The document discusses the challenge of identifying effector genes in the wheat stripe rust fungus Puccinia striiformis f.sp. tritici. Effector genes are small secreted proteins that help the fungus infect wheat plants. Next-generation sequencing allows genomic and transcriptomic analysis but has limitations in assembling repetitive sequences like effectors. The author has analyzed transcriptomes of the fungus grown in planta to predict 100 small secreted protein candidates as potential effector genes for further laboratory tests. Identifying the fungus's effector genes could help develop resistant wheat varieties to reduce annual losses from stripe rust in Australian wheat production.
1. Next-generation sequencing methods such as Roche 454, Illumina GAII, and ABI SOLiD allow for high throughput DNA sequencing through massive parallel sequencing.
2. These methods involve clonal amplification of DNA fragments on solid surfaces or in emulsion PCR followed by sequencing using pyrosequencing, sequencing by synthesis with reversible terminators, or sequencing by ligation approaches.
3. The resulting sequencing data requires high throughput management and analysis pipelines to process the large volumes of sequence data produced.
Neurotech seminar ish wish 2014 madunaTando Maduna
This document discusses in vitro transcription and fluorescent in situ hybridization (FISH) techniques for visualizing gene expression in tissue samples. It describes the process of designing gene-specific primers, amplifying the gene of interest via PCR, synthesizing fluorescently-labeled RNA probes from the PCR product, hybridizing the probes to tissue samples, and using fluorescence microscopy to visualize where in the tissue the gene is expressed at a cellular level. The document provides technical details on each step of the process and discusses ways to optimize and troubleshoot the technique.
The introduction of supernova system: a vector system for single-cell labelin...Div. of Neurogenet., NIG
Here, we introduce the “Supernova system”, which has been reported in the following two papers:
- NMDAR-Regulated Dynamics of Layer 4 Neuronal Dendrites during Thalamocortical Reorganization in Neonates. Mizuno et al., Neuron 2014.
- Supernova: A Versatile Vector System for Single-Cell Labeling and Gene Function Studies in vivo. Luo et al. Sci. Rep.2016.
Lab web site: https://www.nig.ac.jp/labs/NeurGen/
Supernova support site: http://snsupport.webcrow.jp/
contact: tiwasato(at)nig.ac.jp
This document summarizes key events in translation including:
1. tRNAs act as adaptor molecules that pair each mRNA codon to its corresponding amino acid. Francis Crick first proposed this "adaptor hypothesis".
2. tRNAs undergo processing and modification before being charged with their cognate amino acids by aminoacyl tRNA synthetases.
3. The genetic code was deciphered through experiments using RNA polymers and identification of codon frequencies. Wobble base pairing allows multiple codons to code for the same amino acid.
4. Ribosomes catalyze peptide bond formation using rRNA. Bacterial and eukaryotic ribosomes differ in their subunit composition and initiation factors. Elongation
This document summarizes research on rust effectors and rust resistance genes in flax. It discusses how 20 flax rust resistance genes have been cloned and encode receptor components of the plant immune system. Four flax rust avirulence genes have been identified that encode small secreted proteins expressed in haustoria. Recognition of these avirulence proteins occurs through direct interaction with the corresponding resistance proteins. The document also discusses how stem rust effectors are delivered into plant cells and the potential application of knowledge from flax to cereal rust diseases.
This document discusses research into the sociogenetics of fire ants. It describes experiments conducted to identify genes that change activity levels in orphaned young fire ant queens over time after being separated from their colony. RNA was extracted from queens at 0, 6, and 24 hours after orphaning and hybridized to microarrays containing 10,000 ant genes. Analysis found significant changes in the activity of 297 genes, most occurring 24 hours after orphaning. The goal is to understand how orphaning affects gene expression and physiological changes in young queens.
1. Next-generation sequencing methods such as Roche 454, Illumina GAII, and ABI SOLiD allow for high throughput DNA sequencing through massive parallel sequencing.
2. These methods involve clonal amplification of DNA fragments on solid surfaces or in emulsion PCR followed by sequencing using pyrosequencing, sequencing by synthesis with reversible terminators, or sequencing by ligation approaches.
3. The resulting sequencing data requires high throughput management and analysis pipelines to process the large volumes of sequence data produced.
Neurotech seminar ish wish 2014 madunaTando Maduna
This document discusses in vitro transcription and fluorescent in situ hybridization (FISH) techniques for visualizing gene expression in tissue samples. It describes the process of designing gene-specific primers, amplifying the gene of interest via PCR, synthesizing fluorescently-labeled RNA probes from the PCR product, hybridizing the probes to tissue samples, and using fluorescence microscopy to visualize where in the tissue the gene is expressed at a cellular level. The document provides technical details on each step of the process and discusses ways to optimize and troubleshoot the technique.
The introduction of supernova system: a vector system for single-cell labelin...Div. of Neurogenet., NIG
Here, we introduce the “Supernova system”, which has been reported in the following two papers:
- NMDAR-Regulated Dynamics of Layer 4 Neuronal Dendrites during Thalamocortical Reorganization in Neonates. Mizuno et al., Neuron 2014.
- Supernova: A Versatile Vector System for Single-Cell Labeling and Gene Function Studies in vivo. Luo et al. Sci. Rep.2016.
Lab web site: https://www.nig.ac.jp/labs/NeurGen/
Supernova support site: http://snsupport.webcrow.jp/
contact: tiwasato(at)nig.ac.jp
This document summarizes key events in translation including:
1. tRNAs act as adaptor molecules that pair each mRNA codon to its corresponding amino acid. Francis Crick first proposed this "adaptor hypothesis".
2. tRNAs undergo processing and modification before being charged with their cognate amino acids by aminoacyl tRNA synthetases.
3. The genetic code was deciphered through experiments using RNA polymers and identification of codon frequencies. Wobble base pairing allows multiple codons to code for the same amino acid.
4. Ribosomes catalyze peptide bond formation using rRNA. Bacterial and eukaryotic ribosomes differ in their subunit composition and initiation factors. Elongation
This document summarizes research on rust effectors and rust resistance genes in flax. It discusses how 20 flax rust resistance genes have been cloned and encode receptor components of the plant immune system. Four flax rust avirulence genes have been identified that encode small secreted proteins expressed in haustoria. Recognition of these avirulence proteins occurs through direct interaction with the corresponding resistance proteins. The document also discusses how stem rust effectors are delivered into plant cells and the potential application of knowledge from flax to cereal rust diseases.
This document discusses research into the sociogenetics of fire ants. It describes experiments conducted to identify genes that change activity levels in orphaned young fire ant queens over time after being separated from their colony. RNA was extracted from queens at 0, 6, and 24 hours after orphaning and hybridized to microarrays containing 10,000 ant genes. Analysis found significant changes in the activity of 297 genes, most occurring 24 hours after orphaning. The goal is to understand how orphaning affects gene expression and physiological changes in young queens.
Cloning and expression of the Nodamura virus RNA-dependent RNA polymerase
Poster presentation at Society for the Advancement of Chicanos and Native Americans in Science (SACNAS) National Conference, October 2012, Seatltle, WA
The document describes a collection of lentiviral ORF clones called Precision LentiORFs contained in the pLOC lentiviral vector. Key features include:
- The ORF, fluorescent marker, and selection marker are expressed from one promoter for tracking ORF expression.
- It provides two methods (fluorescent marker and antibiotic resistance) to optimize transduction.
- The vector allows addition of fusion tags and works with both transfection and transduction for ORF expression in a variety of cell types.
- Protocols are provided for replicating plates of clones stored in glycerol stock and preparing plasmid DNA from individual clones.
Ever since hominids evolved into humans, they have observed that organisms resemble their blood relatives. For most of human history, people did not know conclusively why people resembled their families. The work of many scientists over many years led to the determination that DNA is why organisms resemble their relatives.
Evolution of the RecA Protein: from Systematics to Structure 1995 talk for CA...Jonathan Eisen
This document discusses the evolution of the RecA protein and its use for bacterial systematics. It finds that phylogenetic trees constructed from RecA sequence data are highly congruent with trees constructed from 16S rRNA sequence data. Both RecA and 16S rRNA trees resolve bacterial relationships with similar degrees of resolution. The analysis supports the use of RecA comparisons for molecular systematics studies of bacteria. It also finds that studying patterns of amino acid substitutions in RecA can provide insights into the protein's structure-function relationships.
1. Molecular markers are powerful tools that can detect genetic variation between individuals, populations, and species. They have revolutionized research on evolution, conservation, natural resource management, and genetic improvement programs.
2. There are two main types of molecular markers - those based on DNA hybridization and those based on PCR amplification. Examples include restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD).
3. Molecular markers have a variety of applications in fisheries, including identifying fish species, studying genetic variation and population structure in natural populations, comparing genetic variation between wild and hatchery populations, and marker-assisted selection in aquaculture.
This document summarizes work done on culturing crocodile cell lines and cloning the parc gene from Pseudomonas keratitis. Primary crocodile cell lines were established from various organs and immortalized using hTERT. The parc gene was cloned from mutant and wild-type Pseudomonas strains and will be expressed and crystallized to study its role in quinolone antibiotic resistance.
