Poster prepared by Francesca Stomeo, Mark Wamalwa, Jagger Harvey, Douglas W. Miano, Neil Boonham, Dora Kilalo, Ian Adams and Appolinaire Djikeng) for the ILRI APM 2013, Addis Ababa, 15-17 May 2013
The Phytobiomes Initiative proposes a systems-level approach to studying the entire microbial community associated with plants, including bacteria, viruses, and eukaryotes in the rhizosphere, phyllosphere, and within plants. Recent advances in metagenomic technologies now allow comprehensive analysis of both culturable and non-culturable microbes. Two recent studies using these methods revealed that root microbial communities are non-random and depend on host genotype and environment. The initiative aims to establish a foundation for understanding how phytobiomes influence plant health and productivity, with the goal of developing strategies to improve crop yields, reduce disease and environmental impacts, and enhance food safety and security.
The document discusses the Plant Microbiome Project which aims to understand the relationships between plants and their associated microbes. Specifically, it seeks to determine what genetic factors influence whether a microbe benefits or harms a plant. The author's role is to sequence microbes found living in seaweed to study their effects when inoculated in Arabidopsis plants and duckweed. Preliminary results found genera like Bacillus and Geobacillus in bacteria isolated from seaweed in Brazil. Future work includes testing the seaweed microbes' effects on plant growth and sequencing any beneficial microbes.
Bioinformatics plays a significant role in the development of the agricultural sector, crop improvement,
agro-based industries, agricultural by-products utilization and better management of the
environment. With the increase of sequencing projects, bioinformatics continues to make
considerable progress in biology by providing scientists with access to the genomic information.
It is believed that we will take on another giant leap in bioinformatics field in next decade, where
computational models of systems wide properties could serve as the basis for experimentation
and discovery. Agricultural bioinform -atics areas that need focus would be are data curation and
need for the use of restricted vocabularies. Being an interface between modern biology and
informatics it involves discovery, development and implementation of computational algorithms
and software tools that facilitate an understanding of the biological processes with the goal to
serve primarily agriculture and healthcare sectors with several spinoffs.
Metagenomics is a set of techniques used to study microbial communities through direct collection and analysis of environmental DNA samples. It allows researchers to study millions of microbial organisms and genetic fragments simultaneously without needing to culture individual microbes in the lab. The main procedures involve sampling an environment, filtering out particles by size, extracting and sequencing DNA fragments. Two common sequencing methods are shotgun sequencing and high-throughput sequencing using platforms like Illumina or SOLiD. Projects like MetaHIT use metagenomics to study the human gut microbiome and its role in health and disease. Potential applications include contributions to earth sciences, life sciences, biomedicine, bioenergy, biotechnology, and microbial forensics.
Bioinformatics is the science of storing, retrieving and analysing large amounts of biological information. It involves biologists, computer scientists, and mathematicians analyzing data like DNA sequences, protein domains, and protein sequences. DNA sequencing determines the order of nucleotides in DNA using various techniques to analyze adenine, guanine, cytosine, and thymine. Protein domains are basic protein units that can fold and function independently, and domain prediction methods are sequence-based or structure-based. Gene expression can be determined by measuring mRNA levels using techniques like microarrays and RNA sequencing.
Computer science plays an important role in biotechnology by enabling the analysis and management of vast amounts of biological and genetic data. Bioinformatics tools allow researchers to gather, store, analyze and integrate various data sources to make new discoveries about gene and protein sequences, structures and functions. These tools include biological databases and software for tasks like sequence alignment, analysis and interpretation of data, and development of algorithms and statistics. The Human Genome Project was a landmark international scientific research project that mapped the human genome with the help of computational analysis and over 3300 billion lines of code.
this ppt contains information regarding Bioinformatics database. introduction, objectives of database, database management, application of database management, types of database management. Its a part of subject pharmacy, 2nd semester computer application.
The Phytobiomes Initiative proposes a systems-level approach to studying the entire microbial community associated with plants, including bacteria, viruses, and eukaryotes in the rhizosphere, phyllosphere, and within plants. Recent advances in metagenomic technologies now allow comprehensive analysis of both culturable and non-culturable microbes. Two recent studies using these methods revealed that root microbial communities are non-random and depend on host genotype and environment. The initiative aims to establish a foundation for understanding how phytobiomes influence plant health and productivity, with the goal of developing strategies to improve crop yields, reduce disease and environmental impacts, and enhance food safety and security.
The document discusses the Plant Microbiome Project which aims to understand the relationships between plants and their associated microbes. Specifically, it seeks to determine what genetic factors influence whether a microbe benefits or harms a plant. The author's role is to sequence microbes found living in seaweed to study their effects when inoculated in Arabidopsis plants and duckweed. Preliminary results found genera like Bacillus and Geobacillus in bacteria isolated from seaweed in Brazil. Future work includes testing the seaweed microbes' effects on plant growth and sequencing any beneficial microbes.
