Quest of DNA signature of species of animal, plant & microbes :
Can we have a PIN code?
Invited talk- National symposium - Punjab University Chandigarh, 17th Feb 2011, Biotechnology department
National Symposium : Frontiers in Biotechnology 17th Feb 2011Biotechnology Department, PU, Chandigarh
Invited Talk-Quest of DNA signature of species of animal, plant & microbes :
Can we have a PIN code?
This document provides an introduction to non-coding RNAs (ncRNAs). It discusses how RNA was proposed to have come before DNA and proteins in the RNA world hypothesis. It notes that RNA can store genetic information like DNA and have catalytic abilities like proteins. The document outlines different types and functions of ncRNAs, including how some act as guides for chemical modifications, regulate gene expression as sponges for small RNAs or proteins, or sense environmental signals as riboswitches or thermosensors. Examples of conserved ncRNA families and mechanisms are briefly described.
Three mini-stories are summarized from a document about genomics and bioinformatics in non-model organisms:
1. Building better gene models for the chicken genome using RNA-seq data helped recover annotated isoforms and detect unknown isoforms, resulting in over 15,000 genes and 46,000 transcripts identified.
2. Digital normalization of sequencing data enabled iterative use of new data by setting aside 90% of redundant sequences, allowing analyses that would otherwise be impossible with limited computing resources.
3. Comparing pathway predictions using Ensembl gene models versus gene models constructed with the Gimme pipeline showed both recovered known pathways but Gimme identified additional pathways, demonstrating effects of gene model completeness on downstream analyses.
Forensic Sciences (DNA Fingerprinting) STR Typing - Case Reportnarmeenarshad
Identification of Human Remains by DNA Analysis of the gastrointestinal contents of Fly Larvae
A case Report that has been explained in form of presentation.
B.Tech Biotechnology II Elements of Biotechnology Unit 4 DNA FingerprintingRai University
This document discusses DNA fingerprinting and its uses in forensics and parental testing. It begins by providing a brief history of DNA fingerprinting and then describes the various hypervariable DNA sequences that are examined, including RFLPs, VNTRs, STRs, SNPs, mitochondrial DNA and Y chromosomal DNA. It discusses the methods used, including Southern blots and PCR, as well as statistical and technical considerations. It also mentions DNA databases and issues of privacy. Examples are provided to illustrate DNA fingerprinting techniques and how probabilities of a DNA match are determined.
- All primer sets were able to successfully amplify mtDNA from ancient goose samples into the correct size fragments. Two samples were identified as specific bird species.
- Universal primer sets were designed that could identify over 97% of North American bird species from mtDNA, through amplifying variable regions of the COI gene. Four primer sets allow for sequential testing to identify unknown samples.
- The primers were tested on ancient goose and other unknown bird samples, identifying several to the species level through DNA sequencing and BLAST searches. The primers provide a tool for identifying bird remains when morphology alone is insufficient.
Applications of biotechnology in forensic sciencesZahra Naz
Biotechnology tools have revolutionized forensic sciences by enabling analysis of biological evidence. Restriction fragment length polymorphism was an early technique using Southern blotting for DNA fingerprinting. Polymerase chain reaction is now preferred as it amplifies DNA, is sensitive, and requires less work. Other techniques profile mitochondrial DNA, Y-chromosomes, microsatellites, and Alu repeats to identify suspects, examine lineages, and study populations. Applications include sample analysis, lineage tracing, suspect identification, anthropology, and population genetics. Biotechnology continues advancing forensic sciences capabilities.
National Symposium : Frontiers in Biotechnology 17th Feb 2011Biotechnology Department, PU, Chandigarh
Invited Talk-Quest of DNA signature of species of animal, plant & microbes :
Can we have a PIN code?
This document provides an introduction to non-coding RNAs (ncRNAs). It discusses how RNA was proposed to have come before DNA and proteins in the RNA world hypothesis. It notes that RNA can store genetic information like DNA and have catalytic abilities like proteins. The document outlines different types and functions of ncRNAs, including how some act as guides for chemical modifications, regulate gene expression as sponges for small RNAs or proteins, or sense environmental signals as riboswitches or thermosensors. Examples of conserved ncRNA families and mechanisms are briefly described.
Three mini-stories are summarized from a document about genomics and bioinformatics in non-model organisms:
1. Building better gene models for the chicken genome using RNA-seq data helped recover annotated isoforms and detect unknown isoforms, resulting in over 15,000 genes and 46,000 transcripts identified.
2. Digital normalization of sequencing data enabled iterative use of new data by setting aside 90% of redundant sequences, allowing analyses that would otherwise be impossible with limited computing resources.
3. Comparing pathway predictions using Ensembl gene models versus gene models constructed with the Gimme pipeline showed both recovered known pathways but Gimme identified additional pathways, demonstrating effects of gene model completeness on downstream analyses.
