This document summarizes research from various institutions on dissecting and utilizing disease QTL for rice and maize. It describes QTL identified for different diseases in rice and maize, near-isogenic lines developed to characterize QTL, and advanced breeding lines with improved disease resistance being tested in Kenya, India, and Indonesia. Results are presented on QTL effects, candidate genes associated with resistance, and histopathological analysis of fungal infection in maize. Deliverables over the project include understanding and dissecting disease traits through QTL mapping, developing resistant lines, and characterizing QTL through near-isogenic lines and histopathology.
3D cultures of Patient derived Gliomas and Breast cancer - Optimized for drug...Rachna Goyal
Three-dimensional (3D) tumor cell culture models have been shown to represent a biologically relevant assay system. We've optimized methods to culture Patient derived Primary tumor cells in 2D & 3D formats. Over 20 + Gliomas and 40+ Breast cancer samples from unique patients have been cultured. These cultures are also enriched in Cancer stem cells !
Pls contact for more details:
Rachna@saarum.com
+91 7032647554
Kinases belong to the family of phosphotransferases and play critical roles in the process known as phosphorylation in which a phosphorylated substrate and ADP are produced.
https://www.creative-biogene.com/products/kinase-stable-cell-lines.html
3D cultures of Patient derived Gliomas and Breast cancer - Optimized for drug...Rachna Goyal
Three-dimensional (3D) tumor cell culture models have been shown to represent a biologically relevant assay system. We've optimized methods to culture Patient derived Primary tumor cells in 2D & 3D formats. Over 20 + Gliomas and 40+ Breast cancer samples from unique patients have been cultured. These cultures are also enriched in Cancer stem cells !
Pls contact for more details:
Rachna@saarum.com
+91 7032647554
Kinases belong to the family of phosphotransferases and play critical roles in the process known as phosphorylation in which a phosphorylated substrate and ADP are produced.
https://www.creative-biogene.com/products/kinase-stable-cell-lines.html
Wolfgang Gruneberg
Biofortified Sweetpotato Available Material, Advances, and Selection Limits
Reuión anual de socios y colaboradores de AgroSalud / 2009
Molecular Identification of Specific Virulence Genes in EnteropathogenicEsche...iosrjce
IOSR Journal of Pharmacy and Biological Sciences(IOSR-JPBS) is a double blind peer reviewed International Journal that provides rapid publication (within a month) of articles in all areas of Pharmacy and Biological Science. The journal welcomes publications of high quality papers on theoretical developments and practical applications in Pharmacy and Biological Science. Original research papers, state-of-the-art reviews, and high quality technical notes are invited for publications.
Aneuploidy in embryos is the leading cause of failure for in vitro fertilization (IVF)
procedures.1 Pre-implantation Genetic Screening (PGS) is used to identify euploid
embryos for implantation to increase successful pregnancies and decrease the number
of cycles required to obtain them. PGS using fluorescence in situ hybridization has
fallen out of favor and been replaced by comparative genome hybridization on
microarrays.1 More recently, high throughput sequencing (HTS) technologies have been
employed for cost-effective PGS on multiple samples.1
We report results using a streamlined Whole Genome Amplification (WGA) and library
generation method followed by HTS and data analysis to detect aneuploidies in single
cells in under 12hr. Using DNA barcodes, we multiplex libraries to reduce the per
sample cost. Our analysis platform compares reads per chromosomal region to an
informatics control built from a baseline of normal cell samples. Using this method, we
show that trisomy of the smallest chromosome (21) can be detected with high sensitivity
and specificity.
Ion Torrent™ semiconductor sequencing, combined with Ion AmpliSeq™ technology, provides simultaneous identification of copy number variants (CNVs), single nucleotide variants (SNVs), and small insertions and deletions (indels) from a research sample by means of a single integrated workflow. 100% of assayed CNV regions (n=34) were detected using a reference set of 31 samples with known chromosomal aberrations. Low-pass whole-genome sequencing data, with approximately 0.01x read coverage, allowed the rapid ≤10 hour analysis of aneuploidies from research samples with extremely low initial input DNA amounts—even from a single cell. Using a control set of 10 samples with known chromosomal aberrations, 100% of the copy number changes were found, ranging from gains or losses of whole chromosomes to subchromosomal alterations tens of megabases (Mb) in size. The Ion PGM™ System minimizes the high cost and complexity of next-generation sequencing and, with Ion Reporter™ Software, facilitates user-defined CNV and aneuploidy detection, with three sensitivity options so that copy number analysis workflows can be tuned to achieve desired levels of sensitivity and specificity.
