This document summarizes a study that used microarray data to assess differentially expressed genes in the storage roots of cassava landraces from Brazil and Colombia. The study aimed to evaluate global gene expression patterns to help explain genetic diversity in pigmented cassava and identify new regulatory genes and biological pathways. Cassava landraces from the two countries were analyzed using a microarray containing over 25,000 cassava cDNA probes. The analysis identified 161 differentially expressed genes between the landraces.
1. The CTAB DNA extraction process involves several steps to access the DNA within plant cells and protect it from degradation. First, the plant tissue is frozen and ground to break open the cell walls and membranes.
2. Next, a hot CTAB buffer is added to disrupt the membranes using detergent properties and protect the DNA using chelating agents and maintaining pH. The DNA is kept in solution using salt.
3. Proteins are then extracted by adding chloroform, which causes them to denature and become soluble in the organic phase, leaving the DNA in the aqueous CTAB solution.
4. Finally, the DNA is precipitated out of solution by removing salt from the CTAB buffer
This document summarizes statistical methods for analyzing cDNA microarray data, including data preprocessing, normalization techniques, and statistical tests. It discusses alignment, background calculation, data transformation, normalization methods like global normalization, housekeeping gene normalization, and intensity-dependent normalization. Statistical tests covered include t-tests, multiple testing adjustments, permutation tests, and significance analysis of microarrays (SAM). The document concludes that no single method is best and different data may require trying different analytical approaches.
1) The document discusses a study analyzing the impact of gene length on detecting differentially expressed genes using RNA-seq technology.
2) The study will first test the reproducibility of RNA-seq and the effect of normalization. It will then compare different statistical tests for identifying differentially expressed genes.
3) Finally, the study will specifically test how gene length impacts the likelihood of a gene being identified as differentially expressed, as longer genes are easier to map with short reads.
There are two types of abdominal fat: subcutaneous and visceral fat. Visceral fat surrounds internal organs in the abdominal cavity while subcutaneous fat lies beneath the skin. Abdominal CT scans can be used to distinguish and measure visceral and subcutaneous fat deposits, which have different impacts on health risks such as inflammation and effects on the liver and kidneys.
Neurodevelopmental consequences of prenatal alcohol exposure behavioural and...BARRY STANLEY 2 fasd
This document describes a study examining the neurodevelopmental consequences of prenatal alcohol exposure using a mouse model. Pregnant mice were injected with ethanol on gestational days 8 and 11 (equivalent to the first trimester in humans), or on days 14 and 16 (equivalent to the second trimester). Resulting offspring underwent behavioural testing from birth to adulthood to assess FASD-relevant behaviours. At postnatal day 70, whole brain tissue was extracted for genome-wide expression analysis using microarrays. Gene expression changes were examined at both short-term (2 hours post-injection on day 16) and long-term (postnatal day 70) time points. Differentially expressed genes were analyzed to identify
This document summarizes a study that investigated the transcriptome profile of mouse mesenteric lymph nodes and allergic reactions in response to common food allergens. Mice were sensitized to peanut agglutinin, ovalbumin, or beta-lactoglobulin and challenged after two weeks. Gene expression was analyzed using microarrays and real-time RT-PCR. Several pathways and genes were differentially expressed, including T-cell receptor signaling and IL-7 signal transduction pathways. The study identified potential biomarker genes for assessing food allergen responses.
1. The CTAB DNA extraction process involves several steps to access the DNA within plant cells and protect it from degradation. First, the plant tissue is frozen and ground to break open the cell walls and membranes.
2. Next, a hot CTAB buffer is added to disrupt the membranes using detergent properties and protect the DNA using chelating agents and maintaining pH. The DNA is kept in solution using salt.
3. Proteins are then extracted by adding chloroform, which causes them to denature and become soluble in the organic phase, leaving the DNA in the aqueous CTAB solution.
4. Finally, the DNA is precipitated out of solution by removing salt from the CTAB buffer
This document summarizes statistical methods for analyzing cDNA microarray data, including data preprocessing, normalization techniques, and statistical tests. It discusses alignment, background calculation, data transformation, normalization methods like global normalization, housekeeping gene normalization, and intensity-dependent normalization. Statistical tests covered include t-tests, multiple testing adjustments, permutation tests, and significance analysis of microarrays (SAM). The document concludes that no single method is best and different data may require trying different analytical approaches.
1) The document discusses a study analyzing the impact of gene length on detecting differentially expressed genes using RNA-seq technology.
2) The study will first test the reproducibility of RNA-seq and the effect of normalization. It will then compare different statistical tests for identifying differentially expressed genes.
3) Finally, the study will specifically test how gene length impacts the likelihood of a gene being identified as differentially expressed, as longer genes are easier to map with short reads.
There are two types of abdominal fat: subcutaneous and visceral fat. Visceral fat surrounds internal organs in the abdominal cavity while subcutaneous fat lies beneath the skin. Abdominal CT scans can be used to distinguish and measure visceral and subcutaneous fat deposits, which have different impacts on health risks such as inflammation and effects on the liver and kidneys.
Neurodevelopmental consequences of prenatal alcohol exposure behavioural and...BARRY STANLEY 2 fasd
This document describes a study examining the neurodevelopmental consequences of prenatal alcohol exposure using a mouse model. Pregnant mice were injected with ethanol on gestational days 8 and 11 (equivalent to the first trimester in humans), or on days 14 and 16 (equivalent to the second trimester). Resulting offspring underwent behavioural testing from birth to adulthood to assess FASD-relevant behaviours. At postnatal day 70, whole brain tissue was extracted for genome-wide expression analysis using microarrays. Gene expression changes were examined at both short-term (2 hours post-injection on day 16) and long-term (postnatal day 70) time points. Differentially expressed genes were analyzed to identify
This document summarizes a study that investigated the transcriptome profile of mouse mesenteric lymph nodes and allergic reactions in response to common food allergens. Mice were sensitized to peanut agglutinin, ovalbumin, or beta-lactoglobulin and challenged after two weeks. Gene expression was analyzed using microarrays and real-time RT-PCR. Several pathways and genes were differentially expressed, including T-cell receptor signaling and IL-7 signal transduction pathways. The study identified potential biomarker genes for assessing food allergen responses.
The document describes a research study aimed at developing biomarkers for detecting potential allergenicity of novel foods, including genetically modified foods. The researcher conducted experiments challenging mice with known food allergens (egg ovomucoid protein and peanut protein) and analyzed gene expression profiles in the mice spleens. Several hundred genes were found to be differentially expressed. After validating some genes, the researcher identified potential biomarker genes that could help detect allergenicity of GM foods. The study provides insights into transcriptomic responses to food allergens and biomarkers that may help evaluate allergenicity of novel foods like GM crops.
This study analyzed gene expression across three stages of arm regeneration in the brittle star Amphiura filiformis using microarray analysis and quantitative PCR. The three stages studied were the blastema stage 7 days post autotomy, the intermediate regenerative stage at 3 weeks with 50% differentiation, and the advanced regenerative stage at 5 weeks with 95% differentiation. The results showed that genes involved in proliferation and energy production were most highly expressed in the early blastema stage, while expression levels generally decreased in later stages as differentiation increased. Certain genes associated with Hox regulation, neuronal development, and bone morphogenic protein 1 were differentially expressed across stages. While no Hox genes were identified, the study provides insight into regeneration molecular mechanisms
This document discusses fatty acid metabolism in humans. It notes that virtually all fatty acids originate from dietary triglycerides, with long-term storage occurring in adipose tissue. Upper body subcutaneous fat accounts for the majority of systemic free fatty acid release, though intra-abdominal fat correlates with higher delivery of free fatty acids to the liver. High levels of free fatty acids can lead to insulin resistance, increased triglycerides, and vascular abnormalities.
