This document provides evidence of recombination between the Sr2 and Fhb1 genes in wheat. It summarizes that a doubled haploid population from a cross between Carberry and AC Cadillac wheat lines showed: 1) recombinants expressing both pseudo-black chaff (PBC, linked to Sr2) and low Fusarium head blight (FHB, linked to Fhb1), 2) genetic mapping identified QTL in the Sr2/Fhb1 region associated with both traits, and 3) haplotype analysis identified recombinants with the Sr2 and Fhb1 marker haplotypes separated.
Chromatin looping as a target for altering gene expressionIvan Krivega
The β-hemoglobinopathies are the most common monogenic disorders in humans, with symptoms arising after birth when the fetal γ-globin genes are silenced and the adult β-globin gene is activated. There is a growing appreciation that genome organization and the folding of chromosomes are key determinants of gene transcription. Underlying this function is the activity of transcriptional enhancers that increase the transcription of target genes over long linear distances. To accomplish this, enhancers engage in close physical contact with target promoters through chromosome folding or looping that is orchestrated by protein complexes that bind to both sites and stabilize their interaction. We find that enhancer activity can be redirected with concomitant changes in gene transcription. Both targeting the β-globin locus control region (LCR) to the γ-globin gene in adult erythroid cells by tethering and epigenetic unmasking of a silenced γ-globin gene lead to increased frequency of LCR/γ-globin contacts and reduced LCR/β-globin contacts. The outcome of these manipulations is robust, pancellular γ-globin transcription activation with a concomitant reduction in β-globin transcription. These examples show that chromosome looping may be considered a therapeutic target for gene activation in β-thalassemia and sickle cell disease.
An approach to describing and analysing bulk biological annotation quality: a...Michael Bell
Motivation:
Annotations are a key feature of many biological databases, used to convey our knowledge of a sequence to the reader. Ideally, annotations are curated manually, however manual curation is costly, time consuming and requires expert knowledge and training. Given these issues and the exponential increase of data, many databases implement automated annotation pipelines in an attempt to avoid un-annotated entries. Both manual and automated annotations vary in quality between databases and annotators, making assessment of annotation reliability problematic for users. The community lacks a generic measure for determining annotation quality and correctness, which we look at addressing within this work. Specifically we investigate word reuse within bulk textual annotations and relate this to Zipf's Principle of Least Effort. We use UniProt Knowledge Base (UniProtKB) as a case study to demonstrate this approach since it allows us to compare annotation change, both over time and between automated and manually curated annotations.
Results:
By applying power-law distributions to word reuse in annotation, we show clear trends in UniProtKB over time, which are consistent with existing studies of quality on free text English. Further, we show a clear distinction between manual and automated analysis and investigate cohorts of protein records as they mature. These results suggest that this approach holds distinct promise as a mechanism for judging annotation quality.
For more information available at the authors website: www.michaeljbell.co.uk
Chromatin looping as a target for altering gene expressionIvan Krivega
The β-hemoglobinopathies are the most common monogenic disorders in humans, with symptoms arising after birth when the fetal γ-globin genes are silenced and the adult β-globin gene is activated. There is a growing appreciation that genome organization and the folding of chromosomes are key determinants of gene transcription. Underlying this function is the activity of transcriptional enhancers that increase the transcription of target genes over long linear distances. To accomplish this, enhancers engage in close physical contact with target promoters through chromosome folding or looping that is orchestrated by protein complexes that bind to both sites and stabilize their interaction. We find that enhancer activity can be redirected with concomitant changes in gene transcription. Both targeting the β-globin locus control region (LCR) to the γ-globin gene in adult erythroid cells by tethering and epigenetic unmasking of a silenced γ-globin gene lead to increased frequency of LCR/γ-globin contacts and reduced LCR/β-globin contacts. The outcome of these manipulations is robust, pancellular γ-globin transcription activation with a concomitant reduction in β-globin transcription. These examples show that chromosome looping may be considered a therapeutic target for gene activation in β-thalassemia and sickle cell disease.
An approach to describing and analysing bulk biological annotation quality: a...Michael Bell
Motivation:
Annotations are a key feature of many biological databases, used to convey our knowledge of a sequence to the reader. Ideally, annotations are curated manually, however manual curation is costly, time consuming and requires expert knowledge and training. Given these issues and the exponential increase of data, many databases implement automated annotation pipelines in an attempt to avoid un-annotated entries. Both manual and automated annotations vary in quality between databases and annotators, making assessment of annotation reliability problematic for users. The community lacks a generic measure for determining annotation quality and correctness, which we look at addressing within this work. Specifically we investigate word reuse within bulk textual annotations and relate this to Zipf's Principle of Least Effort. We use UniProt Knowledge Base (UniProtKB) as a case study to demonstrate this approach since it allows us to compare annotation change, both over time and between automated and manually curated annotations.
