A 3 part talk presented at PAG Asia 2019 in Shenzhen- The Digitalization of Ruili Botanical Garden Project: Production, Curation and Re-Use. Presented by Huan Liu (CNGB), Scott Edmunds (GigaScience) & Stephen Tsui (CUHK). 8th June 2019
Open pacbiomodelorgpaper j_landolin_20150121Jane Landolin
Jane Ladolin's slides on Open Data Paper (http://www.nature.com/articles/sdata201445) presented at Balti and Bioinformatics virtual meeting on Jan. 21st 2015. (http://bit.ly/1KYGxr4)
The presentation includes preliminary information about the big data mainly metagenomic data and discussions related to the hurdles in analyzing using conventional approaches. In the later part, brief introduction about machine learning approaches using biological example for each. In the last, work done with special focus on implementation of a machine learning approach Random Forest for the functional annotation and taxonomic classification of metagenomic data.
Cross-Kingdom Standards in Genomics, Epigenomics and MetagenomicsChristopher Mason
Challenges and biases in preparing, characterizing, and sequencing DNA and RNA can have significant impacts on research in genomics across all kingdoms of life, including experiments in single cells, RNA profiling, and metagenomics. Technical artifacts and contaminations can arise at each point of sample manipulation, extraction, sequencing, and analysis. Thus, the measurement and benchmarking of these potential sources of error are of paramount importance as next-generation sequencing (NGS) projects become more global and ubiquitous.
Fortunately, a variety of methods, standards, and technologies have recently emerged that improve measurements in genomics and sequencing, from the initial input material to the computational pipelines that process and annotate the data.
This webinar will review work to develop standards and their applications in genomics, including the ABRF-NGS Phase II NGS Study on DNA Sequencing; the FDA’s Sequencing Quality Control Consortium (SEQC2); metagenomics standards efforts (ABRF, ATCC, Zymo, Metaquins), and the Epigenomics QC group of the SEQC2. The webinar will also review he computational methods for detection, validation, and implementation of these genomic measures.
Open pacbiomodelorgpaper j_landolin_20150121Jane Landolin
Jane Ladolin's slides on Open Data Paper (http://www.nature.com/articles/sdata201445) presented at Balti and Bioinformatics virtual meeting on Jan. 21st 2015. (http://bit.ly/1KYGxr4)
The presentation includes preliminary information about the big data mainly metagenomic data and discussions related to the hurdles in analyzing using conventional approaches. In the later part, brief introduction about machine learning approaches using biological example for each. In the last, work done with special focus on implementation of a machine learning approach Random Forest for the functional annotation and taxonomic classification of metagenomic data.
Cross-Kingdom Standards in Genomics, Epigenomics and MetagenomicsChristopher Mason
Challenges and biases in preparing, characterizing, and sequencing DNA and RNA can have significant impacts on research in genomics across all kingdoms of life, including experiments in single cells, RNA profiling, and metagenomics. Technical artifacts and contaminations can arise at each point of sample manipulation, extraction, sequencing, and analysis. Thus, the measurement and benchmarking of these potential sources of error are of paramount importance as next-generation sequencing (NGS) projects become more global and ubiquitous.
Fortunately, a variety of methods, standards, and technologies have recently emerged that improve measurements in genomics and sequencing, from the initial input material to the computational pipelines that process and annotate the data.
This webinar will review work to develop standards and their applications in genomics, including the ABRF-NGS Phase II NGS Study on DNA Sequencing; the FDA’s Sequencing Quality Control Consortium (SEQC2); metagenomics standards efforts (ABRF, ATCC, Zymo, Metaquins), and the Epigenomics QC group of the SEQC2. The webinar will also review he computational methods for detection, validation, and implementation of these genomic measures.
Presentation at 2019 ASHG GRC/GIAB workshop describing goals and progress of the telomere-to-telomere consortium to generate a genome assembly that provides representation of all sequences, including repetitive regions.
