Stress and glucocorticoid receptor transcriptional programming in time and space: Implications for the brain-gut axis.

BACKGROUND: Chronic psychological stress is associated with enhanced abdominal pain and altered intestinal barrier function that may result from a perturbation in the hypothalamic-pituitary-adrenal (HPA) axis. The glucocorticoid receptor (GR) exploits diverse mechanisms to activate or suppress congeneric gene expression, with regulatory variation associated with stress-related disorders in psychiatry and gastroenterology. PURPOSE: During acute and chronic stress, corticotropin-releasing hormone drives secretion of adrenocorticotropic hormone from the pituitary, ultimately leading to the release of cortisol (human) and corticosterone (rodent) from the adrenal glands. Cortisol binds with the GR in the cytosol, translocates to the nucleus, and activates the NR3C1 (nuclear receptor subfamily 3, group C, member 1 [GR]) gene. This review focuses on the rapidly developing observations that cortisol is responsible for driving circadian and ultradian bursts of transcriptional activity in the CLOCK (clock circadian regulator) and PER (period circadian clock 1) gene families, and this rhythm is disrupted in major depressive disorder, bipolar disorder, and stress-related gastrointestinal and immune disorders. Glucocorticoid receptor regulates different sets of transcripts in a tissue-specific manner, through pulsatile waves of gene expression that includes occupancy of glucocorticoid response elements located within constitutively open spatial domains in chromatin. Emerging evidence supports a potentially pivotal role for epigenetic regulation of how GR interacts with other chromatin regulators to control the expression of its target genes. Dysregulation of the central and peripheral GR regulome has potentially significant consequences for stress-related disorders affecting the brain-gut axis.

Needs for an expanded ontology-based classification of adverse drug reactions and related mechanisms.

The growing significance of bioinformatics and systems biology in drug safety research requires a system of adverse-event classification that goes beyond a simple vocabulary. This opinion piece outlines the need for development of an ontology-based framework of describing adverse drug reactions (ADRs) and describes the potential applications for such a framework.

Challenges in presenting high dimensional data to aid in triage in the DARPA virtual soldier project.

One of the goals of the DARPA Virtual Soldier Project is to aid the field medic in the triage of a casualty. In Phase I, we are currently collecting 12 baseline experimental physiological variables and a cardiac gated Computed Tomography (CT) imagery for use in an prototyping a futuristic electronic medical record, the "Holomer". We are using physiological models and Kalman filtering to aid in diagnosis and predict outcomes in relation to cardiac injury. The physiological modeling introduces another few hundred variables. Reducing the complexity of the above into easy-to-read text to aid in the triage by the field medic is the challenge with multiple display solutions. A description of the possible techniques follows.

Investigation of ultrafast time gating by spatial filtering.

With a spatial-filtering method of gating, we explore image formation through scattering media using first-arriving light. Gating times of a few femtoseconds and less are produced, and the resolution at these extremely short gating times is investigated.

F-actin, tubulin and spectrin in the organ of Corti: comparative distribution in different cell types and mammalian species.

Laser scanning confocal microscopy was used to determine the distribution of actin, spectrin and tubulin in whole mounts of the organ of Corti of guinea pig, monkey, rat and chinchilla. Actin, spectrin and tubulin were localized in all cell types in the auditory epithelium. No specialized cytoskeletal organization of tubulin was detected in the cytoplasmic domain of hair cells. The only specialized organization of actin and spectrin in the cytoplasmic domain was the infra-cuticular network, found exclusively in apical guinea pig outer hair cells. In contrast, the lateral wall of inner and outer hair cells contained a homogeneous distribution of label specific for actin and spectrin. The label intensity was similar in the base and the apex of the cochlea. These results indicate that the distribution of spectrin and actin in the auditory epithelium is similar to that in other epithelial cells, suggesting that actin and spectrin participate in the formation of cellular shape and possibly in docking molecules to the membrane.

Structure of the reticular lamina and repair after noise injury.

Laser Scanning Confocal Microscopy (LSCM) and specific labeling techniques were employed to examine the distributing of F-actin and microtubules in the reticular lamina of the guinea pig and monkey organ of Corti. Actin specific label was found in the circumferential belt of adherens junction at the borders between cells in the reticular lamina, and in the cuticular plate of hair cells. The distribution of actin in the adherens junction belt was asymmetric. Actin label was not found in the fonticulus, where the microtubule organizing center resides. Actin free areas were also found between the junctional actin and the cuticular plate. Microtubule specific label was very intense in supporting cells. In normal hair cells, the spatial distribution of tubulin at the reticular lamina is mutually exclusive with that of actin. After noise exposure, a belt of actin was found in the central portion of degenerating outer hair cells, possibly representing a constricted circumferential junction. Expanded supporting cells replaced degenerating hair cells and maintained the confluence of the reticular lamina during the dynamic process of scar formation. A complex network of actin-rich cables appeared at sites of degenerating inner hair cells, suggesting that more than two supporting cells are involved in scar formation for inner hair cells. LSCM proved an attractive method for analysis of the organ of Corti since preparation of the tissue is relatively rapid, preparation artefacts are minimized, different markers in the same specimen may be co-localized and out-of focus fluorescence blurring is eliminated.

