Metagenomics is the study of metagenome, genetics material, recovered directly from environmental sample such as soil, water or faeces.
Metagenomics is based on the genomics analysis of microbial DNA directly
from the communities present in samples
Metagenomics technology – genomics on a large scale will probably lead to great advances in medicine, agriculture, energy production and bioremediation.
Metagenomics can unlock the massive uncultured microbial diversity present in the environment for new molecule for therapeutic and biotechnological application.
Metagenomic studies have identified many novel microbial genes coding for metabolic pathways such as energy acquisition, carbon and nitrogen metabolism in natural environments that were previously considered to lack such metabolism
Shotgun metagenomics sequencing allows researchers to comprehensively sample all genes in organisms present in a complex sample without culturing. This provides insights into bacterial diversity, abundance, and uncultured microbes. Bioinformatics pipelines guide analysis including quality filtering, assembly, binning, gene finding, fingerprinting, and phylogeny/diversity modeling to understand communities. Metagenomics has applications in antibiotic/drug discovery, bioremediation, agriculture, human microbiome mapping, and more. Tools like QIIME, Mothur, MEGAN, and MG-RAST facilitate large-scale metagenomic analysis.
Metagenomics is the study of genetic material recovered directly from environmental samples. Metagenomics is a molecular tool used to analyse DNA acquired from environmental samples, in order to study the community of microorganisms present, without the necessity of obtaining pure cultures.
Metagenomics is the study of genetic material recovered directly from environmental samples without culturing. This field enables research on uncultured organisms and microbial communities. There are three main metagenomic approaches: biochemical, whole genome shotgun sequencing, and 16s rRNA sequencing. Metagenomics is being applied to study human microbiomes, discover new genes and enzymes, monitor environmental impacts, and characterize uncultured microbes. Future directions include identifying more novel products from uncultured bacteria and improving culture methods and bioinformatics tools.
Bacterial Identification by 16s rRNA Sequencing.pptRakesh Kumar
Bacteria are the most abundant life forms on Earth, with a single gram of soil containing 40 million bacterial cells. Most bacterial species have yet to be identified due to their abundance. DNA sequencing of the 16s rRNA gene is a common technique used to identify bacterial species. The process involves isolating bacteria from a sample, extracting DNA, amplifying and sequencing the 16s rRNA gene, and comparing the sequence to databases to identify matches. 16s rRNA gene sequencing provides a more accurate identification of bacteria than phenotypic methods.
This document discusses metagenomics, which is the study of genetic material recovered directly from environmental samples without culturing organisms. It outlines the difference between traditional genomics which studies one organism at a time in culture, versus metagenomics which sequences all DNA in a sample without culturing. The document then covers historical events in metagenomics, techniques used including direct DNA extraction and sequencing or function-based screening, applications such as discovering microbial diversity and novel enzymes, and future directions such as understanding human microbiomes and discovering novel pathways and organisms.
Comparative genomics involves comparing genomes to discover similarities and differences. It can provide insights into evolutionary relationships, help predict gene function, and aid in drug discovery. The first step is often aligning genome sequences using tools like BLAST or MUMmer. Genomes can then be compared at various levels, such as overall nucleotide statistics, genome structure, and coding/non-coding regions. Comparing gene and protein content across genomes helps predict functions. Conserved genomic features across species also aid prediction. Insights into genome evolution come from studying molecular events like inversions and duplications. Comparative genomics has impacted phylogenetics and drug target identification.
This document discusses the use of 16S ribosomal RNA (rRNA) gene sequencing for bacterial identification and phylogenetic analysis. It explains that the 16S rRNA gene is highly conserved, making it useful for comparing distantly related organisms. The document outlines the process of 16S rRNA gene sequencing, including PCR amplification using conserved primer regions and sequencing of variable regions. It also discusses various methods that have been developed using 16S rRNA, such as TRFLP profiling and ribotyping, to study microbial communities.
This document discusses yeast artificial chromosomes (YACs) and bacterial artificial chromosomes (BACs). YACs are engineered chromosomes derived from yeast DNA that can clone very large DNA sequences in yeast cells of up to 1 megabase. BACs are cloning vectors derived from bacterial DNA that can clone DNA fragments of up to 300 kilobases in E. coli. Both systems allow cloning and propagation of large DNA fragments, but YACs can hold more DNA while BACs are more stable and better for functional analysis in mammalian cells.
Shotgun metagenomics sequencing allows researchers to comprehensively sample all genes in organisms present in a complex sample without culturing. This provides insights into bacterial diversity, abundance, and uncultured microbes. Bioinformatics pipelines guide analysis including quality filtering, assembly, binning, gene finding, fingerprinting, and phylogeny/diversity modeling to understand communities. Metagenomics has applications in antibiotic/drug discovery, bioremediation, agriculture, human microbiome mapping, and more. Tools like QIIME, Mothur, MEGAN, and MG-RAST facilitate large-scale metagenomic analysis.
Metagenomics is the study of genetic material recovered directly from environmental samples. Metagenomics is a molecular tool used to analyse DNA acquired from environmental samples, in order to study the community of microorganisms present, without the necessity of obtaining pure cultures.
Metagenomics is the study of genetic material recovered directly from environmental samples without culturing. This field enables research on uncultured organisms and microbial communities. There are three main metagenomic approaches: biochemical, whole genome shotgun sequencing, and 16s rRNA sequencing. Metagenomics is being applied to study human microbiomes, discover new genes and enzymes, monitor environmental impacts, and characterize uncultured microbes. Future directions include identifying more novel products from uncultured bacteria and improving culture methods and bioinformatics tools.
Bacterial Identification by 16s rRNA Sequencing.pptRakesh Kumar
Bacteria are the most abundant life forms on Earth, with a single gram of soil containing 40 million bacterial cells. Most bacterial species have yet to be identified due to their abundance. DNA sequencing of the 16s rRNA gene is a common technique used to identify bacterial species. The process involves isolating bacteria from a sample, extracting DNA, amplifying and sequencing the 16s rRNA gene, and comparing the sequence to databases to identify matches. 16s rRNA gene sequencing provides a more accurate identification of bacteria than phenotypic methods.
This document discusses metagenomics, which is the study of genetic material recovered directly from environmental samples without culturing organisms. It outlines the difference between traditional genomics which studies one organism at a time in culture, versus metagenomics which sequences all DNA in a sample without culturing. The document then covers historical events in metagenomics, techniques used including direct DNA extraction and sequencing or function-based screening, applications such as discovering microbial diversity and novel enzymes, and future directions such as understanding human microbiomes and discovering novel pathways and organisms.
Comparative genomics involves comparing genomes to discover similarities and differences. It can provide insights into evolutionary relationships, help predict gene function, and aid in drug discovery. The first step is often aligning genome sequences using tools like BLAST or MUMmer. Genomes can then be compared at various levels, such as overall nucleotide statistics, genome structure, and coding/non-coding regions. Comparing gene and protein content across genomes helps predict functions. Conserved genomic features across species also aid prediction. Insights into genome evolution come from studying molecular events like inversions and duplications. Comparative genomics has impacted phylogenetics and drug target identification.
This document discusses the use of 16S ribosomal RNA (rRNA) gene sequencing for bacterial identification and phylogenetic analysis. It explains that the 16S rRNA gene is highly conserved, making it useful for comparing distantly related organisms. The document outlines the process of 16S rRNA gene sequencing, including PCR amplification using conserved primer regions and sequencing of variable regions. It also discusses various methods that have been developed using 16S rRNA, such as TRFLP profiling and ribotyping, to study microbial communities.
This document discusses yeast artificial chromosomes (YACs) and bacterial artificial chromosomes (BACs). YACs are engineered chromosomes derived from yeast DNA that can clone very large DNA sequences in yeast cells of up to 1 megabase. BACs are cloning vectors derived from bacterial DNA that can clone DNA fragments of up to 300 kilobases in E. coli. Both systems allow cloning and propagation of large DNA fragments, but YACs can hold more DNA while BACs are more stable and better for functional analysis in mammalian cells.
The document discusses genome sequencing and related topics. It begins by defining what a genome is - the complete set of DNA in an organism. It then discusses the different types of genomes, such as prokaryotic and eukaryotic, including nuclear, mitochondrial, and chloroplast genomes. The document also defines genomics as the comprehensive study of whole genomes and all gene interactions, distinguishing it from traditional genetics which focuses on single genes. It outlines some key milestones in genomic sequencing and the technical foundations that enabled sequencing whole genomes. Finally, it describes the main approaches used for genome sequencing projects, including hierarchical shotgun sequencing and whole genome shotgun sequencing.