Bioinformatics plays a significant role in the development of the agricultural sector, crop improvement,
agro-based industries, agricultural by-products utilization and better management of the
environment. With the increase of sequencing projects, bioinformatics continues to make
considerable progress in biology by providing scientists with access to the genomic information.
It is believed that we will take on another giant leap in bioinformatics field in next decade, where
computational models of systems wide properties could serve as the basis for experimentation
and discovery. Agricultural bioinform -atics areas that need focus would be are data curation and
need for the use of restricted vocabularies. Being an interface between modern biology and
informatics it involves discovery, development and implementation of computational algorithms
and software tools that facilitate an understanding of the biological processes with the goal to
serve primarily agriculture and healthcare sectors with several spinoffs.
Metagenomics is a set of techniques used to study microbial communities through direct collection and analysis of environmental DNA samples. It allows researchers to study millions of microbial organisms and genetic fragments simultaneously without needing to culture individual microbes in the lab. The main procedures involve sampling an environment, filtering out particles by size, extracting and sequencing DNA fragments. Two common sequencing methods are shotgun sequencing and high-throughput sequencing using platforms like Illumina or SOLiD. Projects like MetaHIT use metagenomics to study the human gut microbiome and its role in health and disease. Potential applications include contributions to earth sciences, life sciences, biomedicine, bioenergy, biotechnology, and microbial forensics.
Bioinformatics is the science of storing, retrieving and analysing large amounts of biological information. It involves biologists, computer scientists, and mathematicians analyzing data like DNA sequences, protein domains, and protein sequences. DNA sequencing determines the order of nucleotides in DNA using various techniques to analyze adenine, guanine, cytosine, and thymine. Protein domains are basic protein units that can fold and function independently, and domain prediction methods are sequence-based or structure-based. Gene expression can be determined by measuring mRNA levels using techniques like microarrays and RNA sequencing.
Computer science plays an important role in biotechnology by enabling the analysis and management of vast amounts of biological and genetic data. Bioinformatics tools allow researchers to gather, store, analyze and integrate various data sources to make new discoveries about gene and protein sequences, structures and functions. These tools include biological databases and software for tasks like sequence alignment, analysis and interpretation of data, and development of algorithms and statistics. The Human Genome Project was a landmark international scientific research project that mapped the human genome with the help of computational analysis and over 3300 billion lines of code.
this ppt contains information regarding Bioinformatics database. introduction, objectives of database, database management, application of database management, types of database management. Its a part of subject pharmacy, 2nd semester computer application.
The document summarizes a bioinformatics summer camp, including:
1. The camp will cover basic molecular biology and bioinformatics topics like DNA, proteins, gene expression and the genetic code.
2. Students will work on computational analysis projects involving whole genome sequencing, gene expression profiling, and functional and comparative genomics.
3. The camp will teach techniques for analyzing protein structures and interactions, gene expression data, and identifying pockets on protein surfaces.
Bioinformatics is the branch of life science that deals with the use of mathematical, statistical and computer methods to analyze biological and biochemical data.
Types of Bioinformatics (see the slides)
Bioinformatics in biotechnology by kk sahu KAUSHAL SAHU
Introduction
Bioinformatics – definition
History
Required skills
Core areas of bioinformatics
Components of bioinformatics
Nomenclature system in bioinformatics
Biological databases
Types of database
Bioinformatics tools
Applications of bioinformatics
Conclusion
References
The document summarizes microbiome biomarker data from the American Gut Project. It describes the project's goal of characterizing participants' gut, skin, and oral bacteria to better understand relationships between microbiome and lifestyle/health factors. Over 4,600 samples from 3,624 participants have been sequenced and analyzed. The analyzed samples included some from patients that provided multiple sample types (mouth & skin, mouth & stool). T-Bioinfo then performed analyses including mapping samples to identify bacteria, generating abundance tables, and using machine learning methods to identify correlations between bacterial species from different body sites. Preliminary conclusions identified outstanding samples and correlated oral and stool bacteria.
The document discusses applications of DNA technology including the Human Genome Project. The Human Genome Project was a 13-year international project completed in 2003 that mapped and sequenced the entire human genome. Its goals were to identify all human genes, determine the sequence of DNA's 3 billion base pairs, store this information in databases, improve analysis tools, and address ethical issues arising from the research. The project used genetic mapping, physical mapping, and DNA sequencing approaches.
The document summarizes research that screened metagenomic libraries from Puerto Rican forests for protease activity. Culture-independent metagenomic techniques were used to study the uncultured microbial genetics. Two libraries containing 14,000 and 600,000 clones were screened, identifying 20 potential clones producing protease enzymes, which are undergoing further analysis. Proteases have important industrial biotechnology applications.
Bio-banking and metagenomics platforms for pathogen discoveryILRI
Poster by George Michuki, Absolomon Kihara, Alan Orth, Cecilia Rumberia and Steve Kemp presented at the Sequencing, Finishing and Analysis in the Future (SFAF) meeting held at Santa Fe, New Mexico, 29-31 May 2013.
