This document summarizes research on the evolution of animal body plans and insights from genomics studies of marine invertebrates. It finds that basal metazoans like Placozoa, Cnidaria, Porifera, and Ctenophora exhibit a wide variety of body plans and life histories. The genome of Pleurobrachia bachei, a ctenophore, was sequenced which provides insights into the evolution of nervous systems. Analysis of Wnt signaling pathway genes in P. bachei found conservation with other animals and potential roles in development and neurotransmission. The study of P. bachei's genome involved undergraduate students and provided hands-on research experience in genomics.
A systematic approach to Genotype-Phenotype correlationsfisherp
It is increasingly common to combine Microarray and Quantitative Trait Loci data to aid the search for candidate genes responsible for phenotypic variation. Workflows provide a means of systematically processing these large datasets and also represent a framework for the re-use and the explicit declaration of experimental methods. Here we highlight the issues facing the manual analysis of microarray and QTL data for the discovery of candidate genes underlying complex phenotypes. We show how automated approaches provide a systematic means to investigate genotype-phenotype correlations. This methodology was applied to a use case of resistance to African trypanosomiasis in the mouse. Pathways represented in the results identified Daxx as one of the candidate genes within the Tir1 QTL region.
A complete set of chromosomes/genes inherited as a unit from one parent called genome. The entire genetic complement of a living organism.
The total amount of genetic information in the chromosomes of an organism, including its genes and DNA sequences. The genome of eukaryotes is made up of a single, haploid set of chromosomes that is contained in the nucleus of every cell and exists in two copies in the chromosomes of all cells except reproductive and red blood cells. The human genome is made up of about 35,000 genes.
despite of the enormous genomic diversity, the phage genome mapping is being done using a plethora of techniques,which includes both genetic mapping and physical mapping
A systematic approach to Genotype-Phenotype correlationsfisherp
It is increasingly common to combine Microarray and Quantitative Trait Loci data to aid the search for candidate genes responsible for phenotypic variation. Workflows provide a means of systematically processing these large datasets and also represent a framework for the re-use and the explicit declaration of experimental methods. Here we highlight the issues facing the manual analysis of microarray and QTL data for the discovery of candidate genes underlying complex phenotypes. We show how automated approaches provide a systematic means to investigate genotype-phenotype correlations. This methodology was applied to a use case of resistance to African trypanosomiasis in the mouse. Pathways represented in the results identified Daxx as one of the candidate genes within the Tir1 QTL region.
A complete set of chromosomes/genes inherited as a unit from one parent called genome. The entire genetic complement of a living organism.
The total amount of genetic information in the chromosomes of an organism, including its genes and DNA sequences. The genome of eukaryotes is made up of a single, haploid set of chromosomes that is contained in the nucleus of every cell and exists in two copies in the chromosomes of all cells except reproductive and red blood cells. The human genome is made up of about 35,000 genes.
despite of the enormous genomic diversity, the phage genome mapping is being done using a plethora of techniques,which includes both genetic mapping and physical mapping
Genomic conflict-It arises when genes inside a genome are not transmitted by the same rules
Genes that cause such genomic conflict are called selfish genetic elements (also selfish DNA, ultra-selfish genes, genetic parasites) and can be harmful to the individual.
So selfish gene can be defined as stretches of DNA (genes, fragments of genes, noncoding DNA, portions of chromosomes, whole chromosomes, or sets of chromosomes) that act narrowly to advance their own interests—in other words, replication at the expense of the larger organism.
Here it also presented about what is genomic conflict, types of it, cytoplasmic inheritance, its relation with genomic conflict, ABC model, Molecular mechanism of CMS, Pollen hypothesis, ATP hypothesis, etc.
Basic genetics /certified fixed orthodontic courses by Indian dental academy Indian dental academy
Welcome to Indian Dental Academy
The Indian Dental Academy is the Leader in continuing dental education , training dentists in all aspects of dentistry and offering a wide range of dental certified courses in different formats.
Indian dental academy has a unique training program & curriculum that provides students with exceptional clinical skills and enabling them to return to their office with high level confidence and start treating patients
State of the art comprehensive training-Faculty of world wide repute &Very affordable.
