Phonation Threshold Pressure Measurement with a Semi-Occluded Vocal Tract

ERIC Educational Resources Information Center

Titze, Ingo R.

2009-01-01

Purpose: The purpose of this article was to determine if a semi-occluded vocal tract could be used to measure phonation threshold pressure. This is in contrast to the shutter technique, where an alternation between a fully occluded tract and an unoccluded tract is used. Method: Five male and 5 female volunteers phonated through a thin straw held…

Recent development of transcatheter closure of atrial septal defect and patent foramen ovale with occluders.

PubMed

Tang, Baiyu; Su, Feng; Sun, Xiangke; Wu, Qin; Xing, Quansheng; Li, Suming

2018-01-01

Atrial septal defect (ASD) and patent foramen ovale (PFO) are common clinical congenital heart defects. As an effective method for the treatment of ASD and PFO, transcatheter closure with occluders presents many advantages, including safety, ease of operation, minimal invasiveness, and reduced complications. This contribution reviews the various types of occluders currently used in clinical applications and under development, including non degradable occluders, partially degradable occluders, and totally degradable occluders. A number of case studies are described in detail. Comparison is made on the treatment outcomes using different occulders. Future development of transcatheter closure is discussed, in particular the use of totally degradable occluders. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 106B: 433-443, 2018. © 2016 Wiley Periodicals, Inc.

A Taxonomy of 3D Occluded Objects Recognition Techniques

NASA Astrophysics Data System (ADS)

Soleimanizadeh, Shiva; Mohamad, Dzulkifli; Saba, Tanzila; Al-ghamdi, Jarallah Saleh

2016-03-01

The overall performances of object recognition techniques under different condition (e.g., occlusion, viewpoint, and illumination) have been improved significantly in recent years. New applications and hardware are shifted towards digital photography, and digital media. This faces an increase in Internet usage requiring object recognition for certain applications; particularly occulded objects. However occlusion is still an issue unhandled, interlacing the relations between extracted feature points through image, research is going on to develop efficient techniques and easy to use algorithms that would help users to source images; this need to overcome problems and issues regarding occlusion. The aim of this research is to review recognition occluded objects algorithms and figure out their pros and cons to solve the occlusion problem features, which are extracted from occluded object to distinguish objects from other co-existing objects by determining the new techniques, which could differentiate the occluded fragment and sections inside an image.

Form Perception of Partly Occluded Shapes in 4-Month-Old Infants

ERIC Educational Resources Information Center

de Wit, Tessa C. J.; Vrins, Sven; Dejonckheere, Peter J. N.; van Lier, Rob

2008-01-01

Two habituation experiments were conducted to investigate how 4-month-old infants perceive partly occluded shapes. In the first experiment, we presented a simple, partly occluded shape to the infants until habituation was reached. Then we showed either a probable completion (one that would be predicted on the basis of both local and global cues)…

Dynamic representation of partially occluded objects in primate prefrontal and visual cortex

PubMed Central

Choi, Hannah; Shea-Brown, Eric

2017-01-01

Successful recognition of partially occluded objects is presumed to involve dynamic interactions between brain areas responsible for vision and cognition, but neurophysiological evidence for the involvement of feedback signals is lacking. Here, we demonstrate that neurons in the ventrolateral prefrontal cortex (vlPFC) of monkeys performing a shape discrimination task respond more strongly to occluded than unoccluded stimuli. In contrast, neurons in visual area V4 respond more strongly to unoccluded stimuli. Analyses of V4 response dynamics reveal that many neurons exhibit two transient response peaks, the second of which emerges after vlPFC response onset and displays stronger selectivity for occluded shapes. We replicate these findings using a model of V4/vlPFC interactions in which occlusion-sensitive vlPFC neurons feed back to shape-selective V4 neurons, thereby enhancing V4 responses and selectivity to occluded shapes. These results reveal how signals from frontal and visual cortex could interact to facilitate object recognition under occlusion. PMID:28925354

Identification and characterization of steady and occluded water in drinking water distribution systems.

PubMed

Tong, Huiyan; Zhao, Peng; Zhang, Hongwei; Tian, Yimei; Chen, Xi; Zhao, Weigao; Li, Mei

2015-01-01

Deterioration and leakage of drinking water in distribution systems have been a major issue in the water industry for years, which are associated with corrosion. This paper discovers that occluded water in the scales of the pipes has an acidic environment and high concentration of iron, manganese, chloride, sulfate and nitrate, which aggravates many pipeline leakage accidents. Six types of water samples have been analyzed under the flowing and stagnant periods. Both the water in the exterior of the tubercles and stagnant water carry suspended iron particles, which explains the occurrence of "red water" when the system hydraulic conditions change. Nitrate is more concentrated in occluded water under flowing condition in comparison with that in flowing water. However, the concentration of nitrate in occluded water under stagnant condition is found to be less than that in stagnant water. A high concentration of manganese is found to exist in steady water, occluded water and stagnant water. These findings impact secondary pollution and the corrosion of pipes and containers used in drinking water distribution systems. The unique method that taking occluded water from tiny holes which were drilled from the pipes' exteriors carefully according to the positions of corrosion scales has an important contribution to research on corrosion in distribution systems. And this paper furthers our understanding and contributes to the growing body of knowledge regarding occluded environments in corrosion scales. Copyright © 2014 Elsevier Ltd. All rights reserved.

Recognition of partially occluded threat objects using the annealed Hopefield network

NASA Technical Reports Server (NTRS)

Kim, Jung H.; Yoon, Sung H.; Park, Eui H.; Ntuen, Celestine A.

1992-01-01

Recognition of partially occluded objects has been an important issue to airport security because occlusion causes significant problems in identifying and locating objects during baggage inspection. The neural network approach is suitable for the problems in the sense that the inherent parallelism of neural networks pursues many hypotheses in parallel resulting in high computation rates. Moreover, they provide a greater degree of robustness or fault tolerance than conventional computers. The annealed Hopfield network which is derived from the mean field annealing (MFA) has been developed to find global solutions of a nonlinear system. In the study, it has been proven that the system temperature of MFA is equivalent to the gain of the sigmoid function of a Hopfield network. In our early work, we developed the hybrid Hopfield network (HHN) for fast and reliable matching. However, HHN doesn't guarantee global solutions and yields false matching under heavily occluded conditions because HHN is dependent on initial states by its nature. In this paper, we present the annealed Hopfield network (AHN) for occluded object matching problems. In AHN, the mean field theory is applied to the hybird Hopfield network in order to improve computational complexity of the annealed Hopfield network and provide reliable matching under heavily occluded conditions. AHN is slower than HHN. However, AHN provides near global solutions without initial restrictions and provides less false matching than HHN. In conclusion, a new algorithm based upon a neural network approach was developed to demonstrate the feasibility of the automated inspection of threat objects from x-ray images. The robustness of the algorithm is proved by identifying occluded target objects with large tolerance of their features.

21 CFR 882.5150 - Intravascular occluding catheter.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Intravascular occluding catheter. 882.5150 Section 882.5150 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES NEUROLOGICAL DEVICES Neurological Therapeutic Devices § 882.5150 Intravascular...

21 CFR 882.5150 - Intravascular occluding catheter.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Intravascular occluding catheter. 882.5150 Section 882.5150 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES NEUROLOGICAL DEVICES Neurological Therapeutic Devices § 882.5150 Intravascular...

Subintimal Recanalization of Occluded Stents: The Substent Technique

DOE Office of Scientific and Technical Information (OSTI.GOV)

Diamantopoulos, Athanasios, E-mail: adiamant@upatras.gr; Katsanos, Konstantinos; Spiliopoulos, Stavros

2013-08-01

PurposeApplication of metal stents is complicated by neointimal hyperplasia leading to vessel restenosis and reocclusion. Treatment options in cases presenting with complete occlusion of the stented segment and recurrent critical limb ischemia (CLI) are limited. We present the option of the subintimal/substent technique in dealing with occluded stents.MethodsThe study included patients presenting with recurrent CLI due to impaired blood flow as a result of complete occlusion of previously inserted metal stents and unsuccessful intraluminal crossing of the lesion via either the antegrade or retrograde approach. In these cases, crossing the occlusion through the subintimal/substent plane was attempted. Primary end pointsmore » included technical success, safety of the procedure, clinical improvement, and limb salvage, while secondary end points were patient survival, primary patency, and vessel restenosis rates at 1-year follow-up. Study end points were calculated by Kaplan-Meier survival analysis.ResultsBetween July 2006 and October 2011, a total of 14 patients (mean age 69.14 {+-} 12.59 years, 12 men) were treated with the substent technique and included in the analysis. Technical success rate was 85.71 % (12 of 14), with a total lesion length of 193.57 {+-} 90.78 mm. The mean occluded stented segment length was 90.21 {+-} 44.34 mm. In 10 (83.33 %) of 12 cases, a new stent had to be placed by the side of the old occluded one, while the remaining two cases (16.67 %) were treated only with balloon angioplasty. No serious adverse events were noted during the immediate postprocedural period. All successfully treated patients improved clinically. Estimated limb salvage was 90.9 %, and patient survival rate was 90.0 % at 1 year's follow-up. Primary patency was 45.50 % and vessel restenosis 77.30 %.ConclusionSubintimal recanalization of occluded metal stents through the substent plane is a valuable alternative treatment option, especially in patients with recurrent CLI

The Role of Good Form in Young Infants' Perception of Partly Occluded Objects.

ERIC Educational Resources Information Center

Johnson, Scott P.; Bremner, J. Gavin; Slater, Alan M.; Mason, Uschi C.

2000-01-01

Three experiments investigated whether 4-month-olds would attend to and utilize the global configuration ("good form") of a partly occluded, moving object to perceive its unit and coherence behind the occluder. Results indicated that curvature per se provided information in support of completion, in addition to global configuration and…

Distribution and Determinants of Myocardial Perfusion Grade Following Late Mechanical Recanalization of Occluded Infarct-Related Arteries Postmyocardial Infarction: A Report From the Occluded Artery Trial

PubMed Central

Jorapur, Vinod; Steigen, Terje K.; Buller, Christopher E.; Dẑavík, Vladimír; Webb, John G.; Strauss, Bradley H.; Yeoh, Eunice E.S.; Kurray, Peter; Sokalski, Leszek; Machado, Mauricio C.; Kronsberg, Shari S.; Lamas, Gervasio A.; Hochman, Judith S.; John Mancini, G.B.

2010-01-01

Objective To evaluate the distribution and determinants of myocardial perfusion grade (MPG) following late recanalization of persistently occluded infarct-related arteries (IRA). Background MPG reflects microvascular integrity. It is an independent prognostic factor following myocardial infarction, but has been studied mainly in the setting of early reperfusion. The occluded artery trial (OAT) enrolled stable patients with persistently occluded IRAs beyond 24 hr and up to 28 days post-MI. Methods Myocardial blush was assessed using TIMI MPG grading in 261 patients with TIMI 3 epicardial flow following IRA PCI. Patients demonstrating impaired (0–1) versus preserved (2–3) MPG were compared with regard to baseline clinical and pre-PCI angiographic characteristics. Results Impaired MPG was observed in 60 of 261 patients (23%). By univariate analysis, impaired MPG was associated with failed fibrinolytic therapy, higher heart rate, lower systolic blood pressure, lower ejection fraction, LAD occlusion, absence of collaterals (P < 0.01) and ST elevation MI, lower diastolic blood pressure, and higher systolic sphericity index (P < 0.05). By multivariable analysis, higher heart rate, LAD occlusion, absence of collaterals and higher systolic sphericity index (P < 0.01), and lower systolic blood pressure (P < 0.05) were independently associated with impaired MPG. Conclusion Preserved microvascular integrity was present in a high proportion of patients following late recanalization of occluded IRAs post-MI. Presence of collaterals was independently associated with preserved MPG and likely accounted for the high frequency of preserved myocardial perfusion in this clinical setting. Impaired MPG was associated with baseline clinical and angiographic features consistent with larger infarct size. PMID:18798327

Catching what we can't see: manual interception of occluded fly-ball trajectories.

PubMed

Bosco, Gianfranco; Delle Monache, Sergio; Lacquaniti, Francesco

2012-01-01

Control of interceptive actions may involve fine interplay between feedback-based and predictive mechanisms. These processes rely heavily on target motion information available when the target is visible. However, short-term visual memory signals as well as implicit knowledge about the environment may also contribute to elaborate a predictive representation of the target trajectory, especially when visual feedback is partially unavailable because other objects occlude the visual target. To determine how different processes and information sources are integrated in the control of the interceptive action, we manipulated a computer-generated visual environment representing a baseball game. Twenty-four subjects intercepted fly-ball trajectories by moving a mouse cursor and by indicating the interception with a button press. In two separate sessions, fly-ball trajectories were either fully visible or occluded for 750, 1000 or 1250 ms before ball landing. Natural ball motion was perturbed during the descending trajectory with effects of either weightlessness (0 g) or increased gravity (2 g) at times such that, for occluded trajectories, 500 ms of perturbed motion were visible before ball disappearance. To examine the contribution of previous visual experience with the perturbed trajectories to the interception of invisible targets, the order of visible and occluded sessions was permuted among subjects. Under these experimental conditions, we showed that, with fully visible targets, subjects combined servo-control and predictive strategies. Instead, when intercepting occluded targets, subjects relied mostly on predictive mechanisms based, however, on different type of information depending on previous visual experience. In fact, subjects without prior experience of the perturbed trajectories showed interceptive errors consistent with predictive estimates of the ball trajectory based on a-priori knowledge of gravity. Conversely, the interceptive responses of subjects

Reduced Performance of Prey Targeting in Pit Vipers with Contralaterally Occluded Infrared and Visual Senses

PubMed Central

Chen, Qin; Deng, Huanhuan; Brauth, Steven E.; Ding, Li; Tang, Yezhong

2012-01-01

Both visual and infrared (IR) senses are utilized in prey targeting by pit vipers. Visual and IR inputs project to the contralateral optic tectum where they activate both multimodal and bimodal neurons. A series of ocular and pit organ occlusion experiments using the short-tailed pit viper (Gloydius brevicaudus) were conducted to investigate the role of visual and IR information during prey targeting. Compared with unoccluded controls, snakes with either both eyes or pit organs occluded performed more poorly in hunting prey although such subjects still captured prey on 75% of trials. Subjects with one eye and one pit occluded on the same side of the face performed as well as those with bilateral occlusion although these subjects showed a significant targeting angle bias toward the unoccluded side. Performance was significantly poorer when only a single eye or pit was available. Interestingly, when one eye and one pit organ were occluded on opposite sides of the face, performance was poorest, the snakes striking prey on no more than half the trials. These results indicate that, visual and infrared information are both effective in prey targeting in this species, although interference between the two modalities occurs if visual and IR information is restricted to opposite sides of the brain. PMID:22606229

[Percutaneous closure of the patent ductus arteriosus in children with the Amplatzer Duct Occluder II].

PubMed

Parra-Bravo, José Rafael; Osuna-Izaguirre, Manuel Alfredo; Beirana-Palencia, Luisa; Gálvez-Cancino, Franco; Martínez-Monterrosas, Christian; Lazo-Cárdenas, César; Reyes-Vargas, César

2014-01-01

In the last decades, several devices have been used for the percutaneous closure of patent ductus arteriosus, with its own limitations and risks. The Amplatzer Duct Occluder II has been designed to overcome those limitations and reduce risks. We described our initial series of patients who underwent percutaneous closure of patent ductus arteriosus with the Amplatzer Duct Occluder II, emphasis on the technical aspects of the procedure. We reviewed the clinical records of 9 patients with patent ductus arteriosus who underwent percutaneous closure with the Amplatzer Duct Occluder II. Median age was 24 months (range 8-51 months) and the median weight was 10.7kg (range 6-16.3kg). The minimal ductus arteriosus diameter was 2.7mm (1-5mm). Implantation was successful in all cases. The devices most commonly used (33.3%) were the dimensions 4-4mm (3 patients), in 2 patients were used 3-4mm and in the rest of the patients were employed occluder other sizes. Four cases showed slight residual flow immediately after implantation. Total closure was achieved in 24h in 8 of 9 patients (89%). There was no embolization of the occluder or deaths during the procedure and we only observed one minor complication. The Amplatzer Duct Occluder II in this series was effective in 89% of the patients at 24hs after the procedure and 100% follow-up. The implantation was safe and no major complications were observed. The occlusion rate is comparable to those reported for the Amplatzer Duct Occluder I. Copyright © 2013 Instituto Nacional de Cardiología Ignacio Chávez. Published by Masson Doyma México S.A. All rights reserved.

Ileal Varices Treated with Balloon-Occluded Retrograde Transvenous Obliteration.

PubMed

Sato, Takahiro; Yamazaki, Katsu; Toyota, Jouji; Karino, Yoshiyasu; Ohmura, Takumi; Akaike, Jun

2009-04-01

A 55-year-old man with hepatitis B virus antigen-positive liver cirrhosis was admitted to our hospital with anal bleeding. Colonoscopy revealed blood retention in the entire colon, but no bleeding lesion was found. Computed tomography images showed that vessels in the ileum were connected to the right testicular vein, and we suspected ileal varices to be the most probable cause of bleeding. We immediately performed double balloon enteroscopy, but failed to find any site of bleeding owing to the difficulty of fiberscope insertion with sever adhesion. Using a balloon catheter during retrograde transvenous venography, we found ileal varices communicating with the right testicular vein (efferent vein) with the superior mesenteric vein branch as the afferent vein of these varices. We performed balloon occluded retrograde transvenous obliteration by way of the efferent vein of the varices and have detected no further bleeding in this patient one year after treatment.

Amodal representation of occluded surfaces: role of invisible stimuli in apparent motion correspondence.

PubMed

Shimojo, S; Nakayama, K

1990-01-01

A series of demonstrations were created where the perceived depth of targets was controlled by stereoscopic disparity. A closer object (a cloud) was made to jump back and forth horizontally, partially occluding a farther object (a full moon). The more distant moon appeared stationary even though the unoccluded portion of it, a crescent, changed position. Reversal of the relative depth of the moon and cloud gave a totally different percept: the crescent appeared to flip back and forth in the front depth plane. Thus, the otherwise-robust apparent motion of the moon crescents was completely abolished in the cloud-closer case alone. This motion-blocking effect is attributed to the 'amodal presence' of the occluded surface continuing behind the occluding surface. To measure the effect of this occluded 'invisible' surface quantitatively, a bistable apparent motion display was used (Ramachandran and Anstis 1983a): two small rectangular-shaped targets changed their positions back and forth between two frames, and the disparity of a large centrally positioned rectangle was varied. When the perceived depths supported the possibility of amodal completion behind the large rectangle, increased vertical motion of the targets was found, suggesting that the amodal presence of the targets behind the occluder had effectively changed the center position of the moving targets for purposes of motion correspondence. Amodal contours are literally 'invisible', yet it is hypothesized that they have a neural representation at sufficiently early stages of visual processing to alter the correspondence solving process for apparent motion.

Catching What We Can't See: Manual Interception of Occluded Fly-Ball Trajectories

PubMed Central

Bosco, Gianfranco; Delle Monache, Sergio; Lacquaniti, Francesco

2012-01-01

Control of interceptive actions may involve fine interplay between feedback-based and predictive mechanisms. These processes rely heavily on target motion information available when the target is visible. However, short-term visual memory signals as well as implicit knowledge about the environment may also contribute to elaborate a predictive representation of the target trajectory, especially when visual feedback is partially unavailable because other objects occlude the visual target. To determine how different processes and information sources are integrated in the control of the interceptive action, we manipulated a computer-generated visual environment representing a baseball game. Twenty-four subjects intercepted fly-ball trajectories by moving a mouse cursor and by indicating the interception with a button press. In two separate sessions, fly-ball trajectories were either fully visible or occluded for 750, 1000 or 1250 ms before ball landing. Natural ball motion was perturbed during the descending trajectory with effects of either weightlessness (0 g) or increased gravity (2 g) at times such that, for occluded trajectories, 500 ms of perturbed motion were visible before ball disappearance. To examine the contribution of previous visual experience with the perturbed trajectories to the interception of invisible targets, the order of visible and occluded sessions was permuted among subjects. Under these experimental conditions, we showed that, with fully visible targets, subjects combined servo-control and predictive strategies. Instead, when intercepting occluded targets, subjects relied mostly on predictive mechanisms based, however, on different type of information depending on previous visual experience. In fact, subjects without prior experience of the perturbed trajectories showed interceptive errors consistent with predictive estimates of the ball trajectory based on a-priori knowledge of gravity. Conversely, the interceptive responses of subjects

Ileal Varices Treated with Balloon-Occluded Retrograde Transvenous Obliteration

PubMed Central

Sato, Takahiro; Yamazaki, Katsu; Toyota, Jouji; Karino, Yoshiyasu; Ohmura, Takumi; Akaike, Jun

2009-01-01

A 55-year-old man with hepatitis B virus antigen-positive liver cirrhosis was admitted to our hospital with anal bleeding. Colonoscopy revealed blood retention in the entire colon, but no bleeding lesion was found. Computed tomography images showed that vessels in the ileum were connected to the right testicular vein, and we suspected ileal varices to be the most probable cause of bleeding. We immediately performed double balloon enteroscopy, but failed to find any site of bleeding owing to the difficulty of fiberscope insertion with sever adhesion. Using a balloon catheter during retrograde transvenous venography, we found ileal varices communicating with the right testicular vein (efferent vein) with the superior mesenteric vein branch as the afferent vein of these varices. We performed balloon occluded retrograde transvenous obliteration by way of the efferent vein of the varices and have detected no further bleeding in this patient one year after treatment. PMID:27956966

AMPLATZER versus Figulla occluder for transcatheter patent foramen ovale closure.

PubMed

Trabattoni, Daniela; Gaspardone, Achille; Sgueglia, Gregory A; Fabbiocchi, Franco; Gioffrè, Gaetano; Montorsi, Piero; Calligaris, Giuseppe; Iamele, Maria; De Santis, Antonella; Bartorelli, Antonio L

2017-04-20

The aim of this observational study was to compare acute and 12-month results of percutaneous closure of patent foramen ovale (PFO) with two occluder devices. Between June 2007 and October 2014, 406 consecutive patients (48.1±13.3 years, 243 women) underwent percutaneous PFO closure with either the AMPLATZER (n=179) or the Figulla (n=227) device after a stroke or a transient ischaemic attack ascribed to the PFO. A right-to-left shunt grade >1 was previously detected in all patients and atrial septal aneurysm was present in 111 (27.5%) patients. Patients were followed up with a contrast transthoracic echocardiogram and clinically at 24 hours, six months, and 12 months after the procedure. A high procedural success was observed in both groups. Despite a trend towards a higher incidence of acute residual shunt immediately after device deployment among Figulla occluder patients, a residual grade ≥2 right-to-left shunt was observed in 4.5% of patients, independently of the device used for PFO closure. The only difference reported after Figulla device implantation was a lower rate of supraventricular arrhythmias (9% vs. 17%, p=0.02). According to this two-centre study, PFO closure appears safe and effective with the Figulla occluder as well as with the AMPLATZER device.

Recognition of 3-D Scene with Partially Occluded Objects

NASA Astrophysics Data System (ADS)

Lu, Siwei; Wong, Andrew K. C...

1987-03-01

This paper presents a robot vision system which is capable of recognizing objects in a 3-D scene and interpreting their spatial relation even though some objects in the scene may be partially occluded by other objects. An algorithm is developed to transform the geometric information from the range data into an attributed hypergraph representation (AHR). A hypergraph monomorphism algorithm is then used to compare the AHR of objects in the scene with a set of complete AHR's of prototypes. The capability of identifying connected components and interpreting various types of edges in the 3-D scene enables us to distinguish objects which are partially blocking each other in the scene. Using structural information stored in the primitive area graph, a heuristic hypergraph monomorphism algorithm provides an effective way for recognizing, locating, and interpreting partially occluded objects in the range image.

Transcatheter closure of ventricular septal defects with nitinol wire occluders of type patent ductus arteriosus.

PubMed

Wierzyk, Arkadiusz; Szkutnik, Małgorzata; Fiszer, Roland; Banaszak, Paweł; Pawlak, Szymon; Białkowski, Jacek

2014-01-01

Ventricular septal defects closure (VSD) depending on the anatomy and clinical setting can be performed surgically or by a hybrid and transcatheter approach. Two cases of children with VSD will be presented. Patients' defects were closed with various types of occluders made of nitinol wire mesh occluder, patent ductus arteriosus (PDA) type. The first case was a 2.5-year-old boy after cardiosurgical correction of tetralogy of Fallot (TOF). After the procedure, a significant haemodynamic residual VSD was observed, which was not successfully closed during the subsequent reoperation. Despite pharmacological treatment, symptoms of heart failure were observed in this patient. In echocardiographic images the residual VSD was presented as a tunnel-like dissection of the ventricular septum (length 6 mm and diameter 3.4 mm). The defect was closed via arterial access with an Amplatzer Duct Occluder II (ADO II). The procedure was successfully performed without any medical complications. In this child, a significant shunt reduction and a noticeable improvement in the patient's clinical status and diminished symptoms of heart failure were noticed. The second patient was a 4-year-old girl suffering from a multi-perforated perimembranous VSD accompanied by a ventricular septal defect with aneurysm. The defect was closed by a venous approach with a PDA Cardio-O-Fix occluder (very similar to ADO I). No short-term or long-term complications were visible during or after the procedure. Only a mild residual shunt through the VSD was observed 6 months afterwards. Transcatheter VSD closure with a proper morphology, with occluders of type Amplatzer Duct Occluder ADO I or ADO II, constitutes a safe and effective therapeutic alternative.

Molecular dynamics simulation of the last step of a catalytic cycle: product release from the active site of the enzyme chorismate mutase from Mycobacterium tuberculosis.

PubMed

Choutko, Alexandra; van Gunsteren, Wilfred F

2012-11-01

The protein chorismate mutase MtCM from Mycobacterium tuberculosis catalyzes one of the few pericyclic reactions known in biology: the transformation of chorismate to prephenate. Chorismate mutases have been widely studied experimentally and computationally to elucidate the transition state of the enzyme catalyzed reaction and the origin of the high catalytic rate. However, studies about substrate entry and product exit to and from the highly occluded active site of the enzyme have to our knowledge not been performed on this enzyme. Crystallographic data suggest a possible substrate entry gate, that involves a slight opening of the enzyme for the substrate to access the active site. Using multiple molecular dynamics simulations, we investigate the natural dynamic process of the product exiting from the binding pocket of MtCM. We identify a dominant exit pathway, which is in agreement with the gate proposed from the available crystallographic data. Helices H2 and H4 move apart from each other which enables the product to exit from the active site. Interestingly, in almost all exit trajectories, two residues arginine 72 and arginine 134, which participate in the burying of the active site, are accompanying the product on its exit journey from the catalytic site. Copyright © 2012 The Protein Society.

Developments in Young Infants' Reasoning about Occluded Objects

ERIC Educational Resources Information Center

Aguiar, Andrea; Baillargeon, Renee

2002-01-01

Eight experiments were conducted to examine 3- and 3.5-month-old infants' responses to occlusion events. The results revealed two developments, one in infants' knowledge of when objects should and should not be occluded and the other in infants' ability to posit additional objects to make sense of events that would otherwise violate their…

Percutaneous closure of a post-traumatic ventricular septal defect with a patent ductus arteriosus occluder.

PubMed

Xi, Er-Ping; Zhu, Jian; Zhu, Shui-Bo; Yin, Gui-Lin; Liu, Yong; Dong, Yong-Qiang; Zhang, Yu; Xia, Feng

2012-11-01

Ventricular septal defects resulting from post-traumatic cardiac injury are very rare. Percutaneous closure has emerged as a method for treating this disorder. We wish to report our experience in three patients who underwent percutaneous closure of a post-traumatic ventricular septal defect with a patent ductus arteriosus occluder. We treated three patients with post-traumatic ventricular septal defects caused by stab wounds with knives. After the heart wound was repaired, patient examinations revealed ventricular septal defects with pulmonary/systemic flow ratios (Qp/Qs) of over 1.7. The post-traumatic ventricular septal defects were closed percutaneously with a patent ductus arteriosus occluder (Lifetech Scientific (Shenzhen) Co., LTD, Guangdong, China) utilizing standard techniques. Post-operative transthoracic echocardiography revealed no residual left-to-right shunt and indicated normal ventricular function. In addition, 320-slice computerized tomography showed that the occluder was well placed and exhibited normal morphology. Our experiences indicate that closure of a post-traumatic ventricular septal defect using a patent ductus arteriosus occluder is feasible, safe, and effective.

Percutaneous closure of a post-traumatic ventricular septal defect with a patent ductus arteriosus occluder

PubMed Central

Xi, Er-Ping; Zhu, Jian; Zhu, Shui-Bo; Yin, Gui-Lin; Liu, Yong; Dong, Yong-Qiang; Zhang, Yu; Xia, Feng

2012-01-01

OBJECTIVE: Ventricular septal defects resulting from post-traumatic cardiac injury are very rare. Percutaneous closure has emerged as a method for treating this disorder. We wish to report our experience in three patients who underwent percutaneous closure of a post-traumatic ventricular septal defect with a patent ductus arteriosus occluder. METHODS: We treated three patients with post-traumatic ventricular septal defects caused by stab wounds with knives. After the heart wound was repaired, patient examinations revealed ventricular septal defects with pulmonary/systemic flow ratios (Qp/Qs) of over 1.7. The post-traumatic ventricular septal defects were closed percutaneously with a patent ductus arteriosus occluder (Lifetech Scientific (Shenzhen) Co., LTD, Guangdong, China) utilizing standard techniques. RESULTS: Post-operative transthoracic echocardiography revealed no residual left-to-right shunt and indicated normal ventricular function. In addition, 320-slice computerized tomography showed that the occluder was well placed and exhibited normal morphology. CONCLUSION: Our experiences indicate that closure of a post-traumatic ventricular septal defect using a patent ductus arteriosus occluder is feasible, safe, and effective. PMID:23184204

Photodynamic therapy for occluded biliary metal stents

NASA Astrophysics Data System (ADS)

Roche, Joseph V. E.; Krasner, Neville; Sturgess, R.

1999-02-01

In this abstract we describe the use of photodynamic therapy (PDT) to recanalize occluded biliary metal stents. In patients with jaundice secondary to obstructed metal stents PDT was carried out 72 hours after the administration of m THPC. Red laser light at 652 nm was delivered endoscopically at an energy intensity of 50 J/cm. A week later endoscopic retrograde cholangiogram showed complete recanalization of the metal stent.

Efficacy of a Creon delayed-release pancreatic enzyme protocol for clearing occluded enteral feeding tubes.

PubMed

Stumpf, Janice L; Kurian, Rebecca M; Vuong, Jennifer; Dang, Kimberlyn; Kraft, Michael D

2014-04-01

Alkalinized Viokase pancreatic enzyme tablets restored patency to 71.9% of occluded Dobhoff tubes in a prospective study. After removal of Viokase tablets from the US market, the hospital protocol for unclogging enteral feeding tubes was adapted to use Creon pancreatic enzyme delayed-release capsules, despite the lack of published data. To evaluate the effectiveness of a Creon-based protocol to clear occluded enteral feeding tubes. This retrospective study included all adult and pediatric patients seen in the emergency department or in an inpatient setting who received Creon 12 000 units lipase delayed-release capsule dissolved in a solution of sodium bicarbonate 650 mg and sterile water for clearing occluded enteral feeding tubes between May 1 and November 30, 2010. The Creon protocol was deemed effective if tube clearance was documented in the medical record or if enteral feedings were resumed with no note regarding tube replacement. Alkalinized Creon delayed-release capsules were administered to 83 patients with a total of 118 clogged tubes. Three poorly documented cases and 5 tubes with mechanical clogs were excluded from data analysis. Patency was restored to 53 of 110 (48.2%) occluded tubes. More than 1 treatment course was attempted in 5 cases, with success in 3. An alkalinized Creon pancreatic enzyme protocol was effective in clearing approximately half of the occluded enteral feeding tubes in this retrospective study, an efficacy rate much less than that previously reported in the literature with a Viokase-based protocol.

Numerical procedure to determine geometric view factors for surfaces occluded by cylinders

NASA Technical Reports Server (NTRS)

Sawyer, P. L.

1978-01-01

A numerical procedure was developed to determine geometric view factors between connected infinite strips occluded by any number of infinite circular cylinders. The procedure requires a two-dimensional cross-sectional model of the configuration of interest. The two-dimensional model consists of a convex polygon enclosing any number of circles. Each side of the polygon represents one strip, and each circle represents a circular cylinder. A description and listing of a computer program based on this procedure are included in this report. The program calculates geometric view factors between individual strips and between individual strips and the collection of occluding cylinders.

Cotton-Top Tamarins' ("Saguinus Oedipus") Expectations about Occluded Objects: A Dissociation between Looking and Reaching Tasks

ERIC Educational Resources Information Center

Santos, Laurie R.; Seelig, David; Hauser, Marc D.

2006-01-01

Recent work with human infants and toddlers suggests a dissociation between performance on looking and reaching tasks. Specifically, infants appear to generate accurate representations of occluded objects and their actions when tested in expectancy violation looking tasks but often fail to use this information when reaching for occluded objects.…

Closure of the patent ductus arteriosus with the Amplatzer Duct Occluder II: a clinical experience.

PubMed

Karagöz, Tevfik; Akin, Alper; Ertuğrul, Ilker; Aykan, Hayrettin Hakan; Alehan, Dursun; Ozer, Sema; Ozkutlu, Süheyla

2012-12-01

The aim of our study was to share our clinical experience on cases with patent ductus arteriosus treated with the Amplatzer Duct Occluder II. Between 2008 and 2012, 26 of 31 patients with patent ductus arteriosus underwent successful transcatheter closure of patent ductus arteriosus using the Amplatzer Duct Occluder II. Mean age was 3.3 years and mean weight was 15.7 kilograms. The presence of a residual shunt, left pulmonary artery or aortic obstruction was explored by administering contrast material during the procedure. The patients were discharged 24 hours after the procedure. The procedure was successful in 26 of 31 patients and failed in five patients. According to the Krichenko classification, 26 patients had type A, one patient had type B and 4 patients had type C ductus. The mean narrowest ductus diameter was 3.2 mm and the mean ductus length was 6.7 mm. Complete angiographic occlusion occurred immediately after the procedure in 22 out of 26 patients in whom the ductus was closed successfully with the Amplatzer Duct Occluder II. Complete occlusion was achieved in the remaining patients with residual shunt one month after the procedure. The procedure was preceded by closure with an Amplatzer Duct Occluder I in two patients and an Amplatzer Vascular Plug I in one patient. Amplatzer Duct Occluder II is highly effective in transcatheter closure of patent ductus arteriosus. We think that an alternative closure device and alternative techniques can be attempted in patients with type C ductus. The success rate could increase with accumulating experience.

Transcatheter Closure of Bilateral Multiple Huge Pulmonary Arteriovenous Malformations with Homemade Double-Umbrella Occluders

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhong Hongshan, E-mail: zhonghongshan@hotmail.com; Xu Ke; Shao Haibo

2008-07-15

A 28-year-old man underwent successful transcatheter occlusion of three huge pulmonary arteriovenous malformations (PAVMs) using homemade double-umbrella occluders and stainless steel coils. Thoracic CT with three-dimensional reconstruction and pulmonary angiography were used for treatment planning and follow-up. The diameters of the feeding vessels were 11 mm, 13 mm, and 14 mm, respectively. This report demonstrates the novel design and utility of the double-umbrella occluder, an alternative tool for treatment of large PAVMs.

Recanalisation of Chronically Occluded Remote Superficial Femoral Artery Endarterectomy Through Angioplasty for Limb Salvage

DOE Office of Scientific and Technical Information (OSTI.GOV)

Husainy, Mohammad Ali, E-mail: m.husainy@nhs.net; Slim, Hani; Rashid, Hisham

2017-02-15

We report a novel application of balloon angioplasty to recanalise a chronically occluded remote endarterectomy superficial femoral artery. This patient previously had two occluded surgical bypass grafts in an attempt to revascularise the limb and presented with critical limb ischaemia and necrotic foot ulcerations. Following the angioplasty, the patient showed significant improvement in rest pain and healing of the ulcerations. This technique may be useful for limb salvage in patients where surgical options have been exhausted.

Safety and efficacy of nano lamellar TiN coatings on nitinol atrial septal defect occluders in vivo.

PubMed

Zhang, Zhi xiong; Fu, Bu fang; Zhang, De yuan; Zhang, Zhi wei; Cheng, Yan; Sheng, Li yuan; Lai, Chen; Xi, Ting fei

2013-04-01

Atrial septal defect (ASD) occlusion devices made of nickel-titanium (NiTi) have a major shortcoming in that they release nickel into the body. We modified NiTi occluders using Arc Ion Plating technology. Nano lamellar titanium-nitrogen (TiN) coatings were formed on the surfaces of the occluders. The safety and efficacy of the modified NiTi occluders were evaluated in animal model. The results showed that 38 out of 39 rams (97%) survived at the end of the experiment. Fibrous capsules formed on the surfaces of the devices. Gradual endothelialization took place through the attachment of endothelial progenitor cells from the blood and the migration of endothelial cells from adjacent endocardium. The neo-endocardium formed more quickly in the coated group than in the uncoated group, as indicated by the evaluation of the six month study group. After TiN coating, there was no significant difference in endothelial cell cycle. TiN coating significantly reduced the release of nickel in both in vivo and in vitro indicating an improved biocompatibility of the nitinol ASD occluders. Superior and modified ASD occluders may provide a good choice for people with nickel allergies after sFDA registration, which is expected in one to two years. Copyright © 2012 Elsevier B.V. All rights reserved.

Cardi-O-Fix duct occluder versus Amplatzer duct occluder for closure of patent ductus arteriosus.

PubMed

Celebi, Ahmet; Demir, Ibrahim Halil; Saritaş, Türkay; Dedeoğlu, Reyhan; Yucel, Ilker Kemal; Demir, Fadli; Erdem, Abdullah

2013-11-15

We sought to investigate the safety, efficacy, and follow-up results of percutaneous patent ductus arteriosus (PDA) closure using the novel Cardi-O-Fix duct occluder (CDO), a device similar to but less expensive than the Amplatzer duct occluder (ADO). We also aimed to compare these two devices in terms of results. Between March 2005 and May 2012, 167 patients diagnosed with moderate-to-large PDA underwent transcatheter closure. ADO was used in 56 (33.5%) patients with a mean age of 8.1 ± 11.9 years (3.6 months-56 years), whereas CDO was used in 111 (66.5%) patients with a mean age of 12.6 ± 14.6 years (4.8 months-63 years). The narrowest PDA diameter, the used device diameter, procedure time, fluoroscopy time, and residual shunt rates were similar between the two groups. Procedural success rate was 100% in both groups. Although the residual shunt rate was higher in the CDO group immediately after the procedure, the difference was not statistically significant (12.6 vs. 8.9%; P = 0.3). There was no statistically significant difference between groups at discharge and during follow-up. No deaths occurred in any of the groups, and there were no differences in complication rates during the short- and mid-term follow-up periods (CDO 7/111 vs. ADO 5/56; P = 0.5 π). The CDO can be used for PDA closure because of its safety, effectiveness, and simplicity in use. It is available in bigger sizes and can be used in patients with large defects. According to our short- and mid-term findings, the results it yields are similar to those of the ADO; thus, it may be the preferred choice owing to its low cost and large size variability. Copyright © 2013 Wiley Periodicals, Inc.

Translation in cardiovascular stents and occluders: From biostable to fully degradable

PubMed Central

Huang, Yingying; Wong, Yee Shan; Ng, Herr Cheun Anthony; Boey, Freddy Y. C.

2017-01-01

Abstract Cardiovascular disease is a major cause of morbidity and mortality, especially in developed countries. Most academic research efforts in cardiovascular disease management focus on pharmacological interventions, or are concerned with discovering new disease markers for diagnosis and monitoring. Nonpharmacological interventions with therapeutic devices, conversely, are driven largely by novel materials and device design. Examples of such devices include coronary stents, heart valves, ventricular assist devices, and occluders for septal defects. Until recently, development of such devices remained largely with medical device companies. We trace the materials evolution story in two of these devices (stents and occluders), while also highlighting academic contributions, including our own, to the evolution story. Specifically, it addresses not only our successes, but also the challenges facing the translatability of concepts generated via academic research. PMID:29313029

Computational evaluation of aortic occlusion and the proposal of a novel, improved occluder: Constrained endo-aortic balloon occlusion.

PubMed

de Vaal, M H; Gee, M W; Stock, U A; Wall, W A

2016-12-01

Because aortic occlusion is arguably one of the most dangerous aortic manipulation maneuvers during cardiac surgery in terms of perioperative ischemic neurological injury, the purpose of this investigation is to assess the structural mechanical impact resulting from the use of existing and newly proposed occluders. Existing (clinically used) occluders considered include different cross-clamps (CCs) and endo-aortic balloon occlusion (EABO). A novel occluder is also introduced, namely, constrained EABO (CEABO), which consists of applying a constrainer externally around the aorta when performing EABO. Computational solid mechanics are employed to investigate each occluder according to a comprehensive list of functional requirements. The potential of a state of occlusion is also considered for the first time. Three different constrainer designs are evaluated for CEABO. Although the CCs were responsible for the highest strains, largest deformation, and most inefficient increase of the occlusion potential, it remains the most stable, simplest, and cheapest occluder. The different CC hinge geometries resulted in poorer performance of CC used for minimally invasive procedures than conventional ones. CEABO with a profiled constrainer successfully addresses the EABO shortcomings of safety, stability, and positioning accuracy, while maintaining its complexities of operation (disadvantage) and yielding additional functionalities (advantage). Moreover, CEABO is able to achieve the previously unattainable potential to provide a clinically determinable state of occlusion. CEABO offers an attractive alternative to the shortcomings of existing occluders, with its design rooted in achieving the highest patient safety. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Results of the combined U.S. Multicenter Pivotal Study and the Continuing Access Study of the Nit-Occlud PDA device for percutaneous closure of patent ductus arteriosus.

PubMed

Moore, John W; Greene, Jessica; Palomares, Salvadore; Javois, Alexander; Owada, Carl Y; Cheatham, John P; Hoyer, Mark H; Jones, Thomas K; Levi, Daniel S

2014-12-01

This study aimed to compare the efficacy and safety of the Nit-Occlud PDA device (PFM Medical, Cologne, Germany) to benchmarks designed as objective performance criteria (OPC). The Nit-Occlud PDA is a nitinol coil-type patent ductus arteriosus (PDA) occluder with a reverse cone configuration, which is implanted using a controlled delivery system. Patients with <4-mm minimum diameter PDA were prospectively enrolled in the Pivotal and the Continuing Access Studies from 15 sites in the United States and were followed up for 12 months post-procedure. Investigator-reported outcomes were compared to OPC including a composite success criterion, efficacy criteria of successful closure (clinical and echocardiographic), and safety criteria incidence of adverse events (serious and of total). The Pivotal Study enrolled patients between November 1, 2002 and October 31, 2005, and the Continuing Access Study enrolled additional patients between September 1, 2006 and October 31, 2007. A total of 357 patients were enrolled, and 347 had successful device implantations. After 12 months, 96.8% had complete echocardiographic closure (OPC = 85%) and 98.1% had clinical closure (OPC = 95%). There were no deaths or serious adverse events (OPC = 1%). The total adverse event rate was 4.7% (OPC = 6%). Composite success was 95.1% in the study patients (OPC = 80%). Closure of small- and medium-sized PDA with the Nit-Occlud PDA is effective and safe when compared with OPC. Copyright © 2014 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.

Probing the electrostatics of active site microenvironments along the catalytic cycle for Escherichia coli dihydrofolate reductase.

PubMed

Liu, C Tony; Layfield, Joshua P; Stewart, Robert J; French, Jarrod B; Hanoian, Philip; Asbury, John B; Hammes-Schiffer, Sharon; Benkovic, Stephen J

2014-07-23

Electrostatic interactions play an important role in enzyme catalysis by guiding ligand binding and facilitating chemical reactions. These electrostatic interactions are modulated by conformational changes occurring over the catalytic cycle. Herein, the changes in active site electrostatic microenvironments are examined for all enzyme complexes along the catalytic cycle of Escherichia coli dihydrofolate reductase (ecDHFR) by incorporation of thiocyanate probes at two site-specific locations in the active site. The electrostatics and degree of hydration of the microenvironments surrounding the probes are investigated with spectroscopic techniques and mixed quantum mechanical/molecular mechanical (QM/MM) calculations. Changes in the electrostatic microenvironments along the catalytic environment lead to different nitrile (CN) vibrational stretching frequencies and (13)C NMR chemical shifts. These environmental changes arise from protein conformational rearrangements during catalysis. The QM/MM calculations reproduce the experimentally measured vibrational frequency shifts of the thiocyanate probes across the catalyzed hydride transfer step, which spans the closed and occluded conformations of the enzyme. Analysis of the molecular dynamics trajectories provides insight into the conformational changes occurring between these two states and the resulting changes in classical electrostatics and specific hydrogen-bonding interactions. The electric fields along the CN axes of the probes are decomposed into contributions from specific residues, ligands, and solvent molecules that make up the microenvironments around the probes. Moreover, calculation of the electric field along the hydride donor-acceptor axis, along with decomposition of this field into specific contributions, indicates that the cofactor and substrate, as well as the enzyme, impose a substantial electric field that facilitates hydride transfer. Overall, experimental and theoretical data provide evidence for

Probing the Electrostatics of Active Site Microenvironments along the Catalytic Cycle for Escherichia coli Dihydrofolate Reductase

PubMed Central

2015-01-01

Electrostatic interactions play an important role in enzyme catalysis by guiding ligand binding and facilitating chemical reactions. These electrostatic interactions are modulated by conformational changes occurring over the catalytic cycle. Herein, the changes in active site electrostatic microenvironments are examined for all enzyme complexes along the catalytic cycle of Escherichia coli dihydrofolate reductase (ecDHFR) by incorporation of thiocyanate probes at two site-specific locations in the active site. The electrostatics and degree of hydration of the microenvironments surrounding the probes are investigated with spectroscopic techniques and mixed quantum mechanical/molecular mechanical (QM/MM) calculations. Changes in the electrostatic microenvironments along the catalytic environment lead to different nitrile (CN) vibrational stretching frequencies and 13C NMR chemical shifts. These environmental changes arise from protein conformational rearrangements during catalysis. The QM/MM calculations reproduce the experimentally measured vibrational frequency shifts of the thiocyanate probes across the catalyzed hydride transfer step, which spans the closed and occluded conformations of the enzyme. Analysis of the molecular dynamics trajectories provides insight into the conformational changes occurring between these two states and the resulting changes in classical electrostatics and specific hydrogen-bonding interactions. The electric fields along the CN axes of the probes are decomposed into contributions from specific residues, ligands, and solvent molecules that make up the microenvironments around the probes. Moreover, calculation of the electric field along the hydride donor–acceptor axis, along with decomposition of this field into specific contributions, indicates that the cofactor and substrate, as well as the enzyme, impose a substantial electric field that facilitates hydride transfer. Overall, experimental and theoretical data provide evidence for

Externalized decondensed neutrophil chromatin occludes pancreatic ducts and drives pancreatitis

PubMed Central

Leppkes, Moritz; Maueröder, Christian; Hirth, Sebastian; Nowecki, Stefanie; Günther, Claudia; Billmeier, Ulrike; Paulus, Susanne; Biermann, Mona; Munoz, Luis E.; Hoffmann, Markus; Wildner, Dane; Croxford, Andrew L.; Waisman, Ari; Mowen, Kerri; Jenne, Dieter E.; Krenn, Veit; Mayerle, Julia; Lerch, Markus M.; Schett, Georg; Wirtz, Stefan; Neurath, Markus F.; Herrmann, Martin; Becker, Christoph

2016-01-01

Ductal occlusion has been postulated to precipitate focal pancreatic inflammation, while the nature of the primary occluding agents has remained elusive. Neutrophils make use of histone citrullination by peptidyl arginine deiminase-4 (PADI4) in contact to particulate agents to extrude decondensed chromatin as neutrophil extracellular traps (NETs). In high cellular density, NETs form macroscopically visible aggregates. Here we show that such aggregates form inside pancreatic ducts in humans and mice occluding pancreatic ducts and thereby driving pancreatic inflammation. Experimental models indicate that PADI4 is critical for intraductal aggregate formation and that PADI4-deficiency abrogates disease progression. Mechanistically, we identify the pancreatic juice as a strong instigator of neutrophil chromatin extrusion. Characteristic single components of pancreatic juice, such as bicarbonate ions and calcium carbonate crystals, induce aggregated NET formation. Ductal occlusion by aggregated NETs emerges as a pathomechanism with relevance in a plethora of inflammatory conditions involving secretory ducts. PMID:26964500

Patent ductus arteriosus closure using Occlutech® Duct Occluder, experience in Port Elizabeth, South Africa

PubMed Central

Pepeta, Lungile; Greyling, Adele; Nxele, Mahlubandile Fintan; Makrexeni, Zongezile Masonwabe

2017-01-01

Background: Percutaneous closure of patent ductus arteriosus (PDA) has become standard therapy. Experience with the Occlutech® Duct Occluder is limited. Methods: Data regarding ductal closure using Occlutech® Duct Occluder were reviewed and prospectively collected. Demographics, hemodynamic and angiographic characteristics, complications, and outcomes were documented. Results: From March 2013 to June 2016, 65 patients (43 females and 22 males) underwent percutaneous closure of the PDA using Occlutech® Duct Occluder. The median age of the patients was 11 months (range, 1–454 months) and the median weight was 8.5 kg (range 2.5–78 kg). The mean pulmonary artery median pressure was 27 mmHg (range, 12–100 mmHg) and the QP: Qs ratio median was 1.8 (range, 1–7.5), with a pulmonary vascular resistance mean of 2.7 WU (standard deviation [SD] ±2.1). Thirty-two patients had Krichenko Type A duct (49%); 7, Type C (11%); 4, Type D (6%); and 22, Type E (34%). The ductal size (narrowest diameter at the pulmonic end) mean was 3.5 mm (SD ± 1.9 mm). The screening time mean was 17.3 min (SD ± 11.6). Out of 63 patients with successful closure of the PDA using Occlutech® Duct Occluder, there were 15 patients with small PDAs; 25 with moderate PDAs, and 23 with large PDAs. In one patient, the device dislodged to the descending aorta, and in two patients, to the right pulmonary artery immediately following deployment, with successful percutaneous (two) and surgical (one) retrieval. Complete ductal occlusion was achieved in all 63 patients on day one. Conclusion: The Occlutech® Duct Occluder is a safe and effective device for closure of ducts in appropriately selected patients. PMID:28566820

Patent ductus arteriosus closure using Occlutech® Duct Occluder, experience in Port Elizabeth, South Africa.

PubMed

Pepeta, Lungile; Greyling, Adele; Nxele, Mahlubandile Fintan; Makrexeni, Zongezile Masonwabe

2017-01-01

Percutaneous closure of patent ductus arteriosus (PDA) has become standard therapy. Experience with the Occlutech® Duct Occluder is limited. Data regarding ductal closure using Occlutech® Duct Occluder were reviewed and prospectively collected. Demographics, hemodynamic and angiographic characteristics, complications, and outcomes were documented. From March 2013 to June 2016, 65 patients (43 females and 22 males) underwent percutaneous closure of the PDA using Occlutech® Duct Occluder. The median age of the patients was 11 months (range, 1-454 months) and the median weight was 8.5 kg (range 2.5-78 kg). The mean pulmonary artery median pressure was 27 mmHg (range, 12-100 mmHg) and the QP: Qs ratio median was 1.8 (range, 1-7.5), with a pulmonary vascular resistance mean of 2.7 WU (standard deviation [SD] ±2.1). Thirty-two patients had Krichenko Type A duct (49%); 7, Type C (11%); 4, Type D (6%); and 22, Type E (34%). The ductal size (narrowest diameter at the pulmonic end) mean was 3.5 mm (SD ± 1.9 mm). The screening time mean was 17.3 min (SD ± 11.6). Out of 63 patients with successful closure of the PDA using Occlutech® Duct Occluder, there were 15 patients with small PDAs; 25 with moderate PDAs, and 23 with large PDAs. In one patient, the device dislodged to the descending aorta, and in two patients, to the right pulmonary artery immediately following deployment, with successful percutaneous (two) and surgical (one) retrieval. Complete ductal occlusion was achieved in all 63 patients on day one. The Occlutech® Duct Occluder is a safe and effective device for closure of ducts in appropriately selected patients.

Pan-nitinol occluder and special delivery device for closure of patent ductus arteriosus: a canine-model feasibility study.

PubMed

Jiang, Hai-bin; Bai, Yuan; Zong, Gang-jun; Han, Lin; Li, Wei-ping; Lu, Yang; Qin, Yong-wen; Zhao, Xian-xian

2013-01-01

The aim of this study was to evaluate a new type of occluder for patent ductus arteriosus. Patent ductus arteriosus was established in a canine model by anastomosing a length of autologous jugular vein to the descending aorta and the left pulmonary artery in an end-to-side fashion. Transcatheter closure of each patent ductus arteriosus was performed on 10 dogs, which were then monitored for as long as 6 months with aortography, echocardiography, and histologic evaluation. Transcatheter closure with use of the novel pan-nitinol device was successful in all canine models. Postoperative echocardiography showed that the location and shape of the occluders were normal, without any residual shunting. Further histologic evaluation confirmed that the occluder surface was completely endothelialized 3 months after implantation. Transcatheter patent ductus arteriosus closure with the pan-nitinol occluder can be performed safely and successfully in a canine model and shows good biological compatibility and low mortality rates.

Template occluded SBA-15: An effective dissolution enhancer for poorly water-soluble drug

NASA Astrophysics Data System (ADS)

Tingming, Fu; Liwei, Guo; Kang, Le; Tianyao, Wang; Jin, Lu

2010-09-01

The aim of the present work was to improve the dissolution rate of piroxicam by inclusion into template occluded SBA-15. Our strategy involves directly introducing piroxicam into as-prepared SBA-15 occluded with P123 (EO 20PO 70EO 20) by self assembling method in acetonitrile/methylene chloride mixture solution. Ultraviolet spectrometry experiment and thermogravimetric analysis-differential scanning calorimetry (TG-DSC) profiles show that the piroxicam and P123 contents in the inclusion compound are 12 wt% and 28 wt%, respectively. X-ray powder diffraction and DSC analysis reveal that the included piroxicam is arranged in amorphous form. N 2 adsorption-desorption experiment indicates that the piroxicam has been introduced to the mesopores instead of precipitating at the outside of the silica material. The inclusion compound was submitted to in vitro dissolution tests, the results show that the piroxicam dissolve from template occluded inclusion compound more rapidly, than these from the piroxicam crystalline and template removed samples in all tested conditions. Thus a facile method to improve the dissolution rate of poorly water-soluble drug was established, and this discovery opens a new avenue for the utilization of templates used for the synthesis of mesoporous materials.

Identifying the Optimal Water-Occluding Earplugs: A Scientific Simulation Study.

PubMed

Kovoor, Joshua; Al Hussaini, Ali; Backhouse, Steven

2016-12-01

Numerous types of water-occluding earplugs are available as a means of preventing infection in patients with external and middle ear disease. However, little is known about the comparative efficacies of these earplugs with prolonged water exposure. In this study, we assessed the water impermeability of various earplug materials to prolonged water exposure. Nine earplugs were tested: cotton wool mixed with petroleum jelly, cotton wool externally coated with petroleum jelly, Blu-Tack, foam earplugs, silicone putty, silicone earplugs, flanged earplugs, and hard and soft silicone custom-moulds. Precision-engineered cups were filled with 30 mL water and sealed with lids that contained a 10 mm diameter hole to simulate the ear canal. The aperture was occluded with different earplugs, and the cup was inverted. Computer software was used to record the water loss to the nearest 10 milligrams 720 times over a three-hour period. The test was repeated five times for each material. The water permeability onset, rate, and total amount of water loss varied markedly between the materials; cotton wool mixed with petroleum jelly demonstrated the fastest onset of leak and the highest rate of water loss (p < 0.00001), as well as the largest amount of cumulative water loss (p = 0.00213). The soft silicone custom-mould plugs, hard silicone custom-mould plugs, foam plugs, and silicone putty demonstrated no leaks. This study demonstrates a wide range of water permeabilities of commonly used ear-occluding materials during prolonged water exposure. We found that the generally suggested regimen of cotton wool mixed with petroleum jelly may be inefficacious for substantial periods of water exposure.

Lack of benefit from percutaneous intervention of persistently occluded infarct arteries after the acute phase of myocardial infarction is time independent: insights from Occluded Artery Trial

PubMed Central

Menon, Venu; Pearte, Camille A.; Buller, Christopher E.; Steg, Ph.Gabriel; Forman, Sandra A.; White, Harvey D.; Marino, Paolo N.; Katritsis, Demosthenes G.; Caramori, Paulo; Lasevitch, Ricardo; Loboz-Grudzien, Krystyna; Zurakowski, Aleksander; Lamas, Gervasio A.; Hochman, Judith S.

2009-01-01

Aims The Occluded Artery Trial (OAT) (n = 2201) showed no benefit for routine percutaneous intervention (PCI) (n = 1101) over medical therapy (MED) (n = 1100) on the combined endpoint of death, myocardial infarction (MI), and class IV heart failure (congestive heart failure) in stable post-MI patients with late occluded infarct-related arteries (IRAs). We evaluated the potential for selective benefit with PCI over MED for patients enrolled early in OAT. Methods and results We explored outcomes with PCI over MED in patients randomized to the ≤3 calendar days and ≤7 calendar days post-MI time windows. Earlier, times to randomization in OAT were associated with higher rates of the combined endpoint (adjusted HR 1.04/day: 99% CI 1.01–1.06; P < 0.001). The 48-month event rates for ≤3 days, ≤7 days post-MI enrolled patients were similar for PCI vs. MED for the combined and individual endpoints. There was no interaction between time to randomization defined as a continuous (P = 0.55) or categorical variable with a cut-point of 3 days (P = 0.98) or 7 days (P = 0.64) post-MI and treatment effect. Conclusion Consistent with overall OAT findings, patients enrolled in the ≤3 day and ≤7 day post-MI time windows derived no benefit with PCI over MED with no interaction between time to randomization and treatment effect. Our findings do not support routine PCI of the occluded IRA in trial-eligible patients even in the earliest 24–72 h time window. PMID:19028780

Dentinal tubules occluded by bioactive glass-containing toothpaste exhibit high resistance toward acidic soft drink challenge.

PubMed

Bakri, M M; Hossain, M Z; Razak, F A; Saqina, Z H; Misroni, A A; Ab-Murat, N; Kitagawa, J; Saub, R B

2017-06-01

Dentine hypersensitivity is a common problem attributed by patent dentinal tubules. Ingredients incorporated in toothpastes aim to occlude patent dentinal tubules to minimize the dentine hypersensitivity. However, frequent consumption of acidic soft drinks may reverse the dentinal tubules' occlusion. In this in vitro study, the efficacy of dentinal tubules occluded by commercially available toothpastes to withstand different durations of an acidic soft drink challenge was investigated. One hundred and twenty dentine discs were divided into three groups. The discs from each group were brushed with toothpaste containing bioactive glass, arginine and control toothpaste. Each group was then divided into four subgroups and exposed to acidic soft drink over four different time durations. The scoring and the percentage of occluded dentinal tubules by Novamin-containing toothpaste was significantly better compared with arginine or the control toothpaste. Acidic soft drink challenge reduced the extent of dentinal tubules occlusion along with time. Dentinal tubules occluded by Novamin-containing toothpaste withstand the acidic challenge comparatively for a longer period. The findings demonstrated that occlusion of dentinal tubules is more efficient by the bioactive glass-containing toothpaste and thus may contribute to its better resistance to acidic soft drink challenge. © 2016 Australian Dental Association.

Electronic eye occluder with time-counting and reflection control

NASA Astrophysics Data System (ADS)

Karitans, V.; Ozolinsh, M.; Kuprisha, G.

2008-09-01

In pediatric ophthalmology 2 - 3 % of all the children are impacted by a visual pathology - amblyopia. It develops if a clear image isn't presented to the retina during an early stage of the development of the visual system. A common way of treating this pathology is to cover the better-seeing eye to force the "lazy" eye to learn seeing. However, children are often reluctant to wear such an occluder because they are ashamed or simply because they find it inconvenient. This fact requires to find a way how to track the regime of occlusion because results of occlusion is a hint that the actual regime of occlusion isn't that what the optometrist has recommended. We design an electronic eye occluder that allows to track the regime of eye occlusion. We employ real-time clock DS1302 providing time information from seconds to years. Data is stored in the internal memory of the CPU (EEPROM). The MCU (PIC16F676) switches on only if a mechanical switch is closed and temperature has reached a satisfactory level. The occlusion is registered between time moments when the infrared signal appeared and disappeared.

Enzymes with lid-gated active sites must operate by an induced fit mechanism instead of conformational selection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sullivan, Sarah M.; Holyoak, Todd

2008-09-17

The induced fit and conformational selection/population shift models are two extreme cases of a continuum aimed at understanding the mechanism by which the final key-lock or active enzyme conformation is achieved upon formation of the correctly ligated enzyme. Structures of complexes representing the Michaelis and enolate intermediate complexes of the reaction catalyzed by phosphoenolpyruvate carboxykinase provide direct structural evidence for the encounter complex that is intrinsic to the induced fit model and not required by the conformational selection model. In addition, the structural data demonstrate that the conformational selection model is not sufficient to explain the correlation between dynamics andmore » catalysis in phosphoenolpyruvate carboxykinase and other enzymes in which the transition between the uninduced and the induced conformations occludes the active site from the solvent. The structural data are consistent with a model in that the energy input from substrate association results in changes in the free energy landscape for the protein, allowing for structural transitions along an induced fit pathway.« less

Enzymes With Lid-Gated Active Sites Must Operate By An Induced Fit Mechanism Instead of Conformational Selection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sullivan, S.M.; Holyoak, T.

