A computer-based key for identifying 30 genera of plant parasitic nematodes is described. The key uses Lucid software and is multi-access rather than dichotomous, allowing users to choose observable characters without being limited by couplet structure. Character states like stylet length and shape, body size and shape, and tail morphology are used. Images help non-specialists identify specimens. The key aims to aid identification of nematodes in New Zealand for management and biosecurity purposes.
The document discusses RNA interference (RNAi) as a potential tool for insect pest management. It provides an overview of RNAi, including the discovery of RNAi, how small RNA molecules are central to the process, and the different RNAi pathways. It also discusses challenges to applying RNAi for insect control and examples of studies using plant-expressed RNAi to target different insect pests. The conclusion states that RNAi is a target-specific, non-toxic tool that could help with resistance management through gene silencing.
Accelerating Scientific Research Through Machine Learning and GraphNeo4j
Miroculus is a molecular diagnostics company that leverages the potential of microRNAs as biomarkers and has created the most easy-to-use and automated platform for their detection. MicroRNAs are small non-coding RNA molecules, whose primary role is to regulate the expression of our genes. Their discovery in circulation of body fluids such as blood plasma/serum, urine and saliva has been followed up by a multitude of studies, providing evidence that detection of specific microRNA molecules can give clues about a person’s health status and may therefore be used as biomarkers for various conditions.
Loom is an up-to-date snapshot of the scientific literature landscape focused on microRNAs that we built to expedite our own research. As of today, there is no compelling way to access much of the microRNA research. By using Loom's easy-to-use, interactive UI, the researcher is able to quickly locate the relevant sentences across many publications relating specific microRNAs with her disease or gene of interest. With this tool, our objective is to provide a visually compelling and complete overview of how microRNAs relate to specific diseases and genes.
At the backend, Loom is comprised of 4 microservices. The first one is a listener that fetches new publications daily that are available in the NCBI databases: PubMed for abstracts and PMC for full-text, open-access publications. Then, a natural language processor scans the publication, breaking them down into their constituent sentences and detecting mentions of microRNAs, genes and diseases.
Within each sentence, a machine learning scorer evaluates the strength and type of relationship on a scale from 0 to 1 and outputs the results in a graph database. The resulting graph database is then queried in real-time by the UI to retrieve the sentences and relationships the user is interested in.
Variation in responsiveness to environmental RNAi in insects - University of ...OECD Environment
10-12 April 2019: The OECD Conference on RNAi based pesticides provided an overview on the current status and future possibilities for the regulation of externally applied dsRNA-based products that are proposed for use as pesticides. The event facilitated exchanges between policy makers, academia, industry on their implications in health, environment, and regulation.
Background to the draft OECD Working Paper on ‘Environmental Risks from the A...OECD Environment
This document provides an overview and summary of a draft OECD working paper on the environmental risks of dsRNA-based pesticides. The paper discusses the purpose and scope of the document, which is to evaluate data requirements for the ecological risk assessment of dsRNA pesticides. It outlines key sections that will cover exposure potential, hazard identification, and risk assessment considerations. While more data is still needed, the working group's preliminary view is that with some modifications, existing regulatory frameworks and testing guidelines can be applied to dsRNA pesticides, and that these types of products appear to pose minimal risks based on current understanding of exposure barriers and RNAi mechanisms.
Here we update on fundamental systematics research and the development of new potential molecular markers to improve on current diagnostic tools. We also link these molecular tools with physical specimens, documenting the range of morphological variation so as to greatly improve on available resources used to diagnose fruit flies in the field as part of surveillance programmes or at border interceptions.
Isolation of Novel Mycobacteriophages from Tropical Soils of Puerto Rico avargas11
The document contains data from soil samples collected in Puerto Rico by four students - Aida Vargas de Jesus, Danilo Trinidad Pérez Rivera, Lizbeth Perez Castro, and Javier M. Zavala Ayala - as part of the RISE Program in the Department of Biology led by Prof. Eneida Díaz Pérez and Prof. Michael Rubin. The document includes tables with the coordinates, descriptions, locations, and dates of 12 soil samples collected by Danilo Trinidad Pérez Rivera and 7 soil samples collected by Aida Vargas de Jesus.
The document discusses RNA interference (RNAi) as a potential tool for insect pest management. It provides an overview of RNAi, including the discovery of RNAi, how small RNA molecules are central to the process, and the different RNAi pathways. It also discusses challenges to applying RNAi for insect control and examples of studies using plant-expressed RNAi to target different insect pests. The conclusion states that RNAi is a target-specific, non-toxic tool that could help with resistance management through gene silencing.
