Renal Function Underpins the Cyclooxygenase-2: Asymmetric Dimethylarginine Axis in Mouse and Man.

Introduction: Through the production of prostacyclin, cyclooxygenase (COX)-2 protects the cardiorenal system. Asymmetric dimethylarginine (ADMA), is a biomarker of cardiovascular and renal disease. Here we determined the relationship between COX-2/prostacyclin, ADMA, and renal function in mouse and human models. Methods: We used plasma from COX-2 or prostacyclin synthase knockout mice and from a unique individual lacking COX-derived prostaglandins (PGs) because of a loss of function mutation in cytosolic phospholipase A2 (cPLA2), before and after receiving a cPLA2-replete transplanted donor kidney. ADMA, arginine, and citrulline were measured using ultra-high performance liquid-chromatography tandem mass spectrometry. ADMA and arginine were also measured by enzyme-linked immunosorbent assay (ELISA). Renal function was assessed by measuring cystatin C by ELISA. ADMA and prostacyclin release from organotypic kidney slices were also measured by ELISA. Results: Loss of COX-2 or prostacyclin synthase in mice increased plasma levels of ADMA, citrulline, arginine, and cystatin C. ADMA, citrulline, and arginine positively correlated with cystatin C. Plasma ADMA, citrulline, and cystatin C, but not arginine, were elevated in samples from the patient lacking COX/prostacyclin capacity compared to levels in healthy volunteers. Renal function, ADMA, and citrulline were returned toward normal range when the patient received a genetically normal kidney, capable of COX/prostacyclin activity; and cystatin C positively correlated with ADMA and citrulline. Levels of ADMA and prostacyclin in conditioned media of kidney slices were not altered in tissue from COX-2 knockout mice compared to wildtype controls. Conclusion: In human and mouse models, where renal function is compromised because of loss of COX-2/PGI2 signaling, ADMA levels are increased.

Kidney Transplantation in a Patient Lacking Cytosolic Phospholipase A2 Proves Renal Origins of Urinary PGI-M and TX-M.

RATIONALE: The balance between vascular prostacyclin, which is antithrombotic, and platelet thromboxane A2, which is prothrombotic, is fundamental to cardiovascular health. Prostacyclin and thromboxane A2 are formed after the concerted actions of cPLA2α (cytosolic phospholipase A2) and COX (cyclooxygenase). Urinary 2,3-dinor-6-keto-PGF1α (PGI-M) and 11-dehydro-TXB2 (TX-M) have been taken as biomarkers of prostacyclin and thromboxane A2 formation within the circulation and used to explain COX biology and patient phenotypes, despite concerns that urinary PGI-M and TX-M originate in the kidney. OBJECTIVE: We report data from a remarkable patient carrying an extremely rare genetic mutation in cPLA2α, causing almost complete loss of prostacyclin and thromboxane A2, who was transplanted with a normal kidney resulting in an experimental scenario of whole-body cPLA2α knockout, kidney-specific knockin. By studying this patient, we can determine definitively the contribution of the kidney to the productions of PGI-M and TX-M and test their validity as markers of prostacyclin and thromboxane A2 in the circulation. METHODS AND RESULTS: Metabolites were measured using liquid chromatography-tandem mass spectrometry. Endothelial cells were grown from blood progenitors. Before kidney transplantation, the patient's endothelial cells and platelets released negligible levels of prostacyclin (measured as 6-keto-prostaglandin F1α) and thromboxane A2 (measured as TXB2), respectively. Likewise, the urinary levels of PGI-M and TX-M were very low. After transplantation and the establishment of normal renal function, the levels of PGI-M and TX-M in the patient's urine rose to within normal ranges, whereas endothelial production of prostacyclin and platelet production of thromboxane A2 remained negligible. CONCLUSIONS: These data show that PGI-M and TX-M can be derived exclusively from the kidney without contribution from prostacyclin made by endothelial cells or thromboxane A2 by platelets in the general circulation. Previous work relying on urinary metabolites of prostacyclin and thromboxane A2 as markers of whole-body endothelial and platelet function now requires reevaluation.