A Practical Approach to differential diagnosis.
This presentation offers a practical approach in differential diagnosis in head and neck masses in children and it is based on the article by Dr. Bernadette L. Koch published on Statdx.com .
Neck Masses need to be divided in Cystic and Solid and according the location.
Allergy is a hypersensitive reaction to foreign substances called antigens that are harmless to most individuals. It affects 15-30% of the global population, many of them children. Allergies can cause symptoms like sneezing and itching and interfere with daily life. Treating allergies costs billions of dollars annually. There are four main types of allergic reactions that involve different immunoglobulins and immune cells. Common allergens come from natural sources like pollen and foods or chemical sources like drugs.
The document describes the three main layers of the skin:
1. The dermis is the true skin and consists of two layers - the papillary layer containing blood vessels and nerve endings, and the reticular layer made of collagen, elastin and reticulin tissues.
2. Below the dermis is the subcutaneous tissue, a fatty layer that stores energy and protects underlying structures.
3. The deepest layer is the subcutaneous layer, which provides insulation and warmth for the body.
The document summarizes research on fatty acid metabolism and the role of different fat deposits in the body. It finds that while intra-abdominal fat correlates with higher liver fatty acid levels, most systemic fatty acids originate from upper body subcutaneous fat. Greater leg and abdominal fat tissue release fatty acids in obesity, contributing to insulin resistance, dyslipidemia, and other metabolic issues through elevated free fatty acid levels. Regional differences in fat affect health, but the causes of fat distribution and its metabolic effects require more research.
This document discusses lipomas, which are benign soft tissue tumors composed of adipose tissue enclosed in connective tissue. It covers the epidemiology, causes, classification, clinical features, diagnosis, complications and treatment of lipomas. Lipomas most commonly occur in adults aged 40-60 and can be removed surgically, usually via simple excision, for cosmetic reasons or if the diagnosis is uncertain. While generally benign, liposarcomas can rarely develop with similar clinical features and require complete excision and histological examination.
The skin has three main layers - the epidermis, dermis and subcutaneous tissue. The epidermis is the outermost layer and contains no blood vessels. It has multiple layers that cells move through as they are replaced every 28 days. The dermis lies below and contains collagen, elastin and blood vessels that provide structure and nourishment. It has two layers - a papillary layer with nerve endings and a reticular layer with hair follicles and glands. The deepest layer, subcutaneous tissue, contains fat and connects the dermis to underlying structures. Together these layers contain millions of cells, yards of blood vessels and nerves, and various sensory receptors and appendages like hair and glands.
Suggestions:
1) For best quality, download the PDF before viewing.
2) Open at least two windows: One for the Youtube video, one for the screencast (link below), and optionally one for the slides themselves.
3) The Youtube video is shown on the first page of the slide deck, for slides, just skip to page 2.
Screencast: http://youtu.be/VoL7JKJmr2I
Video recording: http://youtu.be/CJRvb8zxRdE (Thanks to Al Friedrich!)
In this talk, we take Deep Learning to task with real world data puzzles to solve.
Data:
- Higgs binary classification dataset (10M rows, 29 cols)
- MNIST 10-class dataset
- Weather categorical dataset
- eBay text classification dataset (8500 cols, 500k rows, 467 classes)
- ECG heartbeat anomaly detection
- Powered by the open source machine learning software H2O.ai. Contributors welcome at: https://github.com/h2oai
- To view videos on H2O open source machine learning software, go to: https://www.youtube.com/user/0xdata
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.
Next Generation Sequencing Technologies and Their Applications in Ornamental ...Ravindra Kumar
This document summarizes research on DNA sequencing and genome sequencing techniques. It discusses early Sanger sequencing and the development of next-generation sequencing platforms like Roche 454, Illumina, Ion Torrent, and SOLiD. The document also presents two case studies, one on sequencing the carnation genome and another on obtaining the rose transcriptome to identify genes related to traits of interest. Overall, the document provides a high-level overview of the evolution of DNA sequencing technologies and their applications in sequencing plant genomes and transcriptomes.
Genome Sequencing in Finger Millet
Genome size estimation
SOLiD Sequencing Technology
Illumina Sequencing Technology
Gene prediction and functional annotation of genes
Mining of plant transcription factors and other genes
This document provides an overview of rice genomics. It discusses the history of genomics from the 1980s development of DNA markers and PCR, to major milestones like the sequencing of rice genomes in 2002. It describes the International Rice Genome Sequencing Project's clone-by-clone sequencing approach. The rice genome was found to contain over 37,000 genes and significant repetitive elements. Comparative genomics with other cereals revealed conserved synteny. The 3,000 Rice Genomes Project aims to sequence a diverse set of rice varieties to explore genetic diversity.
This document describes the CarrAgheen Molecular Marker Database (CaMM-Db), a comprehensive database of molecular markers for the red seaweed Chondrus crispus (carragheen). The database contains over 18,000 microsatellites and 12,000 SNPs identified from carragheen genomic sequences. CaMM-Db provides information on different microsatellite types and properties. It also integrates with primer design software to facilitate wet lab experiments. As the first database of its kind for carragheen, CaMM-Db is expected to be a valuable resource for genetic research on carragheen and other red seaweeds.
The Genetics and Genomics Platform for Rice in Africa provides an interface between National Agricultural Research Systems (NARS) and advanced research institutes. It aims to strengthen NARS through training and laboratory set-up, providing breeders with new tools like marker-assisted selection and breeding to develop improved rice lines. The platform conducts activities such as allelic diversity studies, QTL analysis, marker-assisted breeding, and marker-assisted recurrent selection. It also offers practical training, data analysis, sharing of data and information, and the development of molecular tools.
This document summarizes common bean breeding activities aimed at developing drought tolerance in Andean gene pools through marker-assisted selection. Key activities include screening germplasm for drought tolerance traits, developing genomic resources like SSR and SNP markers, creating mapping populations to identify QTL, introgressing drought tolerance from other gene pools using backcrossing and MARS, and training students in drought breeding and MAS. The overall goal is to develop improved local varieties with improved drought tolerance for Andean regions by 2014 using these genomic and breeding approaches.
DNA barcoding is a method to identify species using short DNA sequences from standardized genes. It involves building a reference library of DNA barcodes from identified specimens and comparing unknown samples to the library. For animals, the CO1 gene is commonly used, while for plants the rbcL, matK, trnH, psbA and ITS genes provide identification. Barcoding has strengths in identifying juveniles, fragments, and through analysis of stomach contents, but relies on reference databases and may have weakness for some taxa. It can help identify herbal supplements, timber, rice varieties and other products.
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.