Accelerating Scientific Research Through Machine Learning and GraphNeo4j
Miroculus is a molecular diagnostics company that leverages the potential of microRNAs as biomarkers and has created the most easy-to-use and automated platform for their detection. MicroRNAs are small non-coding RNA molecules, whose primary role is to regulate the expression of our genes. Their discovery in circulation of body fluids such as blood plasma/serum, urine and saliva has been followed up by a multitude of studies, providing evidence that detection of specific microRNA molecules can give clues about a person’s health status and may therefore be used as biomarkers for various conditions.
Loom is an up-to-date snapshot of the scientific literature landscape focused on microRNAs that we built to expedite our own research. As of today, there is no compelling way to access much of the microRNA research. By using Loom's easy-to-use, interactive UI, the researcher is able to quickly locate the relevant sentences across many publications relating specific microRNAs with her disease or gene of interest. With this tool, our objective is to provide a visually compelling and complete overview of how microRNAs relate to specific diseases and genes.
At the backend, Loom is comprised of 4 microservices. The first one is a listener that fetches new publications daily that are available in the NCBI databases: PubMed for abstracts and PMC for full-text, open-access publications. Then, a natural language processor scans the publication, breaking them down into their constituent sentences and detecting mentions of microRNAs, genes and diseases.
Within each sentence, a machine learning scorer evaluates the strength and type of relationship on a scale from 0 to 1 and outputs the results in a graph database. The resulting graph database is then queried in real-time by the UI to retrieve the sentences and relationships the user is interested in.
Variation in responsiveness to environmental RNAi in insects - University of ...OECD Environment
10-12 April 2019: The OECD Conference on RNAi based pesticides provided an overview on the current status and future possibilities for the regulation of externally applied dsRNA-based products that are proposed for use as pesticides. The event facilitated exchanges between policy makers, academia, industry on their implications in health, environment, and regulation.
Background to the draft OECD Working Paper on ‘Environmental Risks from the A...OECD Environment
This document provides an overview and summary of a draft OECD working paper on the environmental risks of dsRNA-based pesticides. The paper discusses the purpose and scope of the document, which is to evaluate data requirements for the ecological risk assessment of dsRNA pesticides. It outlines key sections that will cover exposure potential, hazard identification, and risk assessment considerations. While more data is still needed, the working group's preliminary view is that with some modifications, existing regulatory frameworks and testing guidelines can be applied to dsRNA pesticides, and that these types of products appear to pose minimal risks based on current understanding of exposure barriers and RNAi mechanisms.
Here we update on fundamental systematics research and the development of new potential molecular markers to improve on current diagnostic tools. We also link these molecular tools with physical specimens, documenting the range of morphological variation so as to greatly improve on available resources used to diagnose fruit flies in the field as part of surveillance programmes or at border interceptions.
Isolation of Novel Mycobacteriophages from Tropical Soils of Puerto Rico avargas11
The document contains data from soil samples collected in Puerto Rico by four students - Aida Vargas de Jesus, Danilo Trinidad Pérez Rivera, Lizbeth Perez Castro, and Javier M. Zavala Ayala - as part of the RISE Program in the Department of Biology led by Prof. Eneida Díaz Pérez and Prof. Michael Rubin. The document includes tables with the coordinates, descriptions, locations, and dates of 12 soil samples collected by Danilo Trinidad Pérez Rivera and 7 soil samples collected by Aida Vargas de Jesus.
The aim of this research project is to establish Australian developed seed testing protocols as an international standard for the detection of viroids and cucumber green mottle mosaic virus (CGMMV) in seed, and to reduce the risks of contaminated traded seed.
Potential for dsRNA-based management of plant diseases - Karl-Heinz Kogel, Ju...OECD Environment
1) dsRNA-based strategies show potential for managing plant diseases caused by fungi, nematodes, insects, and oomycetes.
2) Direct delivery of dsRNA to crop plants (HIGS) or spray application (SIGS) can induce gene silencing in pathogens.
3) Studies have demonstrated the ability of dsRNA to suppress the fungus Fusarium graminearum, both in transgenic Arabidopsis plants and after foliar application to wheat.
4) However, more evidence is still needed to demonstrate efficient control of fungi and oomycetes under field conditions using dsRNA approaches.
This document provides an introduction to non-coding RNAs (ncRNAs). It discusses how RNA was proposed to have come before DNA and proteins in the RNA world hypothesis. It notes that RNA can store genetic information like DNA and have catalytic abilities like proteins. The document outlines different types and functions of ncRNAs, including how some act as guides for chemical modifications, regulate gene expression as sponges for small RNAs or proteins, or sense environmental signals as riboswitches or thermosensors. Examples of conserved ncRNA families and mechanisms are briefly described.
Ecological Risk Assessment Considerations for in planta Expressed and Exogeno...OECD Environment
10-12 April 2019: The OECD Conference on RNAi based pesticides provided an overview on the current status and future possibilities for the regulation of externally applied dsRNA-based products that are proposed for use as pesticides. The event facilitated exchanges between policy makers, academia, industry on their implications in health, environment, and regulation.
