Bioinformatic identification of novel putative photoreceptor specific cis-elements

<p>Abstract</p> <p>Background</p> <p>Cell specific gene expression is largely regulated by different combinations of transcription factors that bind <it>cis</it>-elements in the upstream promoter sequence. However, experimental detection of <it>cis</it>-elements is difficult, expensive, and time-consuming. This provides a motivation for developing bioinformatic methods to identify <it>cis</it>-elements that could prioritize future experimental studies. Here, we use motif discovery algorithms to predict transcription factor binding sites involved in regulating the differences between murine rod and cone photoreceptor populations.</p> <p>Results</p> <p>To identify highly conserved motifs enriched in promoters that drive expression in either rod or cone photoreceptors, we assembled a set of murine rod-specific, cone-specific, and non-photoreceptor background promoter sequences. These sets were used as input to a newly devised motif discovery algorithm called Iterative Alignment/Modular Motif Selection (IAMMS). Using IAMMS, we predicted 34 motifs that may contribute to rod-specific (19 motifs) or cone-specific (15 motifs) expression patterns. Of these, 16 rod- and 12 cone-specific motifs were found in clusters near the transcription start site. New findings include the observation that cone promoters tend to contain TATA boxes, while rod promoters tend to be TATA-less (exempting <it>Rho </it>and <it>Cnga1</it>). Additionally, we identify putative sites for IL-6 effectors (in rods) and RXR family members (in cones) that can explain experimental data showing changes to cell-fate by activating these signaling pathways during rod/cone development. Two of the predicted motifs (NRE and ROP2) have been confirmed experimentally to be involved in cell-specific expression patterns. We provide a full database of predictions as additional data that may contain further valuable information. IAMMS predictions are compared with existing motif discovery algorithms, DME and BioProspector. We find that over 60% of IAMMS predictions are confirmed by at least one other motif discovery algorithm.</p> <p>Conclusion</p> <p>We predict novel, putative <it>cis-</it>elements enriched in the promoter of rod-specific or cone-specific genes. These are candidate binding sites for transcription factors involved in maintaining functional differences between rod and cone photoreceptor populations.</p

Subbarrel patterns in somatosensory cortical barrels can emerge from local dynamic instabilities

Complex spatial patterning, common in the brain as well as in other biological systems, can emerge as a result of dynamic interactions that occur locally within developing structures. In the rodent somatosensory cortex, groups of neurons called "barrels" correspond to individual whiskers on the contralateral face. Barrels themselves often contain subbarrels organized into one of a few characteristic patterns. Here we demonstrate that similar patterns can be simulated by means of local growth-promoting and growth-retarding interactions within the circular domains of single barrels. The model correctly predicts that larger barrels contain more spatially complex subbarrel patterns, suggesting that the development of barrels and of the patterns within them may be understood in terms of some relatively simple dynamic processes. We also simulate the full nonlinear equations to demonstrate the predictive value of our linear analysis. Finally, we show that the pattern formation is robust with respect to the geometry of the barrel by simulating patterns on a realistically shaped barrel domain. This work shows how simple pattern forming mechanisms can explain neural wiring both qualitatively and quantitatively even in complex and irregular domains. © 2009 Ermentrout et al

Human Mas-related G protein-coupled receptors-X1 induce chemokine receptor 2 expression in rat dorsal root ganglia neurons and release of chemokine ligand 2 from the human LAD-2 mast cell line

