282 research outputs found
Development of tools for in situ hybridization in human embryonic stem cells
Abstract only availableOur laboratory uses human embryonic stem cells (hESC) to understand how embryonic cells differentiate into the cells of the placenta. The long term goal of my research is to develop in situ hybridization methods and use them to determine where genes are being expressed within differentiating hESC colonies. I focused my research on two genes that code for transcription factors, OCT 4 and GATA 2. OCT 4 is required to maintain stem cells in an undifferentiated state. GATA 2 is thought to be one of the key transcription factors that promote stem cell differentiation into syncytiotrophoblast, a placental cell type. The first step in in situ hybridization is the development of a labeled RNA probe. I designed primers to amplify a 214bp portion of the GATA2 gene sequence by PCR, and then cloned the PCR product into E. coli bacteria. I confirmed the presence and orientation of the insert by using restriction digestion and DNA sequencing. I used bacteria already transformed with a 182bp OCT4 probe sequence to create a riboprobe. I grew up the bacteria overnight, lysed them, and purified the plasmid DNA. I linearized the plasmid with a restriction enzyme, purified it, and transcribed the DNA to RNA, incorporating digoxygenin (DIG) labeled nucleotides. In the near future, I will utilize the same method to transcribe the GATA2 probe, and use both RNA probes to perform in situ hybridizations on hESC.Life Sciences Undergraduate Research Opportunity Progra
The pace of biological aging helps explain the association between insomnia and chronic low back pain
Chronic low back pain (cLBP) is associated with insomnia and advanced age. Emerging evidence suggests that the severity of both sleep disorders (like insomnia) and chronic pain are associated with a faster pace of biological aging. We aimed to determine whether the pace of biological age mediates the relationship between insomnia and the impact of cLBP in a sample of community-dwelling adults ages 19 to 85 years. Participants (49 with no pain, 32 with low-impact pain, and 37 with high-impact pain) completed sociodemographic, pain, insomnia, and short physical performance battery assessments. We calculated the pace of biological aging using DunedinPACE from blood leukocyte DNA. On average, individuals with high-impact cLBP had significantly faster biological aging than those with low-impact and no chronic pain
Complex temporal patterns in molecular dynamics:a direct measure of the phase-space exploration by the trajectory at macroscopic time scales
Computer simulated trajectories of bulk water molecules form complex spatiotemporal structures at the picosecond time scale. This intrinsic complexity, which underlies the formation of molecular structures at longer time scales, has been quantified using a measure of statistical complexity. The method estimates the information contained in the molecular trajectory by detecting and quantifying temporal patterns present in the simulated data (velocity time series). Two types of temporal patterns are found. The first, defined by the short-time correlations corresponding to the velocity autocorrelation decay times (â‰0.1â€ps), remains asymptotically stable for time intervals longer than several tens of nanoseconds. The second is caused by previously unknown longer-time correlations (found at longer than the nanoseconds time scales) leading to a value of statistical complexity that slowly increases with time. A direct measure based on the notion of statistical complexity that describes how the trajectory explores the phase space and independent from the particular molecular signal used as the observed time series is introduced
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Endogenous aldehyde accumulation generates genotoxicity and exhaled biomarkers in esophageal adenocarcinoma.
Volatile aldehydes are enriched in esophageal adenocarcinoma (EAC) patients' breath and could improve early diagnosis, however the mechanisms of their production are unknown. Here, we show that weak aldehyde detoxification characterizes EAC, which is sufficient to cause endogenous aldehyde accumulation in vitro. Two aldehyde groups are significantly enriched in EAC biopsies and adjacent tissue: (i) short-chain alkanals, and (ii) medium-chain alkanals, including decanal. The short-chain alkanals form DNA-adducts, which demonstrates genotoxicity and confirms inadequate detoxification. Metformin, a putative aldehyde scavenger, reduces this toxicity. Tissue and breath concentrations of the medium-chain alkanal decanal are correlated, and increased decanal is linked to reduced ALDH3A2 expression, TP53 deletion, and adverse clinical features. Thus, we present a model for increased exhaled aldehydes based on endogenous accumulation from reduced detoxification, which also causes therapeutically actionable genotoxicity. These results support EAC early diagnosis trials using exhaled aldehyde analysis
Moyal star product approach to the Bohr-Sommerfeld approximation
The Bohr-Sommerfeld approximation to the eigenvalues of a one-dimensional
quantum Hamiltonian is derived through order (i.e., including the
first correction term beyond the usual result) by means of the Moyal star
product. The Hamiltonian need only have a Weyl transform (or symbol) that is a
power series in , starting with , with a generic fixed point in
phase space. The Hamiltonian is not restricted to the kinetic-plus-potential
form. The method involves transforming the Hamiltonian to a normal form, in
which it becomes a function of the harmonic oscillator Hamiltonian.