Up until mid-2016, citizen science uploads to the Atlas of Living Australia (ALA) included c. 400 bug species, and c. 1,000 beetle species. Given the short time period (c. 3 years) over which most of these records have accumulated, this represents a considerable reporting effort. The key question from a plant biosecurity context is how this level of reporting translates to the detection and reporting of
exotic insect pests in the event of an incursion.
Environmental dissipation of dsRNA in soil, aquatic systems and plants - Pame...OECD Environment
The document discusses quantifying and measuring the environmental dissipation of dsRNA. It describes using the QuantiGene RNA assay to accurately measure dsRNA levels in plant tissues, soil, and water. Laboratory studies show dsRNA degrades rapidly in soil and aquatic systems. Foliar applications may be unstable due to factors like sunlight, microbes, and wash-off by rain. Shade cloth can improve stability, and photochamber studies indicate sunlight alone may not be a major cause of instability. Overall, results indicate low persistence of dsRNA in the environment.
There are many facets involved in the development of biogeochemical markers that might enable the geographic origins of fruit flies to be distinguished.
Highly Discriminatory Diagnostic Primer Design From Whole Genome DataLeighton Pritchard
Presented at the GMI (Global Microbial Identifier) satellite meeting, sponsored by the UK Department for Environment, Food and Rural Affairs (DEFRA), organised by the Food and Environment Research Agency (FERA), Bedern Hall, York, 10th September 2014.
1) The study constructed five cDNA libraries from the vine mealybug, Planococcus ficus, to obtain genetic sequence data for the pest. An RNA extraction protocol was optimized to obtain high quality RNA from the mealybugs.
2) The primary library contained many short inserts, while the fractionated libraries contained size-selected inserts ranging from ~0.25kb to 4kb.
3) A pilot analysis found that 41% of sequences matched databases, mostly being of insect origin. Two potential RNAi targets for mealybug control were identified and seemed unique to arthropods.
An optimal surveillance system is one where the available sampling resources are allocated in time and space to best achieve detection objectives. This project aims to develop new methods for designing optimal surveillance systems that properly account for organism biology, trapping or sampling efficacy, and landscape characteristics.
A perspective on risks associated with dsRNA-based product - Neena Mitter - C...OECD Environment
10-12 April 2019: The OECD Conference on RNAi based pesticides provided an overview on the current status and future possibilities for the regulation of externally applied dsRNA-based products that are proposed for use as pesticides. The event facilitated exchanges between policy makers, academia, industry on their implications in health, environment, and regulation.
With the loss of chemical control options such as Fenthion and Dimethoate for postharvest treatment of horticulture commodities susceptible to fruit fly infestation, it has become even more important to understand how stress-based control techniques such as heat, cold, irradiation and bacteria parasite
can be used most effectively for disinfestation. This project aims to explore the stress-induced molecular response of two fruit fly species of horticultural significance, Mediterranean fruit fly (Ceratitis capitata) and Queensland fruit fly (Bactrocera tryoni), by characterising the cellular pathways involved in both overall and stressor-specific responses.
Benjamin P. Steil has over 15 years of experience in virology research. He received his Ph.D. in Microbiology and Immunology from the University of Colorado Denver in 2008, and has since worked as a postdoctoral fellow and staff scientist developing viral vaccine adjuvants. His skills include viral particle production, nucleic acid techniques, mouse models, and immunological assays. Currently he is seeking a position where he can apply his expertise in vaccine design and development.
Creative Biogene provides world-class packaging services for a variety of viral types using our QVirusTM platform. Creative Biogene's state-of-the-art facilities and highly experienced staff are available in order to assist in all areas of virus vector design and construction, as well as the generation of the virus in a quick turnaround. Our custom viral services are highlighted by a consistent high titer and large delivery viral counts.
Next-generation sequencing (NGS) has revolutionized the way we analyze diseases and commercial outfits such as Illumina, Helicos, QIAGEN and Pacific Biosciences have made significant contributions. In addition, the launch of direct-to-consumer genetic testing solutions has dramatically changed the way consumers access genomics data. Until a few years ago, the cost of sequencing was a major bottleneck. Recent developments have reduced the cost from thousands of dollars to a couple of cents per megabase. When did these changes start? What were the changes in the commercial sector in the last 15 years? This infographic is a timeline of the NGS commercial marketplace.
Sample Prep Solutions for Microbiome ResearchQIAGEN
An accurate molecular analysis of the microbial constituents of a particular community is contingent upon high-yielding and non-biased nucleic acid extraction methodologies. Only by ensuring that all species and classes of microorganisms present in a sample are effectively lysed during extraction will one be able to reliably assess the composition of that sample. An additional challenge faced in nucleic acid extraction is the presence of persistent, co-purifying polymerase inhibitors endogenous to one’s sample. This presentation will focus on nucleic acid extraction tools developed by MO BIO Laboratories that facilitate accurate non-biased community analysis and eliminate common amplification problems via the depletion of endogenous polymerase inhibitors using our patented Inhibitor Removal Technology.
