This document summarizes a presentation on using CRISPR-Cas9 for crop improvement. It begins with an introduction to CRISPR-Cas9 and how it is used to edit genomes by removing, adding, or altering DNA sequences. It then discusses the mechanism of the CRISPR-Cas9 complex and how it creates breaks in DNA that are repaired. The document reviews several case studies where CRISPR was used to modify crops, including creating low-gluten wheat and improving rice. It finds that CRISPR can efficiently edit multiple genes simultaneously with few off-target effects. The conclusion states that CRISPR is revolutionizing agriculture by enabling the creation of higher yielding, more resistant crop varieties without transgenes.
Basics of Primer designing.
Steps involved in designing primers for Prokaryotic expression
Steps involved in designing primers for Eukaryotic expression
The document provides an overview of the history and techniques of transcriptome analysis. It discusses how RNA was separated from DNA with the formulation of the central dogma in 1958. Key developments include the discoveries of messenger RNA, transfer RNA, and ribosomal RNA in the 1960s. The document outlines techniques such as serial analysis of gene expression (SAGE) and RNA sequencing (RNA-seq) that allow comprehensive analysis of gene expression patterns. It provides details on the basic steps and advantages of SAGE and describes how next generation sequencing revolutionized transcriptome analysis through massive parallel sequencing.
Physical maps and their use in annotationsSheetal Mehla
This document discusses physical maps and their use in genome annotation. It provides information on several key topics:
- Physical maps show the relative positions of genes on chromosomes, similar to a topological map of a country. They are created by identifying DNA fragments using genetic markers or restriction enzymes.
- Genetic mapping was first described in 1911 and applied to humans in the 1950s. Whole genome maps were generated by the mid-1990s using improved techniques.
- Physical mapping involves cloning chromosomal fragments, determining their sizes and relative locations to construct a map. Pulsed-field gel electrophoresis and fluorescence-activated cell sorting are used to isolate individual chromosomes.
- Contigs are assembled from overlapping cloned fragments to
1. Forward genetics begins with the identification of an organism with an interesting mutant phenotype and aims to discover the function of genes defective in that mutant. It involves mutagenesis, screening for phenotypes of interest, genetic analysis, and chromosome walking to identify the mutated gene.
2. Reverse genetics starts with a known gene and determines the gene's function by modulating its activity through techniques like virus-induced gene silencing, RNA interference, TILLING, and gene deletion and observing resulting phenotypes in the organism.
3. Both forward and reverse genetics are aided by high-throughput approaches like insertional mutagenesis, which allows for rapid screening of large mutant collections to efficiently link phenotypes to genes.
Techniques of SNP Genotyping can be summarized as follows:
There are several techniques for genotyping SNPs including hybridization methods, enzyme-based methods, and other methods based on physical properties of DNA. Popular hybridization methods include DASH, molecular beacons, and gene chip arrays. Common enzyme-based techniques are RFLP, Invader assay, and oligonucleotide ligation assay. Other physical property-based methods include SSCP, TGGE, and pyrosequencing. Each method has its own pros and cons related to factors like speed, cost, and accuracy. Choosing the appropriate SNP genotyping technique depends on the number of SNPs needed to be analyzed and sample size.
Genomics refers to the study of the entire genome of an organism. It deals with mapping genes on chromosomes and sequencing entire genomes. While work on genomics began with prokaryotes like bacteria, research has now been conducted on crop plants like rice and Arabidopsis thaliana. Genomics is an interdisciplinary field that uses tools from molecular biology, robotics, and computing to study genomes. It provides information on genome size, gene number, gene function, and evolution. Genomics has applications in crop improvement through gene mapping, marker-assisted selection, and transgenic breeding. However, genomic research also faces limitations due to high costs, technical challenges, and complexity of traits.
