Experimental and structural testing module to analyze paralogue-specificity and affinity in the Hsp90 inhibitors series

We here describe the first reported comprehensive analysis of Hsp90 paralogue affinity and selectivity in the clinical Hsp90 inhibitor chemotypes. This has been possible through the development of a versatile experimental assay based on a new FP-probe (16a) that we both describe here. The assay can test rapidly and accurately the binding affinity of all major Hsp90 chemotypes and has a testing range that spans low nanomolar to millimolar binding affinities. We couple this assay with a computational analysis that allows for rationalization of paralogue selectivity and defines not only the major binding modes that relay pan-paralogue binding or, conversely, paralogue selectivity, but also identifies molecular characteristics that impart such features. The methods developed here provide a blueprint for parsing out the contribution of the four Hsp90 paralogues to the perceived biological activity with the current Hsp90 chemotypes and set the ground for the development of paralogue selective inhibitors.

Regional specialisation of the ganglion cell density in the retina of the native duck (Anas platyrhynchos) of Bangladesh

In this study, retinal whole-mount specimens were prepared and stained with 0.1% cresyl violet for the ganglion cell study in the native duck (Anas platyrhynchos). The total number, distribution and size of these cells were determined in different retinal regions. The mean total number of ganglion cells was 1 598 501. The retinal area centralis had the highest ganglion cell density with 11 200 cells/mm(2) . Number of ganglion cell bodies was the highest in temporal area, followed by dorsal, nasal and ventral areas. Ganglion cell size ranged from 5.25 to 80 μm(2) . In the temporal and nasal region, most of the cells were ranged from 15 to 25 μm(2) , and in the dorsal and ventral region, most of the cells were ranged from 12 to 25 μm(2) . There was a marked trend for the retinal ganglion cell size to increase as the population density decrease towards the periphery. A population of small ganglion cells persisted into the central area just above the optic disc and the largest soma area was in the ventral zone of the retina. Thus, the specialisation of ganglion cell densities and their sizes support the notion that the conduction of visual information towards the brain from all regions of the retina is not uniform, and the central area is the fine quality area for vision in native duck.

Interaction between polygenic risk for cigarette use and environmental exposures in the Detroit Neighborhood Health Study

Cigarette smoking is influenced both by genetic and environmental factors. Until this year, all large-scale gene identification studies on smoking were conducted in populations of European ancestry. Consequently, the genetic architecture of smoking is not well described in other populations. Further, despite a rich epidemiologic literature focused on the social determinants of smoking, few studies have examined the moderation of genetic influences (for example, gene-environment interactions) on smoking in African Americans. In the Detroit Neighborhood Health Study (DNHS), a sample of randomly selected majority African American residents of Detroit, we constructed a genetic risk score (GRS), in which we combined top (P-value <5 × 10(-7)) genetic variants from a recent meta-analysis conducted in a large sample of African Americans. Using regression (effective n=399), we first tested for association between the GRS and cigarettes per day, attempting to replicate the findings from the meta-analysis. Second, we examined interactions with three social contexts that may moderate the genetic association with smoking: traumatic events, neighborhood social cohesion and neighborhood physical disorder. Among individuals who had ever smoked cigarettes, the GRS significantly predicted the number of cigarettes smoked per day and accounted for ~3% of the overall variance in the trait. Significant interactions were observed between the GRS and number of traumatic events experienced, as well as between the GRS and average neighborhood social cohesion; the association between genetic risk and smoking was greater among individuals who had experienced an increased number of traumatic events in their lifetimes, and diminished among individuals who lived in a neighborhood characterized by greater social cohesion. This study provides support for the utility of the GRS as an alternative approach to replication of common polygenic variation, and in gene-environment interaction, for smoking behaviors. In addition, this study indicates that environmental determinants have the potential to both exacerbate (traumatic events) and diminish (neighborhood social cohesion) genetic influences on smoking behaviors.