Primate-specific Mas-related G protein-coupled receptors-X1 (MRGPR-X1) are highly enriched in dorsal root ganglia (DRG) neurons and induce acute pain. Herein, we analyzed effects of MRGPR-X1 on serum response factors (SRF) or nuclear factors of activated T cells (NFAT), which control expression of various markers of chronic pain. Using HEK293, DRG neuron-derived F11 cells and cultured rat DRG neurons recombinantly expressing human MRGPR-X1, we found activation of a SRF reporter gene construct and induction of the early growth response protein-1 via extracellular signal-regulated kinases-1/2 known to play a significant role in the development of inflammatory pain. Furthermore, we observed MRGPR-X1-induced up-regulation of the chemokine receptor 2 (CCR2) via NFAT, which is considered as a key event in the onset of neuropathic pain and, so far, has not yet been described for any endogenous neuropeptide. Up-regulation of CCR2 is often associated with increased release of its endogenous agonist chemokine ligand 2 (CCL2). We also found MRGPR-X1-promoted release of CCL2 in a human connective tissue mast cell line endogenously expressing MRGPR-X1. Thus, we provide first evidence to suggest that MRGPR-X1 induce expression of chronic pain markers in DRG neurons and propose a so far unidentified signaling circuit that enhances chemokine signaling by acting on two distinct yet functionally co-operating cell types. Given the important role of chemokine signaling in pain chronification, we propose that interruption of this signaling circuit might be a promising new strategy to alleviate chemokine-promoted pain

Self-reported smoking cessation activities among Swiss primary care physicians

ABSTRACT: BACKGROUND: Individual counselling, pharmacotherapy, and group therapy are evidence-based interventions that help patients stop smoking. Acupuncture, hypnosis, and relaxation have no demonstrated efficacy on smoking cessation, whereas self-help material may only have a small benefit. The purpose of this study is to assess physicians' current clinical practice regarding smokers motivated to stop smoking. METHODS: The survey included 3385 Swiss primary care physicians. Self-reported use of nine smoking cessation interventions was scored. One point was given for each positive answer about practicing interventions with demonstrated efficacy, i.e. nicotine replacement therapy, bupropion, counselling, group therapy, and smoking cessation specialist. No points were given for the recommendation of acupuncture, hypnosis, relaxation, and self-help material. Multivariable logistic analysis was performed to identify factors associated with a good practice score, defined as &gt;1. RESULTS: The response rate was 55%. Respondents were predominately over the age of 40 years (88%), male (79%), and resided in urban areas (74%). Seventeen percent reported being smokers. Most of the physicians prescribed nicotine replacement therapy (84%), bupropion (65%), or provided counselling (70%). A minority of physicians recommended acupuncture (26%), hypnosis (8%), relaxation (7%), or self-help material (24%). A good practice score was obtained by 85% of respondents. Having attended a smoking cessation training program was the only significant predictor of a good practice score (odds ratio: 6.24 , 95% CI 1.95-20.04). CONCLUSION: The majority of respondents practice recommended smoking cessation interventions. However, there is room for improvement and implementing an evidence-based smoking cessation-training program could provide additional benefit

Barriers to the provision of smoking cessation assistance:A qualitative study among Romanian family physicians

BACKGROUND: Smoking cessation is the most effective intervention to prevent and slow down the progression of several respiratory and other diseases and improve patient outcomes. Romania has legislation and a national tobacco control programme in line with the World Health Organization Framework for Tobacco Control. However, few smokers are advised to quit by their family physicians (FPs). AIM: To identify and explore the perceived barriers that prevent Romanian FPs from engaging in smoking cessation with patients. METHODS: A qualitative study was undertaken. A total of 41 FPs were recruited purposively from Bucharest and rural areas within 600 km of the city. Ten FPs took part in a focus group and 31 participated in semistructured interviews. Analysis was descriptive, inductive and themed, according to the barriers experienced. RESULTS: Five main barriers were identified: limited perceived role for FPs; lack of time during consultations; past experience and presence of disincentives; patients' inability to afford medication; and lack of training in smoking cessation skills. Overarching these specific barriers were key themes of a medical and societal hierarchy, which undermined the FP role, stretched resources and constrained care. CONCLUSIONS: Many of the barriers described by the Romanian FPs reflected universally recognised challenges to the provision of smoking cessation advice. The context of a relatively hierarchical health-care system and limitations of time and resources exacerbated many of the problems and created new barriers that will need to be addressed if Romania is to achieve the aims of its National Programme Against Tobacco Consumption

