Development of a Novel Green Fluorescent Protein-Based Binding Assay to Study the Association of Plakins with Intermediate Filament Proteins.

Protein-protein interactions are fundamental for most biological processes, such as the formation of cellular structures and enzymatic complexes or in signaling pathways. The identification and characterization of protein-protein interactions are therefore essential for understanding the mechanisms and regulation of biological systems. The organization and dynamics of the cytoskeleton, as well as its anchorage to specific sites in the plasma membrane and organelles, are regulated by the plakins. These structurally related proteins anchor different cytoskeletal networks to each other and/or to other cellular structures. The association of several plakins with intermediate filaments (IFs) is critical for maintenance of the cytoarchitecture. Pathogenic mutations in the genes encoding different plakins can lead to dramatic manifestations, occurring principally in the skin, striated muscle, and/or nervous system, due to cytoskeletal disorganization resulting in abnormal cell fragility. Nevertheless, it is still unclear how plakins bind to IFs, although some general rules are slowly emerging. We here describe in detail a recently developed protein-protein fluorescence binding assay, based on the production of recombinant proteins tagged with green fluorescent protein (GFP) and their use as fluid-phase fluorescent ligands on immobilized IF proteins. Using this method, we have been able to assess the ability of C-terminal regions of GFP-tagged plakin proteins to bind to distinct IF proteins and IF domains. This simple and sensitive technique, which is expected to facilitate further studies in this area, can also be potentially employed for any kind of protein-protein interaction studies.

A clinically applicable laser-based image-guided system for laparoscopic liver procedures

PURPOSE Laser range scanners (LRS) allow performing a surface scan without physical contact with the organ, yielding higher registration accuracy for image-guided surgery (IGS) systems. However, the use of LRS-based registration in laparoscopic liver surgery is still limited because current solutions are composed of expensive and bulky equipment which can hardly be integrated in a surgical scenario. METHODS In this work, we present a novel LRS-based IGS system for laparoscopic liver procedures. A triangulation process is formulated to compute the 3D coordinates of laser points by using the existing IGS system tracking devices. This allows the use of a compact and cost-effective LRS and therefore facilitates the integration into the laparoscopic setup. The 3D laser points are then reconstructed into a surface to register to the preoperative liver model using a multi-level registration process. RESULTS Experimental results show that the proposed system provides submillimeter scanning precision and accuracy comparable to those reported in the literature. Further quantitative analysis shows that the proposed system is able to achieve a patient-to-image registration accuracy, described as target registration error, of [Formula: see text]. CONCLUSIONS We believe that the presented approach will lead to a faster integration of LRS-based registration techniques in the surgical environment. Further studies will focus on optimizing scanning time and on the respiratory motion compensation.

Towards science-based sediment quality standards-Effects of field-collected sediments in rainbow trout (Oncorhynchus mykiss).

Sediments can act as long-term sinks for environmental pollutants. Within the past decades, dioxin-like compounds (DLCs) such as polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs), polychlorinated biphenyls (PCBs), and polycyclic aromatic hydrocarbons (PAHs) have attracted significant attention in the scientific community. To investigate the time- and concentration-dependent uptake of DLCs and PAHs in rainbow trout (Oncorhynchus mykiss) and their associated toxicological effects, we conducted exposure experiments using suspensions of three field-collected sediments from the rivers Rhine and Elbe, which were chosen to represent different contamination levels. Five serial dilutions of contaminated sediments were tested; these originated from the Prossen and Zollelbe sampling sites (both in the river Elbe, Germany) and from Ehrenbreitstein (Rhine, Germany), with lower levels of contamination. Fish were exposed to suspensions of these dilutions under semi-static conditions for 90 days. Analysis of muscle tissue by high resolution gas chromatography and mass spectrometry and of bile liquid by high-performance liquid chromatography showed that particle-bound PCDD/Fs, PCBs and PAHs were readily bioavailable from re-suspended sediments. Uptake of these contaminants and the associated toxicological effects in fish were largely proportional to their sediment concentrations. The changes in the investigated biomarkers closely reflected the different sediment contamination levels: cytochrome P450 1A mRNA expression and 7-ethoxyresorufin-O-deethylase activity in fish livers responded immediately and with high sensitivity, while increased frequencies of micronuclei and other nuclear aberrations, as well as histopathological and gross pathological lesions, were strong indicators of the potential long-term effects of re-suspension events. Our study clearly demonstrates that sediment re-suspension can lead to accumulation of PCDD/Fs and PCBs in fish, resulting in potentially adverse toxicological effects. For a sound risk assessment within the implementation of the European Water Framework Directive and related legislation, we propose a strong emphasis on sediment-bound contaminants in the context of integrated river basin management plans.