Genomic conflict-It arises when genes inside a genome are not transmitted by the same rules
Genes that cause such genomic conflict are called selfish genetic elements (also selfish DNA, ultra-selfish genes, genetic parasites) and can be harmful to the individual.
So selfish gene can be defined as stretches of DNA (genes, fragments of genes, noncoding DNA, portions of chromosomes, whole chromosomes, or sets of chromosomes) that act narrowly to advance their own interests—in other words, replication at the expense of the larger organism.
Here it also presented about what is genomic conflict, types of it, cytoplasmic inheritance, its relation with genomic conflict, ABC model, Molecular mechanism of CMS, Pollen hypothesis, ATP hypothesis, etc.
Basic genetics /certified fixed orthodontic courses by Indian dental academy Indian dental academy
Welcome to Indian Dental Academy
The Indian Dental Academy is the Leader in continuing dental education , training dentists in all aspects of dentistry and offering a wide range of dental certified courses in different formats.
Indian dental academy has a unique training program & curriculum that provides students with exceptional clinical skills and enabling them to return to their office with high level confidence and start treating patients
State of the art comprehensive training-Faculty of world wide repute &Very affordable.
Horizantal gene transfer in evolution of nematodespriyank mhatre
This is a presentation on Horizontal gene transfer(HGT) in evolution of nematodes which gives us idea about importance of HGT in evolution of nematode parasitism. Here I have covered the historical events about HGT as well.
This is my First seminar in Div of Nematology.
Models of Human Diseases Conference (2010) Tetrahymena model by Dr. R. Pearl...Medical Education Advising
The Ciliate Protozoan Tetrahymena thermophila as an important animal model organism
Dr. R.E. Pearlman, York University
Models of Human Diseases Conference
June 29, 2010
Menders experiments were conducted using garden peas. Why would human.pdfisenbergwarne4100
Menders experiments were conducted using garden peas. Why would humans be an awful
choice for an experimental organism (give at least 3 reasons)? Give an example of an animal that
would be better sorted for genetics experiments. In Mendel\'s experiments, a plant with purple
flowers was crossed with a plant having white flowers. Explain why white flowers disappeared
in the F_1 generation and reappeared in the F_2. Your pet rabbit has curly fur. After seeking
advice from a rabbit breeder, you learn that curly fur is a dominant trait, but you want to know
the precise genotype of your pet. Describe how you could find out. Describe the inheritance of
ABO blood types in humans and explain why individuals with type O are universal donors while
individuals with type AB are universal acceptors. Describe the nature vs. nurture debate. In your
explanation, give an example of a trait that is controlled entirely by nature and one that is heavily
influenced by both nature and nurture.
Solution
Answer:
1. Studying human genetics is unlike studying the genetics of any other organism. In many ways,
humans are very poor model organisms for genetics. Long generation times make for slow
progress when doing genetic crosses, which brings us to another problem with human genetics:
The inability to make controlled crosses.
So, any human geneticist that tried to make controlled human crosses would most likely be
considered a very disturbed criminal and not a brilliant scientist. Besides, humans usually only
have one child at a time, which makes it really difficult to generate numbers of offspring that can
achieve statistical significance. On top of all this, there\'s the issue of genetic manipulation. Key
genetic techniques, like mutation screening and transgenics, are completely off-limits to human
geneticists.
Drosophila melanogaster (Fruit fly) would be better suited as a model organism for genetics
experiments.
1. The relationship between fruit fly and human genes is so close that often the sequences of
newly discovered human genes, including disease genes, can be matched with equivalent genes
in the fly.
2. 75 per cent of the genes that cause disease in humans are also found in the fruit fly.
3. Drosophila have a short, simple reproduction cycle. It is normally about 8-14 days, depending
on the environmental temperature. This means that several generations can be observed in a
matter of months.
4. Fruit fly are small (3 mm long) but not so small that they can’t be seen without a microscope.
This allows scientists to keep millions of them in the laboratory at a time.
5. They are inexpensive to maintain in the laboratory.
6. They require a simple diet consisting of simple sources of carbohydrates (cornmeal) and
proteins (yeast extract).
7. The only care they need is having their food changed regularly (every 10-14 days at 25C or 5-
6 weeks at 18C).
