Huntingtin-associated protein 1: Eutherian adaptation from a TRAK-like protein, conserved gene promoter elements, and localization in the human intestine

Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.Background: Huntingtin-associated Protein 1 (HAP1) is expressed in neurons and endocrine cells, and is critical for postnatal survival in mice. HAP1 shares a conserved “HAP1_N” domain with TRAfficking Kinesin proteins TRAK1 and TRAK2 (vertebrate), Milton (Drosophila) and T27A3.1 (C. elegans). HAP1, TRAK1 and TRAK2 have a degree of common function, particularly regarding intracellular receptor trafficking. However, TRAK1, TRAK2 and Milton (which have a “Milt/TRAK” domain that is absent in human and rodent HAP1) differ in function to HAP1 in that they are mitochondrial transport proteins, while HAP1 has emerging roles in starvation response. We have investigated HAP1 function by examining its evolution, and upstream gene promoter sequences. We performed phylogenetic analyses of the HAP1_N domain family of proteins, incorporating HAP1 orthologues (identified by genomic synteny) from 5 vertebrate classes, and also searched the Dictyostelium proteome for a common ancestor. Computational analyses of mammalian HAP1 gene promoters were performed to identify phylogenetically conserved regulatory motifs. Results: We found that as recently as marsupials, HAP1 contained a Milt/TRAK domain and was more similar to TRAK1 and TRAK2 than to eutherian HAP1. The Milt/TRAK domain likely arose post multicellularity, as it was absent in the Dictyostelium proteome. It was lost from HAP1 in the eutherian lineage, and also from T27A3.1 in C. elegans. The HAP1 promoter from human, mouse, rat, rabbit, horse, dog, Tasmanian devil and opossum contained common sites for transcription factors involved in cell cycle, growth, differentiation, and stress response. A conserved arrangement of regulatory elements was identified, including sites for caudal-related homeobox transcription factors (CDX1 and CDX2), and myc-associated factor X (MAX) in the region of the TATA box. CDX1 and CDX2 are intestine-enriched factors, prompting investigation of HAP1 protein expression in the human duodenum. HAP1 was localized to singly dispersed mucosal cells, including a subset of serotonin-positive enterochromaffin cells. Conclusion: We have identified eutherian HAP1 as an evolutionarily recent adaptation of a vertebrate TRAK protein-like ancestor, and found conserved CDX1/CDX2 and MAX transcription factor binding sites near the TATA box in mammalian HAP1 gene promoters. We also demonstrated that HAP1 is expressed in endocrine cells of the human gut

Regional differences in nutrient-induced secretion of gut serotonin

This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.Enterochromaffin (EC) cells located in the gastrointestinal (GI) tract provide the vast majority of serotonin (5‐HT) in the body and constitute half of all enteroendocrine cells. EC cells respond to an array of stimuli, including various ingested nutrients. Ensuing 5‐HT release from these cells plays a diverse role in regulating gut motility as well as other important responses to nutrient ingestion such as glucose absorption and fluid balance. Recent data also highlight the role of peripheral 5‐HT in various pathways related to metabolic control. Details related to the manner by which EC cells respond to ingested nutrients are scarce and as that the nutrient environment changes along the length of the gut, it is unknown whether the response of EC cells to nutrients is dependent on their GI location. The aim of the present study was to identify whether regional differences in nutrient sensing capability exist in mouse EC cells. We isolated mouse EC cells from duodenum and colon to demonstrate differential responses to sugars depending on location. Measurements of intracellular calcium concentration and 5‐HT secretion demonstrated that colonic EC cells are more sensitive to glucose, while duodenal EC cells are more sensitive to fructose and sucrose. Short‐chain fatty acids (SCFAs), which are predominantly synthesized by intestinal bacteria, have been previously associated with an increase in circulating 5‐HT; however, we find that SCFAs do not acutely stimulate EC cell 5‐HT release. Thus, we highlight that EC cell physiology is dictated by regional location within the GI tract, and identify differences in the regional responsiveness of EC cells to dietary sugars

