Excited-state reaction dynamics of bacteriorhodopsin studied by femtosecond spectroscopy

The photodynamics of bacteriorhodopsin were studied by transient absorption and gain measurements after excitation with femtosecond pulses at 620 nm. With probing pulses at longer wavelengths (λ > 770 nm) the previously reported formation of the J intermediate (with a time constant of 500±100 fs) was confirmed. With probing pulses around 700 nm, a faster process with a relaxation time of 200±70 fs was observed. The data analysis strongly suggests that this kinetic constant describes the reactive motion of the polyatomic molecule on its excited-state potential energy surface, i.e. one observes directly the incipient isomerization of the retinal molecule. The minimum of the S1 potential energy surface reached in 200 fs lies approximately 13300 cm−1 above the ground state of bacteriorhodopsin and from this minimum the intermediate J is formed with a time constant of 500 fs

Predator-Induced Vertical Behavior of a Ctenophore

Although many studies have focused on Mnemiopsis leidyi predation, little is known about the role of this ctenophore as prey when abundant in native and invaded pelagic systems. We examined the response of the ctenophore M. leidyi to the predatory ctenophore Beroe ovata in an experiment in which the two species could potentially sense each other while being physically separated. On average, M. leidyi responded to the predator’s presence by increasing variability in swimming speeds and by lowering their vertical distribution. Such behavior may help explain field records of vertical migration, as well as stratified and near-bottom distributions of M. leidyi

Association of low numbers of CD 206‐positive cells with loss of ICC in the gastric body of patients with diabetic gastroparesis

Background There is increasing evidence for specific cellular changes in the stomach of patients with diabetic ( DG ) and idiopathic ( IG ) gastroparesis. The most significant findings are loss of interstitial cells of Cajal ( ICC ), neuronal abnormalities, and an immune cellular infiltrate. Studies done in diabetic mice have shown a cytoprotective effect of CD 206+ M2 macrophages. To quantify overall immune cellular infiltrate, identify macrophage populations, and quantify CD 206+ and i NOS + cells. To investigate associations between cellular phenotypes and ICC . Methods Full thickness gastric body biopsies were obtained from non‐diabetic controls (C), diabetic controls ( DC ), DG , and IG patients. Sections were labeled for CD 45, CD 206, Kit, i NOS , and putative human macrophage markers ( HAM 56, CD 68, and EMR 1). Immunoreactive cells were quantified from the circular muscle layer. Key Results Significantly fewer ICC were detected in DG and IG tissues, but there were no differences in the numbers of cells immunoreactive for other markers between patient groups. There was a significant correlation between the number of CD 206+ cells and ICC in DG and DC patients, but not in C and IG and a significant correlation between i NOS + cells and ICC in the DC group, but not the other groups. CD 68 and HAM 56 reliably labeled the same cell populations, but EMR 1 labeled other cell types. Conclusions & Inferences Depletion of ICC and correlation with changes in CD 206+ cell numbers in DC and DG patients suggests that in humans, like mice, CD 206+ macrophages may play a cytoprotective role in diabetes. These findings may lead to novel therapeutic options, targeting alternatively activated macrophages. Loss of interstitial cells of Cajal and an immune cell infiltrate have been identified in the gastric smooth muscle of patients with gastroparesis. This study reports a correlation between ICC numbers and CD206‐positive, alternatively activated M2 macrophage numbers in the gastric body of patients with diabetes (Panels B, D), but not in non‐diabetic controls (A) or idiopathic gastroparesis (C). Thus, CD206‐positive macrophages may play a cytoprotective role in the stomach of diabetic patients.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/108285/1/nmo12389-sup-0001-TableS1.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/108285/2/nmo12389.pd

Methyl iodide poisoning presenting as a mimic of acute stroke: a case report

<p>Abstract</p> <p>Introduction</p> <p>Stroke mimics are usually non-vascular disease processes. These raise the possibility of a stroke and are common in clinical practice. It is necessary to distinguish these mimics in order to provide early and appropriate management, as well as reduce possible harm on our patient.</p> <p>Case presentation</p> <p>We report the case of a 50-year-old Caucasian man who developed symptoms suggestive of posterior circulation stroke after he was exposed to methyl iodide at his workplace. Results of stroke investigations of our patient were negative, and a detailed occupational history clinched the diagnosis. Acute presentation with a stroke-like picture is rare in cases of methyl iodide poisoning. We have attempted to discuss the differential diagnosis of stroke mimics through a review of literature.</p> <p>Conclusion</p> <p>Stroke mimics are difficult to diagnose in an emergency room situation and may be initially treated as stroke. This case report underlines the importance of history taking, especially occupational history, in the differential diagnosis of stroke. We also stress the need to recognize mimics at presentation in order to arrive at an early and appropriate management of patients.</p

Combining comparative genomics with de novo motif discovery to identify human transcription factor DNA-binding motifs