Survival of the Fittest – Utilization of Natural selection Mechanisms for Imp...Behnam Taraghi
This document discusses how natural selection mechanisms from Darwin's theory of evolution can be applied to improve personal learning environments (PLEs). It describes selection, variation, and tracking user behavior and preferences to evolve widgets through micro and macro evolution. Selection mechanisms like stabilizing, disruptive, and directed selection act on widgets based on factors like usage frequency and activation to improve the most used and activated widgets over time.
This document provides an overview of bioinformatics. It begins by explaining how bioinformatics emerged from the need to analyze vast amounts of genetic sequence data produced by projects like the Human Genome Project. It then defines bioinformatics as the field that develops tools and methods for understanding biological data by combining computer science, statistics, and other disciplines. The document outlines several goals and applications of bioinformatics, such as identifying genes and their functions, modeling protein structures, comparing genomes, and its uses in medicine, microbial research, and more. It also provides a brief history of important developments in bioinformatics and DNA sequencing.
This document discusses metagenomics, which is the study of microbial communities directly in their natural environments without isolating individual species. It outlines some key aspects of metagenomics including that most prokaryotes cannot be cultured, the use of metagenomics to study viral communities, and approaches such as functional screening and sequence-based screening. Limitations and future directions are also mentioned. Metagenomics provides insights into microbial interactions, metabolism, and genomics that were previously unknown.
This document discusses insect monitoring techniques like pheromone and light traps. Pheromone traps use sex pheromones to attract specific insect species and are useful for tracking populations over time. Light traps attract a variety of insects. Data from these traps is used for pest forecasting through phenology models, which predict development timing based on temperature, and simulation models. The monitoring data and models help time management practices like pesticide applications and scouting.
Bioinformatics & It's Scope in BiotechnologyTuhin Samanta
As an interdisciplinary field of science, bioinformatics consolidates science, software engineering, data building, arithmetic and measurements to dissect and decipher organic information. Bioinformatics has been utilized for in silico investigations of organic inquiries utilizing numerical and measurable methods.
The document provides a summary of the Microbial Genomics 2008 conference held in Lake Arrowhead, California. It discusses several topics that were covered at the conference, including biofuels production using metabolic engineering of E. coli, the Genomic Encyclopedia of Bacteria and Archaea project to sequence bacterial genomes, the Human Microbiome Project to study microbes that live in and on the human body, using metagenomics to study viral ecology in marine environments, identifying essential genes in yeast, studying persister cells in bacterial populations, and discovering new antibacterial targets. Feedback was requested on the training session.
This document provides definitions and descriptions of the field of bioinformatics from multiple perspectives:
- Bioinformatics is the use of computers to analyze and interpret massive amounts of biological data, especially related to genomics, through techniques like modeling, algorithm development, and statistics.
- It involves the convergence of biology, biotechnology, computer science, and information technology to address challenges in managing and understanding biological data.
- Bioinformatics encompasses a range of activities from database management and analysis to developing tools that facilitate biological research and applications in fields like medicine.
Regulatory Status of Genome Editing in Vietnam apaari
Regulatory Status of Genome Editing in Vietnam during the Regional Expert Consultation on Gene Editing in Agriculture and its Regulations Technical Session II
Bioinformatics is a hybrid science that links biological data with techniques for information storage, distribution, and analysis to support multiple areas of scientific research, including biomedicine.
Bioinformatics issues and challanges presentation at s p collegeSKUASTKashmir
This document provides an overview of bioinformatics and some key concepts:
- It discusses the exponential growth of biological data from technologies like PCR and microarrays, and how bioinformatics is needed to analyze this data.
- Bioinformatics is defined as integrating biology and computer science to collect, analyze, and interpret large amounts of molecular-level information. It uses databases and tools to study genomes, proteins, and biological processes.
- Major databases like GenBank, EMBL, and SwissProt store DNA, RNA, protein sequences and provide access to researchers. Tools like BLAST are used to search databases and analyze sequences.
- Benefits of bioinformatics include advances in medicine, agriculture, forensics
Maize Lethal Necrosis: Perspective from the U.S. MidwestCIMMYT
Perspective from the U.S. Midwest on MLN, presented at the International Conference on “MLN Diagnostics and Management in Africa,” organized by AGRA (Alliance for Green Revolution in Africa) and CIMMYT, 12-14 May, 2015
This document analyzes the genetic variability of Watermelon Mosaic Virus-II (WMV-II) in different melon cultivars in South Korea. Researchers inoculated various melon cultivars with WMV-II to investigate their response and analyzed the biological and molecular variability of WMV-II by amplifying its coat protein gene. The goal is to select breeding resources to develop virus-resistant melon cultivars and characterize WMV-II strains through coat protein gene sequencing and comparisons. The research collaborates with KRIBB and expects to receive $100K in funding over 3 years for samples, sequencing, and other activities.
