Effect of Decompressive Craniectomy on Perihematomal Edema in Patients with Intracerebral Hemorrhage.

BACKGROUND Perihematomal edema contributes to secondary brain injury in the course of intracerebral hemorrhage. The effect of decompressive surgery on perihematomal edema after intracerebral hemorrhage is unknown. This study analyzed the course of PHE in patients who were or were not treated with decompressive craniectomy. METHODS More than 100 computed tomography images from our published cohort of 25 patients were evaluated retrospectively at two university hospitals in Switzerland. Computed tomography scans covered the time from admission until day 100. Eleven patients were treated by decompressive craniectomy and 14 were treated conservatively. Absolute edema and hematoma volumes were assessed using 3-dimensional volumetric measurements. Relative edema volumes were calculated based on maximal hematoma volume. RESULTS Absolute perihematomal edema increased from 42.9 ml to 125.6 ml (192.8%) after 21 days in the decompressive craniectomy group, versus 50.4 ml to 67.2 ml (33.3%) in the control group (Δ at day 21 = 58.4 ml, p = 0.031). Peak edema developed on days 25 and 35 in patients with decompressive craniectomy and controls respectively, and it took about 60 days for the edema to decline to baseline in both groups. Eight patients (73%) in the decompressive craniectomy group and 6 patients (43%) in the control group had a good outcome (modified Rankin Scale score 0 to 4) at 6 months (P = 0.23). CONCLUSIONS Decompressive craniectomy is associated with a significant increase in perihematomal edema compared to patients who have been treated conservatively. Perihematomal edema itself lasts about 60 days if it is not treated, but decompressive craniectomy ameliorates the mass effect exerted by the intracerebral hemorrhage plus the perihematomal edema, as reflected by the reduced midline shift.

BIOCHEMICAL CHARACTERIZATION OF BINDING PARTNERS OF TWO HSP70 CO-CHAPERONES IN SACCHAROMYCES CEREVISIAE

Cells are exposed to a variety of environmental and physiological changes including temperature, pH and nutrient availability. These changes cause stress to cells, which results in protein misfolding and altered cellular protein homeostasis. How proteins fold into their three-dimensional functional structure is a fundamental biological process with important relevance to human health. Misfolded and aggregated proteins are linked to multiple neurodegenerative diseases, cardiovascular disease and cystic fibrosis. To combat proteotoxic stress, cells deploy an array of molecular chaperones that assist in the repair or removal of misfolded proteins. Hsp70, an evolutionarily conserved molecular chaperone, promotes protein folding and helps maintain them in a functional state. Requisite co-chaperones, including nucleotide exchange factors (NEFs) strictly regulate and serve to recruit Hsp70 to distinct cellular processes or locations. In yeast and human cells, three structurally non-related cytosolic NEFs are present: Sse1 (Hsp110), Fes1 (HspBP1) and Snl1 (Bag-1). Snl1 is unique among the cytosolic NEFs as it is localized at the ER membrane with its Hsp70 binding (BAG) domain exposed to the cytosol. I discovered that Snl1 distinctly interacts with assembled ribosomes and several lines of evidence indicate that this interaction is both independent of and concurrent with binding to Hsp70 and is not dependent on membrane localization. The ribosome-binding site is identified as a short lysine-rich motif within the amino terminus of the Snl1 BAG domain distinct from the Hsp70 interaction region. In addition, I demonstrate ribosome association with the Snl1 homolog in the pathogenic fungus, Candida albicans and localize this putative NEF to a perinuclear/ER membrane, suggesting functional conservation in fungal BAG domain-containing proteins. As a first step in determining specific domain architecture in fungal BAG proteins, I present the preliminary steps of protein purification and analysis of the minimal Hsp70 binding region in in both S.cerevisiae and C. albicans Snl1. Contrary to previous in vitro evidence which showed the Fes1 NEF to interact with both cytosolic Hsp70s, Ssa and Ssb, Fes1 is shown to interact specifically with Ssa when expressed under normal cellular conditions in S. cerevisiae. This is the first reported evidence of Hsp70 binding selectivity for a cytosolic NEF, and suggests a possible mechanism to achieve specificity in Hsp70-dependent functions. Taken together, the work presented in this dissertation highlights the striking divergence among Hsp70 co-chaperones in selecting binding partners, which may correlate with their specific roles in the cell.