2009-05-26

The induced fit and conformational selection/population shift models are two extreme cases of a continuum aimed at understanding the mechanism by which the final key-lock or active enzyme conformation is achieved upon formation of the correctly ligated enzyme. Structures of complexes representing the Michaelis and enolate intermediate complexes of the reaction catalyzed by phosphoenolpyruvate carboxykinase provide direct structural evidence for the encounter complex that is intrinsic to the induced fit model and not required by the conformational selection model. In addition, the structural data demonstrate that the conformational selection model is not sufficient to explain the correlation between dynamics andmore » catalysis in phosphoenolpyruvate carboxykinase and other enzymes in which the transition between the uninduced and the induced conformations occludes the active site from the solvent. The structural data are consistent with a model in that the energy input from substrate association results in changes in the free energy landscape for the protein, allowing for structural transitions along an induced fit pathway.« less

Occluded Brescia-Cimino Hemodialysis Fistulas: Endovascular Treatment with Both Brachial Arterial and Venous Access Using the Pull-Through Technique

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miyayama, Shiro; Matsui, Osamu; Taki, Keiichi

2005-12-15

We retrospectively evaluated the usefulness of both arterial and venous access with the pull-through technique in endovascular treatment of totally occluded Brescia-Cimino fistulas. We treated 26 patients (17 men, 9 women; age range 43-82 years, mean age 66 years) with occluded Brescia-Cimino fistulas. First, the occluded segment was traversed from the antegrade brachial arterial access using a microcatheter-guidewire system. Second, the vein was retrogradely punctured after confirmation of all diseased segments, and a 0.014- or 0.016-inch guidewire was pulled through the venous access when the occluded segment was long. All interventions including thrombolysis, thromboaspiration, angioplasty, and stent placement were performedmore » via the venous access. The occlusion was successfully crossed via the brachial arterial access in 23 patients (88%). In 2 patients it was done from the venous approach. In the remaining patient it was not possible to traverse the occluded segment. The pull-through technique was successful in all 19 attempts. Clinical success was achieved in 96%, the primary patency rates at 6, 12, and 18 months were 83%, 78%, and 69%, the primary assisted patency rates were 92%, 92%, and 72%, and the secondary patency rates were 92%, 92%, and 92%, respectively. Minor complications in 5 patients included venous perforation in 2 (8%), venous rupture in 1 (4%), and regional hematoma in 2 (8%). Our study suggests that endovascular treatments with both arterial and venous access using the pull-through technique are highly effective in restoring function in totally occluded Brescia-Cimino fistulas.« less

A unified computational model of the development of object unity, object permanence, and occluded object trajectory perception.

PubMed

Franz, A; Triesch, J

2010-12-01

The perception of the unity of objects, their permanence when out of sight, and the ability to perceive continuous object trajectories even during occlusion belong to the first and most important capacities that infants have to acquire. Despite much research a unified model of the development of these abilities is still missing. Here we make an attempt to provide such a unified model. We present a recurrent artificial neural network that learns to predict the motion of stimuli occluding each other and that develops representations of occluded object parts. It represents completely occluded, moving objects for several time steps and successfully predicts their reappearance after occlusion. This framework allows us to account for a broad range of experimental data. Specifically, the model explains how the perception of object unity develops, the role of the width of the occluders, and it also accounts for differences between data for moving and stationary stimuli. We demonstrate that these abilities can be acquired by learning to predict the sensory input. The model makes specific predictions and provides a unifying framework that has the potential to be extended to other visual event categories. Copyright © 2010 Elsevier Inc. All rights reserved.

Safety and efficacy of transcatheter closure of large patent ductus arteriosus in adults with a self-expandable occluder.

PubMed

Yu, Man-Li; Huang, Xin-Miao; Wang, Jia-Feng; Qin, Yong-Wen; Zhao, Xian-Xian; Zheng, Xing

2009-11-01

Most occurrences of large patent ductus arteriosus (PDAs) of > or =10 mm have been surgically closed, and transcatheter closure of these large PDAs was only reported in a few case reports. The present study reviewed our experience in transcatheter closure of such large PDAs with a Chinese self-expandable occluder, which is similar to but much cheaper than the Amplatzer occluder. From July 2000 to January 2008, 23 patients underwent transcatheter closure of large PDA > or =10 mm with this kind of occluder. The mean (SD) age of the patients was 38.0 (15.6) years (range 18-75 years). Radiographs of the chest, electrocardiograms, and echocardiograms were used for follow-up evaluation of the treatment within 1 day, 1 month, 6 months, and then every year after successful closure. The mean (SD) angiographic PDA diameter was 12.8 (2.6) mm (range 10-18 mm) and the mean occluder diameter was 18.0 (2.9) mm (range 16-22 mm). The occluders were delivered successfully and closed the PDA completely in 19 out of the 23 patients. Pulmonary arterial pressures decreased significantly after occlusion in patients with successful treatment: 67.3 (24.7) mmHg (range 29-122 mmHg) before occlusion and 42.3 (22.0) mmHg (range 19-98 mmHg) immediately after the procedure. Radiographs of the chest and echocardiograms showed that the diameters of the left atrium, left ventricle, and the main pulmonary artery decreased, and the ejection fraction (EF) increased at a mean (SD) follow-up of 36.3 (18.7) months (range 6-72 months). No severe complication occurred. The immediate and long-term outcomes suggested that transcatheter closure of PDAs with the native PDA occluder is a safe and effective treatment for adults with large PDA > or =10 mm.

Association between autistic traits and emotion adaptation to partially occluded faces.

PubMed

Luo, Chengwen; Burns, Edwin; Xu, Hong

2017-04-01

Prolonged exposure to a happy face makes subsequently presented faces appear sadder: the facial emotion aftereffect (FEA). People with autism spectrum disorders and their relatives have diminished holistic perception of faces. Levels of autism can be measured continuously in the general population by autistic traits using the autism-quotient (AQ). Prior work has not found any association between AQ and FEA in adults, possibly due to non-holistic processing strategies employed by those at the higher end of the spectrum. In the present study, we tested whether AQ was associated with FEA to partially occluded faces. We hypothesized that inferring emotion from such faces would require participants to process their viewable parts as a gestalt percept, thus we anticipated this ability would diminish as autistic traits increased. In Experiment 1, we partially occluded the adapting faces with aligned or misaligned opaque bars. Both conditions produced significant FEAs, with aftereffects and AQ negatively correlated. In Experiment 2, we adapted participants to obscured faces flickering in luminance, and manipulated the facilitation of holistic perception by varying the synchronization of this flickering. We found significant FEAs in all conditions, but abolished its association with AQ. In Experiment 3, we showed that the association between AQ and FEA in the occluded conditions in Experiment 1 was not due to the recognizability or perceived emotional intensity of our adaptors; although the overall FEAs were linked to emotional intensity. We propose that increasing autistic traits are associated with diminishing abilities in perceiving emotional faces as a gestalt percept. Copyright © 2017 Elsevier Ltd. All rights reserved.

Endovascular treatment of occluded and stenotic visceral vessels in patients with chronic mesenteric ischemia.

PubMed

Christofi, Georgia; Donas, Konstantinos P; Pitoulias, Georgios A; Torsello, Giovanni; Schwindt, Arne G; Stavroulakis, Konstantinos

2017-02-01

Objective Current evidence in the literature about endovascular treatment (ET) of visceral vessels in patients with chronic mesenterial ischemia (CMI) based on morphological characteristics is limited. The aim of this study was the evaluation of ET in occluded and stenotic visceral vessels. Methods Patients undergoing ET for CMI between November 2000 and November 2012 were included in this retrospective study. Primary measure outcome was the symptom-free survival (SFS). Secondary outcomes were primary (PPR), secondary patency (SPR) rates and technical success rate (TSR). A Cox-regression analysis identified risk factors for the primary and secondary measure outcomes. Results Forty patients were included in the present study (men: 21, mean age: 68). The overall number of vessels with intention-to-treat was 62. Fifty-two visceral arteries (18 occlusions and 34 stenoses) were successfully treated by endovascular means. The overall TSR was 84%. Visceral vessel occlusions and atherosclerotic disease of the superior mesenteric artery (SMA) were identified as independent risk factors for poorer TSR ( p < 0.05). The 12-month SFS was 60%. The overall 12-month PPR and SPR were 71% and 94%, respectively. No significant differences were observed between occluded and stenotic vessels ( p > 0.05) concerning the PPR. On the other hand, the subgroup analysis revealed higher SPR among occluded visceral vessels ( p < 0.001) and coeliac axis lesions ( p < 0.001). Conclusions ET was associated with high incidence of symptoms recurrence despite the satisfying patency rates in both occluded and stenotic vessels. Additionally, visceral vessel occlusion and presence of atherosclerotic lesions in the SMA were associated with poorer TSR.

Laser restoration of flow in occluded ventricular shunts for pediatric neurosurgery

NASA Astrophysics Data System (ADS)

Christens-Barry, William A.; Guarnieri, Michael; Carson, Benjamin S.

1998-01-01

We have investigated the use of short pulses of infrared ((lambda) equals 2.09 micrometers ) light from a Ho:YAG laser to photofragment occlusions and restore flow in ventricular shunts, which provide the sole means of maintaining proper intracranial pressure in hydrocephalus patients. These experiments employed model tissues, a polymeric model compound, and patient explants in order to determine appropriate pulse energies and delivery rates for removal of occlusions material. Laser energy doses and rates of occlusion removal were established for these materials. Laser energy doses that do not damage the shunt device or surrounding tissue were identified. Optical fibers (25 ga. or smaller) can be introduced through the dome of current shunt devices and threaded to the occlusion site. Clinical application will require the continued development of an introducer tool for the transcutaneous insertion of the optical fiber into the shunt device and irrigation techniques for removing the occlusion detritus generated by photofragmentation treatment. Using this approach, a minimally invasive and benign procedure for in situ restoration of flow in occluded neurological implant devices becomes possible.

Complications Following Balloon-Occluded Arterial Infusion Chemotherapy for Pelvic Malignancies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sugimoto, Koji; Hirota, Shozo; Imanaka, Kazufumi

Purpose: To evaluate the incidence and causes of complications associated with balloon-occluded arterial infusion chemotherapy (BOAI) for pelvic malignancies. Methods: In 34 courses of BOAI in 22 patients with pelvic malignancies, we analyzed the incidence of complications as well as the effect of the dose of the anticancer drugs, the infusion site, and the number of BOAI administrations on these complications. Complications were divided into two categories: cystitis-like symptoms and neurological complications such as pain, numbness, and paresthesia of the lower extremities and the hip. Results: Eleven patients (50%) suffered from complications, seven (31.8%) from neurological complications and four (18.2%)more » from cystitis-like symptoms. The complications appeared in 14 courses (42.4%) of BOAI, neurological complications in 10 (30.3%) and cystitis-like symptoms in four (12.1%). A high dose of anti-cancer drugs and infusion from the anterior division tended to induce neurological complications more frequently; however, the cystitis-like symptoms were not related to any factors. Conclusion: Our results indicate that a smaller dose of anti-cancer drugs should be infused from the bilateral internal iliac arteries for safer pelvic BOAI.« less

Transcatheter closure of left ventricle to right atrial communication using cera duct occluder.

PubMed

Ganesan, Gnanavelu; Paul, G Justin; Mahadevan, Vaikom S

Left ventricle-right atrial communication could be congenital (Gerbode defect) or acquired as a complication of surgery or infective endocarditis and leads to volume overloading of pulmonary circulation. Two types, direct and indirect types are known depending on the involvement of septal tricuspid leaflet. Transcatheter closure of this defect is feasible and appears an attractive alternative to surgical management. Various devices like Amplatzer duct occluder I, II, Muscular ventricular septal defect device etc. have been used to close this defect. We report two patients, a preteen boy with direct left ventricle-right atrial communication as post operative complication and an adult female with indirect communication who underwent transcatheter closure with Cera duct occluder (Lifetech Scientific (Shenzhen), China). Copyright © 2017. Published by Elsevier B.V.

18 CFR 270.302 - Occluded natural gas produced from coal seams.

Code of Federal Regulations, 2014 CFR

2014-04-01

... produced from coal seams. 270.302 Section 270.302 Conservation of Power and Water Resources FEDERAL ENERGY... produced from coal seams. A person seeking a determination that natural gas is occluded natural gas produced from coal seams must file an application with the jurisdictional agency which contains the...

18 CFR 270.302 - Occluded natural gas produced from coal seams.

Code of Federal Regulations, 2012 CFR

2012-04-01

... produced from coal seams. 270.302 Section 270.302 Conservation of Power and Water Resources FEDERAL ENERGY... produced from coal seams. A person seeking a determination that natural gas is occluded natural gas produced from coal seams must file an application with the jurisdictional agency which contains the...

18 CFR 270.302 - Occluded natural gas produced from coal seams.

Code of Federal Regulations, 2010 CFR

2010-04-01

... produced from coal seams. 270.302 Section 270.302 Conservation of Power and Water Resources FEDERAL ENERGY... produced from coal seams. A person seeking a determination that natural gas is occluded natural gas produced from coal seams must file an application with the jurisdictional agency which contains the...

18 CFR 270.302 - Occluded natural gas produced from coal seams.

Code of Federal Regulations, 2011 CFR

2011-04-01

... produced from coal seams. 270.302 Section 270.302 Conservation of Power and Water Resources FEDERAL ENERGY... produced from coal seams. A person seeking a determination that natural gas is occluded natural gas produced from coal seams must file an application with the jurisdictional agency which contains the...

18 CFR 270.302 - Occluded natural gas produced from coal seams.

Code of Federal Regulations, 2013 CFR

2013-04-01

... produced from coal seams. 270.302 Section 270.302 Conservation of Power and Water Resources FEDERAL ENERGY... produced from coal seams. A person seeking a determination that natural gas is occluded natural gas produced from coal seams must file an application with the jurisdictional agency which contains the...

Intuitive physical reasoning about occluded objects by inexperienced chicks

PubMed Central

Chiandetti, Cinzia; Vallortigara, Giorgio

2011-01-01

Questions concerning the role of nature and nurture in higher cognition appear to be intractable if one restricts one's attention to development in humans. However, in other domains, such as sensory development, much information has been gained from controlled rearing studies with animals. Here, we used a similar experimental strategy to investigate intuitive reasoning about occluded objects. Newborn domestic chicks (Gallus gallus) were reared singly with a small object that became their social partner. They were then accustomed to rejoin such an imprinting object when it was made to move and disappear behind either one of two identical opaque screens. After disappearance of the imprinting object, chicks were faced with two screens of different slants, or of different height or different width, which may or may not have been compatible with the presence of the imprinting object hidden beneath/behind them. Chicks consistently chose the screen of slant/height/width compatible with the presence of the object beneath/behind it. Preventing chicks from touching and pecking at the imprinting object before testing did not affect the results, suggesting that intuitive reasoning about physical objects is largely independent of specific experience of interaction with objects and of objects' occluding events. PMID:21270036

Comparison of three patent foramen ovale closure devices in a randomized trial (Amplatzer versus CardioSEAL-STARflex versus Helex occluder).

PubMed

Taaffe, Margaret; Fischer, Evelyn; Baranowski, Andreas; Majunke, Nicolas; Heinisch, Corinna; Leetz, Michaela; Hein, Ralph; Bayard, Yves; Büscheck, Franziska; Reschke, Madlen; Hoffmann, Ilona; Wunderlich, Nina; Wilson, Neil; Sievert, Horst

2008-05-01

This randomized trial compared procedural complications and 30-day clinical outcomes of 3 patent foramen ovale (PFO) closure devices (Amplatzer, Helex, and CardioSEAL-STARflex). It examined 660 patients (361 men, 299 women, mean age 49.3+/-1.9 years), with 220 patients per group. All patients had a history of paradoxical embolism. All PFO closures were successful technically. Exchange of devices for others was most frequently required for the Helex occluder (7 of 220) and 2 of 220 in either of the other groups. Three device embolizations in the Helex group were retrieved and replaced successfully. One patient with a Helex occluder developed a transient ischemic attack and recovered without treatment. A hemopericardium in that group was punctured without affecting the device. One tamponade in the Amplatzer group required surgical device explantation. In 8 of 660 patients in the CardioSEAL-STARflex group, thrombi resolved after anticoagulation. Sixteen patients (11 in the CardioSEAL-STARflex group, 3 in the Amplatzer group, and 2 in the Helex group) had episodes of atrial fibrillation. PFOs were closed completely in 143 of 220 patients (65%) in the Amplatzer group, 116 of 220 patients (52.7%) in the Helex group, and 137 of 220 patients (62.3%) in the CardioSEAL-STARflex group at 30 days with significant differences between the Helex and Amplatzer occluders (p=0.0005) and the Helex and CardioSEAL-STARflex occluders (p=0.0003). PFO closure can be performed safely with each device. In conclusion, the Helex occluder embolized more frequently. Device thrombus formation and paroxysmal atrial fibrillation were more common with the CardioSEAL-STARflex occluder.

Magnetic targeting to enhance microbubble delivery in an occluded microarterial bifurcation

NASA Astrophysics Data System (ADS)

de Saint Victor, M.; Carugo, D.; Barnsley, L. C.; Owen, J.; Coussios, C.-C.; Stride, E.

2017-09-01

Ultrasound and microbubbles have been shown to accelerate the breakdown of blood clots both in vitro and in vivo. Clinical translation of this technology is still limited, however, in part by inefficient microbubble delivery to the thrombus. This study examines the obstacles to delivery posed by fluid dynamic conditions in occluded vasculature and investigates whether magnetic targeting can improve microbubble delivery. A 2D computational fluid dynamic model of a fully occluded Y-shaped microarterial bifurcation was developed to determine: (i) the fluid dynamic field in the vessel with inlet velocities from 1-100 mm s-1 (corresponding to Reynolds numbers 0.25-25) (ii) the transport dynamics of fibrinolytic drugs; and (iii) the flow behavior of microbubbles with diameters in the clinically-relevant range (0.6-5 µm). In vitro experiments were carried out in a custom-built microfluidic device. The flow field was characterized using tracer particles, and fibrinolytic drug transport was assessed using fluorescence microscopy. Lipid-shelled magnetic microbubbles were fluorescently labelled to determine their spatial distribution within the microvascular model. In both the simulations and experiments, the formation of laminar vortices and an abrupt reduction of fluid velocity were observed in the occluded branch of the bifurcation, severely limiting drug transport towards the occlusion. In the absence of a magnetic field, no microbubbles reached the occlusion, remaining trapped in the first vortex, within 350 µm from the bifurcation center. The number of microbubbles trapped within the vortex decreased as the inlet velocity increased, but was independent of microbubble size. Application of a magnetic field (magnetic flux density of 76 mT, magnetic flux density gradient of 10.90 T m-1 at the centre of the bifurcation) enabled delivery of microbubbles to the occlusion and the number of microbubbles delivered increased with bubble size and with decreasing inlet velocity.

Balloon-Occluded Percutaneous Transhepatic Obliteration of Isolated Vesical Varices Causing Gross Hematuria

PubMed Central

Lim, Dong Hoon; Kim, Min Seok; Kim, Chul Sung

2013-01-01

Gross hematuria secondary to vesical varices is an unusual presentation. We report such a case recurrent gross hematuria in a male patient who had a history of bladder substitution with ileal segments that had been treated by balloon-occluded percutaneous transhepatic obliteration of vesical varices. PMID:23323037

Phonation Threshold Pressure Measurement With a Semi-Occluded Vocal Tract

PubMed Central

Titze, Ingo R.

2015-01-01

Purpose The purpose of this article was to determine if a semi-occluded vocal tract could be used to measure phonation threshold pressure. This is in contrast to the shutter technique, where an alternation between a fully occluded tract and an unoccluded tract is used. Method Five male and 5 female volunteers phonated through a thin straw held between the lips. Oral pressure behind the lips was measured. Mathematical predictions of phonation threshold pressures were compared to the measured ones over a range of frequencies. Results It was shown that, for a 2.5-mm diameter straw, phonation threshold pressures were obtainable over a 2-octave range of fundamental frequency by all volunteers. In magnitude, the pressures agreed with the 0.2–0.5 kPa values obtained in previous investigations. Sensitivity to viscoelastic and geometric properties of the vocal folds was generally not compromised with greater oral impedance, but some differences were predicted theoretically in contrast to an open mouth configuration. Conclusion Because phonation threshold pressure is always dependent on vocal tract interaction, it may be advantageous to choose an exact and fixed oral semi-occlusion for the measurement and interpret the results in light of the known acoustic load. PMID:19641082

Method of preparing sodalite from chloride salt occluded zeolite

DOEpatents

Lewis, Michele A.; Pereira, Candido

1997-01-01

A method for immobilizing waste chloride salts containing radionuclides and hazardous nuclear material for permanent disposal starting with a substantially dry zeolite and sufficient glass to form leach resistant sodalite with occluded radionuclides and hazardous nuclear material. The zeolite and glass are heated to a temperature up to about 1000.degree. K. to convert the zeolite to sodalite and thereafter maintained at a pressure and temperature sufficient to form a sodalite product near theoretical density. Pressure is used on the formed sodalite to produce the required density.

An Infectious Pseudoaneurysm Caused by Ventricular Septal Defect Occluder in Patent Ductus Arteriosus Closure in a Two-Year-Old Child.

PubMed

Li, Dingyang; Qiu, Qiu; Jin, Jing; Zhang, Changdong; Wang, Lijun; Zhang, Gangcheng

2017-12-12

We present a case of an infectious pseudoaneurysm after patent ductus arteriosus (PDA) closure with a ventricular septal defect (VSD) occluder in a two-year-old child. The aneurysm grew rapidly but was successfully removed in time and the patient survived. To our knowledge, this is the first report of an infectious pseudoaneurysm caused by VSD occluder in PDA closure.

Method of preparing sodalite from chloride salt occluded zeolite

DOEpatents

Lewis, M.A.; Pereira, C.

1997-03-18

A method is described for immobilizing waste chloride salts containing radionuclides and hazardous nuclear material for permanent disposal starting with a substantially dry zeolite and sufficient glass to form leach resistant sodalite with occluded radionuclides and hazardous nuclear material. The zeolite and glass are heated to a temperature up to about 1000 K to convert the zeolite to sodalite and thereafter maintained at a pressure and temperature sufficient to form a sodalite product near theoretical density. Pressure is used on the formed sodalite to produce the required density.

Differential contributions to the interception of occluded ballistic trajectories by the temporoparietal junction, area hMT/V5+, and the intraparietal cortex.

PubMed

Delle Monache, Sergio; Lacquaniti, Francesco; Bosco, Gianfranco

2017-09-01

The ability to catch objects when transiently occluded from view suggests their motion can be extrapolated. Intraparietal cortex (IPS) plays a major role in this process along with other brain structures, depending on the task. For example, interception of objects under Earth's gravity effects may depend on time-to-contact predictions derived from integration of visual signals processed by hMT/V5+ with a priori knowledge of gravity residing in the temporoparietal junction (TPJ). To investigate this issue further, we disrupted TPJ, hMT/V5+, and IPS activities with transcranial magnetic stimulation (TMS) while subjects intercepted computer-simulated projectile trajectories perturbed randomly with either hypo- or hypergravity effects. In experiment 1 , trajectories were occluded either 750 or 1,250 ms before landing. Three subject groups underwent triple-pulse TMS (tpTMS, 3 pulses at 10 Hz) on one target area (TPJ | hMT/V5+ | IPS) and on the vertex (control site), timed at either trajectory perturbation or occlusion. In experiment 2 , trajectories were entirely visible and participants received tpTMS on TPJ and hMT/V5+ with same timing as experiment 1 tpTMS of TPJ, hMT/V5+, and IPS affected differently the interceptive timing. TPJ stimulation affected preferentially responses to 1-g motion, hMT/V5+ all response types, and IPS stimulation induced opposite effects on 0-g and 2-g responses, being ineffective on 1-g responses. Only IPS stimulation was effective when applied after target disappearance, implying this area might elaborate memory representations of occluded target motion. Results are compatible with the idea that IPS, TPJ, and hMT/V5+ contribute to distinct aspects of visual motion extrapolation, perhaps through parallel processing. NEW & NOTEWORTHY Visual extrapolation represents a potential neural solution to afford motor interactions with the environment in the face of missing information. We investigated relative contributions by temporoparietal junction

Efficacy and safety of a single 2 mg dose or 4 mg double dose of alteplase for 50 occluded chest ports using a unique instillation technique.

PubMed

Sharma, Rajinder P; Ree, Chung Ja; Ree, Alexander

2008-01-01

To evaluate the effectiveness and safety of a single 2 mg dose or a 4 mg double dose of alteplase for restoring function in occluded chest ports. A prospective, open-label, nonblinded study was performed on 40 enrolled patients with a total of 50 chest ports at the Henry Ford Hospital Interventional Radiology Department (Detroid, Michigan, USA). Alteplase (Cathflo Activase; Genentech, USA), a recombinant tissue plasminogen activator produced by recombinant DNA technology, was used to restore the function of 50 occluded chest ports. Occlusion was defined as the inability to withdraw blood freely from the port, or the inability to flush the port easily. A 2 mg (2 mL) dose of alteplase was injected into the port through a Huber needle, using a gentle push and pull technique, and was left to dwell for 30 min. If the port remained occluded after the initial 2 mg alteplase treatment, an additional 2 mg alteplase treatment was administered with the same dwell time of 30 min. If a port had remained occluded despite the above regimen, this outcome would have been considered a failure and the chest port would have required surgical intervention. However, all ports were successfully treated, and no surgical intervention was required. The safety end points included minor or major hemorrhages, such as intracranial hemorrhages, or sepsis. Safety end points were determined by a 24 h follow-up telephone call. Of the 50 chest ports (30 single ports and 10 double ports) treated with alteplase, 36 required 2 mg (72%) and 14 required 4 mg (28%). The efficacy end point was 100% for all chest ports treated, without any adverse events. High efficacy and safety rates of restoring function in occluded chest ports were obtained with 2 mg or 4 mg doses of alteplase. Part of this high efficacy rate may be due to the gentle push and pull technique used in the present study.

Efficacy and safety of a single 2 mg dose or 4 mg double dose of alteplase for 50 occluded chest ports using a unique instillation technique

PubMed Central

Sharma, Rajinder P; Ree, Chung Ja; Ree, Alexander

2008-01-01

PURPOSE: To evaluate the effectiveness and safety of a single 2 mg dose or a 4 mg double dose of alteplase for restoring function in occluded chest ports. METHODS: A prospective, open-label, nonblinded study was performed on 40 enrolled patients with a total of 50 chest ports at the Henry Ford Hospital Interventional Radiology Department (Detroid, Michigan, USA). Alteplase (Cathflo Activase; Genentech, USA), a recombinant tissue plasminogen activator produced by recombinant DNA technology, was used to restore the function of 50 occluded chest ports. Occlusion was defined as the inability to withdraw blood freely from the port, or the inability to flush the port easily. A 2 mg (2 mL) dose of alteplase was injected into the port through a Huber needle, using a gentle push and pull technique, and was left to dwell for 30 min. If the port remained occluded after the initial 2 mg alteplase treatment, an additional 2 mg alteplase treatment was administered with the same dwell time of 30 min. If a port had remained occluded despite the above regimen, this outcome would have been considered a failure and the chest port would have required surgical intervention. However, all ports were successfully treated, and no surgical intervention was required. The safety end points included minor or major hemorrhages, such as intracranial hemorrhages, or sepsis. Safety end points were determined by a 24 h follow-up telephone call. RESULTS: Of the 50 chest ports (30 single ports and 10 double ports) treated with alteplase, 36 required 2 mg (72%) and 14 required 4 mg (28%). The efficacy end point was 100% for all chest ports treated, without any adverse events. CONCLUSION: High efficacy and safety rates of restoring function in occluded chest ports were obtained with 2 mg or 4 mg doses of alteplase. Part of this high efficacy rate may be due to the gentle push and pull technique used in the present study. PMID:22477414

Indocyanine green videoangiography (ICGV)-guided surgery of parasagittal meningiomas occluding the superior sagittal sinus (SSS).

PubMed

d'Avella, Elena; Volpin, Francesco; Manara, Renzo; Scienza, Renato; Della Puppa, Alessandro

2013-03-01

Maximal safe resection is the goal of correct surgical treatment of parasagittal meningiomas, and it is intimately related to the venous anatomy both near and directly involved by the tumor. Indocyanine green videoangiography (ICGV) has already been advocated as an intra-operative resourceful technique in brain tumor surgery for the identification of vessels. The aim of this study was to investigate the role of ICGV in surgery of parasagittal meningiomas occluding the superior sagittal sinus (SSS). In this study, we prospectively analyzed clinical, radiological and intra-operative findings of patients affected by parasagittal meningioma occluding the SSS, who underwent ICGV assisted-surgery. Radiological diagnosis of complete SSS occlusion was pre-operatively established in all cases. ICGV was performed before dural opening, before and during tumor resection, at the end of the procedure. Five patients were included in our study. In all cases, ICGV guided dural opening, tumor resection, and venous management. The venous collateral pathway was easily identified and preserved in all cases. Radical resection was achieved in four cases. Surgery was uneventful in all cases. Despite the small number of patients, our study shows that ICG videoangiography could play a crucial role in guiding surgery of parasagittal meningioma occluding the SSS. Further studies are needed to define the role of this technique on functional and oncological outcome of these patients.

Septic Complication After Balloon-Occluded Retrograde Transvenous Obliteration of Duodenal Variceal Bleeding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Akasaka, Thai; Shibata, Toshiya, E-mail: ksj@kuhp.kyoto-u.ac.jp; Isoda, Hiroyoshi

2010-12-15

We report a 64-year-old woman with duodenal varices who underwent balloon-occluded retrograde transvenous obliteration (B-RTO) complicated by intraprocedural variceal rupture. The patient developed shivering and a fever higher than 40{sup o}C 3 days after the B-RTO procedure. A blood culture grew Entereobacter cloacoe. This case represents a rare septic complication of B-RTO for duodenal varices.

Normal Modes Expose Active Sites in Enzymes.

PubMed

Glantz-Gashai, Yitav; Meirson, Tomer; Samson, Abraham O

2016-12-01

Accurate prediction of active sites is an important tool in bioinformatics. Here we present an improved structure based technique to expose active sites that is based on large changes of solvent accessibility accompanying normal mode dynamics. The technique which detects EXPOsure of active SITes through normal modEs is named EXPOSITE. The technique is trained using a small 133 enzyme dataset and tested using a large 845 enzyme dataset, both with known active site residues. EXPOSITE is also tested in a benchmark protein ligand dataset (PLD) comprising 48 proteins with and without bound ligands. EXPOSITE is shown to successfully locate the active site in most instances, and is found to be more accurate than other structure-based techniques. Interestingly, in several instances, the active site does not correspond to the largest pocket. EXPOSITE is advantageous due to its high precision and paves the way for structure based prediction of active site in enzymes.

Normal Modes Expose Active Sites in Enzymes

PubMed Central

Glantz-Gashai, Yitav; Samson, Abraham O.

2016-01-01

Accurate prediction of active sites is an important tool in bioinformatics. Here we present an improved structure based technique to expose active sites that is based on large changes of solvent accessibility accompanying normal mode dynamics. The technique which detects EXPOsure of active SITes through normal modEs is named EXPOSITE. The technique is trained using a small 133 enzyme dataset and tested using a large 845 enzyme dataset, both with known active site residues. EXPOSITE is also tested in a benchmark protein ligand dataset (PLD) comprising 48 proteins with and without bound ligands. EXPOSITE is shown to successfully locate the active site in most instances, and is found to be more accurate than other structure-based techniques. Interestingly, in several instances, the active site does not correspond to the largest pocket. EXPOSITE is advantageous due to its high precision and paves the way for structure based prediction of active site in enzymes. PMID:28002427

[Percutaneous closure of ductus arteriosus and muscular ventricular defect with amplatzer occluder in a patient with severe pulmonary hypertension].

PubMed

García-Montes, José Antonio; Zabal Cerdeira, Carlos; Calderón-Colmenero, Juan; Espínola, Nilda; Fernández de la Reguera, Guillermo; Buendía Hernández, Alfonso

2005-01-01

Surgical treatment of multiple muscular ventricular septal defects with associated lesions and severe pulmonary hypertension has a high morbility and mortality. Closure of these defects by the Amplatzer muscular VSD occluder is an alternative to surgery, avoiding the need of cardiopulmonary bypass. We present the case of a 38 year-old woman with signs of heart failure in NYHA functional class IV, with two muscular ventricular septal defects, patent ductus arteriosus and severe pulmonary hypertension, that were treated with three Amplatzer muscular VSD occluders, with significant reduction of pulmonary pressure and functional class improvement.

The localization of occluded matrix proteins in calcareous spicules of sea urchin larvae.

PubMed

Seto, Jong; Zhang, Yang; Hamilton, Patricia; Wilt, Fred

2004-10-01

The sea urchin embryo forms calcareous endoskeletal spicules composed of calcite and an occluded protein matrix. Though the latter is approximately 0.1% of of the mass, the composite has substantially altered material properties, e.g., conchoidal fracture planes and increased hardness. Experiments were conducted to examine the localization of matrix proteins occluded in the mineral by use of immunocytochemistry coupled with scanning electron microscopy (SEM). The isolated, unfixed spicules were etched under relatively gentle conditions and exposed to affinity purified antibodies made against two different matrix proteins, as well as an antibody to the entire constellation of matrix proteins. Immunogold tagged secondary antibody was used to observe antibody localization in the back scatter mode of SEM. All proteins examined were very widely distributed throughout the calcite, supporting a model of the structure in which a multiprotein assemblage is woven with fine texture around microcrystalline domains of calcite. Gentle etching revealed a laminar arrangement of calcite solubility, consistent with a stepwise deposition of matrix and mineral to increase girth of the spicule.

Is It Worthwhile Treating Occluded Cold Stored Venous Allografts by Thrombolysis?

PubMed

Balaz, P; Wohlfahrt, P; Rokosny, S; Maly, S; Bjorck, M

2016-09-01

Thrombolysis has been reported to be suboptimal in occluded vein grafts and cryopreserved allografts, and there are no data on the efficacy of thrombolysis in occluded cold stored venous allografts. The aim was to evaluate early outcomes, secondary patency and limb salvage rates of thrombolysed cold stored venous allograft bypasses and to compare the outcomes with thrombolysis of autologous bypasses. This was a single center study of consecutive patients with acute and non-acute limb ischemia between September 1, 2000, and January 1, 2014, with occlusion of cold stored venous allografts, and between January 1, 2012, and January 1, 2014, with occlusion of autologous bypass who received intra-arterial thrombolytic therapy. Sixty-one patients with occlusion of an infrainguinal bypass using a cold stored venous allograft (n = 35) or an autologous bypass (n = 26) underwent percutaneous intra-arterial thrombolytic therapy. The median duration of thrombolysis was 20 h (IQR 18-24) with no difference between the groups (p = .14). The median follow up was 18.5 months (IQR 11.0-52.0). Secondary patency rates of thrombolysed bypass at 6 and 12 months were 44 ± 9% and 32 ± 9% in patients with a venous allograft bypass and 46 ± 10% and 22 ± 8% with an autologous bypass, with no difference between groups (p = .40). Limb salvage rates at 1, 6, and 12 months after thrombolysis in the venous allograft group were 83 ± 7%, 72 ± 8% and 63 ± 9%, and in the autologous group 91 ± 6%, 76 ± 9%, and 65 ± 13%, with no difference between groups (p = .69). Long-term results of thrombolysis of venous allograft bypasses are similar to those of autologous bypasses. Occluded cold stored venous allograft can be successfully re-opened in most cases with a favorable effect on limb salvage. Copyright © 2016 European Society for Vascular Surgery. Published by Elsevier Ltd. All rights reserved.

Factors Affecting Infants’ Manual Search for Occluded Objects and the Genesis of Object Permanence

PubMed Central

Moore, M. Keith; Meltzoff, Andrew N.

2009-01-01

Two experiments systematically examined factors that influence infants’ manual search for hidden objects (N = 96). Experiment 1 used a new procedure to assess infants’ search for partially versus totally occluded objects. Results showed that 8.75-month-old infants solved partial occlusions by removing the occluder and uncovering the object, but these same infants failed to use this skill on total occlusions. Experiment 2 used sound-producing objects to provide a perceptual clue to the objects’ hidden location. Sound clues significantly increased the success rate on total occlusions for 10-month-olds, but not for 8.75-month-olds. An identity development account is offered for why infants succeed on partial occlusions earlier than total occlusions and why sound helps only the older infants. We propose a mechanism for how infants use object identity as a basis for developing a notion of permanence. Implications are drawn for understanding the dissociation between looking-time and search assessments of object permanence. PMID:18036668

Feasibility and safety of a new generation of gore septal occluder device in children.

PubMed

Lombardi, Maristella; Tagliente, Maria R; Pirolo, Teodoro; Massari, Elena; Milella, Leonardo; Vairo, Ugo

2016-12-01

Transcatheter closure of an ostium secundum atrial septal defect (ASD) is now considered the standard care for most of children with the appropriate anatomy, and is a relatively well-tolerated procedure to reduce the clinical sequelae of ASD, with a low complication rate. The present case reports describe our clinical experience of the percutaneous closure of a secundum ASD in 10 children between December 2011 and November 2012, by means of a new generation of device, the GORE Septal Occluder device. The implantation was successful in all except two cases, the device being properly placed and deployed without malposition or embolization in the catheterization laboratory. No complications were related to the procedure. The successful implant was confirmed and no major adverse events were documented in the following 3-12 months. The new GORE Septal Occluder device appears to be a feasible, well-tolerated and successful tool for the closure of an ASD of 15 mm or less in childhood.

Factors affecting infants' manual search for occluded objects and the genesis of object permanence.

PubMed

Moore, M Keith; Meltzoff, Andrew N

2008-04-01

Two experiments systematically examined factors that influence infants' manual search for hidden objects (N=96). Experiment 1 used a new procedure to assess infants' search for partially versus totally occluded objects. Results showed that 8.75-month-old infants solved partial occlusions by removing the occluder and uncovering the object, but these same infants failed to use this skill on total occlusions. Experiment 2 used sound-producing objects to provide a perceptual clue to the objects' hidden location. Sound clues significantly increased the success rate on total occlusions for 10-month-olds, but not for 8.75-month-olds. An identity development account is offered for why infants succeed on partial occlusions earlier than total occlusions and why sound helps only the older infants. We propose a mechanism for how infants use object identity as a basis for developing a notion of permanence. Implications are drawn for understanding the dissociation between looking time and search assessments of object permanence.

A new coated nitinol occluder for transcatheter closure of ventricular septal defects in a canine model.

PubMed

Zhou, Yong; Chen, Feng; Huang, Xinmiao; Zhao, Xianxian; Wu, Hong; Bai, Yuan; Qin, Yongwen

2013-01-01

This study evaluated feasibility and safety of implanting the polyester-coated nitinol ventricular septal defect occluder (pcVSDO) in the canine model. VSD models were successfully established by transseptal ventricular septal puncture via the right jugular vein in 15 out of 18 canines. Two types of VSDOs were implanted, either with pcVSDOs (n = 8) as the new type occluder group or with the commercial ventricular septal defect occluders (VSDOs, n = 7, Shanghai Sharp Memory Alloy Co. Ltd.) as the control group. Sheath size was 10 French (10 Fr) in two groups. Then the general state of the canines was observed after implantation. ECG and TTE were performed, respectively, at 7, 30, 90 days of follow-up. The canines were sacrificed at these time points for pathological and scanning electron microscopy examination. The devices were successfully implanted in all 15 canines and were retrievable and repositionable. There was no thrombus formation on the device or occurrence of complete heart block. The pcVSDO surface implanted at day 7 was already covered with neotissue by gross examination, and it completed endothelialization at day 30, while the commercial VSDO was covered with the neotissue in 30th day and the complete endothelialization in 90th day. The study shows that pcVSDO is feasible and safe to close canine VSD model and has good biocompatibility and shorter time of endothelialization.

Model-based occluded object recognition using Petri nets

NASA Astrophysics Data System (ADS)

Zhou, Chuan; Hura, Gurdeep S.

1998-09-01

This paper discusses the use of Petri nets to model the process of the object matching between an image and a model under different 2D geometric transformations. This transformation finds its applications in sensor-based robot control, flexible manufacturing system and industrial inspection, etc. A description approach for object structure is presented by its topological structure relation called Point-Line Relation Structure (PLRS). It has been shown how Petri nets can be used to model the matching process, and an optimal or near optimal matching can be obtained by tracking the reachability graph of the net. The experiment result shows that object can be successfully identified and located under 2D transformation such as translations, rotations, scale changes and distortions due to object occluded partially.

A Randomized Controlled Trial of Two Semi-Occluded Vocal Tract Voice Therapy Protocols

ERIC Educational Resources Information Center

Kapsner-Smith, Mara R.; Hunter, Eric J.; Kirkham, Kimberly; Cox, Karin; Titze, Ingo R.

2015-01-01

Purpose: Although there is a long history of use of semi-occluded vocal tract gestures in voice therapy, including phonation through thin tubes or straws, the efficacy of phonation through tubes has not been established. This study compares results from a therapy program on the basis of phonation through a flow-resistant tube (FRT) with Vocal…

2.5-month-old infants' reasoning about when objects should and should not be occluded.

PubMed

Aguiar, A; Baillargeon, R

1999-09-01

The present research examined 2.5-month-old infants' reasoning about occlusion events. Three experiments investigated infants' ability to predict whether an object should remain continuously hidden or become temporarily visible when passing behind an occluder with an opening in its midsection. In Experiment 1, the infants were habituated to a short toy mouse that moved back and forth behind a screen. Next, the infants saw two test events that were identical to the habituation event except that a portion of the screen's midsection was removed to create a large window. In one event (high-window event), the window extended from the screen's upper edge; the mouse was shorter than the bottom of the window and thus did not become visible when passing behind the screen. In the other event (low-window event), the window extended from the screen's lower edge; although the mouse was shorter than the top of the window and hence should have become fully visible when passing behind the screen, it never appeared in the window. The infants tended to look equally at the high- and low-window events, suggesting that they were not surprised when the mouse failed to appear in the low window. However, positive results were obtained in Experiment 2 when the low-window event was modified: a portion of the screen above the window was removed so that the left and right sections of the screen were no longer connected (two-screens event). The infants looked reliably longer at the two-screens than at the high-window event. Together, the results of Experiments 1 and 2 suggested that, at 2.5 months of age, infants possess only very limited expectations about when objects should and should not be occluded. Specifically, infants expect objects (1) to become visible when passing between occluders and (2) to remain hidden when passing behind occluders, irrespective of whether these have openings extending from their upper or lower edges. Experiment 3 provided support for this interpretation. The

Site-directed mutagenesis of Autographa californica nucleopolyhedrovirus (AcNPV) polyhedrin: effect on polyhedron structure.

PubMed

Bravo-Patiño, A; Ibarra, J E

2000-01-01

Amino acids Lys34, His36, and Phe37 were substituted by PCR-mediated, site-directed mutagenesis for three Trp's in the AcNPV polyhedrin sequence. Phase contrast microscopy revealed refringent, amorphous polyhedra in the nuclei of infected cells. Electron microscopy confirmed a great variation in form and size of the mutated polyhedra. Although crystallization of the mutated polyhedrin occurred, it was irregular within each polyhedron. Virion occlusion was also severely affected. Virions were partially occluded, or only one virion was occluded per polyhedron. Results suggest that the substitution of these three amino acids affected the morphology of polyhedra, the uniformity of crystallization within each polyhedron, and the virion occlusion.

Amplatzer angled duct occluder for closure of patent ductus arteriosus larger than the aorta in an infant.

PubMed

Vijayalakshmi, I B; Chitra, N; Rajasri, R; Prabhudeva, A N

2005-01-01

Transcatheter closure of patent ductus arteriosus (PDA) by Amplatzer duct occluder is the treatment of choice. However, closure of very large ducts in infants with low weight is a challenge for the interventionalist because a large device may obstruct the aorta or left pulmonary artery. Difficulty is also encountered in advancing the device around the curve of the right ventricular outflow tract toward the pulmonary artery; this curve is tight, more or less at a right angle in infants, leading to kinking of the sheath, which increases fluoroscopic time. This is the first reported case of a very large PDA (8.7 mm), larger than the aorta (8.2 mm), successfully closed by an Amplatzer angled duct occluder in an infant weighing 5 kg.

Voice Training and Therapy with a Semi-Occluded Vocal Tract: Rationale and Scientific Underpinnings

ERIC Educational Resources Information Center

Titze, Ingo R.

2006-01-01

Purpose: Voice therapy with a semi-occluded vocal tract has a long history. The use of lip trills, tongue trills, bilabial fricatives, humming, and phonation into tubes or straws has been hailed by clinicians, singing teachers, and voice coaches as efficacious for training and rehabilitation. Little has been done, however, to provide the…

A New Coated Nitinol Occluder for Transcatheter Closure of Ventricular Septal Defects in a Canine Model

PubMed Central

Zhou, Yong; Chen, Feng; Huang, Xinmiao; Zhao, Xianxian; Wu, Hong; Bai, Yuan; Qin, Yongwen

2013-01-01

Aims. This study evaluated feasibility and safety of implanting the polyester-coated nitinol ventricular septal defect occluder (pcVSDO) in the canine model. Methods and Results. VSD models were successfully established by transseptal ventricular septal puncture via the right jugular vein in 15 out of 18 canines. Two types of VSDOs were implanted, either with pcVSDOs (n = 8) as the new type occluder group or with the commercial ventricular septal defect occluders (VSDOs, n = 7, Shanghai Sharp Memory Alloy Co. Ltd.) as the control group. Sheath size was 10 French (10 Fr) in two groups. Then the general state of the canines was observed after implantation. ECG and TTE were performed, respectively, at 7, 30, 90 days of follow-up. The canines were sacrificed at these time points for pathological and scanning electron microscopy examination. The devices were successfully implanted in all 15 canines and were retrievable and repositionable. There was no thrombus formation on the device or occurrence of complete heart block. The pcVSDO surface implanted at day 7 was already covered with neotissue by gross examination, and it completed endothelialization at day 30, while the commercial VSDO was covered with the neotissue in 30th day and the complete endothelialization in 90th day. Conclusion. The study shows that pcVSDO is feasible and safe to close canine VSD model and has good biocompatibility and shorter time of endothelialization. PMID:24066289

Controlling the hydration of the skin though the application of occluding barrier creams

PubMed Central

Sparr, Emma; Millecamps, Danielle; Isoir, Muriel; Burnier, Véronique; Larsson, Åsa; Cabane, Bernard

2013-01-01

The skin is a barrier membrane that separates environments with profoundly different water contents. The barrier properties are assured by the outer layer of the skin, the stratum corneum (SC), which controls the transepidermal water loss. The SC acts as a responding membrane, since its hydration and permeability vary with the boundary condition, which is the activity of water at the outer surface of the skin. We show how this boundary condition can be changed by the application of a barrier cream that makes a film with a high resistance to the transport of water. We present a quantitative model that predicts hydration and water transport in SC that is covered by such a film. We also develop an experimental method for measuring the specific resistance to water transport of films made of occluding barrier creams. Finally, we combine the theoretical model with the measured properties of the barrier creams to predict how a film of cream changes the activity of water at the outer surface of the SC. Using the known variations of SC permeability and hydration with the water activity in its environment (i.e. the relative humidity), we can thus predict how a film of barrier cream changes SC hydration. PMID:23269846

Controlling the hydration of the skin though the application of occluding barrier creams.

PubMed

Sparr, Emma; Millecamps, Danielle; Isoir, Muriel; Burnier, Véronique; Larsson, Åsa; Cabane, Bernard

2013-03-06

The skin is a barrier membrane that separates environments with profoundly different water contents. The barrier properties are assured by the outer layer of the skin, the stratum corneum (SC), which controls the transepidermal water loss. The SC acts as a responding membrane, since its hydration and permeability vary with the boundary condition, which is the activity of water at the outer surface of the skin. We show how this boundary condition can be changed by the application of a barrier cream that makes a film with a high resistance to the transport of water. We present a quantitative model that predicts hydration and water transport in SC that is covered by such a film. We also develop an experimental method for measuring the specific resistance to water transport of films made of occluding barrier creams. Finally, we combine the theoretical model with the measured properties of the barrier creams to predict how a film of cream changes the activity of water at the outer surface of the SC. Using the known variations of SC permeability and hydration with the water activity in its environment (i.e. the relative humidity), we can thus predict how a film of barrier cream changes SC hydration.

The Cricoid Force Necessary to Occlude the Esophageal Entrance: Is There a Gender Difference?

PubMed

Zeidan, Ahed M; Salem, M Ramez; Bamadhaj, Munir; Mazoit, Jean-Xavier; Sadek, Hussein; Houjairy, Hassan; Abdulkhaleq, Kamal; Bamadhaj, Nabil

2017-04-01

We tested the hypothesis whether gender differences exist in the applied cricoid force necessary to prevent regurgitation. Real-time visual and dynamic means were used to assess the effectiveness of different applied cricoid forces in occluding the esophageal entrance in men (group 1) and in women (group 2). In anesthetized and paralyzed patients, the glottis and esophageal entrance were visualized with a Glidescope video laryngoscope. Trained operators performed cricoid pressure (CP) and gastric tube insertion trials. Successful gastric tube insertion in the presence of CP was considered ineffective CP, whereas unsuccessful insertion was considered effective CP. The applied cricoid forces were measured with a novel instrument, the cricometer. The first patient in each group received 20 N. The applied cricoid force in successive patients was determined by the response of the previous patient within the same group, using the up-and-down sequential allocation technique. In the 30 men and 30 women who qualified for the study, the median cricoid force (cricoid force = 50) that occluded the esophageal entrance was 30.8 N (95% confidence interval = 28.15-33.5) in men, and 18.7 N in women (95% confidence interval = 17.1-20.3; P < .0001). Patency of the esophageal entrance was observed when CP was not applied and when inadequate forces that allowed successful esophageal cannulation were used. The current study provides evidence that the median force necessary to occlude the esophageal entrance to prevent regurgitation is less in women compared with men. Applying the appropriate cricoid force in women should also decrease airway-related problems that tend to occur with the use of excessive forces. The findings of the current study may only be applicable to patients with normal body habitus.

A retrospective comparative study of tunneled haemodialysis catheters inserted through occluded or collateral veins versus conventional methods.

PubMed

Powell, Steven; Chan, Tze Yuan; Bhat, Rammohan; Lam, Kimberly; Narlawar, Ranjeet S; Cullen, Nicola; Littler, Peter

2010-08-01

Tunneled hemodialysis catheters become essential in dialysis access when there is no possibility of using a functioning arteriovenous fistula. Collateral or occluded veins visible on ultrasound are used for puncture and passage of catheters into the central venous system. Chronically occluded veins are crossed with guidewires to allow dilatation and subsequent passage of hemodialysis catheters. We performed a retrospective analysis of patient demographics, comorbidities, procedural complications, functional survival, performance, and history of previous vascular access. The study group was compared with two control groups in which dialysis catheters were inserted either by radiologists in the interventional suite or by clinicians on the wards. Nineteen patients from the study group were compared with same number of patients in both control groups. The mean age of the study group was higher compared with the control groups. There was no significant difference in mean functional survival, infection rates, dialysis pump speeds in the first 2 weeks, and procedural complications between the study group and the controls. The study group had a significantly higher number of previous vascular access interventions, longer dialysis careers, and more comorbidities. Tunneled dialysis catheter placement by way of collateral or occluded veins appears safe and effective. These techniques give the operator further options when faced with patients possessing challenging vascular access. Indeed, there may be a case for preferential use of these veins to keep patent central veins in reserve.

Dissecting the active site of a photoreceptor protein

NASA Astrophysics Data System (ADS)

Hoff, Wouter; Hara, Miwa; Ren, Jie; Moghadam, Farzaneh; Xie, Aihua; Kumauchi, Masato

While enzymes are quite large molecules, functionally important chemical events are often limited to a small region of the protein: the active site. The physical and chemical properties of residues at such active sites are often strongly altered compared to the same groups dissolved in water. Understanding such effects is important for unraveling the mechanisms underlying protein function and for protein engineering, but has proven challenging. Here we report on our ongoing efforts on using photoactive yellow protein (PYP), a bacterial photoreceptor, as a model system for such effects. We will report on the following questions: How many residues affect active site properties? Are these residues in direct physical contact with the active site? Can functionally important residues be recognized in the crystal structure of a protein? What structural resolution is needed to understand active sites? What spectroscopic techniques are most informative? Which weak interactions dominate active site properties?

Retrieval of large Occlutech Figula Flex septal defect occluders using a commercially available bioptome: proof of concept.

PubMed

Georgiev, Stanimir; Tanase, Daniel; Genz, Thomas; Ewert, Peter; Naumann, Susanne; Pozza, Robert Dalla; Eicken, Andreas

2018-07-01

This study aimed to develop a method for retrieval of the new meshed nitinol atrial septal defect occluders - Ceraflex and Occlutech. The newly developed atrial septal defect occluders have potential benefits considering implantation, but concerns regarding their removal in case of embolisation have been raised. Over 21 years, 1449 patients underwent interventional atrial septal defect occlusion in our institution. We reviewed the cases of embolisation of the device, developed a strategy for device removal, and tested it on the benchside and in animal tests. In 11 patients (0.8%), the intended atrial septal defect occlusion was complicated by an embolisation of the device. In contrast to the Amplatzer septal occluders, retrieval of Occlutech devices larger than 16 mm with snare techniques was impossible. In benchside tests, this was confirmed and a new method for removal of large meshed devices was developed. This involved the commercially available Maslanka® biopsy forceps. The feasibility of this technique in vivo was tested in a pig model. During animal tests, using the Maslanka biopsy forceps it was possible to interventionally retrieve embolised Ceraflex and Occlutech devices of different sizes - 10, 16, 30, and 40 mm - into a 12-F sheath. It was impossible to retrieve Occlutech and Ceraflex devices larger than 16 mm into a large sheath in vivo and during benchside tests. However, this was feasible on the bench and in vivo using the Maslanka biopsy forceps even with the largest available devices.

Active site dynamics of ribonuclease.

PubMed Central

Brünger, A T; Brooks, C L; Karplus, M

1985-01-01

The stochastic boundary molecular dynamics method is used to study the structure, dynamics, and energetics of the solvated active site of bovine pancreatic ribonuclease A. Simulations of the native enzyme and of the enzyme complexed with the dinucleotide substrate CpA and the transition-state analog uridine vanadate are compared. Structural features and dynamical couplings for ribonuclease residues found in the simulation are consistent with experimental data. Water molecules, most of which are not observed in crystallographic studies, are shown to play an important role in the active site. Hydrogen bonding of residues with water molecules in the free enzyme is found to mimic the substrate-enzyme interactions of residues involved in binding. Networks of water stabilize the cluster of positively charged active site residues. Correlated fluctuations between the uridine vanadate complex and the distant lysine residues are mediated through water and may indicate a possible role for these residues in stabilizing the transition state. Images PMID:3866234

In Vitro Ability of a Novel Nanohydroxyapatite Oral Rinse to Occlude Dentine Tubules

PubMed Central

Hill, Robert G.; Chen, Xiaohui; Gillam, David G.

2015-01-01

Objectives. The aim of the study was to investigate the ability of a novel nanohydroxyapatite (nHA) desensitizing oral rinse to occlude dentine tubules compared to selected commercially available desensitizing oral rinses. Methods. 25 caries-free extracted molars were sectioned into 1 mm thick dentine discs. The dentine discs (n = 25) were etched with 6% citric acid for 2 minutes and rinsed with distilled water, prior to a 30-second application of test and control oral rinses. Evaluation was by (1) Scanning Electron Microscopy (SEM) of the dentine surface and (2) fluid flow measurements through a dentine disc. Results. Most of the oral rinses failed to adequately cover the dentine surface apart from the nHa oral rinse. However the hydroxyapatite, 1.4% potassium oxalate, and arginine/PVM/MA copolymer oral rinses, appeared to be relatively more effective than the nHA test and negative control rinses (potassium nitrate) in relation to a reduction in fluid flow measurements. Conclusions. Although the novel nHA oral rinse demonstrated the ability to occlude the dentine tubules and reduce the fluid flow measurements, some of the other oral rinses appeared to demonstrate a statistically significant reduction in fluid flow through the dentine disc, in particular the arginine/PVM/MA copolymer oral rinse. PMID:26161093

Low dielectric response in enzyme active site

PubMed Central

Mertz, Edward L.; Krishtalik, Lev I.

2000-01-01

The kinetics of charge transfer depend crucially on the dielectric reorganization of the medium. In enzymatic reactions that involve charge transfer, atomic dielectric response of the active site and of its surroundings determines the efficiency of the protein as a catalyst. We report direct spectroscopic measurements of the reorganization energy associated with the dielectric response in the active site of α-chymotrypsin. A chromophoric inhibitor of the enzyme is used as a spectroscopic probe. We find that water strongly affects the dielectric reorganization in the active site of the enzyme in solution. The reorganization energy of the protein matrix in the vicinity of the active site is similar to that of low-polarity solvents. Surprisingly, water exhibits an anomalously high dielectric response that cannot be described in terms of the dielectric continuum theory. As a result, sequestering the active site from the aqueous environment inside low-dielectric enzyme body dramatically reduces the dielectric reorganization. This reduction is particularly important for controlling the rate of enzymatic reactions. PMID:10681440

Methanopyrus kandleri topoisomerase V contains three distinct AP lyase active sites in addition to the topoisomerase active site

PubMed Central

Rajan, Rakhi; Osterman, Amy; Mondragón, Alfonso

2016-01-01

Topoisomerase V (Topo-V) is the only topoisomerase with both topoisomerase and DNA repair activities. The topoisomerase activity is conferred by a small alpha-helical domain, whereas the AP lyase activity is found in a region formed by 12 tandem helix-hairpin-helix ((HhH)2) domains. Although it was known that Topo-V has multiple repair sites, only one had been mapped. Here, we show that Topo-V has three AP lyase sites. The atomic structure and Small Angle X-ray Scattering studies of a 97 kDa fragment spanning the topoisomerase and 10 (HhH)2 domains reveal that the (HhH)2 domains extend away from the topoisomerase domain. A combination of biochemical and structural observations allow the mapping of the second repair site to the junction of the 9th and 10th (HhH)2 domains. The second site is structurally similar to the first one and to the sites found in other AP lyases. The 3rd AP lyase site is located in the 12th (HhH)2 domain. The results show that Topo-V is an unusual protein: it is the only known protein with more than one (HhH)2 domain, the only known topoisomerase with dual activities and is also unique by having three AP lyase repair sites in the same polypeptide. PMID:26908655

[Outcome of transcatheter closure of perimembranous ventricular septal defect with modified double-disk occluder device].

PubMed

Liu, Jing; You, Xiao-hua; Zhao, Xian-xian; Hu, Jian-qiang; Cao, Jiang; Xu, Rong-liang; Wu, Hong; Chen, Shao-ping; Zhang, Jian-liang; Zheng, Xing; Qin, Yong-wen

2010-04-01

To evaluate the efficacy and adverse effects of transcatheter closure of perimembranous ventricular septal defect (pmVSD) with modified double-disk occluder device (MDVO). Clinical data including clinical examination, electrocardiography daily after the procedure for a week, chest-X-rays and TTE before discharge and at 3-5 days after the procedure were analyzed from 604 patients underwent percutaneous closure of a pmVSD with MDVO at our department between December 2001 and December 2008. Procedure was successful in 576 out of 604 patients (95.4%) and 583 VSD occluders were placed. Endocarditis, thromboembolism, or deaths were not observed after procedure. Conduction block occurred in 81 patients (56 RBBB, 14 LBBB) and transient nonparoxysmal ventricular tachycardia in 31 patients after the procedure. Complete heart block occurred in 11 patients, 9 of them recovered in 3 weeks, permanent pacemaker was implanted in 2 patients (one had transient III degrees AVB before the procedure, the other underwent simultaneous closure of ventricular septal defect and atrial septal defect). Trivial/small residual shunts were found in 69 patients (12.0%). The residual shunts disappeared in 31 patients and remained unchanged in 38 patients (6.6%) 7 days after procedures. Aortic regurgitation developed in 5 patients (2 trivial/small, 3 small/moderate), and tricuspid regurgitation was present in 35 patients (32 trivial/small, 3 moderate). Five patients developed haemolysis (device retrieved via catheter in 1 patient due to persistent haemolysis, the other 4 patients recovered 3-14 days post procedure). Pseudoaneurysm of femoral artery occurred in 1 patient, and disappeared by pressure dressing. Device was successfully replaced in 2 patients with either device embolization (n = 1) or device misplacement (n = 1) after device retrieval by catheter. It is safe and effective to close congenital perimembranous ventricular septal defect with domestic-made occluder device.

Is it necessary to occlude the ear in bone-conduction testing at 4 kHz, in order to prevent air-borne radiation affecting the results?

PubMed

Tate Maltby, Maryanne; Gaszczyk, David

2015-01-01

To re-evaluate the current BSA recommendation that the test ear should be occluded during the bone-conduction procedure at frequencies above 2 kHz to prevent audible air-borne radiation. Pure-tone audiometry was undertaken during routine hearing tests. The audiograms of fifty-two ears met the criteria for the study and were included. Bone conduction at 4 kHz was tested in three different conditions: test ear open/occluded by earplug and occluded by circumaural earphone. Forty-four adults aged 41-77 years with average hearing levels from normal to severe loss. All complied fully with the test procedure. No audiogram had a significant conductive element. There was no significant difference in each of the three test situations. Only two audiograms showed any (5 dB) difference at 4 kHz when bone conduction was retested with the ear occluded. The errors that result in a false air-bone gap at 4 kHz would not appear to be due to air-borne radiation. Failure to occlude the ear canal at 4 kHz, where air-borne radiation is greatest, makes no significant difference to the audiometric results. It is therefore suggested that it is unnecessary to block the test ear during routine pure-tone bone-conduction testing to prevent audible air-borne radiation, and that this should no longer form part of normal clinical practice.

Transcatheter closure of patent ductus arteriosus with Nit-Occlud coils.

PubMed

Celiker, Alpay; Aypar, Ebru; Karagöz, Tevfik; Dilber, Embiya; Ceviz, Naci

2005-08-01

The detachable coils have been successfully used for transcatheter occlusion of small- to moderate-sized patent ductus arteriosus (PDA). We report our experience regarding the use of the Nit-Occlud coils (NOCs) for transcatheter PDA and major aortopulmonary collateral (MAPCA) occlusion. Single NOCs were used to close PDA in 26 patients, and one small and two large MAPCAs in two patients. Mean age and weight of the patients were 7.7 +/- 5.4 years and 20.6 +/- 11.6 kg. Mean minimum duct diameter was 2.8 +/- 0.8 mm; ampulla, 8.7 +/- 2.4 mm; and PDA length, 9.3 +/- 4.4 mm. Mean pulmonary artery pressure ranged from 9 to 51 mm Hg and pulmonary/systemic flow ratio from 1.1 to 5.8. Ductal shape was conical in 24 patients. Route of approach was venous in 23 and arterial in 3. Successful coil implantation was achieved in 24/26 (92.3%). Mean procedure and fluoroscopy time were 67.2 +/- 22.1 and 14.9 +/- 6.5 min. The three MAPCAs were also successfully occluded using NOC Medium and Flex. Postimplantation angiograms revealed no leak in 3, a trace or small leak in 17, and a medium leak in 4 patients. Mean follow-up was 7 +/- 5 months. Complete occlusion was achieved in 17/24 (71%) at 24 hr, 19/24 (79%) by 1 month, 13/15 (87%) by 3 months, 14/15 (93%) by 6 months, and 10/11 (90%) by 12 months postprocedure. Hemolysis, late embolization, duct recanalization, and flow disturbances were not observed. Transcatheter occlusion of moderate-sized PDAs and MAPCAs using NOCs seems to offer a safe, simple, and controlled method in pediatric patients.

Sympathetic and cardiovascular responses to venous distension in an occluded limb.

