Examining variations on the ZEB1 gene in individuals with cleft lip and palate (CL/P), the researcher found:
(1) 13 new variants in ZEB1, including 1 nonsynonymous change, as well as 7 known SNPs;
(2) Some known SNPs were found at significantly higher frequencies in CL/P cases; and
(3) The newly identified variants showed varying levels of conservation across species. Further research is needed to understand how genetic and environmental factors interact to cause CL/P.
Gene Editing: An Essential Tool For Plant BreedingNoreen Fatima
Gene editing to remove the specie barriers. In many crops it have been used for improvement of crops for particular attribute. in this many tools have been used . these tools consist of nucleases that cut the DNA. So that is used for gene regulation, gene knock out and also use for point mutations.
A complementation test (sometimes called a "cis-trans" test) can be used to test whether the mutations in two strains are in different genes. By taking an example of Benzer's work, complementation has been explained.
Concurrent Determination of ABO RhD Blood Types and the HIV-1 Resistance Mark...Thermo Fisher Scientific
For optimal outcomes when matching bone marrow donors with their recipients, it is preferable to use bone marrow of identical or compatible blood types. Bone marrow registries thus require high resolution HLA genotyping data to match donor specimens with their recipients. We developed a research assay to aid in these investigations, which utilizes buccal swab DNA from potential donors to determine the ABO and Rh-antigen genotypes. In addition, the assay detects a 32 bp deletion in the CCR5 gene. Homozygous carriers of this deletion are resistant to HIV-1 infection, and thus could be valuable stem cell donors for HIV-infected recipients
Loss of pollen-specific phospholipase NOT LIKE DAD triggers gynogenesis in maizePGS
This lecture was a part of Plant Genetics Seminars - PGS 2017/2018 at Assiut University. These seminars organized by Dr. Ahmed Sallam, Department of Genetics, Faculty of Agriculture, Assiut University
Abstract
Gynogenesis is an asexual mode of reproduction common to animals and plants, in which stimuli from the sperm cell trigger the development of the unfertilized egg cell into a haploid embryo. Fine mapping restricted a major maize QTL (quantitative trait locus) responsible for the aptitude of inducer lines to trigger gynogenesis to a zone containing a single gene NOT LIKE DAD (NLD) coding for a patatin-like phospholipase A. In all surveyed inducer lines, NLD carries a 4-bp insertion leading to a predicted truncated protein. This frameshift mutation is responsible for haploid induction because complementation with wild-type NLD abolishes the haploid induction capacity. Activity of the NLD promoter is restricted to mature pollen and pollen tube. The translational NLD::citrine fusion protein likely localizes to the sperm cell plasma membrane. In Arabidopsis roots, the truncated protein is no longer localized to the plasma membrane, contrary to the wild-type NLD protein. In conclusion, an intact pollen-specific phospholipase is required for successful sexual reproduction and its targeted disruption may allow establishing powerful haploid breeding tools in numerous crops.
ShRNA-specific regulation of FMNL2 expression in P19 cellsYousefLayyous
This video encompasses all the steps and data produced for my graduation project in BSc in Biopharmaceutical science. During the course of the project we modified mammalian cells using Short Hairpin RNA to inhibit the correct function of the cytoskelleton. In this way we studied the importance of FMNL2 for the activation and regulation of actin fibers. Among the methods used are Flourescent microscopy, mamallian cell culture, cloning and flow cytometry.
Gene Editing: An Essential Tool For Plant BreedingNoreen Fatima
Gene editing to remove the specie barriers. In many crops it have been used for improvement of crops for particular attribute. in this many tools have been used . these tools consist of nucleases that cut the DNA. So that is used for gene regulation, gene knock out and also use for point mutations.
A complementation test (sometimes called a "cis-trans" test) can be used to test whether the mutations in two strains are in different genes. By taking an example of Benzer's work, complementation has been explained.