Next Generation Sequencing for Joubert Postersptaylor
Targeted resequencing of 14 individuals with Joubert syndrome identified variants in 26 genes, 9 of which had variants in multiple individuals. This approach seeks to discover novel disease genes contributing to Joubert syndrome by combining targeted DNA capture and massively parallel sequencing. While several genes have been identified as causing Joubert syndrome, they only account for about 50% of cases, so the aim is to identify additional causal genes through this sequencing of protein-coding regions in affected individuals.
Next Generation Sequencing for Joubert Syndromesptaylor
Targeted resequencing of 14 individuals with Joubert syndrome identified variants in 26 genes, 9 of which had variants in multiple individuals. This suggests these 9 genes may contribute to or cause Joubert syndrome. The study aimed to discover new disease genes for Joubert syndrome by combining targeted DNA capture and massively parallel sequencing of 14 unrelated affected individuals. A custom gene array was used to capture 180 cilia-related genes, which were then sequenced. Variants were identified and filtered against databases to find novel candidate variants.
GenTegra RNA Overview - Short & long term stabilizationkbebak
GenTegra RNA is a product that stabilizes RNA samples at ambient temperature for long-term storage, transport, and handling. According to ongoing experiments, RNA samples preserved with GenTegra RNA showed no degradation after 3.5 years of mixed temperature dry state storage at ambient temperature. After rehydration, the samples performed identically to frozen controls in downstream applications. GenTegra RNA protects RNA samples by stopping RNase activity in solution and preventing hydrolysis and oxidation when dried, allowing indefinite storage at ambient temperature.
This document discusses the use of molecular markers to study genetic diversity in indigenous food legumes of Pakistan. It provides examples of different types of molecular markers that have been used, including RAPDs, AFLPs, SSRs, and seed protein analyses. It also summarizes some key findings, such as high genetic diversity found within pea (Pisum sativum) accessions using different marker techniques, and lower but still significant diversity found within blackgram (Vigna mungo). The document advocates for the increased use of molecular markers to characterize genetic resources and enable targeted crop improvement efforts in Pakistan.
Nils Poulicard - Relations entre histoire évolutive et capacité d'adaptation ...Seminaire MEE
The document discusses how ancient host adaptation of Rice yellow mottle virus (RYMV) to different rice species modulated its current ability to break plant resistance. RYMV adapted to infect Oryza glaberrima rice around 500,000 years ago. This is evidenced by a threonine residue at codon 49 of the viral genome that enhances infection of O. glaberrima but limits resistance breaking in O. sativa rice. Directed mutations showed codon 49 influences the virus's ability to overcome two major resistance genes in its hosts. Ancient adaptation to a rice species continues to impact RYMV's resistance-breaking potential today.
This research aims to investigate the function of the transcription factor Snail2 during vascular development by generating a loss-of-function zebrafish model using CRISPR/Cas9 genome editing. Three single guide RNAs were designed to target the snai2 gene. Transgenic zebrafish lines were also generated using BAC recombineering to visualize vascular development. The CRISPR/Cas9 system was validated and zebrafish embryos were injected to create mutant lines. Founder fish were identified by crossing with wild type fish and genotyping offspring. This research demonstrates that CRISPR can introduce premature stop codons in snai2 and generate stable transgenic lines for studying gene function during vascular development.
This document summarizes seven strategies that plant viruses use to translate multiple proteins from a single mRNA, which is necessary because the host cell's translation system normally produces only one protein per mRNA. The strategies described are: 1) having a multipartite genome with multiple RNA segments, 2) producing proteins from a polyprotein via proteolytic cleavage, 3) using subgenomic RNAs, 4) read-through of stop codons to produce extended proteins, 5) leaky scanning of ribosomes, 6) internal initiation of translation, and 7) frameshifting during translation. Examples are provided for many plant viruses that employ each strategy, such as bromoviruses having multipartite genomes and potyviruses expressing via a poly
Tag-based transcript sequencing: Comparison of SAGE and CAGEMatthias Harbers
Talk given at the European Meeting on Next Generation Sequencing, August 29 to September 1, 2010, at Leiden University Medical Center, The Netherland.
Data have been published in: Hestand et al.: “Tissue-specific transcript annotation and expression profiling with complementary next-generation sequencing technologies.” Nucleic Acids Res. 2010 Sep;38(16):e165.
PMID: 20615900
The document discusses several topics related to genomics and phenotypes:
1. Genome-wide genotyping and sequencing can detect common and rare genetic variants that contribute to differences between individuals.
2. Knowledge of genetic factors like variants in VKORC1 and CYP2C9 genes can help determine the appropriate drug dose of warfarin for anticoagulation therapy in patients.
3. Targeted cancer therapies like Herceptin and various tyrosine kinase inhibitors are effective for cancers with specific "driver mutations" like EGFR mutations, which can be identified through genomic analysis of each patient's tumor.
The document discusses the history of discoveries related to DNA and genetics from 1859 to 1990. Some key events summarized are:
- In the 1850s-1900s, scientists like Darwin, Mendel, Miescher, and others made discoveries laying the foundations of genetics and heredity.
- In the 1920s-1950s, scientists including Griffith, Avery, Chargaff, Hershey and Chase, Watson and Crick contributed to understanding that DNA is the genetic material and determining its structure.
- In the 1950s-1960s, Nirenberg, Khorana and Ochoa helped decipher the genetic code by which DNA specifies proteins.
- In the 1970s,
This document provides an overview of VectorBase gene sets, including:
- VectorBase provides official gene sets for mosquitoes (Anopheles, Aedes, Culex) and the tick Ixodes scapularis using automated gene modeling initially, with ongoing manual curation.
- Gene sets are made using multiple approaches including aligning proteins to genomes, aligning ESTs, and ab initio gene prediction, which are then combined.
- There are limitations to automated gene sets including missed or incomplete genes due to assembly gaps/errors and lack of evidence, as well as potential merges or splits of genes. Genome assembly issues like gaps, repeats, and polymorphisms can also impact gene sets.
The document summarizes a presentation about developing open access tools to maximize the value of genomic data through the Genome Commons. The Genome Commons Database will be a repository of variants and associated traits. The Genome Commons Navigator will integrate this data and external tools to facilitate basic research, clinical applications, and more. Participation in the Critical Assessment of Genome Interpretation initiative aims to improve predictions of variant impacts on molecular, cellular and organismal phenotypes. Analysis of variants in folate pathway genes found classes of effects on yeast growth and folate remediation.
The document discusses Washington University's cancer mutation profiling test, which uses next-generation sequencing (NGS) to detect somatic mutations including single nucleotide variants (SNVs), insertions/deletions (indels), and structural variation. The test provides 1000x average coverage across 25 clinically reported genes and can detect variants present at 10% allele frequency. Considerations for clinical validation of the assay include DNA input quality and quantity from small biopsies or FFPE samples, as well as detection of low frequency variants due to tumor heterogeneity or presence of non-tumor DNA. Validation also requires accounting for detection of indels, copy number variation, and translocations across different NGS platforms and references.
Cloning and expression of the Nodamura virus RNA-dependent RNA polymerase
Poster presentation at Society for the Advancement of Chicanos and Native Americans in Science (SACNAS) National Conference, October 2012, Seatltle, WA
The document describes a collection of lentiviral ORF clones called Precision LentiORFs contained in the pLOC lentiviral vector. Key features include:
- The ORF, fluorescent marker, and selection marker are expressed from one promoter for tracking ORF expression.
- It provides two methods (fluorescent marker and antibiotic resistance) to optimize transduction.
- The vector allows addition of fusion tags and works with both transfection and transduction for ORF expression in a variety of cell types.
- Protocols are provided for replicating plates of clones stored in glycerol stock and preparing plasmid DNA from individual clones.
Ever since hominids evolved into humans, they have observed that organisms resemble their blood relatives. For most of human history, people did not know conclusively why people resembled their families. The work of many scientists over many years led to the determination that DNA is why organisms resemble their relatives.
Evolution of the RecA Protein: from Systematics to Structure 1995 talk for CA...Jonathan Eisen
This document discusses the evolution of the RecA protein and its use for bacterial systematics. It finds that phylogenetic trees constructed from RecA sequence data are highly congruent with trees constructed from 16S rRNA sequence data. Both RecA and 16S rRNA trees resolve bacterial relationships with similar degrees of resolution. The analysis supports the use of RecA comparisons for molecular systematics studies of bacteria. It also finds that studying patterns of amino acid substitutions in RecA can provide insights into the protein's structure-function relationships.
1. Molecular markers are powerful tools that can detect genetic variation between individuals, populations, and species. They have revolutionized research on evolution, conservation, natural resource management, and genetic improvement programs.
2. There are two main types of molecular markers - those based on DNA hybridization and those based on PCR amplification. Examples include restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD).
3. Molecular markers have a variety of applications in fisheries, including identifying fish species, studying genetic variation and population structure in natural populations, comparing genetic variation between wild and hatchery populations, and marker-assisted selection in aquaculture.