Genomic In-Situ Hybridization (GISH)-Principles, Methods and Applications in ...Banoth Madhu
Banoth Madhu: Genomic In-Situ Hybridization (GISH)-Principles, Methods and Applications in Crop Plants. It is a cytogenetic technique that allows the detection and localization of specific nucleic acid sequences on morphologically preserved chromosomes using genomic DNA of donor specie as probe. It is a cytogenetic technique that allows the detection and localization of specific nucleic acid sequences on morphologically preserved chromosomes using genomic DNA of donor specie as probe
A phylogeny driven genomic encyclopedia of bacteria and archaeaJonathan Eisen
This document summarizes a study that sequenced the genomes of 56 bacteria and archaea selected based on their phylogenetic novelty to maximize phylogenetic diversity, rather than traits of interest. Analyzing these genomes provided benefits over an equivalent random set, including better reconstruction of phylogenetic history, discovery of new protein families and biological properties, and improved prediction of gene functions. The study supports systematic "phylogenomic" efforts to compile a genomic encyclopedia representing the tree of life.
This document describes a comparative analysis of the human gut microbiota of Koreans using barcoded pyrosequencing. It finds that the Korean gut microbiome has high diversity at the species and strain levels, with over 800 species-level phylotypes identified on average per individual. The analysis identifies 14 core genera that are consistently present across Korean guts, including Bacteroides, Prevotella, Clostridium, and Ruminococcus. The phylum-level diversity of the Korean gut microbiome is similar to other human populations.
The document describes a research study aimed at developing biomarkers for detecting potential allergenicity of novel foods, including genetically modified foods. The researcher conducted experiments challenging mice with known food allergens (egg ovomucoid protein and peanut protein) and analyzed gene expression profiles in the mice spleens. Several hundred genes were found to be differentially expressed. After validating some genes, the researcher identified potential biomarker genes that could help detect allergenicity of GM foods. The study provides insights into transcriptomic responses to food allergens and biomarkers that may help evaluate allergenicity of novel foods like GM crops.
This study analyzed gene expression across three stages of arm regeneration in the brittle star Amphiura filiformis using microarray analysis and quantitative PCR. The three stages studied were the blastema stage 7 days post autotomy, the intermediate regenerative stage at 3 weeks with 50% differentiation, and the advanced regenerative stage at 5 weeks with 95% differentiation. The results showed that genes involved in proliferation and energy production were most highly expressed in the early blastema stage, while expression levels generally decreased in later stages as differentiation increased. Certain genes associated with Hox regulation, neuronal development, and bone morphogenic protein 1 were differentially expressed across stages. While no Hox genes were identified, the study provides insight into regeneration molecular mechanisms
This document discusses fatty acid metabolism in humans. It notes that virtually all fatty acids originate from dietary triglycerides, with long-term storage occurring in adipose tissue. Upper body subcutaneous fat accounts for the majority of systemic free fatty acid release, though intra-abdominal fat correlates with higher delivery of free fatty acids to the liver. High levels of free fatty acids can lead to insulin resistance, increased triglycerides, and vascular abnormalities.
A Practical Approach to differential diagnosis.
This presentation offers a practical approach in differential diagnosis in head and neck masses in children and it is based on the article by Dr. Bernadette L. Koch published on Statdx.com .
Neck Masses need to be divided in Cystic and Solid and according the location.
Allergy is a hypersensitive reaction to foreign substances called antigens that are harmless to most individuals. It affects 15-30% of the global population, many of them children. Allergies can cause symptoms like sneezing and itching and interfere with daily life. Treating allergies costs billions of dollars annually. There are four main types of allergic reactions that involve different immunoglobulins and immune cells. Common allergens come from natural sources like pollen and foods or chemical sources like drugs.
The document describes the three main layers of the skin:
1. The dermis is the true skin and consists of two layers - the papillary layer containing blood vessels and nerve endings, and the reticular layer made of collagen, elastin and reticulin tissues.
2. Below the dermis is the subcutaneous tissue, a fatty layer that stores energy and protects underlying structures.
3. The deepest layer is the subcutaneous layer, which provides insulation and warmth for the body.
The document summarizes research on fatty acid metabolism and the role of different fat deposits in the body. It finds that while intra-abdominal fat correlates with higher liver fatty acid levels, most systemic fatty acids originate from upper body subcutaneous fat. Greater leg and abdominal fat tissue release fatty acids in obesity, contributing to insulin resistance, dyslipidemia, and other metabolic issues through elevated free fatty acid levels. Regional differences in fat affect health, but the causes of fat distribution and its metabolic effects require more research.
This document discusses lipomas, which are benign soft tissue tumors composed of adipose tissue enclosed in connective tissue. It covers the epidemiology, causes, classification, clinical features, diagnosis, complications and treatment of lipomas. Lipomas most commonly occur in adults aged 40-60 and can be removed surgically, usually via simple excision, for cosmetic reasons or if the diagnosis is uncertain. While generally benign, liposarcomas can rarely develop with similar clinical features and require complete excision and histological examination.
The skin has three main layers - the epidermis, dermis and subcutaneous tissue. The epidermis is the outermost layer and contains no blood vessels. It has multiple layers that cells move through as they are replaced every 28 days. The dermis lies below and contains collagen, elastin and blood vessels that provide structure and nourishment. It has two layers - a papillary layer with nerve endings and a reticular layer with hair follicles and glands. The deepest layer, subcutaneous tissue, contains fat and connects the dermis to underlying structures. Together these layers contain millions of cells, yards of blood vessels and nerves, and various sensory receptors and appendages like hair and glands.
Suggestions:
1) For best quality, download the PDF before viewing.
2) Open at least two windows: One for the Youtube video, one for the screencast (link below), and optionally one for the slides themselves.
3) The Youtube video is shown on the first page of the slide deck, for slides, just skip to page 2.
Screencast: http://youtu.be/VoL7JKJmr2I
Video recording: http://youtu.be/CJRvb8zxRdE (Thanks to Al Friedrich!)
In this talk, we take Deep Learning to task with real world data puzzles to solve.
Data:
- Higgs binary classification dataset (10M rows, 29 cols)
- MNIST 10-class dataset
- Weather categorical dataset
- eBay text classification dataset (8500 cols, 500k rows, 467 classes)
- ECG heartbeat anomaly detection
- Powered by the open source machine learning software H2O.ai. Contributors welcome at: https://github.com/h2oai
- To view videos on H2O open source machine learning software, go to: https://www.youtube.com/user/0xdata
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.
Next Generation Sequencing Technologies and Their Applications in Ornamental ...Ravindra Kumar
This document summarizes research on DNA sequencing and genome sequencing techniques. It discusses early Sanger sequencing and the development of next-generation sequencing platforms like Roche 454, Illumina, Ion Torrent, and SOLiD. The document also presents two case studies, one on sequencing the carnation genome and another on obtaining the rose transcriptome to identify genes related to traits of interest. Overall, the document provides a high-level overview of the evolution of DNA sequencing technologies and their applications in sequencing plant genomes and transcriptomes.
Genome Sequencing in Finger Millet
Genome size estimation
SOLiD Sequencing Technology
Illumina Sequencing Technology
Gene prediction and functional annotation of genes
Mining of plant transcription factors and other genes
This document provides an overview of rice genomics. It discusses the history of genomics from the 1980s development of DNA markers and PCR, to major milestones like the sequencing of rice genomes in 2002. It describes the International Rice Genome Sequencing Project's clone-by-clone sequencing approach. The rice genome was found to contain over 37,000 genes and significant repetitive elements. Comparative genomics with other cereals revealed conserved synteny. The 3,000 Rice Genomes Project aims to sequence a diverse set of rice varieties to explore genetic diversity.