CRISPR-Cas9 is a revolutionary genome editing tool that allows targeted modifications to DNA. It utilizes the Cas9 endonuclease enzyme, which is guided to a specific location in the genome by a short RNA molecule. When the Cas9 enzyme cuts the DNA, it triggers the cell's repair mechanisms which can introduce changes to the genome at that location. CRISPR-Cas9 has significant advantages over previous genome editing techniques in terms of efficiency and ease of use. It holds promise for curing genetic diseases, advancing biomedical research, and improving crops and livestock. Future directions include optimizing delivery methods and enhancing the precision and control of genome alterations.
This document summarizes a presentation on using CRISPR-Cas9 for crop improvement. It begins with an introduction to CRISPR-Cas9 and how it is used to edit genomes by removing, adding, or altering DNA sequences. It then discusses the mechanism of the CRISPR-Cas9 complex and how it creates breaks in DNA that are repaired. The document reviews several case studies where CRISPR was used to modify crops, including creating low-gluten wheat and improving rice. It finds that CRISPR can efficiently edit multiple genes simultaneously with few off-target effects. The conclusion states that CRISPR is revolutionizing agriculture by enabling the creation of higher yielding, more resistant crop varieties without transgenes.
Basics of Primer designing.
Steps involved in designing primers for Prokaryotic expression
Steps involved in designing primers for Eukaryotic expression
The document provides an overview of the history and techniques of transcriptome analysis. It discusses how RNA was separated from DNA with the formulation of the central dogma in 1958. Key developments include the discoveries of messenger RNA, transfer RNA, and ribosomal RNA in the 1960s. The document outlines techniques such as serial analysis of gene expression (SAGE) and RNA sequencing (RNA-seq) that allow comprehensive analysis of gene expression patterns. It provides details on the basic steps and advantages of SAGE and describes how next generation sequencing revolutionized transcriptome analysis through massive parallel sequencing.
Physical maps and their use in annotationsSheetal Mehla
This document discusses physical maps and their use in genome annotation. It provides information on several key topics:
- Physical maps show the relative positions of genes on chromosomes, similar to a topological map of a country. They are created by identifying DNA fragments using genetic markers or restriction enzymes.
- Genetic mapping was first described in 1911 and applied to humans in the 1950s. Whole genome maps were generated by the mid-1990s using improved techniques.
- Physical mapping involves cloning chromosomal fragments, determining their sizes and relative locations to construct a map. Pulsed-field gel electrophoresis and fluorescence-activated cell sorting are used to isolate individual chromosomes.
- Contigs are assembled from overlapping cloned fragments to
1. Forward genetics begins with the identification of an organism with an interesting mutant phenotype and aims to discover the function of genes defective in that mutant. It involves mutagenesis, screening for phenotypes of interest, genetic analysis, and chromosome walking to identify the mutated gene.
2. Reverse genetics starts with a known gene and determines the gene's function by modulating its activity through techniques like virus-induced gene silencing, RNA interference, TILLING, and gene deletion and observing resulting phenotypes in the organism.
3. Both forward and reverse genetics are aided by high-throughput approaches like insertional mutagenesis, which allows for rapid screening of large mutant collections to efficiently link phenotypes to genes.
Techniques of SNP Genotyping can be summarized as follows:
There are several techniques for genotyping SNPs including hybridization methods, enzyme-based methods, and other methods based on physical properties of DNA. Popular hybridization methods include DASH, molecular beacons, and gene chip arrays. Common enzyme-based techniques are RFLP, Invader assay, and oligonucleotide ligation assay. Other physical property-based methods include SSCP, TGGE, and pyrosequencing. Each method has its own pros and cons related to factors like speed, cost, and accuracy. Choosing the appropriate SNP genotyping technique depends on the number of SNPs needed to be analyzed and sample size.
