Role of Cdx factors in early mesodermal fate decisions.

Murine cardiac and hematopoietic progenitors are derived from mesoderm. Cdx function impacts both yolk sac hematopoiesis and cardiogenesis in zebrafish, suggesting that Cdx family members regulate early mesoderm cell fate decisions. We found that Cdx2 occupies a number of transcription factor loci during embryogenesis, including key regulators of both cardiac and blood development, and that Cdx function is required for normal expression of the cardiogenic transcription factors and Furthermore, Cdx and Brg1, an ATPase subunit of the SWI/SNF chromatin remodeling complex, co-occupy a number of loci, suggesting that Cdx family members regulate target gene expression through alterations in chromatin architecture.

Creation and Online Use of Patient-Centered Videos, Digital Storytelling, and Interactive Self-testing Questions for Teaching Pathophysiology.

Background: Nursing students need to not only understand the pathophysiological basis of disease but also acquire insight into its effects on patients and their families.

Purpose: Digital storytelling was used to engage students in self-directed, online learning, allowing them to identify with patients dealing with disease and its consequences.

Methods: Scripts were written and videos created that simulated patient experiences with select diseases of the gastrointestinal and respiratory systems as well as diabetes.

Towards the optical second: verifying optical clocks at the SI limit.

The pursuit of ever more precise measures of time and frequency motivates redefinition of the second in terms of an optical atomic transition. To ensure continuity with the current definition, based on the microwave hyperfine transition in Cs, it is necessary to measure the absolute frequency of candidate optical standards relative to primary cesium references. Armed with independent measurements, a stringent test of optical clocks can be made by comparing ratios of absolute frequency measurements against optical frequency ratios measured via direct optical comparison.

Optical-Clock-Based Time Scale.

A time scale is a procedure for accurately and continuously marking the passage of time. It is exemplified by Coordinated Universal Time (UTC) and provides the backbone for critical navigation tools such as the Global Positioning System. Present time scales employ microwave atomic clocks, whose attributes can be combined and averaged in a manner such that the composite is more stable, accurate, and reliable than the output of any individual clock.

Cdx2 Regulates Gene Expression through Recruitment of Brg1-associated Switch-Sucrose Non-fermentable (SWI-SNF) Chromatin Remodeling Activity.

The packaging of genomic DNA into nucleosomes creates a barrier to transcription that can be relieved through ATP-dependent chromatin remodeling via complexes such as the switch-sucrose non-fermentable (SWI-SNF) chromatin remodeling complex. The SWI-SNF complex remodels chromatin via conformational or positional changes of nucleosomes, thereby altering the access of transcriptional machinery to target genes. The SWI-SNF complex has limited ability to bind to sequence-specific elements, and, therefore, its recruitment to target loci is believed to require interaction with DNA-associated transcription factors.

Essential roles for Cdx in murine primitive hematopoiesis.

The Cdx transcription factors play essential roles in primitive hematopoiesis in the zebrafish where they exert their effects, in part, through regulation of hox genes. Defects in hematopoiesis have also been reported in Cdx mutant murine embryonic stem cell models, however, to date no mouse model reflecting the zebrafish Cdx mutant hematopoietic phenotype has been described. This is likely due, in part, to functional redundancy among Cdx members and the early lethality of Cdx2 null mutants.

Cdx1 and Cdx2 function as tumor suppressors.

In humans, colorectal cancer is often initiated through APC loss of function, which leads to crypt hyperplasia and polyposis driven by unrestricted canonical Wnt signaling. Such polyps typically arise in the colorectal region and are at risk of transforming to invasive adenocarcinomas. Although colorectal cancer is the third most common cause of cancer-related death worldwide, the processes impacting initiation, transformation, and invasion are incompletely understood.

Identification of novel retinoic acid target genes.

Retinoic acid is required for diverse ontogenic processes and as such identification of the genes and pathways affected by retinoic acid is critical to understanding these pleiotropic effects. The presomitic mesoderm of the E8.5 mouse embryo is composed of undifferentiated cells that are depleted of retinoic acid, yet are competent to respond to the retinoid signal.

A regulatory network controls nephrocan expression and midgut patterning.