This document describes the CarrAgheen Molecular Marker Database (CaMM-Db), a comprehensive database of molecular markers for the red seaweed Chondrus crispus (carragheen). The database contains over 18,000 microsatellites and 12,000 SNPs identified from carragheen genomic sequences. CaMM-Db provides information on different microsatellite types and properties. It also integrates with primer design software to facilitate wet lab experiments. As the first database of its kind for carragheen, CaMM-Db is expected to be a valuable resource for genetic research on carragheen and other red seaweeds.
The Genetics and Genomics Platform for Rice in Africa provides an interface between National Agricultural Research Systems (NARS) and advanced research institutes. It aims to strengthen NARS through training and laboratory set-up, providing breeders with new tools like marker-assisted selection and breeding to develop improved rice lines. The platform conducts activities such as allelic diversity studies, QTL analysis, marker-assisted breeding, and marker-assisted recurrent selection. It also offers practical training, data analysis, sharing of data and information, and the development of molecular tools.
This document summarizes common bean breeding activities aimed at developing drought tolerance in Andean gene pools through marker-assisted selection. Key activities include screening germplasm for drought tolerance traits, developing genomic resources like SSR and SNP markers, creating mapping populations to identify QTL, introgressing drought tolerance from other gene pools using backcrossing and MARS, and training students in drought breeding and MAS. The overall goal is to develop improved local varieties with improved drought tolerance for Andean regions by 2014 using these genomic and breeding approaches.
DNA barcoding is a method to identify species using short DNA sequences from standardized genes. It involves building a reference library of DNA barcodes from identified specimens and comparing unknown samples to the library. For animals, the CO1 gene is commonly used, while for plants the rbcL, matK, trnH, psbA and ITS genes provide identification. Barcoding has strengths in identifying juveniles, fragments, and through analysis of stomach contents, but relies on reference databases and may have weakness for some taxa. It can help identify herbal supplements, timber, rice varieties and other products.
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.
Genomic In-Situ Hybridization (GISH)-Principles, Methods and Applications in ...Banoth Madhu
Banoth Madhu: Genomic In-Situ Hybridization (GISH)-Principles, Methods and Applications in Crop Plants. It is a cytogenetic technique that allows the detection and localization of specific nucleic acid sequences on morphologically preserved chromosomes using genomic DNA of donor specie as probe. It is a cytogenetic technique that allows the detection and localization of specific nucleic acid sequences on morphologically preserved chromosomes using genomic DNA of donor specie as probe
A phylogeny driven genomic encyclopedia of bacteria and archaeaJonathan Eisen
This document summarizes a study that sequenced the genomes of 56 bacteria and archaea selected based on their phylogenetic novelty to maximize phylogenetic diversity, rather than traits of interest. Analyzing these genomes provided benefits over an equivalent random set, including better reconstruction of phylogenetic history, discovery of new protein families and biological properties, and improved prediction of gene functions. The study supports systematic "phylogenomic" efforts to compile a genomic encyclopedia representing the tree of life.
This document describes a comparative analysis of the human gut microbiota of Koreans using barcoded pyrosequencing. It finds that the Korean gut microbiome has high diversity at the species and strain levels, with over 800 species-level phylotypes identified on average per individual. The analysis identifies 14 core genera that are consistently present across Korean guts, including Bacteroides, Prevotella, Clostridium, and Ruminococcus. The phylum-level diversity of the Korean gut microbiome is similar to other human populations.
This document describes an experiment to extract DNA from strawberries using household materials. It explains that all living things contain DNA, which contains the genetic instructions for the organism. The experiment involves smashing strawberries, adding an extraction liquid, filtering the mixture, then adding alcohol to precipitate out the strawberry DNA. Performing the simple extraction allows students to learn more about how DNA can be isolated from cells and gain a basic understanding of genetics.
DNA probes and PCR technology are used to rapidly identify microorganisms by amplifying copies of their DNA or RNA. The amplified DNA can then be detected and quantified to assess how many microorganisms are present and monitor responses to treatment. DNA technology can also break the cycle of disease in nature by intervening in parasites' life cycles. DNA barcoding uses a short, unique DNA sequence to identify species, including establishing new species. It supplements traditional taxonomy. Recovering DNA from fossils through PCR amplification allows comparison to present DNA, determining relationships and identifying ancestors. Tracking human mtDNA and Y chromosomes shows all people originated from an African ancestor. Cloning extinct animals could disrupt nature but may be acceptable for those driven extinct by humans to preserve
Abstract— Taxus Chinensis var. mairei is a valuable plant species for timber and taxoids isolated from this species are very important compounds that are used for cancer treatment. Although chemical investigation on T. chinensis var. mairei are popular, functional identification of genes isolated from this species is rare. In this investigation, we have isolated TCAP3 gene and analyzed its expression pattern in different tissue and developmental stages through Real time-PCR; then we transformed this gene into Arabidopsis and analyzed its function. Our results demonstrated that its cDNA contains 846 bp bases (coding 197 amino acids) constituted by four typical domains, M, I, K, C with conserved motif, Phylogenetic analysis showed that TCAP3 is more ancient than angiosperm B class genes. Alignment of protein sequence demonstrated the conserved motifs, which illustrated that TCAP3 belongs to gymnosperm Gymno B class MADS-box genes with PI-derived, on C-teminal, which is similar structure to the Gymno B class MADS-box genes that they share the same B class gene specific conserved motif. Expression analysis of TCAP3 in different tissue showed that it only expression in male strobilus, not in leaf, bud and female strobilus at different developmental stages. We divided the stages according to paraffin sections of male strobilus. The results indicated that TCAP3 expresses dynamically along with the male strobilus. Heterologous expression of TCAP3 in Arabidopsis demonstrated that TCAP3 was involved in flower, especially the filaments morphological development.
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.
This document describes a new DNA metabarcoding approach for high-throughput biodiversity assessment using environmental DNA. Short DNA barcode markers are amplified from bulk soil or water samples and sequenced on next-generation platforms to identify all taxa present, without needing to isolate individual organisms. The method was tested on soil samples from an alpine meadow, identifying 8 earthworm species from sequence reads of short mtDNA markers. Future applications could include capturing DNA with hundreds of probes and shotgun sequencing of soil eDNA for comprehensive biodiversity surveys at large scales.
India has contributed to the International Rice Genome Sequencing Project by sequencing chromosome 11 through scientists at the University of Delhi and chromosome 12 through scientists at the Indian Agricultural Research Institute. Indian scientists developed a physical map of the target regions, screened a BAC library to identify relevant BAC clones, constructed BAC contigs to cover 70% of the minimum tiling path, and worked to fill gaps in the physical map through chromosome walking and identifying additional BACs. Purity of identified BACs was also checked to ensure high quality sequencing.
This document summarizes information from a student's assignment on plant genome sequencing techniques. It discusses early phenotypic selection methods and their limitations. It then summarizes different sequencing strategies used for important crop plants like rice, poplar, and Arabidopsis. These include BAC-by-BAC, whole genome shotgun, and various next-generation sequencing platforms. The document also summarizes applications of sequencing including identifying genes related to rice yield and flowering time and using sequencing to improve potato and maize varieties.
This document describes an activity where students extract DNA from smashed strawberries using household materials. The activity involves smashing strawberries, adding an extraction liquid, filtering the mixture, and adding alcohol to precipitate out the DNA. It aims to demonstrate in a fun, hands-on way how scientists extract DNA from organisms. The document also summarizes a discovery about proteins that are essential for organizing genes in the nucleus and how this helps understand diseases.