Genomics refers to the study of the entire genome of an organism. It deals with mapping genes on chromosomes and sequencing entire genomes. While work on genomics began with prokaryotes like bacteria, research has now been conducted on crop plants like rice and Arabidopsis thaliana. Genomics is an interdisciplinary field that uses tools from molecular biology, robotics, and computing to study genomes. It provides information on genome size, gene number, gene function, and evolution. Genomics has applications in crop improvement through gene mapping, marker-assisted selection, and transgenic breeding. However, genomic research also faces limitations due to high costs, technical challenges, and complexity of traits.
CRISPR-Cas9 is a revolutionary genome editing tool that allows targeted modifications to DNA. It utilizes the Cas9 endonuclease enzyme, which is guided to a specific location in the genome by a short RNA molecule. When the Cas9 enzyme cuts the DNA, it triggers the cell's repair mechanisms which can introduce changes to the genome at that location. CRISPR-Cas9 has significant advantages over previous genome editing techniques in terms of efficiency and ease of use. It holds promise for curing genetic diseases, advancing biomedical research, and improving crops and livestock. Future directions include optimizing delivery methods and enhancing the precision and control of genome alterations.
Map-based cloning is a technique used to identify the genetic cause of a mutant phenotype by isolating overlapping DNA segments that progress along the chromosome toward a candidate gene. The process involves initially identifying a marker close to the gene of interest and then saturating the region with additional markers. Large populations are screened to find markers that rarely recombine with the gene. Genomic libraries are screened to find clones containing the markers, and chromosomal walking is used to obtain flanking markers on a single clone. DNA fragments between the markers are tested to rescue the wild-type phenotype and identify the candidate gene.
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.
Gene mapping, describes the methods used to identify the locus of a gene and the distances between genes. The essence of all genome mapping is to place a collection of molecular markers onto their respective positions on the genome. Molecular markers come in all forms.
This document defines molecular markers and describes two main types - biochemical markers and molecular genetic markers. Biochemical markers involve studying gene expression products like proteins through electrophoresis. Isoenzymes are variant enzymes that catalyze the same reaction but differ in properties, while alloenzymes are different alleles that can be detected through electrophoresis. Molecular genetic markers involve DNA polymorphisms detected by probes and include RAPD, RFLP, AFLP, SSR, and DNA fingerprinting techniques. These markers allow genome profiling and studying genetic variation.
Gene silencing is a technique that reduces or eliminates protein production from a gene. It occurs through RNA interference, where small interfering RNAs are processed by an enzyme called Dicer and loaded into an RNA-induced silencing complex (RISC) that targets complementary mRNAs for degradation. There are two main types of gene silencing - transcriptional which alters DNA accessibility, and post-transcriptional via RNAi technologies. RNAi has therapeutic applications for cancer, infectious diseases, and neurodegenerative disorders by knocking down target genes. The first approved RNAi drug, Patisiran, treats hereditary transthyretin-mediated amyloidosis.
Introduction
Transcriptome analysis
Goal of functional genomics
Why we need functional genomics
Technique
1. At DNA level
2.At RNA level
3. At protein level
4. loss of function
5. functional genomic and bioinformatics
Application
Latest research and reviews
Websites of functional genomics
Conclusions
Reference
This document discusses genetic analysis techniques including gene mapping and quantitative trait locus (QTL) analysis. It provides an overview of the basic requirements for gene mapping such as near isogenic lines and saturated physical maps. It describes the 5 step process for map-based cloning including gene tagging, high resolution mapping, physical mapping, sequencing, and transformation. It also discusses QTL analysis including principal objectives, factors considered, and methods to detect QTL like single marker analysis and interval mapping. Applications of QTL analysis in plant breeding and pre-breeding are mentioned. The key differences between traditional QTL mapping and association mapping are highlighted.