Volunteers Opening Doors: the Five Keys to Lead Safety

Millions of houses and apartments built before 1978 have paint that contains lead. Chips, dust, and fumes from this paint can be very dangerous if they are not handled properly. Lead is particularly hazardous to unborn babies, infants, and young children. Volunteers in painting and housing-rehabilitation programs often work in homes that contain lead paint. The work they perform can create a lead hazard if they disturb this paint and produce paint chips or dust. Volunteers Opening Doors is a video program for these volunteers. It explains how volunteers can protect housing residents,themselves, and their families from lead poisoning by using the five keys to lead safety: 1. Protect residents and their belongings. 2. Prepare the work area. 3. Protect yourself from dust and debris. 4. Work wet. 5. Work clean.

Current United States stem cell policy considerations and a recommendation for an alternative policy based on guidelines from existing international policies

Embryonic stem cell research is a widely debated topic in modern politics and religion. Differing views on the fetal rights conflict with the rights of an embryo. Those who believe an embryo has the same human qualities as a fetus accordingly believe embryonic stem cell research is unethical because it destroys a potential human life. However, scientists advocate the embryo does not have human qualities and should be used for valuable research in the stem cell field. Stem cell research may lead to vast developments in medical treatments, including cancer and brain conditions and injuries that are currently incurable. ^ The current stem cell policy introduced by President Bush in 2001 in an attempt to balance the moral issues with the need for scientific research has broad negative implications on the furthering of stem cell research. There is a limited diversity of available stem cell lines, there may be constitutional issues, there is an increasing disparity between the public and private research spheres, and the U.S. is struggling to maintain its scientific community. The U.S. must develop a new stem cell research policy that will balance the interest of science and public health with the moral issues that concern the public. ^ The United Kingdom allows researchers great liberty in conducting research, permitting the creation of embryos for the sole purpose of research, while Germany is equally conservative in their laws, as their policies support the philosophy that all embryos deserve the protection of full life. The United States should adopt a policy that takes the "middle ground" approach and permit research on excess embryos created for IVF purposes, rather than simply discarding those potentially valuable research tools. ^

GMZ27 is a new organic arsenic derivative with anti-leukemic activity, via the induction of reactive oxygen species through NADPH oxidase and mitochondrial pathway that lead to leukemia cell apoptosis