Similar to Assessing Differentially Expressed Genes in Storage Root of Cassava Landraces from Brazil and Colombia Using Microarray Data (20)
Durante la Semana de la Agricultura y la Alimentación, el Programa de Investigación del CGIAR en Cambio Climático, Agricultura y Seguridad Alimentaria – CCAFS, la Organización de las Naciones Unidas para la Alimentación y la Agricultura, FAO, y el Centro Internacional de Agricultura Tropical – CIAT, apoyaron la II Reunión Internacional de Ministros y altas autoridades de agricultura sobre agricultura sostenible y cambio climático con un documento base y su presentación sobre los retos que representa el cambio climático para la agricultura en Latino América y el Caribe.
Taller sobre intervenciones en nutrición, género y agricultura: situación actual y oportunidades futuras’, organizado por el CIAT y HarvestPlus en Ciudad de Guatemala. Leer más: http://ow.ly/XNIv30mGYBv
Impacto de las intervenciones agricolas y de salud para reducir la deficienci...CIAT
Este documento resume un estudio realizado en Guatemala para evaluar el impacto de entregar semilla biofortificada de frijol en aspectos socioeconómicos y de salud nutricional. El estudio utilizó un diseño de ensayo clúster aleatorio en comunidades rurales asignadas a recibir semilla biofortificada o no. Los resultados preliminares mostraron pocos cambios socioeconómicos entre grupos. Los resultados de línea base encontraron altas tasas de anemia y deficiencia de hierro, con el frijol contribuyendo signific
Agricultura sensible a la nutrición en el Altiplano. Explorando las perspecti...CIAT
Taller sobre intervenciones en nutrición, género y agricultura: situación actual y oportunidades futuras’, organizado por el CIAT y HarvestPlus en Ciudad de Guatemala. Leer más: http://ow.ly/XNIv30mGYBv
El rol de los padres en la nutrición del hogarCIAT
Este documento presenta los resultados preliminares de un estudio sobre las dinámicas intra-hogar y su impacto en la nutrición de familias agrícolas en Guatemala. Los hallazgos incluyen que las mujeres tienden a estar más desempoderadas que los hombres, y los niños en hogares con mujeres desempoderadas tienen más probabilidades de sufrir retraso en el crecimiento. Además, las preferencias de alimentos y labores varían entre hombres y mujeres dependiendo del ingreso disponible. Considerar tanto a padres como madres es importante para proyectos de nut
Scaling up soil carbon enhancement contributing to mitigate climate changeCIAT
This document summarizes Session 3 of a symposium on scaling up soil carbon enhancement to contribute to climate change mitigation. It discusses: 1) The potential for climate change
Impacto del Cambio Climático en la Agricultura de República DominicanaCIAT
El Banco Interamericano de Desarrollo (BID) y el Centro Internacional de Agricultura Tropical (CIAT), con el apoyo de los Programas de Investigación de CGIAR sobre Políticas, Instituciones y Mercados (PIM) y sobre Cambio Climático, Agricultura y Seguridad Alimentaria (CCAFS), se han asociado para comprender, a través de la ciencia, el impacto del cambio climático en cultivos claves y el impacto económico en la productividad de la agricultura en países de ALC.
BioTerra: Nuevo sistema de monitoreo de la biodiversidad en desarrollo por el...CIAT
BioTerra es un sistema innovador de monitoreo de la biodiversidad y sus amenazas desarrollado por el Programa Riqueza Natural de la Agencia de los Estados Unidos para el Desarrollo Internacional (USAID), y sus socios locales – el Centro Internacional de Agricultura Tropical (CIAT) y el Instituto Alexander von Humboldt (IAvH) – para apoyar al gobierno colombiano en el cumplimiento de las metas y compromisos de conservación de la biodiversidad. Este sistema busca complementar y aunar esfuerzos existentes de monitoreo de la biodiversidad y sus amenazas, a nivel nacional y regional.
Cacao for Peace Activities for Tackling the Cadmium in Cacao Issue in Colo...CIAT
El taller ‘Cacao libre de cadmio’, organizado por el CIAT, CIRAD, y la AFD, se lleva a cabo del 12 al 14 de marzo en la sede del CIAT en Palmira,y tiene como objetivo integrar un consorcio de actores y disciplinas claves de la región, así como elaborar un proyecto de investigación aplicada que dé respuesta a este problema que afecta a los cacaoteros de Colombia, Perú y Ecuador. http://ow.ly/J43p30iU0UZ
Tackling cadmium in cacao and derived products – from farm to forkCIAT
El taller ‘Cacao libre de cadmio’, organizado por el CIAT, CIRAD, y la AFD, se lleva a cabo del 12 al 14 de marzo en la sede del CIAT en Palmira,y tiene como objetivo integrar un consorcio de actores y disciplinas claves de la región, así como elaborar un proyecto de investigación aplicada que dé respuesta a este problema que afecta a los cacaoteros de Colombia, Perú y Ecuador. http://ow.ly/J43p30iU0UZ
Cadmium bioaccumulation and gastric bioaccessibility in cacao: A field study ...CIAT
El taller ‘Cacao libre de cadmio’, organizado por el CIAT, CIRAD, y la AFD, se lleva a cabo del 12 al 14 de marzo en la sede del CIAT en Palmira,y tiene como objetivo integrar un consorcio de actores y disciplinas claves de la región, así como elaborar un proyecto de investigación aplicada que dé respuesta a este problema que afecta a los cacaoteros de Colombia, Perú y Ecuador. http://ow.ly/J43p30iU0UZ
Geographical Information System Mapping for Optimized Cacao Production in Col...CIAT
El taller ‘Cacao libre de cadmio’, organizado por el CIAT, CIRAD, y la AFD, se lleva a cabo del 12 al 14 de marzo en la sede del CIAT en Palmira,y tiene como objetivo integrar un consorcio de actores y disciplinas claves de la región, así como elaborar un proyecto de investigación aplicada que dé respuesta a este problema que afecta a los cacaoteros de Colombia, Perú y Ecuador. http://ow.ly/J43p30iU0UZ
El documento resume los resultados de una investigación sobre el contenido de cadmio en granos de cacao en Perú. La investigación analizó muestras de suelo, hojas y granos de cacao de varias regiones para determinar las relaciones entre los contenidos de cadmio. Los resultados mostraron que eliminar la testa de los granos tiende a disminuir el contenido de cadmio. Además, se proponen nuevos protocolos de poscosecha y prácticas agrícolas para reducir los contenidos de cadmio en el suelo, las plantas y los
Técnicas para disminuir la disponibilidad de cadmio en suelos de cacaoterasCIAT
El taller ‘Cacao libre de cadmio’, organizado por el CIAT, CIRAD, y la AFD, se lleva a cabo del 12 al 14 de marzo en la sede del CIAT en Palmira,y tiene como objetivo integrar un consorcio de actores y disciplinas claves de la región, así como elaborar un proyecto de investigación aplicada que dé respuesta a este problema que afecta a los cacaoteros de Colombia, Perú y Ecuador. http://ow.ly/J43p30iU0UZ
El taller ‘Cacao libre de cadmio’, organizado por el CIAT, CIRAD, y la AFD, se lleva a cabo del 12 al 14 de marzo en la sede del CIAT en Palmira,y tiene como objetivo integrar un consorcio de actores y disciplinas claves de la región, así como elaborar un proyecto de investigación aplicada que dé respuesta a este problema que afecta a los cacaoteros de Colombia, Perú y Ecuador. http://ow.ly/J43p30iU0UZ
El taller ‘Cacao libre de cadmio’, organizado por el CIAT, CIRAD, y la AFD, se lleva a cabo del 12 al 14 de marzo en la sede del CIAT en Palmira,y tiene como objetivo integrar un consorcio de actores y disciplinas claves de la región, así como elaborar un proyecto de investigación aplicada que dé respuesta a este problema que afecta a los cacaoteros de Colombia, Perú y Ecuador. http://ow.ly/J43p30iU0UZ
de la región, así como elaborar un proyecto de investigación aplicada que dé respuesta a este problema que afecta a los cacaoteros de Colombia, Perú y Ecuador. http://ow.ly/J43p30iU0UZ
El taller ‘Cacao libre de cadmio’, organizado por el CIAT, CIRAD, y la AFD, se lleva a cabo del 12 al 14 de marzo en la sede del CIAT en Palmira,y tiene como objetivo integrar un consorcio de actores y disciplinas claves de la región, así como elaborar un proyecto de investigación aplicada que dé respuesta a este problema que afecta a los cacaoteros de Colombia, Perú y Ecuador. http://ow.ly/J43p30iU0UZ
5th LF Energy Power Grid Model Meet-up SlidesDanBrown980551
5th Power Grid Model Meet-up
It is with great pleasure that we extend to you an invitation to the 5th Power Grid Model Meet-up, scheduled for 6th June 2024. This event will adopt a hybrid format, allowing participants to join us either through an online Mircosoft Teams session or in person at TU/e located at Den Dolech 2, Eindhoven, Netherlands. The meet-up will be hosted by Eindhoven University of Technology (TU/e), a research university specializing in engineering science & technology.
