Plastination Procedure @ PCOM: Current Practice and Future Uses

Introduction: Since its invention by German anatomist Gunther von Hagens, the process of forced-impregnation plastination of organic specimens has become the standard for the preservation of biological tissue specimens. This practice serves as the most practical method to preserve these specimens for study and is utilized at PCOM regularly for this purpose. During the steps of plastination, aqueous and lipid tissues are replaced by a curable polymer to produce plastinates that do not decompose, can be handled without gloves, and retain most characteristics of the original specimens. For decades, PCOM used this method to prepare a permanent teaching collection in support of medical education. In the last five years, the lab has been reactivated and prepares specimens for allied health professional education, enrichment of the Doctor of Osteopathy curriculum, and outreach at regional institutions (e.g., The Franklin Institute, The Nebinger School, etc.). Objectives: The purpose of this poster is to inform the PCOM community of current plastination practices and suggest future uses. Methods: To prepare specimens for plastination, they must be preserved in fixative. We currently dissect and stage all tissues after the fixative process. Dissections are prepared by work-study students at PCOM who have completed the relevant anatomy course (interested students please contact Dr. Claeson). After fixation, tissues are dehydrated in progressively more concentrated washes of cold-temperature acetone (-20ºC) until concentration is between 98-100%. After dehydration, they are placed into a silicone polymer bath and brought to room temperature. The room temperature bath technique is the primary deviation from von Hagen (1977). Once at room temperature in the bath, vacuum pressure is used to replace the acetone that fills each cell with silicone. A hardening agent is then administered to finish the process. Results & Conclusions: Current initiatives have included building a collection of heart specimens to support a cardiac workshop which pairs anatomy and physiology. Most recently, a brain anatomy collection is being built. Brain specimens include axial cross sections, whole and half brains, and pathological specimens. These specimens are currently used at many outreach events and will be incorporated into a featured anatomy series as part of the medical school curriculum. Future research initiatives may also begin via current practices

Localization of type 1 diabetes susceptibility to the MHC class I genes HLA-B and HLA-A

The major histocompatibility complex (MHC) on chromosome 6 is associated with susceptibility to more common diseases than any other region of the human genome, including almost all disorders classified as autoimmune. In type 1 diabetes the major genetic susceptibility determinants have been mapped to the MHC class II genes HLA-DQB1 and HLA-DRB1 (refs 1-3), but these genes cannot completely explain the association between type 1 diabetes and the MHC region. Owing to the region's extreme gene density, the multiplicity of disease-associated alleles, strong associations between alleles, limited genotyping capability, and inadequate statistical approaches and sample sizes, which, and how many, loci within the MHC determine susceptibility remains unclear. Here, in several large type 1 diabetes data sets, we analyse a combined total of 1,729 polymorphisms, and apply statistical methods - recursive partitioning and regression - to pinpoint disease susceptibility to the MHC class I genes HLA-B and HLA-A (risk ratios >1.5; Pcombined = 2.01 × 10-19 and 2.35 × 10-13, respectively) in addition to the established associations of the MHC class II genes. Other loci with smaller and/or rarer effects might also be involved, but to find these, future searches must take into account both the HLA class II and class I genes and use even larger samples. Taken together with previous studies, we conclude that MHC-class-I-mediated events, principally involving HLA-B*39, contribute to the aetiology of type 1 diabetes. ©2007 Nature Publishing Group

Electrochemical Deprotection of <i>para</i>-Methoxybenzyl Ethers in a Flow Electrolysis Cell

Electrochemical deprotection of <i>p</i>-methoxybenzyl (PMB) ethers was performed in an undivided electrochemical flow reactor in MeOH solution, leading to the unmasked alcohol and <i>p</i>-methoxybenzaldehyde dimethyl acetal as a byproduct. The electrochemical method removes the need for chemical oxidants, and added electrolyte (BF₄NEt₄) can be recovered and reused. The method was applied to 17 substrates with high conversions in a single pass, yields up to 92%, and up to 7.5 g h^–1 productivity. The PMB protecting group was also selectively removed in the presence of some other common alcohol protecting groups

Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data

Abstract: Crohn Disease (CD) is a complex genetic disorder for which more than 140 genes have been identified using genome wide association studies (GWAS). However, the genetic architecture of the trait remains largely unknown. The recent development of machine learning (ML) approaches incited us to apply them to classify healthy and diseased people according to their genomic information. The Immunochip dataset containing 18,227 CD patients and 34,050 healthy controls enrolled and genotyped by the international Inflammatory Bowel Disease genetic consortium (IIBDGC) has been re-analyzed using a set of ML methods: penalized logistic regression (LR), gradient boosted trees (GBT) and artificial neural networks (NN). The main score used to compare the methods was the Area Under the ROC Curve (AUC) statistics. The impact of quality control (QC), imputing and coding methods on LR results showed that QC methods and imputation of missing genotypes may artificially increase the scores. At the opposite, neither the patient/control ratio nor marker preselection or coding strategies significantly affected the results. LR methods, including Lasso, Ridge and ElasticNet provided similar results with a maximum AUC of 0.80. GBT methods like XGBoost, LightGBM and CatBoost, together with dense NN with one or more hidden layers, provided similar AUC values, suggesting limited epistatic effects in the genetic architecture of the trait. ML methods detected near all the genetic variants previously identified by GWAS among the best predictors plus additional predictors with lower effects. The robustness and complementarity of the different methods are also studied. Compared to LR, non-linear models such as GBT or NN may provide robust complementary approaches to identify and classify genetic markers