PubMed

Cui, Jian; Leuenberger, Urs A; Gao, Zhaohui; Sinoway, Lawrence I

2011-12-01

We recently showed that a fixed volume (i.e., 40 ml) of saline infused into the venous circulation of an arterially occluded vascular bed increases muscle sympathetic nerve activity (MSNA) and blood pressure. In the present report, we hypothesized that the volume and rate of infusion would influence the magnitude of the sympathetic response. Blood pressure, heart rate, and MSNA were assessed in 13 young healthy subjects during forearm saline infusions (arrested circulation). The effects of different volumes of saline (i.e., 2%, 3%, 4%, or 5% forearm volume at 30 ml/min) and different rates of infusion (i.e., 5% forearm volume at 10, 20, or 30 ml/min) were evaluated. MSNA and blood pressure responses were linked with the infusion volume. Infusion of 5% of forearm volume evoked greater MSNA responses than did infusion of 2% of forearm volume (Δ11.6 ± 1.9 vs. Δ3.1 ± 1.8 bursts/min and Δ332 ± 105 vs. Δ38 ± 32 units/min, all P < 0.05). Moreover, greater MSNA responses were evoked by saline infusion at 30 ml/min than 10 ml/min (P < 0.05). Sonographic measurements confirmed that the saline infusions induced forearm venous distension. The results suggest that volume and rate of saline infusion are important factors in evoking sympathetic activation. We postulate that venous distension contributes to cardiovascular autonomic adjustment in humans.

Long-Term Results of Transcatheter Closure of Patent Ductus Arteriosus in Infants Using Amplatzer Duct Occluder

PubMed Central

Behjati-Ardakani, Mostafa; Behjati-Ardakani, Mohammad-Amin; Hosseini, Seyed-Habibolla; Noori, Noormohammad

2013-01-01

Objective Patent ductus arteriosus (PDA) is one of the most frequently seen congenital heart diseases. Its closure is recommended because of the risk of infective endocardis, as well as morbidity and mortality in the long. The aim of this study was to assess the long term results of the transcatheter closure of PDA in infants using amplatzer duct occlude (ADO). Methods From May 2004 to September 2011, forty eight infants underwent transcatheter closure of PDA. A lateral or right anterior oblique view aortogram was done to locate PDA and to measure its size. Before discharge, repeat aortogram was performed to evaluate eventual residual shunt and to confirm the appropriate deployment of the ADO. Follow up evaluations were done with transthoracic echocardiography at discharge, 1 month, 6 months, 12 months and yearly thereafter. Findings The mean age of patients at procedure was 9.18±2.32 (range 3 to 12) months, mean weight 6.73±1.16 (range 4.5 to 10.1) kg. The PDA occluded completely in 20 out of the 48 patients. Twenty four patients had trivial or mild shunt and two patients had moderate residual shunt which disappeared in one patient within 24 hours and other patient with moderate shunt in 1 month. One patient (age 8 months) had mild LPA stenosis. The device emobolization occurred in two patients, immediately after the procedure in one and during night in the other patient Conclusion The long term results suggested that transcatheter closure of PDA using Amplatzer duct occluder is a safe and effective treatment in infants less than 1 year of age with minimal complications. PMID:24427494

Balloon-occluded Retrograde Transvenous Obliteration (BRTO): Technique and Intraprocedural Imaging

PubMed Central

Sabri, Saher S.; Saad, Wael E. A.

2011-01-01

Balloon-occluded retrograde transvenous obliteration (BRTO) is an endovascular technique used as a therapeutic adjunct or alternative to transjugular intrahepatic shunts (TIPS) in the management of gastric varices. Occlusion balloons are strategically placed to modulate flow within the gastrorenal or gastrocaval shunt to allow stagnation of the sclerosant material within the gastric varix. The approach and complexity of the procedure depends on the anatomic classification of inflow and outflow veins of the varix. Ethanolamine oleate has been described as the main sclerosant used in this procedure. Recently, foam sclerosants have gained popularity as alternative embolization agents, which provide the advantage of better variceal wall contact and potentially less dose of sclerosant. PMID:22942548

Transcatheter Closure of Patent Ductus Arteriosus in Children with the Occlutech Duct Occluder.

PubMed

Bilici, Meki; Demir, Fikri; Akın, Alper; Türe, Mehmet; Balık, Hasan; Kuyumcu, Mahir

2017-12-01

The aim of this study was to evaluate the feasibility, efficacy and safety of transcatheter closure of patent ductus arteriosus (PDA) with the Occlutech duct occluder (ODO) in children. We reviewed the clinical records of 71 patients who underwent percutaneous closure of PDA with an ODO between September 2014 and August 2016. The Occlutech duct occluder was applied to 71 patients during the study period (September 2014-August 2016), and the results were analyzed in this study. Forty-two of the patients were female and 29 male. The median age was 20.5 months (range, 6-194 months) and median weight was 16 kg (range, 6-68 kg). The PDA was classified as type A in 54 patients (76.1%), type E in 14 (19.7%), type C in 2 (2.8%) and type B in 1 (1.4%) based on the Krichenko classification. A standard ODO device was used for the transcatheter closure procedure in 66 patients and the long-shank ODO device in 5. In the echocardiographic measurement of PDA, the median smallest diameter was 2.7 mm (range, 1.5-7.0 mm), and in the angiographic measurement, the median smallest diameter was 2.5 mm (range, 1.5-6.5 mm). All 71 patients underwent successful PDA closure with the ODO. Angiography following the procedure showed complete closure in 47 patients (66.2%), mild residual shunt in 13 patients (18.3%) and a trivial shunt in 11 patients (15.5%). Color flow Doppler echocardiogpaphy at 24 h post-implantation showed that complete closure was achieved in 65 patients (91.5%), and 6 patients (8.5%) had mild residual shunt. All patients (100%) had complete closure at 30 days of follow-up. The results of this study showed that the Occlutech PDA occluder device is safe and effective in the closure of PDA. As the pulmonary artery side of the device is wider than the aortic side, protrusion toward the aortic side and embolization are prevented, but there is residual shunt in the early period, although this residual shunt disappeared after a few months.

Transcatheter Retrieval of Embolized Atrial Septal Defect Occluder Device by Waist Capture Technique.

PubMed

Her, Ae-Young; Lim, Kyung-Hun; Shin, Eun-Seok

2018-01-27

This case study describes the successful percutaneous transcatheter retrieval of an embolized Amplatzer occluder device using the "waist capture technique" in a patient with an atrial septal defect. This technique allowed for stability of the Amplatzer device, compression of the atrial discs for easier removal, prevention of further embolization, and minimal injury to vasculature during device retrieval. This novel and effective technique can be used safely for the retrieval of Amplatzer devices in the venous system.

[Lung perfusion studies after percutaneous closure of patent ductus arteriosus using the Amplatzer Duct Occluder in children].

PubMed

Parra-Bravo, José Rafael; Apolonio-Martínez, Adriana; Estrada-Loza, María de Jesús; Beirana-Palencia, Luisa Gracia; Ramírez-Portillo, César Iván

2015-01-01

The closure of patent ductus arteriosus with multiple devices has been associated with a reduction in lung perfusion. We evaluated the pulmonary perfusion after percutaneous closure of patent ductus arteriosus with the Amplatzer Duct Occluder device using perfusion lung scan. Thirty patients underwent successful percutaneous patent ductus arteriosus occlusions using the Amplatzer Duct Occluder device were included in this study. Lung perfusion scans were preformed 6 months after the procedure. Peak flow velocities and protrusion of the device were analyzed by Doppler echocardiography. A left lung perfusion<40% was considered abnormal. The device implantation was successful in all patients. Average perfusion of left lung was 44.7±4.9% (37.8-61.4). Five patients (16.6%) showed decreased perfusion of the left lung. Age, low weight, the length of the ductus arteriosus and the minimum and maximum diameter/length of the ductus arteriosus ratio were statistically significant in patients with abnormalities of lung perfusion. It was observed protrusion the device in 6 patients with a higher maximum flow rate in the left pulmonary artery. The left lung perfusion may be compromised after percutaneous closure of patent ductus arteriosus with the Amplatzer Duct Occluder. The increased flow velocity in the origin of the left pulmonary artery can be a poor indicator of reduction in pulmonary perfusion and can occur in the absence of protrusion of the device. Copyright © 2014 Instituto Nacional de Cardiología Ignacio Chávez. Published by Masson Doyma México S.A. All rights reserved.

Treatment of patent ductus arteriosus by the use of an Amplatz canine ductal occluder device

PubMed Central

White, Pam

2009-01-01

A 7-month-old female, spayed border collie was referred to the Ontario Veterinary College due to a continuous murmur noted by the referring veterinarian prior to ovariohysterectomy. Auscultation confirmed a grade VI/VI continuous murmur. An echocardiogram confirmed patent ductus arteriosus (PDA). An Amplatz canine ductal occluder device was successfully placed for occlusion of blood flow though the ductus. PMID:19436449

An in vivo assessment of the effects of using different implant abutment occluding materials on implant microleakage and the peri-implant microbiome

NASA Astrophysics Data System (ADS)

Rubino, Caroline

Microleakage may be a factor in the progression of peri-implant pathology. Microleakage in implant dentistry refers to the passage of bacteria, fluids, molecules or ions between the abutment-implant interface to and from the surrounding periodontal tissues. This creates a zone of inflammation and reservoir of bacteria at the implant-abutment interface. Bone loss typically occurs within the first year of abutment connection and then stabilizes. It has not yet been definitively proven that the occurrence of microleakage cannot contribute to future bone loss or impede the treatment of peri-implant disease. Therefore, strategies to reduce or eliminate microleakage are sought out. Recent evidence demonstrates that the type of implant abutment channel occluding material can affect the amount of microleakage in an in vitro study environment. Thus, we hypothesize that different abutment screw channel occluding materials will affect the amount of observed microleakage, vis-a-vis the correlation between the microflora found on the abutment screw channel occluding material those found in the peri-implant sulcus. Additional objectives include confirming the presence of microleakage in vivo and assessing any impact that different abutment screw channel occluding materials may have on the peri-implant microbiome. Finally, the present study provides an opportunity to further characterize the peri-implant microbiome. Eight fully edentulous patients restored with at dental implants supporting screw-retained fixed hybrid prostheses were included in the study. At the initial appointment (T1), the prostheses were removed and the implants and prostheses were cleaned. The prostheses were then inserted with polytetrafluoroethylene tape (PTFE, TeflonRTM), cotton, polyvinyl siloxane (PVS), or synthetic foam as the implant abutment channel occluding material and sealed over with composite resin. About six months later (T2), the prostheses were removed and the materials collected. Paper

Activation of phenylalanine hydroxylase by phenylalanine does not require binding in the active site.

PubMed

Roberts, Kenneth M; Khan, Crystal A; Hinck, Cynthia S; Fitzpatrick, Paul F

2014-12-16

Phenylalanine hydroxylase (PheH), a liver enzyme that catalyzes the hydroxylation of excess phenylalanine in the diet to tyrosine, is activated by phenylalanine. The lack of activity at low levels of phenylalanine has been attributed to the N-terminus of the protein's regulatory domain acting as an inhibitory peptide by blocking substrate access to the active site. The location of the site at which phenylalanine binds to activate the enzyme is unknown, and both the active site in the catalytic domain and a separate site in the N-terminal regulatory domain have been proposed. Binding of catecholamines to the active-site iron was used to probe the accessibility of the active site. Removal of the regulatory domain increases the rate constants for association of several catecholamines with the wild-type enzyme by ∼2-fold. Binding of phenylalanine in the active site is effectively abolished by mutating the active-site residue Arg270 to lysine. The k(cat)/K(phe) value is down 10⁴ for the mutant enzyme, and the K(m) value for phenylalanine for the mutant enzyme is >0.5 M. Incubation of the R270K enzyme with phenylalanine also results in a 2-fold increase in the rate constants for catecholamine binding. The change in the tryptophan fluorescence emission spectrum seen in the wild-type enzyme upon activation by phenylalanine is also seen with the R270K mutant enzyme in the presence of phenylalanine. Both results establish that activation of PheH by phenylalanine does not require binding of the amino acid in the active site. This is consistent with a separate allosteric site, likely in the regulatory domain.

Activation of Phenylalanine Hydroxylase by Phenylalanine Does Not Require Binding in the Active Site

PubMed Central

2015-01-01

Phenylalanine hydroxylase (PheH), a liver enzyme that catalyzes the hydroxylation of excess phenylalanine in the diet to tyrosine, is activated by phenylalanine. The lack of activity at low levels of phenylalanine has been attributed to the N-terminus of the protein’s regulatory domain acting as an inhibitory peptide by blocking substrate access to the active site. The location of the site at which phenylalanine binds to activate the enzyme is unknown, and both the active site in the catalytic domain and a separate site in the N-terminal regulatory domain have been proposed. Binding of catecholamines to the active-site iron was used to probe the accessibility of the active site. Removal of the regulatory domain increases the rate constants for association of several catecholamines with the wild-type enzyme by ∼2-fold. Binding of phenylalanine in the active site is effectively abolished by mutating the active-site residue Arg270 to lysine. The kcat/Kphe value is down 104 for the mutant enzyme, and the Km value for phenylalanine for the mutant enzyme is >0.5 M. Incubation of the R270K enzyme with phenylalanine also results in a 2-fold increase in the rate constants for catecholamine binding. The change in the tryptophan fluorescence emission spectrum seen in the wild-type enzyme upon activation by phenylalanine is also seen with the R270K mutant enzyme in the presence of phenylalanine. Both results establish that activation of PheH by phenylalanine does not require binding of the amino acid in the active site. This is consistent with a separate allosteric site, likely in the regulatory domain. PMID:25453233

Dense Accumulation of Lipiodol Emulsion in Hepatocellular Carcinoma Nodule during Selective Balloon-occluded Transarterial Chemoembolization: Measurement of Balloon-occluded Arterial Stump Pressure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Irie, Toshiyuki, E-mail: toshiyuki.irie.rq@hitachi.com; Kuramochi, Masashi, E-mail: masashi.kuramochi.sh@hitachi.com; Takahashi, Nobuyuki, E-mail: nbyktakahashiodn@yahoo.co.jp

2013-06-15

Purpose. To reveal the mechanism of dense accumulation of lipiodol emulsion (LE) in hepatocellular carcinoma (HCC) during selective balloon-occluded transarterial chemoembolization (B-TACE). Methods. Balloon-occluded arterial stump pressure (BOASP) at the embolization portion was measured during selective B-TACE for 43 nodules in 42 patients. Fluoroscopy and digital subtraction angiography were prospectively observed during selective B-TACE to note whether dense LE accumulation in HCC occurred. The LE concentration ratio of HCC to embolized liver parenchyma (LECHL ratio) was also calculated for each treatment on the basis of the computed tomographic scan obtained immediately after selective B-TACE. The relationships between degree of LEmore » accumulation and the BOASP, as well as the LECHL ratio, were analyzed. Results. Arterial flow beyond the catheter tip was maintained even after balloon inflation. In 39 of 43 treatments, LE inflow into the nontumorous liver parenchyma ceased immediately after LE droplets were filled in arteries of the nontumorous liver parenchyma while LE inflow into the HCC nodule continued (group 1). More dense LE accumulation in HCC nodule was obtained in these 39 treatments. In four treatments, LE inflow both into the nontumorous liver parenchyma and into the HCC nodule continued, and no dense LE accumulation in HCC nodule was observed (group 2). In these four treatments, thick anastomotic vessels with collateral artery were noted. The BOASP in group 1 was (mean {+-} SD) 33.8 {+-} 12.8 mmHg (range 13-64 mmHg) and that in group 2 was 92.3 {+-} 7.4 mmHg (range 83-100 mmHg). There was a statistically significant difference in BOASP between groups (p = 0.00004, Welch's t test). The LECHL ratio in group 1 was 18.3 {+-} 13.9 (range 2.9-54.2) and that in group 2 was 2.6 {+-} 1.1 (range 1.7-4.2). There was a statistically significant difference in the LECHL ratio between the groups (p = 0.000034, Welch's t test). Conclusion. Selective B

Non-competitive inhibition by active site binders.

PubMed

Blat, Yuval

2010-06-01

Classical enzymology has been used for generations to understand the interactions of inhibitors with their enzyme targets. Enzymology tools enabled prediction of the biological impact of inhibitors as well as the development of novel, more potent, ones. Experiments designed to examine the competition between the tested inhibitor and the enzyme substrate(s) are the tool of choice to identify inhibitors that bind in the active site. Competition between an inhibitor and a substrate is considered a strong evidence for binding of the inhibitor in the active site, while the lack of competition suggests binding to an alternative site. Nevertheless, exceptions to this notion do exist. Active site-binding inhibitors can display non-competitive inhibition patterns. This unusual behavior has been observed with enzymes utilizing an exosite for substrate binding, isomechanism enzymes, enzymes with multiple substrates and/or products and two-step binding inhibitors. In many of these cases, the mechanisms underlying the lack of competition between the substrate and the inhibitor are well understood. Tools like alternative substrates, testing the enzyme reaction in the reverse direction and monitoring inhibition time dependence can be applied to enable distinction between 'badly behaving' active site binders and true exosite inhibitors.

Long-term outcome of 154 patients receiving balloon-occluded retrograde transvenous obliteration for gastric fundal varices.

PubMed

Imai, Yukinori; Nakazawa, Manabu; Ando, Satsuki; Sugawara, Kayoko; Mochida, Satoshi

2016-11-01

This study aims to clarify the long-term outcome of therapeutic strategies including balloon-occluded retrograde transvenous obliteration (B-RTO) for patients with gastric fundal varices. The subjects were 154 patients with gastric fundal varices fulfilling the criteria for receiving B-RTO. In patients showing variceal bleeding, endoscopic therapies and/or balloon tamponade was performed to achieve hemostasis. B-RTO was accomplished with injection of 5% ethanolamine oleate through a standard balloon catheter except for patients with atypical varices, in whom a microballoon catheter was used to occlude drainage vessels other than a gastrorenal shunt. In patients complicated with esophageal varices at baseline, endoscopic therapies were performed following B-RTO. Balloon-occluded retrograde transvenous obliteration was performed successfully in 147 patients (95%), including 15 patients using a microballoon catheter. Complete variceal obliteration was achieved in all patients. Additional endoscopic therapies for esophageal varices were performed in 31 patients. Gastric varices did not recur in any of these patients. The cumulative survival rates at 1, 3, and 5 years after B-RTO were 91%, 76%, and 72%, respectively. Child-Pugh scores and hepatocellular carcinoma complication were identified as prognostic factors associated with survival rates. The cumulative exacerbation rates of esophageal varices at 1, 3, and 5 years were 13%, 20%, and 27%, respectively, and rupture developed in six patients, which were successfully treated with endoscopic therapies. Therapeutic strategies including B-RTO with a microballoon catheter were useful to achieve a favorable outcome in patients with gastric fundal varices especially in those manifesting Child-Pugh class-A liver damage and/or those without hepatocellular carcinoma complication. © 2016 Journal of Gastroenterology and Hepatology Foundation and John Wiley & Sons Australia, Ltd.

Safety Oversight of Decommissioning Activities at DOE Nuclear Sites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zull, Lawrence M.; Yeniscavich, William

2008-01-15

The Defense Nuclear Facilities Safety Board (Board) is an independent federal agency established by Congress in 1988 to provide nuclear safety oversight of activities at U.S. Department of Energy (DOE) defense nuclear facilities. The activities under the Board's jurisdiction include the design, construction, startup, operation, and decommissioning of defense nuclear facilities at DOE sites. This paper reviews the Board's safety oversight of decommissioning activities at DOE sites, identifies the safety problems observed, and discusses Board initiatives to improve the safety of decommissioning activities at DOE sites. The decommissioning of former defense nuclear facilities has reduced the risk of radioactive materialmore » contamination and exposure to the public and site workers. In general, efforts to perform decommissioning work at DOE defense nuclear sites have been successful, and contractors performing decommissioning work have a good safety record. Decommissioning activities have recently been completed at sites identified for closure, including the Rocky Flats Environmental Technology Site, the Fernald Closure Project, and the Miamisburg Closure Project (the Mound site). The Rocky Flats and Fernald sites, which produced plutonium parts and uranium materials for defense needs (respectively), have been turned into wildlife refuges. The Mound site, which performed R and D activities on nuclear materials, has been converted into an industrial and technology park called the Mound Advanced Technology Center. The DOE Office of Legacy Management is responsible for the long term stewardship of these former EM sites. The Board has reviewed many decommissioning activities, and noted that there are valuable lessons learned that can benefit both DOE and the contractor. As part of its ongoing safety oversight responsibilities, the Board and its staff will continue to review the safety of DOE and contractor decommissioning activities at DOE defense nuclear sites.« less

Cochlear excitation by the near-field component during stimulation through the partially occluded round window

NASA Astrophysics Data System (ADS)

Weddell, Thomas D.; Yarin, Yury M.; Drexl, Markus; Russell, Ian J.; Elliott, Stephen J.; Lukashkin, Andrei N.

2015-12-01

The round window membrane (RW) provides pressure relief when the cochlea is excited by sound. While normal function of the RW is important for effective stimulation of the cochlea through the conventional oval window route, the cochlea can be stimulated successfully in non-conventional ways (e.g. through bone conduction, through the RW, and through perforations in the cochlea's apical turn). We report measurements of cochlear function from guinea pigs when the cochlea was stimulated at acoustic frequencies by movements of a miniature magnet which partially occluded the RW. Neural response latencies to acoustic and RW stimulation were similar and taken to indicate that both means of stimulation resulted in the generation of conventional travelling waves along the cochlear partition. It was concluded that the relatively high impedance of the ossicles, as seen from the cochlea, enabled the region of the RW not occluded by the magnet, to act as a pressure shunt during RW stimulation. We propose that travelling waves, similar to those due to acoustic far-field pressure changes, are driven by a jet-like, near-field component of a complex fluid-pressure field, which is generated by the magnetically vibrated RW.

Impact of National Clinical Guideline Recommendations for Revascularization of Persistently Occluded Infarct-Related Arteries on Clinical Practice in the United States

PubMed Central

Deyell, Marc W.; Buller, Christopher E.; Miller, Louis H.; Wang, Tracy Y.; Dai, David; Lamas, Gervasio A.; Srinivas, Vankeepuram S.; Hochman, Judith S.

2013-01-01

Background The Occluded Artery Trial (OAT) was a large, randomized controlled trial published in 2006 that demonstrated no benefit to routine percutaneous coronary intervention (PCI) of persistently totally occluded infarct-related arteries (IRA) identified a minimum of 24 hours (on calendar days 3–28) after myocardial infarction (MI). The purpose of this study was to determine the impact of OAT results and consequent change in guideline recommendations for PCI for treatment of persistently occluded IRAs. Methods We identified all patients enrolled in the CathPCI Registry, from 2005 to 2008, undergoing catheterization more than 24 hours after MI with a totally occluded native coronary artery and no major OAT exclusion criteria. We examined trends in monthly rates of PCI for occlusions after OAT publication and after guideline revisions. Because reporting of diagnostic catheterizations was not mandatory, we examined trends among hospitals in the highest quartile for reporting of diagnostic procedures. Results A total of 28 780 patient visits from 896 hospitals were included. Overall, we found no significant decline in the adjusted monthly rate of PCI of occlusions after publication of OAT (odds ratio [OR], 0.997; 95% confidence interval [CI], 0.989–1.006) or after guideline revisions (OR, 1.007; 95% CI, 0.992–1.022). Among hospitals consistently reporting diagnostic catheterizations, there was no significant decline after OAT publication (OR, 1.018; 95% CI, 0.995–1.042), and there was a trend toward decline after guideline revisions (OR, 0.963; 95% CI, 0.920–1.000). Conclusion These findings suggest that the results of OAT and consequent guideline revisions have not, to date, been fully incorporated into clinical practice in a large cross-section of hospitals in the United States. PMID:21747002

Efficacy of electrocoagulation in sealing the cystic artery and cystic duct occluded with only one absorbable clip during laparoscopic cholecystectomy.

PubMed

Yang, Chang-Ping; Cao, Jin-Lin; Yang, Ren-Rong; Guo, Hong-Rong; Li, Zhao-Hui; Guo, Hai-Ying; Shao, Yin-Can; Liu, Gui-Bao

2014-02-01

Even though laparoscopic cholecystectomy (LC) emerged over 20 years ago, controversies persist with regard to the best method to ligate the cystic duct and artery. We proposed to assess the effectiveness and safety of electrocoagulation to seal the cystic artery and cystic duct after their occlusion with only one absorbable clip. We retrospectively compared the clinical data for 635 patients undergoing LC using electrocoagulation to seal the cystic artery and cystic duct that were occluded with only one absorbable clip (Group 1) and 728 patients undergoing LC using titanium clips (Group 2). In parallel, 30 rabbits randomized into six groups underwent cholecystectomy. After cystic duct ligation with absorbable or titanium clips, the animals were sacrificed 1, 3, or 6 months later, and intraabdominal adhesions were assessed after celiotomy. The mean operative time was significantly shorter (41.6 versus 58.9 minutes, P<.01) in Group 1 than in Group 2. No cystic duct leaks occurred in any patients from Group 1, compared with seven leaks among the 728 (0.96%) patients from Group 2 (P<.05). The morbidity was significantly higher in Group 2 than in Group 1 (3.43% versus 1.58%). Mean intraoperative blood loss and hospitalization length were not significantly different between the two groups, and no deaths occurred in either group. In animal experiments, adhesion was tighter for absorbable than for titanium clips, but fibrous tissue encapsulation was thinner at the site of titanium clips. Electrocoagulation of the cystic artery and cystic duct that were occluded with only one absorbable clip is safe and effective during LC. This approach is associated with shortened operative times and reduced leakage, compared with the standard method using metal clips.

Transcutaneous closure of chronic broncho-pleuro-cutaneous fistula by duct occluder device

PubMed Central

Marwah, Vikas; Ravikumar, R; Rajput, Ashok Kumar; Singh, Amandeep

2016-01-01

Bronchopleural fistula (BPF) is a well known complication of several pulmonary conditions posing challenging management problem and is often associated with high morbidity and mortality. Though no consensus exists on a definite closure management algorithm, strategies for closure widely include various methods like tube thoracostomy with suction, open surgical closure, bronchoscopy directed glue, coiling and sealants which now also includes use of occlusion devices. We report a case in which a novel method of delivery and closure of recurrent post-operative broncho-pleuro-cutaneous fistula by a duct occluder device was done transcutaneously which has not been previously described in literature. PMID:27051115

Ionizable Side Chains at Catalytic Active Sites of Enzymes

PubMed Central

Jimenez-Morales, David; Liang, Jie

2012-01-01

Catalytic active sites of enzymes of known structure can be well defined by a modern program of computational geometry. The CASTp program was used to define and measure the volume of the catalytic active sites of 573 enzymes in the Catalytic Site Atlas database. The active sites are identified as catalytic because the amino acids they contain are known to participate in the chemical reaction catalyzed by the enzyme. Acid and base side chains are reliable markers of catalytic active sites. The catalytic active sites have 4 acid and 5 base side chains, in an average volume of 1072 Å3. The number density of acid side chains is 8.3 M (in chemical units); the number density of basic side chains is 10.6 M. The catalytic active site of these enzymes is an unusual electrostatic and steric environment in which side chains and reactants are crowded together in a mixture more like an ionic liquid than an ideal infinitely dilute solution. The electrostatics and crowding of reactants and side chains seems likely to be important for catalytic function. In three types of analogous ion channels, simulation of crowded charges accounts for the main properties of selectivity measured in a wide range of solutions and concentrations. It seems wise to use mathematics designed to study interacting complex fluids when making models of the catalytic active sites of enzymes. PMID:22484856

Discriminative structural approaches for enzyme active-site prediction.

PubMed

Kato, Tsuyoshi; Nagano, Nozomi

2011-02-15

Predicting enzyme active-sites in proteins is an important issue not only for protein sciences but also for a variety of practical applications such as drug design. Because enzyme reaction mechanisms are based on the local structures of enzyme active-sites, various template-based methods that compare local structures in proteins have been developed to date. In comparing such local sites, a simple measurement, RMSD, has been used so far. This paper introduces new machine learning algorithms that refine the similarity/deviation for comparison of local structures. The similarity/deviation is applied to two types of applications, single template analysis and multiple template analysis. In the single template analysis, a single template is used as a query to search proteins for active sites, whereas a protein structure is examined as a query to discover the possible active-sites using a set of templates in the multiple template analysis. This paper experimentally illustrates that the machine learning algorithms effectively improve the similarity/deviation measurements for both the analyses.

In vivo production of recombinant proteins using occluded recombinant AcMNPV-derived baculovirus vectors.

PubMed

Guijarro-Pardo, Eva; Gómez-Sebastián, Silvia; Escribano, José M

2017-12-01

Trichoplusia ni insect larvae infected with vectors derived from the Autographa californica multiple nucleopolyhedrovirus (AcMNPV), are an excellent alternative to insect cells cultured in conventional bioreactors to produce recombinant proteins because productivity and cost-efficiency reasons. However, there is still a lot of work to do to reduce the manual procedures commonly required in this production platform that limit its scalability. To increase the scalability of this platform technology, a current bottleneck to be circumvented in the future is the need of injection for the inoculation of larvae with polyhedrin negative baculovirus vectors (Polh-) because of the lack of oral infectivity of these viruses, which are commonly used for production in insect cell cultures. In this work we have developed a straightforward alternative to obtain orally infective vectors derived from AcMNPV and expressing recombinant proteins that can be administered to the insect larvae (Trichoplusia ni) by feeding, formulated in the insect diet. The approach developed was based on the use of a recombinant polyhedrin protein expressed by a recombinant vector (Polh+), able to co-occlude any recombinant Polh- baculovirus vector expressing a recombinant protein. A second alternative was developed by the generation of a dual vector co-expressing the recombinant polyhedrin protein and the foreign gene of interest to obtain the occluded viruses. Additionally, by the incorporation of a reporter gene into the helper Polh+ vector, it was possible the follow-up visualization of the co-occluded viruses infection in insect larvae and will help to homogenize infection conditions. By using these methodologies, the production of recombinant proteins in per os infected larvae, without manual infection procedures, was very similar in yield to that obtained by manual injection of recombinant Polh- AcMNPV-based vectors expressing the same proteins. However, further analyses will be required for a

Ionizable side chains at catalytic active sites of enzymes.

PubMed

Jimenez-Morales, David; Liang, Jie; Eisenberg, Bob

2012-05-01

Catalytic active sites of enzymes of known structure can be well defined by a modern program of computational geometry. The CASTp program was used to define and measure the volume of the catalytic active sites of 573 enzymes in the Catalytic Site Atlas database. The active sites are identified as catalytic because the amino acids they contain are known to participate in the chemical reaction catalyzed by the enzyme. Acid and base side chains are reliable markers of catalytic active sites. The catalytic active sites have 4 acid and 5 base side chains, in an average volume of 1,072 Å(3). The number density of acid side chains is 8.3 M (in chemical units); the number density of basic side chains is 10.6 M. The catalytic active site of these enzymes is an unusual electrostatic and steric environment in which side chains and reactants are crowded together in a mixture more like an ionic liquid than an ideal infinitely dilute solution. The electrostatics and crowding of reactants and side chains seems likely to be important for catalytic function. In three types of analogous ion channels, simulation of crowded charges accounts for the main properties of selectivity measured in a wide range of solutions and concentrations. It seems wise to use mathematics designed to study interacting complex fluids when making models of the catalytic active sites of enzymes.

Spectral analysis of airflow sounds in patent versus occluded tracheostomy tubes: a pilot study in tracheostomized adult patients.

PubMed

Rao, A J; Niwa, H; Watanabe, Y; Fukuta, S; Yanagita, N

1990-05-01

Cannula occlusion is a life-threatening postoperative complication of tracheostomy. Current management largely relies on nursing care for prevention of fatalities because no proven mechanical, machine-based support monitoring exists. The objective of this paper was to address the problem of monitoring the state of cannula patency, based on analysis of airflow acoustic spectral patterns in tracheostomized adult patients in the patent and partially occluded cannula. Tracheal airflow sounds were picked up via a condenser microphone air-coupled to the skin just below the tracheal stoma. Signal output from Mic was amplified, high-pass filtered, digital tape-recorded, and analyzed on a mainframe computer. Although airflow frequencies for patient cannulae were predominantly low-pitched (0.1 to 0.3 kHz), occluded tubes had discrete high-pitched spectral peaks (1.3 to 1.6 kHz). These results suggest that frequency analysis of airflow sounds can identify a change in the status of cannula patency.

Activation of Latent Dihydroorotase from Aquifex aeolicus by Pressure*

PubMed Central

Hervé, Guy; Evans, Hedeel Guy; Fernado, Roshini; Patel, Chandni; Hachem, Fatme; Evans, David R.

2017-01-01

Elevated hydrostatic pressure was used to probe conformational changes of Aquifex aeolicus dihydroorotase (DHO), which catalyzes the third step in de novo pyrimidine biosynthesis. The isolated protein, a 45-kDa monomer, lacks catalytic activity but becomes active upon formation of a dodecameric complex with aspartate transcarbamoylase (ATC). X-ray crystallographic studies of the isolated DHO and of the complex showed that association induces several major conformational changes in the DHO structure. In the isolated DHO, a flexible loop occludes the active site blocking the access of substrates. The loop is mostly disordered but is tethered to the active site region by several electrostatic and hydrogen bonds. This loop becomes ordered and is displaced from the active site upon formation of DHO-ATC complex. The application of pressure to the complex causes its time-dependent dissociation and the loss of both DHO and ATC activities. Pressure induced irreversible dissociation of the obligate ATC trimer, and as a consequence the DHO is also inactivated. However, moderate hydrostatic pressure applied to the isolated DHO subunit mimics the complex formation and reversibly activates the isolated subunit in the absence of ATC, suggesting that the loop has been displaced from the active site. This effect of pressure is explained by the negative volume change associated with the disruption of ionic interactions and exposure of ionized amino acids to the solvent (electrostriction). The interpretation that the loop is relocated by pressure was validated by site-directed mutagenesis and by inhibition by small peptides that mimic the loop residues. PMID:27746403

Half-of-the-Sites Reactivity of the Castor Δ9-18:0-Acyl Carrier Protein Desaturase.

PubMed

Liu, Qin; Chai, Jin; Moche, Martin; Guy, Jodie; Lindqvist, Ylva; Shanklin, John

2015-09-01

Fatty acid desaturases regulate the unsaturation status of cellular lipids. They comprise two distinct evolutionary lineages, a soluble class found in the plastids of higher plants and an integral membrane class found in plants, yeast (Saccharomyces cerevisiae), animals, and bacteria. Both classes exhibit a dimeric quaternary structure. Here, we test the functional significance of dimeric organization of the soluble castor Δ9-18:0-acyl carrier protein desaturase, specifically, the hypothesis that the enzyme uses an alternating subunit half-of-the-sites reactivity mechanism whereby substrate binding to one subunit is coordinated with product release from the other subunit. Using a fluorescence resonance energy transfer assay, we demonstrated that dimers stably associate at concentrations typical of desaturase assays. An active site mutant T104K/S202E, designed to occlude the substrate binding cavity, was expressed, purified, and its properties validated by x-ray crystallography, size exclusion chromatography, and activity assay. Heterodimers comprising distinctly tagged wild-type and inactive mutant subunits were purified at 1:1 stoichiometry. Despite having only one-half the number of active sites, purified heterodimers exhibit equivalent activity to wild-type homodimers, consistent with half-of-the-sites reactivity. However, because multiple rounds of turnover were observed, we conclude that substrate binding to one subunit is not required to facilitate product release from the second subunit. The observed half-of-the-sites reactivity could potentially buffer desaturase activity from oxidative inactivation. That soluble desaturases require only one active subunit per dimer for full activity represents a mechanistic difference from the membrane class of desaturases such as the Δ9-acyl-CoA, Ole1p, from yeast, which requires two catalytically competent subunits for activity. © 2015 American Society of Plant Biologists. All Rights Reserved.

Metal active site elasticity linked to activation of homocysteine in methionine synthases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koutmos, Markos; Pejchal, Robert; Bomer, Theresa M.

2008-04-02

Enzymes possessing catalytic zinc centers perform a variety of fundamental processes in nature, including methyl transfer to thiols. Cobalamin-independent (MetE) and cobalamin-dependent (MetH) methionine synthases are two such enzyme families. Although they perform the same net reaction, transfer of a methyl group from methyltetrahydrofolate to homocysteine (Hcy) to form methionine, they display markedly different catalytic strategies, modular organization, and active site zinc centers. Here we report crystal structures of zinc-replete MetE and MetH, both in the presence and absence of Hcy. Structural investigation of the catalytic zinc sites of these two methyltransferases reveals an unexpected inversion of zinc geometry uponmore » binding of Hcy and displacement of an endogenous ligand in both enzymes. In both cases a significant movement of the zinc relative to the protein scaffold accompanies inversion. These structures provide new information on the activation of thiols by zinc-containing enzymes and have led us to propose a paradigm for the mechanism of action of the catalytic zinc sites in these and related methyltransferases. Specifically, zinc is mobile in the active sites of MetE and MetH, and its dynamic nature helps facilitate the active site conformational changes necessary for thiol activation and methyl transfer.« less

ST-depression in right precordial leads with inferior STEMI and occluded right coronary artery: intertwined anatomy and ischemic areas.

PubMed

De Gennaro, Luisa; Brunetti, Natale Daniele; Ruggiero, Massimo; Rutigliano, David; Locuratolo, Nicola; Di Biase, Matteo; Caldarola, Pasquale

2017-10-01

Right coronary artery (RCA) occlusion in inferior acute myocardial infarction is usually heralded by ST-elevation both in inferior and in right precordial leads. We report the case of a 68-year-old male, who presented marked ST-elevation in inferior leads, mirrored by ST-depression in anterior-septal and lateral leads. Right precordial lead electrocardiogram unexpectedly showed ST-depression V1R-V5R leads. Coronary angiography showed mid-left anterior descending (LAD) coronary near-complete occlusion with distal wrapping LAD. Left circumflex artery was not occluded, while RCA was occluded mid tract. The patient was treated with coronary angioplasty on RCA and LAD. Absence of ST-elevation in right precordial leads may be presumably explained by the presence of a large ischemic area distal to mid-LAD near-occlusive stenosis and of a long-wrapping LAD. Complex coronary anatomy and intertwined ischemic areas may underlie apparently discording electrocardiograms.

Nicotinamide Cofactors Suppress Active-Site Labeling of Aldehyde Dehydrogenases.

PubMed

Stiti, Naim; Chandrasekar, Balakumaran; Strubl, Laura; Mohammed, Shabaz; Bartels, Dorothea; van der Hoorn, Renier A L

2016-06-17

Active site labeling by (re)activity-based probes is a powerful chemical proteomic tool to globally map active sites in native proteomes without using substrates. Active site labeling is usually taken as a readout for the active state of the enzyme because labeling reflects the availability and reactivity of active sites, which are hallmarks for enzyme activities. Here, we show that this relationship holds tightly, but we also reveal an important exception to this rule. Labeling of Arabidopsis ALDH3H1 with a chloroacetamide probe occurs at the catalytic Cys, and labeling is suppressed upon nitrosylation and oxidation, and upon treatment with other Cys modifiers. These experiments display a consistent and strong correlation between active site labeling and enzymatic activity. Surprisingly, however, labeling is suppressed by the cofactor NAD(+), and this property is shared with other members of the ALDH superfamily and also detected for unrelated GAPDH enzymes with an unrelated hydantoin-based probe in crude extracts of plant cell cultures. Suppression requires cofactor binding to its binding pocket. Labeling is also suppressed by ALDH modulators that bind at the substrate entrance tunnel, confirming that labeling occurs through the substrate-binding cavity. Our data indicate that cofactor binding adjusts the catalytic Cys into a conformation that reduces the reactivity toward chloroacetamide probes.

Quantum mechanical design of enzyme active sites.

PubMed

Zhang, Xiyun; DeChancie, Jason; Gunaydin, Hakan; Chowdry, Arnab B; Clemente, Fernando R; Smith, Adam J T; Handel, T M; Houk, K N

2008-02-01

The design of active sites has been carried out using quantum mechanical calculations to predict the rate-determining transition state of a desired reaction in presence of the optimal arrangement of catalytic functional groups (theozyme). Eleven versatile reaction targets were chosen, including hydrolysis, dehydration, isomerization, aldol, and Diels-Alder reactions. For each of the targets, the predicted mechanism and the rate-determining transition state (TS) of the uncatalyzed reaction in water is presented. For the rate-determining TS, a catalytic site was designed using naturalistic catalytic units followed by an estimation of the rate acceleration provided by a reoptimization of the catalytic site. Finally, the geometries of the sites were compared to the X-ray structures of related natural enzymes. Recent advances in computational algorithms and power, coupled with successes in computational protein design, have provided a powerful context for undertaking such an endeavor. We propose that theozymes are excellent candidates to serve as the active site models for design processes.

Learning from oligosaccharide soaks of crystals of an AA13 lytic polysaccharide monooxygenase: crystal packing, ligand binding and active-site disorder.

PubMed

Frandsen, Kristian E H; Poulsen, Jens Christian Navarro; Tovborg, Morten; Johansen, Katja S; Lo Leggio, Leila

2017-01-01

Lytic polysaccharide monooxygenases (LPMOs) are a class of copper-dependent enzymes discovered within the last ten years. They oxidatively cleave polysaccharides (chitin, lignocellulose, hemicellulose and starch-derived), presumably making recalcitrant substrates accessible to glycoside hydrolases. Recently, the first crystal structure of an LPMO-substrate complex was reported, giving insights into the interaction of LPMOs with β-linked substrates (Frandsen et al., 2016). The LPMOs acting on α-linked glycosidic bonds (family AA13) display binding surfaces that are quite different from those of LPMOs that act on β-linked glycosidic bonds (families AA9-AA11), as revealed from the first determined structure (Lo Leggio et al., 2015), and thus presumably the AA13s interact with their substrate in a distinct fashion. Here, several new structures of the same AA13 enzyme, Aspergillus oryzae AA13, are presented. Crystals obtained in the presence of high zinc-ion concentrations were used, as they can be obtained more reproducibly than those used to refine the deposited copper-containing structure. One structure with an ordered zinc-bound active site was solved at 1.65 Å resolution, and three structures from crystals soaked with maltooligosaccharides in solutions devoid of zinc ions were solved at resolutions of up to 1.10 Å. Despite similar unit-cell parameters, small rearrangements in the crystal packing occur when the crystals are depleted of zinc ions, resulting in a more occluded substrate-binding surface. In two of the three structures maltooligosaccharide ligands are bound, but not at the active site. Two of the structures presented show a His-ligand conformation that is incompatible with metal-ion binding. In one of these structures this conformation is the principal one (80% occupancy), giving a rare atomic resolution view of a substantially misfolded enzyme that is presumably rendered inactive.

The Role of Visual Area V4 in the Discrimination of Partially Occluded Shapes

PubMed Central

Kosai, Yoshito; El-Shamayleh, Yasmine; Fyall, Amber M.

2014-01-01

The primate brain successfully recognizes objects, even when they are partially occluded. To begin to elucidate the neural substrates of this perceptual capacity, we measured the responses of shape-selective neurons in visual area V4 while monkeys discriminated pairs of shapes under varying degrees of occlusion. We found that neuronal shape selectivity always decreased with increasing occlusion level, with some neurons being notably more robust to occlusion than others. The responses of neurons that maintained their selectivity across a wider range of occlusion levels were often sufficiently sensitive to support behavioral performance. Many of these same neurons were distinctively selective for the curvature of local boundary features and their shape tuning was well fit by a model of boundary curvature (curvature-tuned neurons). A significant subset of V4 neurons also signaled the animal's upcoming behavioral choices; these decision signals had short onset latencies that emerged progressively later for higher occlusion levels. The time course of the decision signals in V4 paralleled that of shape selectivity in curvature-tuned neurons: shape selectivity in curvature-tuned neurons, but not others, emerged earlier than the decision signals. These findings provide evidence for the involvement of contour-based mechanisms in the segmentation and recognition of partially occluded objects, consistent with psychophysical theory. Furthermore, they suggest that area V4 participates in the representation of the relevant sensory signals and the generation of decision signals underlying discrimination. PMID:24948811

Active and regulatory sites of cytosolic 5'-nucleotidase.

PubMed

Pesi, Rossana; Allegrini, Simone; Careddu, Maria Giovanna; Filoni, Daniela Nicole; Camici, Marcella; Tozzi, Maria Grazia

2010-12-01

Cytosolic 5'-nucleotidase (cN-II), which acts preferentially on 6-hydroxypurine nucleotides, is essential for the survival of several cell types. cN-II catalyses both the hydrolysis of nucleotides and transfer of their phosphate moiety to a nucleoside acceptor through formation of a covalent phospho-intermediate. Both activities are regulated by a number of phosphorylated compounds, such as diadenosine tetraphosphate (Ap₄A), ADP, ATP, 2,3-bisphosphoglycerate (BPG) and phosphate. On the basis of a partial crystal structure of cN-II, we mutated two residues located in the active site, Y55 and T56. We ascertained that the ability to catalyse the transfer of phosphate depends on the presence of a bulky residue in the active site very close to the aspartate residue that forms the covalent phospho-intermediate. The molecular model indicates two possible sites at which adenylic compounds may interact. We mutated three residues that mediate interaction in the first activation site (R144, N154, I152) and three in the second (F127, M436 and H428), and found that Ap₄A and ADP interact with the same site, but the sites for ATP and BPG remain uncertain. The structural model indicates that cN-II is a homotetrameric protein that results from interaction through a specific interface B of two identical dimers that have arisen from interaction of two identical subunits through interface A. Point mutations in the two interfaces and gel-filtration experiments indicated that the dimer is the smallest active oligomerization state. Finally, gel-filtration and light-scattering experiments demonstrated that the native enzyme exists as a tetramer, and no further oligomerization is required for enzyme activation. © 2010 The Authors Journal compilation © 2010 FEBS.

Water in the Active Site of Ketosteroid Isomerase

PubMed Central

Hanoian, Philip; Hammes-Schiffer, Sharon

2011-01-01

Classical molecular dynamics simulations were utilized to investigate the structural and dynamical properties of water in the active site of ketosteroid isomerase (KSI) to provide insight into the role of these water molecules in the enzyme-catalyzed reaction. This reaction is thought to proceed via a dienolate intermediate that is stabilized by hydrogen bonding with residues Tyr16 and Asp103. A comparative study was performed for the wild-type (WT) KSI and the Y16F, Y16S, and Y16F/Y32F/Y57F (FFF) mutants. These systems were studied with three different bound ligands: equilenin, which is an intermediate analog, and the intermediate states of two steroid substrates. Several distinct water occupation sites were identified in the active site of KSI for the WT and mutant systems. Three additional sites were identified in the Y16S mutant that were not occupied in WT KSI or the other mutants studied. The number of water molecules directly hydrogen bonded to the ligand oxygen was approximately two waters in the Y16S mutant, one water in the Y16F and FFF mutants, and intermittent hydrogen bonding of one water molecule in WT KSI. The molecular dynamics trajectories of the Y16F and FFF mutants reproduced the small conformational changes of residue 16 observed in the crystal structures of these two mutants. Quantum mechanical/molecular mechanical calculations of 1H NMR chemical shifts of the protons in the active site hydrogen-bonding network suggest that the presence of water in the active site does not prevent the formation of short hydrogen bonds with far-downfield chemical shifts. The molecular dynamics simulations indicate that the active site water molecules exchange much more frequently for WT KSI and the FFF mutant than for the Y16F and Y16S mutants. This difference is most likely due to the hydrogen-bonding interaction between Tyr57 and an active site water molecule that is persistent in the Y16F and Y16S mutants but absent in the FFF mutant and significantly less

Water in the active site of ketosteroid isomerase.

PubMed

Hanoian, Philip; Hammes-Schiffer, Sharon

2011-08-09

Classical molecular dynamics simulations were utilized to investigate the structural and dynamical properties of water in the active site of ketosteroid isomerase (KSI) to provide insight into the role of these water molecules in the enzyme-catalyzed reaction. This reaction is thought to proceed via a dienolate intermediate that is stabilized by hydrogen bonding with residues Tyr16 and Asp103. A comparative study was performed for the wild-type (WT) KSI and the Y16F, Y16S, and Y16F/Y32F/Y57F (FFF) mutants. These systems were studied with three different bound ligands: equilenin, which is an intermediate analog, and the intermediate states of two steroid substrates. Several distinct water occupation sites were identified in the active site of KSI for the WT and mutant systems. Three additional sites were identified in the Y16S mutant that were not occupied in WT KSI or the other mutants studied. The number of water molecules directly hydrogen bonded to the ligand oxygen was approximately two in the Y16S mutant and one in the Y16F and FFF mutants, with intermittent hydrogen bonding of one water molecule in WT KSI. The molecular dynamics trajectories of the Y16F and FFF mutants reproduced the small conformational changes of residue 16 observed in the crystal structures of these two mutants. Quantum mechanical/molecular mechanical calculations of (1)H NMR chemical shifts of the protons in the active site hydrogen-bonding network suggest that the presence of water in the active site does not prevent the formation of short hydrogen bonds with far-downfield chemical shifts. The molecular dynamics simulations indicate that the active site water molecules exchange much more frequently for WT KSI and the FFF mutant than for the Y16F and Y16S mutants. This difference is most likely due to the hydrogen-bonding interaction between Tyr57 and an active site water molecule that is persistent in the Y16F and Y16S mutants but absent in the FFF mutant and significantly less probable

Active Site Characterization of Proteases Sequences from Different Species of Aspergillus.

PubMed

Morya, V K; Yadav, Virendra K; Yadav, Sangeeta; Yadav, Dinesh

2016-09-01

A total of 129 proteases sequences comprising 43 serine proteases, 36 aspartic proteases, 24 cysteine protease, 21 metalloproteases, and 05 neutral proteases from different Aspergillus species were analyzed for the catalytically active site residues using MEROPS database and various bioinformatics tools. Different proteases have predominance of variable active site residues. In case of 24 cysteine proteases of Aspergilli, the predominant active site residues observed were Gln193, Cys199, His364, Asn384 while for 43 serine proteases, the active site residues namely Asp164, His193, Asn284, Ser349 and Asp325, His357, Asn454, Ser519 were frequently observed. The analysis of 21 metalloproteases of Aspergilli revealed Glu298 and Glu388, Tyr476 as predominant active site residues. In general, Aspergilli species-specific active site residues were observed for different types of protease sequences analyzed. The phylogenetic analysis of these 129 proteases sequences revealed 14 different clans representing different types of proteases with diverse active site residues.

Half-of-the-sites reactivity of outer-membrane phospholipase A against an active-site-directed inhibitor.

PubMed

Ubarretxena-Belandia, I; Cox, R C; Dijkman, R; Egmond, M R; Verheij, H M; Dekker, N

1999-03-01

The reaction of a novel active-site-directed phospholipase A1 inhibitor with the outer-membrane phospholipase A (OMPLA) was investigated. The inhibitor 1-p-nitrophenyl-octylphosphonate-2-tridecylcarbamoyl-3-et hanesulfonyl -amino-3-deoxy-sn-glycerol irreversibly inactivated OMPLA. The inhibition reaction did not require the cofactor calcium or an unprotonated active-site His142. The inhibition of the enzyme solubilized in hexadecylphosphocholine micelles was characterized by a rapid (t1/2 = 20 min) and complete loss of enzymatic activity, concurrent with the covalent modification of 50% of the active-site serines, as judged from the amount of p-nitrophenolate (PNP) released. Modification of the remaining 50% occurred at a much lower rate, indicative of half-of-the-sites reactivity against the inhibitor of this dimeric enzyme. Inhibition of monomeric OMPLA solubilized in hexadecyl-N,N-dimethyl-1-ammonio-3-propanesulfonate resulted in an equimolar monophasic release of PNP, concurrent with the loss of enzymatic activity (t1/2 = 14 min). The half-of-the-sites reactivity is discussed in view of the dimeric nature of this enzyme.

Conserved active site residues limit inhibition of a copper-containing nitrite reductase by small molecules.

PubMed

Tocheva, Elitza I; Eltis, Lindsay D; Murphy, Michael E P

2008-04-15

The interaction of copper-containing dissimilatory nitrite reductase from Alcaligenes faecalis S-6 ( AfNiR) with each of five small molecules was studied using crystallography and steady-state kinetics. Structural studies revealed that each small molecule interacted with the oxidized catalytic type 2 copper of AfNiR. Three small molecules (formate, acetate and nitrate) mimic the substrate by having at least two oxygen atoms for bidentate coordination to the type 2 copper atom. These three anions bound to the copper ion in the same asymmetric, bidentate manner as nitrite. Consistent with their weak inhibition of the enzyme ( K i >50 mM), the Cu-O distances in these AfNiR-inhibitor complexes were approximately 0.15 A longer than that observed in the AfNiR-nitrite complex. The binding mode of each inhibitor is determined in part by steric interactions with the side chain of active site residue Ile257. Moreover, the side chain of Asp98, a conserved residue that hydrogen bonds to type 2 copper-bound nitrite and nitric oxide, was either disordered or pointed away from the inhibitors. Acetate and formate inhibited AfNiR in a mixed fashion, consistent with the occurrence of second acetate binding site in the AfNiR-acetate complex that occludes access to the type 2 copper. A fourth small molecule, nitrous oxide, bound to the oxidized metal in a side-on fashion reminiscent of nitric oxide to the reduced copper. Nevertheless, nitrous oxide bound at a farther distance from the metal. The fifth small molecule, azide, inhibited the reduction of nitrite by AfNiR most strongly ( K ic = 2.0 +/- 0.1 mM). This ligand bound to the type 2 copper center end-on with a Cu-N c distance of approximately 2 A, and was the only inhibitor to form a hydrogen bond with Asp98. Overall, the data substantiate the roles of Asp98 and Ile257 in discriminating substrate from other small anions.

Physical activity and cancer risk: dose-response and cancer, all sites and site-specific.

PubMed

Thune, I; Furberg, A S

2001-06-01

The association between physical activity and overall and site-specific cancer risk is elaborated in relation to whether any observed dose-response association between physical activity and cancer can be interpreted in terms of how much physical activity (type, intensity, duration, frequency) is needed to influence site- and gender-specific cancer risk. Observational studies were reviewed that have examined the independent effect of the volume of occupational physical activity (OPA) and/or leisure time physical activity (LPA) on overall and site-specific cancer risk. The evidence of cohort and case-control studies suggests that both leisure time and occupational physical activity protect against overall cancer risk, with a graded dose-response association suggested in both sexes. Confounding effects such as diet, body weight, and parity are often included as a covariate in the analyses, with little influence on the observed associations. A crude graded inverse dose-response association was observed between physical activity and colon cancer in 48 studies including 40,674 colon/colorectal cancer cases for both sexes. A dose-response effect of physical activity on colon cancer risk was especially observed, when participation in activities of at least moderate activity (>4.5 MET) and demonstrated by activities expressed as MET-hours per week. An observed inverse association with a dose-response relationship between physical activity and breast cancer was also identified in the majority of the 41 studies including 108,031 breast cancer cases. The dose-response relationship was in particular observed in case-control studies and supported by observations in cohort studies when participation in activities of at least moderate activity (>4.5 MET) and demonstrated by activities expressed by MET-hours per week. This association between physical activity and breast cancer risk is possibly dependent on age at exposure, age at diagnosis, menopausal status and other effect

Active Site Metal Occupancy and Cyclic Di-GMP Phosphodiesterase Activity of Thermotoga maritima HD-GYP.

PubMed

Miner, Kyle D; Kurtz, Donald M

2016-02-16

HD-GYPs make up a subclass of the metal-dependent HD phosphohydrolase superfamily and catalyze conversion of cyclic di(3',5')-guanosine monophosphate (c-di-GMP) to 5'-phosphoguanylyl-(3'→5')-guanosine (pGpG) and GMP. Until now, the only reported crystal structure of an HD-GYP that also exhibits c-di-GMP phosphodiesterase activity contains a His/carboxylate ligated triiron active site. However, other structural and phylogenetic correlations indicate that some HD-GYPs contain dimetal active sites. Here we provide evidence that an HD-GYP c-di-GMP phosphodiesterase, TM0186, from Thermotoga maritima can accommodate both di- and trimetal active sites. We show that an as-isolated iron-containing TM0186 has an oxo/carboxylato-bridged diferric site, and that the reduced (diferrous) form is necessary and sufficient to catalyze conversion of c-di-GMP to pGpG, but that conversion of pGpG to GMP requires more than two metals per active site. Similar c-di-GMP phosphodiesterase activities were obtained with divalent iron or manganese. On the basis of activity correlations with several putative metal ligand residue variants and molecular dynamics simulations, we propose that TM0186 can accommodate both di- and trimetal active sites. Our results also suggest that a Glu residue conserved in a subset of HD-GYPs is required for formation of the trimetal site and can also serve as a labile ligand to the dimetal site. Given the anaerobic growth requirement of T. maritima, we suggest that this HD-GYP can function in vivo with either divalent iron or manganese occupying di- and trimetal sites.

Half-of-the-Sites Reactivity of the Castor Δ9-18:0-Acyl Carrier Protein Desaturase1[OPEN

PubMed Central

Liu, Qin; Chai, Jin; Moche, Martin; Guy, Jodie; Lindqvist, Ylva; Shanklin, John

2015-01-01

Fatty acid desaturases regulate the unsaturation status of cellular lipids. They comprise two distinct evolutionary lineages, a soluble class found in the plastids of higher plants and an integral membrane class found in plants, yeast (Saccharomyces cerevisiae), animals, and bacteria. Both classes exhibit a dimeric quaternary structure. Here, we test the functional significance of dimeric organization of the soluble castor Δ9-18:0-acyl carrier protein desaturase, specifically, the hypothesis that the enzyme uses an alternating subunit half-of-the-sites reactivity mechanism whereby substrate binding to one subunit is coordinated with product release from the other subunit. Using a fluorescence resonance energy transfer assay, we demonstrated that dimers stably associate at concentrations typical of desaturase assays. An active site mutant T104K/S202E, designed to occlude the substrate binding cavity, was expressed, purified, and its properties validated by x-ray crystallography, size exclusion chromatography, and activity assay. Heterodimers comprising distinctly tagged wild-type and inactive mutant subunits were purified at 1:1 stoichiometry. Despite having only one-half the number of active sites, purified heterodimers exhibit equivalent activity to wild-type homodimers, consistent with half-of-the-sites reactivity. However, because multiple rounds of turnover were observed, we conclude that substrate binding to one subunit is not required to facilitate product release from the second subunit. The observed half-of-the-sites reactivity could potentially buffer desaturase activity from oxidative inactivation. That soluble desaturases require only one active subunit per dimer for full activity represents a mechanistic difference from the membrane class of desaturases such as the Δ9-acyl-CoA, Ole1p, from yeast, which requires two catalytically competent subunits for activity. PMID:26224800

Diffusional correlations among multiple active sites in a single enzyme.

PubMed

Echeverria, Carlos; Kapral, Raymond

2014-04-07

Simulations of the enzymatic dynamics of a model enzyme containing multiple substrate binding sites indicate the existence of diffusional correlations in the chemical reactivity of the active sites. A coarse-grain, particle-based, mesoscopic description of the system, comprising the enzyme, the substrate, the product and solvent, is constructed to study these effects. The reactive and non-reactive dynamics is followed using a hybrid scheme that combines molecular dynamics for the enzyme, substrate and product molecules with multiparticle collision dynamics for the solvent. It is found that the reactivity of an individual active site in the multiple-active-site enzyme is reduced substantially, and this effect is analyzed and attributed to diffusive competition for the substrate among the different active sites in the enzyme.

Endoscopic management of occluded metal biliary stents: metal versus 10F plastic stents.

PubMed

Yoon, Won Jae; Ryu, Ji Kon; Lee, Jung Won; Ahn, Dong-Won; Kim, Yong-Tae; Yoon, Yong Bum; Woo, Sang Myung; Lee, Woo Jin

2010-11-14

To compare the efficacy of self-expandable metal stents (SEMSs) with 10F plastic stents (PSs) in the endoscopic management of occluded SEMSs. We retrospectively reviewed the medical records of 56 patients who underwent SEMS insertion for palliation of unresectable malignant biliary obstruction between 2000 and 2007 and subsequent endoscopic retrograde biliary drainage (ERBD) with SEMS or PS for initial SEMS occlusion between 2000 and 2008. Subsequent ERBD with SEMS was performed in 29 patients and with PS in 27. The median time to stent occlusion after subsequent ERBD was 186 d in the SEMS group and 101 d in the PS group (P = 0.118). Overall median stent patency was 79 d for the SEMS group and 66 d for the PS group (P = 0.379). The mean number of additional biliary drainage procedures after subsequent ERBD in patients that died (n = 50) during the study period was 2.54 ± 4.12 for the SEMS group and 1.85 ± 1.95 for the PS group (P = 0.457). The mean total cost of additional biliary drainage procedures after the occlusion of subsequent SEMS or PS was $410.04 ± 692.60 for the SEMS group and $630.16 ± 671.63 for the PS group (P = 0.260). Tumor ingrowth as the cause of initial SEMS occlusion was the only factor associated with a shorter time to subsequent stent occlusion (101 d for patients with tumor ingrowth vs 268 d for patients without tumor ingrowth, P = 0.008). Subsequent ERBD with PSs offered similar patency and number of additional biliary drainage procedures compared to SEMSs in the management of occluded SEMS.

Direct instrumental identification of catalytically active surface sites

NASA Astrophysics Data System (ADS)

Pfisterer, Jonas H. K.; Liang, Yunchang; Schneider, Oliver; Bandarenka, Aliaksandr S.

2017-09-01

The activity of heterogeneous catalysts—which are involved in some 80 per cent of processes in the chemical and energy industries—is determined by the electronic structure of specific surface sites that offer optimal binding of reaction intermediates. Directly identifying and monitoring these sites during a reaction should therefore provide insight that might aid the targeted development of heterogeneous catalysts and electrocatalysts (those that participate in electrochemical reactions) for practical applications. The invention of the scanning tunnelling microscope (STM) and the electrochemical STM promised to deliver such imaging capabilities, and both have indeed contributed greatly to our atomistic understanding of heterogeneous catalysis. But although the STM has been used to probe and initiate surface reactions, and has even enabled local measurements of reactivity in some systems, it is not generally thought to be suited to the direct identification of catalytically active surface sites under reaction conditions. Here we demonstrate, however, that common STMs can readily map the catalytic activity of surfaces with high spatial resolution: we show that by monitoring relative changes in the tunnelling current noise, active sites can be distinguished in an almost quantitative fashion according to their ability to catalyse the hydrogen-evolution reaction or the oxygen-reduction reaction. These data allow us to evaluate directly the importance and relative contribution to overall catalyst activity of different defects and sites at the boundaries between two materials. With its ability to deliver such information and its ready applicability to different systems, we anticipate that our method will aid the rational design of heterogeneous catalysts.