Fiber diffraction without fibers

Postprocessing of diffraction patterns of completely randomly oriented helical particles, as measured, for example, in so-called "diffract-and-destroy" experiments with an x-ray free electron laser can yield "fiber diffraction" patterns expected of fibrous bundles of the particles. This will allow "single-axis alignment" to be performed computationally, thus obviating the need to do this by experimental means such as forming fibers and laser or flow alignment. The structure of such particles may then be found by either iterative phasing methods or standard methods of fiber diffraction.

Using 124I-PU-H71 PET imaging to predict intratumoral concentration in patients on a phase I trial of PU-H71

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Background: PU-H71 is a Heat Shock Protein 90 inhibitor that can be labeled with 124I without altering its biochemical properties. Intratumoral drug concentration can be calculated based on 124I-PU-H71 (*PU-H71) region of interest analysis and dilution principle. A microdose pilot study has shown uptake of *PU-H71 in a variety of tumors. *PU-H71 PET is currently being used to estimate intratumoral concentrations in subjects on our phase I study. Methods: Patients with previously treated solid tumors or lymphoma are eligible for this phase 1 trial. PU-H71 is given twice-weekly for 2 weeks each 21 days at escalating dose levels. A mix of *PU-H71 and unlabeled PU-H71 is given during cycle 2 followed by serial PET imaging. Patients on the pilot study are administered a microdose of *PU-H71 alone, followed by serial PET scans. Intratumoral PUH-71 concentration is measured directly in optional pre- and post- treatment core needle tumor biopsies (CNB). Results: To date, 13 patients have received PU-H71 on the phase I trial. Of these, 10 have undergone *PU-H71 PET imaging. 4 imaged patients also volunteered for CNBs, with results reported in the table. Of the 10 patients who underwent *PU-H71 imaging in the phase 1 study, 5 also underwent prior *PU-H71 imaging in the microdose pilot. Intratumoral concentrations as calculated in the pilot and phase I studies were in close concordance. Conclusions: *PU-H71 can be used to visualize PU-H71 uptake in a variety of solid tumors and lymphoma, and *PU-H71 PET scans can be used to estimate intratumoral concentrations of PU-H71. Direct intratumoral measurements of PU-H71 correlate reasonably closely with concentrations calculated from *PU-H71 PET imaging. Further refinement of this imaging tool will allow quantitative assessment of PU-H71 uptake in tumors during the ongoing phase I trial. Clinical trial information: NCT01393509. [Table: see text]

Aspirin-triggered resolvin D1 reduces mucosal inflammation and promotes resolution in a murine model of acute lung injury

Acute lung injury (ALI) is a severe illness with excess mortality and no specific therapy. Protective actions were recently uncovered for docosahexaenoic acid-derived mediators, including D-series resolvins. Here, we used a murine self-limited model of hydrochloric acid-induced ALI to determine the effects of aspirin-triggered resolvin D1 (AT-RvD1; 7S,8R,17R-trihydroxy-4Z,9E,11E,13Z,15E,19Z-docosahexaenoic acid) on mucosal injury. RvD1 and its receptor ALX/FPR2 were identified in murine lung after ALI. AT-RvD1 (~0.5-5 μg kg(-1)) decreased peak inflammation, including bronchoalveolar lavage fluid (BALF) neutrophils by ~75%. Animals treated with AT-RvD1 had improved epithelial and endothelial barrier integrity and decreased airway resistance concomitant with increased BALF epinephrine levels. AT-RvD1 inhibited neutrophil-platelet heterotypic interactions by downregulating both P-selectin and its ligand CD24. AT-RvD1 also significantly decreased levels of BALF pro-inflammatory cytokines, including interleukin (IL)-1β, IL-6, Kupffer cells, and tumor necrosis factor-α, and decreased nuclear factor-κB-phosphorylated p65 nuclear translocation. Taken together, these findings indicate that AT-RvD1 displays potent mucosal protection and promotes catabasis after ALI.

