This document discusses genetic biomarkers and molecular markers. It describes different types of genetic variation like SNPs, indels, inversions, and rearrangements. It also summarizes various DNA-based genetic markers used in research, including RFLPs, RAPDs, AFLPs, ESTs, SNPs, and microsatellites. The document discusses the differences between type I (coding) and type II (non-coding) markers. It provides details on specific marker types and their applications, advantages, and disadvantages.
This document discusses different types of genetic markers that can be used to detect genetic variation, including single nucleotide polymorphisms (SNPs), insertions/deletions, microsatellites, restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPDs), amplified fragment length polymorphisms (AFLPs), and expressed sequence tags (ESTs). It describes how these markers are classified as type I (associated with genes of known function) or type II (associated with anonymous genomic regions) and compares their properties such as polymorphic information content and usefulness in genetic analysis.
Molecular Markers and Applications-Lecture.pdfaisha159367
This document discusses molecular markers, which are short DNA sequences that reveal polymorphisms between individuals. Molecular markers include SNPs, insertions/deletions, and variations in simple sequence repeats. The document describes several types of molecular markers and methods used to detect them, including RFLPs, RAPDs, AFLPs, SSRs, ISSRs, and CAPS. The applications of molecular markers include paternity testing, disease diagnosis, forensic analysis, and varietal identification in plants.
this presentation is about the molecular markers as we all know the molecular markers are the DNA sequences it can be easily detected and its inheritance is easily monitored.so the main basics of the molecular markers is the polymorphic nature so it can used as molecular markers.and this will gives you the idea about AFLP, RFLP, RAPD, SNPS,ETC.
using molecular marker technology in studying genetic diversity salmasaud8892
This document discusses various molecular marker technologies used for studying plant genetic diversity, including their advantages and disadvantages. It describes several types of genetic markers such as morphological traits, protein markers, and DNA markers. DNA markers like RFLP, RAPD, AFLP, microsatellites are discussed in detail, outlining their methodology, applications in areas like breeding, diversity studies, and more. The document provides an overview of important molecular marker techniques for measuring genetic variation at the phenotype and genotype level.
Molecular Markers, their application in crop improvementMrinali Mandape
Molecular markers such as SNPs, SSRs, RAPDs, AFLPs, and RFLPs can be used for crop improvement through applications like marker-assisted selection, linkage mapping, and trait-based selection. Molecular markers are DNA sequences that can identify specific locations in the genome and are linked to important agronomic traits. They are useful because they are selectively neutral, co-segregate with traits of interest, and follow Mendelian inheritance patterns.
Molecular marker General introduction by K. K. SAHU Sir.KAUSHAL SAHU
Introduction
Molecular marker
Characterstics of molecular marker
Types of molecular marker
. Non PCR Based
. PCR Based
RFLP
RAPD
AFLP
SSR
SNP
Conclusion
References
DNA markers can be used in plant breeding to identify plant varieties and track genetic inheritance. There are several types of DNA markers, including morphological markers, protein markers, RFLPs, RAPDs, AFLPs, SSRs, CAPS, SCARs, ISSRs, ESTs, STSs, and SNPs. DNA markers have advantages over morphological markers in that they are abundant, not influenced by environment, and can precisely track inheritance. The document discusses various DNA marker techniques and their applications in plant breeding, including genetic mapping, marker-assisted selection, and germplasm characterization.
Molecular markers- RFLP, RAPD, AFLP, SNP etc.Cherry
Molecular markers are identifiable DNA sequences used to locate genes associated with specific traits or genetic conditions.
A molecular marker is a specific gene fragment present at a specific position called ‘locus’ (pleural loci) in the genome of a cell.
In the pool of unknown DNA or in a whole chromosome, these molecular markers help in identification of particular sequence of DNA at particular location.
This document discusses different types of genetic markers that can be used to detect genetic variation, including single nucleotide polymorphisms (SNPs), insertions/deletions, microsatellites, restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPDs), amplified fragment length polymorphisms (AFLPs), and expressed sequence tags (ESTs). It describes how these markers are classified as type I (associated with genes of known function) or type II (associated with anonymous genomic regions) and compares their properties such as polymorphic information content and usefulness in genetic analysis.
Molecular Markers and Applications-Lecture.pdfaisha159367
This document discusses molecular markers, which are short DNA sequences that reveal polymorphisms between individuals. Molecular markers include SNPs, insertions/deletions, and variations in simple sequence repeats. The document describes several types of molecular markers and methods used to detect them, including RFLPs, RAPDs, AFLPs, SSRs, ISSRs, and CAPS. The applications of molecular markers include paternity testing, disease diagnosis, forensic analysis, and varietal identification in plants.
this presentation is about the molecular markers as we all know the molecular markers are the DNA sequences it can be easily detected and its inheritance is easily monitored.so the main basics of the molecular markers is the polymorphic nature so it can used as molecular markers.and this will gives you the idea about AFLP, RFLP, RAPD, SNPS,ETC.
using molecular marker technology in studying genetic diversity salmasaud8892
This document discusses various molecular marker technologies used for studying plant genetic diversity, including their advantages and disadvantages. It describes several types of genetic markers such as morphological traits, protein markers, and DNA markers. DNA markers like RFLP, RAPD, AFLP, microsatellites are discussed in detail, outlining their methodology, applications in areas like breeding, diversity studies, and more. The document provides an overview of important molecular marker techniques for measuring genetic variation at the phenotype and genotype level.
Molecular Markers, their application in crop improvementMrinali Mandape
Molecular markers such as SNPs, SSRs, RAPDs, AFLPs, and RFLPs can be used for crop improvement through applications like marker-assisted selection, linkage mapping, and trait-based selection. Molecular markers are DNA sequences that can identify specific locations in the genome and are linked to important agronomic traits. They are useful because they are selectively neutral, co-segregate with traits of interest, and follow Mendelian inheritance patterns.
Molecular marker General introduction by K. K. SAHU Sir.KAUSHAL SAHU
Introduction
Molecular marker
Characterstics of molecular marker
Types of molecular marker
. Non PCR Based
. PCR Based
RFLP
RAPD
AFLP
SSR
SNP
Conclusion
References
DNA markers can be used in plant breeding to identify plant varieties and track genetic inheritance. There are several types of DNA markers, including morphological markers, protein markers, RFLPs, RAPDs, AFLPs, SSRs, CAPS, SCARs, ISSRs, ESTs, STSs, and SNPs. DNA markers have advantages over morphological markers in that they are abundant, not influenced by environment, and can precisely track inheritance. The document discusses various DNA marker techniques and their applications in plant breeding, including genetic mapping, marker-assisted selection, and germplasm characterization.