Forensic Sciences (DNA Fingerprinting) STR Typing - Case Reportnarmeenarshad
Identification of Human Remains by DNA Analysis of the gastrointestinal contents of Fly Larvae
A case Report that has been explained in form of presentation.
B.Tech Biotechnology II Elements of Biotechnology Unit 4 DNA FingerprintingRai University
This document discusses DNA fingerprinting and its uses in forensics and parental testing. It begins by providing a brief history of DNA fingerprinting and then describes the various hypervariable DNA sequences that are examined, including RFLPs, VNTRs, STRs, SNPs, mitochondrial DNA and Y chromosomal DNA. It discusses the methods used, including Southern blots and PCR, as well as statistical and technical considerations. It also mentions DNA databases and issues of privacy. Examples are provided to illustrate DNA fingerprinting techniques and how probabilities of a DNA match are determined.
- All primer sets were able to successfully amplify mtDNA from ancient goose samples into the correct size fragments. Two samples were identified as specific bird species.
- Universal primer sets were designed that could identify over 97% of North American bird species from mtDNA, through amplifying variable regions of the COI gene. Four primer sets allow for sequential testing to identify unknown samples.
- The primers were tested on ancient goose and other unknown bird samples, identifying several to the species level through DNA sequencing and BLAST searches. The primers provide a tool for identifying bird remains when morphology alone is insufficient.
Applications of biotechnology in forensic sciencesZahra Naz
Biotechnology tools have revolutionized forensic sciences by enabling analysis of biological evidence. Restriction fragment length polymorphism was an early technique using Southern blotting for DNA fingerprinting. Polymerase chain reaction is now preferred as it amplifies DNA, is sensitive, and requires less work. Other techniques profile mitochondrial DNA, Y-chromosomes, microsatellites, and Alu repeats to identify suspects, examine lineages, and study populations. Applications include sample analysis, lineage tracing, suspect identification, anthropology, and population genetics. Biotechnology continues advancing forensic sciences capabilities.
This document summarizes a presentation given at the Arabidopsis Information Resource (TAIR) workshop. It provides an overview of TAIR, including its role as a curated resource for Arabidopsis thaliana research. Key points include that TAIR integrates experimental data from over 33,000 A. thaliana genes, provides manual literature curation of gene functions, and offers various search and analysis tools for researchers. The presentation also demonstrates how TAIR can be leveraged to study gene functions in other plant species through sequence similarity searches and comparative genomics analyses.
Endosymbiont hunting in the metagenome of Asian citrus psyllid (Diaphorina ci...Surya Saha
The Asian citrus psyllid (D. citri Kuwayama or ACP) is host to 7+ bacterial endosymbionts and is the insect vector of Ca. liberibacter asiaticus (Las), causal agent of citrus greening. To gain a better understanding of endosymbiont and pathogen ecology and develop improved detection strategies for Las, DNA from D. citri was sequenced to 108X coverage. Initial analyses have focused on Wolbachia, an alpha-proteobacterial primary endosymbiont typically found in the reproductive tissues of ACP and other arthropods. The metagenomic sequences were mined for wACP reads using BLAST and 4 sequenced Wolbachia genomes as bait. Putative wACP reads were then assembled using Velvet and MIRA3 assemblers over a range of parameter settings. The resulting wACP contigs were annotated using the RAST pipeline and compared to Wolbachia endosymbiont of Culex quinquefasciatus (wPip). MIRA3 was able to reconstruct a majority of the wPip CDS regions and was selected for scaffolding with Minimus2, SSPACE and SOPRA using large insert mate-pair libraries. The wACP scaffolds were compared to wPip using Abacas and Mauve contig mover to orient and order the contigs. The functional annotation of scaffolds was evaluated by comparing it to wPip genome using RAST. The draft assembly was verified using an OrthoMCL based comparison to the 4 sequenced Wolbachia genomes. We expanded the scope of endosymbiont characterization beyond wACP using 16S rDNA and partial 23S rDNA analysis as a guide. Results will be presented regarding endosymbionts, their potential interactions and their impact on the disease of citrus greening.
Isolation of Novel Mycobacteriophages from Tropical Soils of Puerto Rico avargas11
The document contains data from soil samples collected in Puerto Rico by four students - Aida Vargas de Jesus, Danilo Trinidad Pérez Rivera, Lizbeth Perez Castro, and Javier M. Zavala Ayala - as part of the RISE Program in the Department of Biology led by Prof. Eneida Díaz Pérez and Prof. Michael Rubin. The document includes tables with the coordinates, descriptions, locations, and dates of 12 soil samples collected by Danilo Trinidad Pérez Rivera and 7 soil samples collected by Aida Vargas de Jesus.
1. The document discusses a biohacking project that aims to use microorganisms as a material to store and transmit information.
2. Specifically, the project plans to translate text such as handwritten characters into DNA code, genetically inject this DNA into microbes, culture the microbes, sequence the microbial DNA to extract the stored data, and regenerate the original information.