This document discusses the CRISPR-Cas9 genome editing technique. It begins with an introduction to CRISPR as an adaptive immune system in bacteria. The CRISPR mechanism involves acquiring DNA from invading viruses and using CRISPR RNA and Cas9 proteins to cut matching viral DNA. Scientists now use the Cas9 nuclease guided by a synthetic single guide RNA to make targeted cuts in DNA for genetic engineering. Some applications include modifying crop plants and research in mice embryos. However, using CRISPR in human embryos raises ethical concerns about germline editing and unintended consequences.
SAGE (Serial analysis of Gene Expression)talhakhat
SAGE (Serial Analysis of Gene Expression) is a technique that allows for the rapid and comprehensive analysis of gene expression patterns in a given cell population. It works by isolating mRNA, synthesizing cDNA, ligating short sequence tags to the cDNA, and then counting the number of times each tag is observed to quantify gene expression levels. The tags are concatenated and sequenced to generate vast amounts of data that must be analyzed computationally to identify which genes particular tags correspond to and to compare expression profiles between cell types. SAGE provides an overview of a cell's complete transcriptional activity and has been applied to study differences in cancer vs normal cells and to identify targets of oncogenes and tumor suppressor genes.
The document discusses various methods for synthesizing complementary DNA (cDNA) from messenger RNA (mRNA). It describes the basic three step process of first-strand cDNA synthesis using reverse transcriptase, removal of the RNA template, and second-strand cDNA synthesis using DNA polymerase. Early methods used hairpin priming of the second strand but were later improved using oligo-dT tailing and oligo-dG priming to avoid 5' end losses. Other methods discussed include oligo-capping to select for full-length mRNAs and RACE (rapid amplification of cDNA ends) to amplify cDNA fragments from both ends of transcripts.
Orthologs are homologous sequences that descended from a common ancestral sequence after a speciation event separated two species. Paralogs are homologous sequences related through a gene duplication event in a common ancestor. Xenologs are homologous sequences resulting from horizontal gene transfer between two organisms. The document discusses these three types of sequence homology - orthologs, paralogs, and xenologs - which arise from different evolutionary events involving speciation, duplication, and horizontal transfer of genes.
Crispr cas: A new tool of genome editing palaabhay
The document summarizes a presentation on CRISPR cas9, a new genome editing tool. It discusses the history of CRISPR, how CRISPR functions in bacteria, the classification and components of CRISPR systems, and the mechanism of CRISPR cas9. It then covers applications of CRISPR cas9 in genome editing, databases of CRISPR sequences, case studies using the technology, and future directions of CRISPR research.
The document discusses various methods for predicting protein function, including homology-based transfer of annotation and prediction of functional motifs and domains. Homology-based transfer can infer molecular function from sequence similarity, but biological process is only transferable between orthologs. Orthologs can be detected through phylogenetic trees or automated methods like InParanoid. Each protein domain contributes to molecular function, while short motifs like phosphorylation sites are also important. Functional annotation involves describing proteins at the molecular, biological process, and cellular component levels.
The document discusses techniques for DNA sequencing, including early methods developed in the 1970s by Maxam and Gilbert as well as Sanger. It provides details on how both methods work, such as using specific chemical or enzymatic reactions to generate labeled DNA fragments of different lengths corresponding to nucleotide positions in the sequence. The document also describes how these methods were later automated, using fluorescent tags on dideoxynucleotides and capillary electrophoresis to simultaneously sequence multiple samples in a single gel. This allowed rapid determination of thousands of nucleotides and enabled large genome sequencing projects such as the Human Genome Project.
Open reading frame is part of reading frame that contains no stop codons or region of amino acids coding triple codons.
ORF starts with start codon and ends at stop codon.
This document discusses the process of designing an miRNA. It is by Reza Rakhshi, a master's student in medical biotechnology. It explains how to find the sequence of a chosen miRNA, complete the reverse transcription sequence, and design the F plasmid sequence by selecting nucleotides from the 5' end of the miRNA sequence and adding nucleotides to balance the temperature with the R plasmid sequence.
1. The document discusses hERG safety assays, which evaluate a compound's potential to block the hERG potassium channel and cause cardiac toxicity.