Molecular markers- RFLP, RAPD, AFLP, SNP etc.Cherry
Molecular markers are identifiable DNA sequences used to locate genes associated with specific traits or genetic conditions.
A molecular marker is a specific gene fragment present at a specific position called ‘locus’ (pleural loci) in the genome of a cell.
In the pool of unknown DNA or in a whole chromosome, these molecular markers help in identification of particular sequence of DNA at particular location.
Gene mapping involves identifying the location of genes on chromosomes. It can help identify genes associated with inherited diseases. There are two main types of gene mapping: linkage mapping, which determines the relative distances between genes on a chromosome, and physical mapping, which measures distances in nucleotide bases. Gene mapping is done using various genetic markers, such as single nucleotide polymorphisms, microsatellites, and restriction fragment length polymorphisms. The goal is to better understand gene expression and regulation to help develop treatments and cures for genetic disorders.
Molecular markers are DNA sequences that can be easily detected and whose inheritance can be monitored. They are based on natural polymorphisms and allow studying the inheritance of genes. Common types of molecular markers include RFLPs, RAPDs, AFLPs, SSRs, and SNPs. RFLPs use restriction enzymes to detect differences in fragment lengths. RAPDs use random primers to detect sequence polymorphisms. AFLPs selectively amplify restriction fragments to detect length differences. SSRs detect variability in simple sequence repeats. Molecular markers are useful for applications like gene mapping, phylogenetic studies, and analyzing genetic diversity.
Molecular markers are used to identify DNA sequences and are based on natural DNA polymorphisms like substitutions, additions, or patterns. There are five key characteristics of suitable molecular markers: being polymorphic, co-dominant inheritance, random and frequent distribution, easy and cheap detection, and reproducibility. Common types of markers include RFLPs, AFLPs, RAPDs, VNTRs, microsatellites, SNPs, STRs, and others. These markers have various advantages and disadvantages and can be used for applications like characterization, genetic diagnostics, and forensic analysis.
A genetic marker is a gene or DNA sequence with a known location on a chromosome and associated with a particular gene or trait. It can be described as a variation, which may arise due to mutation or alteration in the genomic loci that can be observed. A genetic marker may be a short DNA sequence, such as a sequence surrounding a single base-pair change (single nucleotide polymorphism, SNP), or a long one, like mini & microsatellites.
DNA MARKERS 2023 DNA FINGERPRINTING TYPE OF METHODS OF DNA FINGERPRINTINGshooterzgame09
Molecular techniques allow for analysis of protein and DNA interactions through techniques like biochips, polymerase chain reaction (PCR), and quantitative real-time PCR. DNA fingerprinting and markers like RAPD, RFLP, AFLP, and SSR can be used to study genetics. Other techniques mentioned include site directed mutagenesis, reverse genetics, gene knockouts using RNAi and gene silencing, and gene therapy. Omics techniques like metagenomics, transcriptomics, and proteomics are also introduced.
Genetic markers are biological features determined by gene alleles that can be transmitted between generations and used to track individuals, tissues, cells, nuclei, chromosomes, or genes. They represent genetic differences between organisms and act as signs near or linked to genes controlling traits of interest without affecting phenotypes. Various types of genetic markers exist, including morphological, cytological, biochemical, and DNA-based markers like RFLPs, AFLPs, RAPDs, SSRs and SNPs. DNA markers detect polymorphisms through molecular techniques and occupy specific genomic positions. Together, genetic markers provide tools for inheritance studies and plant breeding applications.
This document discusses molecular taxonomy and the use of molecular markers for classifying organisms. It describes how taxonomy has shifted from morphology-based to molecular-based as technology has advanced. Molecular markers like DNA, RNA, proteins, and allozymes can be used as they change at the microlevel during speciation. Common molecular markers discussed include mitochondrial DNA, rRNA, RFLPs, microsatellites, and isozymes. Techniques used include PCR, gel electrophoresis, and DNA microarrays. Examples are provided of various studies using molecular markers like COI, rRNA, and isozymes to classify species of bacteria, birds, and protozoa. Molecular taxonomy is concluded to be more accurate than morphology-based taxonomy as
1. Molecular markers are DNA polymorphisms that can be used to identify genetic differences between individuals. They are used for various applications in vegetable crop breeding including assessing genetic diversity, gene tagging, varietal identification, and marker assisted selection.
2. Common molecular marker techniques include RFLP, RAPD, AFLP, SSR, and SNP. Each has advantages and disadvantages such as reproducibility, cost, and amount of DNA required.
3. Molecular markers allow for selection of traits without being influenced by environmental factors and can speed up breeding by identifying superior genotypes earlier. Marker assisted selection is used to improve both qualitative and quantitative traits.
The document discusses DNA markers for genetic variability studies in fish. It describes several types of genetic variation, including single nucleotide polymorphisms (SNPs) and insertions/deletions, that can be revealed using DNA marker technology. It also discusses different types of molecular markers, such as microsatellites and DNA barcoding using the CO1 gene, that can help characterize genetic variation within and among species.
The document discusses various types of genetic markers that can be used to measure genetic diversity, including random amplified polymorphic DNA (RAPD), inter-simple sequence repeats (ISSR), amplified fragment length polymorphism (AFLP), restriction fragment length polymorphism (RFLP), microsatellites, minisatellites, and mitochondrial DNA markers. It provides details on how each type of marker works and its applications in studying genetic variation, relationships, and evolution.
- Molecular markers are segments of DNA that represent genetic differences and can be used for genetic analysis, though they may not correlate with observable traits.
- An ideal molecular marker technique should be polymorphic, provide adequate genetic resolution, generate multiple independent markers simply and inexpensively using small amounts of DNA, and be linked to distinct phenotypes.
- Molecular marker techniques can be categorized as non-PCR based like RFLP analysis or PCR-based like AFLP, RAPD, and SNP analysis, which have been widely used in plant and animal research.