This document summarizes work done on culturing crocodile cell lines and cloning the parc gene from Pseudomonas keratitis. Primary crocodile cell lines were established from various organs and immortalized using hTERT. The parc gene was cloned from mutant and wild-type Pseudomonas strains and will be expressed and crystallized to study its role in quinolone antibiotic resistance.
Next Generation Sequencing for Joubert Postersptaylor
Targeted resequencing of 14 individuals with Joubert syndrome identified variants in 26 genes, 9 of which had variants in multiple individuals. This approach seeks to discover novel disease genes contributing to Joubert syndrome by combining targeted DNA capture and massively parallel sequencing. While several genes have been identified as causing Joubert syndrome, they only account for about 50% of cases, so the aim is to identify additional causal genes through this sequencing of protein-coding regions in affected individuals.
Next Generation Sequencing for Joubert Syndromesptaylor
Targeted resequencing of 14 individuals with Joubert syndrome identified variants in 26 genes, 9 of which had variants in multiple individuals. This suggests these 9 genes may contribute to or cause Joubert syndrome. The study aimed to discover new disease genes for Joubert syndrome by combining targeted DNA capture and massively parallel sequencing of 14 unrelated affected individuals. A custom gene array was used to capture 180 cilia-related genes, which were then sequenced. Variants were identified and filtered against databases to find novel candidate variants.
GenTegra RNA Overview - Short & long term stabilizationkbebak
GenTegra RNA is a product that stabilizes RNA samples at ambient temperature for long-term storage, transport, and handling. According to ongoing experiments, RNA samples preserved with GenTegra RNA showed no degradation after 3.5 years of mixed temperature dry state storage at ambient temperature. After rehydration, the samples performed identically to frozen controls in downstream applications. GenTegra RNA protects RNA samples by stopping RNase activity in solution and preventing hydrolysis and oxidation when dried, allowing indefinite storage at ambient temperature.
This document discusses the use of molecular markers to study genetic diversity in indigenous food legumes of Pakistan. It provides examples of different types of molecular markers that have been used, including RAPDs, AFLPs, SSRs, and seed protein analyses. It also summarizes some key findings, such as high genetic diversity found within pea (Pisum sativum) accessions using different marker techniques, and lower but still significant diversity found within blackgram (Vigna mungo). The document advocates for the increased use of molecular markers to characterize genetic resources and enable targeted crop improvement efforts in Pakistan.
Nils Poulicard - Relations entre histoire évolutive et capacité d'adaptation ...Seminaire MEE
The document discusses how ancient host adaptation of Rice yellow mottle virus (RYMV) to different rice species modulated its current ability to break plant resistance. RYMV adapted to infect Oryza glaberrima rice around 500,000 years ago. This is evidenced by a threonine residue at codon 49 of the viral genome that enhances infection of O. glaberrima but limits resistance breaking in O. sativa rice. Directed mutations showed codon 49 influences the virus's ability to overcome two major resistance genes in its hosts. Ancient adaptation to a rice species continues to impact RYMV's resistance-breaking potential today.
This research aims to investigate the function of the transcription factor Snail2 during vascular development by generating a loss-of-function zebrafish model using CRISPR/Cas9 genome editing. Three single guide RNAs were designed to target the snai2 gene. Transgenic zebrafish lines were also generated using BAC recombineering to visualize vascular development. The CRISPR/Cas9 system was validated and zebrafish embryos were injected to create mutant lines. Founder fish were identified by crossing with wild type fish and genotyping offspring. This research demonstrates that CRISPR can introduce premature stop codons in snai2 and generate stable transgenic lines for studying gene function during vascular development.
This document summarizes seven strategies that plant viruses use to translate multiple proteins from a single mRNA, which is necessary because the host cell's translation system normally produces only one protein per mRNA. The strategies described are: 1) having a multipartite genome with multiple RNA segments, 2) producing proteins from a polyprotein via proteolytic cleavage, 3) using subgenomic RNAs, 4) read-through of stop codons to produce extended proteins, 5) leaky scanning of ribosomes, 6) internal initiation of translation, and 7) frameshifting during translation. Examples are provided for many plant viruses that employ each strategy, such as bromoviruses having multipartite genomes and potyviruses expressing via a poly
Tag-based transcript sequencing: Comparison of SAGE and CAGEMatthias Harbers
Talk given at the European Meeting on Next Generation Sequencing, August 29 to September 1, 2010, at Leiden University Medical Center, The Netherland.
Data have been published in: Hestand et al.: “Tissue-specific transcript annotation and expression profiling with complementary next-generation sequencing technologies.” Nucleic Acids Res. 2010 Sep;38(16):e165.
PMID: 20615900
The document discusses several topics related to genomics and phenotypes:
1. Genome-wide genotyping and sequencing can detect common and rare genetic variants that contribute to differences between individuals.
2. Knowledge of genetic factors like variants in VKORC1 and CYP2C9 genes can help determine the appropriate drug dose of warfarin for anticoagulation therapy in patients.
3. Targeted cancer therapies like Herceptin and various tyrosine kinase inhibitors are effective for cancers with specific "driver mutations" like EGFR mutations, which can be identified through genomic analysis of each patient's tumor.
The document discusses the history of discoveries related to DNA and genetics from 1859 to 1990. Some key events summarized are:
- In the 1850s-1900s, scientists like Darwin, Mendel, Miescher, and others made discoveries laying the foundations of genetics and heredity.
- In the 1920s-1950s, scientists including Griffith, Avery, Chargaff, Hershey and Chase, Watson and Crick contributed to understanding that DNA is the genetic material and determining its structure.
- In the 1950s-1960s, Nirenberg, Khorana and Ochoa helped decipher the genetic code by which DNA specifies proteins.
- In the 1970s,
This document provides an overview of VectorBase gene sets, including:
- VectorBase provides official gene sets for mosquitoes (Anopheles, Aedes, Culex) and the tick Ixodes scapularis using automated gene modeling initially, with ongoing manual curation.
- Gene sets are made using multiple approaches including aligning proteins to genomes, aligning ESTs, and ab initio gene prediction, which are then combined.
- There are limitations to automated gene sets including missed or incomplete genes due to assembly gaps/errors and lack of evidence, as well as potential merges or splits of genes. Genome assembly issues like gaps, repeats, and polymorphisms can also impact gene sets.
The document summarizes a presentation about developing open access tools to maximize the value of genomic data through the Genome Commons. The Genome Commons Database will be a repository of variants and associated traits. The Genome Commons Navigator will integrate this data and external tools to facilitate basic research, clinical applications, and more. Participation in the Critical Assessment of Genome Interpretation initiative aims to improve predictions of variant impacts on molecular, cellular and organismal phenotypes. Analysis of variants in folate pathway genes found classes of effects on yeast growth and folate remediation.
The document discusses Washington University's cancer mutation profiling test, which uses next-generation sequencing (NGS) to detect somatic mutations including single nucleotide variants (SNVs), insertions/deletions (indels), and structural variation. The test provides 1000x average coverage across 25 clinically reported genes and can detect variants present at 10% allele frequency. Considerations for clinical validation of the assay include DNA input quality and quantity from small biopsies or FFPE samples, as well as detection of low frequency variants due to tumor heterogeneity or presence of non-tumor DNA. Validation also requires accounting for detection of indels, copy number variation, and translocations across different NGS platforms and references.
Transcript profiling is used to study gene expression during plant-pathogen interactions. Methods like northern blotting, microarrays, and SAGE analysis are used to analyze changes in host and pathogen transcription during infection. Basal defense responses in the host like accumulation of salicylic acid help resist pathogens. Successful pathogens suppress host defenses through effectors and modulate expression of host genes involved in senescence and cell death. The interaction outcome depends on the interplay between pathogen effectors and host resistance genes.
Avs molecular diagnostic techniques for detection of plant pathogensAMOL SHITOLE
PCR is a technique used to detect plant pathogens through amplification of DNA. It involves denaturing DNA, annealing primers, and polymerizing new strands of DNA. This process is repeated to exponentially increase the amount of target DNA. Nested PCR improves sensitivity by adding a second round of amplification. Other techniques like RT-PCR, IC-PCR, bio-PCR, and co-operational PCR have also been used to detect pathogens through nucleic acid amplification and analysis. PCR provides an efficient way to diagnose and study plant pathogens.
This document discusses various molecular techniques used for diagnosis of infectious diseases. It notes that molecular methods are most useful for pathogens that are difficult to detect by conventional methods, like Mycobacterium tuberculosis and Chlamydia trachomatis. It describes techniques like PCR, NASBA, TBA, SDA, LAMP that amplify nucleic acids from pathogens. Other methods discussed include plasmid profiling, nucleotide sequencing, restriction fragment length polymorphism (RFLP), and nucleic acid hybridization. The document provides details on how several of these techniques work and their applications in microbial identification, detection of antibiotic resistance, and epidemiological studies.