Comparative genomics involves systematically comparing genome sequences from different organisms. It uses computer programs to identify homologous genomic regions and align sequences at the base-pair level. Comparing genomes at different phylogenetic distances can provide insights into gene structure/function, evolution, and characteristics unique to each organism. Key tools for comparative genomics include genome browsers, aligners, and databases that classify orthologous gene clusters conserved across species.
This document discusses the field of metagenomics, which involves directly extracting and sequencing genetic material from environmental samples without culturing individual microbial species. It provides a brief history of metagenomics from early microbiologists in the 17th century to recent large-scale sequencing projects. Methods of metagenomic analysis like sequence-driven and function-driven approaches are described. Applications to studying uncultured symbiotic microbes, extreme environments, and the human gut microbiome are also summarized.
FASTA is a bioinformatics tool and biological database that is used to compare amino acid sequences of proteins or nucleotide sequences of DNA. It was first described in 1985 by Lipman and Pearson. FASTA performs fast homology searches to find similarities between a query sequence and sequences in a database. While similar to BLAST, FASTA is faster for sequence comparisons. It works by identifying patches of sequence similarity that may contain gaps. Some key FASTA programs include FASTA, TFASTA, FASTS, and FASTX/Y. FASTA is useful for applications like identification of species, establishing phylogeny, DNA mapping, and understanding protein function.
Chromosome walking is a technique used to analyze large regions of DNA by identifying overlapping clones. It involves selecting a starting clone, subcloning fragments from the ends, and using those fragments to screen a genomic library and identify neighboring clones with overlapping sequences. This process is repeated to "walk" along the chromosome. Chromosome walking was developed in the 1980s and is useful for finding mutations associated with genetic diseases and detecting single nucleotide polymorphisms, though it has limitations with repetitive sequences.
Chromosome walking is a method used to isolate and clone a particular gene or allele through positional cloning. It involves using overlapping clones that contain DNA fragments near the target gene to "walk" through the chromosome until reaching the gene. Each successive clone is tested to map its precise location until eventually reaching the target gene. Chromosome walking was developed in the early 1980s and can be used to analyze genetically transmitted diseases and find single nucleotide polymorphisms. However, it has limitations such as being a slow process and difficulty walking through repeated sequences.
This document discusses different types of DNA libraries and methods for screening libraries to identify clones containing genes of interest. It describes genomic and cDNA libraries, noting that genomic libraries contain all DNA fragments from an organism's genome while cDNA libraries contain only coding sequences. The key screening methods discussed are colony/plaque hybridization using radiolabeled probes, expression screening using antibodies, and PCR screening using gene-specific primers.
This document discusses the history and various methods of DNA sequencing. It begins with a brief overview of DNA sequencing and its uses. It then outlines some of the major developments in DNA sequencing techniques, including the earliest RNA sequencing in 1972, Sanger sequencing in 1977, and the first complete genome of Haemophilus influenzae in 1995. The document proceeds to provide more detailed explanations of several DNA sequencing methods, such as Sanger sequencing, pyrosequencing, shotgun sequencing, Illumina sequencing, and SOLiD sequencing.
Lectut btn-202-ppt-l3. gene cloning and plasmid vectors (1)Rishabh Jain
The document discusses various types of plasmid vectors and cloning vectors used for gene cloning. It describes the key properties required for a vector, including autonomous replication, small size, selectable markers, and restriction enzyme sites. Some examples of early plasmid vectors discussed are pSC101, ColE1, and pBR322. Later vectors with improved properties include the pUC series, pGEM series, and pET series. A variety of other vector types were also constructed for different applications, such as bacteriophages, cosmids, YACs, BACs, and artificial chromosomes.
Automated sequencing of genomes require automated gene assignment
Includes detection of open reading frames (ORFs)
Identification of the introns and exons
Gene prediction a very difficult problem in pattern recognition
Coding regions generally do not have conserved sequences
Much progress made with prokaryotic gene prediction
Eukaryotic genes more difficult to predict correctly
A gene library is a large collection of DNA fragments cloned from an organism. It contains genomic DNA or cDNA sequences. Gene libraries are constructed using molecular tools like restriction enzymes and ligases to cut and paste DNA fragments into vectors such as plasmids, phages, or artificial chromosomes. The choice of vector depends on the size of the genome being cloned. Libraries allow screening to identify genes of interest through techniques like hybridization or expression screening. cDNA libraries contain only expressed sequences without introns, making them preferable for cloning eukaryotic genes in prokaryotes.
Expressed sequence tag (EST), molecular markerKAUSHAL SAHU
This document discusses expressed sequence tags (ESTs), which are short sequences of cDNA used to identify genes and study gene expression. It provides a brief history of ESTs, noting they were first coined in 1991. ESTs are generated by sequencing fragments of cDNA from mRNA. They provide a quick and inexpensive way to discover new genes and study transcriptomes. Large databases of ESTs exist that can be searched and mined for various applications, including gene discovery, similarity searching, and transcriptome analysis. Pre-processing and clustering/assembling tools are used to improve EST data quality.
This document discusses different expression systems for producing recombinant proteins, including prokaryotic, yeast, insect cell, and mammalian systems. It provides details on some commonly used expression vectors such as pGEX-3X plasmid for prokaryotic expression in E. coli, Saccharomyces cerevisiae and Pichia pastoris yeast expression systems using episomal and integrating plasmids, and baculovirus expression in insect cells using the polyhedrin promoter to drive expression of the gene of interest. The key advantages and limitations of different expression systems are also summarized.
BAC & YAC are artificially prepared chromosomes to clone DNA sequences.yeast artificial chromosome is capable of carrying upto 1000 kbp of inserted DNA sequence
TGGE is a technique used to separate DNA or proteins based on temperature gradients. It allows complex samples to be separated into distinct bands based on small sequence variations. The document discusses the methodology of TGGE, including gel casting and electrophoresis. Several case studies are presented where TGGE was used to analyze microbial communities in various environmental and food samples. The advantages of TGGE are its ability to analyze many samples simultaneously, detect unculturable microbes, and provide semi-quantitative data. Limitations include inability to separate all DNA fragments and potential for co-migration of bands. In conclusion, TGGE is a powerful tool for microbial community analysis when used along with traditional techniques.
After sequencing of the genome has been done, the first thing that comes to mind is "Where are the genes?". Genome annotation is the process of attaching information to the biological sequences. It is an active area of research and it would help scientists a lot to undergo with their wet lab projects once they know the coding parts of a genome.
Genome sequencing is the process of determining the order of nucleotide bases - A, C, G, and T - that make up an organism's DNA. Shotgun sequencing involves randomly breaking the genome into small fragments, sequencing those pieces, and reassembling the sequence by identifying overlapping regions. It was originally used by Sanger to sequence small genomes like viruses and bacteria. There are two main methods - hierarchical shotgun sequencing for larger genomes containing repeats, and whole genome shotgun sequencing for smaller genomes.
This document discusses sequence alignment methods. It describes global and local alignment, and algorithms used for alignment including dot matrix analysis, dynamic programming, and word/k-tuple methods as implemented in FASTA and BLAST programs. BLAST and FASTA are described as popular tools for sequence database searches that use heuristic methods and word matching to quickly identify regions of local similarity.
This document summarizes a seminar presentation on 2D electrophoresis. 2D electrophoresis is a technique used to separate mixed proteins based on their isoelectric point and mass. It involves two sequential electrophoretic steps: iso-electric focusing to separate proteins by charge, followed by SDS-PAGE to separate by molecular weight. The document describes the principles, methods, applications and references for 2D electrophoresis.
Metagenomics by microbiology dept. panjab university2018copydeepankarshashni
Metagenomics is the genomic analysis of microorganisms in an environmental sample without culturing. It allows researchers to study unculturable microbes by extracting DNA directly from samples and sequencing it. While metagenomics has advanced our understanding of microbial diversity, challenges remain in expressing genes from uncultured organisms in a surrogate host for functional screening.