3. The presentation provides background on the speaker and reviews previous studies that have stored large amounts of digital data in DNA, demonstrating the viability of using DNA to encode and store information.
This study analyzed variation in heat shock protein (Hsp) genes between populations of the copepod Tigriopus californicus along the California coast to identify potential functional differences related to local adaptation. The researchers found amino acid variation in two Hsp genes, Hsp70 and Hsp-β, between northern and southern populations. Heterologous expression of the different alleles in E. coli found that the southern Hsp-β allele conferred greater thermotolerance than the northern allele, suggesting functional divergence between populations.
Forensic significance of dna profilingSONiaChahal1
This document discusses various applications of DNA profiling including child swapping cases, missing persons investigations, civil immigration cases, veterinary cases, wildlife and agriculture cases. It covers topics like commercially available STR kits, gender identification using amelogenin, variable number tandem repeats, Y-chromosome DNA analysis, mitochondrial DNA analysis, single nucleotide polymorphisms, non-human DNA identification in animal attacks and wildlife cases. Methods for identifying missing persons through direct and family reference DNA samples are also mentioned.
- The document discusses research on the cotton root-knot nematode (Meloidogyne incognita), an endoparasitic nematode that infects thousands of plant species and causes billions in crop damage worldwide.
- The research uses Arabidopsis thaliana plants, including mutant strains, to study the nematode's infection process. Mutant plants have mutations in an ABC transporter gene (At4g15320) involved in secreting chemicals that nematodes use to locate host plants.
- The goal is to see if the mutant transporter gene affects nematode infection rates compared to wild-type Arabidopsis. Results found the mutant was actually not a true mutant and showed similar nematode infection to the
The document discusses how to interpret a person's genome sequence. It explains that while we can identify genetic variations and inherited conditions, a genome sequence alone does not reveal much because DNA is complex code that is difficult to decipher. Environmental factors and how genes interact also influence traits. The document outlines the process of genome sequencing, mapping reads to a reference, variant calling, and challenges in interpretation due to incomplete knowledge and versioning issues.
113 phillip d. zamore - 7691995 - in vivo production of small interfering r...Mello_Patent_Registry
Phillip D. Zamore, Juanita McLachlan, Gyorgy Hutvagner, Alla Grishok, Craig C. Mello - In Vivo Production of Small Interfering RN's that Mediate Gene Silencing
Recombinant DNA Technology, Forensic DNA Analysis and Human Genome ProjectNateneal Tamerat
Recombinant DNA technology involves joining DNA fragments from different organisms to produce new genetic combinations. It was developed in the 1970s using restriction enzymes, which cut DNA at specific sites. DNA is isolated, cut, and inserted into vectors like plasmids or bacteria, then inserted into host cells. Applications include forensic analysis by matching crime scene DNA to databases, agriculture, diagnosing genetic diseases, and the Human Genome Project, which sequenced the entire human genome in 2001 and revealed insights about human genetics and evolution.
The bat genome data can be found at ENA under project ERP006654. Content based on original slides by Jamie Eadie, edited and expanded by David Martin. Photographs are (C) David Martin and may not be used without permission.
Targeted T-cell receptor beta immune repertoire sequencing in several FFPE ti...Thermo Fisher Scientific
T-cell receptor beta (TCRβ) immune repertoire analysis by next-generation sequencing is a valuable tool for studies of the tumor microenvironment and potential immune responses to cancer immunotherapy. Here we describe a TCRβ sequencing assay that leverages the low sample input requirements of AmpliSeq library preparation technology to extend the capability of targeted immune repertoire sequencing to include FFPE samples which can often be degraded and in short supply
Speeding up sequencing: Sequencing in an hour enables sample to answer in a w...Thermo Fisher Scientific
1) Thermo Fisher Scientific developed improvements to targeted and whole genome sequencing workflows that dramatically decrease overall time from sample to data/answer.
2) For a targeted bacterial identification panel, sequencing and analysis can now be completed in approximately 6.5 hours compared to standard times of 2.5 hours for sequencing and 1 hour for analysis.
3) For whole genome sequencing of bacterial isolates, the entire workflow from library preparation to data can now be finished in approximately 11 hours, compared to standard times of 1.5-3.5 hours for library prep, 2-7 hours for sequencing, and 1 hour for analysis.