Genetic variations can occur in plants produced through plant tissue culture and be detected as changes in genetic characteristics or phenotypes. Variations commonly include changes in chromosome number and structure. Regenerated plants with chromosomal changes often show alterations in traits like leaf shape and color, growth rate, and fertility. These heritable mutations can persist when plants are transplanted to fields. Somaclonal variations are caused by genetic factors like pre-existing variations in explant cells or mutations during tissue culture, and can result in changes in plant characteristics that are useful for crop improvement.
This document discusses methods for detecting plant diseases using information technology. It describes direct detection methods like serological techniques including ELISA and molecular methods like PCR. Indirect detection methods include imaging techniques like fluorescence and hyperspectral imaging, as well as spectroscopic techniques. Various biosensors for disease detection are also outlined, such as bacteriophage-based biosensors, affinity biosensors using antibodies or DNA, and DNA/RNA-based affinity biosensors. Early detection of plant diseases using these IT-based methods can help control diseases and reduce agricultural losses.
MOLECULAR BIOLOGY TECHNIQUES USED IN ZOONOTIC DISEASE Nataraju S M
Zoonotic pathogens cause diseases and death both in human & animals which ultimately leads to man power and economic loss of the country. Traditional diagnostic methods identify a pathogen based on its phenotype.
The correct assessment of a clinical isolate takes more time. Faster and simpler methods of diagnosis is of great advantage. That is why molecular biology technique is the first and foremost choice .
Agricultural biotechnology has been used for over 10,000 years to improve crops and livestock. Modern techniques allow scientists to directly manipulate DNA to develop new traits. While this can increase yields, resist pests and diseases, there are also health, social, and environmental risks to consider. Benefits include higher production, enhanced nutrition, and virus resistance, but risks include allergic reactions, antibiotic resistance, gene flow to weeds, and loss of biodiversity. Careful safety testing and regulation aim to maximize benefits and minimize risks of this developing technology.
This document discusses several types of PCR techniques and their applications. It begins by explaining standard PCR and its development. It then describes several specialized PCR techniques including allele-specific PCR, asymmetric PCR, assembly PCR, hot-start PCR, helicase-dependent amplification, in situ PCR, inverse PCR, ligation-mediated PCR, and multiplex ligation-dependent probe amplification. Each technique is explained and examples of its uses and applications are provided.
This document discusses the plant pathogen Phytophthora. It is an oomycete, not a true fungus, that causes many diseases in plants. Phytophthora reproduces both sexually, requiring two mating types, and asexually through sporangia and zoospores. It infects a wide range of hosts and causes symptoms like leaf spots, stem cankers, root rot, and top dieback. Phytophthora spreads through splashing water or movement of infected plants and soil. It is active in wet and warm conditions. Detection methods include ELISA tests, culturing on selective media, and PCR tests for specific species.
The document summarizes research being conducted on Warburgia ugandensis, an important agroforestry tree used traditionally for malaria treatment. The research aims to identify genes and genomic regions related to active compounds in W. ugandensis. The PhD student is using DNA and RNA-based approaches like PCR, genomic libraries, and microarrays to analyze gene expression and methylation patterns between tissues and genotypes with different anti-malarial properties. The goal is to develop markers for plant breeding to obtain genotypes with high anti-malarial effectiveness and understand how environment impacts this trait. Initial results show promise in identifying new genes involved in sesquiterpene biosynthesis in this underexplored species.
identification of genes and gene-near regions related to active compounds in ...World Agroforestry (ICRAF)
The document summarizes research being conducted on Warburgia ugandensis, an important agroforestry tree used traditionally for malaria treatment. The research aims to identify genes and genomic regions related to active compounds in W. ugandensis. The PhD student is using DNA and RNA-based approaches like PCR, genomic libraries, and microarrays to analyze gene expression and methylation patterns between tissues and genotypes with different anti-malarial properties. The goal is to develop markers for plant breeding to obtain genotypes with high anti-malarial effectiveness and understand how environment impacts this trait. Initial results show promise in isolating housekeeping genes and constructing genomic libraries for further analysis.
The document summarizes research being conducted on Warburgia ugandensis, an important agroforestry tree in East Africa. The research aims to (1) identify genes and genomic regions related to active compounds in W. ugandensis, (2) develop a marker system for selecting genotypes with high anti-malarial effectiveness, and (3) understand the effects of environment on anti-malarial phenotype stability. The researcher is using genomic DNA and RNA approaches, including PCR with degenerate primers and methyl filtration, to isolate candidate genes and differentially expressed sequences for anti-malarial compounds. Initial results show most compounds are related to triterpenes, not sesquiterpenes as expected. The researcher
The document summarizes research being conducted on Warburgia ugandensis, an important agroforestry tree in East Africa. The research aims to 1) identify genes and genomic regions related to active compounds in W. ugandensis, 2) develop a marker system for selecting genotypes with high anti-malarial activity, and 3) understand the effects of environment on anti-malarial phenotype stability. The researcher is using genomic DNA and RNA approaches, including PCR with degenerate primers and microarray analysis of differentially methylated and expressed genomic regions, to identify genes involved in sesquiterpene biosynthesis and develop molecular markers. Progress includes successful PCR amplification, genomic library construction, and initial microarray hybridizations.
Molecular marker and its application to genome mapping and molecular breedingFOODCROPS
Molecular markers are genetic elements that can be used to follow chromosomes or chromosomal segments during genetic analysis. Molecular markers include molecular techniques like single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs). SSRs, also known as microsatellites, are tandem repeats of short DNA motifs that are highly polymorphic due to replication slippage errors. SNPs are single base pair changes that are the most common type of genetic variation. Both SNPs and SSRs are useful molecular markers that can be detected through polymerase chain reaction (PCR) and are important tools for genome mapping and molecular breeding applications.
This document outlines the Phase 2 workplan for an initiative to improve cowpea productivity in marginal environments in Sub-Saharan Africa. The plan involves partners across the cowpea growing region using modern breeding approaches like MARS (Marker-Assisted Recurrent Selection) and MABC (Marker-Assisted Backcrossing) to develop improved cowpea varieties with resistance to drought, pests, and diseases. Key activities include developing genomic resources, employing MARS and MABC, capacity building, and the expected outputs including validated markers, improved breeding lines, and enhanced capacity for cowpea breeding in Africa.
This document outlines the Phase 2 workplan for an initiative to improve cowpea productivity in marginal environments in Sub-Saharan Africa. The plan involves partners across the cowpea growing region using modern breeding approaches like MARS (marker-assisted recurrent selection) and MABC (marker-assisted backcrossing) to develop improved cowpea varieties with resistance to drought, pests and diseases. Key activities include developing genomic resources, employing MARS and MABC to generate breeding lines, and building capacity among African scientists. The goal is to modernize cowpea breeding and expedite the delivery of stress-resistant varieties to increase cowpea production and food security.
This document outlines a draft workplan for improving cowpea productivity in marginal environments in Sub-Saharan Africa from November 2009. It involves partners across the cowpea growing region using modern breeding strategies like MARS and MABC. The workplan builds on outputs from Phase 1 including drought tolerant germplasm, markers for stress resistance, and a high density SNP map. Key activities include developing a MAGIC population, genomic resources to support marker-assisted breeding, and employing MARS and MABC over two cycles to develop improved cowpea varieties for release. The goal is to speed delivery of cowpea varieties resistant to drought, diseases and pests to improve food security.
Isolation of genes differentially expressed during the defense response of Ca...CIAT
Genes differentially expressed in cassava in response to whitefly attack were identified through microarray analysis. Several genes involved in defense responses were found to be upregulated, including genes related to pathogenesis, proteasomes, chitinases, peroxidases, lipases, and heat shock proteins. Pathway analysis indicated that jasmonic acid/ethylene and salicylic acid signaling pathways regulating various defense mechanisms were activated. The microarray analysis provides insight into cassava's gene expression responses when defending against whitefly attack.
Genetic markers are sequences of DNA located at specific positions on chromosomes that can be associated with particular traits. Common types of genetic markers include RFLP, AFLP, RAPD, SNP, and VNTR. These markers allow researchers to locate genes associated with diseases and trace inheritance patterns. While harmless themselves, genetic markers enable the positioning of disease genes along chromosomes to better understand inheritance of traits and diseases.
The document describes the sequencing of the wheat genome, specifically chromosome 3B. Key points:
1. An international effort led by the IWGSC sequenced individual wheat chromosomes including 3B using a physical map-based approach.
2. Sequencing of the 1Gb chromosome 3B generated over 1000 scaffolds covering 995Mb with an N50 of 463kb. Genes and markers were annotated.
3. The sequenced and ordered chromosome 3B provides a foundation for accelerating wheat improvement through map-based cloning, marker development, and integrating genetic and genomic resources.
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 RNA-seq analysis. It begins with an introduction to Mikael Huss, a bioinformatics scientist, and provides an overview of how genomics, RNA profiles, protein profiles, and interactomics relate within systems biology. The document then discusses how gene expression analysis can provide insights into basic research questions regarding tissue and cell identity, as well as insights into diseases by identifying genes that are over- or under-expressed in patients. Finally, it provides a brief overview of the typical workflow for RNA-seq analysis, which involves mapping RNA sequencing reads to a reference genome or transcriptome.