Results:
By applying power-law distributions to word reuse in annotation, we show clear trends in UniProtKB over time, which are consistent with existing studies of quality on free text English. Further, we show a clear distinction between manual and automated analysis and investigate cohorts of protein records as they mature. These results suggest that this approach holds distinct promise as a mechanism for judging annotation quality.
For more information available at the authors website: www.michaeljbell.co.uk
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/
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.
Key Trends Shaping the Future of Infrastructure.pdfCheryl Hung
Keynote at DIGIT West Expo, Glasgow on 29 May 2024.
Cheryl Hung, ochery.com
Sr Director, Infrastructure Ecosystem, Arm.
The key trends across hardware, cloud and open-source; exploring how these areas are likely to mature and develop over the short and long-term, and then considering how organisations can position themselves to adapt and thrive.
Generating a custom Ruby SDK for your web service or Rails API using Smithyg2nightmarescribd
Have you ever wanted a Ruby client API to communicate with your web service? Smithy is a protocol-agnostic language for defining services and SDKs. Smithy Ruby is an implementation of Smithy that generates a Ruby SDK using a Smithy model. In this talk, we will explore Smithy and Smithy Ruby to learn how to generate custom feature-rich SDKs that can communicate with any web service, such as a Rails JSON API.
UiPath Test Automation using UiPath Test Suite series, part 4DianaGray10
Welcome to UiPath Test Automation using UiPath Test Suite series part 4. In this session, we will cover Test Manager overview along with SAP heatmap.
The UiPath Test Manager overview with SAP heatmap webinar offers a concise yet comprehensive exploration of the role of a Test Manager within SAP environments, coupled with the utilization of heatmaps for effective testing strategies.
Participants will gain insights into the responsibilities, challenges, and best practices associated with test management in SAP projects. Additionally, the webinar delves into the significance of heatmaps as a visual aid for identifying testing priorities, areas of risk, and resource allocation within SAP landscapes. Through this session, attendees can expect to enhance their understanding of test management principles while learning practical approaches to optimize testing processes in SAP environments using heatmap visualization techniques
What will you get from this session?
1. Insights into SAP testing best practices
2. Heatmap utilization for testing
3. Optimization of testing processes
4. Demo
Topics covered:
Execution from the test manager
Orchestrator execution result
Defect reporting
SAP heatmap example with demo
Speaker:
Deepak Rai, Automation Practice Lead, Boundaryless Group and UiPath MVP
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.
Encryption in Microsoft 365 - ExpertsLive Netherlands 2024Albert Hoitingh
In this session I delve into the encryption technology used in Microsoft 365 and Microsoft Purview. Including the concepts of Customer Key and Double Key Encryption.
DevOps and Testing slides at DASA ConnectKari Kakkonen
My and Rik Marselis slides at 30.5.2024 DASA Connect conference. We discuss about what is testing, then what is agile testing and finally what is Testing in DevOps. Finally we had lovely workshop with the participants trying to find out different ways to think about quality and testing in different parts of the DevOps infinity loop.
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
Elevating Tactical DDD Patterns Through Object CalisthenicsDorra BARTAGUIZ
After immersing yourself in the blue book and its red counterpart, attending DDD-focused conferences, and applying tactical patterns, you're left with a crucial question: How do I ensure my design is effective? Tactical patterns within Domain-Driven Design (DDD) serve as guiding principles for creating clear and manageable domain models. However, achieving success with these patterns requires additional guidance. Interestingly, we've observed that a set of constraints initially designed for training purposes remarkably aligns with effective pattern implementation, offering a more ‘mechanical’ approach. Let's explore together how Object Calisthenics can elevate the design of your tactical DDD patterns, offering concrete help for those venturing into DDD for the first time!
Builder.ai Founder Sachin Dev Duggal's Strategic Approach to Create an Innova...Ramesh Iyer
In today's fast-changing business world, Companies that adapt and embrace new ideas often need help to keep up with the competition. However, fostering a culture of innovation takes much work. It takes vision, leadership and willingness to take risks in the right proportion. Sachin Dev Duggal, co-founder of Builder.ai, has perfected the art of this balance, creating a company culture where creativity and growth are nurtured at each stage.