Power Grid Model
The global energy transition is placing new and unprecedented demands on Distribution System Operators (DSOs). Alongside upgrades to grid capacity, processes such as digitization, capacity optimization, and congestion management are becoming vital for delivering reliable services.
Power Grid Model is an open source project from Linux Foundation Energy and provides a calculation engine that is increasingly essential for DSOs. It offers a standards-based foundation enabling real-time power systems analysis, simulations of electrical power grids, and sophisticated what-if analysis. In addition, it enables in-depth studies and analysis of the electrical power grid’s behavior and performance. This comprehensive model incorporates essential factors such as power generation capacity, electrical losses, voltage levels, power flows, and system stability.
Power Grid Model is currently being applied in a wide variety of use cases, including grid planning, expansion, reliability, and congestion studies. It can also help in analyzing the impact of renewable energy integration, assessing the effects of disturbances or faults, and developing strategies for grid control and optimization.
What to expect
For the upcoming meetup we are organizing, we have an exciting lineup of activities planned:
-Insightful presentations covering two practical applications of the Power Grid Model.
-An update on the latest advancements in Power Grid -Model technology during the first and second quarters of 2024.
-An interactive brainstorming session to discuss and propose new feature requests.
-An opportunity to connect with fellow Power Grid Model enthusiasts and users.
Fueling AI with Great Data with Airbyte WebinarZilliz
This talk will focus on how to collect data from a variety of sources, leveraging this data for RAG and other GenAI use cases, and finally charting your course to productionalization.
[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.
How to Interpret Trends in the Kalyan Rajdhani Mix Chart.pdfChart Kalyan
A Mix Chart displays historical data of numbers in a graphical or tabular form. The Kalyan Rajdhani Mix Chart specifically shows the results of a sequence of numbers over different periods.
Conversational agents, or chatbots, are increasingly used to access all sorts of services using natural language. While open-domain chatbots - like ChatGPT - can converse on any topic, task-oriented chatbots - the focus of this paper - are designed for specific tasks, like booking a flight, obtaining customer support, or setting an appointment. Like any other software, task-oriented chatbots need to be properly tested, usually by defining and executing test scenarios (i.e., sequences of user-chatbot interactions). However, there is currently a lack of methods to quantify the completeness and strength of such test scenarios, which can lead to low-quality tests, and hence to buggy chatbots.
To fill this gap, we propose adapting mutation testing (MuT) for task-oriented chatbots. To this end, we introduce a set of mutation operators that emulate faults in chatbot designs, an architecture that enables MuT on chatbots built using heterogeneous technologies, and a practical realisation as an Eclipse plugin. Moreover, we evaluate the applicability, effectiveness and efficiency of our approach on open-source chatbots, with promising results.
Your One-Stop Shop for Python Success: Top 10 US Python Development Providersakankshawande
Simplify your search for a reliable Python development partner! This list presents the top 10 trusted US providers offering comprehensive Python development services, ensuring your project's success from conception to completion.
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.
zkStudyClub - LatticeFold: A Lattice-based Folding Scheme and its Application...Alex Pruden
Folding is a recent technique for building efficient recursive SNARKs. Several elegant folding protocols have been proposed, such as Nova, Supernova, Hypernova, Protostar, and others. However, all of them rely on an additively homomorphic commitment scheme based on discrete log, and are therefore not post-quantum secure. In this work we present LatticeFold, the first lattice-based folding protocol based on the Module SIS problem. This folding protocol naturally leads to an efficient recursive lattice-based SNARK and an efficient PCD scheme. LatticeFold supports folding low-degree relations, such as R1CS, as well as high-degree relations, such as CCS. The key challenge is to construct a secure folding protocol that works with the Ajtai commitment scheme. The difficulty, is ensuring that extracted witnesses are low norm through many rounds of folding. We present a novel technique using the sumcheck protocol to ensure that extracted witnesses are always low norm no matter how many rounds of folding are used. Our evaluation of the final proof system suggests that it is as performant as Hypernova, while providing post-quantum security.
Paper Link: https://eprint.iacr.org/2024/257
In the realm of cybersecurity, offensive security practices act as a critical shield. By simulating real-world attacks in a controlled environment, these techniques expose vulnerabilities before malicious actors can exploit them. This proactive approach allows manufacturers to identify and fix weaknesses, significantly enhancing system security.
This presentation delves into the development of a system designed to mimic Galileo's Open Service signal using software-defined radio (SDR) technology. We'll begin with a foundational overview of both Global Navigation Satellite Systems (GNSS) and the intricacies of digital signal processing.
The presentation culminates in a live demonstration. We'll showcase the manipulation of Galileo's Open Service pilot signal, simulating an attack on various software and hardware systems. This practical demonstration serves to highlight the potential consequences of unaddressed vulnerabilities, emphasizing the importance of offensive security practices in safeguarding critical infrastructure.
Programming Foundation Models with DSPy - Meetup SlidesZilliz
Prompting language models is hard, while programming language models is easy. In this talk, I will discuss the state-of-the-art framework DSPy for programming foundation models with its powerful optimizers and runtime constraint system.
What is an RPA CoE? Session 1 – CoE VisionDianaGray10
In the first session, we will review the organization's vision and how this has an impact on the COE Structure.
Topics covered:
• The role of a steering committee
• How do the organization’s priorities determine CoE Structure?