The document discusses genome sequencing and related topics. It begins by defining what a genome is - the complete set of DNA in an organism. It then discusses the different types of genomes, such as prokaryotic and eukaryotic, including nuclear, mitochondrial, and chloroplast genomes. The document also defines genomics as the comprehensive study of whole genomes and all gene interactions, distinguishing it from traditional genetics which focuses on single genes. It outlines some key milestones in genomic sequencing and the technical foundations that enabled sequencing whole genomes. Finally, it describes the main approaches used for genome sequencing projects, including hierarchical shotgun sequencing and whole genome shotgun sequencing.
Comparative genomics involves systematically comparing genome sequences from different organisms. It uses computer programs to identify homologous genomic regions and align sequences at the base-pair level. Comparing genomes at different phylogenetic distances can provide insights into gene structure/function, evolution, and characteristics unique to each organism. Key tools for comparative genomics include genome browsers, aligners, and databases that classify orthologous gene clusters conserved across species.
This document discusses the field of metagenomics, which involves directly extracting and sequencing genetic material from environmental samples without culturing individual microbial species. It provides a brief history of metagenomics from early microbiologists in the 17th century to recent large-scale sequencing projects. Methods of metagenomic analysis like sequence-driven and function-driven approaches are described. Applications to studying uncultured symbiotic microbes, extreme environments, and the human gut microbiome are also summarized.
FASTA is a bioinformatics tool and biological database that is used to compare amino acid sequences of proteins or nucleotide sequences of DNA. It was first described in 1985 by Lipman and Pearson. FASTA performs fast homology searches to find similarities between a query sequence and sequences in a database. While similar to BLAST, FASTA is faster for sequence comparisons. It works by identifying patches of sequence similarity that may contain gaps. Some key FASTA programs include FASTA, TFASTA, FASTS, and FASTX/Y. FASTA is useful for applications like identification of species, establishing phylogeny, DNA mapping, and understanding protein function.
Chromosome walking is a technique used to analyze large regions of DNA by identifying overlapping clones. It involves selecting a starting clone, subcloning fragments from the ends, and using those fragments to screen a genomic library and identify neighboring clones with overlapping sequences. This process is repeated to "walk" along the chromosome. Chromosome walking was developed in the 1980s and is useful for finding mutations associated with genetic diseases and detecting single nucleotide polymorphisms, though it has limitations with repetitive sequences.
Chromosome walking is a method used to isolate and clone a particular gene or allele through positional cloning. It involves using overlapping clones that contain DNA fragments near the target gene to "walk" through the chromosome until reaching the gene. Each successive clone is tested to map its precise location until eventually reaching the target gene. Chromosome walking was developed in the early 1980s and can be used to analyze genetically transmitted diseases and find single nucleotide polymorphisms. However, it has limitations such as being a slow process and difficulty walking through repeated sequences.
This document discusses different types of DNA libraries and methods for screening libraries to identify clones containing genes of interest. It describes genomic and cDNA libraries, noting that genomic libraries contain all DNA fragments from an organism's genome while cDNA libraries contain only coding sequences. The key screening methods discussed are colony/plaque hybridization using radiolabeled probes, expression screening using antibodies, and PCR screening using gene-specific primers.
This document discusses the history and various methods of DNA sequencing. It begins with a brief overview of DNA sequencing and its uses. It then outlines some of the major developments in DNA sequencing techniques, including the earliest RNA sequencing in 1972, Sanger sequencing in 1977, and the first complete genome of Haemophilus influenzae in 1995. The document proceeds to provide more detailed explanations of several DNA sequencing methods, such as Sanger sequencing, pyrosequencing, shotgun sequencing, Illumina sequencing, and SOLiD sequencing.
Lectut btn-202-ppt-l3. gene cloning and plasmid vectors (1)Rishabh Jain
The document discusses various types of plasmid vectors and cloning vectors used for gene cloning. It describes the key properties required for a vector, including autonomous replication, small size, selectable markers, and restriction enzyme sites. Some examples of early plasmid vectors discussed are pSC101, ColE1, and pBR322. Later vectors with improved properties include the pUC series, pGEM series, and pET series. A variety of other vector types were also constructed for different applications, such as bacteriophages, cosmids, YACs, BACs, and artificial chromosomes.
Automated sequencing of genomes require automated gene assignment
Includes detection of open reading frames (ORFs)
Identification of the introns and exons
Gene prediction a very difficult problem in pattern recognition
Coding regions generally do not have conserved sequences
Much progress made with prokaryotic gene prediction
Eukaryotic genes more difficult to predict correctly
A gene library is a large collection of DNA fragments cloned from an organism. It contains genomic DNA or cDNA sequences. Gene libraries are constructed using molecular tools like restriction enzymes and ligases to cut and paste DNA fragments into vectors such as plasmids, phages, or artificial chromosomes. The choice of vector depends on the size of the genome being cloned. Libraries allow screening to identify genes of interest through techniques like hybridization or expression screening. cDNA libraries contain only expressed sequences without introns, making them preferable for cloning eukaryotic genes in prokaryotes.
Expressed sequence tag (EST), molecular markerKAUSHAL SAHU
This document discusses expressed sequence tags (ESTs), which are short sequences of cDNA used to identify genes and study gene expression. It provides a brief history of ESTs, noting they were first coined in 1991. ESTs are generated by sequencing fragments of cDNA from mRNA. They provide a quick and inexpensive way to discover new genes and study transcriptomes. Large databases of ESTs exist that can be searched and mined for various applications, including gene discovery, similarity searching, and transcriptome analysis. Pre-processing and clustering/assembling tools are used to improve EST data quality.
This document discusses different expression systems for producing recombinant proteins, including prokaryotic, yeast, insect cell, and mammalian systems. It provides details on some commonly used expression vectors such as pGEX-3X plasmid for prokaryotic expression in E. coli, Saccharomyces cerevisiae and Pichia pastoris yeast expression systems using episomal and integrating plasmids, and baculovirus expression in insect cells using the polyhedrin promoter to drive expression of the gene of interest. The key advantages and limitations of different expression systems are also summarized.
BAC & YAC are artificially prepared chromosomes to clone DNA sequences.yeast artificial chromosome is capable of carrying upto 1000 kbp of inserted DNA sequence
TGGE is a technique used to separate DNA or proteins based on temperature gradients. It allows complex samples to be separated into distinct bands based on small sequence variations. The document discusses the methodology of TGGE, including gel casting and electrophoresis. Several case studies are presented where TGGE was used to analyze microbial communities in various environmental and food samples. The advantages of TGGE are its ability to analyze many samples simultaneously, detect unculturable microbes, and provide semi-quantitative data. Limitations include inability to separate all DNA fragments and potential for co-migration of bands. In conclusion, TGGE is a powerful tool for microbial community analysis when used along with traditional techniques.
After sequencing of the genome has been done, the first thing that comes to mind is "Where are the genes?". Genome annotation is the process of attaching information to the biological sequences. It is an active area of research and it would help scientists a lot to undergo with their wet lab projects once they know the coding parts of a genome.
Genome sequencing is the process of determining the order of nucleotide bases - A, C, G, and T - that make up an organism's DNA. Shotgun sequencing involves randomly breaking the genome into small fragments, sequencing those pieces, and reassembling the sequence by identifying overlapping regions. It was originally used by Sanger to sequence small genomes like viruses and bacteria. There are two main methods - hierarchical shotgun sequencing for larger genomes containing repeats, and whole genome shotgun sequencing for smaller genomes.
This document discusses sequence alignment methods. It describes global and local alignment, and algorithms used for alignment including dot matrix analysis, dynamic programming, and word/k-tuple methods as implemented in FASTA and BLAST programs. BLAST and FASTA are described as popular tools for sequence database searches that use heuristic methods and word matching to quickly identify regions of local similarity.
This document summarizes a seminar presentation on 2D electrophoresis. 2D electrophoresis is a technique used to separate mixed proteins based on their isoelectric point and mass. It involves two sequential electrophoretic steps: iso-electric focusing to separate proteins by charge, followed by SDS-PAGE to separate by molecular weight. The document describes the principles, methods, applications and references for 2D electrophoresis.
Metagenomics by microbiology dept. panjab university2018copydeepankarshashni
Metagenomics is the genomic analysis of microorganisms in an environmental sample without culturing. It allows researchers to study unculturable microbes by extracting DNA directly from samples and sequencing it. While metagenomics has advanced our understanding of microbial diversity, challenges remain in expressing genes from uncultured organisms in a surrogate host for functional screening.