2. It describes several methods for conducting hERG safety assays, including the automated QPatch HT system, conventional whole-cell patch clamp, and fluorescent flux-based assays.
3. The automated patch clamp system allows for higher throughput screening with better consistency than conventional patch clamp, and fluorescent flux assays can achieve very high throughput in 96-well or 384-well formats.
Map-based cloning is a technique used to identify the genetic cause of a mutant phenotype by isolating overlapping DNA segments that progress along the chromosome toward a candidate gene. The process involves initially identifying a marker close to the gene of interest and then saturating the region with additional markers. Large populations are screened to find markers that rarely recombine with the gene. Genomic libraries are screened to find clones containing the markers, and chromosomal walking is used to obtain flanking markers on a single clone. DNA fragments between the markers are tested to rescue the wild-type phenotype and identify the candidate gene.
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.
Gene mapping, describes the methods used to identify the locus of a gene and the distances between genes. The essence of all genome mapping is to place a collection of molecular markers onto their respective positions on the genome. Molecular markers come in all forms.
This document defines molecular markers and describes two main types - biochemical markers and molecular genetic markers. Biochemical markers involve studying gene expression products like proteins through electrophoresis. Isoenzymes are variant enzymes that catalyze the same reaction but differ in properties, while alloenzymes are different alleles that can be detected through electrophoresis. Molecular genetic markers involve DNA polymorphisms detected by probes and include RAPD, RFLP, AFLP, SSR, and DNA fingerprinting techniques. These markers allow genome profiling and studying genetic variation.
Gene silencing is a technique that reduces or eliminates protein production from a gene. It occurs through RNA interference, where small interfering RNAs are processed by an enzyme called Dicer and loaded into an RNA-induced silencing complex (RISC) that targets complementary mRNAs for degradation. There are two main types of gene silencing - transcriptional which alters DNA accessibility, and post-transcriptional via RNAi technologies. RNAi has therapeutic applications for cancer, infectious diseases, and neurodegenerative disorders by knocking down target genes. The first approved RNAi drug, Patisiran, treats hereditary transthyretin-mediated amyloidosis.
Introduction
Transcriptome analysis
Goal of functional genomics
Why we need functional genomics
Technique
1. At DNA level
2.At RNA level
3. At protein level
4. loss of function
5. functional genomic and bioinformatics
Application
Latest research and reviews
Websites of functional genomics
Conclusions
Reference
This document discusses genetic analysis techniques including gene mapping and quantitative trait locus (QTL) analysis. It provides an overview of the basic requirements for gene mapping such as near isogenic lines and saturated physical maps. It describes the 5 step process for map-based cloning including gene tagging, high resolution mapping, physical mapping, sequencing, and transformation. It also discusses QTL analysis including principal objectives, factors considered, and methods to detect QTL like single marker analysis and interval mapping. Applications of QTL analysis in plant breeding and pre-breeding are mentioned. The key differences between traditional QTL mapping and association mapping are highlighted.
This document discusses the CRISPR-Cas9 genome editing technique. It begins with an introduction to CRISPR as an adaptive immune system in bacteria. The CRISPR mechanism involves acquiring DNA from invading viruses and using CRISPR RNA and Cas9 proteins to cut matching viral DNA. Scientists now use the Cas9 nuclease guided by a synthetic single guide RNA to make targeted cuts in DNA for genetic engineering. Some applications include modifying crop plants and research in mice embryos. However, using CRISPR in human embryos raises ethical concerns about germline editing and unintended consequences.
