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Abstract Background Transcriptomic studies in clinical research are essential tools for deciphering the functional elements of the genome and unraveling underlying disease mechanisms. Various technologies have been developed to deduce and quantify the transcriptome including hybridization and sequencing-based approaches. Recently, high density exon microarrays have been successfully employed for detecting differentially expressed genes and alternative splicing events for biomarker discovery and disease diagnostics. The field of transcriptomics is currently being revolutionized by high throughput DNA sequencing methodologies to map, characterize, and quantify the transcriptome. Methods In an effort to understand the merits and limitations of each of these tools, we undertook a study of the transcriptome in sickle cell disease, a monogenic disease comparing the Affymetrix Human Exon 1.0 ST microarray (Exon array) and Illumina’s deep sequencing technology (RNA-seq) on whole blood clinical specimens. Results Analysis indicated a strong concordance (R = 0.64) between Exon array and RNA-seq data at both gene level and exon level transcript expression. The magnitude of differential expression was found to be generally higher in RNA-seq than in the Exon microarrays. We also demonstrate for the first time the ability of RNA-seq technology to discover novel transcript variants and differential expression in previously unannotated genomic regions in sickle cell disease. In addition to detecting expression level changes, RNA-seq technology was also able to identify sequence variation in the expressed transcripts. Conclusions Our findings suggest that microarrays remain useful and accurate for transcriptomic analysis of clinical samples with low input requirements, while RNA-seq technology complements and extends microarray measurements for novel discoveries.

Abstract Background CD146 is a well described homotypic adhesion molecule found on endothelial cells and a limited number of other cell types. In cells from the peripheral circulation, CD146 has also been reported to be on activated lymphocytes in vitro and in vivo. The function associated with CD146 expression on lymphoid cells is unknown and very little information is available concerning the nature of CD146+ lymphocytes. In the current study, lymphocytes from healthy donors were characterized based upon the presence or absence of CD146 expression. Results CD146 was expressed on a low percentage of circulating T lymphocytes, B lymphocytes, and NK cells in healthy individuals. CD146 expression can be induced and upregulated in vitro on both B cells and T cells, but does not correlate with the expression of other markers of T cell activation. CD146 positive T cells do not represent clonal expansions as determined with the use of anti Vβ reagents. Data suggest that CD146 positive cells have enhanced adherence to endothelial monolayers in vitro. Gene profiling and immunophenotyping studies between CD146+ and CD146- T cells revealed several striking genotypic distinctions such as the upregulation of IL-8 and phenotypic differences including the paucity of CCR7 and CD45RA among CD146 positive T cells, consistent with effector memory function. A number of genes involved in cell adhesion, signal transduction, and cell communication are dramatically upregulated in CD146+ T cells compared to CD146- T cells. Conclusion CD146 appears to identify small, unique populations of T as well as B lymphocytes in the circulation. The T cells have immunophenotypic characteristics of effector memory lymphocytes. The characteristics of these CD146+ lymphocytes in the circulation, together with the known functions in cell adhesion of CD146 on endothelial cells, suggests that these lymphocytes may represent a small subpopulation of cells primed to adhere to the endothelium and possibly extravasate to sites of inflammation.

Fragmentation methods such as MIM (Molecules-in-Molecules) provide a route to accurately model large systems and have been successful in predicting their structures, energies, and spectroscopic properties. However, their use is often limited to systems at equilibrium due to the inherent complications in the choice of fragments in systems away from equilibrium. Furthermore, the presence of charges resulting from any heterolytic bond breaking may increase the fragmentation error. We have previously suggested EE-MIM (Electrostatically Embedded Molecules-In-Molecules) as a method to mitigate the errors resulting from the missing long-range interactions in molecular clusters in equilibrium. Here, we show that the same method can be applied to improve the performance of MIM to solve the longstanding problem of dependency of the fragmentation energy error on the choice of the fragmentation scheme. We chose four widely used acid dissociation reactions (HCl, HClO4, HNO3, and H2SO4) as test cases due to their importance in chemical processes and complex reaction potential energy surfaces. Electrostatic embedding improves the performance at both one and two-layer MIM as shown by lower EE-MIM1 and EE-MIM2 errors. The EE-MIM errors are also demonstrated to be less dependent on the choice of the fragmentation scheme by analyzing the variation in fragmentation energy at the points with more than one possible fragmentation scheme (points where the fragmentation scheme changes). EE-MIM2 with M06-2X as the low-level resulted in a variation of less than 1 kcal/mol for all the cases and 1 kJ/mol for all but three cases, rendering our method fragmentation scheme-independent for acid dissociation processes. [ABSTRACT FROM AUTHOR]