iDiffIR: Identifying differential intron retention from RNA-seqAraport
iDiffIR is a method for identifying differential intron retention from RNA-seq. For more information, please visit http://combi.cs.colostate.edu/idiffir/
Validation of shoot fly resistance introgression lines using SNP markers in S...ICRISAT
Shoot fly is one of the most destructive pest in sorghum causing up to 80% grain and 68% fodder losses. Management of shoot fly with host plant resistance is the most effective means to reduce shoot fly damage as compared to other management practices. In this study, the shoot fly QTL introgressed lines were validated using singlenucleotide polymorphism (SNP) markers tightly linked to shoot fly resistant QTLs.
Results from a Interlaboratory exercise to evaluate NSP kits (C. Browning)EuFMD
The European Commission for the Control of Foot-and-Mouth Disease (EuFMD), one of FAO’s oldest Commissions, came into being on the 12th June 1954, with the pledge of the sixth founding member state to the principles of a coordinated and common action against Foot-and-mouth Disease.
Wolfgang Gruneberg
Biofortified Sweetpotato Available Material, Advances, and Selection Limits
Reuión anual de socios y colaboradores de AgroSalud / 2009
Molecular Identification of Specific Virulence Genes in EnteropathogenicEsche...iosrjce
IOSR Journal of Pharmacy and Biological Sciences(IOSR-JPBS) is a double blind peer reviewed International Journal that provides rapid publication (within a month) of articles in all areas of Pharmacy and Biological Science. The journal welcomes publications of high quality papers on theoretical developments and practical applications in Pharmacy and Biological Science. Original research papers, state-of-the-art reviews, and high quality technical notes are invited for publications.
Aneuploidy in embryos is the leading cause of failure for in vitro fertilization (IVF)
procedures.1 Pre-implantation Genetic Screening (PGS) is used to identify euploid
embryos for implantation to increase successful pregnancies and decrease the number
of cycles required to obtain them. PGS using fluorescence in situ hybridization has
fallen out of favor and been replaced by comparative genome hybridization on
microarrays.1 More recently, high throughput sequencing (HTS) technologies have been
employed for cost-effective PGS on multiple samples.1
We report results using a streamlined Whole Genome Amplification (WGA) and library
generation method followed by HTS and data analysis to detect aneuploidies in single
cells in under 12hr. Using DNA barcodes, we multiplex libraries to reduce the per
sample cost. Our analysis platform compares reads per chromosomal region to an
informatics control built from a baseline of normal cell samples. Using this method, we
show that trisomy of the smallest chromosome (21) can be detected with high sensitivity
and specificity.
Ion Torrent™ semiconductor sequencing, combined with Ion AmpliSeq™ technology, provides simultaneous identification of copy number variants (CNVs), single nucleotide variants (SNVs), and small insertions and deletions (indels) from a research sample by means of a single integrated workflow. 100% of assayed CNV regions (n=34) were detected using a reference set of 31 samples with known chromosomal aberrations. Low-pass whole-genome sequencing data, with approximately 0.01x read coverage, allowed the rapid ≤10 hour analysis of aneuploidies from research samples with extremely low initial input DNA amounts—even from a single cell. Using a control set of 10 samples with known chromosomal aberrations, 100% of the copy number changes were found, ranging from gains or losses of whole chromosomes to subchromosomal alterations tens of megabases (Mb) in size. The Ion PGM™ System minimizes the high cost and complexity of next-generation sequencing and, with Ion Reporter™ Software, facilitates user-defined CNV and aneuploidy detection, with three sensitivity options so that copy number analysis workflows can be tuned to achieve desired levels of sensitivity and specificity.
iDiffIR: Identifying differential intron retention from RNA-seqAraport
iDiffIR is a method for identifying differential intron retention from RNA-seq. For more information, please visit http://combi.cs.colostate.edu/idiffir/
Validation of shoot fly resistance introgression lines using SNP markers in S...ICRISAT
Shoot fly is one of the most destructive pest in sorghum causing up to 80% grain and 68% fodder losses. Management of shoot fly with host plant resistance is the most effective means to reduce shoot fly damage as compared to other management practices. In this study, the shoot fly QTL introgressed lines were validated using singlenucleotide polymorphism (SNP) markers tightly linked to shoot fly resistant QTLs.