Speaker:
Chris Bolin, Senior Intelligent Automation Architect Anika Systems
Main news related to the CCS TSI 2023 (2023/1695)Jakub Marek
An English 🇬🇧 translation of a presentation to the speech I gave about the main changes brought by CCS TSI 2023 at the biggest Czech conference on Communications and signalling systems on Railways, which was held in Clarion Hotel Olomouc from 7th to 9th November 2023 (konferenceszt.cz). Attended by around 500 participants and 200 on-line followers.
The original Czech 🇨🇿 version of the presentation can be found here: https://www.slideshare.net/slideshow/hlavni-novinky-souvisejici-s-ccs-tsi-2023-2023-1695/269688092 .
The videorecording (in Czech) from the presentation is available here: https://youtu.be/WzjJWm4IyPk?si=SImb06tuXGb30BEH .
For the full video of this presentation, please visit: https://www.edge-ai-vision.com/2024/06/temporal-event-neural-networks-a-more-efficient-alternative-to-the-transformer-a-presentation-from-brainchip/
Chris Jones, Director of Product Management at BrainChip , presents the “Temporal Event Neural Networks: A More Efficient Alternative to the Transformer” tutorial at the May 2024 Embedded Vision Summit.
The expansion of AI services necessitates enhanced computational capabilities on edge devices. Temporal Event Neural Networks (TENNs), developed by BrainChip, represent a novel and highly efficient state-space network. TENNs demonstrate exceptional proficiency in handling multi-dimensional streaming data, facilitating advancements in object detection, action recognition, speech enhancement and language model/sequence generation. Through the utilization of polynomial-based continuous convolutions, TENNs streamline models, expedite training processes and significantly diminish memory requirements, achieving notable reductions of up to 50x in parameters and 5,000x in energy consumption compared to prevailing methodologies like transformers.
Integration with BrainChip’s Akida neuromorphic hardware IP further enhances TENNs’ capabilities, enabling the realization of highly capable, portable and passively cooled edge devices. This presentation delves into the technical innovations underlying TENNs, presents real-world benchmarks, and elucidates how this cutting-edge approach is positioned to revolutionize edge AI across diverse applications.
Monitoring and Managing Anomaly Detection on OpenShift.pdfTosin Akinosho
Monitoring and Managing Anomaly Detection on OpenShift
Overview
Dive into the world of anomaly detection on edge devices with our comprehensive hands-on tutorial. This SlideShare presentation will guide you through the entire process, from data collection and model training to edge deployment and real-time monitoring. Perfect for those looking to implement robust anomaly detection systems on resource-constrained IoT/edge devices.
Key Topics Covered
1. Introduction to Anomaly Detection
- Understand the fundamentals of anomaly detection and its importance in identifying unusual behavior or failures in systems.
2. Understanding Edge (IoT)
- Learn about edge computing and IoT, and how they enable real-time data processing and decision-making at the source.
3. What is ArgoCD?
- Discover ArgoCD, a declarative, GitOps continuous delivery tool for Kubernetes, and its role in deploying applications on edge devices.
4. Deployment Using ArgoCD for Edge Devices
- Step-by-step guide on deploying anomaly detection models on edge devices using ArgoCD.
5. Introduction to Apache Kafka and S3
- Explore Apache Kafka for real-time data streaming and Amazon S3 for scalable storage solutions.
6. Viewing Kafka Messages in the Data Lake
- Learn how to view and analyze Kafka messages stored in a data lake for better insights.
7. What is Prometheus?
- Get to know Prometheus, an open-source monitoring and alerting toolkit, and its application in monitoring edge devices.
8. Monitoring Application Metrics with Prometheus
- Detailed instructions on setting up Prometheus to monitor the performance and health of your anomaly detection system.
9. What is Camel K?
- Introduction to Camel K, a lightweight integration framework built on Apache Camel, designed for Kubernetes.
10. Configuring Camel K Integrations for Data Pipelines
- Learn how to configure Camel K for seamless data pipeline integrations in your anomaly detection workflow.
11. What is a Jupyter Notebook?
- Overview of Jupyter Notebooks, an open-source web application for creating and sharing documents with live code, equations, visualizations, and narrative text.
12. Jupyter Notebooks with Code Examples
- Hands-on examples and code snippets in Jupyter Notebooks to help you implement and test anomaly detection models.
"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
"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.
Assessing Differentially Expressed Genes in Storage Root of Cassava Landraces from Brazil and Colombia Using Microarray Data
1. Assessing Differentially Expressed Genes in Storage Root of
Cassava Landraces from Brazil and Colombia Using Microarray Data
Luiz Joaquim Castelo Branco Carvalho1, James V Anderson2, Diana Bernal3, Joe Tohme3, Chikelu
Mba4, Eduardo Alano Vieira5 and Elaine Cunha Moreno1
Laboratory of Biophysics and Biochemistry - LBB, Embrapa Cenargen - DF1; USDA/ARS, Plant Science Research
Unit, Fargo, ND2; CIAT, Cali-Colombia3; IAEA - Vienna, Austria4; EMBRAPA Cerrados5
Introduction
With a functional genomic’s based approach, the high throughput microarray technology sounds to be appropriated to gain information at global level to identify differentially expressed genes among landraces of divergent genetic
background. To date, most efforts using microarrays to study cassava has been focused on expression profiles with restricted genetic background oriented to diseases, abiotic stress and post harvest physiological deterioration. It
has also been claimed that cDNA chip developed for Euphorbiacea family, based on two species (leaf spurge and cassava), may be a useful tool to study gene expression analysis and diversity in cassava at a global base. Our
own work, using HPLC carotenoid profile as diversity sign, has identified color mutated phenotypes in the center of origin and domestication of cassava in Brazil. The present work combines diversity of pigmented cassava
landraces with genetic background from Brazil and Colombian varieties from CIAT to evaluate global gene expression analysis to help explain genetic diversity in pigmented cassava and discover new regulatory genes and
biological pathways in cassava storage root.
Materials and Methods
Domestication hypothesis: Our morphological model for cassava domestication Data analysis: There is no single software that contains all the existing analytical algorithms for gene expression analysis with
considers changes in growth habit, storage root formation and flowering sets of microarray. Our analytical procedure considered four levels of data analysis, included image and data quality evaluation (first
cassava ancestor (M esculenta ssp flabellifolia) to become the cultivated species (M level), statistically differentially expressed genes set identification (second level), functional and ontological genes sub-set classification
esculenta ssp esculenta) as in Figure 6. (third level), and regulatory networks of genes sub-set and biological pathways (fourth level).