Creative Biogene is a biotechnology company that has years of experience working in the field of adenovirus to improve the adenoviral genome's utility in research and its therapeutic potential.
https://www.creative-biogene.com/Services/Custom-Viral-Service/Adenovirus-service.html
Myrtle rust (Puccinia psidii) is an invasive fungus native to South America that was first detected in Australia in 2010. It has spread rapidly along the east coast, and is currently recorded in sites as far north as the Northern Territory and south to Tasmania.
In order to better understand myrtle rust extent and impacts in Australian native and managed landscapes, a survey was sent to national parks, botanical gardens, councils, natural resource
managers, nurseries and forestry agencies in all states where the fungus is present (NT, QLD, NSW, VIC and TAS). The survey revealed that Myrtle rust is widespread in NSW and QLD gardens and streets as well as in native vegetation.
Adenovirus, a DNA virus, was first isolated in the 1950s in adenoid tissue-derived cell cultures, hence the name. A large number of acute respiratory, gastrointestinal and eye infections in humans are caused by adenoviruses.
https://www.creative-biogene.com/Support/Virus.html
Adenoviruses are DNA viruses that are powerful research tools for investigating cellular events and can infect a wide range of mammalian cells with high efficiency, making them a versatile vector for gene delivery and expression. Creative Biogene is a biotechnology company that offers custom adenovirus services including vector design, construction, amplification, and purification to produce high-titer recombinant adenoviruses for use in research applications both in vitro and in vivo. Their services streamline the adenovirus production process which can otherwise be time-consuming and labor-intensive for researchers.
This atlas provides high-resolution electron microscope images that summarize Ortrud Monika Barth's research on the replication and morphogenesis of dengue viruses. Over the past ten years, Barth studied dengue virus type 2 infecting mosquito cells using techniques including transmission electron microscopy, immunoelectron microscopy, and in situ hybridization. The atlas aims to describe the dengue virus lifecycle within infected cells, from viral entry and penetration, through replication in the rough endoplasmic reticulum and smooth membrane structures, maturation and exocytosis in the Golgi complex, and cell lysis. It combines detailed technical observations with discussion, intended as a reference for research on flavivirus morphogenesis and replication.
IRJET- Identification of Malaria Parasites in Cells using Object DetectionIRJET Journal
1) The document proposes a system to identify malaria parasites in cells using object detection with faster R-CNN, which can identify different parasite types and stages more accurately and faster than previous methods.
2) Malaria is caused by plasmodium parasites transmitted by mosquitos. The proposed system uses image processing and faster R-CNN to detect parasites in microscopic images of blood cells to help practitioners diagnose malaria faster and reduce misdiagnoses.
3) Faster R-CNN is trained on labeled images of infected and uninfected cells. It can detect parasite types and stages with 98% accuracy and bounding boxes highlighting the detections. This helps improve malaria diagnosis over traditional microscopic examination.
The aim of this research project is to establish Australian developed seed testing protocols as an international standard for the detection of viroids and cucumber green mottle mosaic virus (CGMMV) in seed, and to reduce the risks of contaminated traded seed.
Potential for dsRNA-based management of plant diseases - Karl-Heinz Kogel, Ju...OECD Environment
1) dsRNA-based strategies show potential for managing plant diseases caused by fungi, nematodes, insects, and oomycetes.
2) Direct delivery of dsRNA to crop plants (HIGS) or spray application (SIGS) can induce gene silencing in pathogens.
3) Studies have demonstrated the ability of dsRNA to suppress the fungus Fusarium graminearum, both in transgenic Arabidopsis plants and after foliar application to wheat.
4) However, more evidence is still needed to demonstrate efficient control of fungi and oomycetes under field conditions using dsRNA approaches.
This document provides an introduction to non-coding RNAs (ncRNAs). It discusses how RNA was proposed to have come before DNA and proteins in the RNA world hypothesis. It notes that RNA can store genetic information like DNA and have catalytic abilities like proteins. The document outlines different types and functions of ncRNAs, including how some act as guides for chemical modifications, regulate gene expression as sponges for small RNAs or proteins, or sense environmental signals as riboswitches or thermosensors. Examples of conserved ncRNA families and mechanisms are briefly described.
Ecological Risk Assessment Considerations for in planta Expressed and Exogeno...OECD Environment
10-12 April 2019: The OECD Conference on RNAi based pesticides provided an overview on the current status and future possibilities for the regulation of externally applied dsRNA-based products that are proposed for use as pesticides. The event facilitated exchanges between policy makers, academia, industry on their implications in health, environment, and regulation.