Arsenic trioxide (ATO) is an inorganic arsenic derivative that is very effective against relapsed acute promyelocytic leukemia. It is being investigated as therapy for other cancers, but the risk/benefit ratio is questionable due to significant side effects. In contrast, organic arsenic derivatives (OAD) are known to be much less toxic than ATO. Based on high activity, we selected GMZ27 (dipropil-s-glycerol arsenic) for further study and have confirmed its potent activity against human acute leukemia cell lines. This anti-leukemic activity is significantly higher than that of ATO. Both in vivo and in vitro tests have shown that GMZ27 is significantly less toxic to normal bone marrow mononuclear cells and normal mice. Therefore, further study of the biological activity of GMZ27 was undertaken. ^ GMZ27, in contrast to ATO, can only marginally induce maturation of leukemic cells. GMZ27 has no effect on cell cycle. The anti-leukemic activity of GMZ27 against acute myeolocytic leukemia cells is not dependent upon degradation of PML-RARα fusion protein. GMZ27 causes dissipation of mitochondrial transmembrane potential, cleavage of caspase 9, caspase 3 activation. Further studies indicated that GMZ27 induces intracellular reactive oxygen species (ROS) production, and modification of intracellular ROS levels had profound effect on its potential to inhibit proliferation of leukemic cells. Therefore ROS production plays a major role in the anti-leukemic activity of GMZ27. ^ To identify how GMZ27 induces ROS, our studies focused on mitochondria and NADPH oxidase. The results indicated that the source of ROS generation induced by GMZ27 is dose dependent. At the low dose (0.3 uM) GMZ27 induces NADPH oxidase activity that leads to late ROS production, while at the high dose (2.0 uM) mitochondria function is disrupted and early ROS production is induced leading to dramatic cell apoptosis. Therefore, late, ROS production can be detected in mitochondria are depleted Rho-0 cells. Our work not only delineates a major biologic pathway for the anti-leukemic activity of GMZ27, but also discusses possible ways of enhancing the effect by the co-application of NADPH oxidase activator. Further study of this interaction may lead to achieving better therapeutic index.^

Dietary patterns and risk of pancreatic cancer in a hospital-based case-control study

Background. It is important to understand the association between diet and risk of pancreatic cancer in order to better understand the etiology of pancreatic cancer.^ Objectives. Describe the dietary patterns of cases of adenocarcinoma of the pancreas and non-cancer controls and evaluate the odds of having a healthy eating pattern among cases and non-cancer controls.^ Design and Methods. An ongoing hospital-based case-control study was conducted in Houston, Texas from 2000-2008 with 678 pancreatic adenocarcinoma cases and 724 controls. Participants completed a food frequency questionnaire and a risk factor questionnaire. Dietary patterns were derived by principal component analysis and associations between dietary patterns and pancreatic cancer risk were assessed using unconditional logistic regression.^ Results. Two dietary patterns were derived: fruit-vegetable and high fat-meat. There were no statistically significant associations between the fruit-vegetable pattern and pancreatic cancer. An inverse association was seen between the high fat-meat pattern and pancreatic cancer risk when comparing those in the upper intake quintile to those scoring in the lowest quintile after adjusting for demographic and risk factor variables (OR=0.67, p=0.03). In sex-stratified analysis adjusted for demographic and risk factor variables, females scoring in the upper intake quintile of the fruit-vegetable pattern had a 49% lower risk of pancreatic cancer compared to females scoring in the lowest quintile (OR=0.51, p=0.03). An inverse relationship was also seen for the high fat-meat pattern when comparing females in the upper intake quintile to females in the lowest quintile (OR=0.50, p=0.03). In males, neither dietary pattern was significantly associated with pancreatic cancer.^ Conclusions. The current findings for the fruit-vegetable pattern are similar to those of previous studies and support the hypothesis that there is an inverse association between a “healthy” diet (comprised of fruits, vegetables, and whole grains) and risk of having pancreatic cancer (in females only). However, the inverse relationship with the high fat-meat pattern and risk of pancreatic cancer is contrary to other results. Further research on dietary patters and pancreatic cancer risk may lead to better understanding of the etiologic cause of pancreatic cancer.^

Network-based genome-wide association study of Crohn's disease

Genome-wide association studies (GWAS) have rapidly become a standard method for disease gene discovery. Many recent GWAS indicate that for most disorders, only a few common variants are implicated and the associated SNPs explain only a small fraction of the genetic risk. The current study incorporated gene network information into gene-based analysis of GWAS data for Crohn's disease (CD). The purpose was to develop statistical models to boost the power of identifying disease-associated genes and gene subnetworks by maximizing the use of existing biological knowledge from multiple sources. The results revealed that Markov random field (MRF) based mixture model incorporating direct neighborhood information from a single gene network is not efficient in identifying CD-related genes based on the GWAS data. The incorporation of solely direct neighborhood information might lead to the low efficiency of these models. Alternative MRF models looking beyond direct neighboring information are necessary to be developed in the future for the purpose of this study.^