The Linac Coherent Light Source.

The Linac Coherent Light Source (LCLS) at the SLAC National Accelerator Laboratory was the first hard X-ray free-electron laser (FEL) to operate as a user facility. After five years of operation, LCLS is now a mature FEL user facility. Our personal views about opportunities and challenges inherent to these unique light sources are discussed.

Optical laser systems at the Linac Coherent Light Source.

Ultrafast optical lasers play an essential role in exploiting the unique capabilities of recently commissioned X-ray free-electron laser facilities such as the Linac Coherent Light Source (LCLS). Pump-probe experimental techniques reveal ultrafast dynamics in atomic and molecular processes and reveal new insights in chemistry, biology, material science and high-energy-density physics. This manuscript describes the laser systems and experimental methods that enable cutting-edge optical laser/X-ray pump-probe experiments to be performed at LCLS.

Aging and uremia: Is there cellular and molecular crossover?

Many observers have noted that the morphological changes that occur in chronic kidney disease (CKD) patients resemble those seen in the geriatric population, with strikingly similar morbidity and mortality profiles and rates of frailty in the two groups, and shared characteristics at a pathophysiological level especially in respect to the changes seen in their vascular and immune systems. However, whilst much has been documented about the shared physical characteristics of aging and uremia, the molecular and cellular similarities between the two have received less attention. In order to bridge this perceived gap we have reviewed published research concerning the common molecular processes seen in aging subjects and CKD patients, with specific attention to altered proteostasis, mitochondrial dysfunction, post-translational protein modification, and senescence and telomere attrition. We have also sought to illustrate how the cell death and survival pathways apoptosis, necroptosis and autophagy are closely interrelated, and how an understanding of these overlapping pathways is helpful in order to appreciate the shared molecular basis behind the pathophysiology of aging and uremia. This analysis revealed many common molecular characteristics and showed similar patterns of cellular dysfunction. We conclude that the accelerated aging seen in patients with CKD is underpinned at the molecular level, and that a greater understanding of these molecular processes might eventually lead to new much needed therapeutic strategies of benefit to patients with renal disease.

Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers.

X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and without radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract meaningful high-resolution signals from fewer diffraction measurements.

Contamination of current-clamp measurement of neuron capacitance by voltage-dependent phenomena.

Measuring neuron capacitance is important for morphological description, conductance characterization, and neuron modeling. One method to estimate capacitance is to inject current pulses into a neuron and fit the resulting changes in membrane potential with multiple exponentials; if the neuron is purely passive, the amplitude and time constant of the slowest exponential give neuron capacitance (Major G, Evans JD, Jack JJ. Biophys J 65: 423-449, 1993). Golowasch et al. (Golowasch J, Thomas G, Taylor AL, Patel A, Pineda A, Khalil C, Nadim F. J Neurophysiol 102: 2161-2175, 2009) have shown that this is the best method for measuring the capacitance of nonisopotential (i.e., most) neurons. However, prior work has not tested for, or examined how much error would be introduced by, slow voltage-dependent phenomena possibly present at the membrane potentials typically used in such work. We investigated this issue in lobster (Panulirus interruptus) stomatogastric neurons by performing current clamp-based capacitance measurements at multiple membrane potentials. A slow, voltage-dependent phenomenon consistent with residual voltage-dependent conductances was present at all tested membrane potentials (-95 to -35 mV). This phenomenon was the slowest component of the neuron's voltage response, and failure to recognize and exclude it would lead to capacitance overestimates of several hundredfold. Most methods of estimating capacitance depend on the absence of voltage-dependent phenomena. Our demonstration that such phenomena make nonnegligible contributions to neuron responses even at well-hyperpolarized membrane potentials highlights the critical importance of checking for such phenomena in all work measuring neuron capacitance. We show here how to identify such phenomena and minimize their contaminating influence.