Up until mid-2016, citizen science uploads to the Atlas of Living Australia (ALA) included c. 400 bug species, and c. 1,000 beetle species. Given the short time period (c. 3 years) over which most of these records have accumulated, this represents a considerable reporting effort. The key question from a plant biosecurity context is how this level of reporting translates to the detection and reporting of
exotic insect pests in the event of an incursion.
Environmental dissipation of dsRNA in soil, aquatic systems and plants - Pame...OECD Environment
The document discusses quantifying and measuring the environmental dissipation of dsRNA. It describes using the QuantiGene RNA assay to accurately measure dsRNA levels in plant tissues, soil, and water. Laboratory studies show dsRNA degrades rapidly in soil and aquatic systems. Foliar applications may be unstable due to factors like sunlight, microbes, and wash-off by rain. Shade cloth can improve stability, and photochamber studies indicate sunlight alone may not be a major cause of instability. Overall, results indicate low persistence of dsRNA in the environment.
There are many facets involved in the development of biogeochemical markers that might enable the geographic origins of fruit flies to be distinguished.
Highly Discriminatory Diagnostic Primer Design From Whole Genome DataLeighton Pritchard
Presented at the GMI (Global Microbial Identifier) satellite meeting, sponsored by the UK Department for Environment, Food and Rural Affairs (DEFRA), organised by the Food and Environment Research Agency (FERA), Bedern Hall, York, 10th September 2014.
1) The study constructed five cDNA libraries from the vine mealybug, Planococcus ficus, to obtain genetic sequence data for the pest. An RNA extraction protocol was optimized to obtain high quality RNA from the mealybugs.
2) The primary library contained many short inserts, while the fractionated libraries contained size-selected inserts ranging from ~0.25kb to 4kb.
3) A pilot analysis found that 41% of sequences matched databases, mostly being of insect origin. Two potential RNAi targets for mealybug control were identified and seemed unique to arthropods.
An optimal surveillance system is one where the available sampling resources are allocated in time and space to best achieve detection objectives. This project aims to develop new methods for designing optimal surveillance systems that properly account for organism biology, trapping or sampling efficacy, and landscape characteristics.
A perspective on risks associated with dsRNA-based product - Neena Mitter - C...OECD Environment
10-12 April 2019: The OECD Conference on RNAi based pesticides provided an overview on the current status and future possibilities for the regulation of externally applied dsRNA-based products that are proposed for use as pesticides. The event facilitated exchanges between policy makers, academia, industry on their implications in health, environment, and regulation.
With the loss of chemical control options such as Fenthion and Dimethoate for postharvest treatment of horticulture commodities susceptible to fruit fly infestation, it has become even more important to understand how stress-based control techniques such as heat, cold, irradiation and bacteria parasite
can be used most effectively for disinfestation. This project aims to explore the stress-induced molecular response of two fruit fly species of horticultural significance, Mediterranean fruit fly (Ceratitis capitata) and Queensland fruit fly (Bactrocera tryoni), by characterising the cellular pathways involved in both overall and stressor-specific responses.
Benjamin P. Steil has over 15 years of experience in virology research. He received his Ph.D. in Microbiology and Immunology from the University of Colorado Denver in 2008, and has since worked as a postdoctoral fellow and staff scientist developing viral vaccine adjuvants. His skills include viral particle production, nucleic acid techniques, mouse models, and immunological assays. Currently he is seeking a position where he can apply his expertise in vaccine design and development.
Creative Biogene provides world-class packaging services for a variety of viral types using our QVirusTM platform. Creative Biogene's state-of-the-art facilities and highly experienced staff are available in order to assist in all areas of virus vector design and construction, as well as the generation of the virus in a quick turnaround. Our custom viral services are highlighted by a consistent high titer and large delivery viral counts.
Next-generation sequencing (NGS) has revolutionized the way we analyze diseases and commercial outfits such as Illumina, Helicos, QIAGEN and Pacific Biosciences have made significant contributions. In addition, the launch of direct-to-consumer genetic testing solutions has dramatically changed the way consumers access genomics data. Until a few years ago, the cost of sequencing was a major bottleneck. Recent developments have reduced the cost from thousands of dollars to a couple of cents per megabase. When did these changes start? What were the changes in the commercial sector in the last 15 years? This infographic is a timeline of the NGS commercial marketplace.
