Genetic Improvement of Indica Group Rice Through Wide HybridizationDr. Md. Nashir Uddin
Indica Group Rice Cultivar IR64 was recurrently crossed with Japonica Group Rice (New Plant Type originated from Indonesia) and developed the Introgression lines (INLs). These INLs showed 30 to 40% increment of Yield than IR64. This wide hybridization method is very useful for crop improvement including rice.
Genome-wide association study (GWAS) technology has been a primary method for identifying the genes responsible for diseases and other traits for the past ten years. GWAS continues to be highly relevant as a scientific method. Over 2,000 human GWAS reports now appear in scientific journals. Our free eBook aims to explain the basic steps and concepts to complete a GWAS experiment.
Genetic Improvement of Indica Group Rice Through Wide HybridizationDr. Md. Nashir Uddin
Indica Group Rice Cultivar IR64 was recurrently crossed with Japonica Group Rice (New Plant Type originated from Indonesia) and developed the Introgression lines (INLs). These INLs showed 30 to 40% increment of Yield than IR64. This wide hybridization method is very useful for crop improvement including rice.
Genome-wide association study (GWAS) technology has been a primary method for identifying the genes responsible for diseases and other traits for the past ten years. GWAS continues to be highly relevant as a scientific method. Over 2,000 human GWAS reports now appear in scientific journals. Our free eBook aims to explain the basic steps and concepts to complete a GWAS experiment.
Breed composition evaluation based on genetic makersILRI
Presented by Yi Zhang (College of Animal Science and Technology, China Agricultural University, Beijing) at the Inception workshop of the AgriTT project: Evaluation of breed composition, productivity and fitness for smallholder dairy cattle in Tanzania, Dar es Salaam, 10-11 June 2014
What can your dog teach you about Genetics?rlanchantin
The following is a presentation to supplement a genetics class. The intention is to help build interest by showing dog breeding and how the scientific method has uncovered remarkable information about the morphological changes in dog breeds.
This presentation covers the basic terminology and key parameters of Population Genetics. Presentation is helpful for the students of Life Sciences and Evolutionary biology.
Read about the Child Life Internship Program at East Tennessee Children's Hospital: http://www.etch.com/employment/internships_professional_education.aspx
Breed composition evaluation based on genetic makersILRI
Presented by Yi Zhang (College of Animal Science and Technology, China Agricultural University, Beijing) at the Inception workshop of the AgriTT project: Evaluation of breed composition, productivity and fitness for smallholder dairy cattle in Tanzania, Dar es Salaam, 10-11 June 2014
What can your dog teach you about Genetics?rlanchantin
The following is a presentation to supplement a genetics class. The intention is to help build interest by showing dog breeding and how the scientific method has uncovered remarkable information about the morphological changes in dog breeds.
This presentation covers the basic terminology and key parameters of Population Genetics. Presentation is helpful for the students of Life Sciences and Evolutionary biology.
Read about the Child Life Internship Program at East Tennessee Children's Hospital: http://www.etch.com/employment/internships_professional_education.aspx
This lecture covers some nice stories about the origins of the words "genome" and the derived word "genomics". the lecture also introduces viral, bacterial, and eukaryotic genomes.
Presentation delivered by Dr. Jesse Poland (Kansas State University, USA) at Borlaug Summit on Wheat for Food Security. March 25 - 28, 2014, Ciudad Obregon, Mexico.
http://www.borlaug100.org
A presentation as a webinar for the Winn Feline Foundation that focuses on recent findings related to the signatures of selection in the domestic cat genome
This was my presentation at the Plant and Animal Genome Conference 2019 in San Diego. My talk was a presentation of the thesis project of my student Mona Abdi. The focus of the presentation and project was the genomic signatures of selection in the domestic cat breeds.
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.
Resource use efficiency in livestock: Bridging the biotechnology-livestock pr...ExternalEvents
Resource use efficiency in livestock: Bridging the biotechnology-livestock productivity gap in East Africa presentation by Denis Mujibi, Nelson Mandela African Institute for Science and Technology, Arusha, Tanzania
Development of a high-throughput high-density SNP genotyping array for bovineAffymetrix
Ali Pirani, Bioinformatics, Affymetrix.Our bioinformatics team first developed a workflow for validating de novo SNPs in animals. They have since applied this successfully in multiple plant species.
DNA fingerprint methods. • The locations for genes for specific traits such as egg number, body weight or carcass quality can be identified using markers and then they can be selected directly.