Designing Great Products: The Power of Design and Leadership by Chief Designe...
2014 bgri de pauw presentation
1. Evidence for Recombination of
Sr2 and Fhb1
#bgri2014 #Borlaug100
R.M. DePauw, R.D. Cuthbert, R.E. Knox, S.
Kumar, A. Singh, A.K. Singh, H. Campbell, S.
Bhavani, D. Singh, F.R. Clarke, and T. Fetch
2. Outline
• Background on genes Sr2 and Fhb1
• Objective: to generate evidence of recombination of
Sr2 and Fhb1 resistance from repulsion to coupling
• Genetic Materials: Carberry/AC Cadillac
• Evidence:
– Pedigree
– Phenotype
– FHB resistance with PBC and stem rust resistance
– Haplotype
2
3. Background: Sr2
– Durable adult plant stem rust resistant gene
– Partial resistance
– Enhances expression of other Lr and Yr rust resistance genes
– 3BS (Yaroslav emmer to Hope and H.44-24 etc)
– QTL analysis of stem rust co-segregation with (microsatellite)
markers in the region of gwm533 and gwm493
– SNP marker XcsSr2 co-segregated with Sr2which is closest
reported marker to date (Mago et al. 2011)
– Tightly linked to PBC (Kota et al. 2006)
– Fine mapping studies have identified recombinants in the region
of gwm533 and gwm493 (Kota et al. 2006, McNeil et al. 2008)
4. Background: Fhb1
– Confers resistance to FHB, a major fungal disease causing loss
of yield and grain quality (mycotoxins harmful to human and
animal health).
– Resistance on 3BS (from landrace Taiwan wheat to Sumai 3).
– QTL analysis of FHB detected co-segregation with
(microsatellite) markers in the region of gwm533 and gwm493.
– Current most tightly linked markers are Xsnp7 and Xsnp11,
Xsts256, and Xsts3B-138 (Bernardo et al. 2012)
– Fine mapping studies have identified recombinants in the
region of gwm533 and gwm493 (Cuthbert et al. 2006, Bernardo et al. 2012).
5. Background:
• Sr2 and Fhb1 are linked with QTL in the Sr2/Fhb1 region
of gwm533 and gwm493 on 3BS.
• ~ 5 cM apart (Bernardo et al. 2012)
• Sr2 and Fhb1 are currently reported only in repulsion.
8. Objective:
• To identify a recombinant of Sr2 and Fhb1 in
coupling from the doubled haploid population of
Carberry/AC Cadillac
• Null Hypothesis: PBC(Sr2) and low FHB will not be
expressed together in a DH line
• Evidence for recombination: a DH line which
expresses both PBC and low FHB symptoms
9. Parental Materials
• AC Cadillac
– resistant to stem rust
– moderately susceptible to FHB
– expresses molecular marker products linked to Sr2
but not to Fhb1 resistance
• Carberry
– resistant to stem rust
– moderately resistant to FHB
– displays molecular marker products linked to Fhb1
but not to Sr2 resistance
• Both parents have gene Lr34/Yr18/Sr57/Pm38/Ltn1 (7DS)
10. Genotyping of the population
• Carberry/AC Cadillac
– Phenotyped 261 DH line subset of doubled haploid
population of 812 lines
• Genotyped with DArT® (578), SSR (54), BAC-derived
(3), CAPS (3), and STS (3) molecular markers
including:
• SSR marker Xumn10 (SNP: Xsnp3BS-11) is reported to be
most diagnostic for Fhb1 (Bernardo et al. 2012)
• XcsSr2 is reported to be most diagnostic for Sr2 (Mago et al.
2011)
11. Evidence: Pedigree
AC Cadillac
Carberry
Thatcher
Hope
H44-24
Marquis
Yaroslav
Emmer
Sumai
#3
AC Cadillac
1.00
Carberry
0.16
1.00
Thatcher
0.60
0.23
1.00
Hope
0.16
0.15
0.25
1.00
H44-24
0.16
0.12
0.25
0.50
1.00
Marquis
0.31
0.18
0.50
0.50
0.50
1.00
Yaroslav
Emmer
0.01
0.05
0.00
0.50
0.50
0.00
1.00
Sumai #3
0.01
0.03
0.00
0.00
0.00
0.00
0.00
1.00
• Both AC Cadillac and Carberry have Yaroslav emmer in their
genealogy
• Only Carberry has Sumai #3 in genealogy
14. Evidence: Stem Rust and Genetic analysis
Stem rust field nurseries:
• Njoro, Kenya: 2010, 11, 12, 13
• Swift Current, Canada: 2011 and 2012, and 2013
Stem Rust QTL (Singh et al. TAG 2013)
• AC Cadillac contributed stem rust resistance QTL on
chromosomes 2B, 3B, 5B, 6D, 7B and 7D
• Carberry contributed resistance QTL on 4B and 5A.