Molecular markers such as RFLP, RAPD, AFLP, SSR, SNPs, and ESTs can be used to detect polymorphisms at the DNA level. SSR markers, also known as microsatellites, detect length polymorphisms in tandem repeats of short nucleotide motifs. SSRs are widely distributed in genomes and show high levels of variation, making them useful for applications like genetic mapping, variety identification, and marker-assisted selection.
1. Molecular markers are DNA sequences that can be used to identify specific locations or genes on chromosomes. Different types of molecular markers include isozymes, restriction fragment length polymorphisms (RFLPs), variable number of tandem repeats (VNTRs), and single nucleotide polymorphisms (SNPs).
2. Molecular markers have a variety of uses in genetics and forensic analysis. RFLPs and VNTRs can be used for DNA fingerprinting and identifying individuals. SNP markers allow for analysis of genetic variations between individuals and populations. Molecular markers are also used for genome mapping and marker-assisted breeding in plants and animals.
3. There are several techniques used to detect molecular markers, including gel electrophoresis, Southern blot
this is a presentation on molecular markers that include what is molecular marker, it's types, biochemical markets (alloenzyme), it's classification, data analysis and it's applications
This document discusses gene mapping and sequencing. It defines key terms like gene, genome, and gene mapping. It describes different types of gene mapping including linkage mapping and physical mapping. It also discusses various genetic markers used in mapping like RFLPs, SNPs, AFLPs, RAPDs, SSLPs, microsatellites, and minisatellites. Details are provided on techniques like RFLP analysis, RAPD, AFLP, and their advantages and limitations. The document also covers Sanger sequencing, the chain termination method, and the chemical cleavage method developed by Maxam and Gilbert.
Molecular markers are DNA sequences that can be used to identify specific locations in the genome. They allow detection of differences between individuals. Common types of molecular markers include RFLP, RAPD, AFLP, SSR, and SNP. RFLP uses restriction enzymes and probes but requires a large amount of high quality DNA. RAPD uses PCR with random primers and needs little DNA but has low reproducibility. AFLP combines restriction enzymes and PCR for higher reproducibility. SSR and SNP detect differences in repetitive DNA sequences and single nucleotides, respectively. Molecular markers have various applications including measuring genetic diversity, fingerprinting, marker-assisted selection, and identifying genotypes.
TYPES OF MOLECULAR MARKERS,ITS ADVANTAGES AND DISADVANTAGESANFAS KT
Types of molecular markers (genetics)
ITS ADVANTAGES AND DISADVANTAGES
What is a genetic marker?
RFLP: Restriction fragment length polymorphism
AFLP: Amplified fragment length polymorphism
RAPD: Random amplification of polymorphic DNA
ISSR: Inter simple sequence repeat
STR: Short tandem repeats
SCAR: Sequence characterized amplified region
SNP: Single nucleotide polymorphism
SSR: Simple sequence repeat
The document discusses different types of molecular markers used in genetics. It describes Restriction Fragment Length Polymorphism (RFLP), Random Amplified Polymorphic DNA (RAPD), and Amplified Fragment Length Polymorphism (AFLP). RFLP involves digesting DNA with restriction enzymes and probing to identify polymorphic sequences. RAPD uses random primers to amplify variable DNA regions via PCR. AFLP combines restriction enzyme digestion with PCR amplification of genomic fragments tagged with adapters. The document compares advantages and disadvantages of RFLP, RAPD, and AFLP techniques.
Gene mapping involves identifying the location of genes on chromosomes. It can help identify genes associated with inherited diseases. There are two main types of gene mapping: linkage mapping, which determines the relative distances between genes on a chromosome, and physical mapping, which measures distances in nucleotide bases. Gene mapping is done using various genetic markers, such as single nucleotide polymorphisms, microsatellites, and restriction fragment length polymorphisms. The goal is to better understand gene expression and regulation to help develop treatments and cures for genetic disorders.
Molecular markers are DNA sequences that can be easily detected and whose inheritance can be monitored. They are based on natural polymorphisms and allow studying the inheritance of genes. Common types of molecular markers include RFLPs, RAPDs, AFLPs, SSRs, and SNPs. RFLPs use restriction enzymes to detect differences in fragment lengths. RAPDs use random primers to detect sequence polymorphisms. AFLPs selectively amplify restriction fragments to detect length differences. SSRs detect variability in simple sequence repeats. Molecular markers are useful for applications like gene mapping, phylogenetic studies, and analyzing genetic diversity.
Molecular markers are used to identify DNA sequences and are based on natural DNA polymorphisms like substitutions, additions, or patterns. There are five key characteristics of suitable molecular markers: being polymorphic, co-dominant inheritance, random and frequent distribution, easy and cheap detection, and reproducibility. Common types of markers include RFLPs, AFLPs, RAPDs, VNTRs, microsatellites, SNPs, STRs, and others. These markers have various advantages and disadvantages and can be used for applications like characterization, genetic diagnostics, and forensic analysis.
A genetic marker is a gene or DNA sequence with a known location on a chromosome and associated with a particular gene or trait. It can be described as a variation, which may arise due to mutation or alteration in the genomic loci that can be observed. A genetic marker may be a short DNA sequence, such as a sequence surrounding a single base-pair change (single nucleotide polymorphism, SNP), or a long one, like mini & microsatellites.
DNA MARKERS 2023 DNA FINGERPRINTING TYPE OF METHODS OF DNA FINGERPRINTINGshooterzgame09
Molecular techniques allow for analysis of protein and DNA interactions through techniques like biochips, polymerase chain reaction (PCR), and quantitative real-time PCR. DNA fingerprinting and markers like RAPD, RFLP, AFLP, and SSR can be used to study genetics. Other techniques mentioned include site directed mutagenesis, reverse genetics, gene knockouts using RNAi and gene silencing, and gene therapy. Omics techniques like metagenomics, transcriptomics, and proteomics are also introduced.
Genetic markers are biological features determined by gene alleles that can be transmitted between generations and used to track individuals, tissues, cells, nuclei, chromosomes, or genes. They represent genetic differences between organisms and act as signs near or linked to genes controlling traits of interest without affecting phenotypes. Various types of genetic markers exist, including morphological, cytological, biochemical, and DNA-based markers like RFLPs, AFLPs, RAPDs, SSRs and SNPs. DNA markers detect polymorphisms through molecular techniques and occupy specific genomic positions. Together, genetic markers provide tools for inheritance studies and plant breeding applications.