Verification of the clinical implementation of the respiratory gated beam delivery technique with synchrotron-based proton irradiation

The clinical advantage for protons over conventional high-energy x-rays stems from their unique depth-dose distribution, which delivers essentially no dose beyond the end of range. In order to achieve it, accurate localization of the tumor volume relative to the proton beam is necessary. For cases where the tumor moves with respiration, the resultant dose distribution is sensitive to such motion. One way to reduce uncertainty caused by respiratory motion is to use gated beam delivery. The main goal of this dissertation is to evaluate the respiratory gating technique in both passive scattering and scanning delivery mode. Our hypothesis for the study was that optimization of the parameters of synchrotron operation and respiratory gating can lead to greater efficiency and accuracy of respiratory gating for all modes of synchrotron-based proton treatment delivery. The hypothesis is tested in two specific aims. The specific aim #1 is to assess the efficiency of respiratory-gated proton beam delivery and optimize the synchrotron operations for the gated proton therapy. A simulation study was performed and introduced an efficient synchrotron operation pattern, called variable Tcyc. In addition, the simulation study estimated the efficiency in the respiratory gated scanning beam delivery mode as well. The specific aim #2 is to assess the accuracy of beam delivery in respiratory-gated proton therapy. The simulation study was extended to the passive scattering mode to estimate the quality of pulsed beam delivery to the residual motion for several synchrotron operation patterns with the gating technique. The results showed that variable Tcyc operation can offer good reproducible beam delivery to the residual motion at a certain phase of the motion. For respiratory gated scanning beam delivery, the impact of motion on the dose distributions by scanned beams was investigated by measurement. The results showed the threshold for motion for a variety of scan patterns and the proper number of paintings for normal and respiratory gated beam deliveries. The results of specific aims 1 and 2 provided supporting data for implementation of the respiratory gating beam delivery technique into both passive and scanning modes and the validation of the hypothesis.

Estimates of hospital and physician costs of epilepsy in the United States for 1995 comparing the provider -based survey method and a patient -based medical charts and billing method