A Measurement of the Interference Structure Function, R_LT, for the 12C(e,e'p) reaction in the Quasielastic Region

The coincidence cross-section and the interference structure function, R_LT, were measured for the 12C(e,e'p) 11B reaction at quasielastic kinematics and central momentum transfer of q=400 MeV/c. The measurement was at an opening angle of theta_pq=11 degrees, covering a range in missing energy of E_m = 0 to 65 MeV. The R_LT structure function is found to be consistent with zero for E_m > 50 MeV, confirming an earlier study which indicated that R_L vanishes in this region. The integrated strengths of the p- and s-shell are compared with a Distorted Wave Impulse Approximation calculation. The s-shell strength and shape are compared with a Hartree Fock-Random Phase Approximation calculation. The DWIA calculation overestimates the cross sections for p- and s-shell proton knockout as expected, but surprisingly agrees with the extracted R_LT value for both shells. The HF-RPA calculation describes the data more consistently, which may be due to the inclusion of 2-body currents in this calculation.Comment: 8 Pages LaTex, 5 postscript figures. Submitted to Phys. Rev.

Tracking the Expression of Excitatory and Inhibitory Neurotransmission-Related Proteins and Neuroplasticity Markers after Noise Induced Hearing Loss

Excessive exposure to loud noise can damage the cochlea and create a hearing loss. These pathologies coincide with a range of CNS changes including reorganisation of frequency representation, alterations in the pattern of spontaneous activity and changed expression of excitatory and inhibitory neurotransmitters. Moreover, damage to the cochlea is often accompanied by acoustic disorders such as hyperacusis and tinnitus, suggesting that one or more of these neuronal changes may be involved in these disorders, although the mechanisms remain unknown. We tested the hypothesis that excessive noise exposure increases expression of markers of excitation and plasticity, and decreases expression of inhibitory markers over a 32-day recovery period. Adult rats (n = 25) were monaurally exposed to a loud noise (16 kHz, 1/10th octave band pass (115 dB SPL)) for 1-hour, or left as non-exposed controls (n = 5). Animals were euthanased at either 0, 4, 8, 16 or 32 days following acoustic trauma. We used Western Blots to quantify protein levels of GABAA receptor subunit α1 (GABAAα1), Glutamic-Acid Decarboxylase-67 (GAD-67), N-Methyl-D-Aspartate receptor subunit 2A (NR2A), Calbindin (Calb1) and Growth Associated Protein 43 (GAP-43) in the Auditory Cortex (AC), Inferior Colliculus (IC) and Dorsal Cochlear Nucleus (DCN). Compared to sham-exposed controls, noise-exposed animals had significantly (p<0.05): lower levels of GABAAα1 in the contralateral AC at day-16 and day-32, lower levels of GAD-67 in the ipsilateral DCN at day-4, lower levels of Calb1 in the ipsilateral DCN at day-0, lower levels of GABAAα1 in the ipsilateral AC at day-4 and day-32. GAP-43 was reduced in the ipsilateral AC for the duration of the experiment. These complex fluctuations in protein expression suggests that for at least a month following acoustic trauma the auditory system is adapting to a new pattern of sensory input

Spraying 2,4-D by Airplane on Sand Sagebrush and Other Plants of the Southern Great Plains

This material was digitized as part of a cooperative project between the Society for Range Management and the University of Arizona Libraries.The Journal of Range Management archives are made available by the Society for Range Management and the University of Arizona Libraries. Contact [email protected] for further information.Migrated from OJS platform August 202

Eight-year Comparisons of Continuous and Rotational Grazing on the Southern Plains Experimental Range

This material was digitized as part of a cooperative project between the Society for Range Management and the University of Arizona Libraries.The Journal of Range Management archives are made available by the Society for Range Management and the University of Arizona Libraries. Contact [email protected] for further information.Migrated from OJS platform August 202