Building a Community Cyberinfrastructure to Support Marine Microbial Ecology ...Larry Smarr
06.09.15
Invited Talk
2006 Synthetic Biology Symposium
Aliso Creek Inn
Title: Building a Community Cyberinfrastructure to Support Marine Microbial Ecology Metagenomics
Laguna Beach, CA
The flood of nextgen sequencing data is changing the landscape of computation biology, pushing the need for more robust infrastructures, tools, and visualization techniques.
Saha UC Davis Plant Pathology seminar Infrastructure for battling the Citrus ...Surya Saha
Rapidly spreading invasive diseases in systems with little or no prior experimental data or resources pose a unique set of challenges for growers, scientists as well as regulators. As a part of a USDA NIFA CAPS project focused on the psyllid, Diaphorina citri, we have released improved genomics resources including high quality genome assemblies and annotation. We have also created an open access web portal for analyses around the Citrus Greening/Huanglongbing disease complex. Citrusgreening.org includes pathosystem-wide resources and bioinformatics tools for multiple Citrus spp. hosts, the Asian citrus psyllid vector (ACP, Diaphorina citri), and multiple pathogens including Candidatus Liberibacter asiaticus (CLas). To the best of our knowledge, this is the first example of a database to use the pathosystem as a holistic framework to understand an insect transmitted plant disease. Users can submit relevant data sets to enable sharing and allow the community to leverage their data within an integrated system. The system includes the metabolic pathway databases CitrusCyc and DiaphorinaCyc with organism specific pathways that can be used to mine metabolomics, transcriptomics and proteomics results to identify pathways and regulatory mechanisms involved in disease response. The Psyllid Expression Network (PEN) contains expression profiles of ACP genes from multiple life stages, tissues, conditions and hosts. The Citrus Expression Network (CEN) contains public expression data from multiple tissues and conditions for various citrus hosts. All tools connect to a central database. The portal also includes electrical penetration graph (EPG) recordings, information about citrus rootstock trials and metabolomics data in addition to traditional omics data types with a goal of combining and mining all information related to the Huanglongbing pathosystem. User-friendly manual curation tools will allow the continuous improvement of knowledge base as more experimental research is published. The portal can be accessed at https://citrusgreening.org/.
10.02.19
Invited talk
Symposium #1816, Managing the Exaflood: Enhancing the Value of Networked Data for Science and Society
Title: Advancing the Metagenomics Revolution
San Diego, CA
Creating a Cyberinfrastructure for Advanced Marine Microbial Ecology Research...Larry Smarr
06.06.27
Invited Talk
ONR Review
Scripps Institution of Oceanography, UCSD
Title: Creating a Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA)—Taking Metagenomics to Light Speed
La Jolla, CA
Using Supercomputers and Supernetworks to Explore the Ocean of LifeLarry Smarr
07.06.07
Director's Colloquium
Los Alamos National Laboratory
Title: Using Supercomputers and Supernetworks to Explore the Ocean of Life
Los Alamos, NM
Visualization of insect vector-plant pathogen interactions in the citrus gree...Surya Saha
The Asian citrus psyllid (ACP,Diaphorina citri) is the insect vector of the bacterium Candidatus Liberibacter asiaticus (CLas), the causal agent for citrus greening disease, which threatens the citrus industry worldwide. The Asian citrus psyllid genome project is a coordinated effort to define the psyllid genome, including the identification and annotation of every psyllid gene. This discovery of psyllid genes regulating CLas acquisition and transmission by the psyllid will transform future vector management strategies for controlling citrus greening. Advances in psyllid genome sequencing to improve genome assembly, including using Pacbio and long-range Hi-C scaffolding, resulted in the identification of 13 psyllid chromosomes, the first description of chromosome number for this economically important hemipteran insect vector. Together with Pacbio IsoSeq technology to sequence psyllid transcripts from different life stages and those reared on CLas + and - trees, approximately 20,000 putative full-length protein coding psyllid genes were identified. Student driven annotation resulted in more than 500 high quality models of genes involved in CLas-ACP interactions. New assemblies and annotations of the Florida strains of the ACP bacterial endosymbionts, Wolbachia, Profftella, and Carsonella were also characterized from the genome sequencing data.