Plant material: Storage root from cassava landraces
CAS36.7, Itauba, Jaboti, Mirasol, Surubim, IAC12-829 from Brazil and 25392 cDNA Array
MTAI16/1, CM2177-2/1, Reina1 and Veronica1 from Colombia (CIAT) were used in the Landrace Diversity Loop Dye Swap GenePix Analysis
Sugary Normal
present study. 23752 QC_Tr
Tissue sampling preparation: Cylinders of storage roots with 30-40 cm long and 4-6 GeneMath Analysis Cassava Data Base
IAC Leafy spurge Data Base
cm diameter were manually dissected in individual tissue layers, immediately frozen in Arabidopsis Data Base
liquid nitrogen and stored in -80°C until use. For RNA extraction we used layer 3
161 DEG
(young secondary growth tissue) because of its closeness of the cambium meristem Intense Yellow Pink Sug
and the most physiological active tissue in the storage root formation. MIPS Analysis Arabidopsis Annotation
Data Base
RNA extraction – tissue system and extraction procedures. RNA
extraction, purification and quantification followed conventional phenol:chloroform 75 ARG
procedure as previously described (de Souza et al, 2004). Ver
Pathway Studio Analysis ResNet Plant Data Base
CIAT Group
Microarrays – experimental design and hybridization procedures: The
Matai16/ GSEA SNEA
experimental design considered Loop-Dye Swap, biological replication 1
Veronica1
(3reps), sample replication (3reps), technical replication (2reps) and the dye CM2177- Reina1
2/1
Rei 34 RG 10 BRG
replication (2reps). cDNA labeling and chip hybridization used kit from Invitrogen
(Kits: Platinum® PCR SuperMix) and followed the procedure recommended. Thirty Pathways Retrieval
microgram of total RNA was used to prepare cDNA probe labeled with Cy3 and Cy5. CM2
Results and Discussions Regulatory
Network
Quality control of hybridization: High quality hybridization signal considered Array design, Image quality Metabolic pathway regulated genes: Figure 4 shows the regulation of genes coding for enzymes on
(background, intensity & reproducibility), Spot quality (center the synthesis and degradation of carotenoid in cassava.
location, background, intensity, noise, specificity, morphology & reproducibility) and Spike controls. The
cutoff limits for image quality threw out top 1% of outliers by using Gigh-PMT and saturation tolerance of expressed protein lycopene epsilon cyclase
0.05%. Under this condition the extent of expressed genes was obtained. Image quality analysis results for 1,2
phytoene desaturase neoxanthin cleavage enzyme nc1
zeta-carotene desaturase p-hydroxyphenylpyruvate dioxygenase
11 probes were representative with more than 93% with high quality hybridization signal ending with more
1
than 23000 elements (out of 25392) in the array with quality to continue the analysis.
0,8
Differentially expressed genes (DEG): Hybridization intensity signal were statistically analyzed to 0,6
determine the extent of expressed gene. A total of 161 genes (Table 1) showed to be differentially
0,4
expressed at a p-value of 0.005. Pattern of DEG data set was examined by two statistical strategies. First by
Principal Component Analysis and then tested by recursive Partitioning for a tentative conclusions on the 0,2
grouping patterns observed in the PCA. The PCA results (Figure 1) indicates the patterns of three groups of
0
genes in DEG that were confirmed with the partitioning grouping results (Figure 2). This grouping pattern is IAC-B-1 IAC-R-1 ITA-B-1 ITA-R-1 Sur-B-1 Sur-R-1
closely associated with the groups of landraces phenotypes. -0,2
Table 1 - Summarized numbers of genes statistically differentially expressed among landraces. -0,4
-0,6
Genome Source Total Anotated Unknown p_Value Coverage
Leaf Spurge 10 7 3 0,005 0,02 -0,8
Cassava 151 75 76 0,005 1,84
TOTAL 161 82 79 0,005 1,86 Exploratory pathways network and candidate regulatory genes: he algorithm Sub Network Enrichment
Statistical Analysis: Differentially Expressed Genes (p Value<0,005) Analysis (SNEA) was used to establish the level of significance (p-value) of regulatory genes in DEG sets
based on three kind of molecular interaction mechanisms (expression target, binding protein, and protein
modification). Statistically significant (p-value<0.05) regulatory genes networks were visualized as an
exploratory pathway network. Figure 5 indicating node operating gene, edge genes which are regulated
1.5e5
(activated or silenced) and their expression level, if up (blue color) or down (pink color) regulated. Among
LD_G I
genes interdependence, visualized in the pathway, regulatory genes such as transcription factors and other
genes products modulating functionality (protein binding and modification) were observed. The node gene in
1.0e5
the network operates the pathway and genes, while in the edge it is observed regulatory genes of a particular
pathway. Table 2 summarizes the list of node genes in the networks unique to each class of landraces when
comparisons were made to cassava ancestor and the elite variety IAC12-829.
5e4
0
Table 2 – Node genes unique to each class of landraces when comparisons were made to normal cassava.DD
LD_G III Pink Sugary Intense Yellow CIAT
-5e4
FLC(ET) *** MPK4(ET) SEU(ET)
ABI1(ET) ABI5(ET) AT1G50240(ET) LUG(ET)
-1.0e5
JAR1(ET) SLY1(PI) BRI1(PI) EDS1(ET)
*** PRL1(PI) *** ***
LD_G II
*** CLPP4(PI) *** ***
-1.5e5
-2.0e5 -1.5e5 -1.0e5 -5e4 0 5e4 1.0e5
Figure 1 - Principal component analysis for DEG. Figure 2 - Gene group partitioned in DEG.
Ontology and functional classification of DEG: The MIPS analyzes identified gene ontology and
functional groups. This information was used to select only regulatory genes sub-set to dissect the
pathway network and inferring on regulatory genes as performed bellow. Data results are summarized in
Figures 3.
99 UNCLASSIFIED
PROTEINS 01 METABOLISM
77 ORGAN LOCALIZATION (76)
02 ENERGY
70 SUBCELLULAR
LOCALIZATION 73 CELL TYPE
10 CELL CYCLE AND DNA
LOCALIZATION
PROCESSING
Glucose responsive pathway MADS-box transcription factors
11 TRANSCRIPTION
Unique to Sugary Unique to Pink
43 CELL TYPE 12 PROTEIN SYNTHESIS
DIFFERENTIATION
14 PROTEIN FATE
(folding, modification, destin
47 ORGAN
ation)
DIFFERENTIATION
42 BIOGENESIS OF
CELLULAR COMPONENTS
41 DEVELOPMENT
(Systemic)
16 PROTEIN WITH
40 CELL FATE BINDING FUNCTION OR
COFACTOR
36 SYSTEMIC REQUIREMENT
INTERACTION WITH THE (118)
ENVIRONMENT FUSED (FU) gene belongs to SEU transcriptional co-regulator of
34 INTERACTION WITH 18 REGULATION OF Ser/Thr protein kinase AGAMOUS
THE ENVIRONMENT METABOLISM AND
PROTEIN FUNCTION Unique to Yellow Unique to CIAT
32 CELL (7)
RESCUE, DEFENSE AND 30 CELLULAR 20 CELLULAR
VIRULENCE COMMUNICATION/SIGNAL TRANSPORT, TRANSPORT
TRANSDUCTION FACILITIES AND
Figure 5 – Diagram showing exploratory pathways network for regulatory genes related to the landrace diversity.
MECHANISM TRANSPORT ROUTES (40) Blue and pink colors symbols are up and down regulated genes.
Figure 3 - Profile of gene sets for DEG
Final Remarks and Future Perspective
Identified regulatory genes sub-sets: The algorithm Gene Set Enrichment Analysis (GSEA) Results indicated that the major genes differentially expressed are largely related to stress response such as up-
established regulatory genes functional statistically significance (p-value) groups in sub-sets for regulated gene for ABA synthesis, transcription factor homolog related to hypoxia, transport proteins for
biological processes, cellular component and molecular function. glucose/ABA and nitrogen, and three unknown genes. Transcript profiles for those genes across landraces
contrasting carotenoid HPLC profiles consistently correlated with end products of carotenoid synthesis.
Quantitative Real Time PCR are planed to confirm the uniqueness of each of pathway associated to a particular
Financial support: Ginés Mera Memorial Fellowship Fund - C-019-08 and color phenotype.
IAEA contract # BRA-13188/R0