Diagrammatic and other techniques with potential applications to other normal
form problems are presented for manipulating higher order terms in the Moyal
series.Comment: 27 pages, no figure
Characterisation of a laser plasma accelerator x-ray source size using a Kirkpatrick-Baez microscope
Laser plasma accelerators are highly versatile and are sources of both radiation and particle beams, with unique properties. The Scottish Centre for Application based Plasma Accelerators (SCAPA) 40 TW and 350 TW laser at the University of Strathclyde has been used to produce both soft and hard x-rays using a laser wakefield accelerator (LWFA). The inherent characteristics of these femtosecond duration pulsed x-rays make them ideal for probing matter and ultrafast imaging applications. To support the development of applications of laser plasma accelerators at the SCAPA facility an adjustable Kirkpatrick-Baez x-ray microscope has been designed to focus 50 eV - 10 KeV x-rays. It is now possible to produce high quality at silicon wafers substrates that can be used for x-ray optics. Platinum-coated (40 nm) silicon wafers have been used in the KB instrument to image the LWFA x-ray source. We simulate the source distribution as part of an investigation to determine the x-ray source size and therefore its transverse coherence and ultimately the peak brilliance. The OASYS SHAODOW-OUI raytracing and wave propagation code has been used to simulate the imaging setup and determine instrument resolution
Genetic overlap between diagnostic subtypes of ischemic stroke
Background and Purpose: Despite moderate heritability, the phenotypic heterogeneity of ischemic stroke has hampered gene discovery, motivating analyses of diagnostic subtypes with reduced sample sizes. We assessed evidence for a shared genetic basis among the 3 major subtypes: large artery atherosclerosis (LAA), cardioembolism, and small vessel disease (SVD), to inform potential cross-subtype analyses. Methods: Analyses used genome-wide summary data for 12 389 ischemic stroke cases (including 2167 LAA, 2405 cardioembolism, and 1854 SVD) and 62 004 controls from the Metastroke consortium. For 4561 cases and 7094 controls, individual-level genotype data were also available. Genetic correlations between subtypes were estimated using linear mixed models and polygenic profile scores. Meta-analysis of a combined LAA-SVD phenotype (4021 cases and 51 976 controls) was performed to identify shared risk alleles. Results: High genetic correlation was identified between LAA and SVD using linear mixed models (rg=0.96, SE=0.47, P=9×10-4) and profile scores (rg=0.72; 95% confid
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Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel
The ENIGMA research consortium develops and applies methods to determine clinical significance of variants in hereditary breast and ovarian cancer genes. An ENIGMA BRCA1/2 classification sub-group, formed in 2015 as a ClinGen external expert panel, evolved into a ClinGen internal Variant Curation Expert Panel (VCEP) to align with Food and Drug Administration recognized processes for ClinVar contributions. The VCEP reviewed American College of Medical Genetics and Genomics/Association of Molecular Pathology (ACMG/AMP) classification criteria for relevance to interpreting BRCA1 and BRCA2 variants. Statistical methods were used to calibrate evidence strength for different data types. Pilot specifications were tested on 40 variants and documentation revised for clarity and ease of use. The original criterion descriptions for 13 evidence codes were considered non-applicable or overlapping with other criteria. Scenario of use was extended or re-purposed for eight codes. Extensive analysis and/or data review informed specification descriptions and weights for all codes. Specifications were applied to pilot variants with pre-existing ClinVar classification as follows: 13 uncertain significance or conflicting, 14 pathogenic and/or likely pathogenic, and 13 benign and/or likely benign. Review resolved classification for 11/13 uncertain significance or conflicting variants and retained or improved confidence in classification for the remaining variants. Alignment of pre-existing ENIGMA research classification processes with ACMG/AMP classification guidelines highlighted several gaps in the research processes and the baseline ACMG/AMP criteria. Calibration of evidence strength was key to justify utility and strength of different data types for gene-specific application. The gene-specific criteria demonstrated value for improving ACMG/AMP-aligned classification of BRCA1 and BRCA2 variants
Malignant mesothelioma
Malignant mesothelioma is a fatal asbestos-associated malignancy originating from the lining cells (mesothelium) of the pleural and peritoneal cavities, as well as the pericardium and the tunica vaginalis. The exact prevalence is unknown but it is estimated that mesotheliomas represent less than 1% of all cancers. Its incidence is increasing, with an expected peak in the next 10–20 years. Pleural malignant mesothelioma is the most common form of mesothelioma. Typical presenting features are those of chest pain and dyspnoea. Breathlessness due to a pleural effusion without chest pain is reported in about 30% of patients. A chest wall mass, weight loss, sweating, abdominal pain and ascites (due to peritoneal involvement) are less common presentations. Mesothelioma is directly attributable to occupational asbestos exposure with a history of exposure in over 90% of cases. There is also evidence that mesothelioma may result from both para-occupational exposure and non-occupational "environmental" exposure. Idiopathic or spontaneous mesothelioma can also occur in the absence of any exposure to asbestos, with a spontaneous rate in humans of around one per million. A combination of accurate exposure history, along with examination radiology and pathology are essential to make the diagnosis. Distinguishing malignant from benign pleural disease can be challenging. The most helpful CT findings suggesting malignant pleural disease are 1) a circumferential pleural rind, 2) nodular pleural thickening, 3) pleural thickening of > 1 cm and 4) mediastinal pleural involvement. Involvement of a multidisciplinary team is recommended to ensure prompt and appropriate management, using a framework of radiotherapy, chemotherapy, surgery and symptom palliation with end of life care. Compensation issues must also be considered. Life expectancy in malignant mesothelioma is poor, with a median survival of about one year following diagnosis
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