Matching Items (8)
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Description
Genes have widely different pertinences to the etiology and pathology of diseases. Thus, they can be ranked according to their disease-significance on a genomic scale, which is the subject of gene prioritization. Given a set of genes known to be related to a disease, it is reasonable to use them

Genes have widely different pertinences to the etiology and pathology of diseases. Thus, they can be ranked according to their disease-significance on a genomic scale, which is the subject of gene prioritization. Given a set of genes known to be related to a disease, it is reasonable to use them as a basis to determine the significance of other candidate genes, which will then be ranked based on the association they exhibit with respect to the given set of known genes. Experimental and computational data of various kinds have different reliability and relevance to a disease under study. This work presents a gene prioritization method based on integrated biological networks that incorporates and models the various levels of relevance and reliability of diverse sources. The method is shown to achieve significantly higher performance as compared to two well-known gene prioritization algorithms. Essentially, no bias in the performance was seen as it was applied to diseases of diverse ethnology, e.g., monogenic, polygenic and cancer. The method was highly stable and robust against significant levels of noise in the data. Biological networks are often sparse, which can impede the operation of associationbased gene prioritization algorithms such as the one presented here from a computational perspective. As a potential approach to overcome this limitation, we explore the value that transcription factor binding sites can have in elucidating suitable targets. Transcription factors are needed for the expression of most genes, especially in higher organisms and hence genes can be associated via their genetic regulatory properties. While each transcription factor recognizes specific DNA sequence patterns, such patterns are mostly unknown for many transcription factors. Even those that are known are inconsistently reported in the literature, implying a potentially high level of inaccuracy. We developed computational methods for prediction and improvement of transcription factor binding patterns. Tests performed on the improvement method by employing synthetic patterns under various conditions showed that the method is very robust and the patterns produced invariably converge to nearly identical series of patterns. Preliminary tests were conducted to incorporate knowledge from transcription factor binding sites into our networkbased model for prioritization, with encouraging results. Genes have widely different pertinences to the etiology and pathology of diseases. Thus, they can be ranked according to their disease-significance on a genomic scale, which is the subject of gene prioritization. Given a set of genes known to be related to a disease, it is reasonable to use them as a basis to determine the significance of other candidate genes, which will then be ranked based on the association they exhibit with respect to the given set of known genes. Experimental and computational data of various kinds have different reliability and relevance to a disease under study. This work presents a gene prioritization method based on integrated biological networks that incorporates and models the various levels of relevance and reliability of diverse sources. The method is shown to achieve significantly higher performance as compared to two well-known gene prioritization algorithms. Essentially, no bias in the performance was seen as it was applied to diseases of diverse ethnology, e.g., monogenic, polygenic and cancer. The method was highly stable and robust against significant levels of noise in the data. Biological networks are often sparse, which can impede the operation of associationbased gene prioritization algorithms such as the one presented here from a computational perspective. As a potential approach to overcome this limitation, we explore the value that transcription factor binding sites can have in elucidating suitable targets. Transcription factors are needed for the expression of most genes, especially in higher organisms and hence genes can be associated via their genetic regulatory properties. While each transcription factor recognizes specific DNA sequence patterns, such patterns are mostly unknown for many transcription factors. Even those that are known are inconsistently reported in the literature, implying a potentially high level of inaccuracy. We developed computational methods for prediction and improvement of transcription factor binding patterns. Tests performed on the improvement method by employing synthetic patterns under various conditions showed that the method is very robust and the patterns produced invariably converge to nearly identical series of patterns. Preliminary tests were conducted to incorporate knowledge from transcription factor binding sites into our networkbased model for prioritization, with encouraging results. To validate these approaches in a disease-specific context, we built a schizophreniaspecific network based on the inferred associations and performed a comprehensive prioritization of human genes with respect to the disease. These results are expected to be validated empirically, but computational validation using known targets are very positive.
ContributorsLee, Jang (Author) / Gonzalez, Graciela (Thesis advisor) / Ye, Jieping (Committee member) / Davulcu, Hasan (Committee member) / Gallitano-Mendel, Amelia (Committee member) / Arizona State University (Publisher)
Created2011
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Description
Sickle cell disease is a genetic disorder that can cause substantial helath problems. It is the result of a mutation in the DNA coding for hemoglobin. As a result of changes in two important amino acids, a person suffering from sickle cell disease will have erythrocytes that do not maintain