This document discusses molecular taxonomy and the use of molecular markers for classifying organisms. It describes how taxonomy has shifted from morphology-based to molecular-based as technology has advanced. Molecular markers like DNA, RNA, proteins, and allozymes can be used as they change at the microlevel during speciation. Common molecular markers discussed include mitochondrial DNA, rRNA, RFLPs, microsatellites, and isozymes. Techniques used include PCR, gel electrophoresis, and DNA microarrays. Examples are provided of various studies using molecular markers like COI, rRNA, and isozymes to classify species of bacteria, birds, and protozoa. Molecular taxonomy is concluded to be more accurate than morphology-based taxonomy as
1. Molecular markers are DNA polymorphisms that can be used to identify genetic differences between individuals. They are used for various applications in vegetable crop breeding including assessing genetic diversity, gene tagging, varietal identification, and marker assisted selection.
2. Common molecular marker techniques include RFLP, RAPD, AFLP, SSR, and SNP. Each has advantages and disadvantages such as reproducibility, cost, and amount of DNA required.
3. Molecular markers allow for selection of traits without being influenced by environmental factors and can speed up breeding by identifying superior genotypes earlier. Marker assisted selection is used to improve both qualitative and quantitative traits.
The document discusses DNA markers for genetic variability studies in fish. It describes several types of genetic variation, including single nucleotide polymorphisms (SNPs) and insertions/deletions, that can be revealed using DNA marker technology. It also discusses different types of molecular markers, such as microsatellites and DNA barcoding using the CO1 gene, that can help characterize genetic variation within and among species.
The document discusses various types of genetic markers that can be used to measure genetic diversity, including random amplified polymorphic DNA (RAPD), inter-simple sequence repeats (ISSR), amplified fragment length polymorphism (AFLP), restriction fragment length polymorphism (RFLP), microsatellites, minisatellites, and mitochondrial DNA markers. It provides details on how each type of marker works and its applications in studying genetic variation, relationships, and evolution.
- Molecular markers are segments of DNA that represent genetic differences and can be used for genetic analysis, though they may not correlate with observable traits.
- An ideal molecular marker technique should be polymorphic, provide adequate genetic resolution, generate multiple independent markers simply and inexpensively using small amounts of DNA, and be linked to distinct phenotypes.
- Molecular marker techniques can be categorized as non-PCR based like RFLP analysis or PCR-based like AFLP, RAPD, and SNP analysis, which have been widely used in plant and animal research.
Molecular markers such as RFLP, RAPD, AFLP, SSR, SNPs, and ESTs can be used to detect polymorphisms at the DNA level. SSR markers, also known as microsatellites, detect length polymorphisms in tandem repeats of short nucleotide motifs. SSRs are widely distributed in genomes and show high levels of variation, making them useful for applications like genetic mapping, variety identification, and marker-assisted selection.
1. Molecular markers are DNA sequences that can be used to identify specific locations or genes on chromosomes. Different types of molecular markers include isozymes, restriction fragment length polymorphisms (RFLPs), variable number of tandem repeats (VNTRs), and single nucleotide polymorphisms (SNPs).
2. Molecular markers have a variety of uses in genetics and forensic analysis. RFLPs and VNTRs can be used for DNA fingerprinting and identifying individuals. SNP markers allow for analysis of genetic variations between individuals and populations. Molecular markers are also used for genome mapping and marker-assisted breeding in plants and animals.
3. There are several techniques used to detect molecular markers, including gel electrophoresis, Southern blot
this is a presentation on molecular markers that include what is molecular marker, it's types, biochemical markets (alloenzyme), it's classification, data analysis and it's applications
This document discusses gene mapping and sequencing. It defines key terms like gene, genome, and gene mapping. It describes different types of gene mapping including linkage mapping and physical mapping. It also discusses various genetic markers used in mapping like RFLPs, SNPs, AFLPs, RAPDs, SSLPs, microsatellites, and minisatellites. Details are provided on techniques like RFLP analysis, RAPD, AFLP, and their advantages and limitations. The document also covers Sanger sequencing, the chain termination method, and the chemical cleavage method developed by Maxam and Gilbert.
Molecular markers are DNA sequences that can be used to identify specific locations in the genome. They allow detection of differences between individuals. Common types of molecular markers include RFLP, RAPD, AFLP, SSR, and SNP. RFLP uses restriction enzymes and probes but requires a large amount of high quality DNA. RAPD uses PCR with random primers and needs little DNA but has low reproducibility. AFLP combines restriction enzymes and PCR for higher reproducibility. SSR and SNP detect differences in repetitive DNA sequences and single nucleotides, respectively. Molecular markers have various applications including measuring genetic diversity, fingerprinting, marker-assisted selection, and identifying genotypes.
TYPES OF MOLECULAR MARKERS,ITS ADVANTAGES AND DISADVANTAGESANFAS KT
Types of molecular markers (genetics)
ITS ADVANTAGES AND DISADVANTAGES
What is a genetic marker?
RFLP: Restriction fragment length polymorphism
AFLP: Amplified fragment length polymorphism
RAPD: Random amplification of polymorphic DNA
ISSR: Inter simple sequence repeat
STR: Short tandem repeats
SCAR: Sequence characterized amplified region
SNP: Single nucleotide polymorphism
SSR: Simple sequence repeat
The document discusses different types of molecular markers used in genetics. It describes Restriction Fragment Length Polymorphism (RFLP), Random Amplified Polymorphic DNA (RAPD), and Amplified Fragment Length Polymorphism (AFLP). RFLP involves digesting DNA with restriction enzymes and probing to identify polymorphic sequences. RAPD uses random primers to amplify variable DNA regions via PCR. AFLP combines restriction enzyme digestion with PCR amplification of genomic fragments tagged with adapters. The document compares advantages and disadvantages of RFLP, RAPD, and AFLP techniques.
hematic appreciation test is a psychological assessment tool used to measure an individual's appreciation and understanding of specific themes or topics. This test helps to evaluate an individual's ability to connect different ideas and concepts within a given theme, as well as their overall comprehension and interpretation skills. The results of the test can provide valuable insights into an individual's cognitive abilities, creativity, and critical thinking skills
Current Ms word generated power point presentation covers major details about the micronuclei test. It's significance and assays to conduct it. It is used to detect the micronuclei formation inside the cells of nearly every multicellular organism. It's formation takes place during chromosomal sepration at metaphase.