1. Reconstitution of RNA interference (RNAi) in Saccharomyces cerevisiae by expressing RNAi components from other species. RNAi was successfully reconstituted using S. castellii Ago1 and Dcr1, but not human Ago2 and S. castellii Dcr1.
2. Inhibition of Hsp90 using geldanamycin did not reduce RNAi in the reconstituted S. cerevisiae strains, indicating Hsp90 is not required for RNAi in this system.
3. S. castellii Ago1 localized to P-bodies in S. cerevisiae independent of Dcr1, but the origin of small RNAs
Dissecting plant genomes with the PLAZA 2.5 comparative genomics platformKlaas Vandepoele
Dissecting plant genomes with the PLAZA comparative genomics platform.
Van Bel M, Proost S, Wischnitzki E, Movahedi S, Scheerlinck C, Van de Peer Y, Vandepoele K.
Plant Physiol. 2012 Feb;158(2):590-600.
With the arrival of low-cost, next-generation sequencing, a multitude of new plant genomes are being publicly released, providing unseen opportunities and challenges for comparative genomics studies. Here, we present PLAZA 2.5, a user-friendly online research environment to explore genomic information from different plants. This new release features updates to previous genome annotations and a substantial number of newly available plant genomes as well as various new interactive tools and visualizations. Currently, PLAZA hosts 25 organisms covering a broad taxonomic range, including 13 eudicots, five monocots, one lycopod, one moss, and five algae. The available data consist of structural and functional gene annotations, homologous gene families, multiple sequence alignments, phylogenetic trees, and colinear regions within and between species. A new Integrative Orthology Viewer, combining information from different orthology prediction methodologies, was developed to efficiently investigate complex orthology relationships. Cross-species expression analysis revealed that the integration of complementary data types extended the scope of complex orthology relationships, especially between more distantly related species. Finally, based on phylogenetic profiling, we propose a set of core gene families within the green plant lineage that will be instrumental to assess the gene space of draft or newly sequenced plant genomes during the assembly or annotation phase.
This document discusses the complexity of the transcriptome and the many sources of technical noise in RNA-Seq experiments. It notes that the transcriptome includes different combinations of exons from genes and that RNA-Seq experiments can be affected by over a dozen technical factors related to sample preparation and sequencing. Accurately analyzing results requires controlling for these sources of variability.
Experimental validation, integration to the linkage map and gene flow pilot s...CIAT
The document summarizes experimental validation of SNP markers for use in common bean (Phaseolus vulgaris) studies. It describes validating 130 soybean-derived SNP markers in 10 common bean genotypes through single base extension in a flow cytometer. Ninety-two SNPs were validated as true polymorphisms. The study also integrated the validated SNPs into an existing common bean genetic linkage map, adding 92 new markers. Finally, the document mentions plans to use validated SNPs to study the relationship between phenotypes and alleles/haplotypes, and to characterize genetic diversity and potential gene flow in a wild-weedy-crop complex of common beans from Colombia.
This document discusses advances in molecular techniques for identifying Phytophthora, Pythium, and related genera. It describes the challenges of morphological identification and outlines desired characteristics for molecular markers. Several nuclear and mitochondrial molecular loci used for species identification are discussed, including rDNA, Î2-tubulin, elicitin genes, and mitochondrial genes like cox1 and cox2. Techniques for molecular identification of isolates and subpopulations are summarized, such as DNA sequencing, PCR-RFLP, and development of species-specific PCR for pathogen detection.
This document summarizes a comparison of stem rust in oats and yellow rust in wheat in Sweden. It finds that stem rust, primarily affecting oats, shows variation expected from a sexually reproducing population, while yellow rust, primarily affecting wheat, can easily survive systemic infection and has a green bridge, allowing it to persist clonally. Sexual reproduction is necessary for stem rust epidemiology but not for yellow rust in the Swedish cropping system. A model is described that could help understand how dominant clones of pathogens appear and are replaced over multiple seasons.
1) In 2013, wheat stem rust outbreaks occurred in Ethiopia and parts of Western Europe for the first time in decades.
2) In Ethiopia, the variety "Digalu" was heavily affected, with some fields experiencing over 90% yield losses. Samples were collected and characterized, identifying the races TTKSK, JRCQC, and RRTTF.
3) In Western Europe, samples were collected from Germany and Denmark and characterized as the TKTT_ race, which had also been identified previously in the Middle East and North Africa.
1) Field trials in Ethiopia identified new stem rust races virulent against genes commonly used in durum wheat breeding programs.
2) Screening of over 6,800 cultivated and wild tetraploid wheat accessions identified sources of resistance, with emmer and wild emmer showing the highest resistance levels.
3) Genetic mapping of resistance genes is underway using biparental crosses to elucidate the genetics of resistance and map genes from tetraploid sources.
Agrovegetal is a farmer-owned seed company in Southern Spain that has been releasing new wheat cultivars for 15 years through collaborative partnerships with CIMMYT. Through multi-location yield trials evaluating disease resistance, quality, and stability, Agrovegetal has released cultivars such as Don Ricardo durum wheat that is highly yielding with good quality and leaf rust resistance. Agrovegetal now holds a 12% market share for durum wheat seeds and 10% for bread wheat seeds in Spain through the commercial success of cultivars developed through its wheat breeding program.
Three key findings from the field pathogenomics study of wheat yellow rust:
1) Gene sequencing of 40 rust samples from UK fields in 2013 found four distinct populations that correlated with location.
2) A small number of genes were specifically differentially expressed between the populations, some of which may encode candidate effector proteins.
3) The pathogen's transcriptome could be matched to wheat varieties, allowing rapid identification of the host variety from RNAseq data alone.
The document discusses the need for public-private partnerships in wheat production in India to boost productivity. It notes that while the public sector has established various research and extension organizations, wheat productivity remains low. The role of the private sector in wheat seed production and marketing has increased in recent years. However, marketing public varieties remains challenging for private companies due to competition and demand forecasting issues. The document advocates for complementary roles between the public and private sectors in research, distribution of public technologies, and marketing/extension. It provides an example of one private company, DCM Shriram Ltd., that has invested in wheat research and seen growing sales of its proprietary varieties in India.
This document discusses the importance and challenges of data and germplasm sharing. It makes the following key points:
1. Sharing knowledge and germplasm has historically been important for progress, but restrictions have slowed in recent decades due to intellectual property laws and treaties.
2. New technologies generate vast amounts of data that is difficult to analyze and share under consistent standards. Improved experimental design is needed to link genotype, phenotype and environment data.
3. Initiatives like BGRI advocate sharing data and germplasm to accelerate breeding for diseases like rust resistance in wheat, but restricted movement of germplasm requires alternative solutions like information sharing.
This document summarizes research on the global occurrence and economic impact of stripe rust, a fungal wheat disease. It finds that stripe rust has spread rapidly in recent decades to new regions due to climate change, susceptible wheat varieties, and pathogen adaptation. Based on survey responses, it estimates that stripe rust causes average annual global wheat yield losses valued at $848 million. It estimates that investing $28 million annually in research could help avert these losses and provide a positive return on investment. The document also analyzes changing spatial patterns of stripe rust outbreaks and losses in the United States over time.
The document describes a study that analyzed genetic data from wheat leaf rust fungus (Puccinia triticina) isolates infecting different wheat genomes to better understand the evolutionary relationships between these host-specific types. The researchers analyzed single nucleotide polymorphism (SNP) markers from 70 fungus samples infecting wheat and found two major clades of common wheat isolates that were distinct from durum wheat isolates. Analysis supported the hypothesis that the original fungus form infected Aegilops speltoides before evolving to infect common wheat and then durum wheat.
The document summarizes molecular characterization of Puccinia striiformis f.sp. tritici (Pst) isolates from Western Canada. Pst isolates were sequenced using Illumina platforms and assembled de novo. Phylogenetic trees were constructed based on rRNA sequences and whole genome assemblies. Comparisons between old isolates from 1990-1993 and new isolates from 2007-2012 identified unique and enriched gene sequences, suggesting genome reorganization in Pst. Functional annotation revealed differences in biological processes between old and new isolates, such as transport and response to exogenous molecules in new isolates.
The document summarizes research on pleiotropic adult plant resistance (PAPR) loci in wheat. Key points:
1. CIMMYT has conducted PAPR research since the 1970s, identifying loci such as Lr34, Lr46, and Lr67 that confer resistance to multiple diseases.
2. Studies mapped additional PAPR QTL in various wheat populations and identified markers for genes like Lr46, Sr2, and Yr54 useful for marker-assisted selection.
3. Research involves fine mapping genes, identifying deletion mutants, and understanding resistance mechanisms to improve durability and pyramide genes in wheat breeding.
4. An international shuttle breeding program
This document summarizes new evidence that the wheat stripe rust fungus Puccinia striiformis f. sp. tritici undergoes sexual reproduction on barberry plants in China. Through surveys, 23 barberry species in China were found to be susceptible hosts for P. striiformis when artificially inoculated. Stripe rust was also observed naturally infecting 3 barberry species in the field. Isolates recovered from infected barberry plants in nature had different virulence patterns than major wheat stripe rust races in China, indicating sexual recombination may contribute to new virulence variations on barberry.
