximum read length of approximately 350 bases. plug, D is the longitudinal diffusion coefficient of the
fragments and t is the separation time. / is a meas-
Scaling considerations and the limits of ure of the selectivity of the separation process and
microelectrophoresis devices depends on the matrix type, fragment size and field
Microelectrophoresis devices can be operated in a strength. For DNA analyses, the essential point is that
nearly ideal regime and free of injection-related broad- D and / are dependent on the field strength,
ening factors. More-conventional slab gels and capil- owing to orientation or conformation changes of the
TIBTECH AUGUST 1999 (VOL 17) 317
4. NANOTECHNOLOGY
data up to a read length of approximately 500 bases
using a 11.5-cm-long device in 20 min or less (Fig. 3).
Somewhat better results and a longer read length will
be possible with very-well-adjusted base-calling software
(B. L. Karger et al., unpublished).
The application of these techniques to genotyping
requires the optimization of different parameters,
particularly for extremely fast separations; for example,
DNA fingerprinting using various 4-base-repeat STR
systems might be achieved in near-real time9. The prin-
cipal alleles from the first three loci of the CTTv STR
system should be resolved in less than 4 sec (4% PAA,
500 V cm 1, 10 m injector, 50 C) but requires an
optimized injector geometry.
Full automation
One of the most important needs for commercial
applications is the full automation of DNA sequenc-
ing. Current commercial technology requires a num-
ber of manual steps (e.g. pouring slab gels, loading
DNA samples), but important inroads are being made
with multicolumn capillaries14,15. Nevertheless, it is
anticipated that microfabricated devices will rapidly
become the format of choice for automated sequenc-
ing. Compared with capillary systems, the microfabri-
cated devices offer identical or improved performance,
bulk manufacture with automated equipment (i.e. no
manual assembly of columns) and the potential to
develop built-in interfaces to a precision robotic front
end (sample and gel loader) and detector (i.e. litho-
graphically defined tolerances at the fluid and data
interfaces of the multichannel device).
Massive parallelism
Given the compelling need for high sample through-
put in DNA sequencing, one obvious question is, how
many samples can be analysed simultaneously on one
system? Microfabrication per se will not be limiting for
many generations of devices, particularly because only
the simplest methods have been used to date. Robots
trends in Biotechnology can easily achieve the spatial resolution required and
should not be cost prohibitive. If a conventional CCD
Figure 3
large-field imaging detector was used, the pixels avail-
DNA sequencing results for a sample run on an electrophoresis
able in the array could limit the device to approximately
microdevice 11.5 cm long and containing a 3% linear polyacrylamide
200 lanes. However, the pixel count requirement ( 50
sieving matrix (molecular weight 6 000 000 Da) separated at
pixels per channel) is not demanding, opening the way
150 V cm 1 and 45 C. The analysis time required is only 20 min,
for the less-conventional use of imaging devices. More-
with 100% accuracy between 30 and 525 base pairs; between 525
over, a scanning detector is certainly capable of greater
and 570 bases, the accuracy decreases to 90%.
than 2000 channels. Consequently, microfabricated
devices of several thousand lanes or more are potentially
possible.
DNA fragments. These dependencies are difficult to
measure but are crucial to generating a predictive model. Conclusions
The greatest improvement in channel performance
Device length and assay speed using microdevices applies to assays such as genotyping,
Based on the measurement of the field-dependent which can take advantage of the unique practicality of
selectivity and lateral-diffusion coefficient8, the maxi- short devices in the new format, but longer sequenc-
mum read length can be predicted12 for a given PAA ing reads will require long devices. However, micro-
concentration, separation length, temperature and bias. fabricated devices have fewer single-channel performance
These calculations, however, require careful measure- advantages over capillary systems as the channel length
ment of field-dependent broadening, mainly anisotropic increases. Systems advantages such as interface compat-
diffusion of the DNA in the presence of a field. ibility, geometrical flexibility, microfluidics integration
Careful measurements of dynamic PAA-sieving per- and ease of device manufacture are all intrinsic to the
formance have only been made in a few cases12. A res- microfabricated format and are relevant to all highly
olution of R 0.5 results in high-quality separation multiplexed applications, even for long-channel systems.
318 TIBTECH AUGUST 1999 (VOL 17)