BACKGROUND: As more and more genomes are sequenced, comparative genomics approaches provide a methodology for identifying conserved regulatory elements that may be involved in gene regulations. RESULTS: We developed a novel method to combine comparative genomics with de novo motif discovery to identify human transcription factor binding motifs that are overrepresented and conserved in the upstream regions of a set of co-regulated genes. The method is validated by analyzing a well-characterized muscle specific gene set, and the results showed that our approach performed better than the existing programs in terms of sensitivity and prediction rate. CONCLUSION: The newly developed method can be used to extract regulatory signals in co-regulated genes, which can be derived from the microarray clustering analysis

Increased platelet counts and platelet activation in early symptomatic versus asymptomatic carotid stenosis and relationship with microembolic status: Results from the Platelets And Carotid Stenosis (PACS) Study

Background: Cerebral microembolic signals (MES) may predict increased stroke risk in carotid stenosis. However, the relationship between platelet counts or platelet activation status and MES in symptomatic versus asymptomatic carotid stenosis has not been comprehensively assessed. Setting: University teaching hospitals. Methods: This prospective, pilot observational study assessed platelet counts and platelet activation status, and the relationship between platelet activation and MES in asymptomatic versus early (≤4 weeks after TIA/stroke) and late phase (≥3 months) symptomatic moderate or severe (≥50%) carotid stenosis patients. Full blood count measurements were performed, and whole blood flow cytometry was used to quantify platelet surface activation marker expression (CD62P and CD63) and circulating leucocyte-platelet complexes. Bilateral simultaneous transcranial Doppler ultrasound monitoring of the middle cerebral arteries was performed for 1 hour to classify patients as MES-positive or MES-negative. Results: Data from 31 asymptomatic patients were compared with 46 symptomatic patients in the early phase, and 35 of these patients followed up to the late phase after symptom onset. The median platelet count (211 vs. 200 x 109/L; p=0.03) and the median % lymphocyte-platelet complexes were higher in early symptomatic than asymptomatic patients (2.8 vs. 2.4%, p=0.001). The % lymphocyte-platelet complexes was higher in early symptomatic than asymptomatic patients with ≥70% carotid stenosis (p=0.0005), and in symptomatic patients recruited within 7 days of symptom onset (p=0.028). Complete TCD data were available in 25 asymptomatic and 31 early phase symptomatic, and 27 late phase symptomatic patients. 12% of asymptomatic versus 32% of early phase symptomatic (p=0.02) and 19% of late phase symptomatic patients (p=0.2) were MES-positive. Early symptomatic MES-negative patients had ahigher % lymphocyte-platelet complexes than asymptomatic MES-negative patients (2.8 vs. 2.3%; p=0.0085). Discussion: Recently symptomatic carotid stenosis patients have higher platelet counts (potentially reflecting increased platelet production, mobilisation or reduced clearance) and platelet activation status than asymptomatic patients. MES were more frequently detected in early symptomatic than asymptomatic patients, but the differences between late symptomatic and asymptomatic groups were not significant. Increased lymphocyte-platelet complex formation in recently symptomatic vs. asymptomatic MES-negative patients indicates enhanced platelet activation in this early symptomatic subgroup. Platelet biomarkers, in combination with TCD, have the potential to aid risk-stratification in asymptomatic and symptomatic carotid stenosis patients

A Bayesian Search for Transcriptional Motifs

Identifying transcription factor (TF) binding sites (TFBSs) is an important step towards understanding transcriptional regulation. A common approach is to use gaplessly aligned, experimentally supported TFBSs for a particular TF, and algorithmically search for more occurrences of the same TFBSs. The largest publicly available databases of TF binding specificities contain models which are represented as position weight matrices (PWM). There are other methods using more sophisticated representations, but these have more limited databases, or aren't publicly available. Therefore, this paper focuses on methods that search using one PWM per TF. An algorithm, MATCHTM, for identifying TFBSs corresponding to a particular PWM is available, but is not based on a rigorous statistical model of TF binding, making it difficult to interpret or adjust the parameters and output of the algorithm. Furthermore, there is no public description of the algorithm sufficient to exactly reproduce it. Another algorithm, MAST, computes a p-value for the presence of a TFBS using true probabilities of finding each base at each offset from that position. We developed a statistical model, BaSeTraM, for the binding of TFs to TFBSs, taking into account random variation in the base present at each position within a TFBS. Treating the counts in the matrices and the sequences of sites as random variables, we combine this TFBS composition model with a background model to obtain a Bayesian classifier. We implemented our classifier in a package (SBaSeTraM). We tested SBaSeTraM against a MATCHTM implementation by searching all probes used in an experimental Saccharomyces cerevisiae TF binding dataset, and comparing our predictions to the data. We found no statistically significant differences in sensitivity between the algorithms (at fixed selectivity), indicating that SBaSeTraM's performance is at least comparable to the leading currently available algorithm. Our software is freely available at: http://wiki.github.com/A1kmm/sbasetram/building-the-tools