SAGE (Serial analysis of Gene Expression)talhakhat
SAGE (Serial Analysis of Gene Expression) is a technique that allows for the rapid and comprehensive analysis of gene expression patterns in a given cell population. It works by isolating mRNA, synthesizing cDNA, ligating short sequence tags to the cDNA, and then counting the number of times each tag is observed to quantify gene expression levels. The tags are concatenated and sequenced to generate vast amounts of data that must be analyzed computationally to identify which genes particular tags correspond to and to compare expression profiles between cell types. SAGE provides an overview of a cell's complete transcriptional activity and has been applied to study differences in cancer vs normal cells and to identify targets of oncogenes and tumor suppressor genes.
The document discusses various methods for synthesizing complementary DNA (cDNA) from messenger RNA (mRNA). It describes the basic three step process of first-strand cDNA synthesis using reverse transcriptase, removal of the RNA template, and second-strand cDNA synthesis using DNA polymerase. Early methods used hairpin priming of the second strand but were later improved using oligo-dT tailing and oligo-dG priming to avoid 5' end losses. Other methods discussed include oligo-capping to select for full-length mRNAs and RACE (rapid amplification of cDNA ends) to amplify cDNA fragments from both ends of transcripts.
Orthologs are homologous sequences that descended from a common ancestral sequence after a speciation event separated two species. Paralogs are homologous sequences related through a gene duplication event in a common ancestor. Xenologs are homologous sequences resulting from horizontal gene transfer between two organisms. The document discusses these three types of sequence homology - orthologs, paralogs, and xenologs - which arise from different evolutionary events involving speciation, duplication, and horizontal transfer of genes.
Crispr cas: A new tool of genome editing palaabhay
The document summarizes a presentation on CRISPR cas9, a new genome editing tool. It discusses the history of CRISPR, how CRISPR functions in bacteria, the classification and components of CRISPR systems, and the mechanism of CRISPR cas9. It then covers applications of CRISPR cas9 in genome editing, databases of CRISPR sequences, case studies using the technology, and future directions of CRISPR research.
The document discusses various methods for predicting protein function, including homology-based transfer of annotation and prediction of functional motifs and domains. Homology-based transfer can infer molecular function from sequence similarity, but biological process is only transferable between orthologs. Orthologs can be detected through phylogenetic trees or automated methods like InParanoid. Each protein domain contributes to molecular function, while short motifs like phosphorylation sites are also important. Functional annotation involves describing proteins at the molecular, biological process, and cellular component levels.
The document discusses techniques for DNA sequencing, including early methods developed in the 1970s by Maxam and Gilbert as well as Sanger. It provides details on how both methods work, such as using specific chemical or enzymatic reactions to generate labeled DNA fragments of different lengths corresponding to nucleotide positions in the sequence. The document also describes how these methods were later automated, using fluorescent tags on dideoxynucleotides and capillary electrophoresis to simultaneously sequence multiple samples in a single gel. This allowed rapid determination of thousands of nucleotides and enabled large genome sequencing projects such as the Human Genome Project.
Open reading frame is part of reading frame that contains no stop codons or region of amino acids coding triple codons.
ORF starts with start codon and ends at stop codon.
This document discusses the process of designing an miRNA. It is by Reza Rakhshi, a master's student in medical biotechnology. It explains how to find the sequence of a chosen miRNA, complete the reverse transcription sequence, and design the F plasmid sequence by selecting nucleotides from the 5' end of the miRNA sequence and adding nucleotides to balance the temperature with the R plasmid sequence.
1. The document discusses hERG safety assays, which evaluate a compound's potential to block the hERG potassium channel and cause cardiac toxicity.
2. It describes several methods for conducting hERG safety assays, including the automated QPatch HT system, conventional whole-cell patch clamp, and fluorescent flux-based assays.
3. The automated patch clamp system allows for higher throughput screening with better consistency than conventional patch clamp, and fluorescent flux assays can achieve very high throughput in 96-well or 384-well formats.
The document summarizes the results of adding long read and linked read sequencing data to the Genome in a Bottle Consortium benchmark. Specifically:
- The benchmark regions now cover over 90% of the genome and include over 139,000 additional SNPs and 16,000 more insertions/deletions, mostly in difficult to sequence regions.