8. Drosophila have ‘polytene’ chromosomes, which means that they are oversized and have
barcode-like banding patterns.
Preliminary data presented at Animal Behavior Society meeting in 2012. Paper is now published in Animal Behaviour: http://www.sciencedirect.com/science/article/pii/S0003347213003473
Essentials of Automations: Optimizing FME Workflows with ParametersSafe Software
Are you looking to streamline your workflows and boost your projects’ efficiency? Do you find yourself searching for ways to add flexibility and control over your FME workflows? If so, you’re in the right place.
Join us for an insightful dive into the world of FME parameters, a critical element in optimizing workflow efficiency. This webinar marks the beginning of our three-part “Essentials of Automation” series. This first webinar is designed to equip you with the knowledge and skills to utilize parameters effectively: enhancing the flexibility, maintainability, and user control of your FME projects.
Here’s what you’ll gain:
- Essentials of FME Parameters: Understand the pivotal role of parameters, including Reader/Writer, Transformer, User, and FME Flow categories. Discover how they are the key to unlocking automation and optimization within your workflows.
- Practical Applications in FME Form: Delve into key user parameter types including choice, connections, and file URLs. Allow users to control how a workflow runs, making your workflows more reusable. Learn to import values and deliver the best user experience for your workflows while enhancing accuracy.
- Optimization Strategies in FME Flow: Explore the creation and strategic deployment of parameters in FME Flow, including the use of deployment and geometry parameters, to maximize workflow efficiency.
- Pro Tips for Success: Gain insights on parameterizing connections and leveraging new features like Conditional Visibility for clarity and simplicity.
We’ll wrap up with a glimpse into future webinars, followed by a Q&A session to address your specific questions surrounding this topic.
Don’t miss this opportunity to elevate your FME expertise and drive your projects to new heights of efficiency.
Transcript: Selling digital books in 2024: Insights from industry leaders - T...BookNet Canada
The publishing industry has been selling digital audiobooks and ebooks for over a decade and has found its groove. What’s changed? What has stayed the same? Where do we go from here? Join a group of leading sales peers from across the industry for a conversation about the lessons learned since the popularization of digital books, best practices, digital book supply chain management, and more.
Link to video recording: https://bnctechforum.ca/sessions/selling-digital-books-in-2024-insights-from-industry-leaders/
Presented by BookNet Canada on May 28, 2024, with support from the Department of Canadian Heritage.
Connector Corner: Automate dynamic content and events by pushing a buttonDianaGray10
Here is something new! In our next Connector Corner webinar, we will demonstrate how you can use a single workflow to:
Create a campaign using Mailchimp with merge tags/fields
Send an interactive Slack channel message (using buttons)
Have the message received by managers and peers along with a test email for review
But there’s more:
In a second workflow supporting the same use case, you’ll see:
Your campaign sent to target colleagues for approval
If the “Approve” button is clicked, a Jira/Zendesk ticket is created for the marketing design team
But—if the “Reject” button is pushed, colleagues will be alerted via Slack message
Join us to learn more about this new, human-in-the-loop capability, brought to you by Integration Service connectors.
And...
Speakers:
Akshay Agnihotri, Product Manager
Charlie Greenberg, Host
GDG Cloud Southlake #33: Boule & Rebala: Effective AppSec in SDLC using Deplo...James Anderson
Effective Application Security in Software Delivery lifecycle using Deployment Firewall and DBOM
The modern software delivery process (or the CI/CD process) includes many tools, distributed teams, open-source code, and cloud platforms. Constant focus on speed to release software to market, along with the traditional slow and manual security checks has caused gaps in continuous security as an important piece in the software supply chain. Today organizations feel more susceptible to external and internal cyber threats due to the vast attack surface in their applications supply chain and the lack of end-to-end governance and risk management.
The software team must secure its software delivery process to avoid vulnerability and security breaches. This needs to be achieved with existing tool chains and without extensive rework of the delivery processes. This talk will present strategies and techniques for providing visibility into the true risk of the existing vulnerabilities, preventing the introduction of security issues in the software, resolving vulnerabilities in production environments quickly, and capturing the deployment bill of materials (DBOM).