Although many regulatory networks involved in defining definitive endoderm have been identified, the mechanisms through which these networks interact to pattern the endoderm are less well understood. To explore the mechanisms involved in midgut patterning, we dissected the transcriptional regulatory elements of nephrocan (Nepn), the earliest known midgut specific gene in mice. We observed that Nepn expression is dramatically reduced in Sox17(-/-) and Raldh2(-/-) embryos compared with wild-type embryos.

Design and implementation of an FPGA-based timing pulse programmer for pulsed-electron paramagnetic resonance applications.

The design, construction and implementation of a field-programmable gate array (FPGA) -based pulse programmer for pulsed-electron paramagnetic resonance (EPR) experiments is described. The FPGA pulse programmer offers advantages in design flexibility and cost over previous pulse programmers, that are based on commercial digital delay generators, logic pattern generators, and application-specific integrated circuit (ASIC) designs. The FPGA pulse progammer features a novel transition-based algorithm and command protocol, that is optimized for the timing structure required for most pulsed magnetic resonance experiments.

Alcohol consumption during pregnancy: cross-sectional survey.

Objective: to assess the prevalence and pattern of alcohol consumption pre-conception and/or during the first trimester using the Alcohol Use Disorders Identification Test (AUDIT), Alcohol Use Disorders Identification Test - Consumption (AUDIT-C) and T-ACE (Tolerance, Annoyance, Cut Down and Eye-Opener) alcohol screening questionnaires, and determine the socio-demographic predictors of drinking in this time period.

Design: cross sectional survey of a consecutive sample of 500 pregnant women attending their first antenatal appointment at approximately 10-11 weeks gestation.

Setting: two antenatal clinics in the South West of England.

Controlled ion ejection from an external trap for extended m/z range in FT-ICR mass spectrometry.

An auxiliary rf waveform of the same amplitude and phase applied to all the rods of an ion accumulation multipole creates an m/z-dependent axial pseudo potential. Controlled decrease of the auxiliary rf amplitude releases ions from the accumulation multipole sequentially from high to low m/z. The slope of the auxiliary rf voltage ramp is adjusted so that ions of different m/z reach the center of the ICR cell at the same time point, which mitigates the typical time dispersion observed in external source FT-ICR and extends the observable mass range for a single data acquisition by 2- to 3-fold.

Expansion of the analytical window for oil spill characterization by ultrahigh resolution mass spectrometry: beyond gas chromatography.

Traditional tools for routine environmental analysis and forensic chemistry of petroleum have relied almost exclusively on gas chromatography-mass spectrometry (GC-MS), although many compounds in crude oil (and its transformation products) are not chromatographically separated or amenable to GC-MS due to volatility. To enhance current and future studies on the fate, transport, and fingerprinting of the Macondo well oil released from the 2010 Deepwater Horizon disaster, we created an extensive molecular library of the unadulterated petroleum to compare to a tar ball collected on the beach of Louisiana. We apply ultrahigh resolution Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry to identify compositional changes at the molecular level between native and weathered crude oil samples and reveal enrichment in polar compounds inaccessible by GC-based characterization.

Charge reversal Fourier transform ion cyclotron resonance mass spectrometry.

We report the first charge reversal experiments performed by tandem-in-time rather than tandem-in-space MS/MS. Precursor odd-electron anions from fullerene C(60), and even-electron ions from 2,7-di-tert-butylfluorene-9-carboxylic acid and 3,3'-bicarbazole were converted into positive product ions ((-)CR(+)) inside the magnet of a Fourier transform ion cyclotron resonance mass spectrometer. Charge reversal was activated by irradiating precursor ions with high energy electrons or UV photons: the first reported use of those activation methods for charge reversal.

Tailored ion radius distribution for increased dynamic range in FT-ICR mass analysis of complex mixtures.

Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) typically utilizes an m/z-independent excitation magnitude to excite all ions to the same cyclotron radius, so that the detected signal magnitude is directly proportional to the relative ion abundance. However, deleterious space charge interaction between ion clouds is maximized for clouds of equal radius. To minimize ion cloud interactions, we induce an m/z-dependent ion radius distribution (30%-45% of the maximum cell radius) that results in a 3-fold increase in mass spectral dynamic range for complex mixtures, consistent with increased ion cloud lifetime for less-abundant ion clouds.

Cdx function is required for maintenance of intestinal identity in the adult.