Genomic aided selection for crop improvementtanvic2
This document summarizes a case study on the draft genome sequence of chickpea. Key points include:
- Researchers sequenced and assembled the ~738Mb genome of a kabuli chickpea variety, identifying an estimated 28,269 genes.
- The genome provides resources for molecular breeding through identification of candidate genes for traits like disease resistance.
- Resequencing of elite varieties provided insights into genome diversity and domestication.
- Analysis found the draft captured over 90% of the gene space through mapping of transcriptome data, and contained homologs for over 98% of core eukaryotic genes.
The document summarizes a bioinformatics summer camp, including:
1. The camp will cover basic molecular biology and bioinformatics topics like DNA, proteins, gene expression and the genetic code.
2. Students will work on computational analysis projects involving whole genome sequencing, gene expression profiling, and functional and comparative genomics.
3. The camp will teach techniques for analyzing protein structures and interactions, gene expression data, and identifying pockets on protein surfaces.
Bioinformatics is the branch of life science that deals with the use of mathematical, statistical and computer methods to analyze biological and biochemical data.
Types of Bioinformatics (see the slides)
Bioinformatics in biotechnology by kk sahu KAUSHAL SAHU
Introduction
Bioinformatics – definition
History
Required skills
Core areas of bioinformatics
Components of bioinformatics
Nomenclature system in bioinformatics
Biological databases
Types of database
Bioinformatics tools
Applications of bioinformatics
Conclusion
References
The document summarizes microbiome biomarker data from the American Gut Project. It describes the project's goal of characterizing participants' gut, skin, and oral bacteria to better understand relationships between microbiome and lifestyle/health factors. Over 4,600 samples from 3,624 participants have been sequenced and analyzed. The analyzed samples included some from patients that provided multiple sample types (mouth & skin, mouth & stool). T-Bioinfo then performed analyses including mapping samples to identify bacteria, generating abundance tables, and using machine learning methods to identify correlations between bacterial species from different body sites. Preliminary conclusions identified outstanding samples and correlated oral and stool bacteria.
The document discusses applications of DNA technology including the Human Genome Project. The Human Genome Project was a 13-year international project completed in 2003 that mapped and sequenced the entire human genome. Its goals were to identify all human genes, determine the sequence of DNA's 3 billion base pairs, store this information in databases, improve analysis tools, and address ethical issues arising from the research. The project used genetic mapping, physical mapping, and DNA sequencing approaches.
The document summarizes research that screened metagenomic libraries from Puerto Rican forests for protease activity. Culture-independent metagenomic techniques were used to study the uncultured microbial genetics. Two libraries containing 14,000 and 600,000 clones were screened, identifying 20 potential clones producing protease enzymes, which are undergoing further analysis. Proteases have important industrial biotechnology applications.
Bio-banking and metagenomics platforms for pathogen discoveryILRI
Poster by George Michuki, Absolomon Kihara, Alan Orth, Cecilia Rumberia and Steve Kemp presented at the Sequencing, Finishing and Analysis in the Future (SFAF) meeting held at Santa Fe, New Mexico, 29-31 May 2013.
Survival of the Fittest – Utilization of Natural selection Mechanisms for Imp...Behnam Taraghi
This document discusses how natural selection mechanisms from Darwin's theory of evolution can be applied to improve personal learning environments (PLEs). It describes selection, variation, and tracking user behavior and preferences to evolve widgets through micro and macro evolution. Selection mechanisms like stabilizing, disruptive, and directed selection act on widgets based on factors like usage frequency and activation to improve the most used and activated widgets over time.
This document provides an overview of bioinformatics. It begins by explaining how bioinformatics emerged from the need to analyze vast amounts of genetic sequence data produced by projects like the Human Genome Project. It then defines bioinformatics as the field that develops tools and methods for understanding biological data by combining computer science, statistics, and other disciplines. The document outlines several goals and applications of bioinformatics, such as identifying genes and their functions, modeling protein structures, comparing genomes, and its uses in medicine, microbial research, and more. It also provides a brief history of important developments in bioinformatics and DNA sequencing.
This document discusses metagenomics, which is the study of microbial communities directly in their natural environments without isolating individual species. It outlines some key aspects of metagenomics including that most prokaryotes cannot be cultured, the use of metagenomics to study viral communities, and approaches such as functional screening and sequence-based screening. Limitations and future directions are also mentioned. Metagenomics provides insights into microbial interactions, metabolism, and genomics that were previously unknown.
This document discusses insect monitoring techniques like pheromone and light traps. Pheromone traps use sex pheromones to attract specific insect species and are useful for tracking populations over time. Light traps attract a variety of insects. Data from these traps is used for pest forecasting through phenology models, which predict development timing based on temperature, and simulation models. The monitoring data and models help time management practices like pesticide applications and scouting.