Major Variation in Branches of the Abdominal Aorta in New Zealand White Rabbit (Orycotolagus Cuniculus)

The aim of the present study was to investigate the arrangement and major vascular variation of abdominal aorta in NZW rabbit. A total of 28 healthy adult rabbits (14 males and 14 females) with an average (1.3 ± 0.5kg) body weight were used in this study. Deep surgical anaesthesia was done by using combination of xylazine and ketamine at the doses of 10mg/kg and 40mg/kg body weight respectively, and was sacrificed by bleeding through the right ventricle of the heart. Cannulation of the thoracic aorta and stained latex (added with ammonium water and red carmine stain) injection were performed, followed by 10% neutral buffered formalin. Asymmetry of the even branches with their distribution and the way of departure of the arteries from the abdominal aorta were observed. However, double pair ovarian arteries were found in a single animal. The diameter of the caudal mesenteric artery showed significant (p?0.05) difference between male and female. In case of male and female, the variability of the origin (number and level of origin) of testicular, ovarian and profound iliac circumflex arteries was also observed. DOI: http://dx.doi.org/10.3329/ijns.v2i4.13218 International Journal of Natural Sciences (2012), 2(4) 91-98

Anatomical study on origin, course and distribution of cranial and caudal mesenteric arteries in the White New Zealand rabbit (Orycotolagus cuniculus)

The present study was carried out on fifteen healthy adult White New Zealand rabbit (Orycotolagus cuniculus) to clarify the obscure mesenteric arteries, which and their branches which are usually involved in intestinal surgery. The mesenteric artery is a high caliber vessel, 2cm in length dependent on the abdominal aorta, right below the emergence of the vessels destined for the liver and stomach. The animals were sacrificed, injecting diazepam (30 mg/kg) in jugular vein. Cannulation of the abdominal aorta, perfusion with warmed water (40ºC) and stained latex injection (Neoprene 450, Capitol Scientific, Austin, U.S.A, Red carmine stain) were performed, followed by fixation. With formalin (10%) the dissection and photographic documents (Casio Cyber-shot, 12.1 mega pixels) made it possible to systemize the arteries and define the vascular patterns of the viscera. The results prone that the cranial mesenteric artery of the White New Zealand rabbit (Orycotolagus cuniculus) arose from the abdominal aorta, at the level of the second lumbar vertebra, entered the cranial mesentery forming its root, then proceeded caudoventrally in the mesojejunum and continued as the last cecal artery. The cranial mesenteric artery gave off: - Caudal pancreaticoduodenal artery to the right lobe of the pancreas and the descending and ascending parts of the duodenum. Middle colic artery, a small vessel (frequently two) arising from the left wall and passing to the transverse colon, Eighteen to twenty jejunal arteries, Ileocecocolic artery to the ileum, cecum, ascending colon, transverse colon and the cranial part of the descending colon. The caudal mesenteric artery arose from the abdominal aorta at the level of the caudal border of the root of the 6th lumbar transverse process, passed caudoventrally in the descending mesocolon, then divided into: left colic artery to the caudal two thirds of the descending colon, and cranial rectal artery to the cranial segment of the rectum. The obtained results were compared with their corresponding in the domestic animals, especially the domestic carnivores and laboratory animals. DOI: http://dx.doi.org/10.3329/ijns.v2i2.11386 International Journal of Natural Sciences (2012), 2(2):54-59

Home foreclosure and risk of psychiatric morbidity during the recent financial crisis

BACKGROUND

A defining feature of the US economic downturn of 2008-2010 was the alarming rate of home foreclosure. Although a substantial number of US households have experienced foreclosure since 2008, the effects of foreclosure on mental health are unknown. We examined the effects of foreclosure on psychiatric symptomatology in a prospective, population-based community survey.

METHOD

Data were drawn from the Detroit Neighborhoods and Health Study (DNHS), waves 1 and 2 (2008-2010). A probability sample of predominantly African-American adults in Detroit, Michigan participated (n=1547). We examined the association between home foreclosure between waves 1 and 2 and increases in symptoms of DSM-IV major depression and generalized anxiety disorder (GAD).