Finally, we developed a data visualization platform, the Psyllid Expression Network (PEN), which is a user-friendly web-based tool for mining gene and protein expression patterns. PEN enabled us to identify tissue and host plant specific changes in ACP genes in response to CLas at the transcript and proteome level. The availability of a high quality reference genome, endosymbiont genomes and tools for analyzing transcriptomics, proteomics and metabolomics data in an integrated, systems biology approach will enable novel approaches to control the transmission of citrus greening disease. The new ACP genome assembly (Diaci v3), PEN and other tools are available on https://citrusgreening.org/ which is our portal for all omics resources for the citrus greening disease.
https://plan.core-apps.com/pag_2019/event/b6da6bc5896fea594de507e257910266
Presentation at 2019 ASHG GRC/GIAB workshop describing goals and progress of the telomere-to-telomere consortium to generate a genome assembly that provides representation of all sequences, including repetitive regions.
Building a Community Cyberinfrastructure to Support Marine Microbial Ecology ...Larry Smarr
06.09.15
Invited Talk
2006 Synthetic Biology Symposium
Aliso Creek Inn
Title: Building a Community Cyberinfrastructure to Support Marine Microbial Ecology Metagenomics
Laguna Beach, CA
The flood of nextgen sequencing data is changing the landscape of computation biology, pushing the need for more robust infrastructures, tools, and visualization techniques.
Saha UC Davis Plant Pathology seminar Infrastructure for battling the Citrus ...Surya Saha
Rapidly spreading invasive diseases in systems with little or no prior experimental data or resources pose a unique set of challenges for growers, scientists as well as regulators. As a part of a USDA NIFA CAPS project focused on the psyllid, Diaphorina citri, we have released improved genomics resources including high quality genome assemblies and annotation. We have also created an open access web portal for analyses around the Citrus Greening/Huanglongbing disease complex. Citrusgreening.org includes pathosystem-wide resources and bioinformatics tools for multiple Citrus spp. hosts, the Asian citrus psyllid vector (ACP, Diaphorina citri), and multiple pathogens including Candidatus Liberibacter asiaticus (CLas). To the best of our knowledge, this is the first example of a database to use the pathosystem as a holistic framework to understand an insect transmitted plant disease. Users can submit relevant data sets to enable sharing and allow the community to leverage their data within an integrated system. The system includes the metabolic pathway databases CitrusCyc and DiaphorinaCyc with organism specific pathways that can be used to mine metabolomics, transcriptomics and proteomics results to identify pathways and regulatory mechanisms involved in disease response. The Psyllid Expression Network (PEN) contains expression profiles of ACP genes from multiple life stages, tissues, conditions and hosts. The Citrus Expression Network (CEN) contains public expression data from multiple tissues and conditions for various citrus hosts. All tools connect to a central database. The portal also includes electrical penetration graph (EPG) recordings, information about citrus rootstock trials and metabolomics data in addition to traditional omics data types with a goal of combining and mining all information related to the Huanglongbing pathosystem. User-friendly manual curation tools will allow the continuous improvement of knowledge base as more experimental research is published. The portal can be accessed at https://citrusgreening.org/.
10.02.19
Invited talk
Symposium #1816, Managing the Exaflood: Enhancing the Value of Networked Data for Science and Society
Title: Advancing the Metagenomics Revolution
San Diego, CA
Creating a Cyberinfrastructure for Advanced Marine Microbial Ecology Research...Larry Smarr
06.06.27
Invited Talk
ONR Review
Scripps Institution of Oceanography, UCSD
Title: Creating a Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA)—Taking Metagenomics to Light Speed
La Jolla, CA
Using Supercomputers and Supernetworks to Explore the Ocean of LifeLarry Smarr
07.06.07
Director's Colloquium
Los Alamos National Laboratory
Title: Using Supercomputers and Supernetworks to Explore the Ocean of Life
Los Alamos, NM
Visualization of insect vector-plant pathogen interactions in the citrus gree...Surya Saha
The Asian citrus psyllid (ACP,Diaphorina citri) is the insect vector of the bacterium Candidatus Liberibacter asiaticus (CLas), the causal agent for citrus greening disease, which threatens the citrus industry worldwide. The Asian citrus psyllid genome project is a coordinated effort to define the psyllid genome, including the identification and annotation of every psyllid gene. This discovery of psyllid genes regulating CLas acquisition and transmission by the psyllid will transform future vector management strategies for controlling citrus greening. Advances in psyllid genome sequencing to improve genome assembly, including using Pacbio and long-range Hi-C scaffolding, resulted in the identification of 13 psyllid chromosomes, the first description of chromosome number for this economically important hemipteran insect vector. Together with Pacbio IsoSeq technology to sequence psyllid transcripts from different life stages and those reared on CLas + and - trees, approximately 20,000 putative full-length protein coding psyllid genes were identified. Student driven annotation resulted in more than 500 high quality models of genes involved in CLas-ACP interactions. New assemblies and annotations of the Florida strains of the ACP bacterial endosymbionts, Wolbachia, Profftella, and Carsonella were also characterized from the genome sequencing data.