The identity of the active site of oxalate decarboxylase and the importance of the stability of active-site lid conformations1

PubMed Central

Just, Victoria J.; Burrell, Matthew R.; Bowater, Laura; McRobbie, Iain; Stevenson, Clare E. M.; Lawson, David M.; Bornemann, Stephen

2007-01-01

Oxalate decarboxylase (EC 4.1.1.2) catalyses the conversion of oxalate into carbon dioxide and formate. It requires manganese and, uniquely, dioxygen for catalysis. It forms a homohexamer and each subunit contains two similar, but distinct, manganese sites termed sites 1 and 2. There is kinetic evidence that only site 1 is catalytically active and that site 2 is purely structural. However, the kinetics of enzymes with mutations in site 2 are often ambiguous and all mutant kinetics have been interpreted without structural information. Nine new site-directed mutants have been generated and four mutant crystal structures have now been solved. Most mutants targeted (i) the flexibility (T165P), (ii) favoured conformation (S161A, S164A, D297A or H299A) or (iii) presence (Δ162–163 or Δ162–164) of a lid associated with site 1. The kinetics of these mutants were consistent with only site 1 being catalytically active. This was particularly striking with D297A and H299A because they disrupted hydrogen bonds between the lid and a neighbouring subunit only when in the open conformation and were distant from site 2. These observations also provided the first evidence that the flexibility and stability of lid conformations are important in catalysis. The deletion of the lid to mimic the plant oxalate oxidase led to a loss of decarboxylase activity, but only a slight elevation in the oxalate oxidase side reaction, implying other changes are required to afford a reaction specificity switch. The four mutant crystal structures (R92A, E162A, Δ162–163 and S161A) strongly support the hypothesis that site 2 is purely structural. PMID:17680775

Role of active site rigidity in activity: MD simulation and fluorescence study on a lipase mutant.

PubMed

Kamal, Md Zahid; Mohammad, Tabrez Anwar Shamim; Krishnamoorthy, G; Rao, Nalam Madhusudhana

2012-01-01

Relationship between stability and activity of enzymes is maintained by underlying conformational flexibility. In thermophilic enzymes, a decrease in flexibility causes low enzyme activity while in less stable proteins such as mesophiles and psychrophiles, an increase in flexibility is associated with enhanced enzyme activity. Recently, we identified a mutant of a lipase whose stability and activity were enhanced simultaneously. In this work, we probed the conformational dynamics of the mutant and the wild type lipase, particularly flexibility of their active site using molecular dynamic simulations and time-resolved fluorescence techniques. In contrast to the earlier observations, our data show that active site of the mutant is more rigid than wild type enzyme. Further investigation suggests that this lipase needs minimal reorganization/flexibility of active site residues during its catalytic cycle. Molecular dynamic simulations suggest that catalytically competent active site geometry of the mutant is relatively more preserved than wild type lipase, which might have led to its higher enzyme activity. Our study implies that widely accepted positive correlation between conformation flexibility and enzyme activity need not be stringent and draws attention to the possibility that high enzyme activity can still be accomplished in a rigid active site and stable protein structures. This finding has a significant implication towards better understanding of involvement of dynamic motions in enzyme catalysis and enzyme engineering through mutations in active site.

Site-specific thromboembolism: a novel animal model for stroke.

PubMed

Ringer, Andrew J; Guterman, Lee R; Hopkins, L Nelson

2004-02-01

To develop a technique for site-specific placement of a thrombus of predetermined volume in an animal model for the purpose of evaluating methods of intravascular thrombolysis and clot retrieval. Six swine were subjected to thrombus injection bilaterally in the ascending pharyngeal artery (APA). Each animal underwent transfemoral angiography while under general anesthesia. A nondetachable balloon catheter and a 3-French microcatheter were then advanced into the common carotid artery through a 7-French guide catheter. With the microcatheter in the proximal APA and the balloon inflated proximally, a bolus of preformed thrombus composed of 0.9 mL of autologous blood and 0.1 mL of bovine thrombin (200 IU/mL) was injected through the microcatheter while local flow arrest was maintained for 15 min. The balloon was deflated and removed. The occluded arteries were observed by serial angiography for 3 hr and then resected for gross examination and hematoxylin and eosin staining. Each APA was occluded angiographically and did not recanalize during the 3-hr observation period. Persistent, proximal progression of thrombus to the superior thyroid artery origin occurred in three animals. Gross inspection revealed that the resected arteries contained thrombus in the proximal APA but not in the common carotid artery. Histologic examination revealed organized thrombus, without evidence of intimal injury. Our model provides a simple, reliable method for site-specific injection of a thrombus of predetermined volume. Site-specific placement is important for evaluation of the efficacy of thrombolytic agents and techniques. Angiographic evidence of brain revascularization can be used to grade revascularization and clot volume. The ability to specifically localize and estimate clot volume makes our model well suited for the evaluation and comparison of thrombolytic agents and endovascular techniques.

40 CFR 61.154 - Standard for active waste disposal sites.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 8 2011-07-01 2011-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an active... visible emissions to the outside air from any active waste disposal site where asbestos-containing waste...

40 CFR 61.154 - Standard for active waste disposal sites.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 9 2013-07-01 2013-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an active... visible emissions to the outside air from any active waste disposal site where asbestos-containing waste...

40 CFR 61.154 - Standard for active waste disposal sites.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 9 2012-07-01 2012-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an active... visible emissions to the outside air from any active waste disposal site where asbestos-containing waste...

40 CFR 61.154 - Standard for active waste disposal sites.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 8 2010-07-01 2010-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an active... visible emissions to the outside air from any active waste disposal site where asbestos-containing waste...

40 CFR 61.154 - Standard for active waste disposal sites.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 9 2014-07-01 2014-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an active... visible emissions to the outside air from any active waste disposal site where asbestos-containing waste...

Management of occluded metal stents in malignant biliary obstruction: similar outcomes with second metal stents compared to plastic stents

PubMed Central

Shah, Tilak; Desai, Svetang; Haque, Mahfuzul; Dakik, Hassan; Fisher, Deborah

2013-01-01

Background Covered or uncovered self expandable metallic stents (SEMS) placed in patients with malignant biliary obstruction can occlude in 19–40%, but optimal management is unclear. Aim We sought to summarize current evidence regarding management of occluded SEMS in patients with malignant biliary obstruction. Methods Two investigators independently searched Pubmed, Embase, and Web of Science using pre-defined search criteria, and reviewed bibliographies of included studies. Data were independently abstracted by two investigators, and analyzed using RevMan. We compared strategies of second SEMS versus plastic stents with respect to the following outcomes: rate of second stent re-occlusion, duration of second stent patency, and survival. Results Ten retrospective studies met inclusion criteria for the systematic review. Management options described were placement of an uncovered SEMS (n=125), covered SEMS (n=106), plastic stent (n=135), percutaneous biliary drain (n=7), mechanical cleaning (n=18), or microwave coagulation (n=7). Relative risk of re-occlusion was not significantly different in patients with second SEMS compared to plastic stents (RR 1.24, 95% CI 0.92, 1.67, I2= 0, p 0.16). Duration of second stent patency was not significantly different between patients who received second SEMS versus plastic stents (weighted mean difference 0.46, 95% CI −0.30, 1.23, I2=83%). Survival was not significantly different among patients who received plastic stents versus SEMS (weighted mean difference −1.13, 95% CI −2.33, 0.07, I2 86%, p 0.07). Conclusions Among patients with malignant biliary obstruction and occluded SEMS, available evidence suggests a strategy of placing a plastic stent may be as effective as second SEMS. Limitations of these findings were that all studies were retrospective and heterogeneity between studies was detected for two of the outcomes. PMID:22732833

Endoscopic management of occluded metal biliary stents: Metal versus 10F plastic stents

PubMed Central

Yoon, Won Jae; Ryu, Ji Kon; Lee, Jung Won; Ahn, Dong-Won; Kim, Yong-Tae; Yoon, Yong Bum; Woo, Sang Myung; Lee, Woo Jin

2010-01-01

AIM: To compare the efficacy of self-expandable metal stents (SEMSs) with 10F plastic stents (PSs) in the endoscopic management of occluded SEMSs. METHODS: We retrospectively reviewed the medical records of 56 patients who underwent SEMS insertion for palliation of unresectable malignant biliary obstruction between 2000 and 2007 and subsequent endoscopic retrograde biliary drainage (ERBD) with SEMS or PS for initial SEMS occlusion between 2000 and 2008. RESULTS: Subsequent ERBD with SEMS was performed in 29 patients and with PS in 27. The median time to stent occlusion after subsequent ERBD was 186 d in the SEMS group and 101 d in the PS group (P = 0.118). Overall median stent patency was 79 d for the SEMS group and 66 d for the PS group (P = 0.379). The mean number of additional biliary drainage procedures after subsequent ERBD in patients that died (n = 50) during the study period was 2.54 ± 4.12 for the SEMS group and 1.85 ± 1.95 for the PS group (P = 0.457). The mean total cost of additional biliary drainage procedures after the occlusion of subsequent SEMS or PS was $410.04 ± 692.60 for the SEMS group and $630.16 ± 671.63 for the PS group (P = 0.260). Tumor ingrowth as the cause of initial SEMS occlusion was the only factor associated with a shorter time to subsequent stent occlusion (101 d for patients with tumor ingrowth vs 268 d for patients without tumor ingrowth, P = 0.008). CONCLUSION: Subsequent ERBD with PSs offered similar patency and number of additional biliary drainage procedures compared to SEMSs in the management of occluded SEMS. PMID:21072899

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2012 CFR

2012-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2011 CFR

2011-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2013 CFR

2013-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2010 CFR

2010-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2014 CFR

2014-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

Limb suction evoked during arterial occlusion causes systemic sympathetic activity in humans

PubMed Central

Cui, Jian; Blaha, Cheryl; Herr, Michael D.; Drew, Rachel C.; Muller, Matthew D.

2015-01-01

Venous saline infusions in an arterially occluded forearm evokes reflex increases in muscle sympathetic nerve activity (MSNA) and blood pressure (BP). We hypothesized that the application of suction to the human limbs would activate this venous distension reflex and raise sympathetic outflow. We placed airtight pressure tanks and applied 100 mmHg negative pressure to an arterially occluded limb (occlusion and suction, O&S) to induce tissue deformation without fluid translocation. BP, heart rate (HR), and MSNA were assessed in 19 healthy subjects during 2 min of arm or leg O&S. Occlusion without suction served as a control. During a separate visit, saline (5% forearm volume) was infused into veins of the arterially occluded arm (n = 13). The O&S increased limb circumference, MSNA burst rate (arm: Δ6.7 ± 0.7; leg: Δ6.8 ± 0.7 bursts/min), and total activity (arm: Δ199 ± 14; leg: Δ172 ± 22 units/min) and BP (arm: Δ4.3 ± 0.3; leg: Δ9.4 ± 1.4 mmHg) from the baseline. The MSNA and BP responses during arm O&S correlated with those during leg O&S. Occlusion alone had no effect on MSNA and BP. MSNA (r = 0.607) responses during arm O&S correlated with those evoked by the saline infusion into the arm. These correlations suggest that sympathetic activation during limb O&S is likely, at least partially, to be evoked via the venous distension reflex. These data suggest that suction of an occluded limb evokes sympathetic activation and that the limb venous distension reflex exists in arms and legs of normal humans. PMID:26136530

Computer simulation of the active site of human serum cholinesterase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kefang Jiao; Song Li; Zhengzheng Lu

1996-12-31

The first 3D-structure of acetylchelinesterase from Torpedo California electric organ (T.AChE) was published by JL. Sussman in 1991. We have simulated 3D-structure of human serum cholinesterase (H.BuChE) and the active site of H.BuChE. It is discovered by experiment that the residue of H.BuChE is still active site after a part of H.BuChE is cut. For example, the part of 21KD + 20KD is active site of H.BuChE. The 20KD as it is. Studies on these peptides by Hemelogy indicate that two active peptides have same negative electrostatic potential maps diagram. These negative electrostatic areas attached by acetyl choline with positivemore » electrostatic potency. We predict that 147...236 peptide of AChE could be active site because it was as 20KD as with negative electrostatic potential maps. We look forward to proving from other ones.« less

De novo active sites for resurrected Precambrian enzymes

NASA Astrophysics Data System (ADS)

Risso, Valeria A.; Martinez-Rodriguez, Sergio; Candel, Adela M.; Krüger, Dennis M.; Pantoja-Uceda, David; Ortega-Muñoz, Mariano; Santoyo-Gonzalez, Francisco; Gaucher, Eric A.; Kamerlin, Shina C. L.; Bruix, Marta; Gavira, Jose A.; Sanchez-Ruiz, Jose M.

2017-07-01

Protein engineering studies often suggest the emergence of completely new enzyme functionalities to be highly improbable. However, enzymes likely catalysed many different reactions already in the last universal common ancestor. Mechanisms for the emergence of completely new active sites must therefore either plausibly exist or at least have existed at the primordial protein stage. Here, we use resurrected Precambrian proteins as scaffolds for protein engineering and demonstrate that a new active site can be generated through a single hydrophobic-to-ionizable amino acid replacement that generates a partially buried group with perturbed physico-chemical properties. We provide experimental and computational evidence that conformational flexibility can assist the emergence and subsequent evolution of new active sites by improving substrate and transition-state binding, through the sampling of many potentially productive conformations. Our results suggest a mechanism for the emergence of primordial enzymes and highlight the potential of ancestral reconstruction as a tool for protein engineering.

Oncogenic and RASopathy-associated K-RAS mutations relieve membrane-dependent occlusion of the effector-binding site.

PubMed

Mazhab-Jafari, Mohammad T; Marshall, Christopher B; Smith, Matthew J; Gasmi-Seabrook, Geneviève M C; Stathopulos, Peter B; Inagaki, Fuyuhiko; Kay, Lewis E; Neel, Benjamin G; Ikura, Mitsuhiko

2015-05-26

K-RAS4B (Kirsten rat sarcoma viral oncogene homolog 4B) is a prenylated, membrane-associated GTPase protein that is a critical switch for the propagation of growth factor signaling pathways to diverse effector proteins, including rapidly accelerated fibrosarcoma (RAF) kinases and RAS-related protein guanine nucleotide dissociation stimulator (RALGDS) proteins. Gain-of-function KRAS mutations occur frequently in human cancers and predict poor clinical outcome, whereas germ-line mutations are associated with developmental syndromes. However, it is not known how these mutations affect K-RAS association with biological membranes or whether this impacts signal transduction. Here, we used solution NMR studies of K-RAS4B tethered to nanodiscs to investigate lipid bilayer-anchored K-RAS4B and its interactions with effector protein RAS-binding domains (RBDs). Unexpectedly, we found that the effector-binding region of activated K-RAS4B is occluded by interaction with the membrane in one of the NMR-observable, and thus highly populated, conformational states. Binding of the RAF isoform ARAF and RALGDS RBDs induced marked reorientation of K-RAS4B from the occluded state to RBD-specific effector-bound states. Importantly, we found that two Noonan syndrome-associated mutations, K5N and D153V, which do not affect the GTPase cycle, relieve the occluded orientation by directly altering the electrostatics of two membrane interaction surfaces. Similarly, the most frequent KRAS oncogenic mutation G12D also drives K-RAS4B toward an exposed configuration. Further, the D153V and G12D mutations increase the rate of association of ARAF-RBD with lipid bilayer-tethered K-RAS4B. We revealed a mechanism of K-RAS4B autoinhibition by membrane sequestration of its effector-binding site, which can be disrupted by disease-associated mutations. Stabilizing the autoinhibitory interactions between K-RAS4B and the membrane could be an attractive target for anticancer drug discovery.

Molecular dynamics explorations of active site structure in designed and evolved enzymes.

PubMed

Osuna, Sílvia; Jiménez-Osés, Gonzalo; Noey, Elizabeth L; Houk, K N

2015-04-21

This Account describes the use of molecular dynamics (MD) simulations to reveal how mutations alter the structure and organization of enzyme active sites. As proposed by Pauling about 70 years ago and elaborated by many others since then, biocatalysis is efficient when functional groups in the active site of an enzyme are in optimal positions for transition state stabilization. Changes in mechanism and covalent interactions are often critical parts of enzyme catalysis. We describe our explorations of the dynamical preorganization of active sites using MD, studying the fluctuations between active and inactive conformations normally concealed to static crystallography. MD shows how the various arrangements of active site residues influence the free energy of the transition state and relates the populations of the catalytic conformational ensemble to the enzyme activity. This Account is organized around three case studies from our laboratory. We first describe the importance of dynamics in evaluating a series of computationally designed and experimentally evolved enzymes for the Kemp elimination, a popular subject in the enzyme design field. We find that the dynamics of the active site is influenced not only by the original sequence design and subsequent mutations but also by the nature of the ligand present in the active site. In the second example, we show how microsecond MD has been used to uncover the role of remote mutations in the active site dynamics and catalysis of a transesterase, LovD. This enzyme was evolved by Tang at UCLA and Codexis, Inc., and is a useful commercial catalyst for the production of the drug simvastatin. X-ray analysis of inactive and active mutants did not reveal differences in the active sites, but relatively long time scale MD in solution showed that the active site of the wild-type enzyme preorganizes only upon binding of the acyl carrier protein (ACP) that delivers the natural acyl group to the active site. In the absence of bound ACP

Transcatheter Closure of a Chronic Iatrogenic Arteriovenous Fistula Between the Carotid Artery and the Brachiocephalic Vein with an Amplatzer Duct Occluder in Combination with a Carotid Stent

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stasek, Josef, E-mail: stasek@fnhk.c; Lojik, Miroslav; Bis, Josef

2009-05-15

We report an original method of transcatheter closure of an arteriovenous fistula using the combination of an Amplatzer PDA occluder and a carotid stent. The fistula was between the left carotid artery and the brachiocephalic vein. The patient had significant left-to-right shunt and was highly symptomatic. Due to the large orifice and pseudoaneurysmatic enlargement of the fistula, we had to use a large Amplatzer PDA occluder and the protruding part of the PDA device disk had to be covered with a carotid stent. The fistula was completely closed. The patient stopped having symptoms and, 2 years after the procedure, themore » effect persists.« less

Relocating the Active-Site Lysine in Rhodopsin: 2. Evolutionary Intermediates.

PubMed

Devine, Erin L; Theobald, Douglas L; Oprian, Daniel D

2016-08-30

The visual pigment rhodopsin is a G protein-coupled receptor that covalently binds its retinal chromophore via a Schiff base linkage to an active-site Lys residue in the seventh transmembrane helix. Although this residue is strictly conserved among all type II retinylidene proteins, we found previously that the active-site Lys in bovine rhodopsin (Lys296) can be moved to three other locations (G90K, T94K, S186K) while retaining the ability to form a pigment with retinal and to activate transducin in a light-dependent manner [ Devine et al. ( 2013 ) Proc. Natl. Acad. Sci. USA 110 , 13351 - 13355 ]. Because the active-site Lys is not functionally constrained to be in helix seven, it is possible that it could relocate within the protein, most likely via an evolutionary intermediate with two active-site Lys. Therefore, in this study we characterized potential evolutionary intermediates with two Lys in the active site. Four mutant rhodopsins were prepared in which the original Lys296 was left untouched and a second Lys residue was substituted for G90K, T94K, S186K, or F293K. All four constructs covalently bind 11-cis-retinal, form a pigment, and activate transducin in a light-dependent manner. These results demonstrate that rhodopsin can tolerate a second Lys in the retinal binding pocket and suggest that an evolutionary intermediate with two Lys could allow migration of the Schiff base Lys to a position other than the observed, highly conserved location in the seventh TM helix. From sequence-based searches, we identified two groups of natural opsins, insect UV cones and neuropsins, that contain Lys residues at two positions in their active sites and also have intriguing spectral similarities to the mutant rhodopsins studied here.

Immediate effects of the semi-occluded vocal tract exercise with LaxVox® tube in singers.

PubMed

Fadel, Congeta Bruniere Xavier; Dassie-Leite, Ana Paula; Santos, Rosane Sampaio; Santos, Celso Gonçalves Dos; Dias, Cláudio Antônio Sorondo; Sartori, Denise Jussara

The purpose of this study was to analyze the immediate effects of the semi-occluded vocal tract exercise (SOVTE) using the LaxVox® tube in singers. Participants were 23 singers, classical singing students, aged 18 to 47 years (mean age = 27.2 years). First, data was collected through the application of a demographic questionnaire and the recording of sustained emission - vowel /ε/, counting 1-10, and a music section from the participants' current repertoire. After that, the participants were instructed and performed the SOVTE using the LaxVox® tube for three minutes. Finally, the same vocal samples were collected immediately after SOVTE performance and the singers responded to a questionnaire on their perception regarding vocal changes after the exercise. The vocal samples were analyzed by referees (speech-language pathologists and singing teachers) and by means of acoustic analysis. Most of the singers reported improved voice post-exercise in both tasks - speech and singing. Regarding the perceptual assessment (sustained vowel, speech, and singing), the referees found no difference between pre- and post-exercise emissions. The acoustic analysis of the sustained vowel showed increased Fundamental Frequency (F0) and reduction of the Glottal to Noise Excitation (GNE) ratio post-exercise. The semi-occluded vocal tract exercise with LaxVox® tube promotes immediate positive effects on the self-assessment and acoustic analysis of voice in professional singers without vocal complains. No immediate significant changes were observed with respect to auditory-perceptual evaluation of speech and singing.

Allosteric site-mediated active site inhibition of PBP2a using Quercetin 3-O-rutinoside and its combination.

PubMed

Rani, Nidhi; Vijayakumar, Saravanan; P T V, Lakshmi; Arunachalam, Annamalai

2016-08-01

Recent crystallographic study revealed the involvement of allosteric site in active site inhibition of penicillin binding protein (PBP2a), where one molecule of Ceftaroline (Cef) binds to the allosteric site of PBP2a and paved way for the other molecule (Cef) to bind at the active site. Though Cef has the potency to inhibit the PBP2a, its adverse side effects are of major concern. Previous studies have reported the antibacterial property of Quercetin derivatives, a group of natural compounds. Hence, the present study aims to evaluate the effect of Quercetin 3-o-rutinoside (Rut) in allosteric site-mediated active site inhibition of PBP2a. The molecular docking studies between allosteric site and ligands (Rut, Que, and Cef) revealed a better binding efficiency (G-score) of Rut (-7.790318) and Cef (-6.194946) with respect to Que (-5.079284). Molecular dynamic (MD) simulation studies showed significant changes at the active site in the presence of ligands (Rut and Cef) at allosteric site. Four different combinations of Rut and Cef were docked and their G-scores ranged between -6.320 and -8.623. MD studies revealed the stability of the key residue (Ser403) with Rut being at both sites, compared to other complexes. Morphological analysis through electron microscopy confirmed that combination of Rut and Cefixime was able to disturb the bacterial cell membrane in a similar fashion to that of Rut and Cefixime alone. The results of this study indicate that the affinity of Rut at both sites were equally good, with further validations Rut could be considered as an alternative for inhibiting MRSA growth.

Influence of active site location on catalytic activity in de novo-designed zinc metalloenzymes.

PubMed

Zastrow, Melissa L; Pecoraro, Vincent L

2013-04-17

While metalloprotein design has now yielded a number of successful metal-bound and even catalytically active constructs, the question of where to put a metal site along a linear, repetitive sequence has not been thoroughly addressed. Often several possibilities in a given sequence may exist that would appear equivalent but may in fact differ for metal affinity, substrate access, or protein dynamics. We present a systematic variation of active site location for a hydrolytically active ZnHis3O site contained within a de novo-designed three-stranded coiled coil. We find that the maximal rate, substrate access, and metal-binding affinity are dependent on the selected position, while catalytic efficiency for p-nitrophenyl acetate hydrolysis can be retained regardless of the location of the active site. This achievement demonstrates how efficient, tailor-made enzymes which control rate, pKa, substrate and solvent access (and selectivity), and metal-binding affinity may be realized. These findings may be applied to the more advanced de novo design of constructs containing secondary interactions, such as hydrogen-bonding channels. We are now confident that changes to location for accommodating such channels can be achieved without location-dependent loss of catalytic efficiency. These findings bring us closer to our ultimate goal of incorporating the secondary interactions we believe will be necessary in order to improve both active site properties and the catalytic efficiency to be competitive with the native enzyme, carbonic anhydrase.

RETINAL DEEP CAPILLARY ISCHEMIA ASSOCIATED WITH AN OCCLUDED CONGENITAL RETINAL MACROVESSEL.

PubMed

Hasegawa, Taiji; Ogata, Nahoko

2017-01-01

To report the case of a patient with an occluded congenital retinal macrovessel accompanied by retinal deep capillary ischemia. A 38-year-old woman presented with a 2-day history of a paracentral scotoma of her right eye. Fundus photograph showed a dilated congenital retinal macrovessel with arteriovenous anastomosis, an intravascular white region indicating the thrombus at arteriovenous anastomotic region, and an area of retinal whitening temporal to the fovea. The spectral domain optical coherence tomography images through the area of retinal whitening showed a thickening and highly reflectivity at the level of the inner nuclear layer, which is likely due to the deep capillary ischemia. After 6 weeks, spectral domain optical coherence tomography images through the same area demonstrated a thinning and atrophy of only the inner nuclear layer, and the patient's paracentral scotoma persisted. Acute capillary hemodynamic changes caused deep capillary ischemia. The spectral domain optical coherence tomography showed a highly reflective lesion at the level of the inner nuclear layer in the acute phase.

Active Sites Environmental Monitoring Program: Mid-FY 1991 report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ashwood, T.L.; Wickliff, D.S.; Morrissey, C.M.

1991-10-01

This report summarizes the activities of the Active Sites Environmental Monitoring Program (ASEMP) from October 1990 through March 1991. The ASEMP was established in 1989 by Solid Waste Operations and the Environmental Sciences Division to provide early detection and performance monitoring at active low-level radioactive waste (LLW) disposal sites in Solid Waste Storage Area (SWSA) 6 and transuranic (TRU) waste storage sites in SWSA 5 as required by chapters II and III of US Department of Energy Order 5820.2A. Monitoring results continue to demonstrate the no LLW is being leached from the storage vaults on the tumulus pads. Loading ofmore » vaults on Tumulus II began during this reporting period and 115 vaults had been loaded by the end of March 1991.« less

Inhibition of plasma membrane Ca(2+)-ATPase by CrATP. LaATP but not CrATP stabilizes the Ca(2+)-occluded state.

PubMed

Moreira, Otacilio C; Rios, Priscila F; Barrabin, Hector

2005-07-15

The bidentate complex of ATP with Cr(3+), CrATP, is a nucleotide analog that is known to inhibit the sarcoplasmic reticulum Ca(2+)-ATPase and the Na(+),K(+)-ATPase, so that these enzymes accumulate in a conformation with the transported ion (Ca(2+) and Na(+), respectively) occluded from the medium. Here, it is shown that CrATP is also an effective and irreversible inhibitor of the plasma membrane Ca(2+)-ATPase. The complex inhibited with similar efficiency the Ca(2+)-dependent ATPase and the phosphatase activities as well as the enzyme phosphorylation by ATP. The inhibition proceeded slowly (T(1/2)=30 min at 37 degrees C) with a K(i)=28+/-9 microM. The inclusion of ATP, ADP or AMPPNP in the inhibition medium effectively protected the enzyme against the inhibition, whereas ITP, which is not a PMCA substrate, did not. The rate of inhibition was strongly dependent on the presence of Mg(2+) but unaltered when Ca(2+) was replaced by EGTA. In spite of the similarities with the inhibition of other P-ATPases, no apparent Ca(2+) occlusion was detected concurrent with the inhibition by CrATP. In contrast, inhibition by the complex of La(3+) with ATP, LaATP, induced the accumulation of phosphoenzyme with a simultaneous occlusion of Ca(2+) at a ratio close to 1.5 mol/mol of phosphoenzyme. The results suggest that the transport of Ca(2+) promoted by the plasma membrane Ca(2+)-ATPase goes through an enzymatic phospho-intermediate that maintains Ca(2+) ions occluded from the media. This intermediate is stabilized by LaATP but not by CrATP.

Voice Quality After a Semi-Occluded Vocal Tract Exercise With a Ventilation Mask in Contemporary Commercial Singers: Acoustic Analysis and Self-Assessments.

PubMed

Fantini, Marco; Succo, Giovanni; Crosetti, Erika; Borragán Torre, Alfonso; Demo, Roberto; Fussi, Franco

2017-05-01

The current study aimed at investigating the immediate effects of a semi-occluded vocal tract exercise with a ventilation mask in a group of contemporary commercial singers. A randomized controlled study was carried out. Thirty professional or semi-professional singers with no voice complaints were randomly divided into two groups on recruitment: an experimental group and a control group. The same warm-up exercise was performed by the experimental group with an occluded ventilation mask placed over the nose and the mouth and by the control group without the ventilation mask. Voice was recorded before and after the exercise. Acoustic and self-assessment analysis were accomplished. The acoustic parameters of the voice samples recorded before and after training were compared, as well as the parameters' variations between the experimental and the control group. Self-assessment results of the experimental and the control group were compared too. Significant changes after the warm-up exercise included jitter, shimmer, and singing power ratio (SPR) in the experimental group. No significant changes were recorded in the control group. Significant differences between the experimental and the control group were found for ΔShimmer and ΔSPR. Self-assessment analysis confirmed a significantly higher phonatory comfort and voice quality perception for the experimental group. The results of the present study support the immediate advantageous effects on singing voice of a semi-occluded vocal tract exercise with a ventilation mask in terms of acoustic quality, phonatory comfort, and voice quality perception in contemporary commercial singers. Long-term effects still remain to be studied. Copyright © 2017 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

Transcatheter closure of a large patent ductus arteriosus in a young child using the Amplatzer duct occluder.

PubMed

Jan, S-L; Hwang, B; Fu, Y-C; Chi, C-S

2005-01-01

The Amplatzer duct occluder (ADO) provides a safe and effective therapy for patients with moderate- to large-sized patent ductus arteriosus (PDA), but there have been few reports of transcatheter closure of very large PDAs in young children and infants. We report a successful transcatheter closure of a very large PDA, 10.5 mm in diameter at the narrowest point, with a 14/12-mm ADO. To our knowledge, this is the largest PDA ever closed by an interventional method in such a young child.

All the catalytic active sites of MoS 2 for hydrogen evolution

DOE PAGES

Li, Guoqing; Zhang, Du; Qiao, Qiao; ...

2016-11-29

MoS 2 presents a promising low-cost catalyst for the hydrogen evolution reaction (HER), but the understanding about its active sites has remained limited. Here we present an unambiguous study of the catalytic activities of all possible reaction sites of MoS 2, including edge sites, sulfur vacancies, and grain boundaries. We demonstrate that, in addition to the well-known catalytically active edge sites, sulfur vacancies provide another major active site for the HER, while the catalytic activity of grain boundaries is much weaker. Here, the intrinsic turnover frequencies (Tafel slopes) of the edge sites, sulfur vacancies, and grain boundaries are estimated tomore » be 7.5 s –1 (65–75 mV/dec), 3.2 s –1 (65–85 mV/dec), and 0.1 s –1 (120–160 mV/dec), respectively. We also demonstrate that the catalytic activity of sulfur vacancies strongly depends on the density of the vacancies and the local crystalline structure in proximity to the vacancies. Unlike edge sites, whose catalytic activity linearly depends on the length, sulfur vacancies show optimal catalytic activities when the vacancy density is in the range of 7–10%, and the number of sulfur vacancies in high crystalline quality MoS 2 is higher than that in low crystalline quality MoS 2, which may be related with the proximity of different local crystalline structures to the vacancies.« less

Machine-Learning Methods Enable Exhaustive Searches for Active Bimetallic Facets and Reveal Active Site Motifs for CO 2 Reduction

DOE PAGES

Ulissi, Zachary W.; Tang, Michael T.; Xiao, Jianping; ...

2017-07-27

Bimetallic catalysts are promising for the most difficult thermal and electrochemical reactions, but modeling the many diverse active sites on polycrystalline samples is an open challenge. Here, we present a general framework for addressing this complexity in a systematic and predictive fashion. Active sites for every stable low-index facet of a bimetallic crystal are enumerated and cataloged, yielding hundreds of possible active sites. The activity of these sites is explored in parallel using a neural-network-based surrogate model to share information between the many density functional theory (DFT) relaxations, resulting in activity estimates with an order of magnitude fewer explicit DFTmore » calculations. Sites with interesting activity were found and provide targets for follow-up calculations. This process was applied to the electrochemical reduction of CO 2 on nickel gallium bimetallics and indicated that most facets had similar activity to Ni surfaces, but a few exposed Ni sites with a very favorable on-top CO configuration. This motif emerged naturally from the predictive modeling and represents a class of intermetallic CO 2 reduction catalysts. These sites rationalize recent experimental reports of nickel gallium activity and why previous materials screens missed this exciting material. Most importantly these methods suggest that bimetallic catalysts will be discovered by studying facet reactivity and diversity of active sites more systematically.« less

Machine-Learning Methods Enable Exhaustive Searches for Active Bimetallic Facets and Reveal Active Site Motifs for CO 2 Reduction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ulissi, Zachary W.; Tang, Michael T.; Xiao, Jianping

Bimetallic catalysts are promising for the most difficult thermal and electrochemical reactions, but modeling the many diverse active sites on polycrystalline samples is an open challenge. Here, we present a general framework for addressing this complexity in a systematic and predictive fashion. Active sites for every stable low-index facet of a bimetallic crystal are enumerated and cataloged, yielding hundreds of possible active sites. The activity of these sites is explored in parallel using a neural-network-based surrogate model to share information between the many density functional theory (DFT) relaxations, resulting in activity estimates with an order of magnitude fewer explicit DFTmore » calculations. Sites with interesting activity were found and provide targets for follow-up calculations. This process was applied to the electrochemical reduction of CO 2 on nickel gallium bimetallics and indicated that most facets had similar activity to Ni surfaces, but a few exposed Ni sites with a very favorable on-top CO configuration. This motif emerged naturally from the predictive modeling and represents a class of intermetallic CO 2 reduction catalysts. These sites rationalize recent experimental reports of nickel gallium activity and why previous materials screens missed this exciting material. Most importantly these methods suggest that bimetallic catalysts will be discovered by studying facet reactivity and diversity of active sites more systematically.« less

Mutation at a strictly conserved, active site tyrosine in the copper amine oxidase leads to uncontrolled oxygenase activity.

PubMed

Chen, Zhi-Wei; Datta, Saumen; Dubois, Jennifer L; Klinman, Judith P; Mathews, F Scott

2010-08-31

The copper amine oxidases carry out two copper-dependent processes: production of their own redox-active cofactor (2,4,5-trihydroxyphenylalanine quinone, TPQ) and the subsequent oxidative deamination of substrate amines. Because the same active site pocket must facilitate both reactions, individual active site residues may serve multiple roles. We have examined the roles of a strictly conserved active site tyrosine Y305 in the copper amine oxidase from Hansenula polymorpha kinetically, spetroscopically (Dubois and Klinman (2006) Biochemistry 45, 3178), and, in the present work, structurally. While the Y305A enzyme is almost identical to the wild type, a novel, highly oxygenated species replaces TPQ in the Y305F active sites. This new structure not only provides the first direct detection of peroxy intermediates in cofactor biogenesis but also indicates the critical control of oxidation chemistry that can be conferred by a single active site residue.

Hand interception of occluded motion in humans: a test of model-based vs. on-line control

PubMed Central

Zago, Myrka; Lacquaniti, Francesco

2015-01-01

Two control schemes have been hypothesized for the manual interception of fast visual targets. In the model-free on-line control, extrapolation of target motion is based on continuous visual information, without resorting to physical models. In the model-based control, instead, a prior model of target motion predicts the future spatiotemporal trajectory. To distinguish between the two hypotheses in the case of projectile motion, we asked participants to hit a ball that rolled down an incline at 0.2 g and then fell in air at 1 g along a parabola. By varying starting position, ball velocity and trajectory differed between trials. Motion on the incline was always visible, whereas parabolic motion was either visible or occluded. We found that participants were equally successful at hitting the falling ball in both visible and occluded conditions. Moreover, in different trials the intersection points were distributed along the parabolic trajectories of the ball, indicating that subjects were able to extrapolate an extended segment of the target trajectory. Remarkably, this trend was observed even at the very first repetition of movements. These results are consistent with the hypothesis of model-based control, but not with on-line control. Indeed, ball path and speed during the occlusion could not be extrapolated solely from the kinematic information obtained during the preceding visible phase. The only way to extrapolate ball motion correctly during the occlusion was to assume that the ball would fall under gravity and air drag when hidden from view. Such an assumption had to be derived from prior experience. PMID:26133803

High dose urokinase for restoration of patency of occluded permanent central venous catheters in hemodialysis patients.

PubMed

Shavit, L; Lifschitz, M; Plaksin, J; Grenader, T; Slotki, I

2010-10-01

Catheter thrombosis is common and results in inadequate dialysis treatment and, frequently, in catheter loss. Since dialysis treatment runs on a strict schedule, occluded catheters need to be restored in a timely and cost effective manner. We present a new shortened protocol of urokinase infusion that allows hemodialysis to be performed within 90 minutes. To chronic hemodialysis patients, who developed complete catheter occlusion, urokinase was infused simultaneously through both lumens of the catheter (125,000 units to each lumen) over 90 minutes. Technical success was defined as restoring blood pump speed to at least 250 ml/min. We determined the average time from catheter placement to first clot event (primary patency PP), recurrent clot event after urokinase treatment (secondary patency SP), catheter salvage rate and cause for removal. 37 catheters developed total thrombosis and urokinase was used to restore patency one or more times (total 47 treatments). Catheter salvage rate was 97 %. The average time of PP was 152 ± 56 days (7 - 784 days). Nine patients (30%) developed recurrent occlusion and the average time of SP was 64 ± 34 days (2 - 364 days). One catheter was removed because of dysfunction due to thrombosis. Other catheters were removed due to infection, fistula maturation or fell out spontaneously. Hemodialysis was performed immediately after treatment with blood speed of 250 ml/min in all patients. Our protocol is highly effective, short, and allows to restore patency of totally occluded central venous catheters with minimal disruption of the dialysis session.

Functional Evolution of PLP-dependent Enzymes based on Active-Site Structural Similarities

PubMed Central

Catazaro, Jonathan; Caprez, Adam; Guru, Ashu; Swanson, David; Powers, Robert

2014-01-01

Families of distantly related proteins typically have very low sequence identity, which hinders evolutionary analysis and functional annotation. Slowly evolving features of proteins, such as an active site, are therefore valuable for annotating putative and distantly related proteins. To date, a complete evolutionary analysis of the functional relationship of an entire enzyme family based on active-site structural similarities has not yet been undertaken. Pyridoxal-5’-phosphate (PLP) dependent enzymes are primordial enzymes that diversified in the last universal ancestor. Using the Comparison of Protein Active Site Structures (CPASS) software and database, we show that the active site structures of PLP-dependent enzymes can be used to infer evolutionary relationships based on functional similarity. The enzymes successfully clustered together based on substrate specificity, function, and three-dimensional fold. This study demonstrates the value of using active site structures for functional evolutionary analysis and the effectiveness of CPASS. PMID:24920327

Chapter 12: Daily Patterns of Marbled Murrelet Activity at Inland Sites

Treesearch

Nancy L. Naslund; Brian P. O’Donnell

1995-01-01

Patterns in the daily activity of Marbled Murrelets (Brachyramphus marmoratus) at inland sites has been studied throughout their range from California to Alaska. Murrelets are most active at inland sites around dawn, and to a lesser degree, at dusk. Throughout their range, peak levels of activity (detections) occur in the hour around dawn, but...

A double-headed cathepsin B inhibitor devoid of warhead

PubMed Central

Schenker, Patricia; Alfarano, Pietro; Kolb, Peter; Caflisch, Amedeo; Baici, Antonio

2008-01-01

Most synthetic inhibitors of peptidases have been targeted to the active site for inhibiting catalysis through reversible competition with the substrate or by covalent modification of catalytic groups. Cathepsin B is unique among the cysteine peptidase for the presence of a flexible segment, known as the occluding loop, which can block the primed subsites of the substrate binding cleft. With the occluding loop in the open conformation cathepsin B acts as an endopeptidase, and it acts as an exopeptidase when the loop is closed. We have targeted the occluding loop of human cathepsin B at its surface, outside the catalytic center, using a high-throughput docking procedure. The aim was to identify inhibitors that would interact with the occluding loop thereby modulating enzyme activity without the help of chemical warheads against catalytic residues. From a large library of compounds, the in silico approach identified [2-[2-(2,4-dioxo-1,3-thiazolidin-3-yl)ethylamino]-2-oxoethyl] 2-(furan-2-carbonylamino) acetate, which fulfills the working hypothesis. This molecule possesses two distinct binding moieties and behaves as a reversible, double-headed competitive inhibitor of cathepsin B by excluding synthetic and protein substrates from the active center. The kinetic mechanism of inhibition suggests that the occluding loop is stabilized in its closed conformation, mainly by hydrogen bonds with the inhibitor, thus decreasing endoproteolytic activity of the enzyme. Furthermore, the dioxothiazolidine head of the compound sterically hinders binding of the C-terminal residue of substrates resulting in inhibition of the exopeptidase activity of cathepsin B in a physiopathologically relevant pH range. PMID:18796695

An Active Site Water Network in the Plasminogen Activator Pla from Yersinia pestis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eren, Elif; Murphy, Megan; Goguen, Jon

2010-08-13

The plasminogen activator Pla from Yersinia pestis is an outer membrane protease (omptin) that is important for the virulence of plague. Here, we present the high-resolution crystal structure of wild-type, enzymatically active Pla at 1.9 {angstrom}. The structure shows a water molecule located between active site residues D84 and H208, which likely corresponds to the nucleophilic water. A number of other water molecules are present in the active site, linking residues important for enzymatic activity. The R211 sidechain in loop L4 is close to the nucleophilic water and possibly involved in the stabilization of the oxyanion intermediate. Subtle conformational changesmore » of H208 result from the binding of lipopolysaccharide to the outside of the barrel, explaining the unusual dependence of omptins on lipopolysaccharide for activity. The Pla structure suggests a model for the interaction with plasminogen substrate and provides a more detailed understanding of the catalytic mechanism of omptin proteases.« less

Arrhythmias after transcatheter closure of perimembranous ventricular septal defects with a modified double-disk occluder: early and long-term results.

PubMed

Li, Pan; Zhao, Xian-xian; Zheng, Xing; Qin, Yong-wen

2012-07-01

With the development of interventional techniques and devices, transcatheter closure of perimembranous ventricular septal defect has been widely performed. However, there has been a lack of long-term follow-up results about postoperative ECG changes of PmVSD patients. We report our experience of early and late arrhythmias after transcatheter closure of PmVSD with a modified double-disk occluder (MDVO). We performed a retrospective review of 79 patients (47 males, 32 females) between September 2002 and May 2007 who underwent transcatheter closure of perimembranous ventricular septal defect. Symmetric and asymmetric PmVSD occluders were used. The diameter of the evaluated defects ranged from 3 to 12 mm, as measured by TTE and 3 to 15 mm by left ventriculography. Most cases of PmVSD were treated successfully with a single procedure, resulting in a successful closure rate of 97% (77/79 patients). There was no death in any of the patients. After the operation, 79 patients were followed-up for a range of 10-76 months (35.3 ± 17.4 months). In this series, 11 cases of incomplete right bundle branch block and five cases of complete right bundle branch block occurred during the early period after operation. During long-term follow-up, these issues declined in prevalence to five and four cases, respectively. Moreover, reversible third-degree AVB occurred during closure or after the procedure, and two of the three patients with reversible AVB received a temporary heart pacemaker implantation. These patients recovered 1 h, 6 days, and 9 days later, respectively. During 10-76 months of follow-up, no complications occurred in any of the patients, including residual shunt, severe aortic valve, or tricuspid valve regurgitation. Device closure of perimembranous ventricular septal defects with a modified double-disk occluder (MDVO) resulted in excellent closure rates and acceptably low arrhythmia rates.

A comparison of the in vivo neoendothelialization and wound healing processes of three atrial septal defect occluders used during childhood in a nonrandomized prospective trial

PubMed Central

Şahin, Derya Aydın; Başpınar, Osman; Sülü, Ayşe; Karslıgil, Tekin; Kul, Seval

2017-01-01

Objective: We prospectively investigated the neoendothelialization of transcatheter secundum atrial septal defect (ASD) closure in children receiving one of three different occluders. Methods: Transcatheter ASD closure was performed for 44 children. The patients were divided into three groups: group I: Amplatzer, group II: Lifetech CeraFlex, and group III: Occlutech Figulla Flex II septal occluder. The data were prospectively analyzed. Markers of the three phases of wound healing were studied in all patients before and on the 1st and 10th days and 1st month post intervention. Results: The mean age of children was 7.08±3.51 years, and the mean weight was 26.07±15.07 kg. The mean ASD diameter was 12.65±3.50 mm. Groups I, II, and III comprised 34.1%, 31.8%, and 34.1% patients, respectively. No significant differences were observed between the groups regarding patient number, age, defect size, device diameter, or total septum/device ratio (p>0.05). Inflammatory and proliferative phase marker levels increased following the procedure (p<0.05). However, scar formation markers did not change after 1 month. No significant differences in neoendothelializaton were observed among the different occluders (p>0.05). Conclusion: All three devices were composed of nitinol with different surface coating techniques. Although the different manufacturing features were claimed to facilitate of neoendothelialization, no differences were observed among the three devices 1 month following the procedure. PMID:28761023

Catalytic surface radical in dye-decolorizing peroxidase: a computational, spectroscopic and site-directed mutagenesis study

PubMed Central

Linde, Dolores; Pogni, Rebecca; Cañellas, Marina; Lucas, Fátima; Guallar, Victor; Baratto, Maria Camilla; Sinicropi, Adalgisa; Sáez-Jiménez, Verónica; Coscolín, Cristina; Romero, Antonio; Medrano, Francisco Javier; Ruiz-Dueñas, Francisco J.; Martínez, Angel T.

2014-01-01

Dye-decolorizing peroxidase (DyP) of Auricularia auricula-judae has been expressed in Escherichia coli as a representative of a new DyP family, and subjected to mutagenic, spectroscopic, crystallographic and computational studies. The crystal structure of DyP shows a buried haem cofactor, and surface tryptophan and tyrosine residues potentially involved in long-range electron transfer from bulky dyes. Simulations using PELE (Protein Energy Landscape Exploration) software provided several binding-energy optima for the anthraquinone-type RB19 (Reactive Blue 19) near the above aromatic residues and the haem access-channel. Subsequent QM/MM (quantum mechanics/molecular mechanics) calculations showed a higher tendency of Trp-377 than other exposed haem-neighbouring residues to harbour a catalytic protein radical, and identified the electron-transfer pathway. The existence of such a radical in H2O2-activated DyP was shown by low-temperature EPR, being identified as a mixed tryptophanyl/tyrosyl radical in multifrequency experiments. The signal was dominated by the Trp-377 neutral radical contribution, which disappeared in the W377S variant, and included a tyrosyl contribution assigned to Tyr-337 after analysing the W377S spectra. Kinetics of substrate oxidation by DyP suggests the existence of high- and low-turnover sites. The high-turnover site for oxidation of RB19 (kcat> 200 s−1) and other DyP substrates was assigned to Trp-377 since it was absent from the W377S variant. The low-turnover site/s (RB19 kcat ~20 s−1) could correspond to the haem access-channel, since activity was decreased when the haem channel was occluded by the G169L mutation. If a tyrosine residue is also involved, it will be different from Tyr-337 since all activities are largely unaffected in the Y337S variant. PMID:25495127

Catalytic surface radical in dye-decolorizing peroxidase: a computational, spectroscopic and site-directed mutagenesis study.

PubMed

Linde, Dolores; Pogni, Rebecca; Cañellas, Marina; Lucas, Fátima; Guallar, Victor; Baratto, Maria Camilla; Sinicropi, Adalgisa; Sáez-Jiménez, Verónica; Coscolín, Cristina; Romero, Antonio; Medrano, Francisco Javier; Ruiz-Dueñas, Francisco J; Martínez, Angel T

2015-03-01

Dye-decolorizing peroxidase (DyP) of Auricularia auricula-judae has been expressed in Escherichia coli as a representative of a new DyP family, and subjected to mutagenic, spectroscopic, crystallographic and computational studies. The crystal structure of DyP shows a buried haem cofactor, and surface tryptophan and tyrosine residues potentially involved in long-range electron transfer from bulky dyes. Simulations using PELE (Protein Energy Landscape Exploration) software provided several binding-energy optima for the anthraquinone-type RB19 (Reactive Blue 19) near the above aromatic residues and the haem access-channel. Subsequent QM/MM (quantum mechanics/molecular mechanics) calculations showed a higher tendency of Trp-377 than other exposed haem-neighbouring residues to harbour a catalytic protein radical, and identified the electron-transfer pathway. The existence of such a radical in H₂O₂-activated DyP was shown by low-temperature EPR, being identified as a mixed tryptophanyl/tyrosyl radical in multifrequency experiments. The signal was dominated by the Trp-377 neutral radical contribution, which disappeared in the W377S variant, and included a tyrosyl contribution assigned to Tyr-337 after analysing the W377S spectra. Kinetics of substrate oxidation by DyP suggests the existence of high- and low-turnover sites. The high-turnover site for oxidation of RB19 (k(cat) > 200 s⁻¹) and other DyP substrates was assigned to Trp-377 since it was absent from the W377S variant. The low-turnover site/s (RB19 k(cat) ~20 s⁻¹) could correspond to the haem access-channel, since activity was decreased when the haem channel was occluded by the G169L mutation. If a tyrosine residue is also involved, it will be different from Tyr-337 since all activities are largely unaffected in the Y337S variant.

Bleeding Duodenal Varices Successfully Treated with Balloon-Occluded Retrograde Transvenous Obliteration (B-RTO) Assisted by CT During Arterial Portography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tsurusaki, Masakatsu, E-mail: he3m-trsk@asahi-net.or.jp; Sugimoto, Koji; Matsumoto, Shinichi

2006-12-15

A 60-year-old woman with massive hemorrhage from duodenal varices was transferred to our hospital for the purpose of transcatheter intervention. Although digital subtraction arterial portography could not depict the entire pathway of collateral circulation, the efferent route of the duodenal varices was clearly demonstrated on subsequent CT during arterial portography. Balloon-occluded retrograde transvenous obliteration (B-RTO) of the varices was performed via the efferent vein and achieved complete thrombosis of the varices.

Anisotropic Covalency Contributions to Superexchange Pathways in Type One Copper Active Sites

PubMed Central

2015-01-01

Type one (T1) Cu sites deliver electrons to catalytic Cu active sites: the mononuclear type two (T2) Cu site in nitrite reductases (NiRs) and the trinuclear Cu cluster in the multicopper oxidases (MCOs). The T1 Cu and the remote catalytic sites are connected via a Cys-His intramolecular electron-transfer (ET) bridge, which contains two potential ET pathways: P1 through the protein backbone and P2 through the H-bond between the Cys and the His. The high covalency of the T1 Cu–S(Cys) bond is shown here to activate the T1 Cu site for hole superexchange via occupied valence orbitals of the bridge. This covalency-activated electronic coupling (HDA) facilitates long-range ET through both pathways. These pathways can be selectively activated depending on the geometric and electronic structure of the T1 Cu site and thus the anisotropic covalency of the T1 Cu–S(Cys) bond. In NiRs, blue (π-type) T1 sites utilize P1 and green (σ-type) T1 sites utilize P2, with P2 being more efficient. Comparing the MCOs to NiRs, the second-sphere environment changes the conformation of the Cys-His pathway, which selectively activates HDA for superexchange by blue π sites for efficient turnover in catalysis. These studies show that a given protein bridge, here Cys-His, provides different superexchange pathways and electronic couplings depending on the anisotropic covalencies of the donor and acceptor metal sites. PMID:25310460

Functional evolution of PLP-dependent enzymes based on active-site structural similarities.

PubMed

Catazaro, Jonathan; Caprez, Adam; Guru, Ashu; Swanson, David; Powers, Robert

2014-10-01

Families of distantly related proteins typically have very low sequence identity, which hinders evolutionary analysis and functional annotation. Slowly evolving features of proteins, such as an active site, are therefore valuable for annotating putative and distantly related proteins. To date, a complete evolutionary analysis of the functional relationship of an entire enzyme family based on active-site structural similarities has not yet been undertaken. Pyridoxal-5'-phosphate (PLP) dependent enzymes are primordial enzymes that diversified in the last universal ancestor. Using the comparison of protein active site structures (CPASS) software and database, we show that the active site structures of PLP-dependent enzymes can be used to infer evolutionary relationships based on functional similarity. The enzymes successfully clustered together based on substrate specificity, function, and three-dimensional-fold. This study demonstrates the value of using active site structures for functional evolutionary analysis and the effectiveness of CPASS. © 2014 Wiley Periodicals, Inc.

External Barium Affects the Gating of KCNQ1 Potassium Channels and Produces a Pore Block via Two Discrete Sites

PubMed Central

Gibor, Gilad; Yakubovich, Daniel; Peretz, Asher; Attali, Bernard

2004-01-01

The pore properties and the reciprocal interactions between permeant ions and the gating of KCNQ channels are poorly understood. Here we used external barium to investigate the permeation characteristics of homomeric KCNQ1 channels. We assessed the Ba2+ binding kinetics and the concentration and voltage dependence of Ba2+ steady-state block. Our results indicate that extracellular Ba2+ exerts a series of complex effects, including a voltage-dependent pore blockade as well as unique gating alterations. External barium interacts with the permeation pathway of KCNQ1 at two discrete and nonsequential sites. (a) A slow deep Ba2+ site that occludes the channel pore and could be simulated by a model of voltage-dependent block. (b) A fast superficial Ba2+ site that barely contributes to channel block and mostly affects channel gating by shifting rightward the voltage dependence of activation, slowing activation, speeding up deactivation kinetics, and inhibiting channel inactivation. A model of voltage-dependent block cannot predict the complex impact of Ba2+ on channel gating in low external K+ solutions. Ba2+ binding to this superficial site likely modifies the gating transitions states of KCNQ1. Both sites appear to reside in the permeation pathway as high external K+ attenuates Ba2+ inhibition of channel conductance and abolishes its impact on channel gating. Our data suggest that despite the high degree of homology of the pore region among the various K+ channels, KCNQ1 channels display significant structural and functional uniqueness. PMID:15226366

A NMDA receptor glycine site partial agonist, GLYX-13, simultaneously enhances LTP and reduces LTD at Schaffer collateral-CA1 synapses in hippocampus.

PubMed

Zhang, Xiao-lei; Sullivan, John A; Moskal, Joseph R; Stanton, Patric K

2008-12-01

N-methyl-D-aspartate glutamate receptors (NMDARs) are a key route for Ca2+ influx into neurons important to both activity-dependent synaptic plasticity and, when uncontrolled, triggering events that cause neuronal degeneration and death. Among regulatory binding sites on the NMDAR complex is a glycine binding site, distinct from the glutamate binding site, which must be co-activated for NMDAR channel opening. We developed a novel glycine site partial agonist, GLYX-13, which is both nootropic and neuroprotective in vivo. Here, we assessed the effects of GLYX-13 on long-term synaptic plasticity and NMDAR transmission at Schaffer collateral-CA1 synapses in hippocampal slices in vitro. GLYX-13 simultaneously enhanced the magnitude of long-term potentiation (LTP) of synaptic transmission, while reducing long-term depression (LTD). GLYX-13 reduced NMDA receptor-mediated synaptic currents in CA1 pyramidal neurons evoked by low frequency Schaffer collateral stimulation, but enhanced NMDAR currents during high frequency bursts of activity, and these actions were occluded by a saturating concentration of the glycine site agonist d-serine. Direct two-photon imaging of Schaffer collateral burst-evoked increases in [Ca2+] in individual dendritic spines revealed that GLYX-13 selectively enhanced burst-induced NMDAR-dependent spine Ca2+ influx. Examining the rate of MK-801 block of synaptic versus extrasynaptic NMDAR-gated channels revealed that GLYX-13 selectively enhanced activation of burst-driven extrasynaptic NMDARs, with an action that was blocked by the NR2B-selective NMDAR antagonist ifenprodil. Our data suggest that GLYX-13 may have unique therapeutic potential as a learning and memory enhancer because of its ability to simultaneously enhance LTP and suppress LTD.

Active-site solvent replenishment observed during human carbonic anhydrase II catalysis.

PubMed

Kim, Jin Kyun; Lomelino, Carrie L; Avvaru, Balendu Sankara; Mahon, Brian P; McKenna, Robert; Park, SangYoun; Kim, Chae Un

2018-01-01

Human carbonic anhydrase II (hCA II) is a zinc metalloenzyme that catalyzes the reversible hydration/dehydration of CO 2 /HCO 3 - . Although hCA II has been extensively studied to investigate the proton-transfer process that occurs in the active site, its underlying mechanism is still not fully understood. Here, ultrahigh-resolution crystallographic structures of hCA II cryocooled under CO 2 pressures of 7.0 and 2.5 atm are presented. The structures reveal new intermediate solvent states of hCA II that provide crystallographic snapshots during the restoration of the proton-transfer water network in the active site. Specifically, a new intermediate water (W I ') is observed next to the previously observed intermediate water W I , and they are both stabilized by the five water molecules at the entrance to the active site (the entrance conduit). Based on these structures, a water network-restructuring mechanism is proposed, which takes place at the active site after the nucleophilic attack of OH - on CO 2 . This mechanism explains how the zinc-bound water (W Zn ) and W1 are replenished, which are directly responsible for the reconnection of the His64-mediated proton-transfer water network. This study provides the first 'physical' glimpse of how a water reservoir flows into the hCA II active site during its catalytic activity.

Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites.

PubMed

Ribeiro, António J M; Holliday, Gemma L; Furnham, Nicholas; Tyzack, Jonathan D; Ferris, Katherine; Thornton, Janet M

2018-01-04

M-CSA (Mechanism and Catalytic Site Atlas) is a database of enzyme active sites and reaction mechanisms that can be accessed at www.ebi.ac.uk/thornton-srv/m-csa. Our objectives with M-CSA are to provide an open data resource for the community to browse known enzyme reaction mechanisms and catalytic sites, and to use the dataset to understand enzyme function and evolution. M-CSA results from the merging of two existing databases, MACiE (Mechanism, Annotation and Classification in Enzymes), a database of enzyme mechanisms, and CSA (Catalytic Site Atlas), a database of catalytic sites of enzymes. We are releasing M-CSA as a new website and underlying database architecture. At the moment, M-CSA contains 961 entries, 423 of these with detailed mechanism information, and 538 with information on the catalytic site residues only. In total, these cover 81% (195/241) of third level EC numbers with a PDB structure, and 30% (840/2793) of fourth level EC numbers with a PDB structure, out of 6028 in total. By searching for close homologues, we are able to extend M-CSA coverage of PDB and UniProtKB to 51 993 structures and to over five million sequences, respectively, of which about 40% and 30% have a conserved active site. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Holographic quantitative imaging of sample hidden by turbid medium or occluding objects

NASA Astrophysics Data System (ADS)

Bianco, V.; Miccio, L.; Merola, F.; Memmolo, P.; Gennari, O.; Paturzo, Melania; Netti, P. A.; Ferraro, P.

2015-03-01

Digital Holography (DH) numerical procedures have been developed to allow imaging through turbid media. A fluid is considered turbid when dispersed particles provoke strong light scattering, thus destroying the image formation by any standard optical system. Here we show that sharp amplitude imaging and phase-contrast mapping of object hidden behind turbid medium and/or occluding objects are possible in harsh noise conditions and with a large field-of view by Multi-Look DH microscopy. In particular, it will be shown that both amplitude imaging and phase-contrast mapping of cells hidden behind a flow of Red Blood Cells can be obtained. This allows, in a noninvasive way, the quantitative evaluation of living processes in Lab on Chip platforms where conventional microscopy techniques fail. The combination of this technique with endoscopic imaging can pave the way for the holographic blood vessel inspection, e.g. to look for settled cholesterol plaques as well as blood clots for a rapid diagnostics of blood diseases.

Active Site Gate Dynamics Modulate the Catalytic Activity of the Ubiquitination Enzyme E2-25K.

PubMed

Rout, Manoj K; Lee, Brian L; Lin, Aiyang; Xiao, Wei; Spyracopoulos, Leo

2018-05-03

The ubiquitin proteasome system (UPS) signals for degradation of proteins through attachment of K48-linked polyubiquitin chains, or alterations in protein-protein recognition through attachment of K63-linked chains. Target proteins are ubiquitinated in three sequential chemical steps by a three-component enzyme system. Ubiquitination, or E2 enzymes, catalyze the central step by facilitating reaction of a target protein lysine with the C-terminus of Ub that is attached to the active site cysteine of the E2 through a thioester bond. E2 reactivity is modulated by dynamics of an active site gate, whose central residue packs against the active site cysteine in a closed conformation. Interestingly, for the E2 Ubc13, which specifically catalyzes K63-linked ubiquitination, the central gate residue adopts an open conformation. We set out to determine if active site gate dynamics play a role in catalysis for E2-25K, which adopts the canonical, closed gate conformation, and which selectively synthesizes K48-linked ubiquitin chains. Gate dynamics were characterized using mutagenesis of key residues, combined with enzyme kinetics measurements, and main chain NMR relaxation. The experimental data were interpreted with all atom MD simulations. The data indicate that active site gate opening and closing rates for E2-25K are precisely balanced.

SABER: A computational method for identifying active sites for new reactions

PubMed Central

Nosrati, Geoffrey R; Houk, K N

2012-01-01

A software suite, SABER (Selection of Active/Binding sites for Enzyme Redesign), has been developed for the analysis of atomic geometries in protein structures, using a geometric hashing algorithm (Barker and Thornton, Bioinformatics 2003;19:1644–1649). SABER is used to explore the Protein Data Bank (PDB) to locate proteins with a specific 3D arrangement of catalytic groups to identify active sites that might be redesigned to catalyze new reactions. As a proof-of-principle test, SABER was used to identify enzymes that have the same catalytic group arrangement present in o-succinyl benzoate synthase (OSBS). Among the highest-scoring scaffolds identified by the SABER search for enzymes with the same catalytic group arrangement as OSBS were l-Ala d/l-Glu epimerase (AEE) and muconate lactonizing enzyme II (MLE), both of which have been redesigned to become effective OSBS catalysts, demonstrated by experiments. Next, we used SABER to search for naturally existing active sites in the PDB with catalytic groups similar to those present in the designed Kemp elimination enzyme KE07. From over 2000 geometric matches to the KE07 active site, SABER identified 23 matches that corresponded to residues from known active sites. The best of these matches, with a 0.28 Å catalytic atom RMSD to KE07, was then redesigned to be compatible with the Kemp elimination using RosettaDesign. We also used SABER to search for potential Kemp eliminases using a theozyme predicted to provide a greater rate acceleration than the active site of KE07, and used Rosetta to create a design based on the proteins identified. PMID:22492397

SABER: a computational method for identifying active sites for new reactions.

PubMed

Nosrati, Geoffrey R; Houk, K N

2012-05-01

A software suite, SABER (Selection of Active/Binding sites for Enzyme Redesign), has been developed for the analysis of atomic geometries in protein structures, using a geometric hashing algorithm (Barker and Thornton, Bioinformatics 2003;19:1644-1649). SABER is used to explore the Protein Data Bank (PDB) to locate proteins with a specific 3D arrangement of catalytic groups to identify active sites that might be redesigned to catalyze new reactions. As a proof-of-principle test, SABER was used to identify enzymes that have the same catalytic group arrangement present in o-succinyl benzoate synthase (OSBS). Among the highest-scoring scaffolds identified by the SABER search for enzymes with the same catalytic group arrangement as OSBS were L-Ala D/L-Glu epimerase (AEE) and muconate lactonizing enzyme II (MLE), both of which have been redesigned to become effective OSBS catalysts, demonstrated by experiments. Next, we used SABER to search for naturally existing active sites in the PDB with catalytic groups similar to those present in the designed Kemp elimination enzyme KE07. From over 2000 geometric matches to the KE07 active site, SABER identified 23 matches that corresponded to residues from known active sites. The best of these matches, with a 0.28 Å catalytic atom RMSD to KE07, was then redesigned to be compatible with the Kemp elimination using RosettaDesign. We also used SABER to search for potential Kemp eliminases using a theozyme predicted to provide a greater rate acceleration than the active site of KE07, and used Rosetta to create a design based on the proteins identified. Copyright © 2012 The Protein Society.