This document discusses factors influencing the adoption of improved wheat varieties by farmers in Kenya. It finds that more educated farmers and those with more wheat farming experience are more likely to adopt new varieties. However, adoption is low overall, especially among small-scale farmers. The major barriers to adoption include a lack of contractual agreements in the wheat market, limited availability and high costs of quality seeds, and insufficient information dissemination regarding new varieties. The document recommends improving awareness and access to seeds, enhancing collective action among farmer groups, and conducting additional surveys and workshops to promote variety adoption.
This document provides evidence of recombination between the Sr2 and Fhb1 genes in wheat. It summarizes that a doubled haploid population from a cross between Carberry and AC Cadillac wheat lines showed: 1) recombinants expressing both pseudo-black chaff (PBC, linked to Sr2) and low Fusarium head blight (FHB, linked to Fhb1), 2) genetic mapping identified QTL in the Sr2/Fhb1 region associated with both traits, and 3) haplotype analysis identified recombinants with the Sr2 and Fhb1 marker haplotypes separated.
This document discusses wheat rust diseases as a potential problem for Norwegian wheat cultivation due to forecasted climate changes. Currently, wheat rusts are not a major issue but stripe rust occasionally causes local outbreaks. However, predicted higher winter temperatures could allow more rust inoculum to survive winters. Milder autumns and springs along with warmer, wetter summers may also promote faster rust development. As a result, the risks of future rust epidemics are expected to increase. The document recommends strategies like growing winter wheat varieties with good rust resistance and breeding for horizontal resistance to control potential rust problems.
This document summarizes research on achieving sustainable leaf rust control in durum wheat. It discusses the importance of leaf rust, major resistance genes that have been identified and overcome by evolving rust races, and efforts to develop slow rusting resistance through gene pyramiding. Key findings include identification of multiple major genes conferring resistance, the breakdown of these genes over time, efforts to combine minor genes to provide more durable slow rusting resistance, and the need to continue broadening genetic resistance.
The Global Rust Reference Center (GRRC) in Denmark aims to manage wheat rust surveillance, act as an early warning system, disseminate results online, maintain pathogen genetic resources, and provide training. It has expanded facilities including quarantine zones, labs, and greenhouse space. The GRRC works with over 40 international collaborators from Asia, Africa, Europe, and South America. It collects and maintains live wheat rust isolates to assist breeding and research. The GRRC also conducts research on rust spread, evolution, genetics, and host-pathogen interactions. Training is provided to students and scientists in wheat rust pathology. Ongoing challenges include understanding global rust dynamics and improving phenotyping methods. Sustained efforts are needed
This document summarizes the Borlaug Global Rust Initiative from 2009-2014. It discusses the initiative's focus on farmers, globally coordinated surveillance efforts, international screening nurseries, and CGIAR wheat breeding programs. It also highlights the importance of leadership, advocacy, communication, and gene stewardship in combating wheat rust diseases on a global scale. The initiative brings together numerous organizations, scientists, and farmers worldwide to fight hunger and improve food security.
This document summarizes research on identifying genetic loci associated with resistance to stripe and stem rust in wheat. Genome-wide association mapping identified several QTLs for stripe rust resistance on chromosomes 1D, 2B, 3B, 3A, 6A, 6D and 7D. Some QTLs corresponded to previously reported resistance genes. Analysis of interactions between loci found negative interactions between some stripe and stem rust QTLs, suggesting they should not be combined in breeding. The goal is to avoid pyramiding loci that interact negatively to compromise resistance to multiple diseases.
This document summarizes research on cloning rust resistance genes from wheat and developing gene pyramids via genetic engineering. Key points include:
- Researchers at the University of Minnesota and other institutions are working to clone multiple rust resistance genes from wheat including Sr2, Sr22, Sr33, Sr35, Sr46, Sr50 and Lr67.
- Cloned genes like Lr34/Yr18, Yr36, and others can be stacked together in transgenic cassettes to provide pyramided resistance in a single locus.
- Preliminary work has successfully stacked two or three resistance genes in transgenic wheat.
- Further work will continue cloning additional genes, validating gene function through transformation, and
Dandelion Hashtable: beyond billion requests per second on a commodity serverAntonios Katsarakis
This slide deck presents DLHT, a concurrent in-memory hashtable. Despite efforts to optimize hashtables, that go as far as sacrificing core functionality, state-of-the-art designs still incur multiple memory accesses per request and block request processing in three cases. First, most hashtables block while waiting for data to be retrieved from memory. Second, open-addressing designs, which represent the current state-of-the-art, either cannot free index slots on deletes or must block all requests to do so. Third, index resizes block every request until all objects are copied to the new index. Defying folklore wisdom, DLHT forgoes open-addressing and adopts a fully-featured and memory-aware closed-addressing design based on bounded cache-line-chaining. This design offers lock-free index operations and deletes that free slots instantly, (2) completes most requests with a single memory access, (3) utilizes software prefetching to hide memory latencies, and (4) employs a novel non-blocking and parallel resizing. In a commodity server and a memory-resident workload, DLHT surpasses 1.6B requests per second and provides 3.5x (12x) the throughput of the state-of-the-art closed-addressing (open-addressing) resizable hashtable on Gets (Deletes).
Driving Business Innovation: Latest Generative AI Advancements & Success StorySafe Software
Are you ready to revolutionize how you handle data? Join us for a webinar where we’ll bring you up to speed with the latest advancements in Generative AI technology and discover how leveraging FME with tools from giants like Google Gemini, Amazon, and Microsoft OpenAI can supercharge your workflow efficiency.
During the hour, we’ll take you through:
Guest Speaker Segment with Hannah Barrington: Dive into the world of dynamic real estate marketing with Hannah, the Marketing Manager at Workspace Group. Hear firsthand how their team generates engaging descriptions for thousands of office units by integrating diverse data sources—from PDF floorplans to web pages—using FME transformers, like OpenAIVisionConnector and AnthropicVisionConnector. This use case will show you how GenAI can streamline content creation for marketing across the board.
Ollama Use Case: Learn how Scenario Specialist Dmitri Bagh has utilized Ollama within FME to input data, create custom models, and enhance security protocols. This segment will include demos to illustrate the full capabilities of FME in AI-driven processes.
Custom AI Models: Discover how to leverage FME to build personalized AI models using your data. Whether it’s populating a model with local data for added security or integrating public AI tools, find out how FME facilitates a versatile and secure approach to AI.
We’ll wrap up with a live Q&A session where you can engage with our experts on your specific use cases, and learn more about optimizing your data workflows with AI.
This webinar is ideal for professionals seeking to harness the power of AI within their data management systems while ensuring high levels of customization and security. Whether you're a novice or an expert, gain actionable insights and strategies to elevate your data processes. Join us to see how FME and AI can revolutionize how you work with data!
How information systems are built or acquired puts information, which is what they should be about, in a secondary place. Our language adapted accordingly, and we no longer talk about information systems but applications. Applications evolved in a way to break data into diverse fragments, tightly coupled with applications and expensive to integrate. The result is technical debt, which is re-paid by taking even bigger "loans", resulting in an ever-increasing technical debt. Software engineering and procurement practices work in sync with market forces to maintain this trend. This talk demonstrates how natural this situation is. The question is: can something be done to reverse the trend?
Ivanti’s Patch Tuesday breakdown goes beyond patching your applications and brings you the intelligence and guidance needed to prioritize where to focus your attention first. Catch early analysis on our Ivanti blog, then join industry expert Chris Goettl for the Patch Tuesday Webinar Event. There we’ll do a deep dive into each of the bulletins and give guidance on the risks associated with the newly-identified vulnerabilities.
"Frontline Battles with DDoS: Best practices and Lessons Learned", Igor IvaniukFwdays
At this talk we will discuss DDoS protection tools and best practices, discuss network architectures and what AWS has to offer. Also, we will look into one of the largest DDoS attacks on Ukrainian infrastructure that happened in February 2022. We'll see, what techniques helped to keep the web resources available for Ukrainians and how AWS improved DDoS protection for all customers based on Ukraine experience
[OReilly Superstream] Occupy the Space: A grassroots guide to engineering (an...Jason Yip
The typical problem in product engineering is not bad strategy, so much as “no strategy”. This leads to confusion, lack of motivation, and incoherent action. The next time you look for a strategy and find an empty space, instead of waiting for it to be filled, I will show you how to fill it in yourself. If you’re wrong, it forces a correction. If you’re right, it helps create focus. I’ll share how I’ve approached this in the past, both what works and lessons for what didn’t work so well.
HCL Notes and Domino License Cost Reduction in the World of DLAUpanagenda
Webinar Recording: https://www.panagenda.com/webinars/hcl-notes-and-domino-license-cost-reduction-in-the-world-of-dlau/
The introduction of DLAU and the CCB & CCX licensing model caused quite a stir in the HCL community. As a Notes and Domino customer, you may have faced challenges with unexpected user counts and license costs. You probably have questions on how this new licensing approach works and how to benefit from it. Most importantly, you likely have budget constraints and want to save money where possible. Don’t worry, we can help with all of this!