Finally, we developed a data visualization platform, the Psyllid Expression Network (PEN), which is a user-friendly web-based tool for mining gene and protein expression patterns. PEN enabled us to identify tissue and host plant specific changes in ACP genes in response to CLas at the transcript and proteome level. The availability of a high quality reference genome, endosymbiont genomes and tools for analyzing transcriptomics, proteomics and metabolomics data in an integrated, systems biology approach will enable novel approaches to control the transmission of citrus greening disease. The new ACP genome assembly (Diaci v3), PEN and other tools are available on https://citrusgreening.org/ which is our portal for all omics resources for the citrus greening disease.
https://plan.core-apps.com/pag_2019/event/b6da6bc5896fea594de507e257910266
Johannes Bergsten lecture on Thursday, Sept 17, 2009, for the Biodiversity Informatics Course, a Swedish Taxonomy Initiative (Svenska Artprojektet) course at the Swedish Natural History Museum, Stockholm, supported by the Swedish Species Service (ArtDatabanken) and the Swedish GBIF node.
Development of FDA MicroDB: A Regulatory-Grade Microbial Reference DatabaseNathan Olson
"Development of FDA MicroDB: A Regulatory-Grade
Microbial Reference Database" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by the National Institute for Standards and Technology October 2014 by Heike Sichtig, PhD from the FDA and Luke Tallon from IGS UMSOM.
Speeding up sequencing: Sequencing in an hour enables sample to answer in a w...Thermo Fisher Scientific
At this time next generation sequencing (NGS) is hindered by slow and often manual workflow procedures. Decreasing overall workflow times is critical for the widespread adoption of targeted and whole genome sequencing (WGS) for many time-sensitive applications, in particular for infectious disease analysis. To this end, we describe improvements to the four main steps of the NGS workflow: i) library preparation; ii) template preparation, iii) sequencing; iv) and data analysis. Together, these advances dramatically decrease the overall turnaround times.
Ion Torrent semiconductor-based sequencing instruments utilities flow sequencing with speed largely dependent on and the number of nucleotide flows (one flow produces ~0.5 base) and the speed of the flows (Figure 2).
VariantSpark: applying Spark-based machine learning methods to genomic inform...Denis C. Bauer
Genomic information is increasingly used in medical practice giving rise to the need for efficient analysis methodology able to cope with thousands of individuals and millions of variants. Here we introduce VariantSpark, which utilizes Hadoop/Spark along with its machine learning library, MLlib, providing the means of parallelisation for population-scale bioinformatics tasks. VariantSpark is the interface to the standard variant format (VCF), offers seamless genome-wide sampling of variants and provides a pipeline for visualising results.
To demonstrate the capabilities of VariantSpark, we clustered more than 3,000 individuals with 80 Million variants each to determine the population structure in the dataset. VariantSpark is 80% faster than the Spark-based genome clustering approach, ADAM, the comparable implementation using Hadoop/Mahout, as well as Admixture, a commonly used tool for determining individual ancestries. It is over 90% faster than traditional implementations using R and Python. These benefits of speed, resource consumption and scalability enables VariantSpark to open up the usage of advanced, efficient machine learning algorithms to genomic data.
The package is written in Scala and available at https://github.com/BauerLab/VariantSpark.