Ocean acidification outweighs nutrient effects in structuring seagrass epiphyte communities

1. Developing a framework for assessing interactions between multiple anthropogenic stressors remains an important goal in environmental research. In coastal ecosystems, the relative effects of aspects of global climate change (e.g. CO2 concentrations) and localized stressors (e.g. eutrophication), in combination, have received limited attention. 2. Using a long-term (11 month) field experiment, we examine how epiphyte assemblages in a tropical seagrass meadow respond to factorial manipulations of dissolved carbon dioxide (CO2(aq)) and nutrient enrichment. In situ CO2(aq) manipulations were conducted using clear, open-top chambers, which replicated carbonate parameter forecasts for the year 2100. Nutrient enrichment consisted of monthly additions of slow-release fertilizer, nitrogen (N) and phosphorus (P), to the sediments at rates equivalent to theoretical maximum rates of anthropogenic loading within the region (1.54 g N/m**2/d and 0.24 g P m**2/d). 3. Epiphyte community structure was assessed on a seasonal basis and revealed declines in the abundance of coralline algae, along with increases in filamentous algae under elevated CO2(aq). Surprisingly, nutrient enrichment had no effect on epiphyte community structure or overall epiphyte loading. Interactions between CO2(aq) and nutrient enrichment were not detected. Furthermore, CO2(aq)-mediated responses in the epiphyte community displayed strong seasonality, suggesting that climate change studies in variable environments should be conducted over extended time-scales. 4. Synthesis. The observed responses indicate that for certain locations, global stressors such as ocean acidification may take precedence over local eutrophication in altering the community structure of seagrass epiphyte assemblages. Given that nutrient-driven algal overgrowth is commonly cited as a widespread cause of seagrass decline, our findings highlight that alternate climate change forces may exert proximate control over epiphyte community structure.

Are fractured cliffs the source of cometary dust jets? Insights from OSIRIS/Rosetta at 67P/Churyumov-Gerasimenko

Context. Dust jets (i.e., fuzzy collimated streams of cometary material arising from the nucleus) have been observed in situ on all comets since the Giotto mission flew by comet 1P/Halley in 1986, and yet their formation mechanism remains unknown. Several solutions have been proposed involving either specific properties of the active areas or the local topography to create and focus the gas and dust flows. While the nucleus morphology seems to be responsible for the larger features, high resolution imagery has shown that broad streams are composed of many smaller jets (a few meters wide) that connect directly to the nucleus surface. Aims. We monitored these jets at high resolution and over several months to understand what the physical processes are that drive their formation and how this affects the surface. Methods. Using many images of the same areas with different viewing angles, we performed a 3-dimensional reconstruction of collimated jets and linked them precisely to their sources on the nucleus. Results. We show here observational evidence that the northern hemisphere jets of comet 67P/Churyumov-Gerasimenko arise from areas with sharp topographic changes and describe the physical processes involved. We propose a model in which active cliffs are the main source of jet-like features and therefore of the regions eroding the fastest on comets. We suggest that this is a common mechanism taking place on all comets.

Reconstruction and development of rural Cambodia : from Krom Samakki to globalization

This paper reveals how rural Cambodian people reconstructed their social relationships after the collapse of the Pol Pot regime by examining farmland, which was the most important means of production in rural areas at that time. Section 1 and 2 illustrate the process of returning from collective farming under the Pol Pot regime to the family farming system. Section 3 analyzes the structure of land ownership created through land distribution by Krom Samakki. Section 4 studies the actualities of tenant farming. Section 5 examines the changes of the land ownership structure during a decade years after the distribution of Krom Samakki. This paper concludes that the legacy of Krom Samakki started to fade as early as the 1990s.