Concurrent Determination of ABO RhD Blood Types and the HIV-1 Resistance Mark...Thermo Fisher Scientific
For optimal outcomes when matching bone marrow donors with their recipients, it is preferable to use bone marrow of identical or compatible blood types. Bone marrow registries thus require high resolution HLA genotyping data to match donor specimens with their recipients. We developed a research assay to aid in these investigations, which utilizes buccal swab DNA from potential donors to determine the ABO and Rh-antigen genotypes. In addition, the assay detects a 32 bp deletion in the CCR5 gene. Homozygous carriers of this deletion are resistant to HIV-1 infection, and thus could be valuable stem cell donors for HIV-infected recipients
Loss of pollen-specific phospholipase NOT LIKE DAD triggers gynogenesis in maizePGS
This lecture was a part of Plant Genetics Seminars - PGS 2017/2018 at Assiut University. These seminars organized by Dr. Ahmed Sallam, Department of Genetics, Faculty of Agriculture, Assiut University
Abstract
Gynogenesis is an asexual mode of reproduction common to animals and plants, in which stimuli from the sperm cell trigger the development of the unfertilized egg cell into a haploid embryo. Fine mapping restricted a major maize QTL (quantitative trait locus) responsible for the aptitude of inducer lines to trigger gynogenesis to a zone containing a single gene NOT LIKE DAD (NLD) coding for a patatin-like phospholipase A. In all surveyed inducer lines, NLD carries a 4-bp insertion leading to a predicted truncated protein. This frameshift mutation is responsible for haploid induction because complementation with wild-type NLD abolishes the haploid induction capacity. Activity of the NLD promoter is restricted to mature pollen and pollen tube. The translational NLD::citrine fusion protein likely localizes to the sperm cell plasma membrane. In Arabidopsis roots, the truncated protein is no longer localized to the plasma membrane, contrary to the wild-type NLD protein. In conclusion, an intact pollen-specific phospholipase is required for successful sexual reproduction and its targeted disruption may allow establishing powerful haploid breeding tools in numerous crops.
ShRNA-specific regulation of FMNL2 expression in P19 cellsYousefLayyous
This video encompasses all the steps and data produced for my graduation project in BSc in Biopharmaceutical science. During the course of the project we modified mammalian cells using Short Hairpin RNA to inhibit the correct function of the cytoskelleton. In this way we studied the importance of FMNL2 for the activation and regulation of actin fibers. Among the methods used are Flourescent microscopy, mamallian cell culture, cloning and flow cytometry.
Validation of RNA interference by RNA-Seq: How to see the big picture - Brend...OECD Environment
10-12 April 2019: The OECD Conference on RNAi based pesticides provided an overview on the current status and future possibilities for the regulation of externally applied dsRNA-based products that are proposed for use as pesticides. The event facilitated exchanges between policy makers, academia, industry on their implications in health, environment, and regulation.
this is all of the information that I have please help Lab 5 In.pdfambikacomputer4301
this is all of the information that I have please help Lab 5 Introduction - Genetic mapping See
figure 5.1 for a schematic of the fly the cross you initially started with, you'll either crosses you
have been working on. Two labs ago, map the distance between the w gene and the m you set up
a pair of reciprocal parental crosses, gene, or between the w gene and the y gene. between mutant
and wild type flies (fig. 5.1a). You had one of two different mutant strains, each with two mutant
phenotypes - either white eyes all F2 individuals will receive only recessive (w) and miniature
wings (m), or white eyes (w) alleles from this parent (fig. 5.1d, orange and and yellow body (y).
The phenotypes of the F1 yellow chromosomes). Because of this, the flies should have indicated
to you that all mutant phenotype of each F2 fly will tell you which phenotypes in question are x-
linked recessive alleles (mutant or WT) were inherited from the (fig. 5.1b). heterozygous female
F1 parent (fig. 5.1d, dark and light blue chromosomes). The first F2 fly Last lab, you used the F1
flies from one of shown in figure 5.1d inherited 'a B' from the your parental crosses to set up an
F1 cross (fig. heterozygous parent and will end up with the consequence. After crossing two pure
breeding this F2, you observe a ABphenotype and parents, F1 offspring will be heterozygous for
therefore know that this fly received 'A B' from nearly all genes in question - the exception is X -
the heterozygous parent. linked genes in the male offspring. Since the Y chromosome is
equivalent to recessive alleles for The goal of genetic mapping is to X-linked genes, these F1
males are recessive for determine the likelihood of cross over between all X-linked genes and act
as a test cross. The two loci/genes. If we score the phenotypes of a heterozygous F1 females and
recessive F1 males large F2 population from our crosses, we can (test cross) can be used to map
the distance determine the recombination frequency of your between the genes causing the two
phenotypes two genes. of your parental mutant female. Depending on
e) F2 phenotype scoring: f) Recombination frequency: Eigure 5.1: Schematic of your Drosophila
crosses, See text of lab 5 intro for description.
For a given F1 gamete for the F2 individual it number of flies, it is easy to calculate the creates),
if no cross over occurs between the two recombinant frequency between your two genes genes in
question, the F2 phenotype will be the (fig. 5.1ef ). same as one of the original parents - either
fully WT or double mutant in this case. In figure 5.1d Recall from last time that a lower
recombinant these have blue chromosomes of a single colour. frequency is observed when
genetic map If a crossover does occur between the two genes, distances are small. When genes
are close to the F2 fly will have a phenotype unlike either of each other, there's a narrow range
on the the parents - a recombinant phenotype (shown chromosome for a random crossover to
land.