This document is a resume for Brandy Marron, M.S. that summarizes her education and extensive experience in research and laboratory work related to animal genetics. She received her M.S. and B.S. in Animal Science from the University of Illinois. For the past 19 years, she has worked as a Research Specialist at the University of Illinois conducting projects on targeted mutagenesis in pigs and identifying disease-causing loci in cattle and sheep to develop diagnostic tests. Her responsibilities include conducting research, presenting findings, collaborating with other labs, training and supervising students, performing DNA/RNA work, and maintaining laboratory equipment and inventory. She has strong skills in wet lab techniques, bioinformatics, and software
This document describes a study that used polymerase chain reaction (PCR) to amplify 16S ribosomal DNA (rDNA) from various bacterial species for phylogenetic analysis. The researchers designed universal primers that could amplify nearly full-length 16S rDNA from many bacterial genera. They demonstrated that this method allowed phylogenetic analysis of fastidious or pathogenic bacteria directly from lyophilized cultures without requiring cultivation. As an example, they amplified, cloned, sequenced and phylogenetically analyzed the 16S rDNA of Anaplasma marginale, placing it within the genera Rickettsia and Ehrlichia.
The rapid expansion of global trade and travel has increased the spread of pathogens. Climate change also influences pathogen communities directly and indirectly. Sudden Oak Death is provided as an example. There are challenges in accurately identifying pathogen species, understanding pathogen diversity in nature, and facilitating global cooperation on knowledge sharing. The Phytophthora Database was created as cyberinfrastructure to support identification and monitoring of Phytophthora species through genetic fingerprinting and phenotypic data on known isolates.
Pat Heslop-Harrison presentation for International Chromosome Conference Prague September 2018 Meiosis, recombination, pairing, mitochondria, evolution, genomics, oligonucleotides, in situ hybridization, breeding, genetics, cytogenetics, ICC, ICC22
This document discusses mitochondrial genomes and DNA barcodes in arthropods. It presents data on the number of genomes, barcodes, and mitochondrial genomes that have been sequenced for arthropod species. It also shows graphs and data on the nucleotide composition of mitochondrial genomes and barcodes across different arthropod groups. A key point discussed is that haplodiploidy in arthropods is associated with faster evolutionary rates of mitochondrial proteins and more insertions/deletions compared to diploid groups. This is hypothesized to be due to co-evolution between mitochondrial and nuclear genomes enabled by the haploid stage in males.
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.
This document summarizes a presentation given at the Arabidopsis Information Resource (TAIR) workshop. It provides an overview of TAIR, including its role as a curated resource for Arabidopsis thaliana research. Key points include that TAIR integrates experimental data from over 33,000 A. thaliana genes, provides manual literature curation of gene functions, and offers various search and analysis tools for researchers. The presentation also demonstrates how TAIR can be leveraged to study gene functions in other plant species through sequence similarity searches and comparative genomics analyses.
Endosymbiont hunting in the metagenome of Asian citrus psyllid (Diaphorina ci...Surya Saha
The Asian citrus psyllid (D. citri Kuwayama or ACP) is host to 7+ bacterial endosymbionts and is the insect vector of Ca. liberibacter asiaticus (Las), causal agent of citrus greening. To gain a better understanding of endosymbiont and pathogen ecology and develop improved detection strategies for Las, DNA from D. citri was sequenced to 108X coverage. Initial analyses have focused on Wolbachia, an alpha-proteobacterial primary endosymbiont typically found in the reproductive tissues of ACP and other arthropods. The metagenomic sequences were mined for wACP reads using BLAST and 4 sequenced Wolbachia genomes as bait. Putative wACP reads were then assembled using Velvet and MIRA3 assemblers over a range of parameter settings. The resulting wACP contigs were annotated using the RAST pipeline and compared to Wolbachia endosymbiont of Culex quinquefasciatus (wPip). MIRA3 was able to reconstruct a majority of the wPip CDS regions and was selected for scaffolding with Minimus2, SSPACE and SOPRA using large insert mate-pair libraries. The wACP scaffolds were compared to wPip using Abacas and Mauve contig mover to orient and order the contigs. The functional annotation of scaffolds was evaluated by comparing it to wPip genome using RAST. The draft assembly was verified using an OrthoMCL based comparison to the 4 sequenced Wolbachia genomes. We expanded the scope of endosymbiont characterization beyond wACP using 16S rDNA and partial 23S rDNA analysis as a guide. Results will be presented regarding endosymbionts, their potential interactions and their impact on the disease of citrus greening.
Isolation of Novel Mycobacteriophages from Tropical Soils of Puerto Rico avargas11
The document contains data from soil samples collected in Puerto Rico by four students - Aida Vargas de Jesus, Danilo Trinidad Pérez Rivera, Lizbeth Perez Castro, and Javier M. Zavala Ayala - as part of the RISE Program in the Department of Biology led by Prof. Eneida Díaz Pérez and Prof. Michael Rubin. The document includes tables with the coordinates, descriptions, locations, and dates of 12 soil samples collected by Danilo Trinidad Pérez Rivera and 7 soil samples collected by Aida Vargas de Jesus.
1. The document discusses a biohacking project that aims to use microorganisms as a material to store and transmit information.
2. Specifically, the project plans to translate text such as handwritten characters into DNA code, genetically inject this DNA into microbes, culture the microbes, sequence the microbial DNA to extract the stored data, and regenerate the original information.