The Characterization of Ribosomal RNA Gene Chromatin from Physarum Polycephalum

We have isolated ribosomal RNA gene (rDNA) chromatin from Physarum polycephalum using a nucleolar isolation procedure that minimizes protein loss from chromatin and, subsequently, either agarose gel electrophoresis or metrizamide gradient centrifugation to purify this chromatin fraction (Amero, S. A., Ogle, R. C., Keating, J. L., Montoya, V. L., Murdoch, W. L., and Grainger, R. M. (1988) J. Biol. Chem. 263, 10725-10733). Metrizamide-purified rDNA chromatin obtained from nucleoli isolated according to the new procedure has a core histone/DNA ratio of 0.77:1. The major core histone classes comigrate electrophoretically with their nuclear counterparts on Triton-acid-urea/sodium dodecyl sulfate two-dimensional gels, although they may not possess the extent of secondary modification evident with the nuclear histones. This purified rDNA chromatin also possesses RNA polymerase I activity, and many other nonhistone proteins, including two very abundant proteins (26 and 38 kDa) that may be either ribonucleoproteins or nucleolar matrix proteins. Micrococcal nuclease digestion of the metrizamide-purified rDNA chromatin produces particles containing 145-base pair DNA fragments identical in length to those in total chromatin and which contain both transcribed and nontranscribed rDNA sequences. Some smaller fragments (30, 70, and 110 base pairs) are also seen, but their sequence content is not known. These particles sediment uniformly at 11 S in sucrose gradients containing 15 mM NaCl, and at 4-11 S in gradients containing 0.35 M NaCl. Particles enriched in gene or nontranscribed spacer sequences are not resolved in these sucrose gradients or in metrizamide gradients. Our findings suggest that the rDNA chromatin fraction we have identified contains transcriptionally active genes and that an organized, particle-containing structure exists in active rDNA chromatin

The Purification of Ribosomal RNA Gene Chromatin from Physarum Polycephalum

We have undertaken the purification of ribosomal RNA gene (rDNA) chromatin from the slime mold Physarum polycephalum, in order to study its chromatin structure. In this organism rDNA exists in nucleoli as highly repeated minichromosomes, and one can obtain crude chromatin fractions highly enriched in rDNA from isolated nucleoli. We first developed a nucleolar isolation method utilizing polyamines as stabilization agents that results in a chromatin fraction containing far more protein than is obtained by the more commonly used divalent cation isolation methods. The latter method appears to result in extensive histone loss during chromatin isolations. Two methods were then used for purifying rDNA chromatin from nucleoli isolated by the polyamine procedure. We found that rDNA chromatin migrates as a single band in agarose gels, well separated from other components in the chromatin preparation. Although the utility of this technique is somewhat limited by low yields and by progressive stripping of protein from rDNA chromatin, it can provide useful information about rDNA chromatin protein composition. The application of this technique to the fractionation of gene and spacer chromatin fragments produced by restriction enzyme digestion is discussed. We also found that rDNA chromatin, if RNase-treated, bands discretely in metrizamide equilibrium density gradients with a density lighter than that of non-nucleolar chromatin. These characteristics suggest that we have identified a transcriptionally active rDNA chromatin fraction which possesses a lower protein to DNA ratio than does non-nucleolar chromatin. This technique yields sufficient purified rDNA chromatin for further biochemical studies and does not cause extensive protein stripping. The procedures developed here should be applicable to the analysis of a variety of chromatin fractions in other systems

Factors contributing to disparities in mortality among patients with non-small-cell lung cancer

Historically, non-small-cell lung cancer (NSCLC) patients who are non-white, have low incomes, low educational attainment, and non-private insurance have worse survival. We assessed whether differences in survival were attributable to sociodemographic factors, clinical characteristics at diagnosis, or treatments received. We surveyed a multiregional cohort of patients diagnosed with NSCLC from 2003 to 2005 and followed through 2012. We used Cox proportional hazard analyses to estimate the risk of death associated with race/ethnicity, annual income, educational attainment, and insurance status, unadjusted and sequentially adjusting for sociodemographic factors, clinical characteristics, and receipt of surgery, chemotherapy, and radiotherapy. Of 3250 patients, 64% were white, 16% black, 7% Hispanic, and 7% Asian; 36% of patients had income

Factors contributing to disparities in mortality among patients with non–small‐cell lung cancer

Historically, non–small‐cell lung cancer (NSCLC) patients who are non‐white, have low incomes, low educational attainment, and non‐private insurance have worse survival. We assessed whether differences in survival were attributable to sociodemographic factors, clinical characteristics at diagnosis, or treatments received. We surveyed a multiregional cohort of patients diagnosed with NSCLC from 2003 to 2005 and followed through 2012. We used Cox proportional hazard analyses to estimate the risk of death associated with race/ethnicity, annual income, educational attainment, and insurance status, unadjusted and sequentially adjusting for sociodemographic factors, clinical characteristics, and receipt of surgery, chemotherapy, and radiotherapy. Of 3250 patients, 64% were white, 16% black, 7% Hispanic, and 7% Asian; 36% of patients had incomes <$20 000/y; 23$60 000/y, not attending college, and not having private insurance were all associated with an increased risk of mortality. Black‐white differences were not statistically significant after adjustment for sociodemographic factors, although patients with patients without a high school diploma and patients with incomes <$40 000/y continued to have an increased risk of mortality. Differences by educational attainment were not statistically significant after adjustment for clinical characteristics. Differences by income were not statistically significant after adjustment for clinical characteristics and treatments. Clinical characteristics and treatments received primarily contributed to mortality disparities by race/ethnicity and socioeconomic status in patients with NSCLC. Additional efforts are needed to assure timely diagnosis and use of effective treatment to lessen these disparities.Using data from the Cancer Care Outcomes Research and Surveillance (CanCORS) consortium, a large, multi‐regional observational study of newly diagnosed cancer patients, we documented higher unadjusted mortality for NSCLC among patients who were black, have lower income, less well‐educated, and with non‐private insurance. We used a series of Cox proportional hazards model to estimate the increased risk of death associated with sociodemographic factors, clinical characteristics, and treatments received to determine what accounted for the disparities. We found that patients’ clinical characteristics and treatments received primarily contributed to the mortality disparities that we observed in patients with NSCLC.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146607/1/cam41796.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146607/2/cam41796_am.pd