IDW2022: A decades experiences in transparent and interactive publication of ...GigaScience, BGI Hong Kong
Scott Edmunds at International Data Week 2022: A decades experiences in transparent and interactive publication of FAIR data and software via an end-to-end XML publishing platform. 21st June 2022
GigaByte Chief Editor Scott Edmunds presents on how to prepare a data paper for the TDR and WHO sponsored call for data papers describing datasets on vectors of human diseases launched in Nov 2021. Presented at the GBIF webinar on 25th January 2022 and aimed at authors interested in submitting a manuscript submitted to the series.
STM Week: Demonstrating bringing publications to life via an End-to-end XML p...GigaScience, BGI Hong Kong
Scott Edmunds at the STM Week 2020 Digital Publishing seminar on Demonstrating bringing publications to life via an End-to-end XML publishing platform. 2nd December 2020
Scott Edmunds: A new publishing workflow for rapid dissemination of genomes u...GigaScience, BGI Hong Kong
Scott Edmunds on a new publishing workflow for rapid dissemination of genomes using GigaByte & GigaDB. Presented at Biodiversity 2020 in the Annotation & Databases track, 9th October 2020.
Scott Edmunds: Quantifying how FAIR is Hong Kong: The Hong Kong Shareability ...GigaScience, BGI Hong Kong
Scot Edmunds talk at CODATA2019 on Quantifying how FAIR is Hong Kong: The Hong Kong Shareability of Hong Kong University Research Experiment. 19th September 2019 in Beijing
Scott Edmunds talk at IARC: How can we make science more trustworthy and FAIR...GigaScience, BGI Hong Kong
Scott Edmunds talk at IARC, Lyon. How can we make science more trustworthy and FAIR? Principled publishing for more evidence based research. 8th July 2019
Democratising biodiversity and genomics research: open and citizen science to...GigaScience, BGI Hong Kong
Scott Edmunds at the China National GeneBank Youth Biodiversity MegaData Forum: Democratising biodiversity and genomics research: open and citizen science to build trust and fill the data gaps. 18th December 2018
Ricardo Wurmus at #ICG13: Reproducible genomics analysis pipelines with GNU Guix. Presented at the GigaScience Prize Track at the International Conference on Genomics, Shezhen 26th October 2018
Paul Pavlidis at #ICG13: Monitoring changes in the Gene Ontology and their im...GigaScience, BGI Hong Kong
Paul Pavlidis talk at the #ICG13 GigaScience Prize Track: Monitoring changes in the Gene Ontology and their impact on genomic data analysis (GOtrack). Shenzhen, 26th October 2018
Stefan Prost at #ICG13: Genome analyses show strong selection on coloration, ...GigaScience, BGI Hong Kong
Stefan Prost presentation for the #ICG13 GigaScience Prize Track: Genome analyses show strong selection on coloration, morphological and behavioral phenotypes in birds-of-paradise. Shenzhen, 26th October, 2018
Lisa Johnson at #ICG13: Re-assembly, quality evaluation, and annotation of 67...GigaScience, BGI Hong Kong
Lisa Johnson's talk at the #ICG13 GigaScience Prize Track: Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes. Shenzhen, 26th October 2018
Reproducible method and benchmarking publishing for the data (and evidence) d...GigaScience, BGI Hong Kong
Scott Edmunds presentation on: Reproducible method and benchmarking publishing for the data (and evidence) driven era. The Silk Road Forensics Conference, Yantai, 18th September 2018
Mary Ann Tuli: What MODs can learn from Journals – a GigaDB curator’s perspec...GigaScience, BGI Hong Kong
Mary Ann Tuli's talk at the International Society of Biocuration meeting : What MODs can learn from Journals – a GigaDB curator’s perspective. Shanghai 9th April 2018
Laurie Goodman: Sharing and Reusing Cell Image Data, ASCB/EMBO 2017 Subgroup ...GigaScience, BGI Hong Kong
Laurie Goodman's pre-prepared slides for the Subgroup S Sharing and Reusing Cell Image Data session at the 2017 ASCB│EMBO meeting in Philadelphia. December 2017
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
PAGAsia19 - The Digitalization of Ruili Botanical Garden Project: Production, Curation and Re-Use
1. The Digitalization of Ruili Botanical Garden Project:
Production, Curation and Re-Use
Stephen Kwok-Wing TsuiHuan Liu Scott C Edmunds
2. • 1,100 hectares, in Yunnan Province
• Rich biodiversity
• Living Biobank of China National
GeneBank
Ruili Botanical Garden
Part 1. Why?