3. The presentation provides background on the speaker and reviews previous studies that have stored large amounts of digital data in DNA, demonstrating the viability of using DNA to encode and store information.
This study analyzed variation in heat shock protein (Hsp) genes between populations of the copepod Tigriopus californicus along the California coast to identify potential functional differences related to local adaptation. The researchers found amino acid variation in two Hsp genes, Hsp70 and Hsp-β, between northern and southern populations. Heterologous expression of the different alleles in E. coli found that the southern Hsp-β allele conferred greater thermotolerance than the northern allele, suggesting functional divergence between populations.
Forensic significance of dna profilingSONiaChahal1
This document discusses various applications of DNA profiling including child swapping cases, missing persons investigations, civil immigration cases, veterinary cases, wildlife and agriculture cases. It covers topics like commercially available STR kits, gender identification using amelogenin, variable number tandem repeats, Y-chromosome DNA analysis, mitochondrial DNA analysis, single nucleotide polymorphisms, non-human DNA identification in animal attacks and wildlife cases. Methods for identifying missing persons through direct and family reference DNA samples are also mentioned.
- The document discusses research on the cotton root-knot nematode (Meloidogyne incognita), an endoparasitic nematode that infects thousands of plant species and causes billions in crop damage worldwide.
- The research uses Arabidopsis thaliana plants, including mutant strains, to study the nematode's infection process. Mutant plants have mutations in an ABC transporter gene (At4g15320) involved in secreting chemicals that nematodes use to locate host plants.
- The goal is to see if the mutant transporter gene affects nematode infection rates compared to wild-type Arabidopsis. Results found the mutant was actually not a true mutant and showed similar nematode infection to the
The document discusses how to interpret a person's genome sequence. It explains that while we can identify genetic variations and inherited conditions, a genome sequence alone does not reveal much because DNA is complex code that is difficult to decipher. Environmental factors and how genes interact also influence traits. The document outlines the process of genome sequencing, mapping reads to a reference, variant calling, and challenges in interpretation due to incomplete knowledge and versioning issues.
113 phillip d. zamore - 7691995 - in vivo production of small interfering r...Mello_Patent_Registry
Phillip D. Zamore, Juanita McLachlan, Gyorgy Hutvagner, Alla Grishok, Craig C. Mello - In Vivo Production of Small Interfering RN's that Mediate Gene Silencing
Recombinant DNA Technology, Forensic DNA Analysis and Human Genome ProjectNateneal Tamerat
Recombinant DNA technology involves joining DNA fragments from different organisms to produce new genetic combinations. It was developed in the 1970s using restriction enzymes, which cut DNA at specific sites. DNA is isolated, cut, and inserted into vectors like plasmids or bacteria, then inserted into host cells. Applications include forensic analysis by matching crime scene DNA to databases, agriculture, diagnosing genetic diseases, and the Human Genome Project, which sequenced the entire human genome in 2001 and revealed insights about human genetics and evolution.
The bat genome data can be found at ENA under project ERP006654. Content based on original slides by Jamie Eadie, edited and expanded by David Martin. Photographs are (C) David Martin and may not be used without permission.
Targeted T-cell receptor beta immune repertoire sequencing in several FFPE ti...Thermo Fisher Scientific
T-cell receptor beta (TCRβ) immune repertoire analysis by next-generation sequencing is a valuable tool for studies of the tumor microenvironment and potential immune responses to cancer immunotherapy. Here we describe a TCRβ sequencing assay that leverages the low sample input requirements of AmpliSeq library preparation technology to extend the capability of targeted immune repertoire sequencing to include FFPE samples which can often be degraded and in short supply
Speeding up sequencing: Sequencing in an hour enables sample to answer in a w...Thermo Fisher Scientific
1) Thermo Fisher Scientific developed improvements to targeted and whole genome sequencing workflows that dramatically decrease overall time from sample to data/answer.
2) For a targeted bacterial identification panel, sequencing and analysis can now be completed in approximately 6.5 hours compared to standard times of 2.5 hours for sequencing and 1 hour for analysis.
3) For whole genome sequencing of bacterial isolates, the entire workflow from library preparation to data can now be finished in approximately 11 hours, compared to standard times of 1.5-3.5 hours for library prep, 2-7 hours for sequencing, and 1 hour for analysis.
This document is a resume for Brandy Marron, M.S. that summarizes her education and extensive experience in research and laboratory work related to animal genetics. She received her M.S. and B.S. in Animal Science from the University of Illinois. For the past 19 years, she has worked as a Research Specialist at the University of Illinois conducting projects on targeted mutagenesis in pigs and identifying disease-causing loci in cattle and sheep to develop diagnostic tests. Her responsibilities include conducting research, presenting findings, collaborating with other labs, training and supervising students, performing DNA/RNA work, and maintaining laboratory equipment and inventory. She has strong skills in wet lab techniques, bioinformatics, and software
This document describes a study that used polymerase chain reaction (PCR) to amplify 16S ribosomal DNA (rDNA) from various bacterial species for phylogenetic analysis. The researchers designed universal primers that could amplify nearly full-length 16S rDNA from many bacterial genera. They demonstrated that this method allowed phylogenetic analysis of fastidious or pathogenic bacteria directly from lyophilized cultures without requiring cultivation. As an example, they amplified, cloned, sequenced and phylogenetically analyzed the 16S rDNA of Anaplasma marginale, placing it within the genera Rickettsia and Ehrlichia.