Optimal Impulsive Collision Avoidance

The problem of optimal impulsive collision avoidance between two colliding objects in 3-dimensional elliptical Keplerian orbits is investigated with the purpose of establishing the optimal impulse direction and orbit location that give rise to the maximum miss distance following the maneuver. Closed-form analytical expressions are provided that predicts such distance and can be employed to perform a full optimization analysis. After verifying the accuracy of the expression for any orbital eccentricity and encounter geometry the optimum maneuver direction is derived as a function of the arc length separation between the maneuver point and the predicted collision point. The provided formulas can be used for high accuracy instantaneous estimation of the outcome of a generic impulsive collision avoidance maneuver and its optimization

Hardware timestamping for image acquisition system based on FlexRIO and IEEE 1588 v2 Standard

Current fusion devices consist of multiple diagnostics and hundreds or even thousands of signals. This situation forces on multiple occasions to use distributed data acquisition systems as the best approach. In this type of distributed systems, one of the most important issues is the synchronization between signals, so that it is possible to have a temporal correlation as accurate as possible between the acquired samples of all channels. In last decades, many fusion devices use different types of video cameras to provide inside views of the vessel during operations and to monitor plasma behavior. The synchronization between each video frame and the rest of the different signals acquired from any other diagnostics is essential in order to know correctly the plasma evolution, since it is possible to analyze jointly all the information having accurate knowledge of their temporal correlation. The developed system described in this paper allows timestamping image frames in a real-time acquisition and processing system using 1588 clock distribution. The system has been implemented using FPGA based devices together with a 1588 synchronized timing card (see Fig.1). The solution is based on a previous system [1] that allows image acquisition and real-time image processing based on PXIe technology. This architecture is fully compatible with the ITER Fast Controllers [2] and offers integration with EPICS to control and monitor the entire system. However, this set-up is not able to timestamp the frames acquired since the frame grabber module does not present any type of timing input (IRIG-B, GPS, PTP). To solve this lack, an IEEE1588 PXI timing device its used to provide an accurate way to synchronize distributed data acquisition systems using the Precision Time Protocol (PTP) IEEE 1588 2008 standard. This local timing device can be connected to a master clock device for global synchronization. The timing device has a buffer timestamp for each PXI trigger line and requires tha- a software application assigns each frame the corresponding timestamp. The previous action is critical and cannot be achieved if the frame rate is high. To solve this problem, it has been designed a solution that distributes the clock from the IEEE 1588 timing card to all FlexRIO devices [3]. This solution uses two PXI trigger lines that provide the capacity to assign timestamps to every frame acquired and register events by hardware in a deterministic way. The system provides a solution for timestamping frames to synchronize them with the rest of the different signals.

Antiviral agent blocks breathing of the common cold virus

A dynamic capsid is critical to the events that shape the viral life cycle; events such as cell attachment, cell entry, and nucleic acid release demand a highly mobile viral surface. Protein mass mapping of the common cold virus, human rhinovirus 14 (HRV14), revealed both viral structural dynamics and the inhibition of such dynamics with an antiviral agent, WIN 52084. Viral capsid digestion fragments resulting from proteolytic time-course experiments provided structural information in good agreement with the HRV14 three-dimensional crystal structure. As expected, initial digestion fragments included peptides from the capsid protein VP1. This observation was expected because VP1 is the most external viral protein. Initial digestion fragments also included peptides belonging to VP4, the most internal capsid protein. The mass spectral results together with x-ray crystallography data provide information consistent with a “breathing” model of the viral capsid. Whereas the crystal structure of HRV14 shows VP4 to be the most internal capsid protein, mass spectral results show VP4 fragments to be among the first digestion fragments observed. Taken together this information demonstrates that VP4 is transiently exposed to the viral surface via viral breathing. Comparative digests of HRV14 in the presence and absence of WIN 52084 revealed a dramatic inhibition of digestion. These results indicate that the binding of the antiviral agent not only causes local conformational changes in the drug binding pocket but actually stabilizes the entire viral capsid against enzymatic degradation. Viral capsid mass mapping provides a fast and sensitive method for probing viral structural dynamics as well as providing a means for investigating antiviral drug efficacy.

