Papers by Katherine Mitsouras
American Journal of Human Genetics, Oct 13, 2003
Sequencing and comparative genomic analysis of 1227 Felis catus cDNA sequences enriched for devel... more Sequencing and comparative genomic analysis of 1227 Felis catus cDNA sequences enriched for developmental, clinical and nutritional phenotypes
Background: Papillomaviruses (PVs) are a group of small, non-encapsulated, species-specific DNA v... more Background: Papillomaviruses (PVs) are a group of small, non-encapsulated, species-specific DNA viruses that have been detected in a variety of mammalian and avian species including humans, canines and felines. PVs cause lesions in the skin and mucous membranes of the host and after persistent infection, a subset of PVs can cause tumors such as cervical malignancies and head and neck squamous cell carcinoma in humans. PVs from several species have been isolated and their genomes have been sequenced, thereby increasing our understanding of the mechanism of viral oncogenesis and allowing for the development of molecular assays for the detection of PV infection. In humans, molecular testing for PV DNA is used to identify patients with persistent infections at risk for developing cervical cancer. In felids, PVs have been isolated and sequenced from oral papillomatous lesions of several wild species including bobcats, Asian lions and snow leopards. Since a number of wild felids are endan...
BMC Medical Education, 2019
Background: Although specific specialties and residency programs have investigated student perfor... more Background: Although specific specialties and residency programs have investigated student performance factors affecting matching, there is a paucity of information from medical schools. Furthermore, factors contributing to matching into first-choice residency have not been examined. This study aimed to identify academic performance factors affecting matching into first-choice residency and highly competitive specialties. Methods: The authors conducted a study of 1726 graduates from their institution from 2010 to 2017 and assessed pre−/post-admission academic variables associated with matching into first choice and highly competitive specialties. Results: 53.9% of graduates matched into their first choice. This was associated with passing COMLEX Level 2 CE (p = 0.01), PE (p = 0.02) on first attempt, and higher COMLEX Level 2 CE and USMLE 2 CK scores (p < 0.001 and 0.002; 14.1 and 3.9-point difference in mean scores respectively). Pre-clinical GPA (p = 0.002) and highest MCAT score (p = 0.02) were associated, however differences in means were < 1 point for both. Factors associated with matching into first choice included: MCAT (OR 0.95, 95% CI = (0.92, 0.98)), Level 2 CE score (OR = 1.01, 95% CI = (1.01, 1.02)) and passing Level 2 PE (OR = 3.68, 95% CI = (1.2, 11.28)). 12% of graduates matched into high-and 63% into lowcompetitiveness specialties. Matching into highly competitive specialties was associated with passing COMLEX Level 1 (p < 0.001), Level 2 CE (p < 0.001), USMLE Step 1 (p < 0.001) and Step 2 CK (p = 0.03) on first attempt. Mean scores of students matching into high-versus low-competitiveness specialties differed as follows: COMLEX Level 1 62.7 points, Level 2 CE 50.5 points, USMLE Step 1 13.6 points, Step 2 CK 7 points (all p < 0.001), as did pre-clinical GPA (2.4 points, p < 0.001). Level 1 score was the strongest predictor for matching into highly competitive specialties (OR = 1.04, 95% CI = (1.02, 1.05)). Conclusions: Licensing exam performance is important for matching into first-choice residency and into highly competitive specialties. Differences in exam scores were more pronounced for matching into highly competitive specialties than into first choice, with a larger difference in mean scores between students matching into specialties of high versus low competitiveness, than between students matching into their first-versus non first-choice residency. These results may help faculty prepare students and inform curriculum design to improve matching.
Journal of alternative and complementary medicine (New York, N.Y.), 2014
To evaluate the opinions of medical cannabis (MC) users on the effects of Cannabis indica vs. tho... more To evaluate the opinions of medical cannabis (MC) users on the effects of Cannabis indica vs. those of Cannabis sativa on conditions and symptoms through an online survey. Survey of 95 non-randomly assigned MC users. A two-sided chi-square test followed by Bonferroni post hoc multiple comparison and Fisher exact test were used to determine correlations. The Cronbach α was used to determine internal consistency. Announcements on 13 MC websites with links to SurveyMonkey.com. Self-identified MC users. Web survey. Species effects were compared regarding health symptoms, conditions, purpose, route, and trust in product label. Trust in the purity, the route of administration, or the purpose (recreational vs. medicinal) did not differ between the two species. A preference for C. indica was statistically significant for pain management (p=0.001), helping with sedation (p=0.015), and sleep (p<0.001). C. sativa was preferred for euphoria (p<0.001) and enhancing energy (p=0.022). The co...