The rapid expansion of global trade and travel has increased the spread of pathogens. Climate change also influences pathogen communities directly and indirectly. Sudden Oak Death is provided as an example. There are challenges in accurately identifying pathogen species, understanding pathogen diversity in nature, and facilitating global cooperation on knowledge sharing. The Phytophthora Database was created as cyberinfrastructure to support identification and monitoring of Phytophthora species through genetic fingerprinting and phenotypic data on known isolates.
Pat Heslop-Harrison presentation for International Chromosome Conference Prague September 2018 Meiosis, recombination, pairing, mitochondria, evolution, genomics, oligonucleotides, in situ hybridization, breeding, genetics, cytogenetics, ICC, ICC22
This document discusses mitochondrial genomes and DNA barcodes in arthropods. It presents data on the number of genomes, barcodes, and mitochondrial genomes that have been sequenced for arthropod species. It also shows graphs and data on the nucleotide composition of mitochondrial genomes and barcodes across different arthropod groups. A key point discussed is that haplodiploidy in arthropods is associated with faster evolutionary rates of mitochondrial proteins and more insertions/deletions compared to diploid groups. This is hypothesized to be due to co-evolution between mitochondrial and nuclear genomes enabled by the haploid stage in males.
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.
This document discusses DNA barcoding, a method that uses short genetic markers to identify species. It provides background on DNA barcoding, including that the cytochrome c oxidase subunit 1 (COI) gene is commonly used. The document reviews past DNA barcoding studies in India and worldwide. A key study barcoded 115 commercially important Indian marine fish species and found COI can accurately identify fish species. DNA barcoding has advantages like identifying fragments and life stages and reducing ambiguity. It has potential applications in fisheries management and conservation by aiding species identification.
The document discusses several topics related to genome evolution, including:
1. Genome evolution involves the acquisition of new genes through gene duplication within genomes or lateral gene transfer between species. Gene duplication can occur at the whole genome level or for individual or groups of genes.
2. Genome evolution also involves rearrangement of existing genes through domain shuffling, where gene segments are joined to form new proteins, or domain duplication where repetitive domains evolve new functions.
3. Introns may have evolved early in ancestral genes and are gradually being lost from genomes ("introns early" hypothesis) or evolved more recently and are accumulating ("introns late"). Early evidence supported "introns early" with conserved intron positions in homologous genes.
Mitochondrial DNA (mtDNA) is small, circular, double-stranded DNA located in cell mitochondria. It is maternally inherited and does not recombine. mtDNA contains 37 genes essential for mitochondrial function and ATP production through oxidative phosphorylation. Compared to nuclear DNA, mtDNA evolves more rapidly, lacks introns, and is not bound in histones. Forensic analysis of mtDNA is useful when evidence is degraded or limited. Methods include DNA extraction, PCR amplification of mtDNA regions, sequencing, and comparing sequences to identify matches or mismatches. mtDNA analysis has applications in fisheries including individual identification, mixed stock analysis, and determining phylogenetic relationships between fish species.
This document discusses chloroplast DNA (cpDNA). Chloroplasts contain their own circular genome of double-stranded DNA ranging from 140-200kb. The cpDNA contains genes that code for proteins involved in photosynthesis as well as rRNA and tRNA. It has a quadripartite structure containing single copy and inverted repeat regions. Tobacco and liverwort were two of the first chloroplast genomes to be sequenced. Molecular studies of cpDNA regions have been useful for plant systematics. Replication of cpDNA is independent of nuclear DNA and involves enzymes like DNA polymerase and helicase.
Mitochondrial DNA is circular DNA located in the mitochondria of cells. It is 16kb in size and encodes 37 genes. Mitochondrial DNA is only inherited from the mother and differs from nuclear DNA in several key ways, such as being maternally inherited only. Mutations in mitochondrial DNA can cause diseases often involving the central nervous system or musculoskeletal system. The high mutation rate of mitochondrial DNA is due to lack of protective histones and DNA repair mechanisms.
This document describes the CarrAgheen Molecular Marker Database (CaMM-Db), a comprehensive database of molecular markers for the red seaweed Chondrus crispus (carragheen). The database contains over 18,000 microsatellites and 12,000 SNPs identified from carragheen genomic sequences. CaMM-Db provides information on different microsatellite types and properties. It also integrates with primer design software to facilitate wet lab experiments. As the first database of its kind for carragheen, CaMM-Db is expected to be a valuable resource for genetic research on carragheen and other red seaweeds.