Ecology under lake ice

Winter conditions are rapidly changing in temperate ecosystems, particularly for those that experi-ence periods of snow and ice cover. Relatively little is known of winter ecology in these systems,due to a historical research focus on summer ‘growing seasons’. We executed the first global quan-titative synthesis on under-ice lake ecology, including 36 abiotic and biotic variables from 42research groups and 101 lakes, examining seasonal differences and connections as well as how sea-sonal differences vary with geophysical factors. Plankton were more abundant under ice thanexpected; mean winter values were 43.2% of summer values for chlorophyll a, 15.8% of summerphytoplankton biovolume and 25.3% of summer zooplankton density. Dissolved nitrogen concen-trations were typically higher during winter, and these differences were exaggerated in smallerlakes. Lake size also influenced winter-summer patterns for dissolved organic carbon (DOC), withhigher winter DOC in smaller lakes. At coarse levels of taxonomic aggregation, phytoplanktonand zooplankton community composition showed few systematic differences between seasons,although literature suggests that seasonal differences are frequently lake-specific, species-specific,or occur at the level of functional group. Within the subset of lakes that had longer time series,winter influenced the subsequent summer for some nutrient variables and zooplankton biomas

Compound inheritance of a low-frequency regulatory SNP and a rare null mutation in exon-junction complex subunit RBM8A causes TAR syndrome

Item does not contain fulltextThe exon-junction complex (EJC) performs essential RNA processing tasks. Here, we describe the first human disorder, thrombocytopenia with absent radii (TAR), caused by deficiency in one of the four EJC subunits. Compound inheritance of a rare null allele and one of two low-frequency SNPs in the regulatory regions of RBM8A, encoding the Y14 subunit of EJC, causes TAR. We found that this inheritance mechanism explained 53 of 55 cases (P < 5 x 10(-228)) of the rare congenital malformation syndrome. Of the 53 cases with this inheritance pattern, 51 carried a submicroscopic deletion of 1q21.1 that has previously been associated with TAR, and two carried a truncation or frameshift null mutation in RBM8A. We show that the two regulatory SNPs result in diminished RBM8A transcription in vitro and that Y14 expression is reduced in platelets from individuals with TAR. Our data implicate Y14 insufficiency and, presumably, an EJC defect as the cause of TAR syndrome

Ecology under lake ice

Winter conditions are rapidly changing in temperate ecosystems, particularly for those that experience periods of snow and ice cover. Relatively little is known of winter ecology in these systems, due to a historical research focus on summer 'growing seasons'. We executed the first global quantitative synthesis on under-ice lake ecology, including 36 abiotic and biotic variables from 42 research groups and 101 lakes, examining seasonal differences and connections as well as how seasonal differences vary with geophysical factors. Plankton were more abundant under ice than expected; mean winter values were 43.2% of summer values for chlorophyll a, 15.8% of summer phytoplankton biovolume and 25.3% of summer zooplankton density. Dissolved nitrogen concentrations were typically higher during winter, and these differences were exaggerated in smaller lakes. Lake size also influenced winter-summer patterns for dissolved organic carbon (DOC), with higher winter DOC in smaller lakes. At coarse levels of taxonomic aggregation, phytoplankton and zooplankton community composition showed few systematic differences between seasons, although literature suggests that seasonal differences are frequently lake-specific, species-specific, or occur at the level of functional group. Within the subset of lakes that had longer time series, winter influenced the subsequent summer for some nutrient variables and zooplankton biomass

Collaborative International Research in Clinical and Longitudinal Experience Study in NMOSD

Objective To develop a resource of systematically collected, longitudinal clinical data and biospecimens for assisting in the investigation into neuromyelitis optica spectrum disorder (NMOSD) epidemiology, pathogenesis, and treatment. Methods To illustrate its research-enabling purpose, epidemiologic patterns and disease phenotypes were assessed among enrolled subjects, including age at disease onset, annualized relapse rate (ARR), and time between the first and second attacks. Results As of December 2017, the Collaborative International Research in Clinical and Longitudinal Experience Study (CIRCLES) had enrolled more than 1,000 participants, of whom 77.5% of the NMOSD cases and 71.7% of the controls continue in active follow-up. Consanguineous relatives of patients with NMOSD represented 43.6% of the control cohort. Of the 599 active cases with complete data, 84% were female, and 76% were anti-AQP4 seropositive. The majority were white/Caucasian (52.6%), whereas blacks/African Americans accounted for 23.5%, Hispanics/Latinos 12.4%, and Asians accounted for 9.0%. The median age at disease onset was 38.4 years, with a median ARR of 0.5. Seropositive cases were older at disease onset, more likely to be black/African American or Hispanic/Latino, and more likely to be female. Conclusions Collectively, the CIRCLES experience to date demonstrates this study to be a useful and readily accessible resource to facilitate accelerating solutions for patients with NMOSD

New gene functions in megakaryopoiesis and platelet formation

Platelets are the second most abundant cell type in blood and are essential for maintaining haemostasis. Their count and volume are tightly controlled within narrow physiological ranges, but there is only limited understanding of the molecular processes controlling both traits. Here we carried out a high-powered meta-analysis of genome-wide association studies (GWAS) in up to 66,867 individuals of European ancestry, followed by extensive biological and functional assessment. We identified 68 genomic loci reliably associated with platelet count and volume mapping to established and putative novel regulators of megakaryopoiesis and platelet formation. These genes show megakaryocyte-specific gene expression patterns and extensive network connectivity. Using gene silencing in Danio rerio and Drosophila melanogaster, we identified 11 of the genes as novel regulators of blood cell formation. Taken together, our findings advance understanding of novel gene functions controlling fate-determining events during megakaryopoiesis and platelet formation, providing a new example of successful translation of GWAS to function