Hand interception of occluded motion in humans: a test of model-based vs. on-line control.

PubMed

La Scaleia, Barbara; Zago, Myrka; Lacquaniti, Francesco

2015-09-01

Two control schemes have been hypothesized for the manual interception of fast visual targets. In the model-free on-line control, extrapolation of target motion is based on continuous visual information, without resorting to physical models. In the model-based control, instead, a prior model of target motion predicts the future spatiotemporal trajectory. To distinguish between the two hypotheses in the case of projectile motion, we asked participants to hit a ball that rolled down an incline at 0.2 g and then fell in air at 1 g along a parabola. By varying starting position, ball velocity and trajectory differed between trials. Motion on the incline was always visible, whereas parabolic motion was either visible or occluded. We found that participants were equally successful at hitting the falling ball in both visible and occluded conditions. Moreover, in different trials the intersection points were distributed along the parabolic trajectories of the ball, indicating that subjects were able to extrapolate an extended segment of the target trajectory. Remarkably, this trend was observed even at the very first repetition of movements. These results are consistent with the hypothesis of model-based control, but not with on-line control. Indeed, ball path and speed during the occlusion could not be extrapolated solely from the kinematic information obtained during the preceding visible phase. The only way to extrapolate ball motion correctly during the occlusion was to assume that the ball would fall under gravity and air drag when hidden from view. Such an assumption had to be derived from prior experience. Copyright © 2015 the American Physiological Society.

'Unconventional' coordination chemistry by metal chelating fragments in a metalloprotein active site.

PubMed

Martin, David P; Blachly, Patrick G; Marts, Amy R; Woodruff, Tessa M; de Oliveira, César A F; McCammon, J Andrew; Tierney, David L; Cohen, Seth M

2014-04-09

The binding of three closely related chelators: 5-hydroxy-2-methyl-4H-pyran-4-thione (allothiomaltol, ATM), 3-hydroxy-2-methyl-4H-pyran-4-thione (thiomaltol, TM), and 3-hydroxy-4H-pyran-4-thione (thiopyromeconic acid, TPMA) to the active site of human carbonic anhydrase II (hCAII) has been investigated. Two of these ligands display a monodentate mode of coordination to the active site Zn(2+) ion in hCAII that is not recapitulated in model complexes of the enzyme active site. This unprecedented binding mode in the hCAII-thiomaltol complex has been characterized by both X-ray crystallography and X-ray spectroscopy. In addition, the steric restrictions of the active site force the ligands into a 'flattened' mode of coordination compared with inorganic model complexes. This change in geometry has been shown by density functional computations to significantly decrease the strength of the metal-ligand binding. Collectively, these data demonstrate that the mode of binding by small metal-binding groups can be significantly influenced by the protein active site. Diminishing the strength of the metal-ligand bond results in unconventional modes of metal coordination not found in typical coordination compounds or even carefully engineered active site models, and understanding these effects is critical to the rational design of inhibitors that target clinically relevant metalloproteins.

Enhanced enzyme kinetic stability by increasing rigidity within the active site.

PubMed

Xie, Yuan; An, Jiao; Yang, Guangyu; Wu, Geng; Zhang, Yong; Cui, Li; Feng, Yan

2014-03-14

Enzyme stability is an important issue for protein engineers. Understanding how rigidity in the active site affects protein kinetic stability will provide new insight into enzyme stabilization. In this study, we demonstrated enhanced kinetic stability of Candida antarctica lipase B (CalB) by mutating the structurally flexible residues within the active site. Six residues within 10 Å of the catalytic Ser(105) residue with a high B factor were selected for iterative saturation mutagenesis. After screening 2200 colonies, we obtained the D223G/L278M mutant, which exhibited a 13-fold increase in half-life at 48 °C and a 12 °C higher T50(15), the temperature at which enzyme activity is reduced to 50% after a 15-min heat treatment. Further characterization showed that global unfolding resistance against both thermal and chemical denaturation also improved. Analysis of the crystal structures of wild-type CalB and the D223G/L278M mutant revealed that the latter formed an extra main chain hydrogen bond network with seven structurally coupled residues within the flexible α10 helix that are primarily involved in forming the active site. Further investigation of the relative B factor profile and molecular dynamics simulation confirmed that the enhanced rigidity decreased fluctuation of the active site residues at high temperature. These results indicate that enhancing the rigidity of the flexible segment within the active site may provide an efficient method for improving enzyme kinetic stability.

GASS-WEB: a web server for identifying enzyme active sites based on genetic algorithms.

PubMed

Moraes, João P A; Pappa, Gisele L; Pires, Douglas E V; Izidoro, Sandro C

2017-07-03

Enzyme active sites are important and conserved functional regions of proteins whose identification can be an invaluable step toward protein function prediction. Most of the existing methods for this task are based on active site similarity and present limitations including performing only exact matches on template residues, template size restraints, despite not being capable of finding inter-domain active sites. To fill this gap, we proposed GASS-WEB, a user-friendly web server that uses GASS (Genetic Active Site Search), a method based on an evolutionary algorithm to search for similar active sites in proteins. GASS-WEB can be used under two different scenarios: (i) given a protein of interest, to match a set of specific active site templates; or (ii) given an active site template, looking for it in a database of protein structures. The method has shown to be very effective on a range of experiments and was able to correctly identify >90% of the catalogued active sites from the Catalytic Site Atlas. It also managed to achieve a Matthew correlation coefficient of 0.63 using the Critical Assessment of protein Structure Prediction (CASP 10) dataset. In our analysis, GASS was ranking fourth among 18 methods. GASS-WEB is freely available at http://gass.unifei.edu.br/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Patent foramen ovale closure with GORE HELEX or CARDIOFORM Septal Occluder vs. antiplatelet therapy for reduction of recurrent stroke or new brain infarct in patients with prior cryptogenic stroke: Design of the randomized Gore REDUCE Clinical Study.

PubMed

Kasner, Scott E; Thomassen, Lars; Søndergaard, Lars; Rhodes, John F; Larsen, Coby C; Jacobson, Joth

2017-12-01

Rationale The utility of patent foramen ovale (PFO) closure for secondary prevention in patients with prior cryptogenic stroke is uncertain despite multiple randomized trials completed to date. Aims The Gore REDUCE Clinical Study (REDUCE) aims to establish superiority of patent foramen ovale closure in conjunction with antiplatelet therapy over antiplatelet therapy alone in reducing the risk of recurrent clinical ischemic stroke or new silent brain infarct in patients who have had a cryptogenic stroke. Methods and design This controlled, open-label trial randomized 664 subjects with cryptogenic stroke at 63 multinational sites in a 2:1 ratio to either antiplatelet therapy plus patent foramen ovale closure (with GORE® HELEX® Septal Occluder or GORE® CARDIOFORM Septal Occluder) or antiplatelet therapy alone. Subjects will be prospectively followed for up to five years. Neuroimaging is required for all subjects at baseline and at two years or study exit. Study outcomes The two co-primary endpoints for the study are freedom from recurrent clinical ischemic stroke through at least 24 months post-randomization and incidence of new brain infarct (defined as clinical ischemic stroke or silent brain infarct) through 24 months. The primary analyses are an unadjusted log-rank test and a binomial test of subject-based proportions, respectively, both on the intent-to-treat population, with adjustment for testing multiplicity. Discussion The REDUCE trial aims to target a patient population with truly cryptogenic strokes. Medical therapy is limited to antiplatelet agents in both arms thereby reducing confounding. The trial should determine whether patent foramen ovale closure with the Gore septal occluders is safe and more effective than medical therapy alone for the prevention of recurrent clinical ischemic stroke or new silent brain infarct; the neuroimaging data will provide an opportunity to further support the proof of concept. The main results are anticipated in 2017

Thulium fiber laser recanalization of occluded ventricular catheters in an ex vivo tissue model

NASA Astrophysics Data System (ADS)

Hutchens, Thomas C.; Gonzalez, David A.; Hardy, Luke A.; McLanahan, C. Scott; Fried, Nathaniel M.

2017-04-01

Hydrocephalus is a chronic medical condition that occurs in individuals who are unable to reabsorb cerebrospinal fluid (CSF) created within the ventricles of the brain. Treatment requires excess CSF to be diverted from the ventricles to another part of the body, where it can be returned to the vascular system via a shunt system beginning with a catheter within the ventricle. Catheter failures due to occlusion by brain tissues commonly occur and require surgical replacement of the catheter. In this preliminary study, minimally invasive clearance of occlusions is explored using an experimental thulium fiber laser (TFL), with comparison to a conventional holmium: yttrium aluminium garnet (YAG) laser. The TFL utilizes smaller optical fibers (<200-μm OD) compared with holmium laser (>450-μm OD), providing critical extra cross-sectional space within the 1.2-mm-inner-diameter ventricular catheter for simultaneous application of an endoscope for image guidance and a saline irrigation tube for visibility and safety. TFL ablation rates using 100-μm core fiber, 33-mJ pulse energy, 500-μs pulse duration, and 20- to 200-Hz pulse rates were compared to holmium laser using a 270-μm core fiber, 325-mJ, 300-μs, and 10 Hz. A tissue occluded catheter model was prepared using coagulated egg white within clear silicone tubing. An optimal TFL pulse rate of 50 Hz was determined, with an ablation rate of 150 μm/s and temperature rise outside the catheter of ˜10°C. High-speed camera images were used to explore the mechanism for removal of occlusions. Image guidance using a miniature, 0.7-mm outer diameter, 10,000 pixel endoscope was explored to improve procedure safety. With further development, simultaneous application of TFL with small fibers, miniature endoscope for image guidance, and irrigation tube for removal of tissue debris may provide a safe, efficient, and minimally invasive method of clearing occluded catheters in the treatment of hydrocephalus.

Structural Basis for the Kexin-like Serine Protease from Aeromonas sobria as Sepsis-causing Factor*

PubMed Central

Kobayashi, Hidetomo; Utsunomiya, Hiroko; Yamanaka, Hiroyasu; Sei, Yoshihisa; Katunuma, Nobuhiko; Okamoto, Keinosuke; Tsuge, Hideaki

2009-01-01

The anaerobic bacterium Aeromonas sobria is known to cause potentially lethal septic shock. We recently proposed that A. sobria serine protease (ASP) is a sepsis-related factor that induces vascular leakage, reductions in blood pressure via kinin release, and clotting via activation of prothrombin. ASP preferentially cleaves peptide bonds that follow dibasic amino acid residues, as do Kex2 (Saccharomyces cerevisiae serine protease) and furin, which are representative kexin family proteases. Here, we revealed the crystal structure of ASP at 1.65 Å resolution using the multiple isomorphous replacement method with anomalous scattering. Although the overall structure of ASP resembles that of Kex2, it has a unique extra occluding region close to its active site. Moreover, we found that a nicked ASP variant is cleaved within the occluding region. Nicked ASP shows a greater ability to cleave small peptide substrates than the native enzyme. On the other hand, the cleavage pattern for prekallikrein differs from that of ASP, suggesting the occluding region is important for substrate recognition. The extra occluding region of ASP is unique and could serve as a useful target to facilitate development of novel antisepsis drugs. PMID:19654332

Long Term Effects of Percutaneous Coronary Intervention of the Totally Occluded Infarct-Related Artery in the Subacute Phase after Myocardial Infarction

PubMed Central

Hochman, Judith S; Reynolds, Harmony R; Džavík, Vladimír; Buller, Christopher E; Ruzyllo, Witold; Sadowski, Zygmunt P; Maggioni, Aldo P; Carvalho, Antonio C; Rankin, James M.; White, Harvey D.; Goldberg, Suzanne; Forman, Sandra A; Mark, Daniel B; Lamas, Gervasio A

2011-01-01

Background Despite observations suggesting a benefit for late opening of occluded infarct-related arteries (IRA) post-myocardial infarction (MI), the Occluded Artery Trial (OAT) demonstrated no reduction in the composite of death, reinfarction and class IV heart failure (HF) over 2.9-yearmean follow-up. Follow-up was extended to determine whether late trends would favor either treatment group. Methods and Results OAT randomized 2201 stable patients with IRA occlusion >24hours (calendar days3-28) after MI. Severe inducible ischemia, rest angina, class III-IV HF and 3-vessel/left main disease were excluded. We conducted extended followed up of enrolled patients for an additional 3 years for the primary endpoint and angina (6-year median survivor follow up, longest 9 years, 12,234 patient-years).Rates of the primary endpoint (HR 1.06, 95% CI 0.88-1.28), fatal and nonfatal MI (HR 1.25, 95% CI 0.89-1.75), death and class IV HF were similar for PCI vs. MED groups. No interaction between baseline characteristics and treatment group on outcomes were observed. The vast majority of patients at each follow-up visit did not report angina. There was less angina in the PCI group through early in follow-up; by 3 years the between group difference was consistently <4 patients per 100 treated and not significantly different though there was a trend toward less angina in the PCI group at 3 and 5 years. The 7-year rate of PCI of the IRA during follow up was 11.1% for the PCI group compared to 14.7% for the MED group (HR 0.79, 95% CI 0.61-1.01. p=0.06). Conclusions Extended follow up of the OAT cohort provides robust evidence for no reduction of long-term rates of clinical events after routine PCI in stable patients with an occluded IRA and without severe inducible ischemia in the subacute phase post-MI. PMID:22025606

Facebook, Twitter Activities Sites, Location and Students' Interest in Learning

ERIC Educational Resources Information Center

Igbo, J. N.; Ezenwaji, Ifeyinwa; Ajuziogu, Christiana U.

2018-01-01

This study was carried out to ascertain the influence of social networking sites activities (twitter and Facebook) on secondary school students' interest in learning It also considered the impact of these social networking sites activities on location of the students. Two research questions and two null hypotheses guided the study. Mean and…

Particle Filtering with Region-based Matching for Tracking of Partially Occluded and Scaled Targets*

PubMed Central

Nakhmani, Arie; Tannenbaum, Allen

2012-01-01

Visual tracking of arbitrary targets in clutter is important for a wide range of military and civilian applications. We propose a general framework for the tracking of scaled and partially occluded targets, which do not necessarily have prominent features. The algorithm proposed in the present paper utilizes a modified normalized cross-correlation as the likelihood for a particle filter. The algorithm divides the template, selected by the user in the first video frame, into numerous patches. The matching process of these patches by particle filtering allows one to handle the target’s occlusions and scaling. Experimental results with fixed rectangular templates show that the method is reliable for videos with nonstationary, noisy, and cluttered background, and provides accurate trajectories in cases of target translation, scaling, and occlusion. PMID:22506088

Suppression of Peripheral Sympathetic Activity Underlies Protease-Activated Receptor 2-Mediated Hypotension

PubMed Central

Kim, Young-Hwan; Ahn, Duck-Sun; Joeng, Ji-Hyun

2014-01-01

Protease-activated receptor (PAR)-2 is expressed in endothelial cells and vascular smooth muscle cells. It plays a crucial role in regulating blood pressure via the modulation of peripheral vascular tone. Although some reports have suggested involvement of a neurogenic mechanism in PAR-2-induced hypotension, the accurate mechanism remains to be elucidated. To examine this possibility, we investigated the effect of PAR-2 activation on smooth muscle contraction evoked by electrical field stimulation (EFS) in the superior mesenteric artery. In the present study, PAR-2 agonists suppressed neurogenic contractions evoked by EFS in endothelium-denuded superior mesenteric arterial strips but did not affect contraction elicited by the external application of noradrenaline (NA). However, thrombin, a potent PAR-1 agonist, had no effect on EFS-evoked contraction. Additionally, ω-conotoxin GVIA (CgTx), a selective N-type Ca2+ channel (ICa-N) blocker, significantly inhibited EFS-evoked contraction, and this blockade almost completely occluded the suppression of EFS-evoked contraction by PAR-2 agonists. Finally, PAR-2 agonists suppressed the EFS-evoked overflow of NA in endothelium-denuded rat superior mesenteric arterial strips and this suppression was nearly completely occluded by ω-CgTx. These results suggest that activation of PAR-2 may suppress peripheral sympathetic outflow by modulating activity of ICa-N which are located in peripheral sympathetic nerve terminals, which results in PAR-2-induced hypotension. PMID:25598663

Active Site Hydrophobicity and the Convergent Evolution of Paraoxonase Activity in Structurally Divergent Enzymes: The Case of Serum Paraoxonase 1

PubMed Central

2016-01-01

Serum paraoxonase 1 (PON1) is a native lactonase capable of promiscuously hydrolyzing a broad range of substrates, including organophosphates, esters, and carbonates. Structurally, PON1 is a six-bladed β-propeller with a flexible loop (residues 70–81) covering the active site. This loop contains a functionally critical Tyr at position 71. We have performed detailed experimental and computational analyses of the role of selected Y71 variants in the active site stability and catalytic activity in order to probe the role of Y71 in PON1’s lactonase and organophosphatase activities. We demonstrate that the impact of Y71 substitutions on PON1’s lactonase activity is minimal, whereas the kcat for the paraoxonase activity is negatively perturbed by up to 100-fold, suggesting greater mutational robustness of the native activity. Additionally, while these substitutions modulate PON1’s active site shape, volume, and loop flexibility, their largest effect is in altering the solvent accessibility of the active site by expanding the active site volume, allowing additional water molecules to enter. This effect is markedly more pronounced in the organophosphatase activity than the lactonase activity. Finally, a detailed comparison of PON1 to other organophosphatases demonstrates that either a similar “gating loop” or a highly buried solvent-excluding active site is a common feature of these enzymes. We therefore posit that modulating the active site hydrophobicity is a key element in facilitating the evolution of organophosphatase activity. This provides a concrete feature that can be utilized in the rational design of next-generation organophosphate hydrolases that are capable of selecting a specific reaction from a pool of viable substrates. PMID:28026940

Active Site Hydrophobicity and the Convergent Evolution of Paraoxonase Activity in Structurally Divergent Enzymes: The Case of Serum Paraoxonase 1.

PubMed

Blaha-Nelson, David; Krüger, Dennis M; Szeler, Klaudia; Ben-David, Moshe; Kamerlin, Shina Caroline Lynn

2017-01-25

Serum paraoxonase 1 (PON1) is a native lactonase capable of promiscuously hydrolyzing a broad range of substrates, including organophosphates, esters, and carbonates. Structurally, PON1 is a six-bladed β-propeller with a flexible loop (residues 70-81) covering the active site. This loop contains a functionally critical Tyr at position 71. We have performed detailed experimental and computational analyses of the role of selected Y71 variants in the active site stability and catalytic activity in order to probe the role of Y71 in PON1's lactonase and organophosphatase activities. We demonstrate that the impact of Y71 substitutions on PON1's lactonase activity is minimal, whereas the k cat for the paraoxonase activity is negatively perturbed by up to 100-fold, suggesting greater mutational robustness of the native activity. Additionally, while these substitutions modulate PON1's active site shape, volume, and loop flexibility, their largest effect is in altering the solvent accessibility of the active site by expanding the active site volume, allowing additional water molecules to enter. This effect is markedly more pronounced in the organophosphatase activity than the lactonase activity. Finally, a detailed comparison of PON1 to other organophosphatases demonstrates that either a similar "gating loop" or a highly buried solvent-excluding active site is a common feature of these enzymes. We therefore posit that modulating the active site hydrophobicity is a key element in facilitating the evolution of organophosphatase activity. This provides a concrete feature that can be utilized in the rational design of next-generation organophosphate hydrolases that are capable of selecting a specific reaction from a pool of viable substrates.

Characterization of the active site properties of CYP4F12.

PubMed

Eksterowicz, John; Rock, Dan A; Rock, Brooke M; Wienkers, Larry C; Foti, Robert S

2014-10-01

Cytochrome P450 4F12 is a drug-metabolizing enzyme that is primarily expressed in the liver, kidney, colon, small intestine, and heart. The properties of CYP4F12 that may impart an increased catalytic selectivity (decreased promiscuity) were explored through in vitro metabolite elucidation, kinetic isotope effect experiments, and computational modeling of the CYP4F12 active site. By using astemizole as a probe substrate for CYP4F12 and CYP3A4, it was observed that although CYP4F12 favored astemizole O-demethylation as the primary route of metabolism, CYP3A4 was capable of metabolizing astemizole at multiple sites on the molecule. Deuteration of astemizole at the site of O-demethylation resulted in an isotope effect of 7.1 as well as an 8.3-fold decrease in the rate of clearance for astemizole by CYP4F12. Conversely, although an isotope effect of 3.8 was observed for the formation of the O-desmethyl metabolite when deuterated astemizole was metabolized by CYP3A4, there was no decrease in the clearance of astemizole. Development of a homology model of CYP4F12 based on the crystal structure of cytochrome P450 BM3 predicted an active site volume for CYP4F12 that was approximately 76% of the active site volume of CYP3A4. As predicted, multiple favorable binding orientations were available for astemizole docked into the active site of CYP3A4, but only a single binding orientation with the site of O-demethylation oriented toward the heme was identified for CYP4F12. Overall, it appears that although CYP4F12 may be capable of binding similar ligands to other cytochrome P450 enzymes such as CYP3A4, the ability to achieve catalytically favorable orientations may be inherently more difficult because of the increased steric constraints of the CYP4F12 active site. Copyright © 2014 by The American Society for Pharmacology and Experimental Therapeutics.

Real life identification of partially occluded weapons in video frames

NASA Astrophysics Data System (ADS)

Hempelmann, Christian F.; Arslan, Abdullah N.; Attardo, Salvatore; Blount, Grady P.; Sirakov, Nikolay M.

2016-05-01

We empirically test the capacity of an improved system to identify not just images of individual guns, but partially occluded guns and their parts appearing in a videoframe. This approach combines low-level geometrical information gleaned from the visual images and high-level semantic information stored in an ontology enriched with meronymic part-whole relations. The main improvements of the system are handling occlusion, new algorithms, and an emerging meronomy. Well-known and commonly deployed in ontologies, actual meronomies need to be engineered and populated with unique solutions. Here, this includes adjacency of weapon parts and essentiality of parts to the threat of and the diagnosticity for a weapon. In this study video sequences are processed frame by frame. The extraction method separates colors and removes the background. Then image subtraction of the next frame determines moving targets, before morphological closing is applied to the current frame in order to clean up noise and fill gaps. Next, the method calculates for each object the boundary coordinates and uses them to create a finite numerical sequence as a descriptor. Parts identification is done by cyclic sequence alignment and matching against the nodes of the weapons ontology. From the identified parts, the most-likely weapon will be determined by using the weapon ontology.

Deletion of loop fragment adjacent to active site diminishes the stability and activity of exo-inulinase.

PubMed

Arjomand, Maryam Rezaei; Habibi-Rezaei, Mehran; Ahmadian, Gholamreza; Hassanzadeh, Malihe; Karkhane, Ali Asghar; Asadifar, Mandana; Amanlou, Massoud

2016-11-01

Inulinases are classified as hydrolases and widely used in the food and medical industries. Here, we report the deletion of a six-membered adjacent active site loop fragment ( 74 YGSDVT 79 sequence) from third Ω-loop of the exo-inulinase containing aspartate residue from Aspergillus niger to study its structural and functional importance. Site-directed mutagenesis was used to create the mutant of the exo-inulinase (Δ6SL). To investigate the stability of the region spanning this loop, MD simulations were performed 80ns for 20-85 residues. Molecular docking was performed to compare the interactions in the active sites of enzymes with fructose as a ligand. Accordingly, the functional thermostability of the exo-inulinase was significantly decreased upon loop fragment deletion. Evaluation of the kinetics parameters (V max , K m , k cat and, k cat /K m ) and activation energy (E a ) of the catalysis of enzymes indicated the importance of the deleted sequence on the catalytic performance of the enzyme. In conclusion, six-membered adjacent active site loop fragment not only plays a crucial role in the stability of the enzyme, but also it involves in the enzyme catalysis through lowering the activation energy of the catalysis and effective improving the catalytic performance. Copyright © 2016. Published by Elsevier B.V.

The Crystal Structure of a Quercetin 2,3-Dioxygenase from Bacillus subtilis Suggests Modulation of Enzyme Activity by a Change in the Metal Ion at the Active Site(s)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gopal, B.; Madan, Lalima L.; Betz, Stephen F.

2010-11-10

Common structural motifs, such as the cupin domains, are found in enzymes performing different biochemical functions while retaining a similar active site configuration and structural scaffold. The soil bacterium Bacillus subtilis has 20 cupin genes (0.5% of the total genome) with up to 14% of its genes in the form of doublets, thus making it an attractive system for studying the effects of gene duplication. There are four bicupins in B. subtilis encoded by the genes yvrK, yoaN, yxaG, and ywfC. The gene products of yvrK and yoaN function as oxalate decarboxylases with a manganese ion at the active site(s),more » whereas YwfC is a bacitracin synthetase. Here we present the crystal structure of YxaG, a novel iron-containing quercetin 2,3-dioxygenase with one active site in each cupin domain. Yxag is a dimer, both in solution and in the crystal. The crystal structure shows that the coordination geometry of the Fe ion is different in the two active sites of YxaG. Replacement of the iron at the active site with other metal ions suggests modulation of enzymatic activity in accordance with the Irving-Williams observation on the stability of metal ion complexes. This observation, along with a comparison with the crystal structure of YvrK determined recently, has allowed for a detailed structure-function analysis of the active site, providing clues to the diversification of function in the bicupin family of proteins.« less

Transcatheter closure of a small atrial septal defect with an Amplatzer™ patent foramen ovale occluder in a working dog with cyanosis and exercise intolerance at high altitude.

PubMed

Shelden, A; Wesselowski, S; Gordon, S G; Saunders, A B

2017-12-01

A 6.5-year-old male Border Collie presented for transcatheter closure of an atrial septal defect due to exercise intolerance and cyanosis while working and training at altitude. A small, left-to-right shunting secundum atrial septal defect was confirmed with no evidence of significant right-sided volume overload. Pulmonary hypertension with subsequent right-to-left interatrial shunting occurring during exercise at high altitude was suspected and prompted the closure of the defect due to the dog's continued athletic requirements. The anatomy of the defect prompted use of a patent foramen ovale occluder rather than an atrial septal defect occluder, which was deployed using a combination of fluoroscopic and transesophageal echocardiographic guidance. The owner did not report continued exercise intolerance or cyanosis and the dog's lifestyle and residence at altitude was unchanged. Copyright © 2017 Elsevier B.V. All rights reserved.

Production of Carbon Occluded in Phytolith Is Season-Dependent in a Bamboo Forest in Subtropical China

PubMed Central

Huang, Zhang-Ting; Jiang, Pei-Kun; Chang, Scott Xiaochuan; Zhang, Yan; Ying, Yu-Qi

2014-01-01

Carbon (C) occluded in phytolith (PhytOC) is a stable form of C; when PhytOC is returned to the soil through litterfall it is stored in the soil which can be an effective way for long-term C sequestration. However, few estimates on the rate of PhytOC input to the soil are available. To better understand the seasonal dynamics of PhytOC production and the annual rate of stable C sequestration through PhytOC input, we quantified the monthly litterfall, phytolith and PhytOC return to the soil over a year in a typical Lei bamboo (Phyllostachys praecox) forest in subtropical China. The monthly litterfall ranged between 14.81 and 131.18 g m−2, and the phytolith concentration in the monthly litterfall samples ranged between 47.21 and 101.68 g kg−1 of litter mass, with the PhytOC concentration in the phytolith ranged between 29.4 and 44.9 g kg−1 of phytolith, equivalent to 1.8–3.6 g kg−1 of PhytOC in the litterfall (based on litterfall dry mass). The amount of phytolith input to the soil system was 292.21±69.12 (mean±SD) kg ha−1 yr−1, sequestering 41.45±9.32 kg CO2−e ha−1 yr−1 of C in the studied Lei bamboo forest. This rate of C sequestration through the formation of PhytOC found in this study falls within the range of rates for other grass-type species reported in the literature. We conclude that return of C occluded in phytolith to the soil can be a substantial source of stable soil C and finding means to increase PhytOC storage in the soil should be able to play a significant role in mitigating the rapidly increasing atmospheric CO2 concentration. PMID:25188462

Aspirex Thrombectomy in Occluded Dialysis Access: A Retrospective Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dyer, Jules, E-mail: Jules.Dyer@nhs.net; Rosa, Joao; Chachlani, Menka

PurposeThis study is the first to present the outcomes of the Straub Aspirex device for the salvage of occluded renal dialysis access fistulae.Materials and MethodsThis is a retrospective study, using data from the Renal Unit and Radiology Department database. It included all the patients between 2010 and 2014 who underwent percutaneous mechanical thrombectomy (PMT) treated by JD. Aspirex is an over-the-wire, 6–10 French catheter within which is a rapidly rotating helix which draws thrombus into a window near the tip which it then macerates and removes. Access survival was assessed using the Kaplan–Meier method, and multi-variant analysis was performed usingmore » the Cox proportional hazards model. Significance was considered if p < 0.05.ResultsA total of 27 procedures were performed for 19 patients. 13 had autologous arterio-venous fistulae, and 14 had synthetic (PTFE) arterio-venous grafts. 15 were males, 4 females. 100 % of the patients successfully had a channel of thrombus removed. This resulted in an 81.5 % initial clinical success, with primary patency rates of 53.6, 44.3 and 33 % by days 30, 90 and 480, respectively, without significant difference of any analysed covariates. No major complication (pulmonary embolus, paradoxical cerebral infarction, limb ischaemia or significant haemorrhage) occurred.ConclusionAspirex has rates of patency and complication similar to other PMT devices. No covariant studied affected outcome.« less

A hybrid QM/MM simulation study of intramolecular proton transfer in the pyridoxal 5'-phosphate in the active site of transaminase: influence of active site interaction on proton transfer.

PubMed

Dutta Banik, Sindrila; Chandra, Amalendu

2014-09-25

Pyridoxal 5'-phosphate (PLP) Schiff base, a versatile cofactor, exhibits a tautomeric equilibrium that involves an intramolecular proton transfer between the N-protonated zwitterionic ketoenamine tautomer and the O-protonated covalent enolimine tautomer. It has been postulated that for the catalytic activity, the PLP has to be in the zwitterionic ketoenamine tautomeric form. However, the exact position of the tautomeric equilibrium of Schiff base in the active site of PLP-dependent enzyme is not known yet. In the present work, we investigated the tautomeric equilibrium for the external aldimine state of PLP aspartate (PLP-Asp) Schiff base in the active site of aspartate aminotransferase (AspAT) using combined quantum mechanical and molecular mechanical simulations. The main focus of the present study is to analyze the factors that control the tautomeric equilibrium in the active sites of various PLP-dependent enzymes. The results show that the ketoenamine tautomer is more preferred than the enolimine tautomer both in the gas and aqueous phases as well as in the active site of AspAT. Current simulations show that the active site of AspAT is more suitable for the ketoenamine tautomer compared to the enolimine tautomer. Interestingly, the Tyr225 acts as a proton donor to the phenolic oxygen in the ketoenamine tautomer, while in the covalent enolimine tautomer, it acts as a proton acceptor to the phenolic oxygen. Finally, the metadynamics study confirms this result. The calculated free energy barrier is about 7.5 kcal/mol. A comparative analysis of the microenvironment created by the active site residues of three different PLP-dependent enzymes (aspartate aminotransferase, Dopa decarboxylase, and Ala-racemase) has been carried out to understand the controlling factor(s) of the tautomeric equilibrium. The analysis shows that the intermolecular hydrogen bonding between active site residues and the phenolic oxygen of PLP shifts the tautomeric equilibrium toward the N

Community Update on Site Activities, July 19, 2013

EPA Pesticide Factsheets

In an effort to engage and inform community members interested in the New Bedford Harbor Superfund Site cleanup, EPA will be issuing periodic topic-based fact sheets that will provide background information and updates about ongoing activities.

Structural and Kinetic Analyses of Macrophage Migration Inhibitory Factor Active Site Interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Crichlow, G.; Lubetsky, J; Leng, L

Macrophage migration inhibitory factor (MIF) is a secreted protein expressed in numerous cell types that counters the antiinflammatory effects of glucocorticoids and has been implicated in sepsis, cancer, and certain autoimmune diseases. Interestingly, the structure of MIF contains a catalytic site resembling the tautomerase/isomerase sites of microbial enzymes. While bona fide physiological substrates remain unknown, model substrates have been identified. Selected compounds that bind in the tautomerase active site also inhibit biological functions of MIF. It had previously been shown that the acetaminophen metabolite, N-acetyl-p-benzoquinone imine (NAPQI), covalently binds to the active site of MIF. In this study, kinetic datamore » indicate that NAPQI inhibits MIF both covalently and noncovalently. The structure of MIF cocrystallized with NAPQI reveals that the NAPQI has undergone a chemical alteration forming an acetaminophen dimer (bi-APAP) and binds noncovalently to MIF at the mouth of the active site. We also find that the commonly used protease inhibitor, phenylmethylsulfonyl fluoride (PMSF), forms a covalent complex with MIF and inhibits the tautomerase activity. Crystallographic analysis reveals the formation of a stable, novel covalent bond for PMSF between the catalytic nitrogen of the N-terminal proline and the sulfur of PMSF with complete, well-defined electron density in all three active sites of the MIF homotrimer. Conclusions are drawn from the structures of these two MIF-inhibitor complexes regarding the design of novel compounds that may provide more potent reversible and irreversible inhibition of MIF.« less

Rac1 GTPase activates the WAVE regulatory complex through two distinct binding sites.

PubMed

Chen, Baoyu; Chou, Hui-Ting; Brautigam, Chad A; Xing, Wenmin; Yang, Sheng; Henry, Lisa; Doolittle, Lynda K; Walz, Thomas; Rosen, Michael K

2017-09-26

The Rho GTPase Rac1 activates the WAVE regulatory complex (WRC) to drive Arp2/3 complex-mediated actin polymerization, which underpins diverse cellular processes. Here we report the structure of a WRC-Rac1 complex determined by cryo-electron microscopy. Surprisingly, Rac1 is not located at the binding site on the Sra1 subunit of the WRC previously identified by mutagenesis and biochemical data. Rather, it binds to a distinct, conserved site on the opposite end of Sra1. Biophysical and biochemical data on WRC mutants confirm that Rac1 binds to both sites, with the newly identified site having higher affinity and both sites required for WRC activation. Our data reveal that the WRC is activated by simultaneous engagement of two Rac1 molecules, suggesting a mechanism by which cells may sense the density of active Rac1 at membranes to precisely control actin assembly.

Monocopper active site for partial methane oxidation in Cu-exchanged 8MR zeolites

DOE PAGES

Kulkarni, Ambarish R.; Zhao, Zhi -Jian; Siahrostami, Samira; ...

2016-08-17

Direct conversion of methane to methanol using oxygen is experiencing renewed interest owing to the availability of new natural gas resources. Copper-exchanged zeolites such as mordenite and ZSM-5 have shown encouraging results, and di- and tri-copper species have been suggested as active sites. Recently, small eight-membered ring (8MR) zeolites including SSZ-13, -16, and -39 have been shown to be active for methane oxidation, but the active sites and reaction mechanisms in these 8MR zeolites are not known. In this work, we use density functional theory (DFT) calculations to systematically evaluate monocopper species as active sites for the partial methane oxidationmore » reaction in Cu-exchanged SSZ-13. On the basis of kinetic and thermodynamic arguments, we suggest that [Cu IIOH] + species in the 8MR are responsible for the experimentally observed activity. Furthermore, our results successfully explain the available spectroscopic data and experimental observations including (i) the necessity of water for methanol extraction and (ii) the effect of Si/Al ratio on the catalyst activity. Monocopper species have not yet been suggested as an active site for the partial methane oxidation reaction, and our results suggest that [Cu IIOH] + active site may provide complementary routes for methane activation in zeolites in addition to the known [Cu–O–Cu] 2+ and Cu 3O 3 motifs.« less

Transcatheter closure of hemodynamic significant patent ductus arteriosus in 32 premature infants by amplatzer ductal occluder additional size-ADOIIAS.

PubMed

Morville, Patrice; Akhavi, Ahmad

2017-10-01

The advent of Amplatzer Duct Occluder II additional Size (ADOIIAS) provided the potential to close hemodynamic significant patent ductus arteriosus (HSPDA) and to analyze the feasibility, safety and efficacy of the device. Treatment of a patent ductus arteriosus (PDA) in very premature neonates is still a dilemma for the neonatalogist who has to consider its significance and has to choose among different treatment options. Because surgical ligation and medical therapy both have their drawbacks, interventional catheterization might provide an alternative means of closing HSPDA. Between September 2013 and June 2015, 32 premature infants with complications related to HSPDA defined by ultrasound (US) underwent transcatheter closure. The procedure was performed in the catheterization laboratory by venous cannulation without angiography. The position of the occluder was directed by X-ray and US. In particular we looked at procedural details, device size selection, complications, and short and mid-term outcomes. Thirty two premature infants, all of whom had clinical complications related to HSPDA, born at gestational ages ranging between 23.6 and 36 weeks (mean ± standard deviation 28 ± 3 weeks) underwent attempted transcatheter PDA closure using the ADOIIAS. Their mean age and weight at the time of procedure was 25 days (range 8-70 days) and 1373 g (range 680-2480 g), respectively. Ten infants weighed ≤1,000g. All ducts were tubular. The mean PDA and device waist diameters were 3.2 ± 0.6mm (range 2.2-4) and 4.4 ± 0.6 mm, respectively, and the mean PDA and device lengths 5.2 ± 2.0 mm (range 2-10) and 3.4 ± 1.3 mm. Median fluoroscopy and procedural times were 11 min (range 3-24) and 28 min (range 10-90), respectively. Complete closure was achieved in all but one patient. There was no device migration. A left pulmonary artery (LPA) obstruction developed in one patient. Five infants died. Four deaths were related to complications of

What Motivates Young Adults to Talk About Physical Activity on Social Network Sites?

PubMed

Zhang, Ni; Campo, Shelly; Yang, Jingzhen; Eckler, Petya; Snetselaar, Linda; Janz, Kathleen; Leary, Emily

2017-06-22

Electronic word-of-mouth on social network sites has been used successfully in marketing. In social marketing, electronic word-of-mouth about products as health behaviors has the potential to be more effective and reach more young adults than health education through traditional mass media. However, little is known about what motivates people to actively initiate electronic word-of-mouth about health behaviors on their personal pages or profiles on social network sites, thus potentially reaching all their contacts on those sites. This study filled the gap by applying a marketing theoretical model to explore the factors associated with electronic word-of-mouth on social network sites about leisure-time physical activity. A Web survey link was sent to undergraduate students at one of the Midwestern universities and 439 of them completed the survey. The average age of the 439 participants was 19 years (SD=1 year, range: 18-24). Results suggested that emotional engagement with leisure-time physical activity (ie, affective involvement in leisure-time physical activity) predicted providing relevant opinions or information on social network sites. Social network site users who perceived stronger ties with all their contacts were more likely to provide and seek leisure-time physical activity opinions and information. People who provided leisure-time physical activity opinions and information were more likely to seek opinions and information, and people who forwarded information about leisure-time physical activity were more likely to chat about it. This study shed light on the application of the electronic word-of-mouth theoretical framework in promoting health behaviors. The findings can also guide the development of future social marketing interventions using social network sites to promote leisure-time physical activity. ©Ni Zhang, Shelly Campo, Jingzhen Yang, Petya Eckler, Linda Snetselaar, Kathleen Janz, Emily Leary. Originally published in the Journal of Medical

What Motivates Young Adults to Talk About Physical Activity on Social Network Sites?

PubMed Central

Campo, Shelly; Yang, Jingzhen; Eckler, Petya; Snetselaar, Linda; Janz, Kathleen; Leary, Emily

2017-01-01

Background Electronic word-of-mouth on social network sites has been used successfully in marketing. In social marketing, electronic word-of-mouth about products as health behaviors has the potential to be more effective and reach more young adults than health education through traditional mass media. However, little is known about what motivates people to actively initiate electronic word-of-mouth about health behaviors on their personal pages or profiles on social network sites, thus potentially reaching all their contacts on those sites. Objective This study filled the gap by applying a marketing theoretical model to explore the factors associated with electronic word-of-mouth on social network sites about leisure-time physical activity. Methods A Web survey link was sent to undergraduate students at one of the Midwestern universities and 439 of them completed the survey. Results The average age of the 439 participants was 19 years (SD=1 year, range: 18-24). Results suggested that emotional engagement with leisure-time physical activity (ie, affective involvement in leisure-time physical activity) predicted providing relevant opinions or information on social network sites. Social network site users who perceived stronger ties with all their contacts were more likely to provide and seek leisure-time physical activity opinions and information. People who provided leisure-time physical activity opinions and information were more likely to seek opinions and information, and people who forwarded information about leisure-time physical activity were more likely to chat about it. Conclusions This study shed light on the application of the electronic word-of-mouth theoretical framework in promoting health behaviors. The findings can also guide the development of future social marketing interventions using social network sites to promote leisure-time physical activity. PMID:28642215

Corrosion Research And Web Site Activities

NASA Technical Reports Server (NTRS)

Heidersbach, Robert H.

2001-01-01

This report covers corrosion-related activities at the NASA Kennedy Space Center during the summer of 2000. The NASA Kennedy Space Center's corrosion web site, corrosion.ksc.nasa.gov, was updated with new information based on feedback over the past two years. The methodology for a two-year atmospheric exposure testing program to study the effectiveness of commercial chemicals sold for rinsing aircraft and other equipment was developed and some preliminary laboratory chemical analyses are presented.

Corrosion Research and Web Site Activities

NASA Technical Reports Server (NTRS)

Heidersbach, Robert H.

2002-01-01

This report covers corrosion-related activities at the NASA Kennedy Space Center during the summer of 2000. The NASA Kennedy Space Center's corrosion web site, corrosion.ksc.nasa.gov, was updated with new information based on feedback over the past two years. The methodology for a two-year atmospheric exposure testing program to study the effectiveness of commercial chemicals sold for rinsing aircraft and other equipment was developed and some preliminary laboratory chemical analyses are presented.

Channeling by Proximity: The Catalytic Advantages of Active Site Colocalization Using Brownian Dynamics.

PubMed

Bauler, Patricia; Huber, Gary; Leyh, Thomas; McCammon, J Andrew

2010-05-06

Nature often colocalizes successive steps in a metabolic pathway. Such organization is predicted to increase the effective concentration of pathway intermediates near their recipient active sites and to enhance catalytic efficiency. Here, the pathway of a two-step reaction is modeled using a simple spherical approximation for the enzymes and substrate particles. Brownian dynamics are used to simulate the trajectory of a substrate particle as it diffuses between the active site zones of two different enzyme spheres. The results approximate distances for the most effective reaction pathways, indicating that the most effective reaction pathway is one in which the active sites are closely aligned. However, when the active sites are too close, the ability of the substrate to react with the first enzyme was hindered, suggesting that even the most efficient orientations can be improved for a system that is allowed to rotate or change orientation to optimize the likelihood of reaction at both sites.

Cooperative activation of cardiac transcription through myocardin bridging of paired MEF2 sites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anderson, Courtney M.; Hu, Jianxin; Thomas, Reuben

2017-03-28

Enhancers frequently contain multiple binding sites for the same transcription factor. These homotypic binding sites often exhibit synergy, whereby the transcriptional output from two or more binding sites is greater than the sum of the contributions of the individual binding sites alone. Although this phenomenon is frequently observed, the mechanistic basis for homotypic binding site synergy is poorly understood. Here in this paper, we identify a bona fide cardiac-specific Prkaa2 enhancer that is synergistically activated by homotypic MEF2 binding sites. We show that two MEF2 sites in the enhancer function cooperatively due to bridging of the MEF2C-bound sites by themore » SAP domain-containing co-activator protein myocardin, and we show that paired sites buffer the enhancer from integration site-dependent effects on transcription in vivo. Paired MEF2 sites are prevalent in cardiac enhancers, suggesting that this might be a common mechanism underlying synergy in the control of cardiac gene expression in vivo.« less

Phosphorus Effects of Mesoporous Bioactive Glass on Occlude Exposed Dentin

PubMed Central

Chen, Wen-Cheng; Chen, Cheng-Hwei; Kung, Jung-Chang; Hsiao, Yu-Cheng; Shih, Chi-Jen; Chien, Chi-Sheng

2013-01-01

In recent studies, sealing of exposed dentinal tubules is generally considered as one of the most effective strategies to treat dentin hypersensitivity. Mesoporous bioactive glass (MBG) is a potential material for treating dentin hypersensitivity due to its highly specific areas for dissolution and re-precipitated reaction for reduction in dentin permeability. The groups of commercial products of PerioGlas®, synthetic MBG and MBG without phosphorus (MBGNP) were compared. The MBG and MBGNP powders were prepared by the sol-gel method and mixed with different calculated ratios of phosphoric acid (PA) and then was brushed onto dentin surfaces. We used X-ray diffractometer (XRD), scanning electronic microscope (SEM), and Fourier transform infrared spectroscopy (FTIR) to investigate the physiochemistry and the occlusion ability of dentinal tubules. The results showed that MBG paste mixed with PA solution has a better ability for occluding dentinal tubules than MBGNP; it has a short reaction time and good operability. The major crystallite phase of MBG agents was monocalcium phosphate monohydrate [Ca(H2PO4)2·H2O] in the early stages of the reactions. MBG pastes that were mixed with 30% and 40% PA had the ability to create excellent penetration depth greater than 80 μm. These agents have the potential to treat dentin hypersensitivity. PMID:28788393

Maturation of the [Ni-4Fe-4S] active site of carbon monoxide dehydrogenases.

PubMed

Merrouch, Mériem; Benvenuti, Martino; Lorenzi, Marco; Léger, Christophe; Fourmond, Vincent; Dementin, Sébastien

2018-02-14

Nickel-containing enzymes are diverse in terms of function and active site structure. In many cases, the biosynthesis of the active site depends on accessory proteins which transport and insert the Ni ion. We review and discuss the literature related to the maturation of carbon monoxide dehydrogenases (CODH) which bear a nickel-containing active site consisting of a [Ni-4Fe-4S] center called the C-cluster. The maturation of this center has been much less studied than that of other nickel-containing enzymes such as urease and NiFe hydrogenase. Several proteins present in certain CODH operons, including the nickel-binding proteins CooT and CooJ, still have unclear functions. We question the conception that the maturation of all CODH depends on the accessory protein CooC described as essential for nickel insertion into the active site. The available literature reveals biological variations in CODH active site biosynthesis.

CASPASE-9 CARD:CORE DOMAIN INTERACTIONS REQUIRE A PROPERLY-FORMED ACTIVE SITE

PubMed Central

Huber, Kristen L.; Serrano, Banyuhay P.; Hardy, Jeanne A.

2018-01-01

Caspase-9 is a critical factor in the initiation of apoptosis, and as a result is tightly regulated by a number of mechanisms. Caspase-9 contains a Caspase Activation and Recruitment Domain (CARD), which enables caspase-9 to form a tight interaction with the apoptosome, a heptameric activating platform. The caspase-9 CARD has been thought to be principally involved in recruitment to the apoptosome, but its roles outside this interaction have yet to be uncovered. In this work we show that the CARD is involved in physical interactions with the catalytic core of caspase-9 in the absence of the apoptosome; this interaction requires a properly formed caspase-9 active site. The active sites of caspases are composed of four extremely mobile loops. When the active-site loops are not properly ordered, the CARD and core domains of caspase-9 do not interact and behave independently, like loosely tethered beads. When the active-site loop bundle is properly ordered, the CARD domain interacts with the catalytic core, forming a single folding unit. Together these findings provide mechanistic insight into a new level of caspase-9 regulation, prompting speculation that the CARD may also play a role in the recruitment or recognition of substrate. PMID:29500231

Prediction of active sites of enzymes by maximum relevance minimum redundancy (mRMR) feature selection.

PubMed

Gao, Yu-Fei; Li, Bi-Qing; Cai, Yu-Dong; Feng, Kai-Yan; Li, Zhan-Dong; Jiang, Yang

2013-01-27

Identification of catalytic residues plays a key role in understanding how enzymes work. Although numerous computational methods have been developed to predict catalytic residues and active sites, the prediction accuracy remains relatively low with high false positives. In this work, we developed a novel predictor based on the Random Forest algorithm (RF) aided by the maximum relevance minimum redundancy (mRMR) method and incremental feature selection (IFS). We incorporated features of physicochemical/biochemical properties, sequence conservation, residual disorder, secondary structure and solvent accessibility to predict active sites of enzymes and achieved an overall accuracy of 0.885687 and MCC of 0.689226 on an independent test dataset. Feature analysis showed that every category of the features except disorder contributed to the identification of active sites. It was also shown via the site-specific feature analysis that the features derived from the active site itself contributed most to the active site determination. Our prediction method may become a useful tool for identifying the active sites and the key features identified by the paper may provide valuable insights into the mechanism of catalysis.

Active site densities, oxygen activation and adsorbed reactive oxygen in alcohol activation on npAu catalysts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Lu-Cun; Friend, C. M.; Fushimi, Rebecca

The activation of molecular O 2as well as the reactivity of adsorbed oxygen species is of central importance in aerobic selective oxidation chemistry on Au-based catalysts. Herein, we address the issue of O 2activation on unsupported nanoporous gold (npAu) catalysts by applying a transient pressure technique, a temporal analysis of products (TAP) reactor, to measure the saturation coverage of atomic oxygen, its collisional dissociation probability, the activation barrier for O 2dissociation, and the facility with which adsorbed O species activate methanol, the initial step in the catalytic cycle of esterification. The results from these experiments indicate that molecular O 2dissociationmore » is associated with surface silver, that the density of reactive sites is quite low, that adsorbed oxygen atoms do not spill over from the sites of activation onto the surrounding surface, and that methanol reacts quite facilely with the adsorbed oxygen atoms. In addition, the O species from O 2dissociation exhibits reactivity for the selective oxidation of methanol but not for CO. The TAP experiments also revealed that the surface of the npAu catalyst is saturated with adsorbed O under steady state reaction conditions, at least for the pulse reaction.« less

Active site densities, oxygen activation and adsorbed reactive oxygen in alcohol activation on npAu catalysts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Lu-Cun; Friend, C. M.; Fushimi, Rebecca

2016-01-01

The activation of molecular O 2as well as the reactivity of adsorbed oxygen species is of central importance in aerobic selective oxidation chemistry on Au-based catalysts. Herein, we address the issue of O 2activation on unsupported nanoporous gold (npAu) catalysts by applying a transient pressure technique, a temporal analysis of products (TAP) reactor, to measure the saturation coverage of atomic oxygen, its collisional dissociation probability, the activation barrier for O 2dissociation, and the facility with which adsorbed O species activate methanol, the initial step in the catalytic cycle of esterification. The results from these experiments indicate that molecular O 2dissociationmore » is associated with surface silver, that the density of reactive sites is quite low, that adsorbed oxygen atoms do not spill over from the sites of activation onto the surrounding surface, and that methanol reacts quite facilely with the adsorbed oxygen atoms. In addition, the O species from O 2dissociation exhibits reactivity for the selective oxidation of methanol but not for CO. The TAP experiments also revealed that the surface of the npAu catalyst is saturated with adsorbed O under steady state reaction conditions, at least for the pulse reaction.« less

Brownian aggregation rate of colloid particles with several active sites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nekrasov, Vyacheslav M.; Yurkin, Maxim A.; Chernyshev, Andrei V., E-mail: chern@ns.kinetics.nsc.ru

2014-08-14

We theoretically analyze the aggregation kinetics of colloid particles with several active sites. Such particles (so-called “patchy particles”) are well known as chemically anisotropic reactants, but the corresponding rate constant of their aggregation has not yet been established in a convenient analytical form. Using kinematic approximation for the diffusion problem, we derived an analytical formula for the diffusion-controlled reaction rate constant between two colloid particles (or clusters) with several small active sites under the following assumptions: the relative translational motion is Brownian diffusion, and the isotropic stochastic reorientation of each particle is Markovian and arbitrarily correlated. This formula was shownmore » to produce accurate results in comparison with more sophisticated approaches. Also, to account for the case of a low number of active sites per particle we used Monte Carlo stochastic algorithm based on Gillespie method. Simulations showed that such discrete model is required when this number is less than 10. Finally, we applied the developed approach to the simulation of immunoagglutination, assuming that the formed clusters have fractal structure.« less

Stepwise Loop Insertion Strategy for Active Site Remodeling to Generate Novel Enzyme Functions.

PubMed

Hoque, Md Anarul; Zhang, Yong; Chen, Liuqing; Yang, Guangyu; Khatun, Mst Afroza; Chen, Haifeng; Hao, Liu; Feng, Yan

2017-05-19

The remodeling of active sites to generate novel biocatalysts is an attractive and challenging task. We developed a stepwise loop insertion strategy (StLois), in which randomized residue pairs are inserted into active site loops. The phosphotriesterase-like lactonase from Geobacillus kaustophilus (GkaP-PLL) was used to investigate StLois's potential for changing enzyme function. By inserting six residues into active site loop 7, the best variant ML7-B6 demonstrated a 16-fold further increase in catalytic efficiency toward ethyl-paraoxon compared with its initial template, that is a 609-fold higher, >10 7 fold substrate specificity shift relative to that of wild-type lactonase. The remodeled variants displayed 760-fold greater organophosphate hydrolysis activity toward the organophosphates parathion, diazinon, and chlorpyrifos. Structure and docking computations support the source of notably inverted enzyme specificity. Considering the fundamental importance of active site loops, the strategy has potential for the rapid generation of novel enzyme functions by loop remodeling.

Orthogonal use of a human tRNA synthetase active site to achieve multifunctionality.

PubMed

Zhou, Quansheng; Kapoor, Mili; Guo, Min; Belani, Rajesh; Xu, Xiaoling; Kiosses, William B; Hanan, Melanie; Park, Chulho; Armour, Eva; Do, Minh-Ha; Nangle, Leslie A; Schimmel, Paul; Yang, Xiang-Lei

2010-01-01

Protein multifunctionality is an emerging explanation for the complexity of higher organisms. In this regard, aminoacyl tRNA synthetases catalyze amino acid activation for protein synthesis, but some also act in pathways for inflammation, angiogenesis and apoptosis. It is unclear how these multiple functions evolved and how they relate to the active site. Here structural modeling analysis, mutagenesis and cell-based functional studies show that the potent angiostatic, natural fragment of human tryptophanyl-tRNA synthetase (TrpRS) associates via tryptophan side chains that protrude from its cognate cellular receptor vascular endothelial cadherin (VE-cadherin). VE-cadherin's tryptophan side chains fit into the tryptophan-specific active site of the synthetase. Thus, specific side chains of the receptor mimic amino acid substrates and expand the functionality of the active site of the synthetase. We propose that orthogonal use of the same active site may be a general way to develop multifunctionality of human tRNA synthetases and other proteins.

In silico analysis of Pycnoporus cinnabarinus laccase active site with toxic industrial dyes.

PubMed

Prasad, Nirmal K; Vindal, Vaibhav; Narayana, Siva Lakshmi; Ramakrishna, V; Kunal, Swaraj Priyaranjan; Srinivas, M

2012-05-01

Laccases belong to multicopper oxidases, a widespread class of enzymes implicated in many oxidative functions in various industrial oxidative processes like production of fine chemicals to bioremediation of contaminated soil and water. In order to understand the mechanisms of substrate binding and interaction between substrates and Pycnoporus cinnabarinus laccase, a homology model was generated. The resulted model was further validated and used for docking studies with toxic industrial dyes- acid blue 74, reactive black 5 and reactive blue 19. Interactions of chemical mediators with the laccase was also examined. The docking analysis showed that the active site always cannot accommodate the dye molecules, due to constricted nature of the active site pocket and steric hindrance of the residues whereas mediators are relatively small and can easily be accommodated into the active site pocket, which, thereafter leads to the productive binding. The binding properties of these compounds along with identification of critical active site residues can be used for further site-directed mutagenesis experiments in order to identify their role in activity and substrate specificity, ultimately leading to improved mutants for degradation of these toxic compounds.

Thermodynamic compensation upon binding to exosite 1 and the active site of thrombin

PubMed Central

Treuheit, Nicholas A.; Beach, Muneera A.; Komives, Elizabeth A.

2011-01-01

Several lines of experimental evidence including amide exchange and NMR suggest that ligands binding to thrombin cause reduced backbone dynamics. Binding of the covalent inhibitor dPhe-Pro-Arg chloromethylketone to the active site serine, as well as non-covalent binding of a fragment of the regulatory protein, thrombomodulin, to exosite 1 on the back side of the thrombin molecule both cause reduced dynamics. However, the reduced dynamics do not appear to be accompanied by significant conformational changes. In addition, binding of ligands to the active site does not change the affinity of thrombomodulin fragments binding to exosite 1, however, the thermodynamic coupling between exosite 1 and the active site has not been fully explored. We present isothermal titration calorimetry experiments that probe changes in enthalpy and entropy upon formation of binary ligand complexes. The approach relies on stringent thrombin preparation methods and on the use of dansyl-L-arginine-(3-methyl-1,5-pantanediyl) amide and a DNA aptamer as ligands with ideal thermodynamic signatures for binding to the active site and to exosite 1. Using this approach, the binding thermodynamic signatures of each ligand alone as well as the binding signatures of each ligand when the other binding site was occupied were measured. Different exosite 1 ligands with widely varied thermodynamic signatures cause the same reduction in ΔH and a concomitantly lower entropy cost upon DAPA binding at the active site. The results suggest a general phenomenon of enthalpy-entropy compensation consistent with reduction of dynamics/increased folding of thrombin upon ligand binding to either the active site or to exosite 1. PMID:21526769

Thermodynamic compensation upon binding to exosite 1 and the active site of thrombin.

PubMed

Treuheit, Nicholas A; Beach, Muneera A; Komives, Elizabeth A

2011-05-31

Several lines of experimental evidence including amide exchange and NMR suggest that ligands binding to thrombin cause reduced backbone dynamics. Binding of the covalent inhibitor dPhe-Pro-Arg chloromethyl ketone to the active site serine, as well as noncovalent binding of a fragment of the regulatory protein, thrombomodulin, to exosite 1 on the back side of the thrombin molecule both cause reduced dynamics. However, the reduced dynamics do not appear to be accompanied by significant conformational changes. In addition, binding of ligands to the active site does not change the affinity of thrombomodulin fragments binding to exosite 1; however, the thermodynamic coupling between exosite 1 and the active site has not been fully explored. We present isothermal titration calorimetry experiments that probe changes in enthalpy and entropy upon formation of binary ligand complexes. The approach relies on stringent thrombin preparation methods and on the use of dansyl-l-arginine-(3-methyl-1,5-pantanediyl)amide and a DNA aptamer as ligands with ideal thermodynamic signatures for binding to the active site and to exosite 1. Using this approach, the binding thermodynamic signatures of each ligand alone as well as the binding signatures of each ligand when the other binding site was occupied were measured. Different exosite 1 ligands with widely varied thermodynamic signatures cause a similar reduction in ΔH and a concomitantly lower entropy cost upon DAPA binding at the active site. The results suggest a general phenomenon of enthalpy-entropy compensation consistent with reduction of dynamics/increased folding of thrombin upon ligand binding to either the active site or exosite 1.

Active-Site Hydration and Water Diffusion in Cytochrome P450cam: A Highly Dynamic Process

PubMed Central

Miao, Yinglong; Baudry, Jerome

2011-01-01

Long-timescale molecular dynamics simulations (300 ns) are performed on both the apo- (i.e., camphor-free) and camphor-bound cytochrome P450cam (CYP101). Water diffusion into and out of the protein active site is observed without biased sampling methods. During the course of the molecular dynamics simulation, an average of 6.4 water molecules is observed in the camphor-binding site of the apo form, compared to zero water molecules in the binding site of the substrate-bound form, in agreement with the number of water molecules observed in crystal structures of the same species. However, as many as 12 water molecules can be present at a given time in the camphor-binding region of the active site in the case of apo-P450cam, revealing a highly dynamic process for hydration of the protein active site, with water molecules exchanging rapidly with the bulk solvent. Water molecules are also found to exchange locations frequently inside the active site, preferentially clustering in regions surrounding the water molecules observed in the crystal structure. Potential-of-mean-force calculations identify thermodynamically favored trans-protein pathways for the diffusion of water molecules between the protein active site and the bulk solvent. Binding of camphor in the active site modifies the free-energy landscape of P450cam channels toward favoring the diffusion of water molecules out of the protein active site. PMID:21943431

Proteinase-Activated Receptor-2 Sensitivity of Amplified TRPA1 Activity in Skeletal Muscle Afferent Nerves and Exercise Pressor Reflex in Rats with Femoral Artery Occlusion

PubMed Central

Xing, Jihong; Li, Jianhua

2017-01-01

Background/Aims Limb ischemia occurs in peripheral artery disease (PAD). Sympathetic nerve activity (SNA) that regulates blood flow directed to the ischemic limb is exaggerated during exercise in this disease, and transient receptor potential channel A1 (TRPA1) in thin-fiber muscle afferents contributes to the amplified sympathetic response. The purpose of the present study was to determine the role of proteinase-activated receptor-2 (PAR2) in regulating abnormal TRPA1 function and the TRPA1-mediated sympathetic component of the exercise pressor reflex. Methods A rat model of femoral artery ligation was employed to study PAD. Dorsal root ganglion (DRG) tissues were obtained to examine the protein levels of PAR2 using western blot analysis. Current responses induced by activation of TRPA1 in skeletal muscle DRG neurons were characterized using whole-cell patch clamp methods. The blood pressure response to static exercise (i.e., muscle contraction) and stimulation of TRPA1 was also examined after a blockade of PAR2. Results The expression of PAR2 was amplified in DRG neurons of the occluded limb, and PAR2 activation with SL-NH2 (a PAR2 agonist) increased the amplitude of TRPA1 currents to a greater degree in DRG neurons of the occluded limb. Moreover, FSLLRY-NH2 (a PAR antagonist) injected into the arterial blood supply of the hindlimb muscles significantly attenuated the pressor response to muscle contraction and TRPA1 stimulation in rats with occluded limbs. Conclusions The PAR2 signal in muscle sensory nerves contributes to the amplified exercise pressor reflex via TRPA1 mechanisms in rats with femoral artery ligation. These findings provide a pathophysiological basis for autonomic responses during exercise activity in PAD, which may potentially aid in the development of therapeutic approaches for improvement of blood flow in this disease. PMID:29131007

Multicenter Off-Label Use of Nit-Occlud Coil in Retrograde Closure of Small Patent Ductus Arteriosus.

PubMed

Zanjani, Keyhan Sayadpour; Sobhy, Rodina; El-Kaffas, Rania; El-Sisi, Amal

2017-04-01

We studied the safety and efficacy of closing patent ductus arteriosus by Nit-Occlud coils via retrograde approach. This is a retrospective study of 46 attempts to close ducts by this method in two hospitals in Egypt and Iran. Ductus arteriosus was crossed by left or right Judkins or endhole catheters. The coil was delivered via the same catheter or the provided endhole catheter after exchange. The procedure was successful in 42 out of 46 attempts. Fluoroscopy and procedural times were significantly shorter when the catheter was not exchanged. This method is effective and safe for the closure of small ducts. Crossing the duct and delivering the coil by a left Judkins catheter is the easiest and fastest way to perform this method.

