Exploring the Importance of Single Nucleotide Polymorphisms of HSPA9 in DNA of Sarcoma Patients

The aim of this project was to identify genetic variants that may influence the risk and progression of sarcoma through targeted genotyping of HSPA9 gene. It is important to look at genetic variants in DNA samples because if a variant is determined to be more likely than another, a screening for the particular variant can be done to identify a patient’s risk of sarcoma. The study population was sarcoma patients from the International Sarcoma Kindred Study. These patients had no mutations in p53 or MDM2. Genotyping data from the HapMap project (hapmap.org) for HSPA9 was used to identify the polymorphisms needed to tag the entire region. In order to genotype the DNA sample, KASP reagents (KBioSciences, UK) were used. KASP uses a two-set PCR process. Allele specific primers are used to preferentially amplify each allele of a given SNP. The specific genetic variations of HSPA9 in sarcoma patient DNA samples with no mutations in p53 or MDM2 amplification are not more or less likely to occur than in DNA samples with the mutation or amplification. If continued research can show that MDM2 is not amplified, but activated through other mechanisms such as the interaction between polymorphisms of mitochondrial genes, p53, or MDM2, we can propose anti-MDM2 therapies to the patients with these polymorphisms

Autism Assessment Scale for Children (AASC): The Development of a DSM-V AIigned Questionnaire to Screen School-Aged Children for High Functioning Autism

The purpose of this dissertation is to analyze the latent factor structure underlying the Ellis Functional Assessment (EFA) for children with high-functioning autism (HFA), to compare the latent factor structures for under-identified subgroups of children (older children, gifted children, female children), and to design a pre-screening assessment for HFA based on those results. The scope of the study is limited to children who have been identified as having HFA and whose parents completed the EFA while patients of a mid-Atlantic clinical practice specializing in autism spectrum disorders. The methodology uses preliminary factor analysis and confirmatory factor analysis to both analyze the data from seven years of clinical practice and develop a new pre-screening assessment. Findings help to explain differences and commonalities between the under-identified subgroups with HFA and the rest of the HFA population. The largest limitation to this study is the sample size (n = 380) which though large for an autism study, is small for the use of preliminary factor analysis relative to the number of items contained in the EFA. This study supports prior research identifying differences between the under-identified subgroups and the identified population with HFA and contributes additional possible identifying differences. This study also develops a potential pre-screening assessment for HFA that is sensitive to under-identified subgroups, reflects the factor structure of the Ellis Functional Assessment, conforms to DSM-V, and has excellent internal reliability

Understanding Fourth Graders\u27 Decline in Reading Motivation from Students\u27 and Teachers\u27 Perspectives

Previous research by Chall and Jacobs (2003) documented the phenomena of the fourth grade slump, a period in which students switch from learning to read to reading to learn and the subsequent loss of motivation to read. The purpose of this research is to present a phenomenological qualitative study of whether a sample of fourth grade students, low-achieving readers and average achieving readers, exhibited a loss in their motivation to read. Students\u27 responses to a standardized conversational survey and questionnaire, the Motivation to Read Profile (Gambrell, Palmer, Codling & Mazzoni, 2007) and teachers\u27 responses to a researcher-developed questionnaire were examined and coded by themes. Results indicated that there was no difference in motivation to read between low-achieving and average-achieving readers. Students\u27 responses showed positive motivation to read, while teachers\u27 response indicated a negative attitude towards students\u27 motivation to read. Research results were inconclusive concerning students\u27 readiness to switch from learning to read to reading to learn. Implications for future research are discussed. A review of pertinent literature is presented

Induced Ferromagnetism and Colossal Magnetoresistance by Ir-Doping in Pr1-xCaxMnO3

The doping of the manganese site by iridium (up to 15%) in the small A cation manganites Pr_{1-x}Ca_xMnO_3 (0.4 < x < 0.8), has been investigated as a new method to suppress charge-ordering and induce CMR effects. Ir doping leads to ferromagnetism and to insulator to metal transitions, with high transition temperatures reaching 180K and CMR ratio in 7T as large as 10^4. The efficiency with which iridium induces ferromagnetism and CMR is compared to previous results obtained with other substitutions (Ru, Rh, Ni, Cr, ...). The ionic radius of the foreign cations and their mixed-valencies are found to be the main parameters governing the ability to collapse the charge-ordered state.Comment: 9 pages, 5 figures, accepted for publication in Eur. Phys. J.