Molecular and Cellular Biology, 2002
HMGB1 (also called HMG-1) is a DNA-bending protein that augments the affinity of diverse regulato... more HMGB1 (also called HMG-1) is a DNA-bending protein that augments the affinity of diverse regulatory proteins for their DNA sites. Previous studies have argued for a specific interaction between HMGB1 and target proteins, which leads to cooperative binding of the complex to DNA. Here we propose a different model that emerged from studying how HMGB1 stimulates enhanceosome formation by the Epstein-Barr viral activator Rta on a target gene, BHLF-1. HMGB1 stimulates binding of individual Rta dimers to multiple sites in the enhancer. DNase I and hydroxyl radical footprinting, electrophoretic mobility shift assays, and immobilized template assays failed to reveal stable binding of HMGB1 within the complex. Furthermore, mutational analysis failed to identify a specific HMGB1 target sequence. The effect of HMGB1 on Rta could be reproduced by individual HMG domains, yeast HMO1, or bacterial HU. These results, combined with the effects of single-amino-acid substitutions within the DNA-binding...
Nucleic Acids Research, 2004
Alternative splicing has recently emerged as a major mechanism of regulation in the human genome,... more Alternative splicing has recently emerged as a major mechanism of regulation in the human genome, occurring in perhaps 40-60% of human genes. Thus, microarray studies of functional regulation could, in principle, be extended to detect not only the changes in the overall expression of a gene, but also changes in its splicing pattern between different tissues. However, since changes in the total expression of a gene and changes in its alternative splicing can be mixed in complex ways among a set of samples, separating these effects can be difficult, and is essential for their accurate assessment. We present a simple and general approach for distinguishing changes in alternative splicing from changes in expression, based on detecting systematic anti-correlation between the log-ratios of two different samples versus a pool containing both samples. We have tested this analysis method on microarray data for five human tissues, generated using a standard microarray platform and experimental protocols shown previously to be sensitive to alternative splicing. Our automatic analysis was able to detect a wide variety of tissue-specific alternative splicing events, such as exon skipping,mutually exclusive exons, alternative 3 0 and alternative 5 0 splicing, alternative initiation and alternative termination, all of which were validated by independent reverse-transcriptase PCR experiments, with validation rates of 70-85%. Our analysis method also enables hierarchical clustering of genes and samples by the level of similarity to their alternative splicing patterns, revealing patterns of tissuespecific regulation that are distinct from those obtained by hierarchical clustering of gene expression from the same microarray data. Our data and analysis source code are available from http:// www.bioinformatics.ucla.edu/ASAP.
Journal of Biological Chemistry, 1998
Journal of Applied Animal Welfare Science, 2009
Until the recent advent of DNA analysis of breed composition, identification of dogs of unknown p... more Until the recent advent of DNA analysis of breed composition, identification of dogs of unknown parentage was done visually, and visual identification is still the most common method of breed identification. We were interested in how often visual identification o f dogs by people, assumed to be knowledgeable about dogs, matched DNA breed identification and how often these people agreed with each other (inter-observer reliability). Over 900 participants who engaged in dog related professions and activities viewed one-minute, color video-clips of 20 dogs of unknown parentage and were asked to identify the dogs' predominant breeds. For 14 of the dogs, fewer than 50% of the respondents visually identified breeds of dogs that matched DNA identification. Agreement among respondents was also very poor. Krippendorf's alpha was used to examine the reliability of the most predominant breed (selected across all dogs identified as mixed breeds) for all respondents, yielding alpha=0.23. For only 7 of the 20 dogs was there agreement among mo re than 50% of the respondents regarding the most predominant breed of a mixed breed and in 3 o f these cases the most commonly agreed upon visual identification was not identified by DNA analysis.
Current Biology, 2001
Gene expression is controlled by interactions between activators and coactivators. These interact... more Gene expression is controlled by interactions between activators and coactivators. These interactions in turn are regulated by signaling pathways and by chromatin remodeling events. Recent studies indicate that the final arbiter of gene regulation is a coactivator scaffold at the promoter.