The diameters of frozen-hydrated chromatin fibers increase with DNA linker length: evidence in support of variable diameter models for chromatin.

The diameters of chromatin fibers from Thyone briareus (sea cucumber) sperm (DNA linker length, n = 87 bp) and Necturus maculosus (mudpuppy) erythrocytes (n = 48 bp) were investigated. Soluble fibers were frozen into vitrified aqueous solutions of physiological ionic strength (124 mM), imaged by cryo-EM, and measured interactively using quantitative computer image-processing techniques. Frozen-hydrated Thyone and Necturus fibers had significantly different mean diameters of 43.5 nm (SD = 4.2 nm; SEM = 0.61 nm) and 32.0 nm (SD = 3.0 nm; SEM = 0.36 nm), respectively. Evaluation of previously published EM data shows that the diameters of chromatin from a large number of sources are proportional to linker length. In addition, the inherent variability in fiber diameter suggests a relationship between fiber structure and the heterogeneity of linker length. The cryo-EM data were in quantitative agreement with space-filling double-helical crossed-linker models of Thyone and Necturus chromatin. The data, however, do not support solenoid or twisted-ribbon models for chromatin that specify a constant 30 nm diameter. To reconcile the concept of solenoidal packing with the data, we propose a variable-diameter solid-solenoid model with a fiber diameter that increases with linker length. In principle, each of the variable diameter models for chromatin can be reconciled with local variations in linker length.

Radial density distribution of chromatin: evidence that chromatin fibers have solid centers.

Fiber diameter, radial distribution of density, and radius of gyration were determined from scanning transmission electron microscopy (STEM) of unstained, frozen-dried chromatin fibers. Chromatin fibers isolated under physiological conditions (ionic strength, 124 mM) from Thyone briareus sperm (DNA linker length, n = 87 bp) and Necturus maculosus erythrocytes (n = 48 bp) were analyzed by objective image-processing techniques. The mean outer diameters were determined to be 38.0 nm (SD = 3.7 nm; SEM = 0.36 nm) and 31.2 nm (SD = 3.6 nm; SEM = 0.32 nm) for Thyone and Necturus, respectively. These data are inconsistent with the twisted-ribbon and solenoid models, which predict constant diameters of approximately 30 nm, independent of DNA linker length. Calculated radial density distributions of chromatin exhibited relatively uniform density with no central hole, although the 4-nm hole in tobacco mosaic virus (TMV) from the same micrographs was visualized clearly. The existence of density at the center of chromatin fibers is in strong disagreement with the hollow-solenoid and hollow-twisted-ribbon models, which predict central holes of 16 and 9 nm for chromatin of 38 and 31 nm diameter, respectively. The cross-sectional radii of gyration were calculated from the radial density distributions and found to be 13.6 nm for Thyone and 11.1 nm for Necturus, in good agreement with x-ray and neutron scattering. The STEM data do not support the solenoid or twisted-ribbon models for chromatin fiber structure. They do, however, support the double-helical crossed-linker models, which exhibit a strong dependence of fiber diameter upon DNA linker length and have linker DNA at the center.

Chromatin fibers are left-handed double helices with diameter and mass per unit length that depend on linker length.

Four classes of models have been proposed for the internal structure of eukaryotic chromosome fibers--the solenoid, twisted-ribbon, crossed-linker, and superbead models. We have collected electron image and x-ray scattering data from nuclei, and isolated chromatin fibers of seven different tissues to distinguish between these models. The fiber diameters are related to the linker lengths by the equation: D(N) = 19.3 + 0.23 N, where D(N) is the external diameter (nm) and N is the linker length (base pairs). The number of nucleosomes per unit length of the fibers is also related to linker length. Detailed studies were done on the highly regular chromatin from erythrocytes of Necturus (mud puppy) and sperm of Thyone (sea cucumber). Necturus chromatin fibers (N = 48 bp) have diameters of 31 nm and have 7.5 +/- 1 nucleosomes per 10 nm along the axis. Thyone chromatin fibers (N = 87 bp) have diameters of 39 nm and have 12 +/- 2 nucleosomes per 10 nm along the axis. Fourier transforms of electron micrographs of Necturus fibers showed left-handed helical symmetry with a pitch of 25.8 +/- 0.8 nm and pitch angle of 32 +/- 3 degrees, consistent with a double helix. Comparable conclusions were drawn from the Thyone data. The data do not support the solenoid, twisted-ribbon, or supranucleosomal particle models. The data do support two crossed-linker models having left-handed double-helical symmetry and conserved nucleosome interactions.