Taras Oleksyk at #ICG12: Innovative assembly strategy contributes to the unde...GigaScience, BGI Hong Kong
Taras Oleksyk at the GigaScience Prize Track at ICG: Innovative assembly strategy contributes to the understanding of evolution and conservation genetics of the critically endangered Solenodon paradoxus from the island of Hispaniola, #ICG12 in Shenzhen, 26th October 2017
The material of a talk that I prepared to give in the online camel conference of Oman. Unfortunately, I had a death in the family the day before the conference and the material was presented by my friend Dr. Mohammed Alabri from Oman. The material is in Arabic and focused for camel breeders.
The material of a two days workshop that I gave at Sultan Qaboos University in Oman about the importance of livestock biobanks and how to establish an organized one. The workshop was given in Arabic.
This is a my lecture about camels title "Journey around the camel". The lecture was in Arabic and is related to a book under preparation with the same title. This part of the journey around the camel introduces the major camel breeds in the Arabian Peninsula and their external phenotypes and groupings.
This lecture covers key findings to the development of genomics as a field. This first part covers briefly Mendel to knowing that DNA is the genetic material by Hershey and Chase
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
This pdf is about the Schizophrenia.
For more details visit on YouTube; @SELF-EXPLANATORY;
https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos
Thanks...!
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
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.
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
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.
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.
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.
1. Hasan Alhaddad, Ph.D.
Kuwait University
January 2016 - University of Missouri
Degree of Bengalness:
A measure of the genomic contribution of Asian
Leopard Cats into Bengal breed cats
2. Barbara Gandolfi
Hasan Alhaddad
Mike Montague
Mona Abdi
Erica K Creighton
Bianca Haase
Maria Longeri
Rashid Saif
Carlyn Peterson
Brian Davis
William Murphy
Ettore Randi
Shannon Joslin
Grace Lan
Jeff Brockman
Mike Hamilton
Nick Dodman
Richard Malik
Clare Rusbridge
Nick Gustafson
Diane Shelton
Robert A Grahn
Jens Haggstrom
Serina Filler
Hannes Lohi
James C Mullikin
Chris Helps
Niels C Pedersen
Wes Warren
Leslie A Lyons
A work team & a teamwork
3. Outline
• Introduction
•Aim1 - Diagnostic panel
•Aim2 - Degree of Bengalness
•Aim3 - Bengal breed
•Conclusion and significance
4. Outline
• Introduction
• Asian Leopard cat and the domestic
cat
• Hybridization and Bengal breed
• Aims
• Aim1 - Diagnostic panel
• Aim2 - Degree of Bengalness
• Aim3 - Bengal breed
• Conclusion and significance
• Introduction
• Asian Leopard cat and the domestic
cat
• Hybridization and Bengal breed
• Aims
5. Introduction
Fig. 5. Relationships among species of Felidae, continued from Fig. 4. Numbers are posterior probability values with a second number representing sup
I. Agnarsson et al. / Molecular Phylogenetics and Evolution 54 (2010) 726–745
I. Agnarsson et al. / Molecular Phylogenetics and Evolution 54 (2010) 726–745 737
P. bengalensis and F.s. catus
Fig. 5. Relationships among species of Felidae, continued from Fig. 4. Numbers are posterior probability values with a second number representing sup
I. Agnarsson et al. / Molecular Phylogenetics and Evolution 54 (2010) 726–745
7. AIMS
1- Diagnostic panel
Identify diagnostic markers of Asian Leopard
Cat (ALC) alleles in the Feline SNP array
2 - Degree of Bengalness
Estimate ALC allele proportions in known
pedigree, Bengal breed, and other cat breeds
3 - Bengal breed
Use “Degree of Bengalness” to understand
and maintain Bengal cat breed
8. AIMS
Aim1- Diagnostic panel
Identify diagnostic markers of Asian Leopard
Cat (ALC) alleles in the Feline SNP array
Dataset-Analysis -Findings
Aim2 - Degree of Bengalness
Aim3 - Bengal breed
Aim1- Diagnostic panel
Identify diagnostic markers of Asian Leopard
Cat (ALC) alleles in the Feline SNP array
Dataset-Analysis -Findings
9. Data and Analysis
ALC
N = 9
63K SNPs
DOM*
N = 1765
63K SNPs
* Non-Bengal, 41 Breeds
• Select markers from the 63K array that are:
1.Fixed with allele 1 (A1) in ALC
2.A1 frequency in domestic cats = 0 or
MAF <= 0.05.