Sickle cell disease is a genetic disorder that can cause substantial helath problems. It is the result of a mutation in the DNA coding for hemoglobin. As a result of changes in two important amino acids, a person suffering from sickle cell disease will have erythrocytes that do not maintain the typical biconcave shape and instead for a crescent shape. Individuals with sickle cell disease may have many health problems tied to their irregular hemoglobin. The unusual shape of the erythrocytes leads to a much shorter cell life, which means that even though bone marrow remains active long past childhood to try to keep up with the loss of erythrocytes, the body is still unable to accommodate the rapid death of erythrocytes. The malformed erythrocytes can also cause vascular occlusion, blocking blood vessels and slowing blood flow. While sickle cell disease has the potential to spread worldwide, it is particularly common in Africa. This may be because people with the sickle cell trait have a high resistance to malaria, making them more likely to survive that ubiquitous disease and pass on their traits to their offspring. However, the mortality rate in young children with sickle cell disease is very high, in part because the spleen, already stressed by filtering out dead erythrocytes, has difficulties filtering out bacteria. One of the keys to stopping the spread of the disease is neonatal screening, but this requires specialized equipment that is fairly uncommon in rural areas, as can be seen in Kenya. Therefore, it would be highly beneficial to develop a more cost-effective and widely available method for testing for sickle cell disease.
ContributorsWold, John (Author) / Caplan, Michael (Thesis director) / LaBelle, Jeffrey (Committee member) / Snyder, Jan (Committee member) / Barrett, The Honors College (Contributor)
Created2012-05
Description

While attending UCLA Brain Research Institute, I completed research, studied, and found an interest in Duplication 15q 11.2-13.1 syndrome. I noticed the lack of awareness on both UCLA and ASU campuses and decided to complete my thesis on raising awareness of this syndrome specifically on the downtown Phoenix campus. Multiple

While attending UCLA Brain Research Institute, I completed research, studied, and found an interest in Duplication 15q 11.2-13.1 syndrome. I noticed the lack of awareness on both UCLA and ASU campuses and decided to complete my thesis on raising awareness of this syndrome specifically on the downtown Phoenix campus. Multiple surveys including in-person interviews were conducted that totaled around 50 participants. Participants in the surveys included pre-medical students at ASU downtown and an ASU mission team for disabilities and empowerment. Data collected from surveys led to the creation of an online research hub that can give a person access to all things Dup15q with one click. This type of awareness is important as misdiagnosis of rare genetic disorders is a leading cause of infant mortality.

ContributorsBennett, Raelahna (Author) / Kingsbury, Jeffrey (Thesis director) / Saravanapandian, Vidya (Committee member) / Barrett, The Honors College (Contributor) / Watts College of Public Service & Community Solut (Contributor) / College of Health Solutions (Contributor)
Created2023-05
Description

In a series of experiments in the late 1970s, Alec J. Jeffreys in the UK and Richard A. Flavell in the Netherlands developed a technique to detect variations in the DNA of different individuals. They compared fragments of DNA from individuals’ beta-globin genes, which produce a protein in hemoglobin. Previously,

In a series of experiments in the late 1970s, Alec J. Jeffreys in the UK and Richard A. Flavell in the Netherlands developed a technique to detect variations in the DNA of different individuals. They compared fragments of DNA from individuals’ beta-globin genes, which produce a protein in hemoglobin. Previously, to identify biological material, scientists focused on proteins rather than on genes. But evidence about proteins enabled scientists only to exclude, but not to identify, individuals as the sources of the biological samples. By 1979, Jeffrey’s experiments on beta-globin genes shifted the analytical approach of scientific identification from proteins to genes to identify an individual’s genetic identity. The ability to match a person to a biological sample developed in the 1980s and impacted many fields including paternity testing, forensics, immigration, and body identification.