The number of sequenced genes having unknown function continues to climb with the continuing decrease in the cost of genome sequencing. In Reverse Genetics (RG), functions of known genes are investigated with targeted modulation of gene activity, and hypothesis regarding gene function directly tested in vivo. Several RG approaches like insertional mutagenesis, fast neutron mutagenesis, TILLING and RNA interference have led to the identification of mutations in candidate genes and subsequent phenotypic analysis of these mutants.
Okabe et al. (2011) employed TILLING technique to screen six ethylene receptor genes in tomato (SlETR1–SlETR6) and two allelic mutants of SlETR1 (Sletr1-1 and Sletr1-2) with reduced ethylene response were identified. Using fast neutron mutagenesis, Li et al. (2001) obtained arabidopsis deletion mutants for bZIP transcription factor viz. AHBP 1b and OBF 5, a key regulator for systemic acquired resistance but their role were compensated by other regulatory factors in mutants. Terada et al. (2007) successfully blocked the expression of the Adh 2 gene through homologous recombination followed by transgenesis in rice however phenotype could not be determined since no differences were observed between wild and transgenic plants. RNA interference (RNAi) works as sequence-specific gene regulation and has been used in determination of function of many genes. Saurabh et al. (2014) reviewed the impact of RNAi in crop improvement and found its application in improvement of nutritional aspects, biotic and abiotic stresses, morphol¬ogy, crafting male sterility, enhanced secondary metabolite synthesis.
In addition, new advances in technology and reduction in sequencing cost may soon make it practical to use whole genome sequencing or gene targeting like ZFN technology and TAL effectors technology on a routine basis to identify or generate mutations in specific genes. Scholze and Boch (2011) mentioned that TAL effectors technology is more specific and predictable than ZFN. RG techniques have their own advantages and disadvantages depending on the species being targeted and the questions being addressed. Finally, with the continuous development of new technologies, the most efficient RG technique in the future may involve high throughput direct sequencing of part or complete genomes of individual plants followed by efficient novel tools to determine the function for utilization in crop improvement.
Research report (alternative splicing, protein structure; retinitis pigmentosa)avalgar
This presentation explains the two major scientific projects I have been involved in.
It extends way further than a CV, but shorter than an actual scientific paper.
Nonsyndromic orofacial clefts (NSOFCs) are the most common craniofacial malformations observed
across the globe. They are classified into three types: (a) cleft palate, (b) cleft lip, and (c) cleft lip and
palate.
Discussion of latest work on simulating "evolve and resequence" experiments. Covers issues brought up by Burke et al.'s 2010 paper and how the simulations in Baldwin-Brown et al. (2014) address them.
Presented at the 2014 Bio-IT World Expo in Boston, this slideshow provides info on the use of Lyons-Weiler's entropy-based measures of genotypic signal to improve concordance among alternative variant calling algorithms and to evaluate various steps in the GATK best practices pipeline. The second part of the talk presented data showing a demarcation bias in the widely used measure of fold change in selected differentially expressed genes, transcripts or proteins from microarray and RNASeq data.
http://www.bio-itworldexpo.com/Next-Gen-Sequencing-Informatics/
Characterization of Novel ctDNA Reference Materials Developed using the Genom...Thermo Fisher Scientific
Liquid biopsy diagnostic technologies have revolutionized cancer testing and therapeutic monitoring. Non-invasive sample collection removes the need for invasive and dangerous biopsies to diagnose cancer and monitor therapeutic efficacy. As liquid biopsy technologies become more sensitive, screening for early detection of cancer DNA using a blood test could become routine clinical practice. However, such technologies cannot be developed without high quality reference materials. In this study, ctDNA reference materials using the NIST Genome in a Bottle GM24385 cell line DNA were developed in a human plasma-EDTA matrix. The allelic frequency (AF), size and stability of the materials were analyzed.
Cleft lip and palate: Examining variations on ZEB1 gene
1. Cleft lip and palate:
Examining variations on the ZEB1 gene
Jingwen Zhang
Thomas Worthington High School ‘14
Research Institute: Murray Lab, University of Iowa
2. Cleft lip and palate: Background
Cleft lip with or without cleft palate (CL/P) is a common birth defect
Affects 0.5-2.5% of live births
CL/P cases have high morbidity rates due to feeding difficulties,
speech impairment, surgical and dental care, etc.
Develops in a variety of phenotypes
Dixon MJ, Marazita ML, Beaty TH, Murray JC. 2011. Cleft lip and palate:
synthesizing genetic and environmental influences. Nat Rev Genet 12(3):167-178.