Bioinformatics & It's Scope in BiotechnologyTuhin Samanta
As an interdisciplinary field of science, bioinformatics consolidates science, software engineering, data building, arithmetic and measurements to dissect and decipher organic information. Bioinformatics has been utilized for in silico investigations of organic inquiries utilizing numerical and measurable methods.
The document provides a summary of the Microbial Genomics 2008 conference held in Lake Arrowhead, California. It discusses several topics that were covered at the conference, including biofuels production using metabolic engineering of E. coli, the Genomic Encyclopedia of Bacteria and Archaea project to sequence bacterial genomes, the Human Microbiome Project to study microbes that live in and on the human body, using metagenomics to study viral ecology in marine environments, identifying essential genes in yeast, studying persister cells in bacterial populations, and discovering new antibacterial targets. Feedback was requested on the training session.
This document provides definitions and descriptions of the field of bioinformatics from multiple perspectives:
- Bioinformatics is the use of computers to analyze and interpret massive amounts of biological data, especially related to genomics, through techniques like modeling, algorithm development, and statistics.
- It involves the convergence of biology, biotechnology, computer science, and information technology to address challenges in managing and understanding biological data.
- Bioinformatics encompasses a range of activities from database management and analysis to developing tools that facilitate biological research and applications in fields like medicine.
Regulatory Status of Genome Editing in Vietnam apaari
Regulatory Status of Genome Editing in Vietnam during the Regional Expert Consultation on Gene Editing in Agriculture and its Regulations Technical Session II
Bioinformatics is a hybrid science that links biological data with techniques for information storage, distribution, and analysis to support multiple areas of scientific research, including biomedicine.
Bioinformatics issues and challanges presentation at s p collegeSKUASTKashmir
This document provides an overview of bioinformatics and some key concepts:
- It discusses the exponential growth of biological data from technologies like PCR and microarrays, and how bioinformatics is needed to analyze this data.
- Bioinformatics is defined as integrating biology and computer science to collect, analyze, and interpret large amounts of molecular-level information. It uses databases and tools to study genomes, proteins, and biological processes.
- Major databases like GenBank, EMBL, and SwissProt store DNA, RNA, protein sequences and provide access to researchers. Tools like BLAST are used to search databases and analyze sequences.
- Benefits of bioinformatics include advances in medicine, agriculture, forensics
Maize Lethal Necrosis: Perspective from the U.S. MidwestCIMMYT
Perspective from the U.S. Midwest on MLN, presented at the International Conference on “MLN Diagnostics and Management in Africa,” organized by AGRA (Alliance for Green Revolution in Africa) and CIMMYT, 12-14 May, 2015
This document analyzes the genetic variability of Watermelon Mosaic Virus-II (WMV-II) in different melon cultivars in South Korea. Researchers inoculated various melon cultivars with WMV-II to investigate their response and analyzed the biological and molecular variability of WMV-II by amplifying its coat protein gene. The goal is to select breeding resources to develop virus-resistant melon cultivars and characterize WMV-II strains through coat protein gene sequencing and comparisons. The research collaborates with KRIBB and expects to receive $100K in funding over 3 years for samples, sequencing, and other activities.
Similar to Plant virome ecology in African farming systems: A genomics and bioinformatics framework for high-throughput virus detection and pathogen discovery
Genomic aided selection for crop improvementtanvic2
This document summarizes a case study on the draft genome sequence of chickpea. Key points include:
- Researchers sequenced and assembled the ~738Mb genome of a kabuli chickpea variety, identifying an estimated 28,269 genes.
- The genome provides resources for molecular breeding through identification of candidate genes for traits like disease resistance.
- Resequencing of elite varieties provided insights into genome diversity and domestication.
- Analysis found the draft captured over 90% of the gene space through mapping of transcriptome data, and contained homologs for over 98% of core eukaryotic genes.
Incidence and Impact of Maize Lethal Necrosis Disease in TanzaniaCIMMYT
Incidence and Impact of Maize Lethal Necrosis Disease in Tanzania, presented at the International Conference on “MLN Diagnostics and Management in Africa,” organized by AGRA (Alliance for Green Revolution in Africa) and CIMMYT, 12-14 May, 2015
Detection of Early Leaf spot of groundnut using Neural Network techniquesIRJET Journal
This document describes a study that used neural network techniques to detect early leaf spot disease in groundnut plants. Specifically, it developed detection models using convolutional neural networks (CNNs) and artificial neural networks (ANNs). Thermal and RGB images of healthy and infected groundnut leaves were collected and preprocessed. An ANN model was developed using the thermal image data to classify temperature differences between healthy and diseased leaf areas. CNN models were also trained on the RGB image data set to identify healthy versus infected leaves. The models achieved high accuracy, demonstrating the potential of neural networks for early and accurate detection of this important groundnut disease.