Simultaneous femtosecond X-ray spectroscopy and diffraction of photosystem II at room temperature.

Intense femtosecond x-ray pulses produced at the Linac Coherent Light Source (LCLS) were used for simultaneous x-ray diffraction (XRD) and x-ray emission spectroscopy (XES) of microcrystals of photosystem II (PS II) at room temperature. This method probes the overall protein structure and the electronic structure of the Mn4CaO5 cluster in the oxygen-evolving complex of PS II. XRD data are presented from both the dark state (S1) and the first illuminated state (S2) of PS II. Our simultaneous XRD-XES study shows that the PS II crystals are intact during our measurements at the LCLS, not only with respect to the structure of PS II, but also with regard to the electronic structure of the highly radiation-sensitive Mn4CaO5 cluster, opening new directions for future dynamics studies.

Determining all parameters necessary to build Hill-type muscle models from experiments on single muscles.

Characterizing muscle requires measuring such properties as force-length, force-activation, and force-velocity curves. These characterizations require large numbers of data points because both what type of function (e.g., linear, exponential, hyperbolic) best represents each property, and the values of the parameters in the relevant equations, need to be determined. Only a few properties are therefore generally measured in experiments on any one muscle, and complete characterizations are obtained by averaging data across a large number of muscles. Such averaging approaches can work well for muscles that are similar across individuals. However, considerable evidence indicates that large inter-individual variation exists, at least for some muscles. This variation poses difficulties for across-animal averaging approaches. Methods to fully describe all muscle's characteristics in experiments on individual muscles would therefore be useful. Prior work in stick insect extensor muscle has identified what functions describe each of this muscle's properties and shown that these equations apply across animals. Characterizing these muscles on an individual-by-individual basis therefore requires determining only the values of the parameters in these equations, not equation form. We present here techniques that allow determining all these parameter values in experiments on single muscles. This technique will allow us to compare parameter variation across individuals and to model muscles individually. Similar experiments can likely be performed on single muscles in other systems. This approach may thus provide a widely applicable method for characterizing and modeling muscles from single experiments.

Energy-dispersive X-ray emission spectroscopy using an X-ray free-electron laser in a shot-by-shot mode.

The ultrabright femtosecond X-ray pulses provided by X-ray free-electron lasers open capabilities for studying the structure and dynamics of a wide variety of systems beyond what is possible with synchrotron sources. Recently, this "probe-before-destroy" approach has been demonstrated for atomic structure determination by serial X-ray diffraction of microcrystals. There has been the question whether a similar approach can be extended to probe the local electronic structure by X-ray spectroscopy. To address this, we have carried out femtosecond X-ray emission spectroscopy (XES) at the Linac Coherent Light Source using redox-active Mn complexes. XES probes the charge and spin states as well as the ligand environment, critical for understanding the functional role of redox-active metal sites. Kß(1,3) XES spectra of Mn(II) and Mn(2)(III,IV) complexes at room temperature were collected using a wavelength dispersive spectrometer and femtosecond X-ray pulses with an individual dose of up to >100 MGy. The spectra were found in agreement with undamaged spectra collected at low dose using synchrotron radiation. Our results demonstrate that the intact electronic structure of redox active transition metal compounds in different oxidation states can be characterized with this shot-by-shot method. This opens the door for studying the chemical dynamics of metal catalytic sites by following reactions under functional conditions. The technique can be combined with X-ray diffraction to simultaneously obtain the geometric structure of the overall protein and the local chemistry of active metal sites and is expected to prove valuable for understanding the mechanism of important metalloproteins, such as photosystem II.

Nanoflow electrospinning serial femtosecond crystallography.

An electrospun liquid microjet has been developed that delivers protein microcrystal suspensions at flow rates of 0.14-3.1 µl min(-1) to perform serial femtosecond crystallography (SFX) studies with X-ray lasers. Thermolysin microcrystals flowed at 0.17 µl min(-1) and diffracted to beyond 4 Å resolution, producing 14,000 indexable diffraction patterns, or four per second, from 140 µg of protein. Nanoflow electrospinning extends SFX to biological samples that necessitate minimal sample consumption.