3. Cleft lip and palate: Background
5-7% CL/P cases syndromic, or
mendelian, caused by specific
chromosomal malformation patterns
Can affect parts of body other than
palate and lip
Van der Woude Syndrome caused by
mutations on IRF6
Most cases non-syndromic, caused by
variety of genetic and environmental
factors interacting to onset CL/P
4. ZEB1: Background
Zinc finger E-box-binding homeobox 1
Gene on chromosome 10
Plays vital role in epithelial-to-mesenchymal transition (EMT)
Expression of ZEB1 decreases expression of epithelial markers such as E-
cadherin, increases mesenchymal markers
E-cadherin Collagen
α-catenin Smooth muscle actin
γ-catenin Fibronectin
5. ZEB1 in present experiment
ZEB1: candidate gene for involvement in CL/P development
Look for variations within the gene that may be related to CL/P
Find mutations that merit further investigation into ZEB1 gene as
potentially involved in CL/P
Predicted: That new variations relating to CL/P would be found in ZEB1
That information regarding previously known SNPs will also be found to
be significant and aid future research in CL/P.
6. Methods
Experiment:
DNA from CL/P cases in the Philippines and Iowa (studied separately)
Polymerase chain reactions (PCR), amplified exons and sections of
nearby introns; gel electrophoresis
Send plates away for sequencing
Analysis:
Analyze clear, successfully sequenced reads on Phred and Phrap Consed
server
Look for variations from control genome (obtained from NCBI dbSNP)
Check for novelty of SNP mutation on UCSC Genome Browser, Exome
Variant Server, 1000 Genomes Browser.
Assess predicted damage of missense mutations on PolyPhen-2.
8. Explanation
13 new mutations found on 10 locations in gene. Indicated by position
numbers, as they have not been documented in browsers/servers yet.
Known SNPs found in 7 locations in gene. Indicated by rs numbers.
Also indicated: Base change, amino acid change (if any), number of
appearances of mutation
9. Results: Minor allele count
30 Minor allele count of known SNPs
25
20
15
10 CL/P cases
Control
5
0
rs7918614 rs7918614 rs41289011 rs12217419 rs2839664 rs220060
10. Results: SNP minor allele ct. significance
Pop. SNP p-value
Phil rs7918614 0.01
Iowa rs7918614 0.22
Iowa rs41289011 0.40
Iowa rs12217419 0.88
Iowa rs2839664 0.03
Phil rs220060 0.35
12. Explanation
Compared the Minor Allele Counts of known SNPs in cases studied to
the minor allele counts from the control population (control data
obtained from NCBI dbSNP).
In several of these SNPs, the minor allele counts of cases were
significantly higher (p<0.05).
One of these SNPs is located in the Iowan population, the other in the
Filipino population, suggesting that CL/P in these isolated populations
may have developed with different mechanisms.
14. Explanation
Only one new mutation was found in a coding section of the gene.
Changes arginine to glycine.
Amino acid is split over exons 2 and 3
Predicted by PolyPhen-2 to be benign, but could possibly affect splicing.
16. Explanation
Minor Allele Frequencies of new SNPs found.
New; most are very rare.
17. Results: Orthologous conservation
SNP conservation
Human
Rhesus
Mouse
Dog
Elephant
Opossum
Chicken
X_tropicalis
Zebrafish
Conserved in: 5/7 7/7 5/5 6/8 8/8 8/9 2/2 6/7 6/9
18. Explanation
Shows orthological conservation (conservation between species) of the
locations of the gene in which new SNPs were found.
Green = conserved; Orange = not conserved; Gray = no data given
Orthological conservation important in speciation and evolutionary
studies; the more conserved a region is through more species, the more
importance it may have.
19. Summary of results
13 new variants – 10 locations
1 new SNP in coding region split across 2 exons
7 locations of known SNPs
Higher minor allele count of known SNPs (rs7918614, rs2839664) in
CL/P cases than in unaffected controls.
– Statistically significant (p<0.05)
– rs2839664 significant in Iowa pop., rs7918614 significant in Filipino pop.
Some new non-coding variations located in conserved regions of introns
20. Future research
Research non-coding SNPs – TF binding sites and gene expression
Explore possible link between frequently recurring known SNPs and
development of CL/P
Research CL/P in a geographical context, exploring how isolated
pathways developed independently
Examine interaction of new genetic factors with environmental factors
and how the two work together to cause CL/P
Broaden scope of experiment
21. Acknowledgements
Dr. Jeff Murray
For giving me the opportunity and resources for this research project
Maria A. Mansilla
For mentoring me throughout the experiment and analysis processes
Elizabeth Leslie
For helping to answer my technical questions
The Murray Lab
For their welcome and support
Editor's Notes
13 new variants were found in 10 different locations on the ZEB1 gene. 7 locations of known SNPs were also found.
13 new variants were found in 10 different locations on the ZEB1 gene. 7 locations of known SNPs were also found.