Dissolution dominating calcification process in polar pteropods close to the point of aragonite undersaturation

Thecosome pteropods are abundant upper-ocean zooplankton that build aragonite shells. Ocean acidification results in the lowering of aragonite saturation levels in the surface layers, and several incubation studies have shown that rates of calcification in these organisms decrease as a result. This study provides a weight-specific net calcification rate function for thecosome pteropods that includes both rates of dissolution and calcification over a range of plausible future aragonite saturation states (Omega_Ar). We measured gross dissolution in the pteropod Limacina helicina antarctica in the Scotia Sea (Southern Ocean) by incubating living specimens across a range of aragonite saturation states for a maximum of 14 days. Specimens started dissolving almost immediately upon exposure to undersaturated conditions (Omega_Ar,0.8), losing 1.4% of shell mass per day. The observed rate of gross dissolution was different from that predicted by rate law kinetics of aragonite dissolution, in being higher at Var levels slightly above 1 and lower at Omega_Ar levels of between 1 and 0.8. This indicates that shell mass is affected by even transitional levels of saturation, but there is, nevertheless, some partial means of protection for shells when in undersaturated conditions. A function for gross dissolution against Var derived from the present observations was compared to a function for gross calcification derived by a different study, and showed that dissolution became the dominating process even at Omega_Ar levels close to 1, with net shell growth ceasing at an Omega_Ar of 1.03. Gross dissolution increasingly dominated net change in shell mass as saturation levels decreased below 1. As well as influencing their viability, such dissolution of pteropod shells in the surface layers will result in slower sinking velocities and decreased carbon and carbonate fluxes to the deep ocean

Beneficial effect of carotid endarterectomy in symptomatic patients with high-grade carotid stenosis

Background. Without strong evidence of benefit, the use of carotid endarterectomy for prophylaxis against stroke rose dramatically until the mid-1980s, then declined. Our investigation sought to determine whether carotid endarterectomy reduces the risk of stroke among patients with a recent adverse cerebrovascular event and ipsilateral carotid stenosis. Method. We conducted a randomized trial at 50 clinical centers throughout the United States and Canada, in patients in two predetermined strata based on the severity of carotid stenosis—30 to 69 percent and 70 to 99 percent. We report here the results in the 659 patients in the latter stratum, who had had a hemispheric or retinal transient ischemic attack or a nondisabling stroke within the 120 days before entry and had stenosis of 70 to 99 percent in the symptomatic carotid artery. All patients received optimal medical care, including antiplatelet therapy. Those assigned to surgical treatment underwent carotid endarterectomy performed by neurosurgeons or vascular surgeons. All patients were examined by neurologists 1, 3, 6, 9, and 12 months after entry and then every 4 months. End points were assessed by blinded, independent case review. No patient was lost to follow-up. Results. Life-table estimates of the cumulative risk of any ipsilateral stroke at two years were 26 percent in the 331 medical patients and 9 percent in the 328 surgical patients—an absolute risk reduction (±SE) of 17±3.5 percent (P\u3c0.001). For a major or fatal ipsilateral stroke, the corresponding estimates were 13.1 percent and 2.5 percent — an absolute risk reduction of 10.6±2.6 percent (P\u3c0.001 ). Conclusion. Carotid endarterectomy was still found to be beneficial when all strokes and deaths were included in the analysis (P\u3c0.001). Carotid endarterectomy is highly beneficial to patients with recent hemispheric and retinal transient ischemic attacks or nondisabling strokes and ipsilateral high-grade stenosis (70 to 99 percent) of the internal carotid artery. (N Engl J Med 1991; 325:445–53.). © 1991, Massachusetts Medical Society. All rights reserved

Discovery of a Sub-Parsec Radio Counterjet in the Nucleus of Centaurus A

A sub-parsec scale radio counterjet has been detected in the nucleus of the closest radio galaxy, Centaurus A (NGC 5128), with VLBI imaging at 2.3 and 8.4 GHz. This is one of the first detections of a VLBI counterjet and provides new constraints on the kinematics of the radio jets emerging from the nucleus of Cen A. A bright, compact core is seen at 8.4 GHz, along with a jet extending along P.A. 51 degrees. The core is completely absorbed at 2.3 GHz. Our images show a much wider gap between the base of the main jet and the counterjet at 2.3 GHz than at 8.4 GHz and also that the core has an extraordinarily inverted spectrum. These observations provide evidence that the innermost 0.4-0.8 pc of the source is seen through a disk or torus of ionized gas which is opaque at low frequencies due to free-free absorption.Comment: 3 pages, 2 postscript figures, scheduled for publication in August 1, 1996 issue of Ap.J. Letter