This investigation compares two different methodologies for calculating the national cost of epilepsy: provider-based survey method (PBSM) and the patient-based medical charts and billing method (PBMC&BM). The PBSM uses the National Hospital Discharge Survey (NHDS), the National Hospital Ambulatory Medical Care Survey (NHAMCS) and the National Ambulatory Medical Care Survey (NAMCS) as the sources of utilization. The PBMC&BM uses patient data, charts and billings, to determine utilization rates for specific components of hospital, physician and drug prescriptions. ^ The 1995 hospital and physician cost of epilepsy is estimated to be $722 million using the PBSM and $1,058 million using the PBMC&BM. The difference of $336 million results from $136 million difference in utilization and $200 million difference in unit cost. ^ Utilization. The utilization difference of $136 million is composed of an inpatient variation of $129 million, $100 million hospital and $29 million physician, and an ambulatory variation of $7 million. The $100 million hospital variance is attributed to inclusion of febrile seizures in the PBSM, $−79 million, and the exclusion of admissions attributed to epilepsy, $179 million. The former suggests that the diagnostic codes used in the NHDS may not properly match the current definition of epilepsy as used in the PBMC&BM. The latter suggests NHDS errors in the attribution of an admission to the principal diagnosis. ^ The $29 million variance in inpatient physician utilization is the result of different per-day-of-care physician visit rates, 1.3 for the PBMC&BM versus 1.0 for the PBSM. The absence of visit frequency measures in the NHDS affects the internal validity of the PBSM estimate and requires the investigator to make conservative assumptions. ^ The remaining ambulatory resource utilization variance is $7 million. Of this amount, $22 million is the result of an underestimate of ancillaries in the NHAMCS and NAMCS extrapolations using the patient visit weight. ^ Unit cost. The resource cost variation is $200 million, inpatient is $22 million and ambulatory is $178 million. The inpatient variation of $22 million is composed of $19 million in hospital per day rates, due to a higher cost per day in the PBMC&BM, and $3 million in physician visit rates, due to a higher cost per visit in the PBMC&BM. ^ The ambulatory cost variance is $178 million, composed of higher per-physician-visit costs of $97 million and higher per-ancillary costs of $81 million. Both are attributed to the PBMC&BM's precise identification of resource utilization that permits accurate valuation. ^ Conclusion. Both methods have specific limitations. The PBSM strengths are its sample designs that lead to nationally representative estimates and permit statistical point and confidence interval estimation for the nation for certain variables under investigation. However, the findings of this investigation suggest the internal validity of the estimates derived is questionable and important additional information required to precisely estimate the cost of an illness is absent. ^ The PBMC&BM is a superior method in identifying resources utilized in the physician encounter with the patient permitting more accurate valuation. However, the PBMC&BM does not have the statistical reliability of the PBSM; it relies on synthesized national prevalence estimates to extrapolate a national cost estimate. While precision is important, the ability to generalize to the nation may be limited due to the small number of patients that are followed. ^

Left, right and interval bivariate censored data: Evaluating screening mammography in the presence of lead -time bias, length bias and over-detection

Of the large clinical trials evaluating screening mammography efficacy, none included women ages 75 and older. Recommendations on an upper age limit at which to discontinue screening are based on indirect evidence and are not consistent. Screening mammography is evaluated using observational data from the SEER-Medicare linked database. Measuring the benefit of screening mammography is difficult due to the impact of lead-time bias, length bias and over-detection. The underlying conceptual model divides the disease into two stages: pre-clinical (T0) and symptomatic (T1) breast cancer. Treating the time in these phases as a pair of dependent bivariate observations, (t0,t1), estimates are derived to describe the distribution of this random vector. To quantify the effect of screening mammography, statistical inference is made about the mammography parameters that correspond to the marginal distribution of the symptomatic phase duration (T1). This shows the hazard ratio of death from breast cancer comparing women with screen-detected tumors to those detected at their symptom onset is 0.36 (0.30, 0.42), indicating a benefit among the screen-detected cases. ^

Metal content of nodules at Sea Scope stations based upon different analysis methods

Information on possible resource value of sea floor manganese nodule deposits in the eastern north Pacific has been obtained by a study of records and collections of the 1972 Sea Scope Expedition.

Lead 210 and silicate profiles from sediments of the equatorial Pacific and South Atlantic

Particle mixing rates have been determined for 5 South Atlantic/Antarctic and 3 equatorial Pacific deep-sea cores using excess 210Pb and 32Si measurements. Radionuclide profiles from these siliceous, calcareous, and clay-rich sediments have been evaluated using a steady state vertical advection diffusion model. In Antarctic siliceous sediments210Pb mixing coefficients (0.04-0.16 cm**2/y) are in reasonable agreement with the 32Si mixing coefficient (0.2 or 0.4 cm**2/y, depending on 32Si half-life). In an equatorial Pacific sediment core, however, the 210Pb mixing coefficient (0.22 cm**2/y) is 3-7 times greater than the 32Si mixing coefficient (0.03 or 0.07 cm**2/y). The difference in 210Pb and 32Si mixing rates in the Pacific sediments results from: (1) non-steady state mixing and differences in characteristic time and depth scales of the two radionuclides, (2) preferential mixing of fine-grained clay particles containing most of the 210Pb activity relative to coarser particles (large radiolaria) containing the 32Si activity, or (3) the supply of 222Rn from the bottom of manganese nodules which increases the measured excess 210Pb activity (relative to 226Ra) at depth and artificially increases the 210Pb mixing coefficient. Based on 32Si data and pore water silica profiles, dissolution of biogenic silica in the sediment column appears to have a minor effect on the 32Si profile in the mixed layer. Deep-sea particle mixing rates reported in this study and the literature do not correlate with sediment type, sediment accumulation rate, or surface productivity. Based on differences in mixing rate among three Antarctic cores collected within 50 km of each other, local variability in the intensity of deep-sea mixing appears to be as important as regional differences in sediment properties.