• Epistatic interactions were observed between loci on
6D and 3B
15. Yellow Rust
• Swift Current, Canada in 2011
• Lincoln, NZ: 2012, 2013
• Njoro, Kenya: 2009, 2011
Yellow Rust QTL
• AC Cadillac was a source of yellow rust resistance
QTL on chromosomes 2A, 2B, 3A, 3B, 5B, and 7B
• Carberry was a source of resistance on
chromosomes 2B, 4B, and 7A. (Singh et al. 2014)
Evidence: Yellow Rust and Genetic Analysis
16. Co-location:
• Yellow rust resistance QTL co-localized with stem
rust resistance QTL on 2B, 3B, and 7B.
• Sr2 and Yr30 reported in same region 3BS
Evidence: Genetic analysis
17. Epistatic Interactions:
• Several epistatic interactions were identified both
for yellow and leaf rust resistance QTL
Trait Environment QTLa
1 QTLb
2
Yr severity Kenya QYr.spa-3B .1 QYr.spa-2B
Lr severity Canada QLr.spa-3B QLr.spa-4B
Yr infection response New Zealand QYr.spa-3B.1 QYr.spa-2A
Yr infection response New Zealand QYr.spa-3B.1 QYr.spa-7B.2
First QTL1
Second QTL2
Source: Singh et al. TAG 2014 (in press)
Evidence:
18. Evidence: Fusarium Head Blight
• FHB nurseries
• PLP 2010, 2011, 2013
• Variables: Incidence, Severity:
Disease Index = (Incidence * Severity)/100
• QTL in AC Cadillac 4B
• QTL in Carberry 3B, 5A, 6D
19. Evidence: Pseudo Black Chaff
• PBC is a dark pigmentation that may occur on the
glumes, peduncle and below stem internodes, but its
level of expression varies with genetic background and
environment.
• Linkage of Sr2 and PBC has not been broken in about 90
yrs
• PBC scoring: an expression in 6 nurseries out of 12
• QTL for pseudo-black chaff:
– AC Cadillac 2B and 3B
– Carberry 6A
23. Genotypic Data Phenotyping
Carberry/AC Cadillac: Haplotpye + Phenotype
Sr2/Pbc
Fhb1
gwm389
csSr2
3B028F08
3B042G11
gwm533
wPt-7341
wPt-8855
wPt-2757
wPt-8446
wPt-1620
wPt-7984
BArc75
wPt-3260
wPt-744251
wPt-1484
wPt-10972
wPt-9066
Barc147
sts3B-142
UMN10
FhbIndex
PBC(#Environment)
SeveritySr
InfectiontypeSr
AC Cadillac
A A A A A A A A A A A A A A A A A A A A 31 6 3 R
Carberry
B B B B B B B B B B B B B B B B B B B B 22 1 5 R
B0767&AT073
B B B A A - B B B B B B B B B B B B B B 15 1 3 R
B0767&BF021
B B B A A B B B B B B B B B B B B B B B 12 2 10 R
B0767&BF115
B B A A A B B B B - B B B B B B B B B B 5 1 15 R
24. Summary of evidence
• Carberry/AC Cadillac: 261 DH phenotyped
• Evidence provided for Sr2 and FHB1: pedigree,
phenotype, genotype
• DH lines expressed variation for: FHB; Stem, Yellow, &
Leaf rust resistance; PBC
• QTL on 3B detected for FHB; Stem, Yellow, & Leaf rust
resistance; PBC
• Co-location of QTL for Sr and Yr and Epistatic
interactions Sr and Yr, and Sr and Lr
• Recovered recombinants with PBC and FHB resistance
• Haplotype recombination in Sr2/Fbh1 region based on
markers reported to be closest linked
25. Acknowledgements
• Colleagues and Support Staff at:
• AAFC, Swift Current, Lethbridge and Winnipeg,
Canada
• CIMMYT, Kenya
• KARI, Njoro, Kenya
• Plant and Food Research, Lincoln, New Zealand
• Funders:
– levy by Farmers of western Canada administered by
Western Grains Research Foundation
– AAFC: Growing Forward and core funding