Modeling and manipulation of plant-aphid interactions: A new avenue for susta...ILRI
1. An international scientific team aims to develop sustainable strategies to manage diseases transmitted by aphids that threaten common bean production in Africa, an important crop for food security.
2. The team is identifying genes involved in host plant resistance and manipulating plant-aphid interactions to control diseases like Bean Common Mosaic Virus and Bean Common Mosaic Necrosis Virus.
3. Successful strategies could be disseminated across Africa through partnerships, preventing yield losses for millions of smallholder farmers and providing lessons for managing diseases in other crops.
Incidence and toxigenicity of fungi contaminating sorghum from NigeriaPremier Publishers
Each Agro ecological zone was transversely delineated into 5 districts and five villages (at least 20 Km from each other) called “locations” were selected in each district. In each district, Sorghum grains in stores, bunches in the field and sorghum grains in the market were sampled from five locations, each approximately 20 km from the previous sampling location. The mycological analytical procedures were performed under aseptic condition. Plates were counted for fungal colonies using a colony counter and the number of fungal colonies per gram of sample was calculated as CFU/g. The fungi species were isolated and subsequently identified using MEA/CYA media for Aspergillus and Penicillium species and PDA for the fusarium species Toxigenicity studies on strains representing species of Aspergillus, Penicillium, Fusarium was carried out to determine their ability to produce aflatoxin B1 (AFB1); aflatoxin B2 (AFB2); aflatoxin G1 (AFG1); aflatoxin G2 (AFG2); OTA, ZEN, DON and FB1. A total of 701 isolates were recorded which consist of 67 confirmed fungal strains. Aspergillus species formed the majority with 346(49.6%) followed by the Fusarium species with 186(26.7%) then Penicillium species with 102(14.6%) while others such as Cuvularia, Phoma, Alternaria, Rhizormucor constitutes 67 (9.0% )strains of the total population.
This document describes the development of an early warning device to detect the Brown Planthopper (BPH) pest in rice fields using wireless sensor networks and image processing. The device uses microscopic cameras connected to sensor nodes that take video of BPH on rice plants. An algorithm analyzes the video using Haar feature-based classifiers to detect BPH. When BPH is detected, the sensor node sends a warning message via SMS to inform farmers. The researchers tested prototypes of the device which could accurately detect BPH 97% of the time and send timely warning messages to help farmers respond to infestations.
Sri Lankan cassava mosaic virus was first detected in Southeast Asia in 2015. Surveillance and a survey of cassava seed networks in Vietnam and Cambodia were conducted. This resulted in two publications integrating this information to model the combined effects on risk of virus spread. Impact network analysis was used to combine environmental risk factors, seed network data, and surveillance data to generate risk maps. This identifies key areas for disease surveillance, predicts likely spread pathways, and identifies areas for clean seed interventions. The model can incorporate updated data to recalibrate predictions in real time.
Sri Lankan cassava mosaic virus was first detected in Southeast Asia in 2015. Surveillance and a survey of cassava seed networks in Vietnam and Cambodia were conducted. This resulted in two publications integrating this information to model the combined effects on risk of virus spread. Impact network analysis was used to combine environmental risk factors, seed network data, and surveillance data to generate risk maps. This identifies key areas for disease surveillance, predicts likely spread pathways, and identifies areas for clean seed interventions. The model can incorporate updated data to recalibrate predictions in real time.
Diversity of plant parasitic nematodes associated with common beans (Phaseolu...Innspub Net
Common beans (Phaseolus vulgaris L.) are the most important legume staple food in Kenya coming second to maize. In Central Highlands of Kenya, the 0.4-0.5ton ha-1 output is below the genetic yield potential of 1.5-2ton ha-1 partly due pests and diseases. Plant parasitic nematodes (PPN) have been reported to cause yield losses of up to 60% on beans. Though bean production is important in the Central highlands of Kenya, information on PPN associated with the beans in the region is lacking. This study was therefore undertaken to establish the diversity of PPN associated with common beans and to assess the root knot nematode damage on beans in the region. The study covered 50 farms (32 in Kirinyaga and 18 in Embu Counties) distributed in eight localities namely Kibirigwi (L1), Makutano (L2), Kagio (L3), Mwea (L4) and Kutus (L5) in Kirinyaga County and Nembure (L6), Manyatta (L7) and Runyenjes (L8) in Embu County and covering three Agro Ecological Zones (AEZs); UM2 (L1, L2, L3 & L4), UM3 (L5, L7 & L8) and UM4 (L6) AEZs. Manyatta (L7) and Nembure (L6), had the highest and second highest gall indices, respectively, while Kibirigwi (L1), Makutano (L2) and Mwea (L4) had some of the lowest gall indices. The most common PPN in bean roots were Meloidogyne spp. Pratylenchus spp. and Scutellonema spp. with a frequency of 94.38%, 78.25% and 59.13%, respectively. This further confirm the importance of these nematodes in bean production systems. Upper Midland 3 (UM3) AEZs and UM4 had higher nematode population densities and diversity than UM2. Disease severity and nematode composition and distribution were notably low in the irrigated areas Kibirigwi, Kagio and Mwea compared to rain-fed areas such as Makutano, Nembure and Manyatta.