This document discusses using a bioinformatic approach for DNA signature-based diagnostics. It describes three main molecular diagnostic methods - biochemical, antibody, and DNA-based. DNA-based methods such as PCR and DNA probes are highlighted as being highly sensitive and specific. The use of DNA barcoding to identify species via unique DNA sequences is discussed. Developing DNA signatures for pathogens like Ug99 stem rust fungus is presented as an important application of bioinformatics.
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.
This document discusses the analysis of microbial communities through sequencing of the 16S rRNA gene. It presents WATERS, a workflow system that automates and bundles various software tools for analyzing 16S rRNA sequence data. The goals of WATERS are to simplify the analysis process for users without specialized bioinformatics expertise and to facilitate reproducibility through tracking of data provenance. WATERS guides users through the typical sequence analysis steps of alignment, chimera filtering, OTU clustering, taxonomy assignment, phylogeny tree building, and ecological analyses and visualization. By integrating existing tools into a single automated workflow, WATERS aims to reduce the effort required for 16S rRNA data analysis and allow researchers to focus on biological interpretation of results.
The document summarizes a study that used DNA barcoding and bioinformatics to identify plant species on the Northwest Nazarene University campus. Researchers extracted DNA from plant samples and used polymerase chain reaction to amplify the RuBisCo large subunit region. They found that the Carolina genomic protocol was more efficient for DNA extraction than the Wizard genomic protocol. The DNA sequences were then uploaded to databases like BOLD and BLAST to match the barcodes to known plant species and confirm identifications. In total, several common plants on campus were identified, though one sample could not be analyzed due to difficulties extracting its DNA. The study demonstrated the effectiveness of these techniques for biodiversity surveys.
This document summarizes research on the origins of Ashkenazi Levites based on analysis of Y-chromosome DNA from 66 Ashkenazi Levites with carefully constructed genealogies. It finds that over 50% of contemporary Ashkenazi Levites belong to a single lineage, Haplogroup R1a, which shows a close genetic relationship to non-Jewish populations in Eastern Europe. The research aims to determine if 4 individuals claiming descent from Yeshaya Horowitz are direct male-line descendants by comparing their Y-DNA to a worldwide phylogeny of R1a lineages. Preliminary results place the Ashkenazi Levites within the European branch of R1a and indicate a most recent common ancestor for the Hor
Role of bioinformatics in life sciences researchAnshika Bansal
1. The document discusses bioinformatics and summarizes some of its key applications and tools. It describes how bioinformatics merges biology and computer science to solve biological problems by applying computational tools to molecular data.
2. It provides examples of common bioinformatics tasks like retrieving sequences from databases, comparing sequences, analyzing genes and proteins, and viewing 3D structures.
3. The document lists several popular databases for nucleotide sequences, protein sequences, literature, and other biological data. It also introduces common bioinformatics tools for tasks like sequence alignment, translation, and structure analysis.
1. Next generation sequencing techniques like 454 sequencing and Illumina sequencing have enabled high-throughput sequencing of genomes and transcriptomes. These techniques can generate billions of bases of sequence data per day.
2. RNA-Seq is a technique that uses next generation sequencing to determine the RNA transcripts present in a cell and their expression levels. It has advantages over previous methods as it is highly sensitive, quantitative, and can discover isoforms and lowly expressed genes.
3. Analyzing RNA-Seq data involves aligning the short reads to a reference genome or transcriptome using tools like Bowtie or BWA. This allows discovery of novel transcripts, splicing patterns, and quantification of expression levels. Numerous studies have used RNA-
DNA barcoding is a method to identify species using short DNA sequences from standardized genes. It involves building a reference library of DNA barcodes from identified specimens and comparing unknown samples to the library. For animals, the CO1 gene is commonly used, while for plants the rbcL, matK, trnH, psbA and ITS genes provide identification. Barcoding has strengths in identifying juveniles, fragments, and through analysis of stomach contents, but relies on reference databases and may have weakness for some taxa. It can help identify herbal supplements, timber, rice varieties and other products.
What can your dog teach you about Genetics?rlanchantin
The following is a presentation to supplement a genetics class. The intention is to help build interest by showing dog breeding and how the scientific method has uncovered remarkable information about the morphological changes in dog breeds.
NCBI has developed a powerful suite of online biomedical and bioinformatics resources, including old friends like PubMed and OMIM and newer resources such as Genome. This collection of databases and tools are widely used by scientists and medical professionals across the world. With such a wealth of information, it is easy to get overwhelmed. Join us for an overview to NCBI resources for the information professional with an emphasis on biodata connectivity. No science degree required!