- The additional data improves variant detection in medically relevant genes and reduces errors compared to using short reads alone.
- However, performance of short read variant callers decreases when evaluated against the new expanded benchmark, highlighting remaining challenges in complex genomic regions.
WDR7 up-regulation upon knocking down of neighboring noncoding RNA using siRN...Vahid Erfani-Moghadam
1) The document examines the effect of silencing the long non-coding RNA lincRNA-RoR using siRNAs delivered by polyamidoamine dendrimers on the expression of the neighboring WDR7 gene in breast cancer cells.
2) The study showed that lincRNA-RoR expression was significantly decreased after transfection with siRNA encapsulated in PAMAM dendrimers. WDR7 expression correspondingly increased significantly upon lincRNA-RoR silencing.
3) This study demonstrates that PAMAM dendrimers can effectively deliver siRNAs to silence lincRNA-RoR and upregulate the adjacent WDR7 gene, suggesting their potential as a non-viral gene therapy vector
This document describes the process of designing primers for the human FOXP2 gene. It discusses the criteria for primer design, including length, melting temperature, and GC content. It outlines the steps taken to design primers using Primer3Plus and Primer-BLAST programs, including selecting the gene sequence, setting parameters, and analyzing potential primers. The document presents a potential forward and reverse primer pair for the FOXP2 gene that met design criteria and passed validation checks.
RAS is one of the most frequently mutated oncogenes in human cancer. KRAS is the isoform most frequently mutated, which constitutes about 85% of RAS mutations. As the most frequently mutated RAS isoform, KRAS is intensively studied in the past years.
In the formulation of KRAS integrated research plan, Medicilon has in-depth communication with customers. The backbone of scientific research has combined the characteristics of each case with years of practical experience and technical accumulation, and carefully submitted high-quality experimental plans and results to customers. Medicilon provides KRAS-targeted drug discovery, CMC research (API + formulation), pharmacodynamics research, PK study, safety evaluation and other services.https://www.medicilon.com/platform/kras/
The technology uses reclaimed CO₂ as the dyeing medium in a closed loop process. When pressurized, CO₂ becomes supercritical (SC-CO₂). In this state CO₂ has a very high solvent power, allowing the dye to dissolve easily.
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.
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...AbdullaAlAsif1
The pygmy halfbeak Dermogenys colletei, is known for its viviparous nature, this presents an intriguing case of relatively low fecundity, raising questions about potential compensatory reproductive strategies employed by this species. Our study delves into the examination of fecundity and the Gonadosomatic Index (GSI) in the Pygmy Halfbeak, D. colletei (Meisner, 2001), an intriguing viviparous fish indigenous to Sarawak, Borneo. We hypothesize that the Pygmy halfbeak, D. colletei, may exhibit unique reproductive adaptations to offset its low fecundity, thus enhancing its survival and fitness. To address this, we conducted a comprehensive study utilizing 28 mature female specimens of D. colletei, carefully measuring fecundity and GSI to shed light on the reproductive adaptations of this species. Our findings reveal that D. colletei indeed exhibits low fecundity, with a mean of 16.76 ± 2.01, and a mean GSI of 12.83 ± 1.27, providing crucial insights into the reproductive mechanisms at play in this species. These results underscore the existence of unique reproductive strategies in D. colletei, enabling its adaptation and persistence in Borneo's diverse aquatic ecosystems, and call for further ecological research to elucidate these mechanisms. This study lends to a better understanding of viviparous fish in Borneo and contributes to the broader field of aquatic ecology, enhancing our knowledge of species adaptations to unique ecological challenges.