We’ll show you how to fix common misconfigurations that cause higher-than-expected user counts, and how to identify accounts which you can deactivate to save money. There are also frequent patterns that can cause unnecessary cost, like using a person document instead of a mail-in for shared mailboxes. We’ll provide examples and solutions for those as well. And naturally we’ll explain the new licensing model.
Join HCL Ambassador Marc Thomas in this webinar with a special guest appearance from Franz Walder. It will give you the tools and know-how to stay on top of what is going on with Domino licensing. You will be able lower your cost through an optimized configuration and keep it low going forward.
These topics will be covered
- Reducing license cost by finding and fixing misconfigurations and superfluous accounts
- How do CCB and CCX licenses really work?
- Understanding the DLAU tool and how to best utilize it
- Tips for common problem areas, like team mailboxes, functional/test users, etc
- Practical examples and best practices to implement right away
AppSec PNW: Android and iOS Application Security with MobSFAjin Abraham
Mobile Security Framework - MobSF is a free and open source automated mobile application security testing environment designed to help security engineers, researchers, developers, and penetration testers to identify security vulnerabilities, malicious behaviours and privacy concerns in mobile applications using static and dynamic analysis. It supports all the popular mobile application binaries and source code formats built for Android and iOS devices. In addition to automated security assessment, it also offers an interactive testing environment to build and execute scenario based test/fuzz cases against the application.
This talk covers:
Using MobSF for static analysis of mobile applications.
Interactive dynamic security assessment of Android and iOS applications.
Solving Mobile app CTF challenges.
Reverse engineering and runtime analysis of Mobile malware.
How to shift left and integrate MobSF/mobsfscan SAST and DAST in your build pipeline.
Have you ever been confused by the myriad of choices offered by AWS for hosting a website or an API?
Lambda, Elastic Beanstalk, Lightsail, Amplify, S3 (and more!) can each host websites + APIs. But which one should we choose?
Which one is cheapest? Which one is fastest? Which one will scale to meet our needs?
Join me in this session as we dive into each AWS hosting service to determine which one is best for your scenario and explain why!
Skybuffer SAM4U tool for SAP license adoptionTatiana Kojar
Manage and optimize your license adoption and consumption with SAM4U, an SAP free customer software asset management tool.
SAM4U, an SAP complimentary software asset management tool for customers, delivers a detailed and well-structured overview of license inventory and usage with a user-friendly interface. We offer a hosted, cost-effective, and performance-optimized SAM4U setup in the Skybuffer Cloud environment. You retain ownership of the system and data, while we manage the ABAP 7.58 infrastructure, ensuring fixed Total Cost of Ownership (TCO) and exceptional services through the SAP Fiori interface.
Northern Engraving | Nameplate Manufacturing Process - 2024Northern Engraving
Manufacturing custom quality metal nameplates and badges involves several standard operations. Processes include sheet prep, lithography, screening, coating, punch press and inspection. All decoration is completed in the flat sheet with adhesive and tooling operations following. The possibilities for creating unique durable nameplates are endless. How will you create your brand identity? We can help!
"Choosing proper type of scaling", Olena SyrotaFwdays
Imagine an IoT processing system that is already quite mature and production-ready and for which client coverage is growing and scaling and performance aspects are life and death questions. The system has Redis, MongoDB, and stream processing based on ksqldb. In this talk, firstly, we will analyze scaling approaches and then select the proper ones for our system.
Digital Banking in the Cloud: How Citizens Bank Unlocked Their MainframePrecisely
Inconsistent user experience and siloed data, high costs, and changing customer expectations – Citizens Bank was experiencing these challenges while it was attempting to deliver a superior digital banking experience for its clients. Its core banking applications run on the mainframe and Citizens was using legacy utilities to get the critical mainframe data to feed customer-facing channels, like call centers, web, and mobile. Ultimately, this led to higher operating costs (MIPS), delayed response times, and longer time to market.
Ever-changing customer expectations demand more modern digital experiences, and the bank needed to find a solution that could provide real-time data to its customer channels with low latency and operating costs. Join this session to learn how Citizens is leveraging Precisely to replicate mainframe data to its customer channels and deliver on their “modern digital bank” experiences.
Digital Banking in the Cloud: How Citizens Bank Unlocked Their Mainframe
Identification and characterization of effector genes from wheat stripe rust
1. Discovering
the
effector
genes
of
Puccinia
striiformis
f.sp.
tri.ci
John
Rathjen
The
Australian
Na;onal
University
2. Stripe
rust
and
Australian
wheat
produc;on
Annual
losses
Control
cost
GM
Murray
&
JP
Brennan
2009.
Grains
Research
&
Development
Corpora?on.
Australian
Government
3. Stripe
rust
and
Australian
wheat
produc;on
Annual
losses
Control
cost
GM
Murray
&
JP
Brennan
2009.
Grains
Research
&
Development
Corpora?on.
Australian
Government
4. Urediniospores
(2n)
Wheat
Teliospores
(2n)
Dikaryo?c
–
Sexual
host
Two
haploid
nuclei
insignificant
in
Australia
Meiosis
alternate
Basidiospores
host
(1n)
Aeciospores
(2n)
Pycniospores
(1n)
Barberry
hAp://www.apsnet.org/edcenter/intropp/lessons/fungi/Basidiomycetes/Pages/StemRust.aspx
5.
6. P.
striiformis
in
Australia
Psd
BGYR
(2000)
Pst-‐1979
Psp
(~20
strains)
Pst-‐WA
(2002)
Puccinia
striiformis
f.sp.
tri0ci
Barley
grass
yellow
rust
(~6
strains)
Psd–
grows
on
Dactylis
glomerata
(Cocksfoot)
Psp
–
grows
on
Poa
pratensis
(Kentucky
blue
grass)
Stripe
rust
of
Phalaris
spp.,
Bromus
spp.,
“wheat
grass”,
etc,
etc
7. How
can
we
define
effector
genes?
• Generally,
effectors
are
thought
to
be
small
secreted
proteins.
• This
is
sufficient
to
build
a
list
of
such
proteins
if
genomic
sequence
is
available.
• In
some
cases,
amino
acid
mo?fs
such
as
RxLR
or
YxC
are
present…but
don’t
seem
to
be
diagnos?c.
• Another
important
criterion
is
expression
of
candidate
effector
genes
in
planta,
where
that
informa?on
is
available.
8. Puccinia genomics
• Pgt (stem rust) genome (Duplessis et al. 2011) is about 90
Mb, encoding about 17,000 genes – Pgt expected to be
similar.
• This was assembled with a lot of “last-generation
sequencing” which helps with scaffolding and sequence
assembly.
• Transposable elements account for about 45% of the
genome.
• Calling genes from NGS assemblies can be problematic, and
can be difficult to detect expression of fungal genes in
infected tissue (but these are the most interesting genes).
• There are ongoing unresolved problems with the
dikaryotic nature of rusts.
• Broad Institute (Cuomo) has a good Pst assembly in the
pipeline.
9. Perils
and
pi`alls
of
next-‐genera?on
sequencing
(NGS).
• NGS
–
boAom
up
or
‘shotgun’
assembly
of
millions
of
small
sequence
reads,
using
high-‐performance
compu?ng.
Technologies
include:
• Illumina
–
millions
of
very
short
reads
(~100
bp).
• Roche-‐454
–
fewer
numbers
of
longer
reads
(~500
bp).
• Tradi?onal
(Sanger)
sequencing
–
long
reads
800-‐1000
bp.
10. DNA
sequencing;
the
impossible
triangle
NGS
Tradi?onal
Sanger
sequencing
of
physical
con?gs
11. Perils
and
pi`alls
of
next-‐genera?on
sequencing
(NGS).
AATATAAAACCAAAGATACTGATATCTTAGCGGCTTTCCGAATGACCCCACAACCTGGAG
13. Detec?ons
of
sequence
polymorphisms
in
small-‐
read
assemblies
X
X
X
X
AATATAAAACCAAAGATACTGATATCTTAGCGGCTTTCCGAATGACCCCACAACCTGGAG
C/G
14. Detec?ons
of
sequence
polymorphisms
in
small-‐
read
assemblies
-‐
II
X
X
X
X
X
X
X
X
AATATAAAACCAAAGATACTGATATCTTAGCGGCTTTCCGAATGACCCCACAACCTGGAG
T/A
C/G
15. Detec?ons
of
sequence
polymorphisms
in
small-‐
read
assemblies
-‐
II
X
X
X
X
X
X
X
X
AATATAAAACCAAAGATACTGATATCTTAGCGGCTTTCCGAATGACCCCACAACCTGGAG
T/A
C/G
T
C
A
C
The
“phase”
problem
T
G
A
G
16. Repeats
and
mul?copy
genes
are
difficult
to
assemble
from
small
reads
Repeats
(transposons…effectors?)
assemble
poorly
or
not
at
all.