Created2017-07-20
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Description

As of 2022, Trisomy 21 is the most common type of trisomy, or a condition where the person has three instead of the normal two copies of one of the chromosomes. Trisomy occurs when abnormal cell division takes place leading to an extra copy of a chromosome. That extra copy

As of 2022, Trisomy 21 is the most common type of trisomy, or a condition where the person has three instead of the normal two copies of one of the chromosomes. Trisomy occurs when abnormal cell division takes place leading to an extra copy of a chromosome. That extra copy of chromosome 21 results in a congenital disorder called Down syndrome, which is characterized by a cluster of specific traits including intellectual disabilities, atypical facial appearance, and a high risk of heart disease. Trisomy 21 changes the way in which a fetus’s brain develops, which accounts for many intellectual disabilities. The United States Centers for Disease Control and Prevention, or CDC, estimates Trisomy 21 occurs approximately once in every 700 human births, averaging about 6,000 live Down syndrome births every year in the US. Down syndrome is a lifelong developmental condition, but there are many resources available to those living with Down syndrome and their families.

Created2022-08-01
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Mitochondrial DNA (mtDNA) is located outside the nucleus in the liquid portion of the cell (cytoplasm) inside cellular organelles called Mitochondria. Mitochondria are located in all complex or eukaryotic cells, including plant, animal, fungi, and single celled protists, which contain their own mtDNA genome. In animals with a backbone, or

Mitochondrial DNA (mtDNA) is located outside the nucleus in the liquid portion of the cell (cytoplasm) inside cellular organelles called Mitochondria. Mitochondria are located in all complex or eukaryotic cells, including plant, animal, fungi, and single celled protists, which contain their own mtDNA genome. In animals with a backbone, or vertebrates, mtDNA is a double stranded, circular molecule that forms a circular genome, which ranges in size from sixteen to eighteen kilo-base pairs, depending on species. Each mitochondrion in a cell can have multiple copies of the mtDNA genome. In humans, the mature egg cell, or oocyte, contains the highest number of mitochondria among human cells, ranging from 100,000 to 600,000 mitochondria per cell, but each mitochondrion contains only one copy of mtDNA. In human embryonic development, the number of mitochondria, the content of mtDNA in each mitochondrion, and the subsequent mtDNA activity affects the production of the oocytes, fertilization of the oocytes, and early embryonic growth and development.

Created2014-12-19
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Julia Bell worked in twentieth-century Britain, discovered Fragile X Syndrome, and helped find heritable elements of other developmental and genetic disorders. Bell also wrote much of the five volume Treasury of Human Inheritance, a collection about genetics and genetic disorders. Bell researched until late in life, authoring an original research

Julia Bell worked in twentieth-century Britain, discovered Fragile X Syndrome, and helped find heritable elements of other developmental and genetic disorders. Bell also wrote much of the five volume Treasury of Human Inheritance, a collection about genetics and genetic disorders. Bell researched until late in life, authoring an original research article on the effects of the rubella virus of fetal development (Congenital Rubella Syndrome) at the age of 80.

Created2012-12-27
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Description

National Geographic's documentary In the Womb: Identical Twins focuses on the prenatal development of human identical twins. Director Lorne Townend uses three-dimensional (3D) and four-dimensional (4D) ultrasound imaging and microscopy to depict twin development , genetic and epigenetic variations in the fetuses, and methods of fetal survival in the confines

National Geographic's documentary In the Womb: Identical Twins focuses on the prenatal development of human identical twins. Director Lorne Townend uses three-dimensional (3D) and four-dimensional (4D) ultrasound imaging and microscopy to depict twin development , genetic and epigenetic variations in the fetuses, and methods of fetal survival in the confines of the womb. Artist renditions of scientific data fill in areas of development inaccessible to the imaging tools. The 50-minute film describes the lives twins live after birth and describes new research that identical twins might not be as identical as once thought. In the womb: Identical Twins is a sequel to the 2005 National Geographic film In the Womb.

Created2012-03-08