The debris of the ‘last major merger’ is dynamically youngSérgio Sacani
The Milky Way’s (MW) inner stellar halo contains an [Fe/H]-rich component with highly eccentric orbits, often referred to as the
‘last major merger.’ Hypotheses for the origin of this component include Gaia-Sausage/Enceladus (GSE), where the progenitor
collided with the MW proto-disc 8–11 Gyr ago, and the Virgo Radial Merger (VRM), where the progenitor collided with the
MW disc within the last 3 Gyr. These two scenarios make different predictions about observable structure in local phase space,
because the morphology of debris depends on how long it has had to phase mix. The recently identified phase-space folds in Gaia
DR3 have positive caustic velocities, making them fundamentally different than the phase-mixed chevrons found in simulations
at late times. Roughly 20 per cent of the stars in the prograde local stellar halo are associated with the observed caustics. Based
on a simple phase-mixing model, the observed number of caustics are consistent with a merger that occurred 1–2 Gyr ago.
We also compare the observed phase-space distribution to FIRE-2 Latte simulations of GSE-like mergers, using a quantitative
measurement of phase mixing (2D causticality). The observed local phase-space distribution best matches the simulated data
1–2 Gyr after collision, and certainly not later than 3 Gyr. This is further evidence that the progenitor of the ‘last major merger’
did not collide with the MW proto-disc at early times, as is thought for the GSE, but instead collided with the MW disc within
the last few Gyr, consistent with the body of work surrounding the VRM.
The ability to recreate computational results with minimal effort and actionable metrics provides a solid foundation for scientific research and software development. When people can replicate an analysis at the touch of a button using open-source software, open data, and methods to assess and compare proposals, it significantly eases verification of results, engagement with a diverse range of contributors, and progress. However, we have yet to fully achieve this; there are still many sociotechnical frictions.
Inspired by David Donoho's vision, this talk aims to revisit the three crucial pillars of frictionless reproducibility (data sharing, code sharing, and competitive challenges) with the perspective of deep software variability.
Our observation is that multiple layers — hardware, operating systems, third-party libraries, software versions, input data, compile-time options, and parameters — are subject to variability that exacerbates frictions but is also essential for achieving robust, generalizable results and fostering innovation. I will first review the literature, providing evidence of how the complex variability interactions across these layers affect qualitative and quantitative software properties, thereby complicating the reproduction and replication of scientific studies in various fields.
I will then present some software engineering and AI techniques that can support the strategic exploration of variability spaces. These include the use of abstractions and models (e.g., feature models), sampling strategies (e.g., uniform, random), cost-effective measurements (e.g., incremental build of software configurations), and dimensionality reduction methods (e.g., transfer learning, feature selection, software debloating).
I will finally argue that deep variability is both the problem and solution of frictionless reproducibility, calling the software science community to develop new methods and tools to manage variability and foster reproducibility in software systems.
Exposé invité Journées Nationales du GDR GPL 2024
Or: Beyond linear.
Abstract: Equivariant neural networks are neural networks that incorporate symmetries. The nonlinear activation functions in these networks result in interesting nonlinear equivariant maps between simple representations, and motivate the key player of this talk: piecewise linear representation theory.
Disclaimer: No one is perfect, so please mind that there might be mistakes and typos.
dtubbenhauer@gmail.com
Corrected slides: dtubbenhauer.com/talks.html
Nucleophilic Addition of carbonyl compounds.pptxSSR02
Nucleophilic addition is the most important reaction of carbonyls. Not just aldehydes and ketones, but also carboxylic acid derivatives in general.
Carbonyls undergo addition reactions with a large range of nucleophiles.
Comparing the relative basicity of the nucleophile and the product is extremely helpful in determining how reversible the addition reaction is. Reactions with Grignards and hydrides are irreversible. Reactions with weak bases like halides and carboxylates generally don’t happen.
Electronic effects (inductive effects, electron donation) have a large impact on reactivity.
Large groups adjacent to the carbonyl will slow the rate of reaction.
Neutral nucleophiles can also add to carbonyls, although their additions are generally slower and more reversible. Acid catalysis is sometimes employed to increase the rate of addition.
Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...Travis Hills MN
Travis Hills of Minnesota developed a method to convert waste into high-value dry fertilizer, significantly enriching soil quality. By providing farmers with a valuable resource derived from waste, Travis Hills helps enhance farm profitability while promoting environmental stewardship. Travis Hills' sustainable practices lead to cost savings and increased revenue for farmers by improving resource efficiency and reducing waste.
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...Sérgio Sacani
Context. With a mass exceeding several 104 M⊙ and a rich and dense population of massive stars, supermassive young star clusters
represent the most massive star-forming environment that is dominated by the feedback from massive stars and gravitational interactions
among stars.
Aims. In this paper we present the Extended Westerlund 1 and 2 Open Clusters Survey (EWOCS) project, which aims to investigate
the influence of the starburst environment on the formation of stars and planets, and on the evolution of both low and high mass stars.
The primary targets of this project are Westerlund 1 and 2, the closest supermassive star clusters to the Sun.
Methods. The project is based primarily on recent observations conducted with the Chandra and JWST observatories. Specifically,
the Chandra survey of Westerlund 1 consists of 36 new ACIS-I observations, nearly co-pointed, for a total exposure time of 1 Msec.
Additionally, we included 8 archival Chandra/ACIS-S observations. This paper presents the resulting catalog of X-ray sources within
and around Westerlund 1. Sources were detected by combining various existing methods, and photon extraction and source validation
were carried out using the ACIS-Extract software.
Results. The EWOCS X-ray catalog comprises 5963 validated sources out of the 9420 initially provided to ACIS-Extract, reaching a
photon flux threshold of approximately 2 × 10−8 photons cm−2
s
−1
. The X-ray sources exhibit a highly concentrated spatial distribution,
with 1075 sources located within the central 1 arcmin. We have successfully detected X-ray emissions from 126 out of the 166 known
massive stars of the cluster, and we have collected over 71 000 photons from the magnetar CXO J164710.20-455217.