Outcomes of primary care delivery by nurse practitioners: Utilization, cost, and quality of care

ObjectiveTo examine whether nurse practitioner (NP)- assigned patients exhibited differences in utilization, costs, and clinical outcomes compared to medical doctor (MD)- assigned patients.Data SourcesVeterans Affairs (VA) administrative data capturing characteristics, outcomes, and provider assignments of 806 434 VA patients assigned to an MD primary care provider (PCP) who left VA practice between 2010 and 2012.Study DesignWe applied a difference- in- difference approach comparing outcomes between patients reassigned to MD and NP PCPs, respectively. We examined measures of outpatient (primary care, specialty care, and mental health) and inpatient (total and ambulatory care sensitive hospitalizations) utilization, costs (outpatient, inpatient and total), and clinical outcomes (control of hemoglobin A1c, LDL, and blood pressure) in the year following reassignment.Principal FindingsCompared to MD- assigned patients, NP- assigned patients were less likely to use primary care and specialty care services and incurred fewer total and ambulatory care sensitive hospitalizations. Differences in costs, clinical outcomes, and receipt of diagnostic tests between groups were not statistically significant.ConclusionsPatients reassigned to NPs experienced similar outcomes and incurred less utilization at comparable cost relative to MD patients. NPs may offer a cost- effective approach to addressing anticipated shortages of primary care physicians.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154625/1/hesr13246_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154625/2/hesr13246-sup-0001-Authormatrix.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154625/3/hesr13246.pd

Nucleotide sequence and analysis of pRC12 and pRC18, two theta-replicating plasmids harbored by Lactobacillus curvatus CRL 705

The nucleotide sequences of plasmids pRC12 (12,342 bp; GC 43.99%) and pRC18 (18,664 bp; GC 34.33%), harbored by the bacteriocin-producer Lactobacillus curvatus CRL 705, were determined and analyzed. Plasmids pRC12 and pRC18 share a region with high DNA identity (> 83% identity between RepA, a Type II toxin-antitoxin system and a tyrosine integrase genes) and are stably maintained in their natural host L. curvatus CRL 705. Both plasmids are low copy number and belong to the theta-type replicating group. While pRC12 is a pUCL287-like plasmid that possesses iterons and the repA and repB genes for replication, pRC18 harbors a 168 amino acid replication protein affiliated to RepB, which was named RepB’. Plasmid pRC18 also possesses a pUCL287-like repA gene but it was disrupted by an 11 kb insertion element that contains RepB’, several transposases/IS elements, and the lactocin Lac705 operon. An Escherichia coli / Lactobacillus shuttle vector, named plasmid p3B1, carrying the pRC18 replicon (i.e. repB’ and replication origin), a chloramphenicol resistance gene and a pBluescript backbone, was constructed and used to define the host range of RepB’. Chloramphenicol-resistant transformants were obtained after electroporation of Lactobacillus plantarum CRL 691, Lactobacillus sakei 23K and a plasmid-cured derivative of L. curvatus CRL 705, but not of L. curvatus DSM 20019 or Lactococcus lactis NZ9000. Depending on the host, transformation efficiency ranged from 102 to 107 per μg of DNA; in the new hosts, the plasmid was relatively stable as 29–53% of recombinants kept it after cell growth for 100 generations in the absence of selective pressure. Plasmid p3B1 could therefore be used for cloning and functional studies in several Lactobacillus species.Fil: Teran, Lucrecia Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; ArgentinaFil: Cuozzo, Sergio Antonio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Planta Piloto de Procesos Industriales Microbiológicos; ArgentinaFil: Aristimuño Ficoseco, Maria Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; ArgentinaFil: Fadda, Silvina G.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; ArgentinaFil: Chaillou, Stéphane. Institut National de la Recherche Agronomique; FranciaFil: Champomier Vergès, Marie Christine. Institut National de la Recherche Agronomique; FranciaFil: Zagorec, Monique. Institut National de la Recherche Agronomique; FranciaFil: Hebert, Elvira Maria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; ArgentinaFil: Raya, Raul Ricardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; Argentin

Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products

Microbial communities of traditional cheeses are complex and insufficiently characterized. The origin, safety and functional role in cheese making of these microbial communities are still not well understood. Metagenomic analysis of these communities by high throughput shotgun sequencing is a promising approach to characterize their genomic and functional profiles. Such analyses, however, critically depend on the availability of appropriate reference genome databases against which the sequencing reads can be aligned. We built a reference genome catalog suitable for short read metagenomic analysis using a low-cost sequencing strategy. We selected 142 bacteria isolated from dairy products belonging to 137 different species and 67 genera, and succeeded to reconstruct the draft genome of 117 of them at a standard or high quality level, including isolates from the genera Kluyvera, Luteococcus and Marinilactibacillus, still missing from public database. To demonstrate the potential of this catalog, we analysed the microbial composition of the surface of two smear cheeses and one blue-veined cheese, and showed that a significant part of the microbiota of these traditional cheeses was composed of microorganisms newly sequenced in our study. Our study provides data, which combined with publicly available genome references, represents the most expansive catalog to date of cheese-associated bacteria. Using this extended dairy catalog, we revealed the presence in traditional cheese of dominant microorganisms not deliberately inoculated, mainly Gram-negative genera such as Pseudoalteromonas haloplanktis or Psychrobacter immobilis, that may contribute to the characteristics of cheese produced through traditional methods.https://doi.org/10.1186/1471-2164-15-110

Functional Characterization of Rare RAB12 Variants and Their Role in Musician's and Other Dystonias

Mutations in RAB (member of the Ras superfamily) genes are increasingly recognized as cause of a variety of disorders including neurological conditions. While musician's dystonia (MD) and writer's dystonia (WD) are task-specific movement disorders, other dystonias persistently affect postures as in cervical dystonia. Little is known about the underlying etiology. Next-generation sequencing revealed a rare missense variant (c.586A> G; p.Ile196Val) in RAB12 in two of three MD/WD families. Next, we tested 916 additional dystonia patients; 512 Parkinson's disease patients; and 461 healthy controls for RAB12 variants and identified 10 additional carriers of rare missense changes among dystonia patients (1.1%) but only one carrier in non-dystonic individuals (0.1%; p = 0.005). The detected variants among index patients comprised p.Ile196Val (n = 6); p.Ala174Thr (n = 3); p.Gly13Asp; p.Ala148Thr; and p.Arg181Gln in patients with MD; cervical dystonia; or WD. Two relatives of MD patients with WD also carried p.Ile196Val. The two variants identified in MD patients (p.Ile196Val; p.Gly13Asp) were characterized on endogenous levels in patient-derived fibroblasts and in two RAB12-overexpressing cell models. The ability to hydrolyze guanosine triphosphate (GTP), so called GTPase activity, was increased in mutants compared to wildtype. Furthermore, subcellular distribution of RAB12 in mutants was altered in fibroblasts. Soluble Transferrin receptor 1 levels were reduced in the blood of all three tested p.Ile196Val carriers. In conclusion, we demonstrate an enrichment of missense changes among dystonia patients. Functional characterization revealed altered enzyme activity and lysosomal distribution in mutants suggesting a contribution of RAB12 variants to MD and other dystonias

Flower-visitor communities of an arcto-alpine plant-Global patterns in species richness, phylogenetic diversity and ecological functioning

Pollination is an ecosystem function of global importance. Yet, who visits the flower of specific plants, how the composition of these visitors varies in space and time and how such variation translates into pollination services are hard to establish. The use of DNA barcodes allows us to address ecological patterns involving thousands of taxa that are difficult to identify. To clarify the regional variation in the visitor community of a widespread flower resource, we compared the composition of the arthropod community visiting species in the genus Dryas (mountain avens, family Rosaceae), throughout Arctic and high-alpine areas. At each of 15 sites, we sampled Dryas visitors with 100 sticky flower mimics and identified specimens to Barcode Index Numbers (BINs) using a partial sequence of the mitochondrial COI gene. As a measure of ecosystem functioning, we quantified variation in the seed set of Dryas. To test for an association between phylogenetic and functional diversity, we characterized the structure of local visitor communities with both taxonomic and phylogenetic descriptors. In total, we detected 1,360 different BINs, dominated by Diptera and Hymenoptera. The richness of visitors at each site appeared to be driven by local temperature and precipitation. Phylogeographic structure seemed reflective of geological history and mirrored trans-Arctic patterns detected in plants. Seed set success varied widely among sites, with little variation attributable to pollinator species richness. This pattern suggests idiosyncratic associations, with function dominated by few and potentially different taxa at each site. Taken together, our findings illustrate the role of post-glacial history in the assembly of flower-visitor communities in the Arctic and offer insights for understanding how diversity translates into ecosystem functioning.Peer reviewe