Cold Spring Harbor Symposia on Quantitative Biology, 1998
Brain Research, 2010
Niemann-Pick Type C disease is an autosomal recessive neurodegenerative disorder with abnormal li... more Niemann-Pick Type C disease is an autosomal recessive neurodegenerative disorder with abnormal lipid storage as the major cellular pathologic hallmark. Genetic analyses have identified mutations in NPC1 gene in the great majority of cases, while mutations in NPC2 account for the remainders. Yet, little is known regarding the cellular mechanisms responsible for NPC pathogenesis, especially for neurodegeneration, which is the usual cause of death. To identify critical steps that could account for the pathological manifestations of the disease in one of the most affected brain structures, we performed global gene expression analysis in the cerebellum from three-week old Npc1+/+ and Npc1-/-mice with two different microarray platforms (Agilent and Illumina). Differentiallyexpressed genes identified by both microarray platforms were then subjected to KEGG pathway analysis. Expression of genes in six pathways was significantly altered in Npc1-/-mice; functionally, these signaling pathways belong to the following three categories: 1) steroid and terpenoid biosynthesis, 2) immune response, and 3) cell adhesion/motility. In addition, the expression of several proteins involved in lipid transport was significantly altered in Npc1-/-mice. Our results provide novel molecular insight regarding the mechanisms of pathogenesis in NPC disease and reveal potential new therapeutic targets.
BMC Veterinary Research, 2011
Background Papillomaviruses (PVs) are a group of small, non-encapsulated, species-specific DNA vi... more Background Papillomaviruses (PVs) are a group of small, non-encapsulated, species-specific DNA viruses that have been detected in a variety of mammalian and avian species including humans, canines and felines. PVs cause lesions in the skin and mucous membranes of the host and after persistent infection, a subset of PVs can cause tumors such as cervical malignancies and head and neck squamous cell carcinoma in humans. PVs from several species have been isolated and their genomes have been sequenced, thereby increasing our understanding of the mechanism of viral oncogenesis and allowing for the development of molecular assays for the detection of PV infection. In humans, molecular testing for PV DNA is used to identify patients with persistent infections at risk for developing cervical cancer. In felids, PVs have been isolated and sequenced from oral papillomatous lesions of several wild species including bobcats, Asian lions and snow leopards. Since a number of wild felids are endang...
BMC Research Notes, 2009
Background: The domestic dog presents an attractive model system for the study of the genetic bas... more Background: The domestic dog presents an attractive model system for the study of the genetic basis of disease. The development of resources such as the canine genome sequence and SNP genotyping platforms has allowed for the implementation of canine genetic studies. Successful implementation of such studies depends not only on the quality of individual DNA samples, but also on the number of samples obtained. The latter can be maximized using a non-invasive DNA collection method that can increase study participation. We compared the DNA yield and quality obtained from blood and buccal swabs to those obtained using a non-invasive saliva collection kit (Oragene ® •ANIMAL kit). We also assessed the success rate of PCR amplification and genotyping accuracy of DNA isolated using these collection methods. Findings: Comparison of DNA yields from matched saliva, blood and buccal swab samples showed that yields from saliva were significantly higher than those from blood (p = 0.0198) or buccal swabs (p = 0.0008). Electrophoretic analysis revealed that blood and saliva produced higher quality DNA than buccal swabs. In addition, a 1.1-kb PCR fragment was successfully amplified using the paired DNA samples and genotyping by PCR-RFLP yielded identical results. Conclusion: We demonstrate that DNA yields from canine saliva are higher than those from blood or buccal swabs. The quality of DNA extracted from saliva is sufficient for successful amplification of a 1.1-kb fragment and for accurate SNP genotyping by PCR-RFLP. We conclude that saliva presents a non-invasive alternative source of high quantities of canine genomic DNA suitable for genotyping studies.
Acta Haematologica, 2010
Background: Kaposi sarcoma-associated herpesvirus (KSHV), or human herpesvirus type 8 (HHV8), is ... more Background: Kaposi sarcoma-associated herpesvirus (KSHV), or human herpesvirus type 8 (HHV8), is consistently identified in 2 human immunodeficiency virus (HIV)-associated lymphoproliferative disorders: primary effusion lymphoma (PEL) and multicentric Castleman disease. Rarely, KSHV/HHV8-positive extracavitary solid tissue lymphomas occur, often at extranodal sites, which are not associated with an effusion. These solid variants of PEL are similar morphologically, immunophenotypically, clinically and genetically to classic PEL. Case Report: Here we report a case of a 46-year-old HIV-positive patient with lymphadenopathy and Kaposi sarcoma of the skin. The lymph node biopsy shows a KSHV/HHV8-positive high-grade B-cell lymphoma with co-infection with Epstein-Barr virus, which supports the diagnosis of a solid variant of PEL. The same lymph node is also multifocally involved in Kaposi sarcoma. Conclusion: Analysis of viral infection is of primary importance to define this solid variant...
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Papers by Katherine Mitsouras