Speakers:
Bob Boule
Robert Boule is a technology enthusiast with PASSION for technology and making things work along with a knack for helping others understand how things work. He comes with around 20 years of solution engineering experience in application security, software continuous delivery, and SaaS platforms. He is known for his dynamic presentations in CI/CD and application security integrated in software delivery lifecycle.
Gopinath Rebala
Gopinath Rebala is the CTO of OpsMx, where he has overall responsibility for the machine learning and data processing architectures for Secure Software Delivery. Gopi also has a strong connection with our customers, leading design and architecture for strategic implementations. Gopi is a frequent speaker and well-known leader in continuous delivery and integrating security into software delivery.
Let's dive deeper into the world of ODC! Ricardo Alves (OutSystems) will join us to tell all about the new Data Fabric. After that, Sezen de Bruijn (OutSystems) will get into the details on how to best design a sturdy architecture within ODC.
Epistemic Interaction - tuning interfaces to provide information for AI supportAlan Dix
Paper presented at SYNERGY workshop at AVI 2024, Genoa, Italy. 3rd June 2024
https://alandix.com/academic/papers/synergy2024-epistemic/
As machine learning integrates deeper into human-computer interactions, the concept of epistemic interaction emerges, aiming to refine these interactions to enhance system adaptability. This approach encourages minor, intentional adjustments in user behaviour to enrich the data available for system learning. This paper introduces epistemic interaction within the context of human-system communication, illustrating how deliberate interaction design can improve system understanding and adaptation. Through concrete examples, we demonstrate the potential of epistemic interaction to significantly advance human-computer interaction by leveraging intuitive human communication strategies to inform system design and functionality, offering a novel pathway for enriching user-system engagements.
UiPath Test Automation using UiPath Test Suite series, part 3DianaGray10
Welcome to UiPath Test Automation using UiPath Test Suite series part 3. In this session, we will cover desktop automation along with UI automation.
Topics covered:
UI automation Introduction,
UI automation Sample
Desktop automation flow
Pradeep Chinnala, Senior Consultant Automation Developer @WonderBotz and UiPath MVP
Deepak Rai, Automation Practice Lead, Boundaryless Group and UiPath MVP
GraphRAG is All You need? LLM & Knowledge GraphGuy Korland
Guy Korland, CEO and Co-founder of FalkorDB, will review two articles on the integration of language models with knowledge graphs.
1. Unifying Large Language Models and Knowledge Graphs: A Roadmap.
https://arxiv.org/abs/2306.08302
2. Microsoft Research's GraphRAG paper and a review paper on various uses of knowledge graphs:
https://www.microsoft.com/en-us/research/blog/graphrag-unlocking-llm-discovery-on-narrative-private-data/
Search and Society: Reimagining Information Access for Radical FuturesBhaskar Mitra
The field of Information retrieval (IR) is currently undergoing a transformative shift, at least partly due to the emerging applications of generative AI to information access. In this talk, we will deliberate on the sociotechnical implications of generative AI for information access. We will argue that there is both a critical necessity and an exciting opportunity for the IR community to re-center our research agendas on societal needs while dismantling the artificial separation between the work on fairness, accountability, transparency, and ethics in IR and the rest of IR research. Instead of adopting a reactionary strategy of trying to mitigate potential social harms from emerging technologies, the community should aim to proactively set the research agenda for the kinds of systems we should build inspired by diverse explicitly stated sociotechnical imaginaries. The sociotechnical imaginaries that underpin the design and development of information access technologies needs to be explicitly articulated, and we need to develop theories of change in context of these diverse perspectives. Our guiding future imaginaries must be informed by other academic fields, such as democratic theory and critical theory, and should be co-developed with social science scholars, legal scholars, civil rights and social justice activists, and artists, among others.
JMeter webinar - integration with InfluxDB and GrafanaRTTS
Watch this recorded webinar about real-time monitoring of application performance. See how to integrate Apache JMeter, the open-source leader in performance testing, with InfluxDB, the open-source time-series database, and Grafana, the open-source analytics and visualization application.
In this webinar, we will review the benefits of leveraging InfluxDB and Grafana when executing load tests and demonstrate how these tools are used to visualize performance metrics.