Active Site Mutations Change the Cleavage Specificity of Neprilysin

PubMed Central

Sexton, Travis; Hitchcook, Lisa J.; Rodgers, David W.; Bradley, Luke H.; Hersh, Louis B.

2012-01-01

Neprilysin (NEP), a member of the M13 subgroup of the zinc-dependent endopeptidase family is a membrane bound peptidase capable of cleaving a variety of physiological peptides. We have generated a series of neprilysin variants containing mutations at either one of two active site residues, Phe563 and Ser546. Among the mutants studied in detail we observed changes in their activity towards leucine5-enkephalin, insulin B chain, and amyloid β1–40. For example, NEPF563I displayed an increase in preference towards cleaving leucine5-enkephalin relative to insulin B chain, while mutant NEPS546E was less discriminating than neprilysin. Mutants NEPF563L and NEPS546E exhibit different cleavage site preferences than neprilysin with insulin B chain and amyloid ß1–40 as substrates. These data indicate that it is possible to alter the cleavage site specificity of neprilysin opening the way for the development of substrate specific or substrate exclusive forms of the enzyme with enhanced therapeutic potential. PMID:22384224

Carbinolamine Formation and Dehydration in a DNA Repair Enzyme Active Site

PubMed Central

Dodson, M. L.; Walker, Ross C.; Lloyd, R. Stephen

2012-01-01

In order to suggest detailed mechanistic hypotheses for the formation and dehydration of a key carbinolamine intermediate in the T4 pyrimidine dimer glycosylase (T4PDG) reaction, we have investigated these reactions using steered molecular dynamics with a coupled quantum mechanics–molecular mechanics potential (QM/MM). We carried out simulations of DNA abasic site carbinolamine formation with and without a water molecule restrained to remain within the active site quantum region. We recovered potentials of mean force (PMF) from thirty replicate reaction trajectories using Jarzynski averaging. We demonstrated feasible pathways involving water, as well as those independent of water participation. The water–independent enzyme–catalyzed reaction had a bias–corrected Jarzynski–average barrier height of approximately for the carbinolamine formation reaction and ) for the reverse reaction at this level of representation. When the proton transfer was facilitated with an intrinsic quantum water, the barrier height was approximately in the forward (formation) reaction and for the reverse. In addition, two modes of unsteered (free dynamics) carbinolamine dehydration were observed: in one, the quantum water participated as an intermediate proton transfer species, and in the other, the active site protonated glutamate hydrogen was directly transferred to the carbinolamine oxygen. Water–independent unforced proton transfer from the protonated active site glutamate carboxyl to the unprotonated N–terminal amine was also observed. In summary, complex proton transfer events, some involving water intermediates, were studied in QM/MM simulations of T4PDG bound to a DNA abasic site. Imine carbinolamine formation was characterized using steered QM/MM molecular dynamics. Dehydration of the carbinolamine intermediate to form the final imine product was observed in free, unsteered, QM/MM dynamics simulations, as was unforced acid-base transfer between the active site

Immobilization of alkaline phosphatase on solid surface through self-assembled monolayer and by active-site protection.

PubMed

Gao, En-Feng; Kang, Kyung Lhi; Kim, Jeong Hee

2014-06-01

Retaining biological activity of a protein after immobilization is an important issue and many studies reported to enhance the activity of proteins after immobilization. We recently developed a new immobilization method of enzyme using active-site protection and minimization of the cross-links between enzyme and surface with a DNA polymerase as a model system. In this study, we extended the new method to an enzyme with a small mono-substrate using alkaline phosphatase (AP) as another model system. A condition to apply the new method is that masking agents, in this case its own substrate needs to stay at the active-site of the enzyme to be immobilized in order to protect the active-site during the harsh immobilization process. This could be achieved by removal of essential divalent ion, Zn2+ that is required for full enzyme activity of AP from the masking solution while active-site of AP was protected with p-nitrophenyl phosphate (pNPP). Approximately 40% of the solution-phase activity was acquired with active-site protected immobilized AP. In addition to protection active-site of AP, the number of immobilization links was kinetically controlled. When the mole fraction of the activated carboxyl group of the linker molecule in self-assembled monolayer (SAM) of 12-mercaptododecanoic acid and 6-mercapto-1-ethanol was varied, 10% of 12-mercaptododecanoic acid gave the maximum enzyme activity. Approximately 51% increase in enzyme activity of the active-site protected AP was observed compared to that of the unprotected group. It was shown that the concept of active-site protection and kinetic control of the number of covalent immobilization bonds can be extended to enzymes with small mono-substrates. It opens the possibility of further extension of the new methods of active-site protection and kinetic control of immobilization bond to important enzymes used in research and industrial fields.

Ultrafast Light-Driven Substrate Expulsion from the Active Site of a Photoswitchable Catalyst.

PubMed

Pescher, Manuel D; van Wilderen, Luuk J G W; Grützner, Susanne; Slavov, Chavdar; Wachtveitl, Josef; Hecht, Stefan; Bredenbeck, Jens

2017-09-25

The photoswitchable piperidine general base catalyst is a prototype structure for light control of catalysis. Its azobenzene moiety moves sterically shielding groups to either protect or expose the active site, thereby changing the basicity and hydrogen-bonding affinity of the compound. The reversible switching dynamics of the catalyst is probed in the infrared spectral range by monitoring hydrogen bond (HB) formation between its active site and methanol (MeOH) as HB donor. Steady-state infrared (IR) and ultrafast IR and UV/Vis spectroscopies are used to uncover ultrafast expulsion of MeOH from the active site within a few picoseconds. Thus, the force generated by the azobenzene moiety even in the final phase of its isomerization is sufficient to break a strong HB within 3 ps and to shut down access to the active site. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dynamic Perturbation of the Active Site Determines Reversible Thermal Inactivation in Glycoside Hydrolase Family 12.

PubMed

Jiang, Xukai; Li, Wen; Chen, Guanjun; Wang, Lushan

2017-02-27

The temperature dependence of enzyme catalysis is highly debated. Specifically, how high temperatures induce enzyme inactivation has broad implications for both fundamental and applied science. Here, we explored the mechanism of the reversible thermal inactivation in glycoside hydrolase family 12 (GH12) using comparative molecular dynamics simulations. First, we investigated the distribution of structural flexibility over the enzyme and found that the active site was the general thermal-sensitive region in GH12 cellulases. The dynamic perturbation of the active site before enzyme denaturation was explored through principal-component analysis, which indicated that variations in the collective motion and conformational ensemble of the active site may precisely correspond to enzyme transition from its active form to the inactive form. Furthermore, the degree of dynamic perturbation of the active site was found to be negatively correlated with the melting temperatures of GH12 enzymes, further proving the importance of the dynamic stability of the active site. Additionally, analysis of the residue-interaction network revealed that the active site in thermophilic enzyme was capable of forming additional contacts with other amino acids than those observed in the mesophilic enzyme. These interactions are likely the key mechanisms underlying the differences in rigidity of the active site. These findings provide further biophysical insights into the reversible thermal inactivation of enzymes and potential applications in future protein engineering.

Non-active site mutation (Q123A) in New Delhi metallo-β-lactamase (NDM-1) enhanced its enzyme activity.

PubMed

Ali, Abid; Azam, Mohd W; Khan, Asad U

2018-06-01

New Delhi metallo β-lactamase-1 is one of the carbapenemases, causing hydrolysis of almost all β-lactamase antibiotics. Seventeen different NDM variants have been reported so far, they varied in their sequences either by single or multiple amino acid substitutions. Hence, it is important to understand its structural and functional relation. In the earlier studies role of active site residues has been studied but non-active site residues has not studied in detail. Therefore, we have initiated to further comprehend its structure and function relation by mutating some of its non-active site residues. A laboratory mutant of NDM-1 was generated by PCR-based site-directed mutagenesis, replacing Q to A at 123 position. The MICs of imipenem and meropenem for NDM-1 Q123A were found increased by 2 fold as compare to wild type and so the hydrolytic activity was enhanced (Kcat/Km) as compared to NDM-1 wild type. GOLD fitness scores were also found in favour of kinetics data. Secondary structure for α-helical content was determined by Far-UV circular dichroism (CD), which showed significant conformational changes. We conclude a noteworthy role of non-active-site amino acid residues in the catalytic activity of NDM-1. This study also provides an insight of emergence of new variants through natural evolution. Copyright © 2018 Elsevier B.V. All rights reserved.

Application of Cardio-O-Fix occluders for transcatheter closure of patent ductus arteriosus and interatrial communications: Preliminary experience.

PubMed

Białkowski, Jacek; Szkutnik, Małgorzata; Fiszer, Roland; Głowacki, Jan; Banaszak, Paweł; Zembala, Marian

2010-01-01

Transcatheter treatment has become the method of choice for treating many heart defects. Recently, Cardio-O-Fix occluder (COF) - a new, self-expandable nitinol wire-mesh device very similar to the Amplatzer device - has been introduced into clinical practice. To the best of our knowledge, this is the first publication related to its application. Five patients aged from six months to 69 years were included in the study: two with atrial septal defect (ASD), one with patent foramen ovale (PFO) after cryptogenic stroke, and two with patent ductus arteriosus (PDA). These latter two comprised one six month old infant with co-existent hypertrophied cardiomyopathy, and a 53 year-old woman with recanalized PDA after previous ligation. All were treated percutaneously with COF. There was no preliminary patient selection. The only limitation was the size of the devices in our possession (16 and 22 mm ASD COF, 25 PFO COF, 4/6 and 6/8 PDA COF). The implantation technique was the same as previously described for Amplatzer occluders. All procedures were finished successfully with complete closure of the shunt. No complications were observed during a six month follow-up. In the child with PDA, we observed decrease of gradient from 80 to 60 mm Hg in hypertrophied left ventricular outflow tract, although a small protrusion of PDA-COF device was noted in the descending aorta (8 mm Hg gradient in ECHO). In the patient with recanalized PDA, the procedure was performed after arterio-venous loop creation. Mean fluoroscopy time was 4.4 (range from 1.6 to 11) minutes. Our preliminary experience indicates that the application of Cardio-O-Fix devices is safe and effective.

Reperfusion of occluded branch retinal arteries by transluminal Nd:YAG laser embolysis combined with intravenous thrombolysis of urokinase

PubMed Central

Chai, Fang; Du, Shanshuang; Zhao, Xiquan

2017-01-01

Purpose: To report successful treatment with transluminal Nd:YAG laser embolysis (TYE) combined with urokinase thrombolysis for reperfusion of occluded branch retinal arteries with visible emboli. Methods: A total of 34 eyes from 34 patients with acute, severe vision loss secondary to a branch retinal artery occlusion with visible emboli and retinal whitening were examined. Each patient was administered TYE therapy, which focused on the embolus, using an ocular contact lens; a 0.3–0.9 mJ laser pulse was delivered directly and gradually according to the reaction. Fundus photographs and fundus fluorescein angiography (FFA) were obtained before and immediately after the laser treatment. All patients received urokinase thrombolysis therapy drops intravenously for 5 days at 10–20 u/d. The follow-up period ranged from 6 to 14 months after therapy. The morphological characteristics of FFA associated with obstruction recovery of arterial fluorescence filling and visual function were analyzed. Results: After TYE therapy, FFA examinations showed that the retinal artery and its branches exhibited completely restored blood flow without obstruction in 13 eyes, accounting for 38.2% of the cases. The blood flow was mostly recovered in 11 eyes (32.4% of patients). FFA examinations following the combined intravenous urokinase thrombolysis therapy showed that the retinal artery and its branches exhibited completely restored blood flow after obstruction in 16 eyes (47.1% of patients). The blood flow was mostly recovered in 15 eyes (44.1% of patients). Conclusion: TYE combined with urokinase thrombolysis is effective for reperfusion of occluded branch retinal arteries and improving visual recovery in patients with visible emboli. PMID:29162667

Interventional Closure of a Patent Ductus Arteriosus Using an Amplatz Canine Duct Occluder in an Alpaca Cria.

PubMed

Chapel, E C; Lozier, J; Lakritz, J; Schober, K E

2017-07-01

A 6-month old female alpaca cria presented to The Ohio State University for evaluation of a cardiac murmur. Echocardiography revealed a left-to-right shunting patent ductus arteriosus, a restrictive left-to-right shunting perimembranous ventricular septal defect, and secondary moderate left atrial and ventricular dilation. Aortic root angiography demonstrated a type IIA patent ductus arteriosus (PDA). Interventional closure of the PDA was successfully performed, without complication, using an Amplatz canine duct occluder. This case report describes the materials and methods used for interventional closure of a PDA in an alpaca cria. Copyright © 2017 The Authors. Journal of Veterinary Internal Medicine published by Wiley Periodicals, Inc. on behalf of the American College of Veterinary Internal Medicine.

Multiple active site residues are important for photochemical efficiency in the light-activated enzyme protochlorophyllide oxidoreductase (POR).

PubMed

Menon, Binuraj R K; Hardman, Samantha J O; Scrutton, Nigel S; Heyes, Derren J

2016-08-01

Protochlorophyllide oxidoreductase (POR) catalyzes the light-driven reduction of protochlorophyllide (Pchlide), an essential, regulatory step in chlorophyll biosynthesis. The unique requirement of the enzyme for light has provided the opportunity to investigate how light energy can be harnessed to power biological catalysis and enzyme dynamics. Excited state interactions between the Pchlide molecule and the protein are known to drive the subsequent reaction chemistry. However, the structural features of POR and active site residues that are important for photochemistry and catalysis are currently unknown, because there is no crystal structure for POR. Here, we have used static and time-resolved spectroscopic measurements of a number of active site variants to study the role of a number of residues, which are located in the proposed NADPH/Pchlide binding site based on previous homology models, in the reaction mechanism of POR. Our findings, which are interpreted in the context of a new improved structural model, have identified several residues that are predicted to interact with the coenzyme or substrate. Several of the POR variants have a profound effect on the photochemistry, suggesting that multiple residues are important in stabilizing the excited state required for catalysis. Our work offers insight into how the POR active site geometry is finely tuned by multiple active site residues to support enzyme-mediated photochemistry and reduction of Pchlide, both of which are crucial to the existence of life on Earth. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Heterogeneous Electrocatalyst with Molecular Cobalt Ions Serving as the Center of Active Sites.

PubMed

Wang, Jiong; Ge, Xiaoming; Liu, Zhaolin; Thia, Larissa; Yan, Ya; Xiao, Wei; Wang, Xin

2017-02-08

Molecular Co 2+ ions were grafted onto doped graphene in a coordination environment, resulting in the formation of molecularly well-defined, highly active electrocatalytic sites at a heterogeneous interface for the oxygen evolution reaction (OER). The S dopants of graphene are suggested to be one of the binding sites and to be responsible for improving the intrinsic activity of the Co sites. The turnover frequency of such Co sites is greater than that of many Co-based nanostructures and IrO 2 catalysts. Through a series of carefully designed experiments, the pathway for the evolution of the Co cation-based molecular catalyst for the OER was further demonstrated on such a single Co-ion site for the first time. The Co 2+ ions were successively oxidized to Co 3+ and Co 4+ states prior to the OER. The sequential oxidation was coupled with the transfer of different numbers of protons/hydroxides and generated an active Co 4+ ═O fragment. A side-on hydroperoxo ligand of the Co 4+ site is proposed as a key intermediate for the formation of dioxygen.

Catalysis-dependent selenium incorporation and migration in the nitrogenase active site iron-molybdenum cofactor.

PubMed

Spatzal, Thomas; Perez, Kathryn A; Howard, James B; Rees, Douglas C

2015-12-16

Dinitrogen reduction in the biological nitrogen cycle is catalyzed by nitrogenase, a two-component metalloenzyme. Understanding of the transformation of the inert resting state of the active site FeMo-cofactor into an activated state capable of reducing dinitrogen remains elusive. Here we report the catalysis dependent, site-selective incorporation of selenium into the FeMo-cofactor from selenocyanate as a newly identified substrate and inhibitor. The 1.60 Å resolution structure reveals selenium occupying the S2B site of FeMo-cofactor in the Azotobacter vinelandii MoFe-protein, a position that was recently identified as the CO-binding site. The Se2B-labeled enzyme retains substrate reduction activity and marks the starting point for a crystallographic pulse-chase experiment of the active site during turnover. Through a series of crystal structures obtained at resolutions of 1.32-1.66 Å, including the CO-inhibited form of Av1-Se2B, the exchangeability of all three belt-sulfur sites is demonstrated, providing direct insights into unforeseen rearrangements of the metal center during catalysis.

Glucose Transporters are Abundant in Cells with "Occluding" Junctions at the Blood-Eye Barriers

NASA Astrophysics Data System (ADS)

Harik, Sami I.; Kalaria, Rajesh N.; Whitney, Paul M.; Andersson, Lars; Lundahl, Per; Ledbetter, Steven R.; Perry, George

1990-06-01

We studied the distribution of the "erythroid/brain" glucose transporter protein in the human and rat eye by immunocytochemistry with monoclonal and polyclonal antibodies to the C terminus of the human erythrocyte glucose transporter. We found intense immunocytochemical staining in the endothelium of microvessels of the retina, optic nerve, and iris but not in microvessels of the choroid, ciliary body, sclera, and other retro-orbital tissues. In addition, we found marked immunocytochemical staining of retinal pigment epithelium, ciliary body epithelium, and posterior epithelium of the iris. The common feature of all those endothelial and epithelial cells that stained intensely for the glucose transporter is the presence of "occluding" intercellular junctions, which constitute the anatomical bases of the blood-eye barriers. We propose that a high density of the glucose transporter is a biochemical concomitant of epithelial and endothelial cells with barrier characteristics, at least in tissues that have a high metabolic requirement for glucose.

Methylation of an alpha-foetoprotein gene intragenic site modulates gene activity.

PubMed Central

Opdecamp, K; Rivière, M; Molné, M; Szpirer, J; Szpirer, C

1992-01-01

By comparing the methylation pattern of Mspl/Hpall sites in the 5' region of the mouse alpha-foetoprotein (AFP) gene of different cells (hepatoma cells, foetal and adult liver, fibroblasts), we found a correlation between gene expression and unmethylation of a site located in the first intron of the gene. Other sites did not show this correlation. In transfection experiments of unmethylated and methylated AFP-CAT chimeric constructions, we then showed that methylation of the intronic site negatively modulates expression of CAT activity. We also found that a DNA segment centered on this site binds nuclear proteins; however methylation did not affect protein binding. Images PMID:1371343

Assessing Soil Organic C Stability at the Continental Scale: An Analysis of Soil C and Radiocarbon Profiles Across the NEON Sites

NASA Astrophysics Data System (ADS)

Heckman, K. A.; Gallo, A.; Hatten, J. A.; Swanston, C.; McKnight, D. M.; Strahm, B. D.; Sanclements, M.

2017-12-01

Soil carbon stocks have become recognized as increasingly important in the context of climate change and global C cycle modeling. As modelers seek to identify key parameters affecting the size and stability of belowground C stocks, attention has been drawn to the mineral matrix and the soil physiochemical factors influenced by it. Though clay content has often been utilized as a convenient and key explanatory variable for soil C dynamics, its utility has recently come under scrutiny as new paradigms of soil organic matter stabilization have been developed. We utilized soil cores from a range of National Ecological Observatory Network (NEON) experimental plots to examine the influence of physicochemical parameters on soil C stocks and turnover, and their relative importance in comparison to climatic variables. Soils were cored at NEON sites, sampled by genetic horizon, and density separated into light fractions (particulate organics neither occluded within aggregates nor associated with mineral surfaces), occluded fractions (particulate organics occluded within aggregates), and heavy fractions (organics associated with mineral surfaces). Bulk soils and density fractions were measured for % C and radiocarbon abundance (as a measure of C stability). Carbon and radiocarbon abundances were examined among fractions and in the context of climatic variables (temperature, precipitation, elevation) and soil physiochemical variables (% clay and pH). No direct relationships between temperature and soil C or radiocarbon abundances were found. As a whole, soil radiocarbon abundance in density fractions decreased in the order of light>heavy>occluded, highlighting the importance of both surface sorption and aggregation to the preservation of organics. Radiocarbon abundance was correlated with pH, with variance also grouping by dominate vegetation type. Soil order was also identified as an important proxy variable for C and radiocarbon abundance. Preliminary results suggest that

Comparison of outcomes among secondary covered metallic, uncovered metallic, and plastic biliary stents in treating occluded primary metallic stents in malignant distal biliary obstruction.

PubMed

Cho, Jae Hee; Jeon, Tae Joo; Park, Jeong Youp; Kim, Hee Man; Kim, Yoon Jae; Park, Seung Woo; Chung, Jae Bock; Song, Si Young; Bang, Seungmin

2011-02-01

The self-expandable metallic stent (SEMS) has been widely used for unresectable malignant biliary obstruction but eventually becomes occluded by tumor ingrowth/overgrowth and sludge. Therefore, we aimed to determine the therapeutic effectiveness of secondary stents and to find differences according to various combinations of the first and second stents for the management of occluded SEMSs in patients with malignant distal biliary obstruction. Between 1999 and November 2008, 77 patients with malignant biliary obstruction underwent secondary biliary stent placement as "stent-in-stent" at three university hospitals in Korea (40 covered, 26 uncovered, and 11 plastic stents). The membrane of the covered SEMS was regarded as the barrier against tumor ingrowth. We categorized the patients into three groups based on whether the covered SEMS was either the first or the second stent: membrane-SEMS (18 covered-covered; 9 covered-uncovered; 22 uncovered-covered SEMS), bare-SEMS (17 uncovered-uncovered SEMS), and plastic stent (3 covered-plastic; 8 uncovered-plastic). The median patency of second stents was 138, 109, and 88 days (covered, uncovered, and plastic stents). The second covered SEMSs had a significantly longer patency than plastic stents (p=0.047). In a multivariate analysis including membrane-SEMS, bare-SEMS, and plastic stent groups, the bare-SEMS had a worse cumulative stent patency (HR=2.04, CI=1.08-3.86) and survival time (HR=2.37, CI=1.25-4.49) than the membrane-SEMS. Patients with ampulla of Vater cancer had better stent patency (HR=0.27, CI=0.08-0.98) and survival (HR=0.17, CI=0.04-0.77) than those with other pancreatobiliary malignancies. In addition, antitumor treatment prolonged survival time (HR=0.50, CI=0.26-0.99). The placement of additional biliary stents using the "stent-in-stent" method is an effective treatment for an occluded metallic primary stent. In addition, double biliary SEMS placement using at least one covered SEMS (in the primary and

Effect of naringin on hemodynamic changes and left ventricular function in renal artery occluded renovascular hypertension in rats

PubMed Central

Visnagri, Asjad; Adil, Mohammad; Kandhare, Amit D.; Bodhankar, Subhash L.

2015-01-01

Background: Renal artery occlusion (RAO) induced hypertension is a major health problem associated with structural and functional variations of the renal and cardiac vasculature. Naringin a flavanone glycoside derived possesses metal-chelating, antioxidant and free radical scavenging properties. Objective: The objective of this study was to investigate the antihypertensive activity of naringin in RAO induced hypertension in rats. Material and Methods: Male Wistar rats (180-200 g) were divided into five groups Sham, RAO, naringin (20, 40 and 80 mg/kg). Animals were pretreated with naringin (20, 40 and 80 mg/kg p.o) for 4 weeks. On the last day of the experiment, left renal artery was occluded with renal bulldog clamp for 4 h. After assessment of hemodynamic and left ventricular function various biochemical (superoxide dismutase [SOD], glutathione [GSH] and malondialdehyde [MDA]) and histological parameters were determined in the kidney. Results: RAO group significantly (P < 0.001) increased hemodynamic parameters at 15, 30 and 45 min of clamp removal. Naringin (40 and 80 mg/kg) treated groups showed a significant decrease in hemodynamic parameters at 15 min. after clamp removal that remained sustained for 60 min. Naringin (40 and 80 mg/kg) treated groups showed significant improvement in left ventricular function at 15, 30 and 45 min after clamp removal. Alteration in level of SOD, GSH and MDA was significantly restored by naringin (40 and 80 mg/kg) treatment. It also reduced histological aberration induced in kidney by RAO. Conclusion: It is concluded that the antihypertensive activity of naringin may result through inhibition of oxidative stress. PMID:25883516

Molecular imprint of enzyme active site by camel nanobodies: rapid and efficient approach to produce abzymes with alliinase activity.

PubMed

Li, Jiang-Wei; Xia, Lijie; Su, Youhong; Liu, Hongchun; Xia, Xueqing; Lu, Qinxia; Yang, Chunjin; Reheman, Kalbinur

2012-04-20

Screening of inhibitory Ab1 antibodies is a critical step for producing catalytic antibodies in the anti-idiotypic approach. However, the incompatible surface of the active site of the enzyme and the antigen-binding site of heterotetrameric conventional antibodies become the limiting step. Because camelid-derived nanobodies possess the potential to preferentially bind to the active site of enzymes due to their small size and long CDR3, we have developed a novel approach to produce antibodies with alliinase activities by exploiting the molecular mimicry of camel nanobodies. By screening the camelid-derived variable region of the heavy chain cDNA phage display library with alliinase, we obtained an inhibitory nanobody VHHA4 that recognizes the active site. Further screening with VHHA4 from the same variable domain of the heavy chain of a heavy-chain antibody library led to a higher incidence of anti-idiotypic Ab2 abzymes with alliinase activities. One of the abzymes, VHHC10, showed the highest activity that can be inhibited by Ab1 VHHA4 and alliinase competitive inhibitor penicillamine and significantly suppressed the B16 tumor cell growth in the presence of alliin in vitro. The results highlight the feasibility of producing abzymes via anti-idiotypic nanobody approach.

Synthesis of a molecularly defined single-active site heterogeneous catalyst for selective oxidation of N-heterocycles.

PubMed

Zhang, Yujing; Pang, Shaofeng; Wei, Zhihong; Jiao, Haijun; Dai, Xingchao; Wang, Hongli; Shi, Feng

2018-04-13

Generally, a homogeneous catalyst exhibits good activity and defined active sites but it is difficult to recycle. Meanwhile, a heterogeneous catalyst can easily be reused but its active site is difficult to reveal. It is interesting to bridge the gap between homogeneous and heterogeneous catalysis via controllable construction of a heterogeneous catalyst containing defined active sites. Here, we report that a molecularly defined, single-active site heterogeneous catalyst has been designed and prepared via the oxidative polymerization of maleimide derivatives. These polymaleimide derivatives can be active catalysts for the selective oxidation of heterocyclic compounds to quinoline and indole via the recycling of -C=O and -C-OH groups, which was confirmed by tracing the reaction with GC-MS using maleimide as the catalyst and by FT-IR analysis with polymaleimide as the catalyst. These results might promote the development of heterogeneous catalysts with molecularly defined single active sites exhibiting a comparable activity to homogeneous catalysts.

Structural Dynamics as a Contributor to Error-prone Replication by an RNA-dependent RNA Polymerase*

PubMed Central

Moustafa, Ibrahim M.; Korboukh, Victoria K.; Arnold, Jamie J.; Smidansky, Eric D.; Marcotte, Laura L.; Gohara, David W.; Yang, Xiaorong; Sánchez-Farrán, María Antonieta; Filman, David; Maranas, Janna K.; Boehr, David D.; Hogle, James M.; Colina, Coray M.; Cameron, Craig E.

2014-01-01

RNA viruses encoding high- or low-fidelity RNA-dependent RNA polymerases (RdRp) are attenuated. The ability to predict residues of the RdRp required for faithful incorporation of nucleotides represents an essential step in any pipeline intended to exploit perturbed fidelity as the basis for rational design of vaccine candidates. We used x-ray crystallography, molecular dynamics simulations, NMR spectroscopy, and pre-steady-state kinetics to compare a mutator (H273R) RdRp from poliovirus to the wild-type (WT) enzyme. We show that the nucleotide-binding site toggles between the nucleotide binding-occluded and nucleotide binding-competent states. The conformational dynamics between these states were enhanced by binding to primed template RNA. For the WT, the occluded conformation was favored; for H273R, the competent conformation was favored. The resonance for Met-187 in our NMR spectra reported on the ability of the enzyme to check the correctness of the bound nucleotide. Kinetic experiments were consistent with the conformational dynamics contributing to the established pre-incorporation conformational change and fidelity checkpoint. For H273R, residues comprising the active site spent more time in the catalytically competent conformation and were more positively correlated than the WT. We propose that by linking the equilibrium between the binding-occluded and binding-competent conformations of the nucleotide-binding pocket and other active-site dynamics to the correctness of the bound nucleotide, faithful nucleotide incorporation is achieved. These studies underscore the need to apply multiple biophysical and biochemical approaches to the elucidation of the physical basis for polymerase fidelity. PMID:25378410

Biological role of site-specific O-glycosylation in cell adhesion activity and phosphorylation of osteopontin.

PubMed

Oyama, Midori; Kariya, Yoshinobu; Kariya, Yukiko; Matsumoto, Kana; Kanno, Mayumi; Yamaguchi, Yoshiki; Hashimoto, Yasuhiro

2018-05-09

Osteopontin (OPN) is an extracellular glycosylated phosphoprotein that promotes cell adhesion by interacting with several integrin receptors. We previously reported that an OPN mutant lacking five O-glycosylation sites (Thr 134 /Thr 138 /Thr 143 /Thr 147 /Thr 152 ) in the threonine/proline-rich region increased cell adhesion activity and phosphorylation compared with the wild type. However, the role of O-glycosylation in cell adhesion activity and phosphorylation of OPN remains to be clarified. Here, we show that site-specific O-glycosylation in the threonine/proline-rich region of OPN affects its cell adhesion activity and phosphorylation independently and/or synergistically. Using site-directed mutagenesis, we found that OPN mutants with substitution sets of Thr 134 /Thr 138 or Thr 143 /Thr 147 /Thr 152 had decreased and increased cell adhesion activity, respectively. In contrast, the introduction of a single mutation into the O-glycosylation sites had no effect on OPN cell adhesion activity. An adhesion assay using function-blocking antibodies against αvβ3 and β1 integrins, as well as αvβ3 integrin-overexpressing A549 cells, revealed that site-specific O-glycosylation affected the association of OPN with the two integrins. Phosphorylation analyses using phos-tag and LC-MS/MS indicated that phosphorylation levels and sites were influenced by the O-glycosylation status, although the number of O-glycosylation sites was not correlated with the phosphorylation level in OPN. Furthermore, a correlation analysis between phosphorylation level and cell adhesion activity in OPN mutants with the site-specific O-glycosylation showed that they were not always correlated. These results provide conclusive evidence of a novel regulatory mechanism of cell adhesion activity and phosphorylation of OPN by site-specific O-glycosylation. © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Interactive flare sites within an active region complex

NASA Technical Reports Server (NTRS)

Poletto, G.; Gary, G. A.; Machado, M. E.

1993-01-01

We examine here a set of images of an active region complex, acquired on June 24-25, 1980, by the Hard X-ray Imaging Spectrometer on SMM, with the purpose of establishing whether there was any interplay between the frequent activity observed at different sites in the activity center and, in such a case, how the interaction was established. By analyzing both quiet and active orbits we show that, as a rule, activity originating in one region triggers the other region's activity. However, we find little unambiguous evidence for the presence of large-scale interconnecting loops. A comparison of X-ray images with magnetic field observations suggested that we interpret the active region behavior in terms of the interaction between different loop systems, in a scenario quite analogous to the interacting bipole representation of individual flares. We conclude that active region interplay provides an easily observable case to study the time-dependent topology and the mechanisms for the spreading of activity in transient events over all energy scales.

Ultrafast infrared spectroscopy reveals water-mediated coherent dynamics in an enzyme active site.

PubMed

Adamczyk, Katrin; Simpson, Niall; Greetham, Gregory M; Gumiero, Andrea; Walsh, Martin A; Towrie, Michael; Parker, Anthony W; Hunt, Neil T

2015-01-01

Understanding the impact of fast dynamics upon the chemical processes occurring within the active sites of proteins and enzymes is a key challenge that continues to attract significant interest, though direct experimental insight in the solution phase remains sparse. Similar gaps in our knowledge exist in understanding the role played by water, either as a solvent or as a structural/dynamic component of the active site. In order to investigate further the potential biological roles of water, we have employed ultrafast multidimensional infrared spectroscopy experiments that directly probe the structural and vibrational dynamics of NO bound to the ferric haem of the catalase enzyme from Corynebacterium glutamicum in both H 2 O and D 2 O. Despite catalases having what is believed to be a solvent-inaccessible active site, an isotopic dependence of the spectral diffusion and vibrational lifetime parameters of the NO stretching vibration are observed, indicating that water molecules interact directly with the haem ligand. Furthermore, IR pump-probe data feature oscillations originating from the preparation of a coherent superposition of low-frequency vibrational modes in the active site of catalase that are coupled to the haem ligand stretching vibration. Comparisons with an exemplar of the closely-related peroxidase enzyme family shows that they too exhibit solvent-dependent active-site dynamics, supporting the presence of interactions between the haem ligand and water molecules in the active sites of both catalases and peroxidases that may be linked to proton transfer events leading to the formation of the ferryl intermediate Compound I. In addition, a strong, water-mediated, hydrogen bonding structure is suggested to occur in catalase that is not replicated in peroxidase; an observation that may shed light on the origins of the different functions of the two enzymes.

Unmasking tandem site interaction in human acetylcholinesterase. Substrate activation with a cationic acetanilide substrate.

PubMed

Johnson, Joseph L; Cusack, Bernadette; Davies, Matthew P; Fauq, Abdul; Rosenberry, Terrone L

2003-05-13

Acetylcholinesterase (AChE) contains a narrow and deep active site gorge with two sites of ligand binding, an acylation site (or A-site) at the base of the gorge, and a peripheral site (or P-site) near the gorge entrance. The P-site contributes to catalytic efficiency by transiently binding substrates on their way to the acylation site, where a short-lived acyl enzyme intermediate is produced. A conformational interaction between the A- and P-sites has recently been found to modulate ligand affinities. We now demonstrate that this interaction is of functional importance by showing that the acetylation rate constant of a substrate bound to the A-site is increased by a factor a when a second molecule of substrate binds to the P-site. This demonstration became feasible through the introduction of a new acetanilide substrate analogue of acetylcholine, 3-(acetamido)-N,N,N-trimethylanilinium (ATMA), for which a = 4. This substrate has a low acetylation rate constant and equilibrates with the catalytic site, allowing a tractable algebraic solution to the rate equation for substrate hydrolysis. ATMA affinities for the A- and P-sites deduced from the kinetic analysis were confirmed by fluorescence titration with thioflavin T as a reporter ligand. Values of a >1 give rise to a hydrolysis profile called substrate activation, and the AChE site-specific mutant W86F, and to a lesser extent wild-type human AChE itself, showed substrate activation with acetylthiocholine as the substrate. Substrate activation was incorporated into a previous catalytic scheme for AChE in which a bound P-site ligand can also block product dissociation from the A-site, and two additional features of the AChE catalytic pathway were revealed. First, the ability of a bound P-site ligand to increase the substrate acetylation rate constant varied with the structure of the ligand: thioflavin T accelerated ATMA acetylation by a factor a(2) of 1.3, while propidium failed to accelerate. Second, catalytic rate

Portal response related to shunt occlusion by balloon-occluded retrograde transvenous obliteration may determine the prognosis of cirrhosis.

PubMed

Kobayashi, Kazufumi; Maruyama, Hitoshi; Kiyono, Soichiro; Sekimoto, Tadashi; Kondo, Takayuki; Shimada, Taro; Takahashi, Masanori; Okugawa, Hidehiro; Yokosuka, Osamu

2016-12-01

To determine the prognostic effect of portal hemodynamic responses after balloon-occluded retrograde transvenous obliteration (B-RTO) for gastric varices (GV) in cirrhosis patients. This retrospective study consisted of 37 cirrhosis patients (aged 62.5 ± 9.7 years) with medium- or large-grade GV treated with B-RTO. Portal hemodynamic response was assessed by the changes in flow volume in the portal trunk (PFV, mL/min) before and after the treatment. Group I showed increased PFV and group II showed no increase in PFV. The median observation period was 49.8 months (range, 4.7-150.3 months). All patients showed complete embolization of GV without any recurrence. There were 30 patients in group I and 7 patients in group II (decreased PFV in 6 and unchanged PFV in 1). The PFV at baseline was significantly lower in the former (583.5 ± 232.0 mL/min) than in the latter (880.7 ± 345.9 mL/min; P = 0.009). The survival rate was significantly lower in group II (83.3% at 1 year and 66.7% at 3 years) than in group I (96.7% at 1 year, 81.5% at 3 years, and 61.8% at 5 years; P = 0.012). The incidence of deterioration of the esophageal varices was 18/30 (60%) in group I and 5/7 (71.4%; P = 0.687) in group II. Multivariate analysis identified only no increase in portal response (hazard ratio, 8.086; P = 0.005) as an independent factor for poor prognosis. Balloon-occluded retrograde transvenous obliteration for GV may result in a poor prognosis when portal hemodynamics shows no increase in portal response. © 2016 The Japan Society of Hepatology.

Long-Term Primary Patency Rate After Nitinol Self-Expandable Stents Implantation in Long, Totally Occluded Femoropopliteal (TASC II C & D) Lesions.

PubMed

Elmahdy, Mahmoud Farouk; Buonamici, Piergiovanni; Trapani, Maurizio; Valenti, Renato; Migliorini, Angela; Parodi, Guido; Antoniucci, David

2017-06-01

Endovascular therapy for long femoropopliteal lesions using percutaneous transluminal balloon angioplasty or first-generation of peripheral stents has been associated with unacceptable one-year restenosis rates. However, with recent advances in equipment and techniques, a better primary patency rate is expected. This study was conducted to detect the long-term primary patency rate of nitinol self-expandable stents implanted in long, totally occluded femoropopliteal lesions TransAtlantic Inter-Society Census (TASC II type C & D), and determine the predictors of reocclusion or restenosis in the stented segments. The demographics, clinical, anatomical, and procedural data of 213 patients with 240 de novo totally occluded femoropopliteal (TASC II type C & D) lesions treated with nitinol self-expandable stents were retrospectively analysed. Of these limbs, 159 (66.2%) presented with intermittent claudication, while 81 (33.8%) presented with critical limb ischaemia. The mean-time of follow-up was 36±22.6 months, (range: 6.3-106.2 months). Outcomes evaluated were, primary patency rate and predictors of reocclusion or restenosis in the stented segments. The mean age of the patients was 70.9±9.3 years, with male gender 66.2%. Mean pre-procedural ABI was 0.45±0.53. One-hundred-and-seventy-five (73%) lesions were TASC II type C, while 65 (27%) were type D lesions. The mean length of the lesions was 17.9±11.3mm. Procedure related complications occurred in 10 (4.1%) limbs. There was no periprocedural mortality. Reocclusion and restenosis were detected during follow-up in 45 and 30 limbs respectively, and all were re-treated by endovascular approach. None of the patients required major amputation. Primary patency rates were 81.4±1.1%, 77.7±1.9% and 74.4±2.8% at 12, 24, and 36 months respectively. Male gender, severe calcification, and TASC II D lesion were independent predictors for reocclusion, while predictors of restenosis were DM, smoking and TASC II D lesions

n-Dodecyl β-D-maltoside specifically competes with general anesthetics for anesthetic binding sites.

PubMed

Xu, Longhe; Matsunaga, Felipe; Xi, Jin; Li, Min; Ma, Jingyuan; Liu, Renyu

2014-01-01

We recently demonstrated that the anionic detergent sodium dodecyl sulfate (SDS) specifically interacts with the anesthetic binding site in horse spleen apoferritin, a soluble protein which models anesthetic binding sites in receptors. This raises the possibility of other detergents similarly interacting with and occluding such sites from anesthetics, thereby preventing the proper identification of novel anesthetic binding sites. n-Dodecyl β-D-maltoside (DDM) is a non-ionic detergent commonly used during protein-anesthetic studies because of its mild and non-denaturing properties. In this study, we demonstrate that SDS and DDM occupy anesthetic binding sites in the model proteins human serum albumin (HSA) and horse spleen apoferritin and thereby inhibit the binding of the general anesthetics propofol and isoflurane. DDM specifically interacts with HSA (Kd = 40 μM) with a lower affinity than SDS (Kd = 2 μM). DDM exerts all these effects while not perturbing the native structures of either model protein. Computational calculations corroborated the experimental results by demonstrating that the binding sites for DDM and both anesthetics on the model proteins overlapped. Collectively, our results indicate that DDM and SDS specifically interact with anesthetic binding sites and may thus prevent the identification of novel anesthetic sites. Special precaution should be taken when undertaking and interpreting results from protein-anesthetic investigations utilizing detergents like SDS and DDM.

Engineering streptokinase for generation of active site-labeled plasminogen analogs*

PubMed Central

Laha, Malabika; Panizzi, Peter; Nahrendorf, Matthias; Bock, Paul E.

2011-01-01

We previously demonstrated that streptokinase (SK) can be used to generate active site-labeled fluorescent analogs of plasminogen (Pg) by virtue of its non-proteolytic activation of the zymogen. The method is versatile and allows for stoichiometric and active site-specific incorporation of any one of many molecular probes. The limitation of the labeling approach is that it is both time-consuming and low yield. Here we demonstrate an improved method for the preparation of labeled Pg analogs by the use of an engineered SK mutant fusion protein with both COOH- and NH2-terminal His6-tags. The NH2-terminal tag is followed by a tobacco etch virus proteinase cleavage site to ensure that the SK Ile1 residue, essential for conformational activation of Pg, is preserved. The SK COOH-terminal Lys414 residue and residues Arg253-Leu260 in the SK β-domain were deleted to prevent cleavage by plasmin (Pm), and to disable Pg substrate binding to the SK·Pg*/Pm catalytic complexes, respectively. Near-elimination of Pm generation with the SKΔ(R253-L260)ΔK414-His6 mutant increased the yield of labeled Pg 2.6-fold and reduced the time required >2-fold. The versatility of the labeling method was extended to the application of Pg labeled with a near-infrared probe to quantitate Pg receptors on immune cells by flow cytometry. PMID:21570944

Quantifying the density and utilization of active sites in non-precious metal oxygen electroreduction catalysts

PubMed Central

Sahraie, Nastaran Ranjbar; Kramm, Ulrike I.; Steinberg, Julian; Zhang, Yuanjian; Thomas, Arne; Reier, Tobias; Paraknowitsch, Jens-Peter; Strasser, Peter

2015-01-01

Carbon materials doped with transition metal and nitrogen are highly active, non-precious metal catalysts for the electrochemical conversion of molecular oxygen in fuel cells, metal air batteries, and electrolytic processes. However, accurate measurement of their intrinsic turn-over frequency and active-site density based on metal centres in bulk and surface has remained difficult to date, which has hampered a more rational catalyst design. Here we report a successful quantification of bulk and surface-based active-site density and associated turn-over frequency values of mono- and bimetallic Fe/N-doped carbons using a combination of chemisorption, desorption and 57Fe Mössbauer spectroscopy techniques. Our general approach yields an experimental descriptor for the intrinsic activity and the active-site utilization, aiding in the catalyst development process and enabling a previously unachieved level of understanding of reactivity trends owing to a deconvolution of site density and intrinsic activity. PMID:26486465

Exploring the Active Site of the Tungsten, Iron-Sulfur Enzyme Acetylene Hydratase▿ †

PubMed Central

tenBrink, Felix; Schink, Bernhard; Kroneck, Peter M. H.

2011-01-01

The soluble tungsten, iron-sulfur enzyme acetylene hydratase (AH) from mesophilic Pelobacter acetylenicus is a member of the dimethyl sulfoxide (DMSO) reductase family. It stands out from its class as it catalyzes a nonredox reaction, the addition of H2O to acetylene (H—C☰C—H) to form acetaldehyde (CH3CHO). Caught in its active W(IV) state, the high-resolution three-dimensional structure of AH offers an excellent starting point to tackle its unique chemistry and to identify catalytic amino acid residues within the active site cavity: Asp13 close to W(IV) coordinated to two molybdopterin-guanosine-dinucleotide ligands, Lys48 which couples the [4Fe-4S] cluster to the W site, and Ile142 as part of a hydrophobic ring at the end of the substrate access channel designed to accommodate the substrate acetylene. A protocol was developed to express AH in Escherichia coli and to produce active-site variants which were characterized with regard to activity and occupancy of the tungsten and iron-sulfur centers. By this means, fusion of the N-terminal chaperone binding site of the E. coli nitrate reductase NarG to the AH gene improved the yield and activity of AH and its variants significantly. Results from site-directed mutagenesis of three key residues, Asp13, Lys48, and Ile142, document their important role in catalysis of this unusual tungsten enzyme. PMID:21193613

Comparison of the active-site design of molybdenum oxo-transfer enzymes by quantum mechanical calculations.

PubMed

Li, Jilai; Ryde, Ulf

2014-11-17

There are three families of mononuclear molybdenum enzymes that catalyze oxygen atom transfer (OAT) reactions, named after a typical example from each family, viz., dimethyl sulfoxide reductase (DMSOR), sulfite oxidase (SO), and xanthine oxidase (XO). These families differ in the construction of their active sites, with two molybdopterin groups in the DMSOR family, two oxy groups in the SO family, and a sulfido group in the XO family. We have employed density functional theory calculations on cluster models of the active sites to understand the selection of molybdenum ligands in the three enzyme families. Our calculations show that the DMSOR active site has a much stronger oxidative power than the other two sites, owing to the extra molybdopterin ligand. However, the active sites do not seem to have been constructed to make the OAT reaction as exergonic as possible, but instead to keep the reaction free energy close to zero (to avoid excessive loss of energy), thereby making the reoxidation (SO and XO) or rereduction of the active sites (DMSOR) after the OAT reaction facile. We also show that active-site models of the three enzyme families can all catalyze the reduction of DMSO and that the DMSOR model does not give the lowest activation barrier. Likewise, all three models can catalyze the oxidation of sulfite, provided that the Coulombic repulsion between the substrate and the enzyme model can be overcome, but for this harder reaction, the SO model gives the lowest activation barrier, although the differences are not large. However, only the XO model can catalyze the oxidation of xanthine, owing to its sulfido ligand.

Enzyme/non-enzyme discrimination and prediction of enzyme active site location using charge-based methods.

PubMed

Bate, Paul; Warwicker, Jim

2004-07-02

Calculations of charge interactions complement analysis of a characterised active site, rationalising pH-dependence of activity and transition state stabilisation. Prediction of active site location through large DeltapK(a)s or electrostatic strain is relevant for structural genomics. We report a study of ionisable groups in a set of 20 enzymes, finding that false positives obscure predictive potential. In a larger set of 156 enzymes, peaks in solvent-space electrostatic properties are calculated. Both electric field and potential match well to active site location. The best correlation is found with electrostatic potential calculated from uniform charge density over enzyme volume, rather than from assignment of a standard atom-specific charge set. Studying a shell around each molecule, for 77% of enzymes the potential peak is within that 5% of the shell closest to the active site centre, and 86% within 10%. Active site identification by largest cleft, also with projection onto a shell, gives 58% of enzymes for which the centre of the largest cleft lies within 5% of the active site, and 70% within 10%. Dielectric boundary conditions emphasise clefts in the uniform charge density method, which is suited to recognition of binding pockets embedded within larger clefts. The variation of peak potential with distance from active site, and comparison between enzyme and non-enzyme sets, gives an optimal threshold distinguishing enzyme from non-enzyme. We find that 87% of the enzyme set exceeds the threshold as compared to 29% of the non-enzyme set. Enzyme/non-enzyme homologues, "structural genomics" annotated proteins and catalytic/non-catalytic RNAs are studied in this context.

Active Site Flexibility of Mycobacterium tuberculosis Isocitrate Lyase in Dimer Form.

PubMed

Lee, Yie-Vern; Choi, Sy Bing; Wahab, Habibah A; Choong, Yee Siew

2017-09-25

Tuberculosis (TB) still remains a global threat due to the emergence of a drug-resistant strain. Instead of focusing on the drug target of active stage TB, we are highlighting the isocitrate lyase (ICL) at the dormant stage TB. ICL is one of the persistent factors for Mycobacterium tuberculosis (MTB) to survive during the dormant phase. In addition, the absence of ICL in human has made ICL a potential drug target for TB therapy. However, the dynamic details of ICL which could give insights to the ICL-ligand interaction have yet to be solved. Therefore, a series of ICL dimer dynamics studies through molecular dynamics simulation were performed in this work. The ICL active site entrance gate closure is contributed to by hydrogen bonding and electrostatic interactions with the C-terminal. Analysis suggested that the open-closed behavior of the ICL active site entrance depends on the type of ligand present in the active site. We also observed four residues (Ser91, Asp108, Asp153, and Cys191) which could possibly be the nucleophiles for nucleophilic attack on the cleavage of isocitrate at the C 2 -C 3 bond. We hope that the elucidation of ICL dynamics can benefit future works such as lead identification or antibody design against ICL for TB therapeutics.

The off-label use of the Amplatzer muscular VSD occluder for large patent ductus arteriosus: a case report and review.

PubMed

Cubeddu, Roberto J; Babin, Ivan; Inglessis, Ignacio

2014-07-01

A percutaneous approach to the closure of patent ductus arteriosus (PDA) is the preferred procedure in the majority of cases. However, there is little experience with percutaneous closure of unusually large PDA. We report the case of a 28-year-old female with moderate left ventricular dilation and pulmonary hypertension resulting from a large 16 mm PDA. Percutaneous closure was successfully performed using an off-label Amplatzer muscular ventricular septal defect occluder after intravascular ultrasound assessment. Technical challenges, including accurate assessment of defect size and device selection are exemplified along with a comprehensive overview of the available literature.

Blogs and Social Network Sites as Activity Systems: Exploring Adult Informal Learning Process through Activity Theory Framework

ERIC Educational Resources Information Center

Heo, Gyeong Mi; Lee, Romee

2013-01-01

This paper uses an Activity Theory framework to explore adult user activities and informal learning processes as reflected in their blogs and social network sites (SNS). Using the assumption that a web-based space is an activity system in which learning occurs, typical features of the components were investigated and each activity system then…

Counting Active Sites on Titanium Oxide-Silica Catalysts for Hydrogen Peroxide Activation through In Situ Poisoning with Phenylphosphonic Acid

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eaton, Todd R.; Boston, Andrew M.; Thompson, Anthony B.

2015-06-04

Quantifying specific active sites in supported catalysts improves our understanding and assists in rational design. Supported oxides can undergo significant structural changes as surface densities increase from site-isolated cations to monolayers and crystallites, which changes the number of kinetically relevant sites. Herein, TiO x domains are titrated on TiO x–SiO 2 selectively with phenylphosphonic acid (PPA). An ex situ method quantifies all fluid-accessible TiO x, whereas an in situ titration during cis-cyclooctene epoxidation provides previously unavailable values for the number of tetrahedral Ti sites on which H 2O 2 activation occurs. We use this method to determine the active sitemore » densities of 22 different catalysts with different synthesis methods, loadings, and characteristic spectra and find a single intrinsic turnover frequency for cis-cyclooctene epoxidation of (40±7) h -1. This simple method gives molecular-level insight into catalyst structure that is otherwise hidden when bulk techniques are used.« less

Activity-Based Probes for Isoenzyme- and Site-Specific Functional Characterization of Glutathione S -Transferases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stoddard, Ethan G.; Killinger, Bryan J.; Nair, Reji N.

Glutathione S-transferases (GSTs) comprise a highly diverse family of phase II drug metabolizing enzymes whose shared function is the conjugation of reduced glutathione to various endo- and xenobiotics. Although the conglomerate activity of these enzymes can be measured by colorimetric assays, measurement of the individual contribution from specific isoforms and their contribution to the detoxification of xenobiotics in complex biological samples has not been possible. For this reason, we have developed two activity-based probes that characterize active glutathione transferases in mammalian tissues. The GST active site is comprised of a glutathione binding “G site” and a distinct substrate binding “Hmore » site”. Therefore, we developed (1) a glutathione-based photoaffinity probe (GSH-ABP) to target the “G site”, and (2) a probe designed to mimic a substrate molecule and show “H site” activity (GST-ABP). The GSH-ABP features a photoreactive moiety for UV-induced covalent binding to GSTs and glutathione-binding enzymes. The GST-ABP is a derivative of a known mechanism-based GST inhibitor that binds within the active site and inhibits GST activity. Validation of probe targets and “G” and “H” site specificity was carried out using a series of competitors in liver homogenates. Herein, we present robust tools for the novel characterization of enzyme- and active site-specific GST activity in mammalian model systems.« less

Identification and characterization of the sodium-binding site of activated protein C.

PubMed

He, X; Rezaie, A R

1999-02-19

Activated protein C (APC) requires both Ca2+ and Na+ for its optimal catalytic function. In contrast to the Ca2+-binding sites, the Na+-binding site(s) of APC has not been identified. Based on a recent study with thrombin, the 221-225 loop is predicted to be a potential Na+-binding site in APC. The sequence of this loop is not conserved in trypsin. We engineered a Gla domainless form of protein C (GDPC) in which the 221-225 loop was replaced with the corresponding loop of trypsin. We found that activated GDPC (aGDPC) required Na+ (or other alkali cations) for its amidolytic activity with dissociation constant (Kd(app)) = 44.1 +/- 8.6 mM. In the presence of Ca2+, however, the requirement for Na+ by aGDPC was eliminated, and Na+ stimulated the cleavage rate 5-6-fold with Kd(app) = 2.3 +/- 0.3 mM. Both cations were required for efficient factor Va inactivation by aGDPC. In the presence of Ca2+, the catalytic function of the mutant was independent of Na+. Unlike aGDPC, the mutant did not discriminate among monovalent cations. We conclude that the 221-225 loop is a Na+-binding site in APC and that an allosteric link between the Na+ and Ca2+ binding loops modulates the structure and function of this anticoagulant enzyme.

Orthogonal use of a human tRNA synthetase active site to achieve multi-functionality

PubMed Central

Zhou, Quansheng; Kapoor, Mili; Guo, Min; Belani, Rajesh; Xu, Xiaoling; Kiosses, William B.; Hanan, Melanie; Park, Chulho; Armour, Eva; Do, Minh-Ha; Nangle, Leslie A.; Schimmel, Paul; Yang, Xiang-Lei

2011-01-01

Protein multi-functionality is an emerging explanation for the complexity of higher organisms. In this regard, while aminoacyl tRNA synthetases catalyze amino acid activation for protein synthesis, some also act in pathways for inflammation, angiogenesis, and apoptosis. How multiple functions evolved and their relationship to the active site is not clear. Here structural modeling analysis, mutagenesis, and cell-based functional studies show that the potent angiostatic, natural fragment of human TrpRS associates via Trp side chains that protrude from the cognate cellular receptor VE-cadherin. Modeling indicates that (I prefer the way it was because the conclusion was reached not only by modeling, but more so by experimental studies.)VE-cadherin Trp side chains fit into the Trp-specific active site of the synthetase. Thus, specific side chains of the receptor mimic (?) amino acid substrates and expand the functionality of the active site of the synthetase. We propose that orthogonal use of the same active site may be a general way to develop multi-functionality of human tRNA synthetases and other proteins. PMID:20010843

Active Layer and Moisture Measurements for Intensive Site 0 and 1, Barrow, Alaska

DOE Data Explorer

John Peterson

2015-04-17

These are measurements of Active Layer Thickness collected along several lines beginning in September, 2011 to the present. The data were collected at several time periods along the Site0 L2 Line, the Site1 AB Line, and an ERT Monitoring Line near Area A in Site1.

Oscillatory Activity in the Infant Brain and the Representation of Small Numbers.

PubMed

Leung, Sumie; Mareschal, Denis; Rowsell, Renee; Simpson, David; Iaria, Leon; Grbic, Amanda; Kaufman, Jordy

2016-01-01

Gamma-band oscillatory activity (GBA) is an established neural signature of sustained occluded object representation in infants and adults. However, it is not yet known whether the magnitude of GBA in the infant brain reflects the quantity of occluded items held in memory. To examine this, we compared GBA of 6-8 month-old infants during occlusion periods after the representation of two objects vs. that of one object. We found that maintaining a representation of two objects during occlusion resulted in significantly greater GBA relative to maintaining a single object. Further, this enhancement was located in the right occipital region, which is consistent with previous object representation research in adults and infants. We conclude that enhanced GBA reflects neural processes underlying infants' representation of small numbers.

Stereospecific suppression of active site mutants by methylphosphonate substituted substrates reveals the stereochemical course of site-specific DNA recombination

PubMed Central

Rowley, Paul A.; Kachroo, Aashiq H.; Ma, Chien-Hui; Maciaszek, Anna D.; Guga, Piotr; Jayaram, Makkuni

2015-01-01

Tyrosine site-specific recombinases, which promote one class of biologically important phosphoryl transfer reactions in DNA, exemplify active site mechanisms for stabilizing the phosphate transition state. A highly conserved arginine duo (Arg-I; Arg-II) of the recombinase active site plays a crucial role in this function. Cre and Flp recombinase mutants lacking either arginine can be rescued by compensatory charge neutralization of the scissile phosphate via methylphosphonate (MeP) modification. The chemical chirality of MeP, in conjunction with mutant recombinases, reveals the stereochemical contributions of Arg-I and Arg-II. The SP preference of the native reaction is specified primarily by Arg-I. MeP reaction supported by Arg-II is nearly bias-free or RP-biased, depending on the Arg-I substituent. Positional conservation of the arginines does not translate into strict functional conservation. Charge reversal by glutamic acid substitution at Arg-I or Arg-II has opposite effects on Cre and Flp in MeP reactions. In Flp, the base immediately 5′ to the scissile MeP strongly influences the choice between the catalytic tyrosine and water as the nucleophile for strand scission, thus between productive recombination and futile hydrolysis. The recombinase active site embodies the evolutionary optimization of interactions that not only favor the normal reaction but also proscribe antithetical side reactions. PMID:25999343

Systematic Functional Analysis of Active-Site Residues in l-Threonine Dehydrogenase from Thermoplasma volcanium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Desjardins, Morgan; Mak, Wai Shun; O’Brien, Terrence E.

Enzymes have been through millions of years of evolution during which their active-site microenvironments are fine-tuned. Active-site residues are commonly conserved within protein families, indicating their importance for substrate recognition and catalysis. In this work, we systematically mutated active-site residues of l-threonine dehydrogenase from Thermoplasma volcanium and characterized the mutants against a panel of substrate analogs. Our results demonstrate that only a subset of these residues plays an essential role in substrate recognition and catalysis and that the native enzyme activity can be further enhanced roughly 4.6-fold by a single point mutation. Kinetic characterization of mutants on substrate analogs showsmore » that l-threonine dehydrogenase possesses promiscuous activities toward other chemically similar compounds not previously observed. Quantum chemical calculations on the hydride-donating ability of these substrates also reveal that this enzyme did not evolve to harness the intrinsic substrate reactivity for enzyme catalysis. Our analysis provides insights into connections between the details of enzyme active-site structure and specific function. Finally, these results are directly applicable to rational enzyme design and engineering.« less

Systematic Functional Analysis of Active-Site Residues in l-Threonine Dehydrogenase from Thermoplasma volcanium

DOE PAGES

Desjardins, Morgan; Mak, Wai Shun; O’Brien, Terrence E.; ...

2017-07-07

Enzymes have been through millions of years of evolution during which their active-site microenvironments are fine-tuned. Active-site residues are commonly conserved within protein families, indicating their importance for substrate recognition and catalysis. In this work, we systematically mutated active-site residues of l-threonine dehydrogenase from Thermoplasma volcanium and characterized the mutants against a panel of substrate analogs. Our results demonstrate that only a subset of these residues plays an essential role in substrate recognition and catalysis and that the native enzyme activity can be further enhanced roughly 4.6-fold by a single point mutation. Kinetic characterization of mutants on substrate analogs showsmore » that l-threonine dehydrogenase possesses promiscuous activities toward other chemically similar compounds not previously observed. Quantum chemical calculations on the hydride-donating ability of these substrates also reveal that this enzyme did not evolve to harness the intrinsic substrate reactivity for enzyme catalysis. Our analysis provides insights into connections between the details of enzyme active-site structure and specific function. Finally, these results are directly applicable to rational enzyme design and engineering.« less

Active site of tripeptidyl peptidase II from human erythrocytes is of the subtilisin type

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tomkinson, B.; Wernstedt, C.; Hellman, U.

1987-11-01

The present report presents evidence that the amino acid sequence around the serine of the active site of human tripeptidyl peptidase II is of the subtilisin type. The enzyme from human erythrocytes was covalently labeled at its active site with (/sup 3/H)diisopropyl fluorophosphate, and the protein was subsequently reduced, alkylated, and digested with trypsin. The labeled tryptic peptides were purified by gel filtration and repeated reversed-phase HPLC, and their amino-terminal sequences were determined. Residue 9 contained the radioactive label and was, therefore, considered to be the active serine residue. The primary structure of the part of the active site (residuesmore » 1-10) containing this residue was concluded to be Xaa-Thr-Gln-Leu-Met-Asx-Gly-Thr-Ser-Met. This amino acid sequence is homologous to the sequence surrounding the active serine of the microbial peptidases subtilisin and thermitase. These data demonstrate that human tripeptidyl peptidase II represents a potentially distinct class of human peptidases and raise the question of an evolutionary relationship between the active site of a mammalian peptidase and that of the subtilisin family of serine peptidases.« less

Active site of tripeptidyl peptidase II from human erythrocytes is of the subtilisin type.

PubMed Central

Tomkinson, B; Wernstedt, C; Hellman, U; Zetterqvist, O

1987-01-01

The present report presents evidence that the amino acid sequence around the serine of the active site of human tripeptidyl peptidase II is of the subtilisin type. The enzyme from human erythrocytes was covalently labeled at its active site with [3H]diisopropyl fluorophosphate, and the protein was subsequently reduced, alkylated, and digested with trypsin. The labeled tryptic peptides were purified by gel filtration and repeated reversed-phase HPLC, and their amino-terminal sequences were determined. Residue 9 contained the radioactive label and was, therefore, considered to be the active serine residue. The primary structure of the part of the active site (residues 1-10) containing this residue was concluded to be Xaa-Thr-Gln-Leu-Met-Asx-Gly-Thr-Ser-Met. This amino acid sequence is homologous to the sequence surrounding the active serine of the microbial peptidases subtilisin and thermitase. These data demonstrate that human tripeptidyl peptidase II represents a potentially distinct class of human peptidases and raise the question of an evolutionary relationship between the active site of a mammalian peptidase and that of the subtilisin family of serine peptidases. PMID:3313395

Calorimetric studies of the interactions of metalloenzyme active site mimetics with zinc-binding inhibitors.