Room temperature femtosecond X-ray diffraction of photosystem II microcrystals.

Most of the dioxygen on earth is generated by the oxidation of water by photosystem II (PS II) using light from the sun. This light-driven, four-photon reaction is catalyzed by the Mn(4)CaO(5) cluster located at the lumenal side of PS II. Various X-ray studies have been carried out at cryogenic temperatures to understand the intermediate steps involved in the water oxidation mechanism. However, the necessity for collecting data at room temperature, especially for studying the transient steps during the O-O bond formation, requires the development of new methodologies. In this paper we report room temperature X-ray diffraction data of PS II microcrystals obtained using ultrashort (< 50 fs) 9 keV X-ray pulses from a hard X-ray free electron laser, namely the Linac Coherent Light Source. The results presented here demonstrate that the "probe before destroy" approach using an X-ray free electron laser works even for the highly-sensitive Mn(4)CaO(5) cluster in PS II at room temperature. We show that these data are comparable to those obtained in synchrotron radiation studies as seen by the similarities in the overall structure of the helices, the protein subunits and the location of the various cofactors. This work is, therefore, an important step toward future studies for resolving the structure of the Mn(4)CaO(5) cluster without any damage at room temperature, and of the reaction intermediates of PS II during O-O bond formation.

Large-scale pose-invariant face recognition using cellular simultaneous recurrent network.

In this work, we propose a novel technique for face recognition with +/-90 degrees pose variations in image sequences using a cellular simultaneous recurrent network (CSRN). We formulate the recognition problem with such large-pose variations as an implicit temporal prediction task for CSRN. We exploit a face extraction algorithm based on the scale-space method and facial structural knowledge as a preprocessing step. Further, to reduce computational cost, we obtain eigenfaces for a set of image sequences for each person and use these reduced pattern vectors as the input to CSRN. CSRN learns how to associate each face class/person in the training phase. A modified distance metric between successive frames of test and training output pattern vectors indicate either a match or mismatch between the two corresponding face classes. We extensively evaluate our CSRN-based face recognition technique using the publicly available VidTIMIT Audio-Video face dataset. Our simulation shows that for this dataset with large-scale pose variations, we can obtain an overall 77% face recognition rate.

Pyloric neuron morphology in the stomatogastric ganglion of the lobster, Panulirus interruptus.

The pyloric network of decapod crustaceans has been intensively studied electrophysiologically in the infraorders Astacidea, Brachyura, and Palinura. The morphology of some or all pyloric neurons has been well described in Astacidea and Brachyura, but less so in Palinura. Given the large evolutionary distance between these three groups, and the large amount of electrophysiology that has been performed in palinuroid species, it is important to fill this gap. We describe here the gross morphology of all six pyloric neuron types in a palinuroid, P. interruptus. All pyloric neurons had complicated, extended dendritic trees that filled the majority of the neuropil, with most small diameter processes present in a shell near the surface of the ganglion. Certain neuron types showed modest preferences for somata location in the ganglion, but these differences were too weak to use as identifying characteristics. Quantitative measurements of secondary branch number, maximum branch order, total process length, and neuron somata diameter were also, in general, insufficient to distinguish among the neurons, although AB and LP neuron somata diameters differed from those of the other types. One neuron type (VD) had a distinctive neurite branching pattern consisting of a small initial branch followed shortly by a bifurcation of the main neurite. The processes arising from these two branches occupied largely non-overlapping neuropil. Electrophysiological recordings showed that each major branch had its own spike initiation zone and that, although the zones fired correlated spikes, they generated spikes independently. VD neurons in the other infraorders have similar morphologies, suggesting that having two arbors is important for the function of this neuron. These data are similar to those previously obtained in Brachyura and Astacidea. It thus appears that, despite their long evolutionary separation, neuron morphology in these three infraorders has not greatly diverged.