Sample Prep Solutions for Microbiome ResearchQIAGEN
An accurate molecular analysis of the microbial constituents of a particular community is contingent upon high-yielding and non-biased nucleic acid extraction methodologies. Only by ensuring that all species and classes of microorganisms present in a sample are effectively lysed during extraction will one be able to reliably assess the composition of that sample. An additional challenge faced in nucleic acid extraction is the presence of persistent, co-purifying polymerase inhibitors endogenous to one’s sample. This presentation will focus on nucleic acid extraction tools developed by MO BIO Laboratories that facilitate accurate non-biased community analysis and eliminate common amplification problems via the depletion of endogenous polymerase inhibitors using our patented Inhibitor Removal Technology.
Creative Biogene is a biotechnology company that has years of experience working in the field of adenovirus to improve the adenoviral genome's utility in research and its therapeutic potential.
https://www.creative-biogene.com/Services/Custom-Viral-Service/Adenovirus-service.html
Myrtle rust (Puccinia psidii) is an invasive fungus native to South America that was first detected in Australia in 2010. It has spread rapidly along the east coast, and is currently recorded in sites as far north as the Northern Territory and south to Tasmania.
In order to better understand myrtle rust extent and impacts in Australian native and managed landscapes, a survey was sent to national parks, botanical gardens, councils, natural resource
managers, nurseries and forestry agencies in all states where the fungus is present (NT, QLD, NSW, VIC and TAS). The survey revealed that Myrtle rust is widespread in NSW and QLD gardens and streets as well as in native vegetation.
Adenovirus, a DNA virus, was first isolated in the 1950s in adenoid tissue-derived cell cultures, hence the name. A large number of acute respiratory, gastrointestinal and eye infections in humans are caused by adenoviruses.
https://www.creative-biogene.com/Support/Virus.html
Adenoviruses are DNA viruses that are powerful research tools for investigating cellular events and can infect a wide range of mammalian cells with high efficiency, making them a versatile vector for gene delivery and expression. Creative Biogene is a biotechnology company that offers custom adenovirus services including vector design, construction, amplification, and purification to produce high-titer recombinant adenoviruses for use in research applications both in vitro and in vivo. Their services streamline the adenovirus production process which can otherwise be time-consuming and labor-intensive for researchers.
This atlas provides high-resolution electron microscope images that summarize Ortrud Monika Barth's research on the replication and morphogenesis of dengue viruses. Over the past ten years, Barth studied dengue virus type 2 infecting mosquito cells using techniques including transmission electron microscopy, immunoelectron microscopy, and in situ hybridization. The atlas aims to describe the dengue virus lifecycle within infected cells, from viral entry and penetration, through replication in the rough endoplasmic reticulum and smooth membrane structures, maturation and exocytosis in the Golgi complex, and cell lysis. It combines detailed technical observations with discussion, intended as a reference for research on flavivirus morphogenesis and replication.
IRJET- Identification of Malaria Parasites in Cells using Object DetectionIRJET Journal
1) The document proposes a system to identify malaria parasites in cells using object detection with faster R-CNN, which can identify different parasite types and stages more accurately and faster than previous methods.
2) Malaria is caused by plasmodium parasites transmitted by mosquitos. The proposed system uses image processing and faster R-CNN to detect parasites in microscopic images of blood cells to help practitioners diagnose malaria faster and reduce misdiagnoses.
3) Faster R-CNN is trained on labeled images of infected and uninfected cells. It can detect parasite types and stages with 98% accuracy and bounding boxes highlighting the detections. This helps improve malaria diagnosis over traditional microscopic examination.
Viruses are thought to have originated through three main hypotheses:
1. The progressive hypothesis states that viruses arose from mobile genetic elements that gained the ability to move between cells.
2. The regressive hypothesis asserts that viruses are remnants of once free-living cellular organisms that became increasingly parasitic over time.
3. The virus-first hypothesis proposes that viruses predated cells and may have coevolved with the first cellular life.
Viruses evolve over long periods through mechanisms like genetic variation, natural selection, host adaptation, recombination, and mutation. Case studies of plant viruses like begomoviruses that infect tomatoes illustrate their evolution and relationships through analysis of genetic sequences using software like MEGA.
A Deep Learning Method for Plant Disease Diagnosis and Detection in Smart Agr...AakashRoy30
Creating and training a CNN model from scratch is a tedious process, this model can be used to detect and classification of other plant disease too, by simply training the model using respected datasets
This document presents a matrix key for identifying families, subfamilies, and tribes of Lepidoptera (moths and butterflies) found in Canada. It summarizes the key's development based on examination of over 1600 specimens covering approximately 85% of Canadian Lepidoptera genera. The key uses 73 observable external morphological characters to narrow identifications to 222 taxon groups, allowing identification of most microlepidoptera and providing a starting point for macrolepidoptera. It is intended to provide non-experts with a reliable identification tool using only a dissecting microscope.
This document summarizes the work of the DIPO team at the Station Biologique de Roscoff on studying plankton diversity and interactions using molecular tools and databases. It discusses the creation of the PR2 database to catalog small subunit rRNA sequences from unicellular eukaryotes. The database has been expanded and updated over time through various research projects. Current work involves incorporating additional novel sequences, updating taxonomy, and developing new online tools and databases like AQUASYMBIO to record known symbiotic interactions in aquatic systems.