This document discusses metagenomics and its applications in bioremediation. It begins by defining bioremediation as using biological entities like microorganisms to clean up pollution. It then explains that metagenomics uses genetic material directly extracted from environments to analyze culturable and non-culturable microorganisms. Metagenomics seeks to identify genes involved in bioremediation to better understand microbial diversity and activities in polluted environments to improve bioremediation processes. Bioinformatics plays an important role in analyzing the large amounts of metagenomic data generated.
This document provides an overview of modern genetics. It begins by defining genetics as the study of heredity and genes. It describes Gregor Mendel's foundational work in genetics and how his work led to the modern understanding of genes and inheritance being controlled by DNA. Key experiments that established DNA as the genetic material, such as Griffith's transformation experiment and Hershey and Chase's experiment, are summarized. The central dogma of biology involving DNA replication, transcription of DNA to mRNA, and translation of mRNA to proteins is explained at a high level. Concepts covered include DNA and RNA structure, mutation, genetic engineering techniques like recombinant DNA, and applications to medical genetics research.
Metagenomics is the study of genetic material recovered directly from environmental samples. It provides a new approach to studying microbes that are not easily cultured in a laboratory and enables investigation of microbial communities in their natural habitats. Metagenomics involves directly extracting DNA from samples, sequencing it, and analyzing the genetic information obtained from entire communities of organisms simultaneously. This provides insights into uncultured microbes and their roles in various environments.
M Pharm Pharmacognosy Semester 2, MEDICINAL PLANT BIOTECHNOLOGY UNIT 1, Introduction to Plant biotechnology: Historical perspectives, prospects for development of plant biotechnology as a source of
medicinal agents. Applications in pharmacy and allied fields. Genetic and molecular biology as applied to pharmacognosy, study of DNA, RNA and protein replication, genetic code, regulation of gene expression, structure and complicity of
genome, cell signaling, DNA recombinant technology.
This slide lecture is for students seeking help regarding Metagenomics. Do remember me in your prayers.
Metagenomics Applications, Metagenomics working principles , Metagenomic libraries
, Metagenomic Techniques , Metagenomics limitations and other topics are elaborated in this Slideshare.
This document provides an overview of genomics, including its history, major research areas, and applications. Genomics is concerned with studying the genomes of organisms, including determining entire DNA sequences and genetic mapping. Major research areas discussed include bacteriophage, human, computational, and comparative genomics. Applications of genomics discussed include functional genomics, predictive medicine, metagenomics for medicine, biofuels and more. The first genomes sequenced were small viruses and mitochondria, while the human genome project aimed to map the entire human DNA sequence.
The document summarizes key aspects of the human genome and genome projects. It discusses that a genome contains an organism's complete DNA including all genes. It describes the physical structure of human DNA including nuclear DNA, mitochondrial DNA, and RNA. It provides details on the goals and completion of the Human Genome Project in 2003, two years ahead of schedule. The project aimed to identify all human genes and map the 3 billion base pairs of human DNA.
Metagenomics is the study of genetic material recovered directly from environmental samples without culturing organisms. It allows researchers to study the 99.9% of microorganisms that cannot be cultured. Metagenomic analyses of ocean samples revealed over a million new genes and unexpected light-energy pathways in bacteria. Metagenomics has two main approaches - sequence-driven which sequences DNA and compares to databases, and function-driven which screens DNA clones for a desired function. Both approaches have limitations but are complementary. Metagenomics has applications in discovering new antibiotics and enzymes and studying human microbiomes and antibiotic resistance.
The transformational role of polymerase chain reaction (pcr) in environmental...Alexander Decker
This document discusses the transformational role of polymerase chain reaction (PCR) in environmental health research. PCR allows for exponential amplification of target DNA sequences, which has enabled rapid and sensitive detection of pathogens in environmental samples as an alternative to traditional culture methods. While PCR is widely used in developed countries, its benefits have yet to be fully realized in developing countries like Nigeria. The document provides background on DNA replication and the basics of how PCR works to exponentially amplify DNA. It argues that PCR could greatly aid environmental health monitoring and disease diagnosis in Nigeria.
Describe in your own words the benefits, but also the problems of ha.pdfarenamobiles123
Describe in your own words the benefits, but also the problems of having the human genome
deciphered. Write several paragraphs.
Solution
The history of the human race has been filled with curiosity and discovery about our abilities and
limitations. As an egotistical creature with a seemingly unstoppable desire for new
accomplishments, we attempt feats with emotion and tenacity. People worldwide raced to be the
first to discover the secrets and the ability of flight. Enormous amounts of monies were spent on
sending people into space and the race to land on the moon. With the rapid growth of scientific
knowledge and experimental methods, humans have begun to unravel and challenge another
mystery, the discovery of the entire genetic make-up of the human body.
This endeavor, the Human Genome Project (HGP), has created hopes and expectations about
better health care. It has also brought forth serious social issues. To understand the potential
positive and negative issues, we must first understand the history and technical aspects of the
HGP.
History of the Human Genome Project
The HGP has an ultimate goal of identifying and locating the positions of all genes in the human
body. A researcher named Renato Dulbecco first suggested the idea of such a project while the
U.S. Department of Energy (DOE) was also considering the same project because issues related
to radiation and chemical exposure were being raised. Military and civilian populations were
being exposed to radiation and possible carcinogenic chemicals through atomic testing, the use
of Agent Orange in Vietnam, and possible nuclear power facility accidents. Genetic knowledge
was needed to determine the resiliency of the human genome.
Worldwide discussion about a HGP began in 1985. In 1986, the DOE announced its\' Human
Genome Initiative which emphasized the development of resources and technologies for genome
mapping, sequencing, computation, and infrastructure support that would lead to the entire
human genome map. United States involvement began in October 1990 and was coordinated by
the DOE and the National Institute of Health (NIH). With an estimated cost of 3 billion dollars,
sources of funding also include the National Science Foundation (NSF) and the Howard Hughes
Medical Institute (HHMI). Because of the involvement of the NIH, DOE, and NSF who receive
U.S. Congressional funding, the HGP is partly funded through federal tax dollars. Expected to
last 15 years, technological advancements have accelerated the expected date of completion to
the year 2003. This completion date would coincide with the 50th anniversary of Watson and
Crick\'s description of the structure of DNA molecule.
Human Genome Project Goals
The specific goals of the HGP are to::
Technical Aspects of the HGP
Mapping Strategies
To sequence the human genome, maps are needed. Physical maps are a series of overlapping
pieces of DNA isolated in bacteria. Physical maps are used to describe the DNA\'s chemical
characteristics..
This document summarizes key concepts from Chapter 20 of an AP Biology textbook. It discusses several topics:
1) Genomics is the study of genomes and how they are organized and regulated. Genome sequences provide insights into fundamental biological questions.
2) Computer analysis can identify protein-coding genes in DNA sequences by looking for start/stop signals and other features. With 25,000 genes in humans, this analysis is a huge undertaking without technology.
3) Genome sizes vary greatly between organisms, but size does not always correlate with complexity. Some plants have genomes much larger than humans despite fewer genes.
This document provides information about a lecture series on methods in molecular biology. The course is titled "Methods in Molecular Biology" and is worth 3 credit hours. It will be taught by Dr. Sumera Shaheen in the department of biochemistry at Govt. College Women University Faisalabad. The lectures will cover topics such as recombinant DNA technology, vectors, PCR, DNA sequencing, gel electrophoresis, expression of recombinant proteins, antibodies, and blotting techniques. Recommended textbooks for the course are also listed.
B.sc. agri i pog unit 1 introduction to geneticsRai University
The document provides an overview of genetics principles including:
1) DNA serves as the repository for genetic information in cells and replicates through a complex process to minimize errors. The flow of information goes from DNA to RNA to protein.
2) Early experiments by Griffith, Avery, MacLeod, and McCarty demonstrated that DNA carries genetic information by showing it was responsible for bacterial transformation. Further work by Hershey and Chase using bacteriophage showed that viral DNA, not protein, entered host cells to direct new virus production.
3) The relationships between DNA, RNA, and protein were established as the central dogma of molecular biology, where DNA is transcribed into RNA which is then translated into protein
Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, a...Jonathan Eisen
This document describes research into using metagenomic data to search for novel lineages in the tree of life. The researchers developed methods to search for deeply branching small subunit rRNA genes in Global Ocean Sampling data, but were unable to robustly identify any novel lineages due to difficulties aligning short, distantly related sequences. They had more success identifying novel branches in the RecA and RpoB gene families. Some novel sequences likely come from unknown viruses or ancient paralogs, while others may represent truly novel cellular lineages not previously characterized. Metagenomic analysis offers potential for discovering major undiscovered branches in the tree of life.