Ruili Botanical
Garden
3. • 1st Phase of 10KP
• The 1st digitalized botanical garden
• Show the biodiversity and phyletic evolution and
interactions between environment, ecosystem, and
evolution
• Result of phase 1 is published in GigaScience
• Voucher specimen stored at HCNGB (CNGB Herbarium)
1,093 Samples
1093 Voucher
Specimen
49 Order
137 Family
761 Deep-
sequenced
689 Vascular
Species
54TB Data
DRBG
Result
4. Order
Raw
base(Gb)
Alismatales 66.3873
Apiales 70.0075
Araucariales 74.14
Arecales 68.8318
Asparagales 70.3465
Asterales 67.8382
Brassicales 68.474
Buxales 65.44
Caryophyllales 68.6558
Celastrales 75.8133
Commelinales 65.02
Cornales 76.396
Crossosomatale
s
60.2
Cucurbitales 65.11
Cupressales 73.54
Cyatheales 75.76
Dioscoreales 78.9
Dipsacales 58.6267
Equisetales 67.3
Ericales 68.1109
Fabales 69.9439
Fagales 68.14
Gentianales 70.1155
Gnetales 71.1267
Lamiales 69.3291
Laurales 71.9425
Liliales 71.4133
Magnoliales 69.0988
Malpighiales 68.1842
Malvales 66.2106
Myrtales 70.7924
Oxalidales 68.3533
Pandanales 72.6733
Pinales 61.04
Piperales 63.2533
Poales 69.6407
Polypodiales 68.588
Proteales 69.0733
Ranunculales 67.5644
Rosales 70.0468
Santalales 69.07
Sapindales 70.5628
Saxifragales 70.84
Schizaeales 62.57
Solanales 72.2389
Vitales 65.235
Zingiberales 67.4956
10 10 11 12 16
16
17
18
18
21
21
22
24
36
35
3543
41
50
50
54
64
>10 orders
Zingiberales Alismatales Ranunculales Fagales Apiales Arecales
Malvales Solanales Magnoliales Polypodiales Caryophyllales Myrtales
Ericales Asparagales Gentianales Sapindales Asterales Malpighiales
Lamiales Poales Rosales Fabales
1. 54 Tb of sequencing data with an average sequencing depth of 60X per species;
2. Reference phylogeny was re-constructed with 78 chloroplast genes for molecular
identification and other possible applications
3. Data publicly accessible at CNGBdb; https://db.cngb.org/cnsa
Scan and Visit
CNGBdb
Data
5. Huan Liu et. al., GigaScience, 2019
• Survey data of these 761 samples contributed greatly to the genome sequencing
and assembly
• Assembled chloroplast genome of each sample with annotation
• Selected 78 coding gene to construct phylogenetic tree of Ruili Botanical Garden
to present the biodiversity and phyletic evolution, and interactions between
environment, ecosystem, and evolution
Research and Application
8. EM(ectomycorrhizal)
Nitrogen fixer
AM (arbuscular mycorrhizal)
Future Work
• Phylogenetic and molecular evolutionary of controlling symbiosis establishment
• Digitalize major symbiosis species for different order of trees
• Unravel the genetic factors driving the symbiotic
relationship
• Understand the mechanisms underlying beneficial
plant-microbe interactions
9. Part 2: Dissemination
What is the most useful way to share 54TB of
unassembled sequencing data?
Scott Edmunds
10. The Ruili data challenge
• >1000 specimens & 54TB of raw sequencing data
• 60GB short read (BGISEQ 500), single library – usable?
• High-throughput imaging, building new herbarium
• Version-of-record, but species IDs evolving target
• How can we maximise the discoverability & usability?