This document discusses the use of bioinformatics tools to analyze gene expression data and detect tumors and mutations in tissues. It summarizes the PhyloMap technique, which integrates principal coordinate analysis, vector quantization, and phylogenetic tree construction to provide improved visualization of large genomic data sets. PhyloMap allows researchers to better analyze and predict evolutionary relationships among influenza A virus genes. The document concludes that PhyloMap is an efficient algorithm for analyzing phylogenetic relationships in large genomic data compared to other techniques.
This document discusses documentation of taxonomic and systematic research through publications like floras, monographs, and journals. It describes different types of floras based on geographic scope, from local to continental. Identification keys are introduced as analytical tools that use contrasting statements in couplets to identify plants through a process of comparison. Single access or dichotomous keys follow a fixed sequence, while multi-access keys allow free choice of characteristics. Guidelines for constructing accurate and useful keys are provided.
This manual aims to assist in training laboratory technicians and health workers to identify intestinal parasites. It provides outlines of topics to cover, required equipment, and focuses on locally relevant parasites. The accompanying slide set illustrates parasites based on the Bench Aids, with some slides reordered or added. The manual and slides can be used together to teach identification of helminth eggs, larvae, and protozoan stages found in stool samples.
This document provides an overview of the field of bioinformatics, including its history and applications. It discusses how bioinformatics merges biology, computer science, and information technology. It also summarizes key applications like using bioinformatics for human and animal genomics, molecular medicine, microbiology, and more. Microarray technology is introduced, explaining how DNA microarrays work to analyze gene expression levels. Different types of microarrays and platforms are also outlined.
This document provides an overview of the field of bioinformatics, including its history and applications. It discusses how bioinformatics merges biology, computer science, and information technology. It also summarizes key applications like using bioinformatics for human and animal genomics, molecular medicine, microbiology, and more. Microarray technology is introduced, explaining how DNA microarrays work to analyze gene expression levels. Different types of microarrays and platforms are also outlined.
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
INSECT SHAPE DETECTION AND CLASSIFICATION USING DIGITAL IMAGE PROCESSINGIRJET Journal
1) The document presents a method for insect shape detection and classification in digital images using image processing techniques and machine learning.
2) It involves preprocessing images, segmenting them using edge detection, extracting features, and classifying insect shapes using KNN machine learning.
3) The method was tested on images of various crop pests like click beetles, moths, and sward grass insects, and showed it could accurately detect shapes and classify the insect images.
DNA barcoding is a tool to identify insects. It includes various steps like DNA extraction, amplification, sequencing and data analysis. In data analysis we shall match the recognized sequence with the available database to find the specimen collected.
Viral Metagenomics (CABBIO 20150629 Buenos Aires)bedutilh
This is a one-hour lecture about metagenomics, focusing on discovery of viruses and unknown sequence elements. It is part of a one-day workshop about metagenome assembly of crAssphage, a bacteriophage virus found in human gut. The hands-on workflow can be found at http://tbb.bio.uu.nl/dutilh/CABBIO/ and should be doable in one afternoon with supervision. There is also an iPython notebook about this here: https://github.com/linsalrob/CrAPy
This presentation is a thorough guide to the use of Web Apollo, with details on User Navigation, Functionality, and the thought process behind manual annotation.
During this workshop, participants:
- Learn to identify homologs of known genes of interest in a newly sequenced genome.
- Become familiar with the environment and functionality of the Web Apollo genome annotation editing tool.
- Learn how to corroborate or modify automatically annotated gene models using available evidence in Web Apollo.
- Understand the process of curation in the context of genome annotation.