“I think the biggest innovations of the 21st century will be at the intersection of biology and technology. A new era is beginning.” — Steve Jobs
While analyzing the effects of radio frequency heating on hypothermia in the year 1941, Canadian electrical engineer John Hopps read that if the heart stops beating due to an acute drop in temperature, it could successfully be brought back to life artificially using mechanical or electrical stimulation.
This document provides an overview of bioinformatics and genomics. It begins with an acknowledgement and abstract section. The introduction defines bioinformatics and its role in analyzing genetic sequences and biological data through computational methods. Major research areas of bioinformatics discussed include sequence analysis, genome annotation, evolutionary biology, measuring biodiversity, gene expression analysis, protein analysis, cancer mutation analysis, and protein structure prediction. Comparative genomics and modeling biological systems are also summarized. The document concludes with a definition of genomics as the study of genomes through sequencing efforts and mapping genetic interactions.
The basic food law is intended to assure consumers that foods are pure and wholesome, safe to eat, and produced under sanitary conditions. Generally, food law prohibits importation and distribution of food products that are adulterated, or have labels that are false or misleading in any context.
Soil and water conditions. ...
Keep an eye on the forecast for heavy rainfall events. ...
Calibrate, inspect, and maintain manure application equipment. ...
Separation distances for land application. ...
Irrigation of manure sources. ...
Savvy stockpiling and dry manure management.
Based on the mode of action, the major food preservation techniques can be categorized as: (1) slowing down or inhibiting chemical deterioration and microbial growth, (2) directly inactivating bacteria, yeasts, molds, or enzymes, and (3) avoiding recontamination before and after processing.
Food processing waste is derived from the processing of biological materials and is, in the main, biodegradable. Biowaste is defined in the landfill directive as 'waste capable of undergoing anaerobic or aerobic decomposition such as food and garden waste, and paper and cardboard
Water plays a key role in food processing and has various scientific uses. It acts as a solvent, carrier, and lubricant in processes like washing, leaching, extraction, and cooling. Proper management and treatment of water is important for food safety and quality in processing plants.
The environmental damage of food production from conventional agriculture is not limited to deforestation and pollutants associated with crop growth. Harvesting the crop represents a significant amount of nutrients, water, and energy being taken from the land.
The basis for sanitation is the removal of soils from the manufacturing environment. There are many benefits to this process. From a food safety standpoint, there is the removal of pathogenic organisms, prevention of the formation of biofilms and removal of potentially harmful chemicals from food contact surfaces.
Food packaging is defined as enclosing food to protect it from tampering or contamination from physical, chemical, and biological sources, with active packaging being the most common packaging system used for preserving food products.
Sugar, salt, nitrites, butylated hydroxy anisol (BHA), butylated hydroxyl toluene (BHT), tert-butylhydroquinone (TBHQ), vinegar, citric acid, and calcium propionate are all chemicals that preserve foods. Salt, sodium nitrite, spices, vinegar, and alcohol have been used to preserve foods for centuries.
Sugaring is a food preservation method similar to pickling. Sugaring is the process of desiccating a food by first dehydrating it, then packing it with pure sugar. This sugar can be crystalline in the form of table or raw sugar, or it can be a high sugar density liquid such as honey, syrup or molasses.
Removing the moisture from food helps prevent bacterial and fungal growth which would ruin stored foods. Smoking is a method of drying that also imparts flavor to the food (usually meat items), and smoke helps keep bacteria-carrying-insects away during the drying process.
Microwave penetrates inside the food materials resulting in entire internal cooking of whole volume of food rapidly and uniformly reducing the processing time and energy. This fast heat transfer in turn results in preservation of nutrients, vitamins contents, flavor, sensory characteristics, and color of food
Food irradiation (the application of ionizing radiation to food) is a technology that improves the safety and extends the shelf life of foods by reducing or eliminating microorganisms and insects. Like pasteurizing milk and canning fruits and vegetables, irradiation can make food safer for the consumer
Food irradiation is the process of exposing food and food packaging to ionizing radiation, such as from gamma rays, x-rays, or electron beams. Wikipedia
Low dose (up to 1 kGy): Inhibit sprouting (potatoes, onions, yams, garlic)
Lowering the temperature of food so that microbes and enzymes are inactivated.
Moisture is changed to ice and microbes become inactive without water.
Packaging food maintains the colour, flavour and texture.
Fast freezing (-25ºC) helps maintain nutritive value and texture of food.
Chilling is an important activity in food processing. Foods are chilled to extend shelf life by reducing biochemical reactions and microbial activity. Temperature control is essential in order to prevent spoilage and food safety concerns during storage.1
Drying is a mass transfer process consisting of the removal of water or another solvent by evaporation from a solid, semi-solid or liquid. This process is often used as a final production step before selling or packaging products.
Food drying is a method of food preservation in which food is dried (dehydrated or desiccated). Drying inhibits the growth of bacteria, yeasts, and mold through the removal of water.
Dehydration has been used widely for this purpose since ancient times; the earliest known practice is 12,000 B.C. by inhabitants of the modern Middle East and Asia regions. Drying is a simple method for preserving food.
Dried foods make great healthy and tasty snacks. They are good for lunches, travel, backpacking, hiking, and camping plus many other activities. Most types of foods can be dried. Drying is an ancient method of food preservation.
Most foods will not support the growth of bacteria if their water activity is less than 0.85, because at this water activity there is not enough water available for the bacteria to grow.
However, yeasts can grow at water activities as low as 0.70, while some molds will grow even at water activities as low as 0.60!
Foods with water activities in this range usually have preservatives added to prevent the growth of yeasts and molds.
Acidic foods with a pH less than 4.6, such as tomato sauce, retard the growth of microorganisms. Thus an acidic food with a water activity less than 0.85 is relatively shelf stable, especially if it is stored in the refrigerator.
In this case, low pH, water activity and temperature combine to provide good insurance against the growth of harmful pathogens.
Sorption is a physical and chemical process by which one substance becomes attached to another.
Sorption includes both adsorption & absorption
e.g., liquids being absorbed by a solid or gases being absorbed by a liquid, cotton dipped in ink.
Sorption the process in which one substance takes up or holds another; adsorption or absorption
Sorption is a process in which a solute moves from a fluid to a particulate solid.
The food sorption isotherm describes the thermodynamic relationship between water activity and the equilibrium of the moisture content of a food product at constant temperature and pressure. ...
The typical shape of an isotherm reflects the way in which the water binds the system.
Water plays many very important roles in food. It affects texture (dry and brittle versus moist and soft), enables the activity of enzymes and chemical reactions to occur (acts as a solvent), supports the growth of microorganisms, makes it possible for large molecules like polysaccharides and proteins to move about and interact, and conducts heat within food.
Many foods such as meat, poultry, seafood, fruits and vegetables are composed of 75% and more water, so water is the most abundant component in many fresh foods. Other foods such as dairy products, and fresh baked goods also contain high levels of water (about 35% or more). Foods that are high in moisture are at
risk of contamination from the growth of microorganisms such as bacteria, yeast and mold, while dry foods like pasta generally have long shelf lives.
The Microsoft 365 Migration Tutorial For Beginner.pptxoperationspcvita
This presentation will help you understand the power of Microsoft 365. However, we have mentioned every productivity app included in Office 365. Additionally, we have suggested the migration situation related to Office 365 and how we can help you.
You can also read: https://www.systoolsgroup.com/updates/office-365-tenant-to-tenant-migration-step-by-step-complete-guide/
Ivanti’s Patch Tuesday breakdown goes beyond patching your applications and brings you the intelligence and guidance needed to prioritize where to focus your attention first. Catch early analysis on our Ivanti blog, then join industry expert Chris Goettl for the Patch Tuesday Webinar Event. There we’ll do a deep dive into each of the bulletins and give guidance on the risks associated with the newly-identified vulnerabilities.
AppSec PNW: Android and iOS Application Security with MobSFAjin Abraham
Mobile Security Framework - MobSF is a free and open source automated mobile application security testing environment designed to help security engineers, researchers, developers, and penetration testers to identify security vulnerabilities, malicious behaviours and privacy concerns in mobile applications using static and dynamic analysis. It supports all the popular mobile application binaries and source code formats built for Android and iOS devices. In addition to automated security assessment, it also offers an interactive testing environment to build and execute scenario based test/fuzz cases against the application.