With the finalization of the ICH Q14 Analytical Procedure Development guideline, how to apply enhanced approaches (such as analytical quality by design (AQbD)) to develop an analytical procedure, and to propose Established Conditions (ECs) and corresponding reporting categories, is increasingly being discussed. To gain practical experience in applying an enhanced approach for method development and identifying ECs, we developed, validated, and implemented an analytical procedure for a nitrosamine drug substance-related impurity (NDSRI). Here, as an example of the application of Q12 Lifecycle Management guideline principles in regards to analytical procedures, we briefly elaborate how: 1) the principles documented in the ICH Q14 guideline for analytical procedure development were applied, with the focus on identifying an Analytical Target Profile (ATP), knowledge management and risk assessment; 2) analytical procedure robustness according to the recommendations in ICH Q2(R2) Validation of Analytical Procedure guideline and Q14, were evaluated; and 3) mass spectrometry ECs and associated proposed reporting categories were proposed. [ABSTRACT FROM AUTHOR]

Antibacterial nanocomposite films of poly(butylene adipate-co-terephthalate) (PBAT) incorporated with different weight percentage of octakis (3-chloropropyl)octasilsesquioxane (chloropropyl functionalized POSS [Cl-fn-POSS]) nanofiller were prepared. The mechanical, thermal, morphological, barrier, and antimicrobial properties were examined. The mechanical properties of the nanocomposite films were enhanced by the addition of Cl-fn-POSS nanofiller. An optimum filler loading of 3 wt% is identified to be best suited for maximum enhancement in tensile strength (24 MPa for 3 wt% filled PBAT vs 11 MPa for neat PBAT) while a 1 wt% filler loading was adequate to double the tensile strength. The barrier properties (WVTR and oxygen transmission rate) of PBAT was improved by the presence of Cl-fn-POSS. A volume of 3 wt% filler loading results in 50% reduction of water permeation and 10% reduction in oxygen transmission. The thermogravimetric analyses of the nanocomposites indicated that the filler enabled the enhancement of thermal stability of PBAT. The nanocomposite films revealed antimicrobial activity with this activity increasing with increasing filler content. PBAT is compostable under suitable conditions and with a low weight percentage of filler that is largely made of silicon dioxide these nanocomposite films can find application as biodegradable food packaging material given their flexibility. KEYWORDS antibacterial, compostable films, green packaging, nanofiller, octakis(3-chloropropyl) octasilsesquioxane, PBAT, strength enhancement, 1 | INTRODUCTION The environmental problems posed by commodity plastics, such as poly(ethylene), poly(propylene), poly(styrene), and poly(vinyl chloride), which are produced in very large volume, have necessitated the study of [...]

Genome-wide association studies (GWAS) have identified numerous loci associated with blood pressure (BP). The molecular mechanisms underlying BP regulation, however, remain unclear. We investigated BP-associated molecular mechanisms by integrating BP GWAS with whole blood mRNA expression profiles in 3,679 individuals, using network approaches. BP transcriptomic signatures at the single-gene and the coexpression network module levels were identified. Four coexpression modules were identified as potentially causal based on genetic inference because expression-related SNPs for their corresponding genes demonstrated enrichment for BP GWAS signals. Genes from the four modules were further projected onto predefined molecular interaction networks, revealing key drivers. Gene subnetworks entailing molecular interactions between key drivers and BP-related genes were uncovered. As proof-of-concept, we validated SH2B3, one of the top key drivers, using Sh2b3(-/-) mice. We found that a significant number of genes predicted to be regulated by SH2B3 in gene networks are perturbed in Sh2b3(-/-) mice, which demonstrate an exaggerated pressor response to angiotensin II infusion. Our findings may help to identify novel targets for the prevention or treatment of hypertension.

Genome-wide association studies (GWAS) have uncovered numerous genetic variants (SNPs) that are associated with blood pressure (BP). Genetic variants may lead to BP changes by acting on intermediate molecular phenotypes such as coded protein sequence or gene expression, which in turn affect BP variability. Therefore, characterizing genes whose expression is associated with BP may reveal cellular processes involved in BP regulation and uncover how transcripts mediate genetic and environmental effects on BP variability. A meta-analysis of results from six studies of global gene expression profiles of BP and hypertension in whole blood was performed in 7017 individuals who were not receiving antihypertensive drug treatment. We identified 34 genes that were differentially expressed in relation to BP (Bonferroni-corrected p