This document summarizes research highlights from the RTB Annual Planning Meeting on managing priority pests and diseases of root, tuber and banana crops. It describes ongoing work on several major diseases affecting banana (banana Xanthomonas wilt, Fusarium wilt), cassava (cassava mosaic virus disease, cassava brown streak disease), potato (pest risk assessments, IPM strategies), sweet potato (virus diagnostics, virome analysis), and yam (virus surveillance, diagnostic tool development). It also discusses plans to establish a pan-African crop surveillance network and diagnostic network to monitor and control these important diseases.
The Production of Triploid Clariobranchus in Indoor HatcheryIOSR Journals
This study evaluated the interactive effects of rhizobium and virus inocula on three cowpea cultivars. The cultivars were inoculated with two rhizobium strains (R25B and IRj2180A) and two virus strains (CABMV and CYMV) at two different times. Viral inoculation significantly reduced nodulation, biomass production, and grain yields across all cultivars. Maximum reductions occurred without rhizobium inoculation. Early inoculation had a greater effect than late inoculation. The interaction of rhizobium and virus strains showed that viral severity was not reduced by rhizobium presence. Cultivar IT90K-277-2 performed best
molecular-determination-and-characterization-of-phytoplasma-16s-rrna-gene-in-...Adam Juma
This study sought to detect and identify phytoplasma strains infecting wild grasses in western Kenya using the 16S ribosomal RNA gene. DNA was extracted from 646 wild grass samples and tested for phytoplasmas using nested PCR. Two subgroups of phytoplasmas (16SrXI and 16SrXIV) were detected infecting eight grass species near infected Napier fields. Only one phytoplasma (16SrXI) was related to the phytoplasma causing Napier stunt disease. There was a strong association between phytoplasma infection proportions and grass species. The study identified potential wild host reservoirs of phytoplasmas that could threaten important crops and pose challenges for managing Napier stunt disease
Development of ecologically based rodent management for sadc regionLukas Mandema
The ECORAT project aims to develop ecologically-based rodent management in southern Africa by investigating rodent problems affecting small-scale farmers. The project is coordinated by scientists in the UK and involves organizations in Namibia, Swaziland, Tanzania, and South Africa. As part of his training, the author was recruited by the National Museum of Namibia to participate in ECORAT's fieldwork in Namibia, where they are monitoring rodents and their impacts in Mukwe constituency. Their goals are to strengthen sustainable rodent management strategies for small-scale farmers in the region.
Knowledge of the magnitude of genetic variability, heritability and genetic gains in selection of desirable characters could assist the plant breeder in ascertaining criteria to be used for the breeding programmes. Ten open pollinated maize varieties were evaluated at the Teaching and Research farm, University of Ilorin, Nigeria, during 2005 and 2006 cropping seasons to estimate genetic variability, heritability and genetic advance of grain yield and its component characters. The effect of genotype and genotype by year interaction were significant for ear weight and grain yield, while the effect of year was highly significant (P< 0.01) for all the characters. High magnitude of phenotypic and genotypic coefficient of variations as well as high heritability along with high genetic advance recorded for grain yield, number of grains ear-1, ear weight, plant and ear heights provides evidence that these parameters were under the control of additive gene effects and effective selection could be possible for improvement for these characters. Tze Comp3 C2, Acr 94 Tze Comp5, Tze Comp 4-Dmr Srbc2 and Acr 90 Pool 16-Dt were identified as outstanding genotypes for maize grain yield and should be tested at multilocation for their yield performance.
Rift Valley fever virus lineages from selected sites in Kenya, 1997–2020ILRI
Poster by Konongoi Limbaso, John Juma, Solomon Langat, Kristina Roesel, Rosemary Sang, Bernard Bett and Samuel Oyola presented at the Boosting Uganda's Investment in Livestock Development (BUILD) project annual planning meeting, Kampala, Uganda, 20–22 September 2022.
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1. Mobilizing biosciences for Africa’s development
This document is licensed for use under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported License May
2013
Plant virome ecology in African farming systems:
A genomics and bioinformatics framework for high-throughput
Virus detection and Pathogen Discovery
This document is licensed for use under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported License May
2013
1Biosciences Eastern and Central Africa (BecA) - ILRI Hub, Nairobi, PO Box 30709, 00100, Kenya (f.stomeo@cgiar.org; m.wamalwa@cgiar.org) - 2Kenya Agricultural Research
Institute (KARI), Nairobi, PO Box 14733-00800, Kenya - 3Food and Environment Research Agency (FERA), Sand Hutton, York, YO41 1LZ, UK - 4University of Nairobi, Kenya
Francesca Stomeo1, Mark Wamalwa1, Jagger Harvey1, Douglas W. Miano2, Neil Boonham3,Dora Kilalo4, Ian Adams3, Appolinaire Djikeng1
This project is funded by the Swedish Ministry for Foreign Affairs through SIDA. For more info: http://hub.africabiosciences.org/
Outputs
• Confirmation of known diseases/pathogens
• Pathogen Discovery
• Host range and vector information
• Risk analysis based on AEZs and dynamics of disease spread/climate change
• Information to help guide decisions and activities of policy makers, donors and
researchers
• Application of these methodologies to viruses will make it possible to explore viral
diversity through automatically constructed time-measured phylogenies and perform
comparison against their viromes.