Lead isotopes inthe Eastern Equatorial Pacific

The influence of atmospheric dust on climate and biogeochemical cycles in the oceans is well understood but poorly quantified. Glacial atmospheric dust loads were generally greater than those during the Holocene, as shown, for example, by the covariation of dust fluxes in the Equatorial Pacific and Antarctic ice cores. Nevertheless, it remains unclear whether these increases in dust flux were associated with changes in sources of dust, which would in turn suggest variations in wind patterns, climate or paleo-environment. Such questions can be answered using radiogenic isotope tracers of dust provenance. Here, we present a 160-kyr high-precision lead isotope time-series of dust input to the Eastern Equatorial Pacific (EEP) from core ODP Leg 138, Site 849 (0°11.59' N, 110°31.18' W). The Pb isotope record, combined with Nd isotope data, rules out contributions from Northern Hemisphere dust sources, north of the Intertropical Convergence Zone, such as Asia or North Africa/Sahara; similarly, eolian sources in Australia, Central America, the Northern Andes and Patagonia appear insignificant based upon the radiogenic isotope data. Fluctuations in Pb isotope ratios throughout the last 160 kyr show, instead, that South America remained the prevailing source of dusts to the EEP. There are two distinct South American Pb isotope end-members, constrained to be located in the south Central Volcanic Zone (CVZ, 22° S - 27.5° S) and the South Volcanic Zone (SVZ, 33° S - 43° S), with the former most likely originating in the Atacama Desert. Dust availability in the SVZ appears to be related to the weathering of volcanic deposits and the development of ash-derived Andosols, and influenced by local factors that might include vegetation cover. Variations in the dust fluxes from the two sources are in phase with both the dust flux and temperature records from Antarctican ice cores. We show that the forcing of dust provenance over time in the EEP overall is influenced by high-southerly-latitude climate conditions, leading to changes in the latitudinal position and strength of the South Westerlies as well as the coastal winds that blow northward along the Chilean margin. The net result is a modulation of dust emission from the Atacama Desert and the SVZ via a northward migration of the South Westerlies during cold periods and southward retreat during glacial terminations.

Daily pan-Arctic sea-ice lead maps for 2003-2015, with links to maps in netCDF format

The presence of sea-ice leads represents a key feature of the Arctic sea ice cover. Leads promote the flux of sensible and latent heat from the ocean to the cold winter atmosphere and are thereby crucial for air-sea-ice-ocean interactions. We here apply a binary segmentation procedure to identify leads from MODIS thermal infrared imagery on a daily time scale. The method separates identified leads into two uncertainty categories, with the high uncertainty being attributed to artifacts that arise from warm signatures of unrecognized clouds. Based on the obtained lead detections, we compute quasi-daily pan-Arctic lead maps for the months of January to April, 2003-2015. Our results highlight the marginal ice zone in the Fram Strait and Barents Sea as the primary region for lead activity. The spatial distribution of the average pan-Arctic lead frequencies reveals, moreover, distinct patterns of predominant fracture zones in the Beaufort Sea and along the shelf-breaks, mainly in the Siberian sector of the Arctic Ocean as well as the well-known polynya and fast-ice locations. Additionally, a substantial inter-annual variability of lead occurrences in the Arctic is indicated.