The homeodomain transcription factors Cdx1 and Cdx2 are expressed in the intestinal epithelium from early development, with expression persisting throughout the life of the animal. While our understanding of the function of Cdx members in intestinal development has advanced significantly, their roles in the adult intestine is relatively poorly understood. In the present study, we found that ablation of Cdx2 in the adult small intestine severely impacted villus morphology, proliferation and intestinal gene expression patterns, resulting in the demise of the animal.

Cdx regulates Dll1 in multiple lineages.

Vertebrate Cdx genes encode homeodomain transcription factors related to caudal in Drosophila. The murine Cdx homologues Cdx1, Cdx2 and Cdx4 play important roles in anterior-posterior patterning of the embryonic axis and the intestine, as well as axial elongation. While our understanding of the ontogenic programs requiring Cdx function has advanced considerably, the molecular bases underlying these functions are less well understood.

Electrically compensated Fourier transform ion cyclotron resonance cell for complex mixture mass analysis.

Complex natural organic mixtures such as petroleum require ultrahigh mass spectral resolution to separate and identify thousands of elemental compositions. Here, we incorporate a custom-built, voltage-compensated ICR cell for Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS), based on a prior design by Tolmachev to produce optimal mass resolution. The compensated ICR cell installed in a custom-built 9.

International year of Chemistry 2011. A guide to the history of clinical chemistry.

Background: This review was written as part of the celebration of the International Year of Chemistry 2011.

Content: In this review we provide a chronicle of the history of clinical chemistry, with a focus on North America. We outline major methodological advances and trace the development of professional societies and journals dedicated to clinical chemistry.

Cdx mediates neural tube closure through transcriptional regulation of the planar cell polarity gene Ptk7.

The vertebrate Cdx genes (Cdx1, Cdx2 and Cdx4) encode homeodomain transcription factors with well-established roles in anteroposterior patterning. To circumvent the peri-implantation lethality inherent to Cdx2 loss of function, we previously used the Cre-loxP system to ablate Cdx2 at post-implantation stages and confirmed a crucial role for Cdx2 function in events related to axial extension. As considerable data suggest that the Cdx family members functionally overlap, we extended this analysis to assess the consequence of concomitant loss of both Cdx1 and Cdx2.

Parts-per-billion Fourier transform ion cyclotron resonance mass measurement accuracy with a "walking" calibration equation.

Ion cyclotron resonance frequency, f, is conventionally converted to ion mass-to-charge ratio, m/z (mass "calibration") by fitting experimental data spanning the entire detected m/z range to the relation, m/z = A/f + B/f(2), to yield rms mass error as low as ~200 ppb for ~10,000 resolved components of a petroleum crude oil. Analysis of residual error versus m/z and peak abundance reveals that systematic errors limit mass accuracy and thus the confidence in elemental composition assignments. Here, we present a calibration procedure in which the spectrum is divided into dozens of adjoining segments, and a separate calibration is applied to each, thereby eliminating systematic error with respect to m/z.

Cdx4 is a Cdx2 target gene.

The products of the Cdx genes, Cdx1, Cdx2 and Cdx4, play multiple roles in early vertebrate development, and have been proposed to serve to relay signaling information from Wnt, RA and FGF pathways to orchestrate events related to anterior-posterior vertebral patterning and axial elongation. In addition, Cdx1 and Cdx2 have been reported to both autoregulate and to be subject to cross regulation by other family members. We have now found that Cdx4 expression is significantly down regulated in Cdx2(-/-) mutants suggesting previously unrecognized cross-regulatory interactions.

Cdx2 regulates patterning of the intestinal epithelium.

Cdx1, Cdx2 and Cdx4 encode homeodomain transcription factors that are involved in vertebral anterior-posterior (AP) patterning. Cdx1 and Cdx2 are also expressed in the intestinal epithelium during development, suggesting a role in this tissue. Intestinal defects have not been reported in Cdx1 null mutants, while Cdx2 null mutants die at embryonic day 3.

Cdx2 regulation of posterior development through non-Hox targets.

The homeodomain transcription factors Cdx1, Cdx2 and Cdx4 play essential roles in anteroposterior vertebral patterning through regulation of Hox gene expression. Cdx2 is also expressed in the trophectoderm commencing at E3.5 and plays an essential role in implantation, thus precluding assessment of the cognate-null phenotype at later stages.