This
is
obvious
in
NGS
genome
assemblies.
It’s
a
considerable
problem
for
genomics
of
Puccinia
spp.
18. 454 sequencing of
isolated haustoria
transcriptome
16831 contigs
Contamina;on
removal
14682 contigs
Secreted
proteins
predic;on
Non-‐transmembrane
domains
1299 ORFs-SP
Unique
or
non-‐overlapping
ORFs
515 ORFs-SP
Illumina
Protein
length
≤
300aa
sequencing
418 ORFs-SP
High
expression
100 ORFs-SP Lab tests
19. Prediction of small secreted proteins
(SSPs) from the haustorial transcriptome
433
≤
300
aa
Protein
length
No
memes
98
>
300
aa
No
clusters/tribes
311
≤
4
Cysteines
Cysteine
content
220
>
4
Cysteines
91
have
1
mo?f
,
18
in
the
‘correct’
loca?on
Y/F/WxC
mo?f
42
have
2
mo?ves,
23
correct
loca?on
9
have
3
or
more
mo?ves,
8
correct
loca?on
Invertase
BLASTn
BLASTx
1,3-‐β-‐glucosidase
Pgt
hypothe?cal
protein
74
211
Pepsin
A
e-‐val
≤
10-‐25
Chi?n
deacetylase
Glucose-‐regulated
it
rotein
from
Pgt)
Specific
h p (most
38
29
Previous
SP
from
Pst
e-‐val
>
10-‐25
Not
available
419
291
20. Validation and investigation of effector candidates
AvrM
type-‐III
delivery/
P.
fluorescens
AvrM
75
avrM
24
Agro/AvrM
Narayana
Upadhyaya
and
Diana
Garnica
100
sequenced
and
cloned
in
TOPO
Ø R-‐AvrR
recogni?on
assay
Ø Inhibi?on
of
plant
cell
death
Ø Localisa?on
Ø Influence
on
host
metabolism
21. PST-80 housekeeping genes are not
single allele
Housekeeping
Gene
Copy
Number
10
9
8
7
Copy
number
6
5
4
3
2
1
0
18
39
60
81
221
102
123
144
165
186
207
233
254
275
312
333
368
389
418
453
483
521
295
467
443
511
Boeva
V,
et
al.
(2011)
Control-‐FREEC:
Bioinforma?cs.
2011
Dec
6
22. PST-80 Effector genes are present
with variable copy number
Effector
gene
copy
number
PST_80
Effector
Allele
Number
7
Effector
Allele
Number,
6
6
5
Copy
number
Allele
Number
4
3
2
1
0
1
21
41
61
81
101
121
141
161
181
201
221
241
261
281
326
346
366
415
456
290
486
471
519
308
494
434
Effector
gene,
nominal
ranking
23. Effector copy number variations
between Pst-80 and BGYR
Effector
gAllele
Number
Effector
ene
copy
number
7
6
Axis
umber
5
Copy
nTitle
4
3
2
1
0
1
51
101
151
201
251
301
351
401
451
501
Effector
rAxis
Tnominal)
ank
( itle
24. Copy
nNumber
Allele
umber
0
2
4
6
8
10
12
1
13
25
37
49
61
73
85
97
109
Cantu
et
al.
PLOS
One
(2011)
121
133
145
157
169
181
193
205
217
229
241
253
265
277
289
Effector
Number
301
313
325
337
349
361
Effector
gene
copy
number
Effector
number
(nominal)
373
PST_130
Effector
Allele
Number
385
397
409
421
433
445
457
469
Effector copy number variations
481
493
between Pst-80 and Pst-130 (US)
505
517
Allele
Effector
Number
25. Housekeeping
genes
do
not
show
the
same
degree
of
varia?on
in
copy
number
Conserved
Gene
Copy
Number
BGYR
Control-‐FREEC
predic?on
of
CNVs
Pst-‐80
7
Predicted
Copy
N umber
6
5
4
3
2
1
0
1 51 101 151 201 251 301 351 401 451 501
Gene
Boeva
V,
et
al.
(2011)
Control-‐FREEC:
Bioinforma?cs.
2011
Dec
6
26. Copy
number
varia?on
in
Pst
effectors
• Copy
number
varia?ons
are
readily
apparent
in
Pst
effector
genes,
with
many
single
copy.
• Sequence
polymorphisms
are
also
apparent,
but
these
are
harder
to
annotate
because
of
NGS
assemblies.
• Single-‐copy
effectors
may
allow
the
pathogen
to
mutate
rapidly
to
virulence.
27. Barley grass yellow rust (BGYR) – a
stripe rust that jumped?
wheat
Barley
grass
BGYR
(2000)
Wheat
stripe
(1980)
Stripe
rust
and
BGYR
99+%
iden?cal
in
effector
genes
so
far
sequenced
28. Sequencing summary
• We amplified and sequenced the PCR products of 50 candidate
effector genes from Pst-80 and BGYR and found 99 single
nucleotide polymorphisms (SNPs).
• These were ALWAYS of a particular pattern – twin peak
‘dimorphisms’, rather than clear SNPs (dSNPs).
• 50 of these were'informative' dSNPs - 34 from BGYR, and 16
from Pst-80.
• We amplified and sequenced these alleles from BGYR and
Pst-80.
• When we did this, we found that BGYR ALWAYS shared an allele
with Pst-80, and the alternative allele was divergent.
• We think that this is related to the dikaryotypic nature of P.
striiformis.
31. Model for the origins of BGYR
Pst
BGYR unknown ancestor
Anastamosis +
Heterokaryosis
BGYR
32. Where did BGYR come from?
• One line of evidence suggests that heterokaryosis is
an underlying mechanism for the host jump – but we
need to address the phase problem.
• In the 1950’s, this was proposed as a mechanism to
explain frequent mutation to virulence of stem rust
on wheat.
• We have detected four deleted effector genes, and
will test these for recognition on barley grass by
bacterial delivery.
• Heterokaryosis potentially increases effector
hemizygosity, which could both increase the effective
effector compliment (for virulence) and allow rapid
deletion of recognised effectors.
33. Acknowledgments
• Diana
Garnica
• William
Jackson
• CSIRO
Black
Mountain
• Narayana
Upadhyaya
• Peter
Dodds
• Jeff
Ellis
• Univ
Sydney
CobbiAy
• Colin
Wellings
Robert
Park
• Univ
Exeter,
UK
• David
Studholme
34.
35. Germinated
spores:
Ø Use
lipid
reserves
to
generate
energy
Ø Grow
(DNA
replica?on,
cell
division)
Ø Modify
chi?n
to
avoid
recogni?on
Haustoria:
Ø Take
nutrients
(sugars
and
aminoacids)
from
host
Ø Generate
precursors
of
metabolites
and
energy
Ø Biosynthesise
compounds
necessary
for
the
ul?mate
produc?on
of
spores
Ø Secrete
pathogenicity
factors
(effectors)
36. Many effector genes are single copy
PST_80
Effector
Copy
Number,
Allele
Number
and
SNP
14
80
Number
12
70
Copy,
Allele
and
SNP
Number
60
10
Effec
50
tor
8
Cand
40
idate
6
Copy
30
Num
4
ber
20
2
10
0
0
1
23
45
69
91
113
135
157
179
201
223
245
267
336
409
431
492
290
436
517
502
398
314
358
Effector
Number
37. Copy,
Allele
and
SNP
Number
0
2
4
6
8
10
12
14
16
1
13
25
38
50
62
74
86
98
110
122
134
146
159
172
185
198
211
223
235
247
259
271
283
Effector
Number
295
307
320
332
344
356
368
380
PST_130
Effector
Gene
Variability
392
404
416
428
440
452
464
476
488
500
512
PST_80 effector genes in PST_130
0
20
100
120
have undergone significant modification
40
SNP
Copy
Allele
Effector
60
Effector
80
Effector
Number
Number
Number
38. Mapping
BGYR
genomic
reads
against
500
‘conserved’
Pst
genes
Conserved
Gene
Copy
Number
BGYR
Control-‐FREEC
predic?on
of
CNVs
Pst-‐79
7
Predicted
Copy
N umber
6
5
4
3
2
1
0
1 51 101 151 201 251 301 351 401 451 501
Gene
Boeva
V,
et
al.
(2011)
Control-‐FREEC:
Bioinforma?cs.
2011
Dec
6
39. Mapping
BGYR
genomic
reads
against
500
Pst
effector
candidates
Effector
Candidate
Copy
Number
BGYR
Control-‐FREEC
predic?on
of
CNVs
Pst-‐79
8
6
4
2
0
1 51 101 151 201 251 301 351 401 451 501
Gene
Boeva
V,
et
al.
(2011)
Control-‐FREEC:
Bioinforma?cs.
2011
Dec
6
40. ToxA
cell
death
dependent
on
Tsn1
is
suppressed
by
stripe
rust
infec;on
+ToxA
+H2O
+ToxA
+
stripe
rust
stripe
rust
Diana
Garnica
with
help
from
the
Solomon
lab