Length: 30 minutes
Session Overview
-------------------------------------------
During this webinar, we will cover the following topics while demonstrating the integrations of JMeter, InfluxDB and Grafana:
- What out-of-the-box solutions are available for real-time monitoring JMeter tests?
- What are the benefits of integrating InfluxDB and Grafana into the load testing stack?
- Which features are provided by Grafana?
- Demonstration of InfluxDB and Grafana using a practice web application
To view the webinar recording, go to:
https://www.rttsweb.com/jmeter-integration-webinar
3. Modified from
Pang et al 2010
Combination of markersEST Sequences
Phylogenomic Data
Morphological Data 18S rDNA
Phylogenomic Data + More ESTs
The position of Ctenophora on the
Metazoan tree is unresolved
4. Placozoa – creeping detritivore/algavore,
diploblastic, continually change shape
Cnidaria – planktonic or sessile predators,
diploblastic, radial symmetry
Basal Metazoans exhibit a wide variety of body plans
and life history strategies
Porifera (Sponges) – sessile filter feeders,
no true tissues, asymmetry
Ctenophora (Comb Jellies) – active
predators in the plankton,
triploblastic, bi-radial symmetry
Joint Genome Institute
5. Andrea Kohn Leonid Moroz
Billie Swalla
Mat Citrella
2010 and 2012
Genomics
Apprenticeships
At FHL
6. The Early Evolution of Nervous System
Development:
Genomics of Pleurobrachiabachia
7. Undergraduate Research
Apprenticeship
Genome Biology
• Undergraduate students engaged in field activities
• Enhance computational skills
• Clone genes and examine gene expression to study evolution of nerve
networks with marine invertebrates as a collaborative research experience.
• Instructors and/or themes vary from year to year
• FHL has housing, dining facilities & a computer classroom
• Students are recruited from UW and other universities
8. Friday Harbor Labs - San Juan Island
Beautiful setting, amazing biological diversity, all students doing research in the course, few
distractions for them.
9. New Computer Lab for teaching Computational Methods
Bioinformatics/Modelling/Phylogenetics/Genomics
10. Specific genes inform us about animals
Cell-Cell adhesion (Collagens) Nathan
Germ Line
(Piwi) - Caleb
(Nanos)-Gabby
Epigenomics (DNMT) - Emily
Cell-Cell signaling (WNTs) - Rebecca
Mesoderm ?
(Brachyury, BarX) - Isaac
(Tropomyosin, Calponin, ß catenin) -
Zander
Neuronal Development (LIMs) - Rachel
Neuronal Signaling (Glutamatergic
pathway) - Josh
Neuropeptides - David
Evolution of Animal Body Plans
Insights from Marine Genomics
FHL Apprenticeship 2012
14. The Apical Organ - one of the
first centralized nervous
systems
Comb Rows
BalancersStatolith
Dome
Polar Fields(PF)
15. The PleurobrachiabacheiGenome
• First ever genome from an
FHL animal to be sequenced.
– Being the first ctenophore
genome is both exciting and
challenging because without
the genomes of related
organisms assembly must be
done de novo.
– Having the genome allows
for comparison of
homologies between phyla –
other attempts to place them
are “speculative”.
• Size of genome = ~100-160
megabases
Photo Credit: Mat Citarella
16. The Pleurobrachia Genome
• Five separate libraries (3 fragmented, 2 paired-end) were
constructed, but satisfactory annotation and assembly of
the genome has not yet been accomplished.
–This is due to short fragments from sequencing technology and
highly repetitive regions of the genome that cause problems in
assembly.
• Currently:
–Sequences: 5,431,390 reads
–Bases: 1,924,202,519 bases
–Coverage: 10X
–Number of Contigs: 211,869
–Average Contig Size: 1,086 base pairs
–Scaffold
18. Importance of The Wnt Signaling
Pathway
• gastrulation
• germ layer specification
• axial polarity
• Patterning of limbs
• Central Nervous System Development
• Wntpathway is oncogenic when mutated
• Evolved in the metazoan common ancestor
22. Wnt Frizzled Dickkopf WIF Ceberus
Homo 19 Yes Yes Yes Yes
Saccoglossus
Branchiostoma 10+? Yes Yes No No
Drosophila 7 Yes No Yes No
Caenorhabditis 5 4 No No No
Capitella 12 Yes No? Yes No?