Results from a Interlaboratory exercise to evaluate NSP kits (C. Browning)EuFMD
The European Commission for the Control of Foot-and-Mouth Disease (EuFMD), one of FAO’s oldest Commissions, came into being on the 12th June 1954, with the pledge of the sixth founding member state to the principles of a coordinated and common action against Foot-and-mouth Disease.
Rice breeding is both challenged and benefited by the fact that a successful varietal improvement program must embrace both the integration single genes that segregate in a simple Mendelian fashion as well as complex traits that are inherited in more quantitative ways. For decades the rice genetics community has produced a wealth of knowledge about these single genes and has developed markers that allow a breeder to track them in a population. However, marker assisted selection (MAS) alone is insufficient to drive the rates of genetic gain for more complex traits that are equally necessary. This presentation will describe the attempts made in the Favorable Environments Breeding program at IRRI to integrate the selection for single genes appropriate for MAS into a more complex population improvement strategy designed to improve quantitatively inherited traits.
M. Bonierbale, E. Mihovilovich, W. Amoros, J. Landeo and M. Orrillo
Sustaining and Projecting Genetic Diversity for Potatoes Adapted To Changing Environments
14th Australasian Plant Breeding and 11th SABRAO Conference, Cairns, Queensland, Australia, 10-14 August 2009
AGBT 2013: Home Brewed Personalized Genomics - The Quest for Meaningful Analy...Golden Helix Inc
Personalized genomics may be moving into a new era with whole-exome and whole-genome sequencing becoming affordable and available to consumers. 23andMe recently piloted a more affordable 80x exome to their existing customers. But it remains to be seen whether this wealth of raw genomic data can be analyzed to provide meaningful results for both healthy and symptomatic individuals.
By acquiring 23andMe exomes on his family, Gabe puts himself in the position of a bioinformatically inclined consumer, but non-clinician, to approach this question with his own analysis. His trio consists of a healthy father and son, and a mother with clinically-diagnosed idiopathic rheumatoid arthritis.
The following goals were set for the analysis: 1) How accurate are variant calls from direct-to-consumer NGS services? 2) How useful and durable is the list of risk variants provided by 23andMe? 3) Can a healthy individual's exome provide additional risk information over standard genotype-array-based risk prediction? and 4) Can the state of our current understanding of the complex genomic architecture of autoimmune diseases be enough to to find potential driver variants and genes to explain the diagnosis of a single case?
Here Gabe presents his findings of this analysis and discuss how individualized genomics might change in the world of affordable sequencing.
Cip bangladesh research reports on potato-2009-10Mohidul Hasan
CIP-Bangladesh Annual Report 2009-10 compiled by Md. Mohidul Hasan. There are 5 experiments were looking at different locations of Bangladesh and presented at home and abroad by Md. Mohidul Hasan. Laght Blight, Virus, heat, salt and drought tolerance trials were conduct by Md. Mohidul Hasan Manik.
Advances in host plant resistance and identification of broad-based stable so...ICRISAT
Host Plant Resistance is the most effective and economical management option for Fusarium wilt (Fusarium udum Butler) of pigeonpea (Figure 1) either alone or as a major component of IDM. The disease can cause yield losses of up to 100% in susceptible cultivars. ICRISAT has developed large numbers of high yielding wilt resistant lines by selecting them under high disease pressure in field screening. These resistant lines if found to possess stable resistance across locations, could be utilized in pigeonpea disease resistance breeding program.
Presentation made by the GCP Director during the CGIAR Fund Council (FC) visit to CIMMYT (GCP's host), on the sidelines of the FC meeting in Mexico in May 2014.
Presentation by the GCP Director at an international workshop on genomics and integrated breeding, February 2014. More on the workshop: http://bit.ly/MwpliD You can also view the presentation on video here: http://bit.ly/1mVmVdS
A quick introduction to the CGIAR Generation Challenge Programme (GCP) -- its history, network, research organisation, outputs and challenges. GCP is a virtual network of partnerships working on modern crop breeding for food security
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
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.