11. The approach
• Credit early release of data with Data Note articles
• Have GigaDB repository to bring together and host datasets
• Create individually citeable Datacite DOIs
• Curation team organise structure & metadata (with guidance by peer
reviewers)
• Papers static, but GigaDB entries can be updated and linked (via
metadata & links/popups)
• GigaDB pages allow widgets for interaction
• Approach used for Rice3K & Avian Phylogenomic project
16. Does rich metadata increase discoverability? Testing
with RCT
https://osf.io/wzps8/
17. Added protocols to protocols.io
http://dx.doi.org/10.17504/protocols.io.pzqdp5w
https://www.protocols.io/groups/gigascience-journal
18. Data now available, so can people use it?
B. Purpurea = motherB. Variegata = father
19. Part 3. Genomic Analysis of Bauhinia Species
from the Ruili Botanical Garden Project
TSUI Kwok-Wing Stephen
Professor, School of Biomedical Sciences
Programme Director, MSc in Genomics and Bioinformatics
Associate Director, CUHK-BGI Innovative Institute of Trans-omics
Director, Centre for Microbial Genomics and Proteomics
Director, Hong Kong Bioinformatics Centre
20. Hong Kong Flora Emblem - Bauhinia blakeana
Bauhinia blakeana
(洋紫荊)
Hong Kong Emblem
21. Bauhinia blakeana – A Hybrid Plant
Bauhinia blakeana (洋紫荊, hybrid), Hong Kong Orchid
Tree, is a hybrid between Bauhinia variegata (宮粉羊蹄
甲, male) and Bauhinia purpurea (紅花羊蹄甲, female).
Bauhinia variegata
(宮粉羊蹄甲)
Bauhinia purpurea
(紅花羊蹄甲)
Bauhinia blakeana
(洋紫荊)
22. WGS Data from BGI 10K Project
• Organism: vascular plants Bauhinia
variegata
• Biosample: SAMN08770810
• NCBI number: SRR7121897
• Platform: BGISEQ-500
• Insert size: 200 bp
• Read number: 377,370,160*2
• Total read length: 75.47 Gbp
• Coverage depth: 300 X
23. Statistics of WGS data
• The 27-mer spectrum was
computed
• First peak (Coverage: 63X;
heterozygous)
• Second peak (Coverage: 127X;
homozygous)
• Estimated genome size: 245Mb
• Estimated heterozygous rate:
1.06%
24. Statistics of Bauhinia variegata Genome
Genome size 249 Mbp
Scaffold No. 30,075
Scaffold N50 20,620
Longest contig 292 kbp
Gap size 1.30 Mbp
Gap number 13,033
BUSCO Completeness 92.7%
25. Annotation of the Bauhinia variegata Genome
Gene prediction
• 31,248 genes
• 724 tRNA genes
• 18 rRNA genes
Repetitive sequences
• bases masked: 6,525,846 bp (2.67 %)
• Simple repeats: 4,899,189 bp (2.00 %)
• Low complexity: 1,631,550 bp (0.67 %)
27. Ruili Botanical Garden
In summary
• This project provides insight into the feasibility and technical
requirements for “planetary-scale” projects such as 10KP and the
EBP. 1K+ projects are achievable with current technology
• Current data very usable for gene discovery, plastid, and
mitochondrial assembly.
• Reference genomes difficult with this quality of data, but have
demonstrated species of interest can be studied – very suitable
for short postgrad or postdoc project.
• Species identification and genome improvement (Hi-C) on-going.
Plus root metagenomes – watch this space for updates…
• Use the data – join the project. Help yourself to reprints.
Read the research: https://doi.org/10.1093/gigascience/giz007
Download the data: http://dx.doi.org/10.5524/100502
Take the virtual tour: http://720yunnan.com/tour/a2b8096d43d7226d?scene=scene_d3627cc2a43314d
Editor's Notes
Includes sample metadata (in database only, not DataCite) and cross-species results (gene alignments & trees)
It showed us people in Hong Kong want to know more about this subject if given the opportunity. Working with the universities here to train students with this data, Stephen Tsui got his Masters students at the Chinese University of Hong Kong to already assemble most of this data.