PubMed

Robinson, Sophia G; Burns, Philip T; Miceli, Amanda M; Grice, Kyle A; Karver, Caitlin E; Jin, Lihua

2016-07-19

The binding of drugs to metalloenzymes is an intricate process that involves several interactions, including binding of the drug to the enzyme active site metal, as well as multiple interactions between the drug and the enzyme residues. In order to determine the free energy contribution of Zn(2+) binding by known metalloenzyme inhibitors without the other interactions, valid active site zinc structural mimetics must be formed and binding studies need to be performed in biologically relevant conditions. The potential of each of five ligands to form a structural mimetic with Zn(2+) was investigated in buffer using Isothermal Titration Calorimetry (ITC). All five ligands formed strong 1 : 1 (ligand : Zn(2+)) binary complexes. The complexes were used in further ITC experiments to study their interaction with 8-hydroxyquinoline (8-HQ) and/or acetohydroxamic acid (AHA), two bidentate anionic zinc-chelating enzyme inhibitors. It was found that tetradentate ligands were not suitable for creating zinc structural mimetics for inhibitor binding in solution due to insufficient coordination sites remaining on Zn(2+). A stable binary complex, [Zn(BPA)](2+), which was formed by a tridentate ligand, bis(2-pyridylmethyl)amine (BPA), was found to bind one AHA in buffer or a methanol : buffer mixture (60 : 40 by volume) at pH 7.25 or one 8-HQ in the methanol : buffer mixture at pH 6.80, making it an effective structural mimetic for the active site of zinc metalloenzymes. These results are consistent with the observation that metalloenzyme active site zinc ions have three residues coordinated to them, leaving one or two sites open for inhibitors to bind. Our findings indicate that Zn(BPA)X2 can be used as an active site structural mimetic for zinc metalloenzymes for estimating the free energy contribution of zinc binding to the overall inhibitor active site interactions. Such use will help aid in the rational design of inhibitors to a variety of zinc metalloenzymes.

Expertise differences in anticipatory judgements during a temporally and spatially occluded task.

PubMed

Causer, Joe; Smeeton, Nicholas J; Williams, A Mark

2017-01-01

There is contradictory evidence surrounding the role of critical cues in the successful anticipation of penalty kicks in soccer. In the current study, skilled and less-skilled soccer goalkeepers were required to anticipate when viewing penalty kicks that were both spatially (full body; hip region) and temporally (-160 ms, -80 ms before, foot-ball contact) occluded. The skilled group outperformed the less-skilled group in all conditions. Participants performed better in the full body condition when compared to hip region condition. Performance in the hip only condition was significantly better than chance for the skilled group across all occlusion conditions. However, the less-skilled group were no better than chance in the hip condition for the early occlusion points when predicting direction and height. Later temporal occlusion conditions were associated with increased performance both in the correct response and correct direction analyses, but not for correct height. These data suggest that postural information solely from the hip region may be used by skilled goalkeepers to make accurate predictions of penalty kick direction, however, information from other sources are needed in order to make predictions of height. Findings demonstrate how the importance of anticipation cues evolve over time, which has implications for the design of training programs to enhance perceptual-cognitive skill.

Treating amblyopia in adults with prosthetic occluding contact lenses.

PubMed

Garcia-Romo, Esperanza; Perez-Rico, Consuelo; Roldán-Díaz, Isabel; Arévalo-Serrano, Juan; Blanco, Román

2018-05-01

To investigate the feasibility, effectiveness and acceptability of using prosthetic occluding contact lenses (OCLs) to treat moderate amblyopia in adults and of the role of the multifocal visual evoked potential (mfVEP) as a predictor of postamblyopic therapy. A comparative, prospective, interventional, case series pilot study with amblyopic adults (mean age: 40 years, range 20-50 years) allocated into two intervention groups: eye patching and OCL. The primary outcome variable was logarithm of the minimum angle of resolution (logMAR) best-corrected visual acuity (BCVA), and secondary outcomes were mfVEP amplitude and latency and patients' health-related quality of life National Eye Institute Visual Function Questionnaire (NEI VFQ-25). Significant improvements in pre- to postamblyopic therapy BCVA were seen at 1.5 months in the OCL group [0.29 logMAR, 95% confidence interval (CI): 0.10-0.47 versus 0.11 logMAR, 95% CI: 0.02-0.19; p < 0.001] and eye patching group (0.29 logMAR, 95% CI: 0.17-0.40 versus 0.18 logMAR, 95% CI: 0.12-0.23; p < 0.01). Post-treatment BCVA was inversely related to age (R: 0.009, 95% CI: -0.02 to -0.001; p = 0.04) and the presence of strabismus (R: -0.3, 95% CI: -0.434 to -0.17; p = 0.001). No significant changes in the number and size of the abnormal mfVEP amplitude and latency defects were observed after occlusion. The NEI VFQ-25 composite score showed significant improvement in the OCL users at 12 months compared to eye patching. Significant vision improvement can be achieved, making occlusion with OCLs an effective and more acceptable therapy for adults with amblyopia. © 2017 Acta Ophthalmologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

Active site electrostatics protect genome integrity by blocking abortive hydrolysis during DNA recombination

PubMed Central

Ma, Chien-Hui; Rowley, Paul A; Macieszak, Anna; Guga, Piotr; Jayaram, Makkuni

2009-01-01

Water, acting as a rogue nucleophile, can disrupt transesterification steps of important phosphoryl transfer reactions in DNA and RNA. We have unveiled this risk, and identified safeguards instituted against it, during strand cleavage and joining by the tyrosine site-specific recombinase Flp. Strand joining is threatened by a latent Flp endonuclease activity (type I) towards the 3′-phosphotyrosyl intermediate resulting from strand cleavage. This risk is not alleviated by phosphate electrostatics; neutralizing the negative charge on the scissile phosphate through methylphosphonate (MeP) substitution does not stimulate type I endonuclease. Rather, protection derives from the architecture of the recombination synapse and conformational dynamics within it. Strand cleavage is protected against water by active site electrostatics. Replacement of the catalytic Arg-308 of Flp by alanine, along with MeP substitution, elicits a second Flp endonuclease activity (type II) that directly targets the scissile phosphodiester bond in DNA. MeP substitution, combined with appropriate active site mutations, will be useful in revealing anti-hydrolytic mechanisms engendered by systems that mediate DNA relaxation, DNA transposition, site-specific recombination, telomere resolution, RNA splicing and retrohoming of mobile introns. PMID:19440204

Expansion of access tunnels and active-site cavities influence activity of haloalkane dehalogenases in organic cosolvents.

PubMed

Stepankova, Veronika; Khabiri, Morteza; Brezovsky, Jan; Pavelka, Antonin; Sykora, Jan; Amaro, Mariana; Minofar, Babak; Prokop, Zbynek; Hof, Martin; Ettrich, Rudiger; Chaloupkova, Radka; Damborsky, Jiri

2013-05-10

The use of enzymes for biocatalysis can be significantly enhanced by using organic cosolvents in the reaction mixtures. Selection of the cosolvent type and concentration range for an enzymatic reaction is challenging and requires extensive empirical testing. An understanding of protein-solvent interaction could provide a theoretical framework for rationalising the selection process. Here, the behaviour of three model enzymes (haloalkane dehalogenases) was investigated in the presence of three representative organic cosolvents (acetone, formamide, and isopropanol). Steady-state kinetics assays, molecular dynamics simulations, and time-resolved fluorescence spectroscopy were used to elucidate the molecular mechanisms of enzyme-solvent interactions. Cosolvent molecules entered the enzymes' access tunnels and active sites, enlarged their volumes with no change in overall protein structure, but surprisingly did not act as competitive inhibitors. At low concentrations, the cosolvents either enhanced catalysis by lowering K(0.5) and increasing k(cat), or caused enzyme inactivation by promoting substrate inhibition and decreasing k(cat). The induced activation and inhibition of the enzymes correlated with expansion of the active-site pockets and their occupancy by cosolvent molecules. The study demonstrates that quantitative analysis of the proportions of the access tunnels and active-sites occupied by organic solvent molecules provides the valuable information for rational selection of appropriate protein-solvent pair and effective cosolvent concentration. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Using Carbohydrate Interaction Assays to Reveal Novel Binding Sites in Carbohydrate Active Enzymes.

PubMed

Cockburn, Darrell; Wilkens, Casper; Dilokpimol, Adiphol; Nakai, Hiroyuki; Lewińska, Anna; Abou Hachem, Maher; Svensson, Birte

2016-01-01

Carbohydrate active enzymes often contain auxiliary binding sites located either on independent domains termed carbohydrate binding modules (CBMs) or as so-called surface binding sites (SBSs) on the catalytic module at a certain distance from the active site. The SBSs are usually critical for the activity of their cognate enzyme, though they are not readily detected in the sequence of a protein, but normally require a crystal structure of a complex for their identification. A variety of methods, including affinity electrophoresis (AE), insoluble polysaccharide pulldown (IPP) and surface plasmon resonance (SPR) have been used to study auxiliary binding sites. These techniques are complementary as AE allows monitoring of binding to soluble polysaccharides, IPP to insoluble polysaccharides and SPR to oligosaccharides. Here we show that these methods are useful not only for analyzing known binding sites, but also for identifying new ones, even without structural data available. We further verify the chosen assays discriminate between known SBS/CBM containing enzymes and negative controls. Altogether 35 enzymes are screened for the presence of SBSs or CBMs and several novel binding sites are identified, including the first SBS ever reported in a cellulase. This work demonstrates that combinations of these methods can be used as a part of routine enzyme characterization to identify new binding sites and advance the study of SBSs and CBMs, allowing them to be detected in the absence of structural data.

Using Carbohydrate Interaction Assays to Reveal Novel Binding Sites in Carbohydrate Active Enzymes

PubMed Central

Wilkens, Casper; Dilokpimol, Adiphol; Nakai, Hiroyuki; Lewińska, Anna; Abou Hachem, Maher; Svensson, Birte

2016-01-01

Carbohydrate active enzymes often contain auxiliary binding sites located either on independent domains termed carbohydrate binding modules (CBMs) or as so-called surface binding sites (SBSs) on the catalytic module at a certain distance from the active site. The SBSs are usually critical for the activity of their cognate enzyme, though they are not readily detected in the sequence of a protein, but normally require a crystal structure of a complex for their identification. A variety of methods, including affinity electrophoresis (AE), insoluble polysaccharide pulldown (IPP) and surface plasmon resonance (SPR) have been used to study auxiliary binding sites. These techniques are complementary as AE allows monitoring of binding to soluble polysaccharides, IPP to insoluble polysaccharides and SPR to oligosaccharides. Here we show that these methods are useful not only for analyzing known binding sites, but also for identifying new ones, even without structural data available. We further verify the chosen assays discriminate between known SBS/CBM containing enzymes and negative controls. Altogether 35 enzymes are screened for the presence of SBSs or CBMs and several novel binding sites are identified, including the first SBS ever reported in a cellulase. This work demonstrates that combinations of these methods can be used as a part of routine enzyme characterization to identify new binding sites and advance the study of SBSs and CBMs, allowing them to be detected in the absence of structural data. PMID:27504624

Short-Term Effect of Two Semi-Occluded Vocal Tract Training Programs on the Vocal Quality of Future Occupational Voice Users: "Resonant Voice Training Using Nasal Consonants" versus "Straw Phonation"

ERIC Educational Resources Information Center

Meerschman, Iris; Van Lierde, Kristiane; Peeters, Karen; Meersman, Eline; Claeys, Sofie; D'haeseleer, Evelien

2017-01-01

Purpose: The purpose of this study was to determine the short-term effect of 2 semi-occluded vocal tract training programs, "resonant voice training using nasal consonants" versus "straw phonation," on the vocal quality of vocally healthy future occupational voice users. Method: A multigroup pretest--posttest randomized control…

Active-site protein dynamics and solvent accessibility in native Achromobacter cycloclastes copper nitrite reductase.

PubMed

Sen, Kakali; Horrell, Sam; Kekilli, Demet; Yong, Chin W; Keal, Thomas W; Atakisi, Hakan; Moreau, David W; Thorne, Robert E; Hough, Michael A; Strange, Richard W

2017-07-01

Microbial nitrite reductases are denitrifying enzymes that are a major component of the global nitrogen cycle. Multiple structures measured from one crystal (MSOX data) of copper nitrite reductase at 240 K, together with molecular-dynamics simulations, have revealed protein dynamics at the type 2 copper site that are significant for its catalytic properties and for the entry and exit of solvent or ligands to and from the active site. Molecular-dynamics simulations were performed using different protonation states of the key catalytic residues (Asp CAT and His CAT ) involved in the nitrite-reduction mechanism of this enzyme. Taken together, the crystal structures and simulations show that the Asp CAT protonation state strongly influences the active-site solvent accessibility, while the dynamics of the active-site 'capping residue' (Ile CAT ), a determinant of ligand binding, are influenced both by temperature and by the protonation state of Asp CAT . A previously unobserved conformation of Ile CAT is seen in the elevated temperature series compared with 100 K structures. DFT calculations also show that the loss of a bound water ligand at the active site during the MSOX series is consistent with reduction of the type 2 Cu atom.

An active site-tail interaction in the structure of hexahistidine-tagged Thermoplasma acidophilum citrate synthase

DOE PAGES

Murphy, Jesse R.; Donini, Stefano; Kappock, T. Joseph

2015-10-01

Citrate synthase (CS) plays a central metabolic role in aerobes and many other organisms. The CS reaction comprises two half-reactions: a Claisen aldol condensation of acetyl-CoA (AcCoA) and oxaloacetate (OAA) that forms citryl-CoA (CitCoA), and CitCoA hydrolysis. Protein conformational changes that `close' the active site play an important role in the assembly of a catalytically competent condensation active site. CS from the thermoacidophile Thermoplasma acidophilum (TpCS) possesses an endogenous Trp fluorophore that can be used to monitor the condensation reaction. The 2.2 Å resolution crystal structure of TpCS fused to a C-terminal hexahistidine tag (TpCSH6) reported here is an `open'more » structure that, when compared with several liganded TpCS structures, helps to define a complete path for active-site closure. One active site in each dimer binds a neighboring His tag, the first nonsubstrate ligand known to occupy both the AcCoA and OAA binding sites. Solution data collectively suggest that this fortuitous interaction is stabilized by the crystalline lattice. In conclusion, as a polar but almost neutral ligand, the active site-tail interaction provides a new starting point for the design of bisubstrate-analog inhibitors of CS.« less

An active site-tail interaction in the structure of hexahistidine-tagged Thermoplasma acidophilum citrate synthase.

PubMed

Murphy, Jesse R; Donini, Stefano; Kappock, T Joseph

2015-10-01

Citrate synthase (CS) plays a central metabolic role in aerobes and many other organisms. The CS reaction comprises two half-reactions: a Claisen aldol condensation of acetyl-CoA (AcCoA) and oxaloacetate (OAA) that forms citryl-CoA (CitCoA), and CitCoA hydrolysis. Protein conformational changes that `close' the active site play an important role in the assembly of a catalytically competent condensation active site. CS from the thermoacidophile Thermoplasma acidophilum (TpCS) possesses an endogenous Trp fluorophore that can be used to monitor the condensation reaction. The 2.2 Å resolution crystal structure of TpCS fused to a C-terminal hexahistidine tag (TpCSH6) reported here is an `open' structure that, when compared with several liganded TpCS structures, helps to define a complete path for active-site closure. One active site in each dimer binds a neighboring His tag, the first nonsubstrate ligand known to occupy both the AcCoA and OAA binding sites. Solution data collectively suggest that this fortuitous interaction is stabilized by the crystalline lattice. As a polar but almost neutral ligand, the active site-tail interaction provides a new starting point for the design of bisubstrate-analog inhibitors of CS.

A simplified method for active-site titration of lipases immobilised on hydrophobic supports.

PubMed

Nalder, Tim D; Kurtovic, Ivan; Barrow, Colin J; Marshall, Susan N

2018-06-01

The aim of this work was to develop a simple and accurate protocol to measure the functional active site concentration of lipases immobilised on highly hydrophobic supports. We used the potent lipase inhibitor methyl 4-methylumbelliferyl hexylphosphonate to titrate the active sites of Candida rugosa lipase (CrL) bound to three highly hydrophobic supports: octadecyl methacrylate (C18), divinylbenzene crosslinked methacrylate (DVB) and styrene. The method uses correction curves to take into account the binding of the fluorophore (4-methylumbelliferone, 4-MU) by the support materials. We showed that the uptake of the detection agent by the three supports is not linear relative to the weight of the resin, and that the uptake occurs in an equilibrium that is independent of the total fluorophore concentration. Furthermore, the percentage of bound fluorophore varied among the supports, with 50 mg of C18 and styrene resins binding approximately 64 and 94%, respectively. When the uptake of 4-MU was calculated and corrected for, the total 4-MU released via inhibition (i.e. the concentration of functional lipase active sites) could be determined via a linear relationship between immobilised lipase weight and total inhibition. It was found that the functional active site concentration of immobilised CrL varied greatly among different hydrophobic supports, with 56% for C18, compared with 14% for DVB. The described method is a simple and robust approach to measuring functional active site concentration in immobilised lipase samples. Copyright © 2018 Elsevier Inc. All rights reserved.

Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase.

PubMed

Fenwick, Michael K; Mehta, Angad P; Zhang, Yang; Abdelwahed, Sameh H; Begley, Tadhg P; Ealick, Steven E

2015-03-27

Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to generate a 5'-deoxyadenosyl radical. Canonical radical SAM enzymes are characterized by a β-barrel-like fold and SAM anchors to the differentiated iron of the cluster, which is located near the amino terminus and within the β-barrel, through its amino and carboxylate groups. Here we show that ThiC, the thiamin pyrimidine synthase in plants and bacteria, contains a tethered cluster-binding domain at its carboxy terminus that moves in and out of the active site during catalysis. In contrast to canonical radical SAM enzymes, we predict that SAM anchors to an additional active site metal through its amino and carboxylate groups. Superimposition of the catalytic domains of ThiC and glutamate mutase shows that these two enzymes share similar active site architectures, thus providing strong evidence for an evolutionary link between the radical SAM and adenosylcobalamin-dependent enzyme superfamilies.

Long-term intensive management increased carbon occluded in phytolith (PhytOC) in bamboo forest soils

NASA Astrophysics Data System (ADS)

Huang, Zhang-Ting; Li, Yong-Fu; Jiang, Pei-Kun; Chang, Scott X.; Song, Zhao-Liang; Liu, Juan; Zhou, Guo-Mo

2014-01-01

Carbon (C) occluded in phytolith (PhytOC) is highly stable at millennium scale and its accumulation in soils can help increase long-term C sequestration. Here, we report that soil PhytOC storage significantly increased with increasing duration under intensive management (mulching and fertilization) in Lei bamboo (Phyllostachys praecox) plantations. The PhytOC storage in 0-40 cm soil layer in bamboo plantations increased by 217 Mg C ha-1, 20 years after being converted from paddy fields. The PhytOC accumulated at 79 kg C ha-1 yr-1, a rate far exceeding the global mean long-term soil C accumulation rate of 24 kg C ha-1 yr-1 reported in the literature. Approximately 86% of the increased PhytOC came from the large amount of mulch applied. Our data clearly demonstrate the decadal scale management effect on PhytOC accumulation, suggesting that heavy mulching is a potential method for increasing long-term organic C storage in soils for mitigating global climate change.

[Nuclease activity of the recombinant plancitoxin-1-like proteins with mutations in the active site from Trichinella spiralis].

PubMed

Liao, Chengshui; Wang, Xiaoli; Tian, Wenjing; Zhang, Mengke; Zhang, Chunjie; Li, Yinju; Wu, Tingcai; Cheng, Xiangchao

2017-08-25

Although there are 125 predicted DNase Ⅱ-like family genes in the Trichinella spiralis genome, plancitoxin-1-like (Ts-Pt) contains the HKD motif, a typical conserved region of DNase Ⅱ, in N- and C-terminal. It is generally believed that histidine is the active site in DNase Ⅱ. To study the nuclease activity of recombinant Ts-Pt with mutations in the active site from T. spiralis, different fragments of the mutated Ts-Pt genes were cloned using overlap PCR technique and inserted into the expressing vector pET-28a(+), and transformed into Escherichia coli Rosseta (DE3). The fusion proteins were purified by Ni-NTA affinity chromatography and SDS-PAGE. Nuclease activity of the recombinant proteins was detected by agarose gel electrophoresis and nuclease-zymography. The recombinant plasmids harboring the mutated Ts-Pt genes were constructed and expressed as inclusive body in a prokaryotic expression system. After renaturation in vitro, the recombinant proteins had no nuclease activity according to agarose gel electrophoresis. However, the expressed proteins as inclusive body displayed the ability to degrade DNA after renaturation in gel. And the nuclease activity was not affected after subjected to mutation of active site in N- and C-termini of Ts-Pt. These results provide the basis to study the relationship between DNase Ⅱ-like protein family and infection of T. spiralis.

A Variable Active Site Residue Influences the Kinetics of Response Regulator Phosphorylation and Dephosphorylation.

PubMed

Immormino, Robert M; Silversmith, Ruth E; Bourret, Robert B

2016-10-04

Two-component regulatory systems, minimally composed of a sensor kinase and a response regulator protein, are common mediators of signal transduction in microorganisms. All response regulators contain a receiver domain with conserved active site residues that catalyze the signal activating and deactivating phosphorylation and dephosphorylation reactions. We explored the impact of variable active site position T+1 (one residue C-terminal to the conserved Thr/Ser) on reaction kinetics and signaling fidelity, using wild type and mutant Escherichia coli CheY, CheB, and NarL to represent the three major sequence classes observed across response regulators: Ala/Gly, Ser/Thr, and Val/Ile/Met, respectively, at T+1. Biochemical and structural data together suggested that different amino acids at T+1 impacted reaction kinetics by altering access to the active site while not perturbing overall protein structure. A given amino acid at position T+1 had similar effects on autodephosphorylation in each protein background tested, likely by modulating access of the attacking water molecule to the active site. Similarly, rate constants for CheY autophosphorylation with three different small molecule phosphodonors were consistent with the steric constraints on access to the phosphorylation site arising from combination of specific phosphodonors with particular amino acids at T+1. Because other variable active site residues also influence response regulator phosphorylation biochemistry, we began to explore how context (here, the amino acid at T+2) affected the influence of position T+1 on CheY autocatalytic reactions. Finally, position T+1 affected the fidelity and kinetics of phosphotransfer between sensor kinases and response regulators but was not a primary determinant of their interaction.

Insights into the glycyl radical enzyme active site of benzylsuccinate synthase: a computational study.

PubMed

Bharadwaj, Vivek S; Dean, Anthony M; Maupin, C Mark

2013-08-21

The fumarate addition reaction, catalyzed by the enzyme benzylsuccinate synthase (BSS), is considered to be one of the most intriguing and energetically challenging reactions in biology. BSS belongs to the glycyl radical enzyme family and catalyzes the fumarate addition reaction, which enables microorganisms to utilize hydrocarbons as an energy source under anaerobic conditions. Unfortunately, the extreme sensitivity of the glycyl radical to oxygen has hampered the structural and kinetic characterization of BSS, thereby limiting our knowledge on this enzyme. To enhance our molecular-level understanding of BSS, a computational approach involving homology modeling, docking studies, and molecular dynamics (MD) simulations has been used to deduce the structure of BSS's catalytic subunit (BSSα) and illuminate the molecular basis for the fumarate addition reaction. We have identified two conserved and distinct binding pockets at the BSSα active site: a hydrophobic pocket for toluene binding and a polar pocket for fumaric acid binding. Subsequent dynamical and energetic evaluations have identified Glu509, Ser827, Leu390, and Phe384 as active site residues critical for substrate binding. The orientation of substrates at the active site observed in MD simulations is consistent with experimental observations of the syn addition of toluene to fumaric acid. It is also found that substrate binding tightens the active site and restricts the conformational flexibility of the thiyl radical, leading to hydrogen transfer distances conducive to the proposed reaction mechanism. The stability of substrates at the active site and the occurrence of feasible radical transfer distances between the thiyl radical, substrates, and the active site glycine indicate a substrate-assisted radical transfer pathway governing fumarate addition.

Flexibility and Stability Trade-Off in Active Site of Cold-Adapted Pseudomonas mandelii Esterase EstK.

PubMed

Truongvan, Ngoc; Jang, Sei-Heon; Lee, ChangWoo

2016-06-28

Cold-adapted enzymes exhibit enhanced conformational flexibility, especially in their active sites, as compared with their warmer-temperature counterparts. However, the mechanism by which cold-adapted enzymes maintain their active site stability is largely unknown. In this study, we investigated the role of conserved D308-Y309 residues located in the same loop as the catalytic H307 residue in the cold-adapted esterase EstK from Pseudomonas mandelii. Mutation of D308 and/or Y309 to Ala or deletion resulted in increased conformational flexibility. Particularly, the D308A or Y309A mutant showed enhanced substrate affinity and catalytic rate, as compared with wild-type EstK, via enlargement of the active site. However, all mutant EstK enzymes exhibited reduced thermal stability. The effect of mutation was greater for D308 than Y309. These results indicate that D308 is not preferable for substrate selection and catalytic activity, whereas hydrogen bond formation involving D308 is critical for active site stabilization. Taken together, conformation of the EstK active site is constrained via flexibility-stability trade-off for enzyme catalysis and thermal stability. Our study provides further insights into active site stabilization of cold-adapted enzymes.

Well-Defined Metal-O6 in Metal-Catecholates as a Novel Active Site for Oxygen Electroreduction.

PubMed

Liu, Xuan-He; Hu, Wei-Li; Jiang, Wen-Jie; Yang, Ya-Wen; Niu, Shuai; Sun, Bing; Wu, Jing; Hu, Jin-Song

2017-08-30

Metal-nitrogen coordination sites, M-N x (M = Fe, Co, Ni, etc.), have shown great potential to replace platinum group materials as electrocatalysts for oxygen reduction reaction (ORR). However, the real active site in M-N x is still vague to date due to their complicated structure and composition. It is therefore highly desirable but challenging to develop ORR catalysts with novel and clear active sites, which could meet the needs of comprehensive understanding of structure-function relationships and explore new cost-effective and efficient ORR electrocatalysts. Herein, well-defined M-O 6 coordination in metal-catecholates (M-CATs, M = Ni or Co) is discovered to be catalytically active for ORR via a four-electron-dominated pathway. In view of no pyrolysis involved and unambiguous crystalline structure of M-CATs, the M-O 6 octahedral coordination site with distinct structure is determined as a new type of active site for ORR. These findings extend the scope of metal-nonmetal coordination as an active site for ORR and pave a way for bottom-up design of novel electrocatalysts containing M-O 6 coordination.

The structure of amylosucrase from Deinococcus radiodurans has an unusual open active-site topology.

PubMed

Skov, Lars K; Pizzut-Serin, Sandra; Remaud-Simeon, Magali; Ernst, Heidi A; Gajhede, Michael; Mirza, Osman

2013-09-01

Amylosucrases (ASes) catalyze the formation of an α-1,4-glucosidic linkage by transferring a glucosyl unit from sucrose onto an acceptor α-1,4-glucan. To date, several ligand-bound crystal structures of wild-type and mutant ASes from Neisseria polysaccharea and Deinococcus geothermalis have been solved. These structures all display a very similar overall conformation with a deep pocket leading to the site for transglucosylation, subsite -1. This has led to speculation on how sucrose enters the active site during glucan elongation. In contrast to previous studies, the AS structure from D. radiodurans presented here has a completely empty -1 subsite. This structure is strikingly different from other AS structures, as an active-site-lining loop comprising residues Leu214-Asn225 is found in a previously unobserved conformation. In addition, a large loop harbouring the conserved active-site residues Asp133 and Tyr136 is disordered. The result of the changed loop conformations is that the active-site topology is radically changed, leaving subsite -1 exposed and partially dismantled. This structure provides novel insights into the dynamics of ASes and comprises the first structural support for an elongation mechanism that involves considerable conformational changes to modulate accessibility to the sucrose-binding site and thereby allows successive cycles of glucosyl-moiety transfer to a growing glucan chain.

Active chemisorption sites in functionalized ionic liquids for carbon capture.

PubMed

Cui, Guokai; Wang, Jianji; Zhang, Suojiang

2016-07-25

Development of novel technologies for the efficient and reversible capture of CO2 is highly desired. In the last decade, CO2 capture using ionic liquids has attracted intensive attention from both academia and industry, and has been recognized as a very promising technology. Recently, a new approach has been developed for highly efficient capture of CO2 by site-containing ionic liquids through chemical interaction. This perspective review focuses on the recent advances in the chemical absorption of CO2 using site-containing ionic liquids, such as amino-based ionic liquids, azolate ionic liquids, phenolate ionic liquids, dual-functionalized ionic liquids, pyridine-containing ionic liquids and so on. Other site-containing liquid absorbents such as amine-based solutions, switchable solvents, and functionalized ionic liquid-amine blends are also investigated. Strategies have been discussed for how to activate the existent reactive sites and develop novel reactive sites by physical and chemical methods to enhance CO2 absorption capacity and reduce absorption enthalpy. The carbon capture mechanisms of these site-containing liquid absorbents are also presented. Particular attention has been paid to the latest progress in CO2 capture in multiple-site interactions by amino-free anion-functionalized ionic liquids. In the last section, future directions and prospects for carbon capture by site-containing ionic liquids are outlined.

Structural evolution of luciferase activity in Zophobas mealworm AMP/CoA-ligase (protoluciferase) through site-directed mutagenesis of the luciferin binding site.

PubMed

Prado, R A; Barbosa, J A; Ohmiya, Y; Viviani, V R

2011-07-01

The structural origin and evolution of bioluminescent activity of beetle luciferases from AMP/CoA ligases remains a mystery. Previously we cloned the luciferase-like enzyme from Zophobas morio mealworm, a reasonable protoluciferase model that could shine light on this mystery. Kinetic characterization and studies with D- and L-luciferin and their adenylates showed that stereoselectivity constitutes a critical feature for the origin of luciferase activity in AMP/CoA ligases. Comparison of the primary structures and modeling studies of this protoluciferase and the three main families of beetle luciferases showed that the carboxylic acid substrate binding site of this enzyme is smaller and more hydrophobic than the luciferin binding site of beetle luciferases, showing several substitutions of otherwise conserved residues. Thus, here we performed a site-directed mutagenesis survey of the carboxylic binding site motifs of the protoluciferase by replacing their residues by the respective conserved ones found in beetle luciferases in order to identify the structural determinants of luciferase/oxygenase activity. Although most of the substitutions had negative impact on the luminescence activity of the protoluciferase, only the substitution I327T improved the luminescence activity, resulting in a broad and 15 nm blue-shifted luminescence spectrum. Such substitution indicates the importance of the loop motif 322YGMSEI327 (341YGLTETT347 in Photinus pyralis luciferase) for luciferase activity, and indicates a possible route for the evolution of bioluminescence function of beetle luciferases.

Probing the Active Surface Sites for CO Reduction on Oxide-Derived Copper Electrocatalysts

DOE PAGES

Verdaguer-Casadevall, Arnau; Li, Christina W.; Johansson, Tobias P.; ...

2015-07-30

CO electroreduction activity on oxide-derived Cu (OD-Cu) was found to correlate with metastable surface features that bind CO strongly. OD-Cu electrodes prepared by H 2 reduction of Cu 2O precursors reduce CO to acetate and ethanol with nearly 50% Faradaic efficiency at moderate overpotential. Temperature-programmed desorption of CO on OD-Cu revealed the presence of surface sites with strong CO binding that are distinct from the terraces and stepped sites found on polycrystalline Cu foil. After annealing at 350 °C, the surface-area corrected current density for CO reduction is 44-fold lower and the Faradaic efficiency is less than 5%. These changesmore » are accompanied by a reduction in the proportion of strong CO binding sites. Here, we propose that the active sites for CO reduction on OD-Cu surfaces are strong CO binding sites that are supported by grain boundaries. Uncovering these sites is a first step toward understanding the surface chemistry necessary for efficient CO electroreduction.« less

Substrate Shuttling Between Active Sites of Uroporphyrinogen Decarboxylase in Not Required to Generate Coproporphyrinogen

DOE Office of Scientific and Technical Information (OSTI.GOV)

Phillips, J.; Warby, C; Whitby, F

2009-01-01

Uroporphyrinogen decarboxylase (URO-D; EC 4.1.1.37), the fifth enzyme of the heme biosynthetic pathway, is required for the production of heme, vitamin B12, siroheme, and chlorophyll precursors. URO-D catalyzes the sequential decarboxylation of four acetate side chains in the pyrrole groups of uroporphyrinogen to produce coproporphyrinogen. URO-D is a stable homodimer, with the active-site clefts of the two subunits adjacent to each other. It has been hypothesized that the two catalytic centers interact functionally, perhaps by shuttling of reaction intermediates between subunits. We tested this hypothesis by construction of a single-chain protein (single-chain URO-D) in which the two subunits were connectedmore » by a flexible linker. The crystal structure of this protein was shown to be superimposable with wild-type activity and to have comparable catalytic activity. Mutations that impaired one or the other of the two active sites of single-chain URO-D resulted in approximately half of wild-type activity. The distributions of reaction intermediates were the same for mutant and wild-type sequences and were unaltered in a competition experiment using I and III isomer substrates. These observations indicate that communication between active sites is not required for enzyme function and suggest that the dimeric structure of URO-D is required to achieve conformational stability and to create a large active-site cleft.« less

A DFT Study of Tungsten-Methylidene Formation on a W/ZSM-5 Zeolite: The Metathesis Active Site.

PubMed

Maihom, Thana; Probst, Michael; Limtrakul, Jumras

2015-10-26

Tungsten-methylidene formation from ethene on either the W(IV) , W(V) , or W(VI) active sites of a W/ZSM-5 zeolite is investigated by using the M06-L functional. The reaction is assumed to proceed in two steps; the first step is the [2+2] cycloaddition between ethene and the W-O active site to form an oxametallacycle intermediate. The intermediate is then decomposed to produce the W-methylidene active site from the metathesis reaction. The overall activation barrier of the reaction on W(VI) (27.3 kcal mol(-1) ) is considerably lower than the ones for W(IV) and W(V) (69.4 and 37.1 kcal mol(-1) , respectively). Moreover, the reaction involving the W(VI) site also stabilizes intermediates and products to a larger extent than the ones on the W(IV) and W(V) sites. As a result, we have demonstrated that the reaction of the W-methylidene metathesis active site is both kinetically and thermodynamically favored to occur on the W(VI) active site of the zeolite. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Artificial Metalloproteins Containing Co 4O 4Cubane Active Sites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Olshansky, Lisa; Huerta-Lavorie, Raul; Nguyen, Andy I.

Artificial metalloproteins (ArMs) containing Co 4O 4 cubane active sites were constructed via biotin-streptavidin technology. Stabilized by hydrogen bonds (H-bonds), terminal and cofacial Co III-OH 2 moieties are observed crystallographically in a series of immobilized cubane sites. Solution electrochemistry provided correlations of oxidation potential and pH. For variants containing Ser and Phe adjacent to the metallocofactor, 1e -/1H + chemistry predominates until pH 8, above which the oxidation becomes pH-independent. Installation of Tyr proximal to the Co 4O 4 active site provided a single H-bond to one of a set of cofacial Co III-OH 2 groups. With this variant, multi-emore » - /multi-H + chemistry is observed, along with a change in mechanism at pH 9.5 that is consistent with Tyr deprotonation. Finally, with structural similarities to both the oxygen-evolving complex of photosystem II (H-bonded Tyr) and to thin film water oxidation catalysts (Co 4O 4 core), these findings bridge synthetic and biological systems for water oxidation, highlighting the importance of secondary sphere interactions in mediating multi-e - /multi-H + reactivity.« less

Artificial Metalloproteins Containing Co 4O 4Cubane Active Sites

DOE PAGES

Olshansky, Lisa; Huerta-Lavorie, Raul; Nguyen, Andy I.; ...

2018-02-05

Artificial metalloproteins (ArMs) containing Co 4O 4 cubane active sites were constructed via biotin-streptavidin technology. Stabilized by hydrogen bonds (H-bonds), terminal and cofacial Co III-OH 2 moieties are observed crystallographically in a series of immobilized cubane sites. Solution electrochemistry provided correlations of oxidation potential and pH. For variants containing Ser and Phe adjacent to the metallocofactor, 1e -/1H + chemistry predominates until pH 8, above which the oxidation becomes pH-independent. Installation of Tyr proximal to the Co 4O 4 active site provided a single H-bond to one of a set of cofacial Co III-OH 2 groups. With this variant, multi-emore » - /multi-H + chemistry is observed, along with a change in mechanism at pH 9.5 that is consistent with Tyr deprotonation. Finally, with structural similarities to both the oxygen-evolving complex of photosystem II (H-bonded Tyr) and to thin film water oxidation catalysts (Co 4O 4 core), these findings bridge synthetic and biological systems for water oxidation, highlighting the importance of secondary sphere interactions in mediating multi-e - /multi-H + reactivity.« less

Management of a large atrial septal occluder embolized to the left ventricular outflow tract without the use of cardiac surgery.

PubMed

Loh, Joshua P; Satler, Lowell F; Slack, Michael C

2014-09-01

Transcatheter closure of secundum-type atrial septal defects (ASDs) using the AMPLATZER™ Septal Occluder (ASO) has been in use for more than a decade since its US Food and Drug Administration approval in 2001. Device embolization remains an uncommon complication, which can sometimes occur after the initial deployment. Previous reports of ASO devices embolized to the left ventricle have primarily been managed by open-heart surgical retrieval. We present a case of an ASO device embolized to the left ventricular outflow tract (LVOT) 18 hr after initial implantation, which was successfully retrieved percutaneously, followed by successful closure of the ASD using a larger device. © 2014 Wiley Periodicals, Inc.

Understanding Which Residues of the Active Site and Loop Structure of a Tyrosine Aminomutase Define Its Mutase and Lyase Activities.

PubMed

Attanayake, Gayanthi; Walter, Tyler; Walker, Kevin D

2018-05-30

Site-directed mutations and substrate analogues were used to gain insights into the branch-point reaction of the 3,5-dihydro-5-methylidene-4 H-imidazol-4-one (MIO)-tyrosine aminomutase from Oryza sativa ( OsTAM). Exchanging the active residues of OsTAM (Y125C/N446K) for those in a phenylalanine aminomutase TcPAM altered its substrate specificity from tyrosine to phenylalanine. The aminomutase mechanism of OsTAM surprisingly changed almost exclusively to that of an ammonia lyase making cinnamic acid (>95%) over β-phenylalanine [Walter, T., et al. (2016) Biochemistry 55, 3497-3503]. We hypothesized that the missing electronics or sterics on the aryl ring of the phenylalanine substrate, compared with the sizable electron-donating hydroxyl of the natural tyrosine substrate, influenced the unexpected lyase reactivity of the OsTAM mutant. The double mutant was incubated with 16 α-phenylalanine substituent analogues of varying electronic strengths and sterics. The mutant converted each analogue principally to its acrylate with ∼50% conversion of the p-Br substrate, making only a small amount of the β-amino acid. The inner loop structure over the entrance to the active site was also mutated to assess how the lyase and mutase activities are affected. An OsTAM loop mutant, matching the loop residues of TcPAM, still chiefly made >95% of the acrylate from each substrate. A combined active site:loop mutant was most reactive but remained a lyase, making 10-fold more acrylates than other mutants did. While mutations within the active site changed the substrate specificity of OsTAM, continued exploration is needed to fully understand the interplay among the inner loop, the substrate, and the active site in defining the mutase and lyase activities.

Oxygen Activation at the Active Site of a Fungal Lytic Polysaccharide Monooxygenase

DOE Office of Scientific and Technical Information (OSTI.GOV)

O'Dell, William B.; Agarwal, Pratul K.; Meilleur, Flora

Lytic polysaccharide monooxygenases have attracted vast attention owing to their abilities to disrupt glycosidic bonds via oxidation instead of hydrolysis and to enhance enzymatic digestion of recalcitrant substrates including chitin and cellulose. Here, we determined the high-resolution X-ray crystal structures of an enzyme from Neurospora crassa in the resting state and of a copper(II) dioxo intermediate complex formed in the absence of substrate. X-ray crystal structures also revealed “pre-bound” molecular oxygen adjacent to the active site. An examination of protonation states enabled by neutron crystallography and density functional theory calculations identified a role for a conserved histidine in promoting oxygenmore » activation. Our results provide a new structural description of oxygen activation by substrate free lytic polysaccharide monooxygenases and provide insights that can be extended to reactivity in the enzyme–substrate complex.« less

Oxygen Activation at the Active Site of a Fungal Lytic Polysaccharide Monooxygenase

DOE PAGES

O'Dell, William B.; Agarwal, Pratul K.; Meilleur, Flora

2016-12-22

Lytic polysaccharide monooxygenases have attracted vast attention owing to their abilities to disrupt glycosidic bonds via oxidation instead of hydrolysis and to enhance enzymatic digestion of recalcitrant substrates including chitin and cellulose. Here, we determined the high-resolution X-ray crystal structures of an enzyme from Neurospora crassa in the resting state and of a copper(II) dioxo intermediate complex formed in the absence of substrate. X-ray crystal structures also revealed “pre-bound” molecular oxygen adjacent to the active site. An examination of protonation states enabled by neutron crystallography and density functional theory calculations identified a role for a conserved histidine in promoting oxygenmore » activation. Our results provide a new structural description of oxygen activation by substrate free lytic polysaccharide monooxygenases and provide insights that can be extended to reactivity in the enzyme–substrate complex.« less

Fragment-based identification of determinants of conformational and spectroscopic change at the ricin active site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carra,J.; McHugh, C.; Mulligan, S.

2007-01-01

We found that amide ligands can bind weakly but specifically to the ricin active site, producing significant shifts in positions of the critical active site residues Arg180 and Tyr80. These results indicate that fragment-based drug discovery methods are capable of identifying minimal bonding determinants of active-site side-chain rearrangements and the mechanistic origins of spectroscopic shifts. Our results suggest that tryptophan fluorescence provides a sensitive probe for the geometric relationship of arginine-tryptophan pairs, which often have significant roles in protein function. Using the unusual characteristics of the RTA system, we measured the still controversial thermodynamic changes of site-specific urea binding tomore » a protein, results that are relevant to understanding the physical mechanisms of protein denaturation.« less

Active Site Desolvation and Thermostability Trade-Offs in the Evolution of Catalytically Diverse Triazine Hydrolases.

PubMed

Sugrue, Elena; Carr, Paul D; Scott, Colin; Jackson, Colin J

2016-11-15

The desolvation of ionizable residues in the active sites of enzymes and the subsequent effects on catalysis and thermostability have been studied in model systems, yet little about how enzymes can naturally evolve to include active sites with highly reactive and desolvated charges is known. Variants of triazine hydrolase (TrzN) with significant differences in their active sites have been isolated from different bacterial strains: TrzN from Nocardioides sp. strain MTD22 contains a catalytic glutamate residue (Glu241) that is surrounded by hydrophobic and aromatic second-shell residues (Pro214 and Tyr215), whereas TrzN from Nocardioides sp. strain AN3 has a noncatalytic glutamine residue (Gln241) at an equivalent position, surrounded by hydrophilic residues (Thr214 and His215). To understand how and why these variants have evolved, a series of TrzN mutants were generated and characterized. These results show that desolvation by second-shell residues increases the pK a of Glu241, allowing it to act as a general acid at neutral pH. However, significant thermostability trade-offs are required to incorporate the ionizable Glu241 in the active site and to then enclose it in a hydrophobic microenvironment. Analysis of high-resolution crystal structures shows that there are almost no structural changes to the overall configuration of the active site due to these mutations, suggesting that the changes in activity and thermostability are purely based on the altered electrostatics. The natural evolution of these enzyme isoforms provides a unique system in which to study the fundamental process of charged residue desolvation in enzyme catalysis and its relative contribution to the creation and evolution of an enzyme active site.

76 FR 30696 - Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-26

... DEPARTMENT OF ENERGY Reimbursement for Costs of Remedial Action at Active Uranium and Thorium...) acceptance of claims in FY 2011 from eligible active uranium and thorium processing site licensees for... incurred by licensees at active uranium and thorium processing sites to remediate byproduct material...

Oscillatory Activity in the Infant Brain and the Representation of Small Numbers

PubMed Central

Leung, Sumie; Mareschal, Denis; Rowsell, Renee; Simpson, David; Iaria, Leon; Grbic, Amanda; Kaufman, Jordy

2016-01-01

Gamma-band oscillatory activity (GBA) is an established neural signature of sustained occluded object representation in infants and adults. However, it is not yet known whether the magnitude of GBA in the infant brain reflects the quantity of occluded items held in memory. To examine this, we compared GBA of 6–8 month-old infants during occlusion periods after the representation of two objects vs. that of one object. We found that maintaining a representation of two objects during occlusion resulted in significantly greater GBA relative to maintaining a single object. Further, this enhancement was located in the right occipital region, which is consistent with previous object representation research in adults and infants. We conclude that enhanced GBA reflects neural processes underlying infants’ representation of small numbers. PMID:26903821

Active Site and Remote Contributions to Catalysis in Methylthioadenosine Nucleosidases

DOE PAGES

Thomas, Keisha; Cameron, Scott A.; Almo, Steven C.; ...

2015-03-25

5'-Methylthioadenosine/S-adenosyl-l-homocysteine nucleosidases (MTANs) catalyze the hydrolysis of 5'-methylthioadenosine to adenine and 5-methylthioribose. The amino acid sequences of the MTANs from Vibrio cholerae (VcMTAN) and Escherichia coli (EcMTAN) are 60% identical and 75% similar. Protein structure folds and kinetic properties are similar. However, binding of transition-state analogues is dominated by favorable entropy in VcMTAN and by enthalpy in EcMTAN. Catalytic sites of VcMTAN and EcMTAN in contact with reactants differ by two residues; Ala113 and Val153 in VcMTAN are Pro113 and Ile152, respectively, in EcMTAN. Here, we mutated the VcMTAN catalytic site residues to match those of EcMTAN in anticipation ofmore » altering its properties toward EcMTAN. Inhibition of VcMTAN by transition-state analogues required filling both active sites of the homodimer. However, in the Val153Ile mutant or double mutants, transition-state analogue binding at one site caused complete inhibition. Therefore, a single amino acid, Val153, alters the catalytic site cooperativity in VcMTAN. The transition-state analogue affinity and thermodynamics in mutant VcMTAN became even more unlike those of EcMTAN, the opposite of expectations from catalytic site similarity; thus, catalytic site contacts in VcMTAN are unable to recapitulate the properties of EcMTAN. X-ray crystal structures of EcMTAN, VcMTAN, and a multiple-site mutant of VcMTAN most closely resembling EcMTAN in catalytic site contacts show no major protein conformational differences. In conclusion, the overall protein architectures of these closely related proteins are implicated in contributing to the catalytic site differences.« less

Active Site and Remote Contributions to Catalysis in Methylthioadenosine Nucleosidases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thomas, Keisha; Cameron, Scott A.; Almo, Steven C.

5'-Methylthioadenosine/S-adenosyl-l-homocysteine nucleosidases (MTANs) catalyze the hydrolysis of 5'-methylthioadenosine to adenine and 5-methylthioribose. The amino acid sequences of the MTANs from Vibrio cholerae (VcMTAN) and Escherichia coli (EcMTAN) are 60% identical and 75% similar. Protein structure folds and kinetic properties are similar. However, binding of transition-state analogues is dominated by favorable entropy in VcMTAN and by enthalpy in EcMTAN. Catalytic sites of VcMTAN and EcMTAN in contact with reactants differ by two residues; Ala113 and Val153 in VcMTAN are Pro113 and Ile152, respectively, in EcMTAN. Here, we mutated the VcMTAN catalytic site residues to match those of EcMTAN in anticipation ofmore » altering its properties toward EcMTAN. Inhibition of VcMTAN by transition-state analogues required filling both active sites of the homodimer. However, in the Val153Ile mutant or double mutants, transition-state analogue binding at one site caused complete inhibition. Therefore, a single amino acid, Val153, alters the catalytic site cooperativity in VcMTAN. The transition-state analogue affinity and thermodynamics in mutant VcMTAN became even more unlike those of EcMTAN, the opposite of expectations from catalytic site similarity; thus, catalytic site contacts in VcMTAN are unable to recapitulate the properties of EcMTAN. X-ray crystal structures of EcMTAN, VcMTAN, and a multiple-site mutant of VcMTAN most closely resembling EcMTAN in catalytic site contacts show no major protein conformational differences. In conclusion, the overall protein architectures of these closely related proteins are implicated in contributing to the catalytic site differences.« less

Jack bean urease: the effect of active-site binding inhibitors on the reactivity of enzyme thiol groups.

PubMed

Krajewska, Barbara; Zaborska, Wiesława

2007-10-01

In view of the complexity of the role of the active site flap cysteine in the urease catalysis, in this work we studied how the presence of typical active-site binding inhibitors of urease, phenylphosphorodiamidate (PPD), acetohydroxamic acid (AHA), boric acid and fluoride, affects the reactivity of enzyme thiol groups, the active site flap thiol in particular. For that the inhibitor-urease complexes were prepared with excess inhibitors and had their thiol groups titrated with DTNB. The effects observed were analyzed in terms of the structures of the inhibitor-urease complexes reported in the literature. We found that the effectiveness in preventing the active site cysteine from the modification by disulfides, varied among the inhibitors studied, even though they all bind to the active site. The variations were accounted for by different extents of geometrical distortion in the active site that the inhibitors introduced upon binding, leaving the flap either open in AHA-, boric acid- and fluoride-inhibited urease, like in the native enzyme or closed in PPD-inhibited urease. Among the inhibitors, only PPD was found to be able to thoroughly protect the flap cysteines from the further reaction with disulfides, this apparently resulting from the closed conformation of the flap. Accordingly, in practical terms PPD may be regarded as the most suitable inhibitor for active-site protection experiments in inhibition studies of urease.

Stringency of the 2-His–1-Asp Active-Site Motif in Prolyl 4-Hydroxylase

PubMed Central

Gorres, Kelly L.; Pua, Khian Hong; Raines, Ronald T.

2009-01-01

The non-heme iron(II) dioxygenase family of enzymes contain a common 2-His–1-carboxylate iron-binding motif. These enzymes catalyze a wide variety of oxidative reactions, such as the hydroxylation of aliphatic C–H bonds. Prolyl 4-hydroxylase (P4H) is an α-ketoglutarate-dependent iron(II) dioxygenase that catalyzes the post-translational hydroxylation of proline residues in protocollagen strands, stabilizing the ensuing triple helix. Human P4H residues His412, Asp414, and His483 have been identified as an iron-coordinating 2-His–1-carboxylate motif. Enzymes that catalyze oxidative halogenation do so by a mechanism similar to that of P4H. These halogenases retain the active-site histidine residues, but the carboxylate ligand is replaced with a halide ion. We replaced Asp414 of P4H with alanine (to mimic the active site of a halogenase) and with glycine. These substitutions do not, however, convert P4H into a halogenase. Moreover, the hydroxylase activity of D414A P4H cannot be rescued with small molecules. In addition, rearranging the two His and one Asp residues in the active site eliminates hydroxylase activity. Our results demonstrate a high stringency for the iron-binding residues in the P4H active site. We conclude that P4H, which catalyzes an especially demanding chemical transformation, is recalcitrant to change. PMID:19890397

Improving the neutral phytase activity from Bacillus amyloliquefaciens DSM 1061 by site-directed mutagenesis.

PubMed

Xu, Wei; Shao, Rong; Wang, Zupeng; Yan, Xiuhua

2015-03-01

Neutral phytase is used as a feed additive for degradation of anti-nutritional phytate in aquatic feed industry. Site-directed mutagenesis of Bacillus amyloliquefaciens DSM 1061 phytase was performed with an aim to increase its activity. Mutation residues were chosen based on multiple sequence alignments and structure analysis of neutral phytsaes from different microorganisms. The mutation sites on surface (D148E, S197E and N156E) and around the active site (D52E) of phytase were selected. Analysis of the phytase variants showed that the specific activities of mutants D148E and S197E remarkably increased by about 35 and 13% over a temperature range of 40-75 °C at pH 7.0, respectively. The k cat of mutants D148E and S197E were 1.50 and 1.25 times than that of the wild-type phytase, respectively. Both D148E and S197E showed much higher thermostability than that of the wild-type phytase. However, mutants N156E and D52E led to significant loss of specific activity of the enzyme. Structural analysis revealed that these mutations may affect conformation of the active site of phytase. The present mutant phytases D148E and S197E with increased activities and thermostabilities have application potential as additives in aquaculture feed.

Transfer hydrogenation over sodium-modified ceria: Enrichment of redox sites active for alcohol dehydrogenation

DOE PAGES

Nelson, Nicholas C.; Boote, Brett W.; Naik, Pranjali; ...

2017-01-17

Ceria (CeO 2) and sodium-modified ceria (Ce-Na) were prepared through combustion synthesis. Palladium was deposited onto the supports (Pd/CeO 2 and Pd/Ce-Na) and their activity for the aqueous-phase transfer hydrogenation of phenol using 2-propanol under liquid flow conditions was studied. Pd/Ce-Na showed a marked increase (6×) in transfer hydrogenation activity over Pd/CeO 2. Material characterization indicated that water-stable sodium species were not doped into the ceria lattice, but rather existed as subsurface carbonates. Modification of ceria by sodium provided more adsorption and redox active sites (i.e. defects) for 2-propanol dehydrogenation. This effect was an intrinsic property of the Ce-Na supportmore » and independent of Pd. The redox sites active for 2-propanol dehydrogenation were thermodynamically equivalent on both supports/catalysts. At high phenol concentrations, the reaction was limited by 2-propanol adsorption. Furthermore, the difference in catalytic activity was attributed to the different numbers of 2-propanol adsorption and redox active sites on each catalyst.« less

Improved ethanol electrooxidation performance by shortening Pd-Ni active site distance in Pd-Ni-P nanocatalysts

NASA Astrophysics Data System (ADS)

Chen, Lin; Lu, Lilin; Zhu, Hengli; Chen, Yueguang; Huang, Yu; Li, Yadong; Wang, Leyu

2017-01-01

Incorporating oxophilic metals into noble metal-based catalysts represents an emerging strategy to improve the catalytic performance of electrocatalysts in fuel cells. However, effects of the distance between the noble metal and oxophilic metal active sites on the catalytic performance have rarely been investigated. Herein, we report on ultrasmall (~5 nm) Pd-Ni-P ternary nanoparticles for ethanol electrooxidation. The activity is improved up to 4.95 A per mgPd, which is 6.88 times higher than commercial Pd/C (0.72 A per mgPd), by shortening the distance between Pd and Ni active sites, achieved through shape transformation from Pd/Ni-P heterodimers into Pd-Ni-P nanoparticles and tuning the Ni/Pd atomic ratio to 1:1. Density functional theory calculations reveal that the improved activity and stability stems from the promoted production of free OH radicals (on Ni active sites) which facilitate the oxidative removal of carbonaceous poison and combination with CH3CO radicals on adjacent Pd active sites.

Testing the applicability of rapid on-site enzymatic activity detection for surface water monitoring

NASA Astrophysics Data System (ADS)

Stadler, Philipp; Vogl, Wolfgang; Juri, Koschelnik; Markus, Epp; Maximilian, Lackner; Markus, Oismüller; Monika, Kumpan; Peter, Strauss; Regina, Sommer; Gabriela, Ryzinska-Paier; Farnleitner Andreas, H.; Matthias, Zessner

2015-04-01

On-site detection of enzymatic activities has been suggested as a rapid surrogate for microbiological pollution monitoring of water resources (e.g. using glucuronidases, galactosidases, esterases). Due to the possible short measuring intervals enzymatic methods have high potential as near-real time water quality monitoring tools. This presentation describes results from a long termed field test. For twelve months, two ColiMinder devices (Vienna Water Monitoring, Austria) for on-site determination of enzymatic activity were tested for stream water monitoring at the experimental catchment HOAL (Hydrological Open Air Laboratory, Center for Water Resource Systems, Vienna University of Technology). The devices were overall able to follow and reflect the diverse hydrological and microbiological conditions of the monitored stream during the test period. Continuous data in high temporal resolution captured the course of enzymatic activity in stream water during diverse rainfall events. The method also proofed sensitive enough to determine diurnal fluctuations of enzymatic activity in stream water during dry periods. The method was able to capture a seasonal trend of enzymatic activity in stream water that matches the results gained from Colilert18 analysis for E. coli and coliform bacteria of monthly grab samples. Furthermore the comparison of ColiMinder data with measurements gained at the same test site with devices using the same method but having different construction design (BACTcontrol, microLAN) showed consistent measuring results. Comparative analysis showed significant differences between measured enzymatic activity (modified fishman units and pmol/min/100ml) and cultivation based analyses (most probable number, colony forming unit). Methods of enzymatic activity measures are capable to detect ideally the enzymatic activity caused by all active target bacteria members, including VBNC (viable but nonculturable) while cultivation based methods cannot detect VBNC

Agonist activation of α7 nicotinic acetylcholine receptors via an allosteric transmembrane site

PubMed Central

Gill, JasKiran K.; Savolainen, Mari; Young, Gareth T.; Zwart, Ruud; Sher, Emanuele; Millar, Neil S.

2011-01-01

Conventional nicotinic acetylcholine receptor (nAChR) agonists, such as acetylcholine, act at an extracellular “orthosteric” binding site located at the interface between two adjacent subunits. Here, we present evidence of potent activation of α7 nAChRs via an allosteric transmembrane site. Previous studies have identified a series of nAChR-positive allosteric modulators (PAMs) that lack agonist activity but are able to potentiate responses to orthosteric agonists, such as acetylcholine. It has been shown, for example, that TQS acts as a conventional α7 nAChR PAM. In contrast, we have found that a compound with close chemical similarity to TQS (4BP-TQS) is a potent allosteric agonist of α7 nAChRs. Whereas the α7 nAChR antagonist metyllycaconitine acts competitively with conventional nicotinic agonists, metyllycaconitine is a noncompetitive antagonist of 4BP-TQS. Mutation of an amino acid (M253L), located in a transmembrane cavity that has been proposed as being the binding site for PAMs, completely blocks agonist activation by 4BP-TQS. In contrast, this mutation had no significant effect on agonist activation by acetylcholine. Conversely, mutation of an amino acid located within the known orthosteric binding site (W148F) has a profound effect on agonist potency of acetylcholine (resulting in a shift of ∼200-fold in the acetylcholine dose-response curve), but had little effect on the agonist dose-response curve for 4BP-TQS. Computer docking studies with an α7 homology model provides evidence that both TQS and 4BP-TQS bind within an intrasubunit transmembrane cavity. Taken together, these findings provide evidence that agonist activation of nAChRs can occur via an allosteric transmembrane site. PMID:21436053

A remote palm domain residue of RB69 DNA polymerase is critical for enzyme activity and influences the conformation of the active site.

PubMed

Jacewicz, Agata; Trzemecka, Anna; Guja, Kip E; Plochocka, Danuta; Yakubovskaya, Elena; Bebenek, Anna; Garcia-Diaz, Miguel

2013-01-01

Non-conserved amino acids that are far removed from the active site can sometimes have an unexpected effect on enzyme catalysis. We have investigated the effects of alanine replacement of residues distant from the active site of the replicative RB69 DNA polymerase, and identified a substitution in a weakly conserved palm residue (D714A), that renders the enzyme incapable of sustaining phage replication in vivo. D714, located several angstroms away from the active site, does not contact the DNA or the incoming dNTP, and our apoenzyme and ternary crystal structures of the Pol(D714A) mutant demonstrate that D714A does not affect the overall structure of the protein. The structures reveal a conformational change of several amino acid side chains, which cascade out from the site of the substitution towards the catalytic center, substantially perturbing the geometry of the active site. Consistent with these structural observations, the mutant has a significantly reduced k pol for correct incorporation. We propose that the observed structural changes underlie the severe polymerization defect and thus D714 is a remote, non-catalytic residue that is nevertheless critical for maintaining an optimal active site conformation. This represents a striking example of an action-at-a-distance interaction.

Balloon-Occluded Carbon Dioxide Gas Angiography for Internal Iliac Arteriography and Intervention.

PubMed

Kishino, Mitsuhiro; Nakaminato, Shuichiro; Kitazume, Yoshio; Miyasaka, Naoyuki; Kudo, Toshifumi; Saida, Yukihisa; Tateishi, Ukihide

2018-07-01

The usefulness of carbon dioxide (CO 2 ) gas digital subtraction angiography (DSA) has been reported for patients with renal insufficiency and allergy to iodinated contrast agents. However, CO 2 gas cannot replace the iodinated contrast agent in all cases owing to some disadvantages. We describe balloon-occluded CO 2 DSA (B-CO 2 DSA) as an improved CO 2 DSA procedure for interventions in the internal iliac artery (IIA) region and compare the quality of images obtained using conventional CO 2 DSA and B-CO 2 DSA. B-CO 2 DSA-guided embolization was performed for one case of genital bleeding with an acute anaphylactic reaction to the iodinated contrast agent and for three cases of type II endoleaks after endovascular abdominal aortic aneurysm repair with renal dysfunction. A 9-mm occlusion balloon catheter was placed just after the orifice of the IIA. Then, 10-15 ml of CO 2 gas was injected manually via the catheter with and without balloon occlusion. The quality of sequential digital subtraction angiograms was analyzed based on a scoring criterion. In all four cases, image quality was improved with B-CO 2 DSA; the poor quality of images without balloon occlusion was because of reflux of the CO 2 gas. B-CO 2 DSA improves the image quality of CO 2 DSA in the IIA region and is useful for vascular intervention. Level IV.

Analysis of the activation of acetylcholinesterase by carbon nanoparticles using a monolithic immobilized enzyme microreactor: role of the water molecules in the active site gorge.

PubMed

Ibrahim, Firas; Andre, Claire; Iutzeler, Anne; Guillaume, Yves Claude

2013-10-01

A biochromatographic system was used to study the direct effect of carbon nanoparticles (CNPs) on the acetylcholinesterase (AChE) activity. The AChE enzyme was covalently immobilized on a monolithic CIM-disk via its NH2 residues. Our results showed an increase in the AChE activity in presence of CNPs. The catalytic constant (k(cat)) was increased while the Michaelis constant (K(m)) was slightly decreased. This indicated an increase in the enzyme efficiency with increase of the substrate affinity to the active site. The thermodynamic data of the activation mechanism of the enzyme, i.e. ΔH* and ΔS*, showed no change in the substrate interaction mechanism with the anionic binding site. The increase of the enthalpy (ΔH*) and the entropy (ΔS*) with decrease in the free energy of activation (Ea) was related to structural conformation change in the active site gorge. This affected the stability of water molecules in the active site gorge and facilitated water displacement by substrate for entering to the active site of the enzyme.

Work-site wellness programmes in Sweden: a cross-sectional study of physical activity, self-efficacy, and health.