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
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.
ARM 2008: Dissection, characterisation and utilisation of disease QTL -- R Nelson
1. Indonesia
- Bustamam
- Utut
KARI
- Gethi
Cornell
Dissection,
characterization
and utilization
of disease QTL
IRRI
- Vera Cruz
- Leung
- Brar
CSU
- Leach
- Nelson
- Smith
NCSU
- Balint-Kurti
Rice Maize
Generation Challenge
Program
Project #8
Update 2008
2. 5 6 7 8 9
10
9
8
7
6
5
Gray Leaf Spot E-MBLUP
Northern Leaf Blight E-MBLUP
disease GLS NLB
SLB ***0.61 ***0.62
GLS - ***0.45
SLB
a: Unknown gene
b: tasselseed2
c: Glutathione S-Transferase
4
GLS
NLB
3
2
1
Randy Wisser
1 2 3 4 5 6 7 8 9
1 2 3 4
0
Southern Leaf Blight E-MBLUP
E
E
Association mapping
population (Buckler;
n=~300): 11 datasets
for three diseases
-0.4 -0.2 0.0 0.2 0.4 0.6 0.8 1.0
allele effect
a
b
c
{
{
{
3. QTL identified in NAM for NLB , SLB and GLS
0 QTL identified in NAM for NLB , SLB and GLS
-1
-2
-3
-4
-5
Nested association
mapping population
(Buckler et al.; n=5,000):
6 datasets for 3 diseases
FLECKS
-6
-7
-8
-9
-10
SLB
NLB
GLS
12 of 13 NLB-QTL in full NAM
analysis are present both years
K. Kump/PBK et al., NCSU; J. Poland and J. Benson/RJN et al., CU
6. NLB:
histopathology
Field
Infection efficiency (2 days after inoculation)
0
0.2
0.4
0.6
0.8
1
Tx3 03
B73
Maize genotype
TBBC3_38_05F
T BBC 3_42 _10E _2
I n f e c ti o n e ffi c i e n c y
(s u c c e s s f u l in f e c t io n /
g e rm in a t e d c o n id ia )
Tx303 allele at the NLB QTL
in bin 1.06
QTL x E
reduces fungal penetration
SLB: Field
Growth Chamber
Incidence of E. turcicum growing into the xylem
(4 days after inoculation)
0
0.1
0.2
0.3
0.4
0.5
0.6
Tx303
B73
Maize genotype
TBBC3_38_05F
TBBC3_42_10E_2
Incidence
(hyphae in xylem / infection site)
B73 allele at the NLB QTL in
bin 1.02
More robust relative to
reduces fungal colonization
environments?
of the vasculature
7. QTL isolines with impressive phenotypic effects
in the field
+ QTL – chr. 6 - QTL – chr. 6 + QTL – 1.02 - QTL – 1.02
8. A. flavus biomass estimated by
Quantitative Real-Time PCR is
strongly correlated with aflatoxin
concentration
4
3
2
1
0
log Infection Coefficient
2 3 4 5 6 7 8
log (ppb+1)
A. flavus Infection Coefficient (log IC)
Aflatoxin Concentration (log ppb)
Pearson correlation == 00..8855**** nn==2200
QTL mapping for
silk and young
kernel resistance
to colonization
• CML322 x B73 RILs
• Tx303 NILs (B73 background)
Bin 7.02-7.03
• CML52 HIFs (B73) Bin 6.05
To be confirmed with 2008 field data (analysis in progress) S. Mideros, Cornell
11. Deliverables over project lifetime
• Understanding the trait
• Dissecting the trait
– QTL syntheses: published
– Selection mapping: published
– Deletion mapping by dot-blot &
microarray: pub. & submitted
– Large-scale QTL analyses
• SLB, NLB and GLS
– Sets of QTL NILs (maize, rice)
– Deletions in 14 rice mutants
– Association analysis for MDR: in mapped
preparation
– Phylogenomics of candidate genes
– Win-win and win-lose QTL
• Improving the trait
– QTL characterization
– Histopathology
– Fine-mapping in progress for
several QTL in maize
– Maize lines with MDR in advanced trials in Kenya
– Disease resistant elite rice lines in India and
Indonesia