This talk covers:
Using MobSF for static analysis of mobile applications.
Interactive dynamic security assessment of Android and iOS applications.
Solving Mobile app CTF challenges.
Reverse engineering and runtime analysis of Mobile malware.
How to shift left and integrate MobSF/mobsfscan SAST and DAST in your build pipeline.
Northern Engraving | Nameplate Manufacturing Process - 2024Northern Engraving
Manufacturing custom quality metal nameplates and badges involves several standard operations. Processes include sheet prep, lithography, screening, coating, punch press and inspection. All decoration is completed in the flat sheet with adhesive and tooling operations following. The possibilities for creating unique durable nameplates are endless. How will you create your brand identity? We can help!
Skybuffer SAM4U tool for SAP license adoptionTatiana Kojar
Manage and optimize your license adoption and consumption with SAM4U, an SAP free customer software asset management tool.
SAM4U, an SAP complimentary software asset management tool for customers, delivers a detailed and well-structured overview of license inventory and usage with a user-friendly interface. We offer a hosted, cost-effective, and performance-optimized SAM4U setup in the Skybuffer Cloud environment. You retain ownership of the system and data, while we manage the ABAP 7.58 infrastructure, ensuring fixed Total Cost of Ownership (TCO) and exceptional services through the SAP Fiori interface.
For the full video of this presentation, please visit: https://www.edge-ai-vision.com/2024/06/temporal-event-neural-networks-a-more-efficient-alternative-to-the-transformer-a-presentation-from-brainchip/
Chris Jones, Director of Product Management at BrainChip , presents the “Temporal Event Neural Networks: A More Efficient Alternative to the Transformer” tutorial at the May 2024 Embedded Vision Summit.
The expansion of AI services necessitates enhanced computational capabilities on edge devices. Temporal Event Neural Networks (TENNs), developed by BrainChip, represent a novel and highly efficient state-space network. TENNs demonstrate exceptional proficiency in handling multi-dimensional streaming data, facilitating advancements in object detection, action recognition, speech enhancement and language model/sequence generation. Through the utilization of polynomial-based continuous convolutions, TENNs streamline models, expedite training processes and significantly diminish memory requirements, achieving notable reductions of up to 50x in parameters and 5,000x in energy consumption compared to prevailing methodologies like transformers.
Integration with BrainChip’s Akida neuromorphic hardware IP further enhances TENNs’ capabilities, enabling the realization of highly capable, portable and passively cooled edge devices. This presentation delves into the technical innovations underlying TENNs, presents real-world benchmarks, and elucidates how this cutting-edge approach is positioned to revolutionize edge AI across diverse applications.
Taking AI to the Next Level in Manufacturing.pdfssuserfac0301
Read Taking AI to the Next Level in Manufacturing to gain insights on AI adoption in the manufacturing industry, such as:
1. How quickly AI is being implemented in manufacturing.
2. Which barriers stand in the way of AI adoption.
3. How data quality and governance form the backbone of AI.
4. Organizational processes and structures that may inhibit effective AI adoption.
6. Ideas and approaches to help build your organization's AI strategy.
How information systems are built or acquired puts information, which is what they should be about, in a secondary place. Our language adapted accordingly, and we no longer talk about information systems but applications. Applications evolved in a way to break data into diverse fragments, tightly coupled with applications and expensive to integrate. The result is technical debt, which is re-paid by taking even bigger "loans", resulting in an ever-increasing technical debt. Software engineering and procurement practices work in sync with market forces to maintain this trend. This talk demonstrates how natural this situation is. The question is: can something be done to reverse the trend?
HCL Notes and Domino License Cost Reduction in the World of DLAUpanagenda
Webinar Recording: https://www.panagenda.com/webinars/hcl-notes-and-domino-license-cost-reduction-in-the-world-of-dlau/
The introduction of DLAU and the CCB & CCX licensing model caused quite a stir in the HCL community. As a Notes and Domino customer, you may have faced challenges with unexpected user counts and license costs. You probably have questions on how this new licensing approach works and how to benefit from it. Most importantly, you likely have budget constraints and want to save money where possible. Don’t worry, we can help with all of this!
We’ll show you how to fix common misconfigurations that cause higher-than-expected user counts, and how to identify accounts which you can deactivate to save money. There are also frequent patterns that can cause unnecessary cost, like using a person document instead of a mail-in for shared mailboxes. We’ll provide examples and solutions for those as well. And naturally we’ll explain the new licensing model.
Join HCL Ambassador Marc Thomas in this webinar with a special guest appearance from Franz Walder. It will give you the tools and know-how to stay on top of what is going on with Domino licensing. You will be able lower your cost through an optimized configuration and keep it low going forward.
These topics will be covered
- Reducing license cost by finding and fixing misconfigurations and superfluous accounts
- How do CCB and CCX licenses really work?
- Understanding the DLAU tool and how to best utilize it
- Tips for common problem areas, like team mailboxes, functional/test users, etc
- Practical examples and best practices to implement right away
Main news related to the CCS TSI 2023 (2023/1695)Jakub Marek
An English 🇬🇧 translation of a presentation to the speech I gave about the main changes brought by CCS TSI 2023 at the biggest Czech conference on Communications and signalling systems on Railways, which was held in Clarion Hotel Olomouc from 7th to 9th November 2023 (konferenceszt.cz). Attended by around 500 participants and 200 on-line followers.
The original Czech 🇨🇿 version of the presentation can be found here: https://www.slideshare.net/slideshow/hlavni-novinky-souvisejici-s-ccs-tsi-2023-2023-1695/269688092 .
The videorecording (in Czech) from the presentation is available here: https://youtu.be/WzjJWm4IyPk?si=SImb06tuXGb30BEH .
What is an RPA CoE? Session 1 – CoE VisionDianaGray10
In the first session, we will review the organization's vision and how this has an impact on the COE Structure.
Topics covered:
• The role of a steering committee
• How do the organization’s priorities determine CoE Structure?
Speaker:
Chris Bolin, Senior Intelligent Automation Architect Anika Systems
Introduction of Cybersecurity with OSS at Code Europe 2024Hiroshi SHIBATA
I develop the Ruby programming language, RubyGems, and Bundler, which are package managers for Ruby. Today, I will introduce how to enhance the security of your application using open-source software (OSS) examples from Ruby and RubyGems.
The first topic is CVE (Common Vulnerabilities and Exposures). I have published CVEs many times. But what exactly is a CVE? I'll provide a basic understanding of CVEs and explain how to detect and handle vulnerabilities in OSS.
Next, let's discuss package managers. Package managers play a critical role in the OSS ecosystem. I'll explain how to manage library dependencies in your application.
I'll share insights into how the Ruby and RubyGems core team works to keep our ecosystem safe. By the end of this talk, you'll have a better understanding of how to safeguard your code.
Generating privacy-protected synthetic data using Secludy and MilvusZilliz
During this demo, the founders of Secludy will demonstrate how their system utilizes Milvus to store and manipulate embeddings for generating privacy-protected synthetic data. Their approach not only maintains the confidentiality of the original data but also enhances the utility and scalability of LLMs under privacy constraints. Attendees, including machine learning engineers, data scientists, and data managers, will witness first-hand how Secludy's integration with Milvus empowers organizations to harness the power of LLMs securely and efficiently.
2. o The term metagenomics first used by Jo
Handelsman, Jon Clarly, Robert M.
Goodman and first appeared in
publication in 1998.
o Metagenomics defined as “the genomics
analysis of microorganism by direct
extraction and cloning DNA from an
assemblage of microorganism.”
o In Greek, meta means “transcendent”
(combination of separate analysis)
Genomics refers to the study of
the genome
Jo Handelsman
3. Metagenomics is the study of metagenome, genetics material, recovered
directly from environmental sample such as soil, water or faeces.
Metagenomics is based on the genomics analysis of microbial DNA directly
from the communities present in samples
Metagenomics technology – genomics on a large scale will probably lead to
great advances in medicine, agriculture, energy production and bioremediation.
Metagenomics can unlock the massive uncultured microbial diversity present in
the environment for new molecule for therapeutic and biotechnological
application.
Metagenomic studies have identified many novel microbial genes coding for
metabolic pathways such as energy acquisition, carbon and nitrogen
metabolism in natural environments that were previously considered to lack
such metabolism
4. The science of metagenomics, only a few years old, will make it
possible to investigate microbes in their natural environments, the
complex communities in which they normally live.