Phenomics assisted breeding in crop improvementIshaGoswami9
As the population is increasing and will reach about 9 billion upto 2050. Also due to climate change, it is difficult to meet the food requirement of such a large population. Facing the challenges presented by resource shortages, climate
change, and increasing global population, crop yield and quality need to be improved in a sustainable way over the coming decades. Genetic improvement by breeding is the best way to increase crop productivity. With the rapid progression of functional
genomics, an increasing number of crop genomes have been sequenced and dozens of genes influencing key agronomic traits have been identified. However, current genome sequence information has not been adequately exploited for understanding
the complex characteristics of multiple gene, owing to a lack of crop phenotypic data. Efficient, automatic, and accurate technologies and platforms that can capture phenotypic data that can
be linked to genomics information for crop improvement at all growth stages have become as important as genotyping. Thus,
high-throughput phenotyping has become the major bottleneck restricting crop breeding. Plant phenomics has been defined as the high-throughput, accurate acquisition and analysis of multi-dimensional phenotypes
during crop growing stages at the organism level, including the cell, tissue, organ, individual plant, plot, and field levels. With the rapid development of novel sensors, imaging technology,
and analysis methods, numerous infrastructure platforms have been developed for phenotyping.
2. Introduction
•
All organisms are subject to mutations as
a result of normal cellular operations or
interactions with the environment, leading
to genetic variation (polymorphism).
•
For this variation to be useful, it must be
(1) heritable and (2) discernable.
3. Introduction
•
Types of genetic variation include:
base substitutions, commonly referred to as
single nucleotide polymorphisms (SNPs).
insertions or deletions of nucleotide sequences
(indels) within a locus.
inversion of a segment of DNA within a locus.
rearrangement of DNA segments around a locus
of interest
4. DNA-based genetic markers
•
In the past, allozyme and mtDNA markers.
•
More recent marker types include:
restriction fragment length polymorphism (RFLP) (1)
randomly amplified polymorphic DNA (RAPD)
amplified fragment length polymorphism (AFLP)
expressed sequence tag (EST) markers
single nucleotide polymorphism (SNP)
microsatellite
5. Type I (coding) vs. type II (non coding)
markers
•
Molecular markers are classified into two
categories:
type I are markers associated with genes
of known function.
type II markers are associated with
anonymous genomic segments
6. Type I vs. type II markers
•
Most RFLP markers are type I markers because
they were identified during analysis of known
genes.
•
Allozyme markers are type I markers because the
protein they encode has known function.
•
RAPD markers are type II markers because RAPD
bands are amplified from anonymous genomic
regions via the polymerase chain reaction (PCR).
7. Type I vs. type II markers
• AFLP markers are type II because they are also
amplified from anonymous genomic regions.
• EST markers are type I markers because they
represent transcripts of genes, it is more common in
animals and plants research.
• SNP markers are mostly type II markers unless they
are developed from expressed sequences (eSNP or
cSNP) (type l).
• Microsatellite markers are type II markers unless
they are associated with genes of known function
(type l).
8. polymorphic
information content (PIC)
• The usefulness of molecular markers can be
measured based on their PIC.
• PIC refers to the value of a marker for detecting
polymorphism in a population.
• PIC depends on the number of detectable alleles
and the distribution of their frequencies.
• The greater the number of alleles, the greater the
PIC
9. Allozyme markers
• Allozymes are allelic variants of proteins produced
by a single gene locus, and are of interest as
markers because polymorphism exists and
because they represent protein products of genes.
• Amino acid differences in the polypeptide chains of
the different allelic forms of an enzyme reflect
changes in the underlying DNA sequence.
10. Allozyme markers
• Depending on the nature of the amino acid
changes, the resulting protein products may migrate
at different rates (due to charge and size
differences) when run through a starch gel
subjected to an electrical field.
• Differences in the presence/absence and relative
frequencies of alleles are used to quantify genetic
variation and distinguish among genetic units at the
levels of populations, species, and higher taxonomic
designations.
11. Allozyme markers
• Disadvantages:
heterozygote deficiencies due to null (enzymatically
inactive) alleles and the amount and quality of tissue
samples required.
some changes in DNA sequence are masked at the
protein level, reducing the level of detectable variation.
some changes in nucleotide sequence do not change
the encoded polypeptide (silent substitutions).
some polypeptide changes do not alter the mobility of
the protein in an electrophoretic gel (synonymous
substitutions).
12. Mitochondrial DNA markers
• Sequence divergence accumulates more rapidly in
mitochondrial than in nuclear DNA due to a faster
mutation rate result from a lack of repair
mechanisms during replication.
• Due to its non-Mendelian mode of inheritance, the
mtDNA molecule must be considered a single
locus in genetic investigations.
• Disadvantage: mtDNA data may not reflect those of
the nuclear genome.
13. Restriction fragment length
polymorphism (RFLP)
• Restriction endonucleases are bacterial enzymes that
recognize specific 4, 5, 6, or 8 bp nucleotide sequences
and cut DNA wherever these sequences are
encountered, so that changes in the DNA sequence due
to indels, base substitutions, or rearrangements
involving the restriction sites can result in the gain, loss,
or relocation of a restriction site.
• Digestion of DNA with restriction enzymes results in
fragments whose number and size can vary among
individuals, populations, and species.
14. Restriction fragment length
polymorphism (RFLP)
• Traditionally, fragments were separated using Southern
blot analysis, Most recent analyses replace it with PCR.
• If flanking sequences are known for a locus, the
segment containing the RFLP region is amplified via
PCR.
• If the length polymorphism is caused by a relatively
large (> approx. 100 bp depending on the size of the
undigested PCR product) deletion or insertion, gel
electrophoresis of the PCR products should reveal the
size difference.
15. Restriction fragment length
polymorphism (RFLP)
• By using a ‘universal’ primers on a target DNA, PCR
products can be digested with restriction enzymes and
visualized by simple staining with ethidium bromide due to
the increased amount of DNA produced by the PCR
method.
• Advantage: they are codominant markers, because the
size difference is often large, scoring is relatively easy.
• Disadvantage: the relatively low level of polymorphism. In
addition, either sequence information (for PCR analysis)
or probes (for Southern blot analysis) are required,
making it difficult and time-consuming
16.
17. Random amplified polymorphic
DNA (RAPD)
• RAPD procedures were using PCR to randomly
amplify anonymous segments of nuclear DNA with
an identical pair of primers 8 – 10 bp in length.