Lottiagigantea 11 Yes No? Yes No?
Nematostella 11 Yes Yes Yes No
Trichoplax 3 Yes No No No
Amphimedon
3 Yes No No No
Pleurobrachia 3 Yes No No No
Mnemiopsis 4 Yes No No No
Monosiga 0 No No No No
Choanoflagellates
Ctenophores
Sponges
Placozoans
Cnidarians
Deuterostomes
Evolution of Wnt in the Animal Kingdom
Bilaterians
Ecdysozoa
Lophotrochozoa
23. Common Wnt Pathway Components present and
missing in basal metazoans
Gene P. bachei M. leidyi A. queenslandica
Wnt 3 4 3
Frizzled (Fzd) 2 2 2
Secreted-frizzled
related protein
(Srfp)
Present Present Present
LRP Present Present Present
APC No? Partial Present Missing domains
Axin Dix-domain like
protein
Dix-domain like
protein
Axin domain with
no B-Catenin
binding domain
GSK3 Present Present Present
Dishevelled Present Present Present
B-catenin Present Present Present
TCF/LEF Present Present Present
CK1 Present Present Present
groucho Present Present Present
WIF Absent Absent Absent
Dickkopf Absent Absent Absent
Cerberus Absent Absent Absent
CREB-biding
Protein (CBP)
Present Present Present
24. Scientific Conclusions
• Pleurobrachiacan show us the minimum
members ofsignaling pathways needed for
function
• Wnt, TGFßand other developmental signals
areexpressed in adult Pleurobrachia
• There may beinvolved as neurotransmitters in
Pleurobrachia
25. Education Conclusions
• Students learn computational skills easily when
they are immersed in a research experience
• Students become more engaged when they have
their own specific project
• Speaking and writing skills are best taught over a
period of time, with repetition.
• Some students work better in a team, others
individually, but computational analyses allow
flexibility in projects.
26. Acknowledgements
• Wonderful Professors:
Dr. Andrea Kohn,Dr. LenoidMoroz, Dr. Billie
Swalla
• Amazing TAs: Gabrielle Winters, Caleb
Bostwick, Emily Dabe, and Kevin Kocot.
• The Best Bioinformaticians: Mat Citarella
and David Girardo.
• Funding: FHL, NIH, and NSF.
Editor's Notes
Ctenophores- also called comb jellies (Greek- ctene= comb, phore= carry)A phylum of small jelly-filled animals that live all throughout the world in marine habitats.Size- Pleurobrachiabachei – pea sized to large grapeMain feature are their combs or ctenes which are rows of cilia used for swimming. Predators which eat small marine animals.
Ctenophores are one of the most basally branched organisms. Relationship between all the basal metazoans has been an issue of debate. Placozoa- one species in this phyla “trichoplaxadhaerens”Cnidarians – jelliesPorifera – SpongesOur ctenophoresChoanozoa – choanoflagellates - outgroup- single celled organisms that aren’t considered animals, but are the closest relative of animals. Highly debated whether porifera or ctenophora branched off first.This tree supported from ***
Ctenophore anatomy-Highly coordinated ciliary movement and predation skills suggests complex nervous systemApical organ- nervous system structure
Apical organ- early brain?Their basal position in the Metazoa, along with the presence of a nervous system containing a nerve net and an apical organ make ctenophores the ideal candidate for studies concerning the early evolution of the nervous system
WHAT IS A SIGNALING PATHWAY EXPLAIN-Signaling pathway transduces a signal from the outside of the cell to the inside of the cell and interacts in a cascade of events to induce a specific response WHY ARE PLEUROBRACHIA a good system to look at this in??-Because they are a basal metazoan so we can gain key insight onto the early evolution of this pathway.
Things missing in PB-FOUND by doing genome wide search why having a sequenced genome is so nice
EXPLAIN THAT THIS IS ONE OF 3 WNT Genes found in PBWnt domain contains common charactorists of a secretory peptideContains signal peptide N- glycosylation sites22 conserved cysteines used for disulfide bonds
EXPLAIN THAT PB is missing a homolog to WNT A
Explain expansion occurs in common ancestor to cnidarians and bilitarians