Stirring and mixing : 1999 Program of Summer Study in Geophysical Fluid Dynamics

The central theme of the 1999 GFD Program was the stirring, transport, reaction and mixing of passive and active tracers in turbulent, stratified, rotating fluids. The problem of mixing in fluids has applications in areas ranging from oceanography to engineering and astrophysics. In geophysical settings, mixing spans and unites a broad range of scales -- from micrometers to megameters. The mixing of passive tracers is of fundamental importance in environmental and industrial problems, such as pollution, and in determining the large-scale heat and salt balance of the worlds oceans. The transport of active tracers, on the other hand, such as vorticity, plays a key role in the turbulence that occurs in most geophysical and astrophysical fluids. William R. Young (Scripps Institution of Oceanography) gave a series of principal lectures, the notes of which as taken by the fellows, appear in this volume. Report of the projects of the student fellows makes up the second half of this volume.Funding was provided by the National Science Foundation under Grant No. OCE-9810647 and the Office of Naval Research under Grant No. NOO0l4-97-1-0934

The trans-Golgi SNARE syntaxin 6 is recruited to the chlamydial inclusion membrane

Chlamydia trachomatis is an obligate intracellular pathogen that replicates within a parasitophorous vacuole termed an inclusion. The chlamydial inclusion is isolated from the endocytic pathway but fusogenic with Golgi-derived exocytic vesicles containing sphingomyelin and cholesterol. Sphingolipids are incorporated into the chlamydial cell wall and are considered essential for chlamydial development and viability. The mechanisms by which chlamydiae obtain eukaryotic lipids are poorly understood but require chlamydial protein synthesis and presumably modification of the inclusion membrane to initiate this interaction. A polarized cell model of chlamydial infection has demonstrated that chlamydiae preferentially intercept basolaterally directed, sphingomyelin-containing exocytic vesicles. Here we examine the localization and potential function of trans-Golgi and/or basolaterally associated soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins in chlamydia-infected cells. The trans-Golgi SNARE protein syntaxin 6 is recruited to the chlamydial inclusion in a manner that requires chlamydial protein synthesis and is conserved among all chlamydial species examined. The localization of syntaxin 6 to the chlamydial inclusion requires a tyrosine motif or plasma membrane retrieval signal (YGRL). Thus in addition to expression of at least two inclusion membrane proteins that contain SNARE-like motifs, chlamydiae also actively recruit eukaryotic SNARE-family proteins

Ontogeny-Driven rDNA Rearrangement, Methylation, and Transcription, and Paternal Influence

Gene rearrangement occurs during development in some cell types and this genome dynamics is modulated by intrinsic and extrinsic factors, including growth stimulants and nutrients. This raises a possibility that such structural change in the genome and its subsequent epigenetic modifications may also take place during mammalian ontogeny, a process undergoing finely orchestrated cell division and differentiation. We tested this hypothesis by comparing single nucleotide polymorphism-defined haplotype frequencies and DNA methylation of the rDNA multicopy gene between two mouse ontogenic stages and among three adult tissues of individual mice. Possible influences to the genetic and epigenetic dynamics by paternal exposures were also examined for Cr(III) and acid saline extrinsic factors. Variables derived from litters, individuals, and duplicate assays in large mouse populations were examined using linear mixed-effects model. We report here that active rDNA rearrangement, represented by changes of haplotype frequencies, arises during ontogenic progression from day 8 embryos to 6-week adult mice as well as in different tissue lineages and is modifiable by paternal exposures. The rDNA methylation levels were also altered in concordance with this ontogenic progression and were associated with rDNA haplotypes. Sperm showed highest level of methylation, followed by lungs and livers, and preferentially selected haplotypes that are positively associated with methylation. Livers, maintaining lower levels of rDNA methylation compared with lungs, expressed more rRNA transcript. In vitro transcription demonstrated haplotype-dependent rRNA expression. Thus, the genome is also dynamic during mammalian ontogeny and its rearrangement may trigger epigenetic changes and subsequent transcriptional controls, that are further influenced by paternal exposures

The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.Comment: Major update of previous version. This is the reference document for LBNE science program and current status. Chapters 1, 3, and 9 provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess. 288 pages, 116 figure

Improving teaching on an inpatient pediatrics service: a retrospective analysis of a program change