• Because the primers are short and relatively low
annealing temperatures (often 36– 40 C) are used,
the likelihood of amplifying multiple products is
great, with each product representing a different
locus.
18. Random amplified polymorphic
DNA (RAPD)
• The potential power is relatively high for detection of
polymorphism; typically, 5 –20 bands can be
produced using a given primer pair, and multiple sets
of random primers can be used to scan the entire
genome for differential RAPD bands.
• Because each band is considered a bi-allelic locus
(presence or absence of an amplified product), PIC
values for RAPDs fall below those for microsatellites
and SNPs, and RAPDs may not be as informative as
AFLPs because fewer loci are generated
simultaneously.
19.
20.
21.
22. Amplified fragment length
polymorphism (AFLP)
• AFLP is a PCR-based, multi-locus fingerprinting
technique that combines the strengths and
overcomes the weaknesses of the RFLP and RAPD
methods.
• Like RFLPs, the molecular basis of AFLP
polymorphisms includes indels between restriction
sites and base substitutions at restriction sites; like
RAPDs, it also includes base substitutions at PCR
primer binding sites.
23. Amplified fragment length
polymorphism (AFLP)
• The unique feature of the technique is the addition
of adaptors of known sequence to DNA fragments
generated by digestion of whole genomic DNA.
• This allows for the subsequent PCR amplification of
a subset of the total fragments for ease of
separation by gel electrophoresis.
• It is the same as RFLP, but instead of analyzing
one locus at a time, it allows for the analysis of
many loci simultaneously.
24.
25. Single nucleotide polymorphism
(SNP)
• It describes polymorphisms caused by point
mutations that give rise to different alleles
containing alternative bases at a given nucleotide
position within a locus. lt is used for DNA
sequencing.
• SNP markers are inherited as co-dominant
markers.
• Its PIC is not as high as multi-allele microsatellites.
• Random shotgun sequencing, amplicon
sequencing using PCR, and comparative EST
analysis are among the most popular sequencing
methods for SNP discovery.
26. Expressed sequence tags (ESTs)
• ESTs are single-pass sequences generated from
random sequencing of cDNA clones used for gene
profiling and genomic mapping.
• It offers a rapid and valuable first look at genes
expressed in specific tissue types, under specific
physiological conditions, or during specific
developmental stages.
• ESTs are useful for the development of cDNA
microarrays that allow analysis of differentially
expressed genes.
27. What is microsatellites & SSRs?
• Microsatellites or simple sequence repeats (SSRs),
represent codominant molecular genetic markers, i.e., both
allele in an individual are present in the analysis.
• Microsatellites are stretches of DNA consisting of tandemly
repeated short units of 1–6 base pairs (bp) in length. SSRs
typically span between twenty and a few hundred bases
• Due to their high level of polymorphism, relatively small size,
multiallelic nature, codominant inheritance and rapid
detection protocols, easily amplified with the PCR using two
unique oligonucleotide primers that flank the microsatellite
and hence define the microsatellite locus, these markers are
widely used in a variety of fundamental and applied fields of
life and medical sciences.
28. Microsatellites &SSRs
• Application in biology and medicine including:
forensics, molecular epidemiology, parasitology,
population and conservation genetics, genetic
mapping and genetic dissection of complex traits.
• Microsatellites are considered selectively neutral
markers, found anywhere in the genome, both in
protein-encoding (9-15%) and noncoding DNA.
• SSRs contribute to DNA structure, chromatin
organization, regulation of DNA recombination,
transcription and translation, gene expression and
cell cycle dynamics.
29. Microsatellites &SSRs
• The majority of microsatellites (30–67%) found are
dinucleotides, mostly represented by poly (A/T)
tracts, which are the most frequent classes of
SSRs, where (tri-, tetra-, penta-and
hexanucluotides) are about 1.5-fold less common in
genomic DNA.
• In the human genome, one microsatellite was found
every 6 kb and one CA repeat (the most common
type of tandem repeat) occurred every 30 kb of
DNA.
30. Microsatellites &SSRs
• Di- and tetranucleotide motifs are mostly clustered
in noncoding regions. In vertebrates, they are
distributed 42- and 30-fold less frequently in exons
than in intronic sequences and intergenic regions,
respectively.
• Long dimeric motifs are highly unstable within
expressed sequences, while in noncoding regions
most dinucleotide repeats can have surprisingly
long stretches, probably due to the high tolerance of
noncoding DNA to mutations.
31. Microsatellites &SSRs
• In contrast, triplets are found in both coding and
non-coding genomic regions with a high frequency.
• In humans, the expansion of trinucleotides,
encoding polyproline (CCG)n, polyarginine
(CGG)n, polyalanine [(GCC)n and (GCG)n] and
polyglutamine (CAG)n tracts within exons has been
described.
• Such expansions can lead to various
neurodegenerative and neuromuscular disorders,
including myotonic distrophy, fragile X syndrome,
Huntington's disease and spinocerebellar ataxia.
32. Function of microsatellites
1. DNA & chromosome structure
• Microsatellites are involved in forming a wide variety of
unusual DNA structures with simple and complex loop-
folding patterns.
• Telomeric and centromeric chromosome regions have
been shown to be rich in long arrays of a variety of
mono-, di-, tri-, tetra-and hexanucleotide motifs.
• The (TTAGGG)n hexamer sequence is recognized by
ribonucleoprotein polymerase, a telomerase, which
synthesizes telomere repeats onto the chromosome
ends to overcome the loss of sequences during DNA
replication, whereas other proteins prevent nucleolytic
degradation and confer stability of chromosomes.
33. Function of microsatellites
2. DNA recombination
• Dinucleotide motifs are preferential sites for
recombination events due to their high affinity for
recombination enzymes.
• Some SSR sequences, such as GT, CA, CT, GA
and others, may influence recombination through
their effects on DNA structure.
• SSRs were shown to be associated with the
assignment of some Rh phenotypes, and to be
involved in the molecular evolution of the human Rh
gene family and its orthologs in other eukaryotes
via replication slippage and recombination (gene
conversion) mechanisms.