An Improved Slide Culture Technique for the Microscopic Identification of Fun...ijtsrd
Several phyto pathogenic fungi have been discovered by numerous researchers who continue to be saddled with the problem of proper identification of these fungal agents. The conventional method requires plating out the diseased tissues of such plant materials onto culture media and observing their gross morphological features on agar plates. As soon as their colonial characteristics have been studied, the microscopic examination of fungal reproductive structures spores and mycelia must be done as a confirmative method of identification which must be followed by Molecular identification in order to ensure complete identification. This step often disturbs the fragile spore hypha arrangements, thus, leading difficulties in interpretation of morphological results owing to the teasing effect in the preparation of wet mounts. The slide culture method of identification developed by Riddel in 1950 which uses an agar block of medium transferred to a glass slide and put in a moist petri dish have since been used with various modifications that have not really taken care of the slight disturbance of the mycelial arrangement of the study fungi that occurs during removal and replacement of coverslips during lactophenol cotton blue stain. We have developed a rapid slide culture method that can diminsh this problem to the barest minimum. Agu, Kingsley Chukwuebuka | Chidozie, Chiamaka Perpetua "An Improved Slide Culture Technique for the Microscopic Identification of Fungal Species" Published in International Journal of Trend in Scientific Research and Development (ijtsrd), ISSN: 2456-6470, Volume-6 | Issue-1 , December 2021, URL: https://www.ijtsrd.com/papers/ijtsrd45058.pdf Paper URL: https://www.ijtsrd.com/biological-science/microbiology/45058/an-improved-slide-culture-technique-for-the-microscopic-identification-of-fungal-species/agu-kingsley-chukwuebuka
Development of Dot-blot Hybridization Based on 522 bp Repetitive Sequence (R5...Tenri Ashari Wanahari
Toxoplasmosis, arising from infection by Toxoplasma gondii, is one of the most common parasitic diseases in humans and other warm-blooded animals. In humans, infections are usually asymptomatic but severe disease can occur in immunocompromized individuals and newborns. Due to the importance of the disease and in order to take suitable measures, an early diagnosis of the disease is essential, particularly for pregnant women and in industry of domestic animals. The genome of T. gondii contains repeat sequences B1 and R522 which constitute ideal targets for genome-based detection methods. The 522 base pairs repeat sequences R522 are the most promising due to the high copy number, evaluated to be 200 to 300 units within the genome. We developed a simple dot-blot hybridization based on R522 sequences. The method is simple and does not require sophisticated devices. The test of the method, using cloned R522 as target, showed that the parasite detection method was sensitive and proved to be promising for use in routine health controls as well as for the survey of Toxoplasma infections.
Key words: DIG-probe, dot blot hybridization, repeat sequences, R522, Toxoplasma gondii.
This document discusses the analysis of microbial communities through sequencing of the 16S rRNA gene. It presents WATERS, a workflow system that automates and bundles various software tools for analyzing 16S rRNA sequence data. The goals of WATERS are to simplify the analysis process for users without specialized bioinformatics expertise and to facilitate reproducibility through tracking of data provenance. WATERS guides users through the typical sequence analysis steps of alignment, chimera filtering, OTU clustering, taxonomy assignment, phylogeny tree building, and ecological analyses and visualization. By integrating existing tools into a single automated workflow, WATERS aims to reduce the effort required for 16S rRNA data analysis and allow researchers to focus on biological interpretation of results.
This document discusses regulatory plant pathology and the spread of plant diseases globally. It summarizes several plant diseases and insects that have spread between continents due to global trade and movement of plant materials. It then outlines the various international, regional, federal, and state organizations that regulate the movement of plants and plant pests, including the International Plant Protection Convention (IPPC) and the North American Plant Protection Organization (NAPPO). It also provides details on regulations in the US, the Plant Protection Act, and the roles of the USDA and Department of Homeland Security in inspecting imports and preventing the introduction of invasive plant pests.
This document provides information about the Red Palm Weevil (RPW), a serious palm pest that has spread globally from Southeast Asia. RPW larvae bore inside palm tissue and tunnels, eventually killing infested palms. Adults are large reddish-brown beetles that vary in pattern. While not present in Hawaii currently, RPW poses a major threat if introduced as it could devastate the state's palm crops and native species. The public is asked to monitor palms for signs of infestation and report any to authorities.
The document summarizes key information about flies in the insect order Diptera. It notes that Diptera have one pair of wings, with the hindwings reduced to halteres. They undergo complete metamorphosis from egg to larva to pupa to adult. As adults, they are usually strong fliers and have large, multifaceted eyes. The order is divided into the suborders Nematocera and Brachycera. Larvae generally lack legs and have chewing mouthparts, while adults feed on liquids and some transmit diseases. Both beneficial and damaging species are discussed.
This document provides a key to identify families of Lepidoptera (butterflies and moths) found in the southwestern United States. It outlines distinguishing characteristics such as whether they are diurnal or nocturnal, presence of frenulum on hindwings, wing pigmentation, antennae features, leg morphology, and markings. The families are grouped by morphological characteristics with the most common ones that will be seen in the field highlighted in bold and marked with an asterisk.
This document summarizes a study on the mechanisms of resistance to the sorghum shoot fly, Atherigona soccata, in sorghum. The study evaluated different components of resistance (antixenosis, antibiosis, tolerance) in resistant and susceptible sorghum genotypes under field and greenhouse conditions. Key findings include: 1) Resistant genotypes experienced lower deadheart formation, produced more productive tillers, and insects fed on resistant genotypes had longer larval periods and lower survival rates. 2) Physico-chemical traits like leaf glossiness and trichome density were associated with resistance while chlorophyll content and leaf wetness were associated with susceptibility. 3) Deadheart formation, eggs on leaves, leaf gloss