Linking field-based ecological data with remotely sensed data using a geographic information system in two malaria endemic urban areas of Kenya

BACKGROUND: Remote sensing technology provides detailed spectral and thermal images of the earth's surface from which surrogate ecological indicators of complex processes can be measured. METHODS: Remote sensing data were overlaid onto georeferenced entomological and human ecological data randomly sampled during April and May 2001 in the cities of Kisumu (population ≈ 320,000) and Malindi (population ≈ 81,000), Kenya. Grid cells of 270 meters × 270 meters were used to generate spatial sampling units for each city for the collection of entomological and human ecological field-based data. Multispectral Thermal Imager (MTI) satellite data in the visible spectrum at five meter resolution were acquired for Kisumu and Malindi during February and March 2001, respectively. The MTI data were fit and aggregated to the 270 meter × 270 meter grid cells used in field-based sampling using a geographic information system. The normalized difference vegetation index (NDVI) was calculated and scaled from MTI data for selected grid cells. Regression analysis was used to assess associations between NDVI values and entomological and human ecological variables at the grid cell level. RESULTS: Multivariate linear regression showed that as household density increased, mean grid cell NDVI decreased (global F-test = 9.81, df 3,72, P-value = <0.01; adjusted R(2 )= 0.26). Given household density, the number of potential anopheline larval habitats per grid cell also increased with increasing values of mean grid cell NDVI (global F-test = 14.29, df 3,36, P-value = <0.01; adjusted R(2 )= 0.51). CONCLUSIONS: NDVI values obtained from MTI data were successfully overlaid onto georeferenced entomological and human ecological data spatially sampled at a scale of 270 meters × 270 meters. Results demonstrate that NDVI at such a scale was sufficient to describe variations in entomological and human ecological parameters across both cities

CMB polarimetry with BICEP: instrument characterization, calibration, and performance

BICEP is a ground-based millimeter-wave bolometric array designed to target the primordial gravity wave signature on the polarization of the cosmic microwave background (CMB) at degree angular scales. Currently in its third year of operation at the South Pole, BICEP is measuring the CMB polarization with unprecedented sensitivity at 100 and 150 GHz in the cleanest available 2% of the sky, as well as deriving independent constraints on the diffuse polarized foregrounds with select observations on and off the Galactic plane. Instrument calibrations are discussed in the context of rigorous control of systematic errors, and the performance during the first two years of the experiment is reviewed.Comment: 12 pages, 15 figures, updated version of a paper accepted for Millimeter and Submillimeter Detectors and Instrumentation for Astronomy IV, Proceedings of SPIE, 7020, 200

Individual Response to Risk As a Function of Normative Social Pressure: A Pilot Study of Seat Belt Use

The authors attempt to clarify some of the variables that influence whether people act appropriately when a Risk is substantial and subject to individual control. They do so by reporting results of a pilot study of seat belt use. Also, the authors believe their approach to be generalizable to problems such as encouraging people to test for radon, to use condoms to prevent AIDS or to quit smoking

Urologic manifestations of Goldenhar syndrome

ObjectiveGoldenhar syndrome (oculoauriculovertebral dysplasia) is associated with anomalies in multiple organ systems. Renal abnormalities have also been reported with the complex, but the incidence of associated genitourinary malformations has not been defined.MethodWe have reviewed our experience with 28 children with Goldenhar syndrome evaluated during the past twelve years. Twenty children underwent imaging evaluation of the urinary tract and 14 (70% of those imaged) children had urinary tract anomalies.ResultsThe majority of anomalies presented as an incidental finding on a screening ultrasound (8 patients) or during cardiac catheterization (2 patients). Two children presented with urinary tract infection, 1 child presented with renal failure, and another was diagnosed antenatally. The genitourinary anomalies included the following: ectopic and/or fused kidneys (8 patients), renal agenesis (7), vesicoureteral reflux (5), ureteropelvic junction obstruction (2), ureteral duplication (2), and multicystic kidney (1 patient). Four children have undergone surgical intervention.ConclusionOur experience in children with Goldenhar syndrome suggests that the incidence of genitourinary anomalies is higher than previously reported. A screening ultrasound in the neonatal period allows for early intervention in those children with significant urologic abnormalities.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/31881/1/0000833.pd