ESR spectroscopy in liquid food and beverages.pptxPRIYANKA PATEL
With increasing population, people need to rely on packaged food stuffs. Packaging of food materials requires the preservation of food. There are various methods for the treatment of food to preserve them and irradiation treatment of food is one of them. It is the most common and the most harmless method for the food preservation as it does not alter the necessary micronutrients of food materials. Although irradiated food doesn’t cause any harm to the human health but still the quality assessment of food is required to provide consumers with necessary information about the food. ESR spectroscopy is the most sophisticated way to investigate the quality of the food and the free radicals induced during the processing of the food. ESR spin trapping technique is useful for the detection of highly unstable radicals in the food. The antioxidant capability of liquid food and beverages in mainly performed by spin trapping technique.
Authoring a personal GPT for your research and practice: How we created the Q...Leonel Morgado
Thematic analysis in qualitative research is a time-consuming and systematic task, typically done using teams. Team members must ground their activities on common understandings of the major concepts underlying the thematic analysis, and define criteria for its development. However, conceptual misunderstandings, equivocations, and lack of adherence to criteria are challenges to the quality and speed of this process. Given the distributed and uncertain nature of this process, we wondered if the tasks in thematic analysis could be supported by readily available artificial intelligence chatbots. Our early efforts point to potential benefits: not just saving time in the coding process but better adherence to criteria and grounding, by increasing triangulation between humans and artificial intelligence. This tutorial will provide a description and demonstration of the process we followed, as two academic researchers, to develop a custom ChatGPT to assist with qualitative coding in the thematic data analysis process of immersive learning accounts in a survey of the academic literature: QUAL-E Immersive Learning Thematic Analysis Helper. In the hands-on time, participants will try out QUAL-E and develop their ideas for their own qualitative coding ChatGPT. Participants that have the paid ChatGPT Plus subscription can create a draft of their assistants. The organizers will provide course materials and slide deck that participants will be able to utilize to continue development of their custom GPT. The paid subscription to ChatGPT Plus is not required to participate in this workshop, just for trying out personal GPTs during it.
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
1. GRNA DESIGN
Faculty of Advanced Technologies of Medical Sciences
Reza Rakhshi
Master student of medical biotechnology
2. CHOPCHOP SITE:
REZA RAKHSHI, MASTER STUDENT OF MEDICAL BIOTECHNOLOGY
RefSeq/ENSEMBL/gene name
or genomic coordinates.
Choose an Organism
3. CHOPCHOP SITE:
REZA RAKHSHI, MASTER STUDENT OF MEDICAL BIOTECHNOLOGY
Change default PAM and
guide length in Options.
Choose your goal
4. CHOPCHOP SITE- OPTIONS:
REZA RAKHSHI, MASTER STUDENT OF MEDICAL BIOTECHNOLOGY
Better than we target CDS or First and
Second exon
Optimum range for GC content is
40-60%
Self complementary is ZERO
5. CHOPCHOP SITE- OPTIONS:
REZA RAKHSHI, MASTER STUDENT OF MEDICAL BIOTECHNOLOGY
Optimum range is between 19-20
Depends on Cas choose best sequence
Optimum range for first parameter is 3
And for second parameter is ZERO
G20 so important to us
Depends on our cell line
GG or NG/GN important for my RNA
Polymerase (T7 and U6)
Finally PRESS
“ find the target site”
6. RESULT:
REZA RAKHSHI, MASTER STUDENT OF MEDICAL BIOTECHNOLOGY
Analyze results and
choose the best.
1. PAM seq.
2. G20
3. The 5′
base
4. Repeated base
7. DATA ANALYZE:
REZA RAKHSHI, MASTER STUDENT OF MEDICAL BIOTECHNOLOGY
Low mismatch in 3′
is
better than
Possibility of
framshift
Possibility of
deletion
8. CAS-OFFINDER- PRECISE ANALYSIS OF MISMATCH:
REZA RAKHSHI, MASTER STUDENT OF MEDICAL BIOTECHNOLOGY
Choose your PAM seq
Write your gRNA seq.
without PAM seq.
Respectively
Write:
3
1
1
finally