34. Function of microsatellites
3. DNA replication
• Human genes encoding important cell fidelity and
growth factors, such as the B-cell
leukemia/lymphoma 2 (BCL2)-associated X protein,
insulin-like growth factor 2 receptor (IGF2R), breast
cancer early onset protein 2 (BRCA2) and
transforming growth factor beta 2 (TGF-β2), contain
short repeated sequences.
• Frame-shift mutations, resulting in both insertions
and deletions of repeat units within these
sequences that affect these genes and could
therefore initiate tumorigenes and can affect
enzymes controlling mutation rate and cell cycles.
35. Function of microsatellites
4. Gene expression
• SSRs located in promoter regions can influence drastic
or quantitative variations in gene expression and
change the level of promoter activity. The human insulin
minisatellite is highly polymorphic, and some of its
alleles were shown to regulate the expression of the
insulin gene.
• Intronic SSRs also can affect gene transcription affect
mRNA stability, representing binding sites for
translation factors. For example, such an effect was
measured for the tetrameric microsatellite located in
intron 1 of the human tyrosine hydroxylase gene and
the (CA)n dinucleotide repeat in the first intron of the
human epidermal growth factor receptor gene.
36. Development of type I (coding) and type II
(non-coding) microsatellite markers
• Type I markers are more difficult to develop. While non-
gene sequences are free to mutate, causing higher levels
of polymorphism, sequences within protein-coding regions
generally show lower levels of polymorphism because of
functional selection pressure.
• The most effective and rapid way for producing type I
microsatellites is the sequencing of clones from cDNA
libraries. Both 5′- and 3′-ends of a cDNA clone can be
sequenced to produce expressed sequence tags (ESTs).
• An EST represents a short, usually 200–600 bp-long
nucleotide sequence, which represents a uniquely
expressed region of the genome.
37. Development of type I (coding) and type II
(non-coding) microsattellite markers
• EST sequences are archived in a special branch of the
GenBank nucleotide database (dbEST). In Nov. 2005, the
EST database contained more than 31.3 million sequence
entries from around 500 species.
• A typical strategy for the development of ESTderived
microsatellite markers (data mining) includes preliminary
analysis of EST sequences from the DNA database to
remove poly(A) and poly(T) stretches which are common in
ESTs developed from the 3′-ends of cDNA clones and
correspond to the poly(A)-tails in eukaryotic mRNA.
• Sequences are further screened for putative SSRs (all
SSR-containing EST sequences). Following the
identification of ESTs, flanking primers should be designed
to amplify a microsatellite.
38. Applications of microsatellites
1. Genetic mapping
2. Individual DNA identification and
parentage assignment
3. Phylogeny, population and conservation
genetics
4. Molecular epidemiology and pathology
5. Quantitative trait loci mapping
6. Marker-assisted selection
39. 1. Genetic mapping
• SSRs remain the markers of choice for the
construction of linkage maps, because they are
highly polymorphic (and highly informative) and
require a small amount of DNA for each test.
• However, type II (noncoding) microsatellites are
very helpful for building a dense linkage map
framework into which type I (coding) markers can
then be incorporated (type I markers directly shows
the location of genes within the linkage map).
40. 1. Genetic mapping
• Linkage map is known as recombination maps and define
the order and distance of loci along a chromosome on the
basis of inheritance in families or populations.
• During meiosis, one random copy of each chromosome
pair is passed on to the gamete. Only genes located next
to each other are tightly linked.
• Crossingover results from physical exchange of
chromosome segments between two homologous
chromosomes of meiosis.
• Recombination results in the exchange of grandparental
alleles of genes further apart on that chromosome
41. 1. Genetic mapping
• Genetic distance is usually measured in
centimorgans (cM), where 1 cM is equivalent to
1% recombination between markers.
• Linkage map length differs between sexes. In
species with the XY sex determination system,
the female map is usually longer than the male
map because of higher recombination rates in
females compared to males.
42. 2. Individual DNA identification and
parentage assignment
• Microsatellites represent codominant single-locus DNA
markers. For each SSR, a progeny inherits one allele from
the father and another allele from the mother.
• Appropriate mathematical tools are available to evaluate
genetic relatedness and inheritance in these systems.
• A suitable methodology should be chosen for accurate and
correct analysis of genotyping data to reconstruct parentage
and pedigree structure.
• Due to the small size of SSRs, they are relatively stable in
degraded DNA. This is one reason why polymorphic SSRs
are widely used in forensic science, as microsatellite loci
remain relatively stable in bone remnants and dental tissue,
providing the basis for the successful application of ancient
DNA.
43. 3. Phylogeny, population and
conservation genetics
• By using variability within stretches of tandem
repeats, which evolve significantly more rapidly
than flanking regions.
• Flanking regions of microsatellites have proven
their value in establishing phylogenetic
relationships between species and families,
because they evolve much more slowly than
numbers of tandem repeats.
• Phylogeographical applications of micro-satellites
are eminently suitable, where population structure
is observed over a large geographical scale.
44. 4. Molecular epidemiology and
pathology
• Genomic instability of microsatellites has been extensively
evaluated in the field of carcinogenesis, where chromosomal
rearrangements (e.g., translocations, insertions and
deletions of genomic regions) occur.
• Carcinogenic events often happen within a genomic region
harboring a tumour suppressor gene and hence inactivate
the gene.
• Carcinogenic rearrangements are associated with loss of
heterozygosity (LOH) in microsatellites located within the
affected chromosome region.
• Thus, detecting microsatellite LOH in tumour tissues
contributes not only to molecular diagnosis of cancer, but
also points the possible location of a tumour suppressor
gene.
45. 5. Quantitative trait loci mapping
• A quantitative trait is one that has measurable
phenotypic variation owing to genetic and/or
environmental influences.
• The variation can be measured numerically (for
example, height, size or blood pressure) and
quantified.
• Generally, quantitative traits are complex
(multifactorial) and influenced by several
polymorphic genes and by environmental
conditions.
46. 6. Marker-assisted selection
• Marker-assisted selection is based on the concept that it
is possible to infer the presence of a gene from the
presence of a marker tightly linked to that gene.
• So, it is important to have high-density and high-resolution
genetic maps, which are saturated by markers in the
vicinity of a target locus (gene) that will be selected.
• The degree of saturation is the proportion of the genome
that will be covered by markers at the density such that
the maximum separation between markers is no greater
than a few centimorgans (usually 1–2 cM), within which
linkage of markers can be detected.