10. Findings
SNP Relative Position (Mb)
A1
A2
A3
B1
B2
B3
B4
C1
C2
D1
D2
D3
D4
E1
E2
E3
F1
F2
X
0 25 50 75 100 125 150 175 200 225 250
674 markers identified
11. Findings
• To be concerned about:
• Number of markers
• Inter-marker distances
• Linkage disequilibrium
13. AIMS
Aim1- Diagnostic panel
Aim2 - Degree of Bengalness
Estimate ALC allele proportions in known
pedigree, Bengal breed, and other cat breeds
Dataset-Analysis -Findings
Aim3 - Bengal breed
Aim2 - Degree of Bengalness
Estimate ALC allele proportions in known
pedigree, Bengal breed, and other cat breeds
Dataset-Analysis -Findings
14. Data and Analysis
ALC-DOM
pedigree
N = 98
Bengal cats
N = 98
33 cat
breeds
N = 1452
• Use only autosomal markers (262 SNPs).
• Calculate % ALC alleles in each individual
(degree bengalness).
• Use pedigree to validate degree of bengalness.
17. Findings
ALC
% ALC Allele
frequency
0 20 40 60 80 100
02468
BxL
% ALC Allele
frequency
0 20 40 60 80 100
01234
LxD
% ALC Allele
frequency
0 20 40 60 80 100
0246810
BxD
% ALC Allele
frequency
0 20 40 60 80 100
0246810
Bengal
% ALC Allele
frequency
0 20 40 60 80 100
05101520253035
Other Domestic
% ALC Allele
frequency
0 20 40 60 80 100
0200400600800
Theoretical and Observed degree of bengalness
are in agreement
18. %Bengalness
0255075100
ALC LxD BEN ACURL BOM BUR CREX EGY MANEE PERM MCOON MUNCH ORI PBALD RBLUE SREX SIR SPH VAN
BxL BxD ABY BIR BSH CHR DREX JBOB KOR LYK MANX NFC PER RAG SFOLD SIA SOM TREX WIR
Findings
• Bengal breed and its unique degree of bengalness.
• Turkish Van (probably T. Angora)
and high degree bengalness (?).
19. AIMS
Aim1- Diagnostic panel
Aim2 - Degree of Bengalness
Aim3 - Bengal breed
Use “Degree of Bengalness” to understand
and maintain Bengal cat breed
Dataset-Analysis -Findings
Aim3 - Bengal breed
Use “Degree of Bengalness” to understand
and maintain Bengal cat breed
Dataset-Analysis -Findings
20. Data and Analysis
Bengal cats
N = 98
• Use degree of bengalness to understand
breeding history of Bengal breed.
• % Bengalness = 100 x (1/2)#generations
ALC-DOM
pedigree
N = 98
21. Findings
0 1 2 3 4 5 10 15 20 25
0
1.6875
3.375
6.75
12.5
25
50
100
Generation Crossed to Domestic
%Bengalness
Theoritical
Asian Leopard Cats
BxL
LxD
BxD
Random Bengal Breed cats
10 15 20 25
Generation Crossed to Domestic
Theoritical
Asian Leopard Cats
BxL
LxD
BxD
Random Bengal Breed cats
• Variation in backcrosses.
• Less variation in Bengals cats.
• Generation 4 (6.75%).
• Bengalness equilibrium in
Bengal cats.
22. Conclusion and Significance
• Genome-wide SNP panel is selected to
measure degree of bengalness in Bengal cat
breed.
• The panel can be used to study the genetics
of ALC-DOM hybrid zones and the
conservation genetics of ALC.
23. Leslie A. Lyons, PhD
Barbara Gandolfi, PhD
Department of Veterinary Medicine and Surgery
Acknowledgment
Mona Abdi, M.Sc. student
Department of Biological Sciences
Robert A Grahn, PhD
Veterinary Genetics Laboratory
25. Disclaimer
Figures, photos, and graphs in my lectures are
collected using google searches. I do not claim to have
personally produced all the material (except for some).
I do cite only articles or books used. I thank all owners
of the visual aid that I use and apologize for not citing
each individual item. If anybody finds the inclusion of
their material into my lectures a violation of their copy
rights, please contact me via email.
hhalhaddad@gmail.com