RESULTS

The most common reasons for foreclosure were an increase in monthly payments, an increase in non-medical expenses and a reduction in family income. Exposure to foreclosure between waves 1 and 2 predicted symptoms of major depression and GAD at wave 2, controlling for symptoms at wave 1. Even after adjusting for wave 1 symptoms, sociodemographics, lifetime history of psychiatric disorder at wave 1 and exposure to other financial stressors between waves 1 and 2, foreclosure was associated with an increased rate of symptoms of major depression [incidence density ratio (IDR) 2.4, 95% confidence interval (CI) 1.6-3.6] and GAD (IDR 1.9, 95% CI 1.4-2.6).

CONCLUSIONS

We provide the first prospective evidence linking foreclosure to the onset of mental health problems. These results, combined with the high rate of home foreclosure since 2008, suggest that the foreclosure crisis may have adverse effects on the mental health of the US population.

Reconstructing an icosahedral virus from single-particle diffraction experiments

The first experimental data from single-particle scattering experiments from free electron lasers (FELs) are now becoming available. The first such experiments are being performed on relatively large objects such as viruses, which produce relatively low-resolution, low-noise diffraction patterns in so-called "diffract-and-destroy" experiments. We describe a very simple test on the angular correlations of measured diffraction data to determine if the scattering is from an icosahedral particle. If this is confirmed, the efficient algorithm proposed can then combine diffraction data from multiple shots of particles in random unknown orientations to generate a full 3D image of the icosahedral particle. We demonstrate this with a simulation for the satellite tobacco necrosis virus (STNV), the atomic coordinates of whose asymmetric unit is given in Protein Data Bank entry 2BUK.

Epigenetic and inflammatory marker profiles associated with depression in a community-based epidemiologic sample

BACKGROUND

Recent work suggests that epigenetic differences may be associated with psychiatric disorders. Here we investigate, in a community-based sample, whether methylation profiles distinguish between individuals with and without lifetime depression. We also investigate the physiologic consequences that may be associated with these profiles.

METHOD

Using whole blood-derived genomic DNA from a subset of participants in the Detroit Neighborhood Health Study (DNHS), we applied methylation microarrays to assess genome-wide methylation profiles for over 14 000 genes in 33 persons who reported a lifetime history of depression and 67 non-depressed adults. Bioinformatic functional analyses were performed on the genes uniquely methylated and unmethylated in each group, and inflammatory biomarkers [interleukin (IL)-6 and C-reactive protein (CRP)] were measured to investigate the possible functional significance of the methylation profiles observed.

RESULTS

Uniquely unmethylated gene sets distinguished between those with versus without lifetime depression. In particular, some processes (e.g. brain development, tryptophan metabolism) showed patterns suggestive of increased methylation among individuals with depression whereas others (e.g. lipoprotein) showed patterns suggestive of decreased methylation among individuals with depression. IL-6 and CRP levels were elevated among those with lifetime depression and, among those with depression only, IL-6 methylation showed an inverse correlation with circulating IL-6 and CRP.

CONCLUSIONS

Genome-wide methylation profiles distinguish individuals with versus without lifetime depression in a community-based setting, and show coordinated signals with pathophysiological mechanisms previously implicated in the etiology of this disorder. Examining epigenetic mechanisms in concert with other dynamic markers of physiologic functioning should improve our understanding of the neurobiology of depression.

Caesarean of Lion (Panthera leo) at Dulahajra Safari Park, Bangladesh

A six years eight months pregnant lioness at the Dulahajara Safari Park, Chakoria, Cox�s Bazar, Bangladesh, was presented with dystocia. This paper described the pre-, intra- and postoperative procedures including anesthetic protocol carried out and performing a caesarean section to remove dead fetuses and the successful recovery of the lioness without complications.