RNA-Seq To Identify Novel Markers For Research on Neural Tissue DifferentiationThermo Fisher Scientific
Neural tissue differentiated and cultured from derived stem cells is expected to revolutionize the treatment of brain and spinal injuries and diseases. Critical for these cellular therapies is accurate control and monitoring of differentiation but current methods for such cell typing are limited to qPCR and immunocytochemisty (ICC) which is not sufficient to discriminate between the numerous (likely >100,000) possible neural cell-types. Research using RNA sequencing (RNA-Seq) permits the characterization and discovery of much-needed novel markers. To define the temporal transcriptional signature of neural stem cells, cultured human embryonic stem cells (H9) were compared to induced neural stem cells (NSCs) at d0, d7 and d14. Total RNA was isolated over the time course from the undifferentiated and differentiated cells. Ion Torrent™ libraries were created to profile expression of miRNAs and whole transcriptomes for each cell population. Multiplexed Ion Proton™ sequencing and Torrent Suite™ Software analysis yielded ≥2.5 million small RNA reads and ≥29 million whole transcriptome reads per sample. Cluster analysis of the RNA-Seq profiles indicates that the cell populations have characteristic molecular signatures. Among genes that are decreased in induced cells are OCT4 (POU5F1), JARID2, NANOG, consistent with the differentiation of iPSCs into neurons. Among genes that showed increased expressions are NTRK2, POU3F2, and a number of HOX family genes. Recently, Ion AmpliSeq™ Transcriptome Human Gene Expression Kit has been launched, and the results from this analysis corroborated with whole transcriptome RNA-Seq results.
This document outlines a DNA barcoding protocol for Census of Marine Life (CoML) investigators to determine DNA barcodes from collected specimens. The protocol recommends preserving specimens in 95% ethanol, amplifying and sequencing the cytochrome c oxidase subunit I (COI) gene as the primary barcode marker, and submitting sequences to public databases linked to specimen data. Alternate targets may be needed for some taxa. The goal is to provide a uniform method for species identification that will aid CoML research and have broader scientific applications.
1) The study analyzed genetic diversity in 66 finger millet accessions from Ethiopia and Eritrea using RAPD markers.
2) A total of 123 RAPD fragments were amplified using 15 primers, of which 89 (72%) were found to be polymorphic.
3) Genetic similarity between accessions ranged from 0.585 to 0.984. Cluster analysis grouped the 66 accessions into nine clusters at a similarity index of 0.83, showing high genetic variability among the accessions.
Human genetic variation and its contribution to complex traitsgroovescience
This document summarizes a meeting discussing the human genome and human genetic variation.
The key points are:
1) In June 2000, the first draft of the human genome was announced, with fully sequenced publications in 2001. This marked a major milestone in understanding the human genome.
2) Since then, over 11 million SNPs and thousands of structural variants have been discovered through projects like HapMap and large sequencing studies. However, the majority of rare variants are still unknown.
3) Genome-wide association studies since 2006 have identified over 300 genetic loci associated with over 80 human traits and diseases. However, determining the functional consequences and molecular mechanisms remains a major challenge.
DNA Barcoding and its application in species identificationsupriya k
1) The document introduces a seminar on DNA barcoding and its role in discriminating plant species, given by Kaldate Supriya.
2) DNA barcoding is a technique that uses short, standardized gene sequences from organisms as a genetic barcode for species identification and discrimination.
3) The most common plant barcoding markers are chloroplast genes matK and rbcL, which provide sufficient variability to discriminate most plant species.
DNA Barcoding and its application in species identification
17022011
1. National Symposium : Frontiers in Biotechnology 17 th Feb 2011 Biotechnology Department, PU, Chandigarh Quest of DNA signature of species of animal, plant & microbes : Can we have a PIN code? Dinesh Kumar , B.Sc. Hons Zoo(BHU), M.Sc. Biotechnology(BHU), Ph.D. Biotechnology (BHU), PDF(USA) Senior Scientist(Animal Biotechnology) National Bureau of Animal Genetic Resources, Karnal-132 001, Haryana, INDIA Email: dineshkumarbhu@gmail.com, dinesh@iastate.edu
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3. How DNA signature is made for each species? The number of nucleic acid or amino acid differences between two organisms is proportional to the time since they diverged from a common ancestor . TIME MOLECULAR DIFFERENCES 1 AAGG C TA 2 AAGG G TA 3 AAGG AT G Example Rate of Evolution = 1bp per 100 years 1 2 3 100years 200 years
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12. Can we use microsatellite in Fungi? 02/17/11 Dinesh-PU-Talk-17-02-2011
59. Dinesh-PU-Talk-17-02-2011 Acknowledgements Dr Jagdeep Kaur , Dr Jagtar Singh & team, Biotechnology Department , Punjab University, Chandigarh My students- Prashant, Prem, Nishant, Dhiraj (NBAGR) My UG/PG students- Pooja(NISER) & Uday(GU) Dr James Reecy & his group, Iowa State University, USA Dr DK Arora, NBAIM(ICAR) Dr Rameshwar Singh & Dr SK Tomar, NDRI 02/17/11