Background: The traditional role of the faculty inpatient attending providing clinical care and effectively teaching residents and medical students is threatened by increasing documentation requirements, pressures to increase clinical productivity, and insufficient funding available for medical education. In order to sustain and improve clinical education on a general pediatric inpatient service, we instituted a comprehensive program change. Our program consisted of creating detailed job descriptions, setting clear expectations, and providing salary support for faculty inpatient attending physicians serving in clinical and educational roles. This study was aimed at assessing the impact of this program change on the learners’ perceptions of their faculty attending physicians and learners’ experiences on the inpatient rotations. Methods: We analyzed resident and medical student electronic evaluations of both clinical and teaching faculty attending physician characteristics, as well as resident evaluations of an inpatient rotation experience. We compared the proportions of “superior” ratings versus all other ratings prior to the educational intervention (2005–2006, baseline) with the two subsequent years post intervention (2006–2007, year 1; 2007–2008, year 2). We also compared medical student scores on a comprehensive National Board of Medical Examiners clinical subject examination pre and post intervention. Results: When compared to the baseline year, pediatric residents were more likely to rate as superior the quality of didactic teaching (OR=1.7 [1.0-2.8] year 1; OR=2.0 [1.1-3.5] year 2) and attendings’ appeal as a role model (OR=1.9 [1.1-3.3] year 2). Residents were also more likely to rate as superior the quality of feedback and evaluation they received from the attending (OR=2.1 [1.2-3.7] year 1; OR=3.9 [2.2-7.1] year 2). Similar improvements were also noted in medical student evaluations of faculty attendings. Most notably, medical students were significantly more likely to rate feedback on their data gathering and physical examination skills as superior (OR=4.2 [2.0-8.6] year 1; OR=6.4 [3.0-13.6] year 2). Conclusions: A comprehensive program which includes clear role descriptions along with faculty expectations, as well as salary support for faculty in clinical and educational roles, can improve resident and medical student experiences on a general pediatric inpatient service. The authors provide sufficient detail to replicate this program to other settings.JH Libraries Open Access Promotion Fun

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Alternate Paths from Epidermal Growth Factor Receptor to Akt in Malignant Versus Nontransformed Lung Epithelial Cells: ErbB3 Versus Gab1

In many human lung adenocarcinoma cell lines, a pathway involving epidermal growth factor receptor (EGFR), ErbB2 and ErbB3 receptors, phosphatidyl inositol 3-kinase (PI3K), Akt, glycogen synthase kinase 3-β (GSK3-β), and cyclin D1 controls cell growth, survival, and invasiveness. We have investigated this pathway in paired transformed/nontransformed cell lines from murine peripheral lung epithelium, E9/E10 and A5/C10. The E9 and A5 carcinoma lines expressed ErbB3 and transforming growth factor-α (TGF-α) and responded to TGF-α stimulation with protein complex formation including the p85 regulatory subunit of PI3K, activation of Akt, phosphorylation of GSK3-β, and increased cyclin D1 protein and the cell cycle. ErbB3 and TGF-α were not detected in the nontransformed E10 and C10 cell lines. Nevertheless, exposure of E10 or C10 cells to TGF-α activated PI3K and Akt and increased cyclin D1 and cell growth. The effector pathway from the EGFR to PI3K in these nontransformed cells included the adaptor Grb2, the docking protein Gab1, and the phosphatase Shp2. Gab1 was highly expressed in E10 and C10 cells but not in the malignant E9 and A5 sister lines. Complexes of EGFR/Grb2/Gab1/Shp2 after TGF-α stimulation were prominent only in E10 and C10 cells. Thus, alternate pathways downstream of EGFR regulate mitosis in these paired malignant versus nontransformed lung cell lines

Air Displacement Plethysmography versus Dual-Energy X-Ray Absorptiometry in Underweight, Normal-Weight, and Overweight/Obese Individuals

BACKGROUND:Accurately estimating fat percentage is important for assessing health and determining treatment course. Methods of estimating body composition such as hydrostatic weighing or dual-energy x-ray absorptiometry (DXA), however, can be expensive, require extensive operator training, and, in the case of hydrostatic weighing, be highly burdensome for patients. Our objective was to evaluate air displacement plethysmography via the Bod Pod, a less burdensome method of estimating body fat percentage. In particular, we filled a gap in the literature by testing the Bod Pod at the lower extreme of the Body Mass Index (BMI) distribution. FINDINGS:Three BMI groups were recruited and underwent both air displacement plethysmography and dual-energy x-ray absorptiometry. We recruited 30 healthy adults at the lower BMI distribution from the Calorie Restriction (CR) Society and followers of the CR Way. We also recruited 15 normal weight and 19 overweight/obese healthy adults from the general population. Both Siri and Brozek equations derived body fat percentage from the Bod Pod, and Bland-Altman analyses assessed agreement between the Bod Pod and DXA. Compared to DXA, the Bod Pod overestimated body fat percentage in thinner participants and underestimated body fat percentage in heavier participants, and the magnitude of difference was larger for underweight BMI participants, reaching 13% in some. The Bod Pod and DXA had smaller discrepancies in normal weight and overweight/obese participants. CONCLUSIONS:While less burdensome, clinicians should be aware that Bod Pod estimates may deviate from DXA estimates particularly at the lower end of the BMI distribution