PubMed

Gånedahl, H; Zsaludek Viklund, P; Carlén, K; Kylberg, E; Ekberg, J

2015-05-01

In Sweden, a work-site wellness programme implies reimbursing some of the expenses for health-promoting activities. Although work-site wellness programmes are readily available in Sweden, a large number of employees elect not to participate. The aim of this study was to investigate the association of physical activity, self-reported general health assessment and self-efficacy with participation in a work-site wellness programme. A cross-sectional study design was used. An online questionnaire was distributed to employees of a manufacturing company with 2500 employees in southwest Sweden. Those who took advantage of the work-site wellness programme assessed their general health as better and had higher assessment of physical activity. The study showed that being enlisted also implies a higher level of physical activity and general health; however, the effect sizes of these correlations were small. Self-efficacy, i.e. perceived behavioural control, was not associated with participation in the work-site wellness programme. However, self-efficacy was correlated with both general health assessment and physical activity. A regression analysis to determine explanatory contributions to the general health assessment score showed no significant contribution from participation in a work-site wellness programme, but was instead explained by perceived behavioural control and physical activity. Given the small effect size of the difference in physical activity between participators and non-participators in the work-site wellness programme, it is probable that only a small proportion of participators changed their health-promoting activities as a result of the work-site wellness programme. Copyright © 2015 The Royal Society for Public Health. Published by Elsevier Ltd. All rights reserved.

Activity of N-coordinated multi-metal-atom active site structures for Pt-free oxygen reduction reaction catalysis: Role of *OH ligands

DOE PAGES

Holby, Edward F.; Taylor, Christopher D.

2015-03-19

We report calculated oxygen reduction reaction energy pathways on multi-metal-atom structures that have previously been shown to be thermodynamically favorable. We predict that such sites have the ability to spontaneously cleave the O₂ bond and then will proceed to over-bind reaction intermediates. In particular, the *OH bound state has lower energy than the final 2 H₂O state at positive potentials. Contrary to traditional surface catalysts, this *OH binding does not poison the multi-metal-atom site but acts as a modifying ligand that will spontaneously form in aqueous environments leading to new active sites that have higher catalytic activities. These *OH boundmore » structures have the highest calculated activity to date.« less

The Diverse AAA+ Machines that Repair Inhibited Rubisco Active Sites

PubMed Central

Mueller-Cajar, Oliver

2017-01-01

Gaseous carbon dioxide enters the biosphere almost exclusively via the active site of the enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco). This highly conserved catalyst has an almost universal propensity to non-productively interact with its substrate ribulose 1,5-bisphosphate, leading to the formation of dead-end inhibited complexes. In diverse autotrophic organisms this tendency has been counteracted by the recruitment of dedicated AAA+ (ATPases associated with various cellular activities) proteins that all use the energy of ATP hydrolysis to remodel inhibited Rubisco active sites leading to release of the inhibitor. Three evolutionarily distinct classes of these Rubisco activases (Rcas) have been discovered so far. Green and red-type Rca are mostly found in photosynthetic eukaryotes of the green and red plastid lineage respectively, whereas CbbQO is associated with chemoautotrophic bacteria. Ongoing mechanistic studies are elucidating how the various motors are utilizing both similar and contrasting strategies to ultimately perform their common function of cracking the inhibited Rubisco active site. The best studied mechanism utilized by red-type Rca appears to involve transient threading of the Rubisco large subunit C-terminal peptide, reminiscent of the action performed by Clp proteases. As well as providing a fascinating example of convergent molecular evolution, Rca proteins can be considered promising crop-improvement targets. Approaches aiming to replace Rubisco in plants with improved enzymes will need to ensure the presence of a compatible Rca protein. The thermolability of the Rca protein found in crop plants provides an opportunity to fortify photosynthesis against high temperature stress. Photosynthesis also appears to be limited by Rca when light conditions are fluctuating. Synthetic biology strategies aiming to enhance the autotrophic CO2 fixation machinery will need to take into consideration the requirement for Rubisco activases

Differential regulation of the transcriptional activity of the glucocorticoid receptor through site-specific phosphorylation.

PubMed

Kumar, Raj; Calhoun, William J

2008-12-01

Post-translational modifications such as phosphorylation are known to play an important role in the gene regulation by the transcription factors including the nuclear hormone receptor superfamily of which the glucocorticoid receptor (GR) is a member. Protein phosphorylation often switches cellular activity from one state to another. Like many other transcription factors, the GR is a phosphoprotein, and phosphorylation plays an important role in the regulation of GR activity. Cell signaling pathways that regulate phosphorylation of the GR and its associated proteins are important determinants of GR function under various physiological conditions. While the role of many phosphorylation sites in the GR is still not fully understood, the role of others is clearer. Several aspects of transcription factor function, including DNA binding affinity, interaction of transactivation domains with the transcription initiation complex, and shuttling between the cytoplasmic compartments, have all been linked to site-specific phosphorylation. All major phosphorylation sites in the human GR are located in the N-terminal domain including the major transactivation domain, AF1. Available literature clearly indicates that many of these potential phosphorylation sites are substrates for multiple kinases, suggesting the potential for a very complex regulatory network. Phosphorylated GR interacts favorably with critical coregulatory proteins and subsequently enhances transcriptional activity. In addition, the activities and specificities of coregulators may be subject to similar regulation by phosphorylation. Regulation of the GR activity due to phosphorylation appears to be site-specific and dependent upon specific cell signaling cascade. Taken together, site-specific phosphorylation and related kinase pathways play an important role in the action of the GR, and more precise mechanistic information will lead to fuller understanding of the complex nature of gene regulation by the GR- and

Energy landscape of the reactions governing the Na+ deeply occluded state of the Na+/K+-ATPase in the giant axon of the Humboldt squid

PubMed Central

Castillo, Juan P.; De Giorgis, Daniela; Basilio, Daniel; Gadsby, David C.; Rosenthal, Joshua J. C.; Latorre, Ramon; Holmgren, Miguel; Bezanilla, Francisco

2011-01-01

The Na+/K+ pump is a nearly ubiquitous membrane protein in animal cells that uses the free energy of ATP hydrolysis to alternatively export 3Na+ from the cell and import 2K+ per cycle. This exchange of ions produces a steady-state outwardly directed current, which is proportional in magnitude to the turnover rate. Under certain ionic conditions, a sudden voltage jump generates temporally distinct transient currents mediated by the Na+/K+ pump that represent the kinetics of extracellular Na+ binding/release and Na+ occlusion/deocclusion transitions. For many years, these events have escaped a proper thermodynamic treatment due to the relatively small electrical signal. Here, taking the advantages offered by the large diameter of the axons from the squid Dosidicus gigas, we have been able to separate the kinetic components of the transient currents in an extended temperature range and thus characterize the energetic landscape of the pump cycle and those transitions associated with the extracellular release of the first Na+ from the deeply occluded state. Occlusion/deocclusion transition involves large changes in enthalpy and entropy as the ion is exposed to the external milieu for release. Binding/unbinding is substantially less costly, yet larger than predicted for the energetic cost of an ion diffusing through a permeation pathway, which suggests that ion binding/unbinding must involve amino acid side-chain rearrangements at the site. PMID:22143771

Energy landscape of the reactions governing the Na+ deeply occluded state of the Na+/K+-ATPase in the giant axon of the Humboldt squid.

PubMed

Castillo, Juan P; De Giorgis, Daniela; Basilio, Daniel; Gadsby, David C; Rosenthal, Joshua J C; Latorre, Ramon; Holmgren, Miguel; Bezanilla, Francisco

2011-12-20

The Na(+)/K(+) pump is a nearly ubiquitous membrane protein in animal cells that uses the free energy of ATP hydrolysis to alternatively export 3Na(+) from the cell and import 2K(+) per cycle. This exchange of ions produces a steady-state outwardly directed current, which is proportional in magnitude to the turnover rate. Under certain ionic conditions, a sudden voltage jump generates temporally distinct transient currents mediated by the Na(+)/K(+) pump that represent the kinetics of extracellular Na(+) binding/release and Na(+) occlusion/deocclusion transitions. For many years, these events have escaped a proper thermodynamic treatment due to the relatively small electrical signal. Here, taking the advantages offered by the large diameter of the axons from the squid Dosidicus gigas, we have been able to separate the kinetic components of the transient currents in an extended temperature range and thus characterize the energetic landscape of the pump cycle and those transitions associated with the extracellular release of the first Na(+) from the deeply occluded state. Occlusion/deocclusion transition involves large changes in enthalpy and entropy as the ion is exposed to the external milieu for release. Binding/unbinding is substantially less costly, yet larger than predicted for the energetic cost of an ion diffusing through a permeation pathway, which suggests that ion binding/unbinding must involve amino acid side-chain rearrangements at the site.

MX Siting Investigation. Water Resources Program Industry Activity Inventory, Nevada-Utah.

DTIC Science & Technology

1980-09-02

sites. New and revived mining activities and the cooling needs of possible new coal -fired electric power plants represent the chief competitors with MX...34 !- ---- ON CO. Figure .-. Ma showing araipce yUaIoto f𔃻XMsieCmlx 1 3 include new mining activity and coal -fired, geothermal, and hydroelectric j energy...in northeastern Juab County. The Soil Conservation Service has been actively pushing land treatment programs to increase the productivity of irrigated

Pacman in the sky with shadows: the effect of cast shadows on the perceptual completion of occluded figures by chimpanzees and humans.

PubMed

Tomonaga, Masaki; Imura, Tomoko

2010-07-08

Humans readily perceive whole shapes as intact when some portions of these shapes are occluded by another object. This type of amodal completion has also been widely reported among nonhuman animals and is related to pictorial depth perception. However, the effect of a cast shadow, a critical pictorial-depth cue for amodal completion has been investigated only rarely from the comparative-cognitive perspective. In the present study, we examined this effect in chimpanzees and humans. Chimpanzees were slower in responding to a Pacman target with an occluding square than to the control condition, suggesting that participants perceptually completed the whole circle. When a cast shadow was added to the square, amodal completion occurred in both species. On the other hand, however, critical differences between the species emerged when the cast shadow was added to the Pacman figure, implying that Pacman was in the sky casting a shadow on the square. The cast shadow prevented, to a significant extent, compulsory amodal completion in humans, but had no effect on chimpanzees. These results suggest that cast shadows played a critical role in enabling humans to infer the spatial relationship between Pacman and the square. For chimpanzees, however, a cast shadow may be perceived as another "object". A limited role for cast shadows in the perception of pictorial depth has also been reported with respect to human cognitive development. Further studies on nonhuman primates using a comparative-developmental perspective will clarify the evolutionary origin of the role of cast shadows in visual perception.

Enthalpic Breakdown of Water Structure on Protein Active-Site Surfaces

PubMed Central

Haider, Kamran; Wickstrom, Lauren; Ramsey, Steven; Gilson, Michael K.; Kurtzman, Tom

2016-01-01

The principles underlying water reorganization around simple non-polar solutes are well understood and provide the framework for classical hydrophobic effect, whereby water molecules structure themselves around solutes so that they maintain favorable energetic contacts with both the solute and with other water molecules. However, for certain solute surface topographies, water molecules, due to their geometry and size, are unable to simultaneously maintain favorable energetic contacts with both the surface and neighboring water molecules. In this study, we analyze the solvation of ligand-binding sites for six structurally diverse proteins using hydration site analysis and measures of local water structure, in order to identify surfaces at which water molecules are unable to structure themselves in a way that maintains favorable enthalpy relative to bulk water. These surfaces are characterized by a high degree of enclosure, weak solute-water interactions, and surface constraints that induce unfavorable pair interactions between neighboring water molecules. Additionally, we find that the solvation of charged side-chains in an active site generally results in favorable enthalpy but can also lead to pair interactions between neighboring water molecules that are significantly unfavorable relative to bulk water. We find that frustrated local structure can occur not only in apolar and weakly polar pockets, where overall enthalpy tends to be unfavorable, but also in charged pockets, where overall water enthalpy tends to be favorable. The characterization of local water structure in these terms may prove useful for evaluating the displacement of water from diverse protein active-site environments. PMID:27169482

Nevada National Security Site Industrial Sites Project Closeout - 12498

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cabble, Kevin; Krauss, Mark; Matthews, Pat

The U.S. Department of Energy (DOE), National Nuclear Security Administration Nevada Site Office is responsible for environmental restoration (ER) at the Nevada National Security Site (NNSS). This includes remediation at Industrial Sites where past nuclear testing activities and activities that supported nuclear testing may have or are known to have resulted in the release of contaminants into the environment. Industrial Sites at the NNSS have included nuclear facilities that supported the nuclear rocket/missile development programs, gas stations, landfills, spill sites, ordnance sites, and numerous other waste disposal and release sites. The NNSS Industrial Sites activities neared completion at the endmore » of fiscal year 2011 while other activities required under the Federal Facility Agreement and Consent Order (FFACO) and part of the same NNSS ER Project are forecasted to extend to 2027 or beyond. With the majority of Industrial Sites corrective action units (CAUs) completed (more than 250 CAUs and over 1,800 corrective action sites), it was determined that an activity closeout process should be implemented to ensure that the work completed over the past 15 years is well documented in a comprehensive and concise summary. While the process used to close each individual CAU is described in approved documents, no single document describes in summary fashion the work completed to close the many individual Industrial Sites. The activity closeout process will be used to develop an Industrial Sites closeout document that describes these years of work. This document will summarize the number of Industrial Sites closed under the FFACO and provide general descriptions of projects, contaminants removed, and sites closed in place with corresponding Use Restrictions. Other pertinent information related to Industrial Sites work such as the project history, closure decisions, historical declarations, remediation strategies, and final CAU status will be included in the

Dual Active Site in the Endolytic Transglycosylase gp144 of Bacteriophage phiKZ.

PubMed

Chertkov, O V; Armeev, G A; Uporov, I V; Legotsky, S A; Sykilinda, N N; Shaytan, A K; Klyachko, N L; Miroshnikov, K A

2017-01-01

Lytic transglycosylases are abundant peptidoglycan lysing enzymes that degrade the heteropolymers of bacterial cell walls in metabolic processes or in the course of a bacteriophage infection. The conventional catalytic mechanism of transglycosylases involves only the Glu or Asp residue. Endolysin gp144 of Pseudomonas aeruginosa bacteriophage phiKZ belongs to the family of Gram-negative transglycosylases with a modular composition and C -terminal location of the catalytic domain. Glu115 of gp144 performs the predicted role of a catalytic residue. However, replacement of this residue does not completely eliminate the activity of the mutant protein. Site-directed mutagenesis has revealed the participation of Tyr197 in the catalytic mechanism, as well as the presence of a second active site involving Glu178 and Tyr147. The existence of the dual active site was supported by computer modeling and monitoring of the molecular dynamics of the changes in the conformation and surface charge distribution as a consequence of point mutations.

Active sites for CO 2 hydrogenation to methanol on Cu/ZnO catalysts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kattel, Shyam; Ramírez, Pedro J.; Chen, Jingguang G.

The active sites over commercial copper/zinc oxide/aluminum oxide (Cu/ZnO/Al 2O 3) catalysts for carbon dioxide (CO 2) hydrogenation to methanol, the Zn-Cu bimetallic sites or ZnO-Cu interfacial sites, have recently been the subject of intense debate. Here, we report a direct comparison between the activity of ZnCu and ZnO/Cu model catalysts for methanol synthesis. By combining x-ray photoemission spectroscopy, density functional theory, and kinetic Monte Carlo simulations, we can identify and characterize the reactivity of each catalyst. Both experimental and theoretical results agree that ZnCu undergoes surface oxidation under the reaction conditions so that surface Zn transforms into ZnO andmore » allows ZnCu to reach the activity of ZnO/Cu with the same Zn coverage. These results highlight a synergy of Cu and ZnO at the interface that facilitates methanol synthesis via formate intermediates.« less

Active sites for CO 2 hydrogenation to methanol on Cu/ZnO catalysts

DOE PAGES

Kattel, Shyam; Ramírez, Pedro J.; Chen, Jingguang G.; ...

2017-03-23

The active sites over commercial copper/zinc oxide/aluminum oxide (Cu/ZnO/Al 2O 3) catalysts for carbon dioxide (CO 2) hydrogenation to methanol, the Zn-Cu bimetallic sites or ZnO-Cu interfacial sites, have recently been the subject of intense debate. Here, we report a direct comparison between the activity of ZnCu and ZnO/Cu model catalysts for methanol synthesis. By combining x-ray photoemission spectroscopy, density functional theory, and kinetic Monte Carlo simulations, we can identify and characterize the reactivity of each catalyst. Both experimental and theoretical results agree that ZnCu undergoes surface oxidation under the reaction conditions so that surface Zn transforms into ZnO andmore » allows ZnCu to reach the activity of ZnO/Cu with the same Zn coverage. These results highlight a synergy of Cu and ZnO at the interface that facilitates methanol synthesis via formate intermediates.« less

Influence of a Confined Methanol Solvent on the Reactivity of Active Sites in UiO-66.

PubMed

Caratelli, Chiara; Hajek, Julianna; Rogge, Sven M J; Vandenbrande, Steven; Meijer, Evert Jan; Waroquier, Michel; Van Speybroeck, Veronique

2018-02-19

UiO-66, composed of Zr-oxide bricks and terephthalate linkers, is currently one of the most studied metal-organic frameworks due to its exceptional stability. Defects can be introduced in the structure, creating undercoordinated Zr atoms which are Lewis acid sites. Here, additional Brønsted sites can be generated by coordinated protic species from the solvent. In this Article, a multilevel modeling approach was applied to unravel the effect of a confined methanol solvent on the active sites in UiO-66. First, active sites were explored with static periodic density functional theory calculations to investigate adsorption of water and methanol. Solvent was then introduced in the pores with grand canonical Monte Carlo simulations, followed by a series of molecular dynamics simulations at operating conditions. A hydrogen-bonded network of methanol molecules is formed, allowing the protons to shuttle between solvent methanol, adsorbed water, and the inorganic brick. Upon deprotonation of an active site, the methanol solvent aids the transfer of protons and stabilizes charged configurations via hydrogen bonding, which could be crucial in stabilizing reactive intermediates. The multilevel modeling approach adopted here sheds light on the important role of a confined solvent on the active sites in the UiO-66 material, introducing dynamic acidity in the system at finite temperatures by which protons may be easily shuttled from various positions at the active sites. © 2018 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Impact of single-site axonal GABAergic synaptic events on cerebellar interneuron activity.

PubMed

de San Martin, Javier Zorrilla; Jalil, Abdelali; Trigo, Federico F

2015-12-01

Axonal ionotropic receptors are present in a variety of neuronal types, and their function has largely been associated with the modulation of axonal activity and synaptic release. It is usually assumed that activation of axonal GABA(A)Rs comes from spillover, but in cerebellar molecular layer interneurons (MLIs) the GABA source is different: in these cells, GABA release activates presynaptic GABA(A) autoreceptors (autoRs) together with postsynaptic targets, producing an autoR-mediated synaptic event. The frequency of presynaptic, autoR-mediated miniature currents is twice that of their somatodendritic counterparts, suggesting that autoR-mediated responses have an important effect on interneuron activity. Here, we used local Ca(2+) photolysis in MLI axons of juvenile rats to evoke GABA release from individual varicosities to study the activation of axonal autoRs in single release sites. Our data show that single-site autoR conductances are similar to postsynaptic dendritic conductances. In conditions of high [Cl(-)](i), autoR-mediated conductances range from 1 to 5 nS; this corresponds to ∼30-150 GABA(A) channels per presynaptic varicosity, a value close to the number of channels in postsynaptic densities. Voltage responses produced by the activation of autoRs in single varicosities are amplified by a Na(v)-dependent mechanism and propagate along the axon with a length constant of 91 µm. Immunolabeling determination of synapse location shows that on average, one third of the synapses produce autoR-mediated signals that are large enough to reach the axon initial segment. Finally, we show that single-site activation of presynaptic GABA(A) autoRs leads to an increase in MLI excitability and thus conveys a strong feedback signal that contributes to spiking activity. © 2015 Zorrilla de San Martin et al.

Impact of single-site axonal GABAergic synaptic events on cerebellar interneuron activity

PubMed Central

Zorrilla de San Martin, Javier; Jalil, Abdelali

2015-01-01

Axonal ionotropic receptors are present in a variety of neuronal types, and their function has largely been associated with the modulation of axonal activity and synaptic release. It is usually assumed that activation of axonal GABAARs comes from spillover, but in cerebellar molecular layer interneurons (MLIs) the GABA source is different: in these cells, GABA release activates presynaptic GABAA autoreceptors (autoRs) together with postsynaptic targets, producing an autoR-mediated synaptic event. The frequency of presynaptic, autoR-mediated miniature currents is twice that of their somatodendritic counterparts, suggesting that autoR-mediated responses have an important effect on interneuron activity. Here, we used local Ca2+ photolysis in MLI axons of juvenile rats to evoke GABA release from individual varicosities to study the activation of axonal autoRs in single release sites. Our data show that single-site autoR conductances are similar to postsynaptic dendritic conductances. In conditions of high [Cl−]i, autoR-mediated conductances range from 1 to 5 nS; this corresponds to ∼30–150 GABAA channels per presynaptic varicosity, a value close to the number of channels in postsynaptic densities. Voltage responses produced by the activation of autoRs in single varicosities are amplified by a Nav-dependent mechanism and propagate along the axon with a length constant of 91 µm. Immunolabeling determination of synapse location shows that on average, one third of the synapses produce autoR-mediated signals that are large enough to reach the axon initial segment. Finally, we show that single-site activation of presynaptic GABAA autoRs leads to an increase in MLI excitability and thus conveys a strong feedback signal that contributes to spiking activity. PMID:26621773

Recent Experience Using Active Love Wave Techniques to Characterize Seismographic Station Sites

NASA Astrophysics Data System (ADS)

Martin, A. J.; Yong, A.; Salomone, L.

2014-12-01

Active-source Love waves recorded by the multi-channel analysis of surface wave (MASLW) technique were recently analyzed in two site characterization projects. Between 2010 and 2011, the 2009 American Recovery and Reinvestment Act (ARRA) funded GEOVision to conduct geophysical investigations at 189 seismographic stations—185 in California and 4 in the Central Eastern U.S. (CEUS). The original project plan was to utilize active and passive Rayleigh wave-based techniques to obtain shear-wave velocity (VS) profiles to a minimum depth of 30 m and the time-averaged VS of the upper 30 meters (VS30). Early in the investigation it became evident that Rayleigh wave techniques, such as multi-channel analysis of surface waves (MASRW), were not effective at characterizing all sites. Shear-wave seismic refraction and MASLW techniques were therefore applied. The MASLW technique was deployed at a total of 38 sites, in addition to other methods, and used as the primary technique to characterize 22 sites, 5 of which were also characterized using Rayleigh wave techniques. In 2012, the Electric Power Research Institute funded characterization of 33 CEUS station sites. Based on experience from the ARRA investigation, both MASRW and MASLW data were acquired by GEOVision at 24 CEUS sites—the remaining 9 sites and 2 overlapping sites were characterized by University of Texas, Austin. Of the 24 sites characterized by GEOVision, 16 were characterized using MASLW data, 4 using both MASLW and MASRW data and 4 using MASRW data. Love wave techniques were often found to perform better, or at least yield phase velocity data that could be more readily modeled using the fundamental mode assumption, at shallow rock sites, sites with steep velocity gradients, and, sites with a thin, low velocity, surficial soil layer overlying stiffer sediments. These types of velocity structure often excite dominant higher modes in Rayleigh wave data, but not in Love wave data. At such sites, it may be possible

Human 15-LOX-1 active site mutations alter inhibitor binding and decrease potency.

PubMed

Armstrong, Michelle; van Hoorebeke, Christopher; Horn, Thomas; Deschamps, Joshua; Freedman, J Cody; Kalyanaraman, Chakrapani; Jacobson, Matthew P; Holman, Theodore

2016-11-01

Human 15-lipoxygenase-1 (h15-LOX-1 or h12/15-LOX) reacts with polyunsaturated fatty acids and produces bioactive lipid derivatives that are implicated in many important human diseases. One such disease is stroke, which is the fifth leading cause of death and the first leading cause of disability in America. The discovery of h15-LOX-1 inhibitors could potentially lead to novel therapeutics in the treatment of stroke, however, little is known about the inhibitor/active site interaction. This study utilizes site-directed mutagenesis, guided in part by molecular modeling, to gain a better structural understanding of inhibitor interactions within the active site. We have generated eight mutants (R402L, R404L, F414I, F414W, E356Q, Q547L, L407A, I417A) of h15-LOX-1 to determine whether these active site residues interact with two h15-LOX-1 inhibitors, ML351 and an ML094 derivative, compound 18. IC 50 values and steady-state inhibition kinetics were determined for the eight mutants, with four of the mutants affecting inhibitor potency relative to wild type h15-LOX-1 (F414I, F414W, E356Q and L407A). The data indicate that ML351 and compound 18, bind in a similar manner in the active site to an aromatic pocket close to F414 but have subtle differences in their specific binding modes. This information establishes the binding mode for ML094 and ML351 and will be leveraged to develop next-generation inhibitors. Copyright © 2016 Elsevier Ltd. All rights reserved.

Active Site Detection by Spatial Conformity and Electrostatic Analysis—Unravelling a Proteolytic Function in Shrimp Alkaline Phosphatase

PubMed Central

Chakraborty, Sandeep; Minda, Renu; Salaye, Lipika; Bhattacharjee, Swapan K.; Rao, Basuthkar J.

2011-01-01

Computational methods are increasingly gaining importance as an aid in identifying active sites. Mostly these methods tend to have structural information that supplement sequence conservation based analyses. Development of tools that compute electrostatic potentials has further improved our ability to better characterize the active site residues in proteins. We have described a computational methodology for detecting active sites based on structural and electrostatic conformity - C ata L ytic A ctive S ite P rediction (CLASP). In our pipelined model, physical 3D signature of any particular enzymatic function as defined by its active sites is used to obtain spatially congruent matches. While previous work has revealed that catalytic residues have large pKa deviations from standard values, we show that for a given enzymatic activity, electrostatic potential difference (PD) between analogous residue pairs in an active site taken from different proteins of the same family are similar. False positives in spatially congruent matches are further pruned by PD analysis where cognate pairs with large deviations are rejected. We first present the results of active site prediction by CLASP for two enzymatic activities - β-lactamases and serine proteases, two of the most extensively investigated enzymes. The results of CLASP analysis on motifs extracted from Catalytic Site Atlas (CSA) are also presented in order to demonstrate its ability to accurately classify any protein, putative or otherwise, with known structure. The source code and database is made available at www.sanchak.com/clasp/. Subsequently, we probed alkaline phosphatases (AP), one of the well known promiscuous enzymes, for additional activities. Such a search has led us to predict a hitherto unknown function of shrimp alkaline phosphatase (SAP), where the protein acts as a protease. Finally, we present experimental evidence of the prediction by CLASP by showing that SAP indeed has protease activity in vitro

The role of the peripheral benzodiazepine receptor in photodynamic activity of certain pyropheophorbide ether photosensitizers: albumin site II as a surrogate marker for activity.

PubMed

Dougherty, Thomas J; Sumlin, Adam B; Greco, William R; Weishaupt, Kenneth R; Vaughan, Lurine A; Pandey, Ravindra K

2002-07-01

A study has been carried out to define the importance of the peripheral benzodiazepine receptor (PBR) as a binding site for a series of chlorin-type photosensitizers, pyropheophorbide-a ethers, the subject of a previous quantitative structure-activity relationship study by us. The effects of the PBR ligand PK11195 on the photodynamic activity have been determined in vivo for certain members of this series of alkyl-substituted ethers: two of the most active derivatives (hexyl and heptyl), the least active derivative (dodecyl [C12]) and one of intermediate activity (octyl [C8]). The photodynamic therapy (PDT) effect was inhibited by PK11195 for both of the most active derivatives, but no effect on PDT activity was found for the less active C12 or C8 ethers. The inhibitory effects of PK11195 were predicted by the binding of only the active derivatives to the benzodiazepine site on albumin, ie. human serum albumin (HSA)-Site II. Thus, as with certain other types of photosensitizers, it has been demonstrated with this series of pyropheophorbide ethers that in vitro binding to HSA-Site II is a predictor of both optimal in vivo activity and binding to the PBR in vivo.

Long-term intensive management increased carbon occluded in phytolith (PhytOC) in bamboo forest soils

PubMed Central

Huang, Zhang-ting; Li, Yong-fu; Jiang, Pei-kun; Chang, Scott X.; Song, Zhao-liang; Liu, Juan; Zhou, Guo-mo

2014-01-01

Carbon (C) occluded in phytolith (PhytOC) is highly stable at millennium scale and its accumulation in soils can help increase long-term C sequestration. Here, we report that soil PhytOC storage significantly increased with increasing duration under intensive management (mulching and fertilization) in Lei bamboo (Phyllostachys praecox) plantations. The PhytOC storage in 0–40 cm soil layer in bamboo plantations increased by 217 Mg C ha−1, 20 years after being converted from paddy fields. The PhytOC accumulated at 79 kg C ha−1 yr−1, a rate far exceeding the global mean long-term soil C accumulation rate of 24 kg C ha−1 yr−1 reported in the literature. Approximately 86% of the increased PhytOC came from the large amount of mulch applied. Our data clearly demonstrate the decadal scale management effect on PhytOC accumulation, suggesting that heavy mulching is a potential method for increasing long-term organic C storage in soils for mitigating global climate change. PMID:24398703

Gonioscopy findings and prevalence of occludable angles in a Burmese population: the Meiktila Eye Study.

PubMed

Casson, R J; Newland, H S; Muecke, J; McGovern, S; Abraham, L M; Shein, W K; Selva, D; Aung, T

2007-07-01

To determine the prevalence of preglaucomatous angle-closure disease in central Myanmar. A population-based survey of inhabitants >or=40 years in the Meiktila District was carried out; 2481 subjects were identified, 2076 participated and 2060 underwent gonioscopy of at least one eye. Eyes with angles traditionally described as "occludable" were recorded as primary angle-closure suspects (PACS); eyes with PACS and peripheral anterior synechiae (PAS), or an increased intraocular pressure but without primary angle-closure glaucoma, were recorded as primary angle closure (PAC). The prevalence of PACS in at least one eye was 5.7% (95% CI 4.72 to 6.62); prevalence increased with age and was more common in women (p<0.001). The prevalence of PAC in at least one eye was 1.50% (95% CI 1.47 to 1.53). All participants with PAS had at least 90 degrees of closure (range 90-360 degrees). The prevalence of preglaucomatous angle-closure disease (PACS and PAC) in this population was 5.7% and 1.5%, respectively. PACS was more common in women, and its prevalence increased with age.

Enzyme Active Site Interactions by Raman/FTIR, NMR, and Ab Initio Calculations

PubMed Central

Deng, Hua

2017-01-01

Characterization of enzyme active site structure and interactions at high resolution is important for the understanding of the enzyme catalysis. Vibrational frequency and NMR chemical shift measurements of enzyme-bound ligands are often used for such purpose when X-ray structures are not available or when higher resolution active site structures are desired. This review is focused on how ab initio calculations may be integrated with vibrational and NMR chemical shift measurements to quantitatively determine high-resolution ligand structures (up to 0.001 Å for bond length and 0.01 Å for hydrogen bonding distance) and how interaction energies between bound ligand and its surroundings at the active site may be determined. Quantitative characterization of substrate ionic states, bond polarizations, tautomeric forms, conformational changes and its interactions with surroundings in enzyme complexes that mimic ground state or transition state can provide snapshots for visualizing the substrate structural evolution along enzyme-catalyzed reaction pathway. Our results have shown that the integration of spectroscopic studies with theoretical computation greatly enhances our ability to interpret experimental data and significantly increases the reliability of the theoretical analysis. PMID:24018325

Improved ethanol electrooxidation performance by shortening Pd–Ni active site distance in Pd–Ni–P nanocatalysts

PubMed Central

Chen, Lin; Lu, Lilin; Zhu, Hengli; Chen, Yueguang; Huang, Yu; Li, Yadong; Wang, Leyu

2017-01-01

Incorporating oxophilic metals into noble metal-based catalysts represents an emerging strategy to improve the catalytic performance of electrocatalysts in fuel cells. However, effects of the distance between the noble metal and oxophilic metal active sites on the catalytic performance have rarely been investigated. Herein, we report on ultrasmall (∼5 nm) Pd–Ni–P ternary nanoparticles for ethanol electrooxidation. The activity is improved up to 4.95 A per mgPd, which is 6.88 times higher than commercial Pd/C (0.72 A per mgPd), by shortening the distance between Pd and Ni active sites, achieved through shape transformation from Pd/Ni–P heterodimers into Pd–Ni–P nanoparticles and tuning the Ni/Pd atomic ratio to 1:1. Density functional theory calculations reveal that the improved activity and stability stems from the promoted production of free OH radicals (on Ni active sites) which facilitate the oxidative removal of carbonaceous poison and combination with CH3CO radicals on adjacent Pd active sites. PMID:28071650

Dithiolato-bridged nickel-iron complexes as models for the active site of [NiFe]-hydrogenases.

PubMed

Song, Li-Cheng; Yang, Xi-Yue; Cao, Meng; Gao, Xiu-Yun; Liu, Bei-Bei; Zhu, Liang; Jiang, Feng

2017-03-30

The structural and functional modeling of the active site of [NiFe]-hydrogenases has been proved to be challenging to a great extent. Herein, we report the synthesis, structures, and some properties of the NiFe-based dicarbonyl, terminal hydride, and μ-hydroxo models for the active site of [NiFe]-hydrogenases.

Design and Nuclear Magnetic Resonance (NMR) Structure Determination of the Second Extracellular Immunoglobulin Tyrosine Kinase A (TrkAIg2) Domain Construct for Binding Site Elucidation in Drug Discovery

PubMed Central

2014-01-01

The tyrosine kinase A (TrkA) receptor is a validated therapeutic intervention point for a wide range of conditions. TrkA activation by nerve growth factor (NGF) binding the second extracellular immunoglobulin (TrkAIg2) domain triggers intracellular signaling cascades. In the periphery, this promotes the pain phenotype and, in the brain, cell survival or differentiation. Reproducible structural information and detailed validation of protein–ligand interactions aid drug discovery. However, the isolated TrkAIg2 domain crystallizes as a β-strand-swapped dimer in the absence of NGF, occluding the binding surface. Here we report the design and structural validation by nuclear magnetic resonance spectroscopy of the first stable, biologically active construct of the TrkAIg2 domain for binding site confirmation. Our structure closely mimics the wild-type fold of TrkAIg2 in complex with NGF (1WWW.pdb), and the 1H–15N correlation spectra confirm that both NGF and a competing small molecule interact at the known binding interface in solution. PMID:25454499

Use of an Improved Matching Algorithm to Select Scaffolds for Enzyme Design Based on a Complex Active Site Model.

PubMed

Huang, Xiaoqiang; Xue, Jing; Lin, Min; Zhu, Yushan

2016-01-01

Active site preorganization helps native enzymes electrostatically stabilize the transition state better than the ground state for their primary substrates and achieve significant rate enhancement. In this report, we hypothesize that a complex active site model for active site preorganization modeling should help to create preorganized active site design and afford higher starting activities towards target reactions. Our matching algorithm ProdaMatch was improved by invoking effective pruning strategies and the native active sites for ten scaffolds in a benchmark test set were reproduced. The root-mean squared deviations between the matched transition states and those in the crystal structures were < 1.0 Å for the ten scaffolds, and the repacking calculation results showed that 91% of the hydrogen bonds within the active sites are recovered, indicating that the active sites can be preorganized based on the predicted positions of transition states. The application of the complex active site model for de novo enzyme design was evaluated by scaffold selection using a classic catalytic triad motif for the hydrolysis of p-nitrophenyl acetate. Eighty scaffolds were identified from a scaffold library with 1,491 proteins and four scaffolds were native esterase. Furthermore, enzyme design for complicated substrates was investigated for the hydrolysis of cephalexin using scaffold selection based on two different catalytic motifs. Only three scaffolds were identified from the scaffold library by virtue of the classic catalytic triad-based motif. In contrast, 40 scaffolds were identified using a more flexible, but still preorganized catalytic motif, where one scaffold corresponded to the α-amino acid ester hydrolase that catalyzes the hydrolysis and synthesis of cephalexin. Thus, the complex active site modeling approach for de novo enzyme design with the aid of the improved ProdaMatch program is a promising approach for the creation of active sites with high catalytic

Use of an Improved Matching Algorithm to Select Scaffolds for Enzyme Design Based on a Complex Active Site Model

PubMed Central

Huang, Xiaoqiang; Xue, Jing; Lin, Min; Zhu, Yushan

2016-01-01

Active site preorganization helps native enzymes electrostatically stabilize the transition state better than the ground state for their primary substrates and achieve significant rate enhancement. In this report, we hypothesize that a complex active site model for active site preorganization modeling should help to create preorganized active site design and afford higher starting activities towards target reactions. Our matching algorithm ProdaMatch was improved by invoking effective pruning strategies and the native active sites for ten scaffolds in a benchmark test set were reproduced. The root-mean squared deviations between the matched transition states and those in the crystal structures were < 1.0 Å for the ten scaffolds, and the repacking calculation results showed that 91% of the hydrogen bonds within the active sites are recovered, indicating that the active sites can be preorganized based on the predicted positions of transition states. The application of the complex active site model for de novo enzyme design was evaluated by scaffold selection using a classic catalytic triad motif for the hydrolysis of p-nitrophenyl acetate. Eighty scaffolds were identified from a scaffold library with 1,491 proteins and four scaffolds were native esterase. Furthermore, enzyme design for complicated substrates was investigated for the hydrolysis of cephalexin using scaffold selection based on two different catalytic motifs. Only three scaffolds were identified from the scaffold library by virtue of the classic catalytic triad-based motif. In contrast, 40 scaffolds were identified using a more flexible, but still preorganized catalytic motif, where one scaffold corresponded to the α-amino acid ester hydrolase that catalyzes the hydrolysis and synthesis of cephalexin. Thus, the complex active site modeling approach for de novo enzyme design with the aid of the improved ProdaMatch program is a promising approach for the creation of active sites with high catalytic

Chemical Modification of Papain and Subtilisin: An Active Site Comparison

ERIC Educational Resources Information Center

St-Vincent, Mireille; Dickman, Michael

2004-01-01

An experiment using methyle methanethiosulfonate (MMTS) and phenylmethylsulfonyl flouride (PMSF) to specifically modify the cysteine and serine residues in the active sites of papain and subtilism respectively is demonstrated. The covalent modification of these enzymes and subsequent rescue of papain shows the beginning biochemist that proteins…

Active-site copper reduction promotes substrate binding of fungal lytic polysaccharide monooxygenase and reduces stability.

PubMed

Kracher, Daniel; Andlar, Martina; Furtmüller, Paul G; Ludwig, Roland

2018-02-02

Lytic polysaccharide monooxygenases (LPMOs) are a class of copper-containing enzymes that oxidatively degrade insoluble plant polysaccharides and soluble oligosaccharides. Upon reductive activation, they cleave the substrate and promote biomass degradation by hydrolytic enzymes. In this study, we employed LPMO9C from Neurospora crassa , which is active toward cellulose and soluble β-glucans, to study the enzyme-substrate interaction and thermal stability. Binding studies showed that the reduction of the mononuclear active-site copper by ascorbic acid increased the affinity and the maximum binding capacity of LPMO for cellulose. The reduced redox state of the active-site copper and not the subsequent formation of the activated oxygen species increased the affinity toward cellulose. The lower affinity of oxidized LPMO could support its desorption after catalysis and allow hydrolases to access the cleavage site. It also suggests that the copper reduction is not necessarily performed in the substrate-bound state of LPMO. Differential scanning fluorimetry showed a stabilizing effect of the substrates cellulose and xyloglucan on the apparent transition midpoint temperature of the reduced, catalytically active enzyme. Oxidative auto-inactivation and destabilization were observed in the absence of a suitable substrate. Our data reveal the determinants of LPMO stability under turnover and non-turnover conditions and indicate that the reduction of the active-site copper initiates substrate binding. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Critical Amino Acids in the Active Site of Meprin Metalloproteinases for Substrate and Peptide Bond Specificity*

PubMed Central

Villa, James P.; Bertenshaw, Greg P.; Bond, Judith S.

2008-01-01

SUMMARY The protease domains of the evolutionarily-related α and ß subunits of meprin metalloproteases are approximately 55% identical at the amino acid level, however, their substrate and peptide bond specificities differ markedly. The meprin ß subunit favors acidic residues proximal to the scissile bond, while the α subunit prefers small or aromatic amino acids flanking the scissile bond. Thus gastrin, a peptide that contains a string of five Glu residues, is an excellent substrate for meprin ß while it is not hydrolyzed by meprin α. Work herein aimed to identify critical amino acids in the meprin active sites that determine the substrate specificity differences. Sequence alignments and homology models, based on the crystal structure of the crayfish astacin, showed electrostatic differences within the meprin active sites. Site-directed mutagenesis of active site residues demonstrated that replacement of a hydrophobic residue by a basic amino acid enabled the meprin α protease to cleave gastrin. The meprin αY199K mutant was most effective; the corresponding mutation of meprin ßK185Y resulted in decreased activity toward gastrin. Peptide cleavage site determinations and kinetic analyses using a variety of peptides extended evidence that meprin αTyr199/ßLys185 are substrate specificity determinants in meprin active sites. These studies shed light on the molecular basis for the substrate specificity differences of astacin metalloproteinases. PMID:12888571

How Force Might Activate Talin's Vinculin Binding Sites: SMD Reveals a Structural Mechanism

PubMed Central

Hytönen, Vesa P; Vogel, Viola

2008-01-01

Upon cell adhesion, talin physically couples the cytoskeleton via integrins to the extracellular matrix, and subsequent vinculin recruitment is enhanced by locally applied tensile force. Since the vinculin binding (VB) sites are buried in the talin rod under equilibrium conditions, the structural mechanism of how vinculin binding to talin is force-activated remains unknown. Taken together with experimental data, a biphasic vinculin binding model, as derived from steered molecular dynamics, provides high resolution structural insights how tensile mechanical force applied to the talin rod fragment (residues 486–889 constituting helices H1–H12) might activate the VB sites. Fragmentation of the rod into three helix subbundles is prerequisite to the sequential exposure of VB helices to water. Finally, unfolding of a VB helix into a completely stretched polypeptide might inhibit further binding of vinculin. The first events in fracturing the H1–H12 rods of talin1 and talin2 in subbundles are similar. The proposed force-activated α-helix swapping mechanism by which vinculin binding sites in talin rods are exposed works distinctly different from that of other force-activated bonds, including catch bonds. PMID:18282082

Identification of the fatty acid activation site on human ClC-2.

PubMed

Cuppoletti, John; Tewari, Kirti P; Chakrabarti, Jayati; Malinowska, Danuta H

2017-06-01

Fatty acids (including lubiprostone and cobiprostone) are human ClC-2 (hClC-2) Cl - channel activators. Molecular and cellular mechanisms underlying this activation were examined. Role of a four-amino acid PKA activation site, RGET 691 , of hClC-2 was investigated using wild-type (WT) and mutant (AGET, RGEA, and AGAA) hClC-2 expressed in 293EBNA cells as well as involvement of PKA, intracellular cAMP concentration ([cAMP] i ), EP 2 , or EP 4 receptor agonist activity. All fatty acids [lubiprostone, cobiprostone, eicosatetraynoic acid (ETYA), oleic acid, and elaidic acid] caused significant rightward shifts in concentration-dependent Cl - current activation (increasing EC 50 s) with mutant compared with WT hClC-2 channels, without changing time and voltage dependence, current-voltage rectification, or methadone inhibition of the channel. As with lubiprostone, cobiprostone activation of hClC-2 occurred with PKA inhibitor (myristoylated protein kinase inhibitor) present or when using double PKA activation site (RRAA 655 /RGEA 691 ) mutant. Cobiprostone did not activate human CFTR. Fatty acids did not increase [cAMP] i in hClC-2/293EBNA or T84 cells. Using T84 CFTR knockdown cells, cobiprostone increased hClC-2 Cl - currents without increasing [cAMP] i, while PGE 2 and forskolin-IBMX increased both. Fatty acids were not agonists of EP 2 or EP 4 receptors. L-161,982, a supposed EP 4 -selective inhibitor, had no effect on lubiprostone-activated hClC-2 Cl - currents but significantly decreased T84 cell barrier function measured by transepithelial resistance and fluorescent dextran transepithelial movement. The present findings show that RGET 691 of hClC-2 (possible binding site) plays an important functional role in fatty acid activation of hClC-2. PKA, [cAMP] i , and EP 2 or EP 4 receptors are not involved. These studies provide the molecular basis for fatty acid regulation of hClC-2. Copyright © 2017 the American Physiological Society.

Computational active site analysis of molecular pathways to improve functional classification of enzymes.

PubMed

Ozyurt, A Sinem; Selby, Thomas L

2008-07-01

This study describes a method to computationally assess the function of homologous enzymes through small molecule binding interaction energy. Three experimentally determined X-ray structures and four enzyme models from ornithine cyclo-deaminase, alanine dehydrogenase, and mu-crystallin were used in combination with nine small molecules to derive a function score (FS) for each enzyme-model combination. While energy values varied for a single molecule-enzyme combination due to differences in the active sites, we observe that the binding energies for the entire pathway were proportional for each set of small molecules investigated. This proportionality of energies for a reaction pathway appears to be dependent on the amino acids in the active site and their direct interactions with the small molecules, which allows a function score (FS) to be calculated to assess the specificity of each enzyme. Potential of mean force (PMF) calculations were used to obtain the energies, and the resulting FS values demonstrate that a measurement of function may be obtained using differences between these PMF values. Additionally, limitations of this method are discussed based on: (a) larger substrates with significant conformational flexibility; (b) low homology enzymes; and (c) open active sites. This method should be useful in accurately predicting specificity for single enzymes that have multiple steps in their reactions and in high throughput computational methods to accurately annotate uncharacterized proteins based on active site interaction analysis. 2008 Wiley-Liss, Inc.

Elucidating Oxygen Reduction Active Sites in Pyrolyzed Metal–Nitrogen Coordinated Non-Precious-Metal Electrocatalyst Systems

PubMed Central

2015-01-01

Detailed understanding of the nature of the active centers in non-precious-metal-based electrocatalyst, and their role in oxygen reduction reaction (ORR) mechanistic pathways will have a profound effect on successful commercialization of emission-free energy devices such as fuel cells. Recently, using pyrolyzed model structures of iron porphyrins, we have demonstrated that a covalent integration of the Fe–Nx sites into π-conjugated carbon basal plane modifies electron donating/withdrawing capability of the carbonaceous ligand, consequently improving ORR activity. Here, we employ a combination of in situ X-ray spectroscopy and electrochemical methods to identify the various structural and functional forms of the active centers in non-heme Fe/N/C catalysts. Both methods corroboratively confirm the single site 2e– × 2e– mechanism in alkaline media on the primary Fe2+–N4 centers and the dual-site 2e– × 2e– mechanism in acid media with the significant role of the surface bound coexisting Fe/FexOy nanoparticles (NPs) as the secondary active sites. PMID:24817921

Elucidating Oxygen Reduction Active Sites in Pyrolyzed Metal-Nitrogen Coordinated Non-Precious-Metal Electrocatalyst Systems.

PubMed

Tylus, Urszula; Jia, Qingying; Strickland, Kara; Ramaswamy, Nagappan; Serov, Alexey; Atanassov, Plamen; Mukerjee, Sanjeev

2014-05-01

Detailed understanding of the nature of the active centers in non-precious-metal-based electrocatalyst, and their role in oxygen reduction reaction (ORR) mechanistic pathways will have a profound effect on successful commercialization of emission-free energy devices such as fuel cells. Recently, using pyrolyzed model structures of iron porphyrins, we have demonstrated that a covalent integration of the Fe-N x sites into π-conjugated carbon basal plane modifies electron donating/withdrawing capability of the carbonaceous ligand, consequently improving ORR activity. Here, we employ a combination of in situ X-ray spectroscopy and electrochemical methods to identify the various structural and functional forms of the active centers in non-heme Fe/N/C catalysts. Both methods corroboratively confirm the single site 2e - × 2e - mechanism in alkaline media on the primary Fe 2+ -N 4 centers and the dual-site 2e - × 2e - mechanism in acid media with the significant role of the surface bound coexisting Fe/Fe x O y nanoparticles (NPs) as the secondary active sites.

Linde FUSRAP Site Remediation: Engineering Challenges and Solutions of Remedial Activities on an Active Industrial Facility - 13506

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beres, Christopher M.; Fort, E. Joseph; Boyle, James D.

2013-07-01

The Linde FUSRAP Site (Linde) is located in Tonawanda, New York at a major research and development facility for Praxair, Inc. (Praxair). Successful remediation activities at Linde combines meeting cleanup objectives of radiological contamination while minimizing impacts to Praxair business operations. The unique use of Praxair's property coupled with an array of active and abandoned utilities poses many engineering and operational challenges; each of which has been overcome during the remedial action at Linde. The U.S. Army Corps of Engineers - Buffalo District (USACE) and CABRERA SERVICES, INC. (CABRERA) have successfully faced engineering challenges such as relocation of an abovegroundmore » structure, structural protection of an active water line, and installation of active mechanical, electrical, and communication utilities to perform remediation. As remediation nears completion, continued success of engineering challenges is critical as remaining activities exist in the vicinity of infrastructure essential to business operations; an electrical substation and duct bank providing power throughout the Praxair facility. Emphasis on engineering and operations through final remediation and into site restoration will allow for the safe and successful completion of the project. (authors)« less

Radiocarbon dating of prehistoric phytoliths: a preliminary study of archaeological sites in China

NASA Astrophysics Data System (ADS)

Zuo, Xinxin; Lu, Houyuan; Zhang, Jianping; Wang, Can; Sun, Guoping; Zheng, Yunfei

2016-05-01

Phytoliths can occlude some organic carbon during their deposition in plants. This carbon fraction is recognised as an ideal dating material because of its high resistance to decomposition and post-deposition contamination at the time of phytolith formation. However, the reliability of phytolith radiocarbon dating has recently been questioned. The development of a new extraction protocol for phytoliths, with paired dating between phytoliths and other materials from the same sediment, may provide further evidence for the reliability of phytolith dating. We present an improved method for extracting phytoliths from soils. We compared the dating of phytoliths and other materials (e.g., charcoal and plant seeds) recovered at the same depth from seven pits at six archaeological sites in China. The estimated ages of the phytoliths and other materials were generally consistent, except for one outlier. We attribute this inconsistency to the post-depositional processes of phytoliths in soil, rather than to the uptake of old carbon from the soil. Our results clearly show the potential for phytolith carbon dating at archaeological sites in the absence of other dating materials.

Greenhouse Gas Fluxes at the Tablelands, NL, Canada: A Site of Active Serpentinization

NASA Astrophysics Data System (ADS)

Morrill, P. L.; Morrissey, L. S.; Cumming, E.

2016-12-01

Active sites of serpentinization have been proposed as sites for carbon capture and storage (CCS) projects. However, in addition to their ability to convert carbon dioxide to carbonate rock, sites of serpentinization also have the potential release methane, which is a more power greenhouse gas than carbon dioxide. Very little is known about the natural flux of carbon dioxide sequestered and methane released into the atmosphere from active sites of serpentinization. In this study we measured carbon dioxide, methane, and nitrous oxide gas fluxes at a pool of ultra-basic water discharging from serpentinized rock in Winterhouse Canyon, Gros Morne, Newfoundland. We found that the flux of methane released was 4.6 x 10-7 mol/m2/min and the carbon dioxide sequestered was 1.9 x 10-5 mol/m2/min, while the concentrations of nitrous oxide showed little change. Based on these fluxes we calculated predictive climate change parameters such as net radiative forcing and global warming potential which predicted that despite the methane being released the site still had an overall long-term atmospheric cooling effect based on the natural rate of carbon dioxide sequestration.

Quantum delocalization of protons in the hydrogen-bond network of an enzyme active site.

PubMed

Wang, Lu; Fried, Stephen D; Boxer, Steven G; Markland, Thomas E

2014-12-30

Enzymes use protein architectures to create highly specialized structural motifs that can greatly enhance the rates of complex chemical transformations. Here, we use experiments, combined with ab initio simulations that exactly include nuclear quantum effects, to show that a triad of strongly hydrogen-bonded tyrosine residues within the active site of the enzyme ketosteroid isomerase (KSI) facilitates quantum proton delocalization. This delocalization dramatically stabilizes the deprotonation of an active-site tyrosine residue, resulting in a very large isotope effect on its acidity. When an intermediate analog is docked, it is incorporated into the hydrogen-bond network, giving rise to extended quantum proton delocalization in the active site. These results shed light on the role of nuclear quantum effects in the hydrogen-bond network that stabilizes the reactive intermediate of KSI, and the behavior of protons in biological systems containing strong hydrogen bonds.

Substituting Tyr138 in the active site loop of human phenylalanine hydroxylase affects catalysis and substrate activation.

PubMed

Leandro, João; Stokka, Anne J; Teigen, Knut; Andersen, Ole A; Flatmark, Torgeir

2017-07-01

Mammalian phenylalanine hydroxylase (PAH) is a key enzyme in l-phenylalanine (l-Phe) metabolism and is active as a homotetramer. Biochemical and biophysical work has demonstrated that it cycles between two states with a variably low and a high activity, and that the substrate l-Phe is the key player in this transition. X-ray structures of the catalytic domain have shown mobility of a partially intrinsically disordered Tyr 138 -loop to the active site in the presence of l-Phe. The mechanism by which the loop dynamics are coupled to substrate binding at the active site in tetrameric PAH is not fully understood. We have here conducted functional studies of four Tyr 138 point mutants. A high linear correlation ( r 2 = 0.99) was observed between their effects on the catalytic efficiency of the catalytic domain dimers and the corresponding effect on the catalytic efficiency of substrate-activated full-length tetramers. In the tetramers, a correlation ( r 2 = 0.96) was also observed between the increase in catalytic efficiency (activation) and the global conformational change (surface plasmon resonance signal response) at the same l-Phe concentration. The new data support a similar functional importance of the Tyr 138 -loop in the catalytic domain and the full-length enzyme homotetramer.

Inhibitor-based validation of a homology model of the active-site of tripeptidyl peptidase II.

PubMed

De Winter, Hans; Breslin, Henry; Miskowski, Tamara; Kavash, Robert; Somers, Marijke

2005-04-01

A homology model of the active site region of tripeptidyl peptidase II (TPP II) was constructed based on the crystal structures of four subtilisin-like templates. The resulting model was subsequently validated by judging expectations of the model versus observed activities for a broad set of prepared TPP II inhibitors. The structure-activity relationships observed for the prepared TPP II inhibitors correlated nicely with the structural details of the TPP II active site model, supporting the validity of this model and its usefulness for structure-based drug design and pharmacophore searching experiments.

Effects of mutations on active site conformation and dynamics of RNA-dependent RNA polymerase from Coxsackievirus B3.

PubMed

Shen, Hujun; Deng, Mingsen; Zhang, Yachao

2017-10-01

Recent crystal structures of RNA-dependent RNA polymerase (3D pol ) from Coxsackievirus B3 (CVB3) revealed that a tyrosine mutation at Phe364 (F364Y) resulted in structures with open active site whereas a hydrophobic mutation at Phe364 (F364A) led to conformations with closed active site. Besides, the crystal structures showed that the F364W mutation had no preference between the open and closed active sites, similar to wild-type. In this paper, we present a molecular dynamics (MD) study on CVB3 3D pol in order to address some important questions raised by experiments. First, MD simulations of F364Y and F364A were carried out to explore how these mutations at Phe364 influence active site dynamics and conformations. Second, MD simulations of wild-type and mutants were performed to discover the connection between active site dynamics and polymerase function. MD simulations reveal that the effect of mutations on active site dynamics is associated with the interaction between the structural motifs A and D in CVB3 3D pol . Interestingly, we discover that the active site state is influenced by the formation of a hydrogen bond between backbone atoms of Ala231 (in motif A) and Ala358 (in motif D), which has never been revealed before. Copyright © 2017 Elsevier Inc. All rights reserved.

Asymmetric mutations in the tetrameric R67 dihydrofolate reductase reveal high tolerance to active-site substitutions.

PubMed

Ebert, Maximilian C C J C; Morley, Krista L; Volpato, Jordan P; Schmitzer, Andreea R; Pelletier, Joelle N

2015-04-01

Type II R67 dihydrofolate reductase (DHFR) is a bacterial plasmid-encoded enzyme that is intrinsically resistant to the widely-administered antibiotic trimethoprim. R67 DHFR is genetically and structurally unrelated to E. coli chromosomal DHFR and has an unusual architecture, in that four identical protomers form a single symmetrical active site tunnel that allows only one substrate binding/catalytic event at any given time. As a result, substitution of an active-site residue has as many as four distinct consequences on catalysis, constituting an atypical model of enzyme evolution. Although we previously demonstrated that no single residue of the native active site is indispensable for function, library selection here revealed a strong bias toward maintenance of two native protomers per mutated tetramer. A variety of such "half-native" tetramers were shown to procure native-like catalytic activity, with similar KM values but kcat values 5- to 33-fold lower, illustrating a high tolerance for active-site substitutions. The selected variants showed a reduced thermal stability (Tm ∼12°C lower), which appears to result from looser association of the protomers, but generally showed a marked increase in resilience to heat denaturation, recovering activity to a significantly greater extent than the variant with no active-site substitutions. Our results suggest that the presence of two native protomers in the R67 DHFR tetramer is sufficient to provide native-like catalytic rate and thus ensure cellular proliferation. © 2014 The Protein Society.

The effectiveness of cricoid pressure for occluding the esophageal entrance in anesthetized and paralyzed patients: an experimental and observational glidescope study.

PubMed

Zeidan, Ahed M; Salem, M Ramez; Mazoit, Jean-Xavier; Abdullah, Mohamad Ali; Ghattas, Tharwat; Crystal, George J

2014-03-01

In the last 2 decades, the effectiveness of cricoid pressure (CP) in occluding the esophageal entrance has been questioned. Recent magnetic resonance imaging studies yielded conflicting conclusions. We used real-time visual and mechanical means to assess the patency of the esophageal entrance with and without CP in anesthetized and paralyzed adult patients. One hundred seven, nonobese ASA physical status I and II patients were recruited for the study. A cricoid force of 30 N was used. This force was standardized by using a weighing scale before application of CP in each patient. After oxygen administration, anesthetic induction, neuromuscular blockade, and establishment of manual ventilation with FIO2 = 1.0, the view of the glottis and esophageal entrance was visualized, and video recordings were obtained by using a Glidescope video laryngoscope. Attempts to insert 2 gastric tubes (GTs), size 12 and 20 F, into the esophagus were made by a "blinded" operator without and with CP, the timing of which was randomized. A successful insertion of a GT in the presence of CP was considered evidence of a patent esophageal entrance (ineffective CP), whereas an unsuccessful insertion of a GT was considered evidence of an occluded esophageal entrance (effective CP). After the attempts to insert the GTs were completed, tracheal intubation was performed while CP was applied. The position of the esophageal entrance in relation to the glottis (midline versus lateral) was assessed from the video recordings, with and without CP. We stopped the study when 79 patients (41 men and 38 women) qualified for and completed the study (2-sided Clopper-Pearson confidence interval (CI) 95% to 100%, n = 72). Advancement of either size GT into the esophagus could not be accomplished during CP in any patient but was easily done in all subjects when CP was not applied. This occurred whether the esophageal entrance was in a midline position or in a left or right lateral position relative to the

A tentative record of the last 1,000 years of Greenland temperature from occluded air in the GISP2 ice core

NASA Astrophysics Data System (ADS)

Kobashi, T.; Severinghaus, J. P.; Barnola, J.; Kawamura, K.; Beaudette, R.

2005-12-01

Ice borehole temperature inversion has been used to reconstruct Greenland surface temperature during the last millennium (Dahl-Jensen et al, Science, 1998). However, this technique does not preserve high frequencies because of diffusion of heat in the ice. Here, we present a tentative reconstruction of the past 1,000 years of central Greenland temperature using nitrogen and argon isotopes from occluded air in the GISP2 ice core. This technique preserves decadal-to-centennial-scale temperature variations and complements the borehole technique. Nitrogen and argon isotopes in the porous snow layer (~80m) experience two isotopic fractionations by gravitation and temperature gradients (ΔT) between the top and bottom of the snow layer. The simultaneous analysis of argon and nitrogen isotopes allows us to separate these two effects, and obtain a history of ΔT in the layer. To a first approximation, ΔT change on decadal to centennial time scales is a surface temperature history because the heat conductivity of snow is much smaller than that of ice, and the heat capacity of the ice sheet is quite large. The preliminary ΔT history (20-year interval) shows a Medieval Warm Period in the 11th to 12th centuries and the Little Ice Age in the 15th to 19th centuries. Furthermore, the record shows a clear similarity with the Be-10 record (a proxy for solar activity) with Wolf, Sporer, Maunder, and Dalton minima clearly seen in the cold periods. This finding is consistent with the hypothesis that solar activity influenced Greenland temperature during the past 1000 years.

LASIC: Light Activated Site-Specific Conjugation of Native IgGs.

PubMed

Hui, James Z; Tamsen, Shereen; Song, Yang; Tsourkas, Andrew

2015-08-19

Numerous biological applications, from diagnostic assays to immunotherapies, rely on the use of antibody-conjugates. The efficacy of these conjugates can be significantly influenced by the site at which Immunoglobulin G (IgG) is modified. Current methods that provide control over the conjugation site, however, suffer from a number of shortfalls and often require large investments of time and cost. We have developed a novel adapter protein that, when activated by long wavelength UV light, can covalently and site-specifically label the Fc region of nearly any native, full-length IgG, including all human IgG subclasses. Labeling occurs with unprecedented efficiency and speed (>90% after 30 min), with no effect on IgG affinity. The adapter domain can be bacterially expressed and customized to contain a variety of moieties (e.g., biotin, azide, fluorophores), making reliable and efficient conjugation of antibodies widely accessible to researchers at large.

ATP binding at noncatalytic sites of soluble chloroplast F1-ATPase is required for expression of the enzyme activity.

PubMed

Milgrom, Y M; Ehler, L L; Boyer, P D

1990-11-05

The F1-ATPase from chloroplasts (CF1) lacks catalytic capacity for ATP hydrolysis if ATP is not bound at noncatalytic sites. CF1 heat activated in the presence of ADP, with less than one ADP and no ATP at non-catalytic sites, shows a pronounced lag in the onset of ATP hydrolysis after exposure to 5-20 microM ATP. The onset of activity correlates well with the binding of ATP at the last two of the three noncatalytic sites. The dependence of activity on the presence of ATP at non-catalytic sites is shown at relatively low or high free Mg2+ concentrations, with or without bicarbonate as an activating anion, and when the binding of ATP at noncatalytic sites is slowed 3-4-fold by sulfate. The latent CF1 activated by dithiothreitol also requires ATP at noncatalytic sites for ATPase activity. A similar requirement by other F1-ATPases and by ATP synthases seems plausible.

c-rel activates but v-rel suppresses transcription from kappa B sites.

PubMed Central

Inoue, J; Kerr, L D; Ransone, L J; Bengal, E; Hunter, T; Verma, I M

1991-01-01

We show that the product of the protooncogene c-rel is a constituent of an NF-kappa B-like complex that binds to the kappa B site originally identified in the enhancer of immunoglobulin kappa light chain gene. c-rel protein synthesized in bacteria binds to the kappa B site in a sequence-specific manner. The rel-kappa B complex can be disrupted by incubation with anti-rel antibodies. The rel protein can form oligomers. The c-rel protein can activate transcription from promoters containing kappa B sites; v-rel, on the other hand, suppresses the transcription of genes linked to kappa B sites. Thus, v-rel may interfere with the normal transcriptional machinery of the cell by acting as a dominant negative mutant. Images PMID:2023921