Introduction
Crop diseases are one of the major constraints to crop production of sub-Saharan Africa (SSA) small-scale farmers. Small farm ecosystems are a complex mix of crop, non-crop plants,
insects, vectors, fungal, bacterial and virus pathogens. The 'maize mixed' farming system, typically including maize and a selection of different crops (potatoes, banana, rice, sorghum,
cassava, etc.), is among the most common small farming systems in SSA. These ecosystems support greater pathogen (and vector) diversity. This project aims to assess the diversity of
viruses thriving in the 'maize mixed' farming systems in Kenya through a combined genomics – bioinformatics approach. Metagenomics sequencing offers significant advantages over
traditional diagnostics and presents a novel opportunity for understanding virus evolution and the genetic diversity present in these environments, and allows outbreaks to be
monitored in detail. The identification of emerging diseases and associated risks is paramount for improving African sustainability and ensuring food security, especially in the face of
climate change.
• In order to elucidate the presence of pathogens in the soils and their
characteristics, soils were collected from the two farms.
• Genomics and Bioinformatics approaches will be used to gain a better
understanding of the potential factors influencing the spread of viruses (in
space and time) in this ecosystem. Next generation sequencing (NGS) will be
carried out to elucidate the complex mix of hosts, vectors, and viruses.
• Total RNA/siRNA/ds-RNA and DNA will be extracted and sequenced using
NGS techniques (Illumina MiSeq) in order to elucidate the most efficient
nucleic acid class for virus discovery.
• Furthermore, a 16S rRNA gene metagenomics approach will be conducted
to elucidate the diversity of pathogens thriving in the selected
environments (plants and soils) and shade light into their relationships.
Materials and Methods
• Selected crops (maize, beans, irish potatoes, sorghum, sweet potato, millet,
etc.) vegetables (cabbage, onions, etc.), pastures (Napier grass and kikuyu
grass, etc.) and potential vectors (aphids, beetles, etc.) will be sampled from
three Kenyan agro-ecological zones: Bomet, Narok and Trans Nzoia/Uasin
Gishu, representing different climatic zones. To date, samples have been
collected from the Bomet area in the lower highlands (Figure 1a), from two
farms, characterized by mixed cropping systems and different crops diseases.
• Moreover, our effort will concentrate on farming systems affected by the
Maize lethal necrosis (MLN) triggered by a combination of Maize Chlorotic
mottle virus (MCMV) and Sugarcane mosaic virus (SMV) that is causing
severe losses in Kenya (Figure 1b).
Aims and Objectives
• Assessment of the overall diversity of viruses thriving in the 'maize mixed‘
farming systems in Kenya.
• Virome comparisons, geographical distribution and spatial characterization
through a viral metagenome analysis pipeline.
• Development of methods for pathogens detection.
• To make biological data available to scientists and policy makers.
Figure 1 a: Map showing main crop zones of Kenya. 1b: The Maize Lethal Necrosis (MLN) disease in maize
plantations in the Bomet district (Kenya).
b
Photo: CIMMYT
Bomet
a
Symptomatic and asymptomatic crops and pastures leaves were collected
together with the potential vectors (aphids and beetles) responsible for diseases
transmission.
Results
Complete metagenomes are in the pipeline for sequencing with the MiSeq Illumina
system. A preliminary analysis of 16S rRNA gene T-RFLP profiles suggest that plant and soil
ecosystems are characterized by different microbial communities and can be grouped
into two separate clusters.
A semi-automated sample tracking interface that tracks the progress of viral samples from
acquisition to GenBank submission was created (Figure 2) using Drupal version 7.15 and
MySQL database.
A prototype web framework for high-throughput virus detection and pathogen discovery
with a customizable web server for fast metagenomic analysis was developed. The
webserver includes commonly used tools (quality control, tRNA and rRNA prediction,
taxonomic analysis and functional annotation) and provides users with rapid
metagenomic data analysis using published tools (Figure 3). The webserver is temporarily
available at http://localhost:8080/Drupal7/. We are yet to benchmark this tool to others
such as MEGAN and MG-RAST.
Figure 3. Automated sample processing and annotation workflow
Figure 2. A semi-automated workflow that tracks the progress of samples from
acquisition through to NCBI submission