It will bring about a transformation in biology, medicine, ecology, and
biotechnology that may be as profound as that initiated by the invention
of the microscope.
All plants and animals have closely associated microbial communities
that make necessary nutrients(carbon, nitrogen, oxygen, and sulfur)
metals, and vitamins available to their hosts.
We depend on microbes to remediate toxins in the environment—both
the ones that are produced naturally and the ones that are the byproducts
of human activities, such as oil and chemical spills.
5. In 1985 Pace and coworker introduced the idea a cloning DNA
directly from environmental samples.
In 1991 Schmidt and coworker cloning of DNA from
Picoplankton in a phase vector subsequent 16S rRNA gene
sequence analyses.
In 1995, Healy reported first successful function driven
metagenomics library was screened and termed that Zoolibraies.
In 2002, Mya Breitbart and Forest Rohwer, used shotgun
sequencing to show that 200 liters of seawater contain over 5000
different viruses.
6.
7. Science of metagenomics make it possible to
investigate resource for the development of novel
genes, enzymes and chemical compounds for use in
biotechnology.
Microbes, as communities, are key players in
maintaining environmental stability.
Investigate microbes in their natural environment,
the complex communities in which they normally
live in.
High-throughput gene-level studies of communities.
8.
9.
10. Sample processing is the first and most crucial step in metagenomics.
DNA extracted should be representative of all cells present in the sample and sufficient amounts of
high quality nucleic acids must be obtained for subsequent library production and sequencing.
Sample fractionation steps should be checked to ensure that sufficient enrichment of the target is
achieved and that minimal contamination of non-target material occurs.
Physical separation and isolation of cells from the samples might also be important to maximize DNA
yield or avoid co-extraction of enzymatic inhibitors that might interfere with subsequent processing.
Direct lysis of cells versus indirect lysis has a quantifiable bias in terms of microbial diversity, DNA
yield, and resulting sequence fragment length.
Some type of sample such as biopsies or ground water often yield very small amounts of DNA but in
library production for most sequencing technologies require high amounts of DNA (ng or µg ), and
hence amplification of starting material might be required.
Multiple displacement amplification (MDA) using random hexamers and phage phi29 polymerase
is one option employed to increase DNA yields, this method has been widely used in single-cell
genomics and to a certain extent in metagenomics.
11. Dispersing misconceptions and identifying opportunities for the use of 'omics' in soil microbial ecology
James I. Prosser
Nature Reviews Microbiology 13, 439–446 (2015)
13. There are two basic types of
Metagenomics studies
I. Sequence-based Metagenomics-
involves sequencing and analysis of DNA
from environmental samples
II. Function-based Metagenomics
involves screening for a particular
function or activity
14. Sequence-based metagenomics studies can be used to assemble genomes,
identify genes, find complete metabolic pathways, and compare
organisms of different communities.
Genome assembly requires lots of computer power but it can lead to a
better understanding of how certain genes help organisms survive in a
particular environment.
Sequence-based metagenomics can also be used to establish the degree
of diversity and the number of different bacterial species existing in a
particular sample.
Analyzing microbial diversity is less costly and less computer intensive
than assembling genomes and it can provide valuable information about
the ecology of microbes in a sample.
15. Whole genome sequencing developed
by J. Craig Venter and Hamilton Smith
in 1995.
Whole genome sequencing can help to
reconstruct large fragments or even
complete genome from organism in a
community without previous isolation,
allowing the characterization of a large
number of coding and non-coding
sequence can used as phylogenetic
marker.
Whole genome sequencing provides
information both about which organism
are present & what metabolic processes
are possible in the community. J. Craig Venter
16. WHOLE GENOME
SEQUENCING
Whole genome sequencing
based on basic four steps
I. Library construction
II. Random sequencing
III. Fragment Alignment and
gap closure
IV. Editing
17. Carl Woese and coworker started to analyze and sequence
the 16S rDNA genes of various bacteria, using DNA
sequencing, a state-of-the-art technology at that time, and
used the sequences for phylogenetic studies.
16S rRNA is a part of the ribosomal RNA of prokaryotic cell
which is about 1,542 nucleotide.
16S gene contain region that are highly conserved between
species and also variable region that are species specific.
I. Conserved region provide excellent amplification targets.
II. Variable region are highly informative for taxonomic
classification.
Thus is the powerful tool used for classification and
genome analysis
18. Evidence for horizontal gene transfer
exchange of genetic material between two
genomes without a parental relationship.
19. DNA sequencing is one of the most important platforms for the
study of biological systems today. (Ronaghi, 2001)
A. Next generation DNAsequencing
I. 454 life sciences or pyrosequencing
II. Solexa/Illumina
III. Sequencing by ligation (SOLiD technology)
IV. Ion Torrent or PGM
20. Sequence determination is most commonly performed using di-
deoxy chain termination technology, also known as Sanger
sequencing, was developed by Frederick Sanger and collègues
(Sanger et al., 1977).
Pyrosequencing technology is a novel DNA sequencing technology,
the first alternative to the conventional Sanger method for de novo
DNA sequencing.(Md. Fakruddin et al., 2012)
Pyrosequencing has the potential advantages of accuracy, flexibility,
parallel processing, and can be easily automated. (Md. Fakruddin et al.,
2012)
21. Pyrosequencing a DNA sequencing technique that relies on
detection of pyrophosphate release upon nucleotide incorporation
rather than chain termination with dideoxynucleotides.
In Pyrosequencing (Nyren and Skarpnack, 2001) the sequencing
primer is hybridized to a single-stranded DNA biotin-labeled
template and mixed with the enzymes; DNA polymerase, ATP
sulfurylase, luciferase and apyrase, and the substrates adenosine 5′
phosphosulfate (APS) and luciferin (Gharizadeh et al., 2007).
Cycles of four deoxynucleotide triphosphates (dNTPs) are
separately added to the reaction mixture iteratively.
The cascade starts with a nucleic acid polymerization reaction in
which inorganic PPi is released as a result of nucleotide
incorporation by polymerase.
22. Each nucleotide incorporation event is followed by release of inorganic
pyrophosphate (PPi) in a quantity equimolar to the amount of
incorporated nucleotide.
The released PPi is quantitatively converted to ATP by ATP sulfurylase
in the presence ofAPS.
The generated ATP drives the luciferase-mediated conversion of
luciferin to oxyluciferin, producing visible light in amounts that are
proportional to the amount ofATPs.
The light in the luciferase-catalyzed reaction with a maximum of 560
nm wavelength is then detected by a photon detection device such as a
charge coupled device (CCD) camera or photomultiplier.
Apyrase is a nucleotide-degrading enzyme, which continuously
degradesATPand non-incorporated dNTPs in the reaction mixture.
27. Binning is the process of grouping reads or contigs into individual genomes and
assigning the group to specific species, subspecies or genus.
More innovative binning approaches include co-abundance gene segregation across
a series of metagenomic sample thus facilating the assembly of microbial genomes
without the need for reference sequences.
Important considerations for using any binning algorithm are the type of input data
available and the existence of a suitable training dataset or reference genomes.
Binning methods can be characterized in two different ways depending on
information contained within a given DNA sequence
1. Composition based binning
2. Similarity or homology based binning
28. Composition based binning is based on the observation that individual
genomes have a unique distribution of k-mer sequence is known as
genomic signatures.
Binning makes use of this conserved species-specific nucleotide
composition (such as GC) are capable of grouping sequences into their
respective genomes.
Compositional based binning algorithms include phylopythia, successor
phylopythiaS, S-GSOM, PCAHIER, TACAO, TETRA, ESOM and
ClaMS.
Composition based binning is not reliable for short reads as they do not
contain enough information.
29. Similarity based binning refer to the process of using alignment
algorithms such as BLAST or profile hidden markov models
(pHMMs) to obtain similarity information about specific sequences/
genes from publically available databases.
Similarity based binning algorithms include IMG/M, MG-RAST,
MEGAN, CARMA, Sort-ITEMS and Metaphyler.
Similarity based binning fail to do so accurately while reads of
short length, the metagenome under consideration consists of
numerous closely related species.
30.
31. Annotation is the process of assigning functional, positional, and species-
of-origin information to the genes in a database.
Annotation of metagenome is specifically designed to work with mixtures
of genomes and contig of varying length.
Annotation is included the four preprocessing steps
A. Trimming of low quality reads–using platform specific tool such as
FASTX-Toolkit, SolexaQA, and Lucy2 the threshold of which depend
on sequencing technology.
B. Masking of low complexity reads-performed using tool such as DUST.
C. A de-replication step that removes sequence that more than 95%
identical.
D. A screening –the pipeline provided the option of removing reads that are
near exact match to the genome of a handful of model organism
including fly, mouse, cow and human.
Identification of genes within the reads/ assembly contig, a process often
denoted as “gene calling”
32. Gene are labeled as coding DNA sequence (CDS) identified using a number of
tool including Meta-gene mark, meta-gene or phedia and FragGene scan all of
which utilize ab inito gene prediction algorithms.
Non-coding RNAs such as t-RNA are predicted using programs like tRNA Scan,
ribosomal RNA (rRNA) gene (5S, 16S and 23S) are predicted using internally
developed rRNA model for IMG/MER and MG-RAST use similarity to compare
known database to predict rRNA.
Annotation pipeline involves functional assignment to the predicted protein
coding genes. This is currently achieved by homology based searches of query
sequences against databases containing known functional and/or taxonomic
information.
Both IMG/MER and MGRAST are widely used data management repositories
and comparative genomics environments. They are fully automated pipelines that
provide quality control, gene prediction, and functional annotation.
33. ADVANTAGES OF ASSEMBLING METAGENOMES ARE:
(1) The possibility of analysing the genome context (i.e.,
operons);
(2) Increasing the probability of complete genes and genomes
reconstruction, arising the confidence of sequence
annotation;
(3) Analysis simplification by mapping long contigs instead of
short reads (Thomas et al., 2012; Luo et al., 2013; Segata
et al., 2013).
34. NCBI is mandated to store all metagenomic data, however, the sheer volume of data being
generated means there is an urgent need for appropriate ways of storing vast amounts of
sequences.
Tools such as IMG/MER, CAMERA, MGRAST, and EBI metagenomics (which also
incorporates QIIME) provide an integrated environment for analysis, management, storage,
and sharing of metagenome projects.
The GSC is currently investing heavily toward a widely accepted language that shares
ontologies and nomenclatures thereby providing a common standard for exchange of data
derived from the analysis of metagenomic projects.
A suite of standard languages for metadata is currently provided by the Minimum
Information about any (x) Sequence checklists (MIxS).
MIxS is an umbrella term to describe MIMS (Minimum Information about a Metagenome
Sequence) and MIMARKS (Minimum Information about a MARKer Sequence) have been
devised, providing a scheme of standard languages for metadata annotation.
35. Functional metagenomics is a powerful experimental approach for studying gene
function, starting from the extracted DNA of mixed microbial populations.
A functional approach relies on the construction and screening of metagenomic
libraries—physical libraries that contain DNA cloned from environmental
metagenomes.
Functional metagenomics begins with the construction of a metagenomic library,
Cosmid- or fosmid-based libraries are often preferred due to their large and consistent
insert size and high cloning efficiency.
The information obtained from functional metagenomics can help in future
annotation of gene function and serve as a complement to sequence – based
metagenomics.
Using this function-based approach allows for discovery of novel enzymes whose
functions would not be predicted based on DNA sequence alone.
36. Total metagenomic DNA is extracted from a microbial community
sample, sheared, and ligated into an expression vector and is subsequently
transformed into a suitable library host to create a metagenomic library.
The library is then plated on media containing antibiotics inhibitory to the
wild-type host to select for metagenomic fragments conferring antibiotic
fragments present in colonies growing on antibiotic
resistance.
Metagenomic
selection media are then PCR amplified and sequenced using either
traditional Sanger sequencing or next-generation sequencing methods.
Finally, reads are assembled and annotated in order to identify the
causative antibiotic resistance genes
37.
38. FUNCTIONAL METAGENOME ANALYSIS
Reconstruction of metabolic pathway from enzyme coding gene is
a relevant matter in the metagenome analysis.
There are two options to perform functional annotation from
shotgun sequences, one is using sequencing reads directly and
another is read assembly.
39. GENE PREDICTION
Gene prediction determine which metagenomics reads contain
coding sequence.
Metagenome assembly, gene prediction and annotation are similar
to the framework followed in whole genome characterization
(Yandell and Ence 2012, Richardson and Watson, 2013)
Gene prediction by three ways
I. Gene fragments requirements
II. Protein family classification
III. De novo gene prediction
40. METABOLIC PATHWAY RECONSTRUCTION
Pathway reconstruction of the metagenome data is one of the annotation
goals and the term “inter-organismic meta- routes” or “meta-pathways”
has been proposed for this kind of analysis (De Filippo et al., 2012).
The concept of metabolic pathway in microbial ecology should be
understood as the flow of information through different species.
Function annotation has to be used to find each gene in an appropriate
metabolic context, filling missing enzymes in pathways and find optimal
metabolic states to perform the best pathway reconstructions.
Programs available are MinPath (Ye and Doak, 2009) and MetaPath (Liu
and Pop, 2010). Both use information deposited in KEGG (Ogata et al.,
1999) and MetaCyc (Caspi et al., 2014) repositories.
Metabolic pathway reconstruction could be completed with information
provided by the data context such as gene function interactions, synteny,
and copy number of annotated genes to integrate the metabolic potential
of consortium.
44. APPLICATION OF METAGENOMICS
Metagenomics has the potential to advance knowledge in
a wide variety of field.
III.
I. Medicine
II. Engineering
Agriculture
IV. Ecology
V. Biotechnology.
45. APPLICATION
Metagenomics can improve strategies for monitoring the impact of pollutants on ecosystems
and for cleaning up contaminated environments. Increased understanding of bioaugmentation or
biostimulation trials to succeed.
Recent progress in mining the rich genetic resource of nonculturable microbes has led to the
discovery of new gene, enzymes and natural products. The impact of metagenomics is
witnessed in the development of commodity and fine chemicals, agrochemicals and
pharmaceuticals where the benefit of enzyme catalyzed chiral synthesis is increasingly
recognized.
Metagenomics libraries are, indeed, an essential tool for the discovery of new enzymatic
activities, facilitating genetic tracking for all biotechnological applications of interest for the
future.
Metagenomics sequencing is being used to characterize the microbial communities. This is part
of the human micro-biome initiative with primary goals to determine if there is a core human
micro-biome, to understand the changes in the human micro-biome that can be correlated with
human health, and to develop new technological and bioinformatics tools to support these
goals.
It is well known that the vast majority of microbes have not been cultivated. Functional
metagenomics strategies are being used to explore the interactions between plants and microbes
through cultivation-independent study of the microbial communities.
46.
47. • New enzymes, antibiotics, and other reagents identified
• More exotic habitats can be intently studied
• Can only progress as library technology progresses, including
sequencing technology
• Improved bioinformatics will quicken analysis for library
profiling
• Investigating ancient DNAremnants
• Discoveries such as phylogenic tags (rRNAgenes, etc) will give
momentum to the growing field
• Learning novel pathways will lead to knowledge about the
current nonculturable bacteria to then culture these systems
48. LIMITATION
To much data.
Most gene are not identifiable
Contamination, chimeric clone sequences
Extraction problem
Requires proteomics or expression studies to demonstrate phenotypic characteristics
Need a standard method for annotating genomes
Can only progress as library technology progresses, including sequencing technology.
Requires high throughput instrumentation not readily available to most institutions.
49. CONCLUSION
Metagenomics has benefited in the past few years from many
visionary investments in both financial and intellectual terms.
The science of metagenomics is currently in its pioneering stages
of development as a field, and many tools and technologies are
undergoing rapid evolution.
The best use of the metagenomics as a tool to address
fundamental question of microbial ecology, evolution and
diversity and to derive and test new hypothesis.
As datasets more
analysis,
complex and
storage, and
comprehensive,
become increasingly
novel tools for
visualization will be required.
50. Metagenomics allows us to discover new genes and proteins or
even the complete genomes of non-cultivable organisms in less
time and with better accuracy than classical microbiology or
molecular methods.
In addition to the phenotypic dimension of human biology, such as
gene expression profiling, proteomics, and metabolomics, perhaps
we need to extend our concept of the human genome to include
the more comprehensive and plastic human metagenome in
laboratory medicine.
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52. CONT..
Patake R. S. and Patake G. R (2011) A Mini Review on Metagenomics and its
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