Identification of 5′-deoxyribose phosphate lyase activity in human DNA polymerase γ and its role in mitochondrial base excision repair in vitro

Mitochondria have been proposed to possess base excision repair processes to correct oxidative damage to the mitochondrial genome. As the only DNA polymerase (pol) present in mitochondria, pol γ is necessarily implicated in such processes. Therefore, we tested the ability of the catalytic subunit of human pol γ to participate in uracil-provoked base excision repair reconstituted in vitro with purified components. Subsequent to actions of uracil-DNA glycosylase and apurinic/apyrimidinic endonuclease, human pol γ was able to fill a single nucleotide gap in the presence of a 5′ terminal deoxyribose phosphate (dRP) flap. We report here that the catalytic subunit of human pol γ catalyzes release of the dRP residue from incised apurinic/apyrimidinic sites to produce a substrate for DNA ligase. The heat sensitivity of this activity suggests the dRP lyase function requires a three-dimensional protein structure. The dRP lyase activity does not require divalent metal ions, and the ability to trap covalent enzyme-DNA complexes with NaBH4 strongly implicates a Schiff base intermediate in a β-elimination reaction mechanism.

Structural mimicry of a native protein by a minimized binding domain

The affinity between molecules depends both on the nature and presentation of the contacts. Here, we observe coupling of functional and structural elements when a protein binding domain is evolved to a smaller functional mimic. Previously, a 38-residue form of the 59-residue B-domain of protein A, termed Z38, was selected by phage display. Z38 contains 13 mutations and binds IgG only 10-fold weaker than the native B-domain. We present the solution structure of Z38 and show that it adopts a tertiary structure remarkably similar to that observed for the first two helices of B-domain in the B-domain/Fc complex [Deisenhofer, J. (1981) Biochemistry 20, 2361–2370], although it is significantly less stable. Based on this structure, we have improved on Z38 by designing a 34-residue disulfide-bonded variant (Z34C) that has dramatically enhanced stability and binds IgG with 9-fold higher affinity. The improved stability of Z34C led to NMR spectra with much greater chemical shift dispersion, resulting in a more precisely determined structure. Z34C, like Z38, has a structure virtually identical to the equivalent region from native protein A domains. The well-defined hydrophobic core of Z34C reveals key structural features that have evolved in this small, functional domain. Thus, the stabilized two-helix peptide, about half the size and having one-third of the remaining residues altered, accurately mimics both the structure and function of the native domain.

X-ray analysis of azido-thymidine diphosphate binding to nucleoside diphosphate kinase

To be effective as antiviral agent, AZT (3′-azido-3′-deoxythymidine) must be converted to a triphosphate derivative by cellular kinases. The conversion is inefficient and, to understand why AZT diphosphate is a poor substrate of nucleoside diphosphate (NDP) kinase, we determined a 2.3-Å x-ray structure of a complex with the N119A point mutant of Dictyostelium NDP kinase. It shows that the analog binds at the same site and, except for the sugar ring pucker which is different, binds in the same way as the natural substrate thymidine diphosphate. However, the azido group that replaces the 3′OH of the deoxyribose in AZT displaces a lysine side chain involved in catalysis. Moreover, it is unable to make an internal hydrogen bond to the oxygen bridging the β- and γ-phosphate, which plays an important part in phosphate transfer.

A transmembrane form of annexin XII detected by site-directed spin labeling

Previous studies of the annexin family of Ca2+ binding proteins identified a soluble monomer in the absence of Ca2+ and a trimer adsorbed on the membrane surface in the presence of Ca2+. On the basis of site-directed spin-labeling studies of annexin XII at low pH, we now report a membrane-inserted form of the protein with a dramatically different structure. The data suggest that upon insertion a continuous transmembrane α-helix is reversibly formed from a helix–loop–helix motif in the solution structure. Other regions with similar membrane-insertion potential were identified in the amino acid sequence, and we propose that the corresponding helices come together to form an aqueous pore that mediates the ion channel activity reported for several annexins.

Two different neurodegenerative diseases caused by proteins with similar structures

The downstream prion-like protein (doppel, or Dpl) is a paralog of the cellular prion protein, PrPC. The two proteins have ≈25% sequence identity, but seem to have distinct physiologic roles. Unlike PrPC, Dpl does not support prion replication; instead, overexpression of Dpl in the brain seems to cause a completely different neurodegenerative disease. We report the solution structure of a fragment of recombinant mouse Dpl (residues 26–157) containing a globular domain with three helices and a small amount of β-structure. Overall, the topology of Dpl is very similar to that of PrPC. Significant differences include a marked kink in one of the helices in Dpl, and a different orientation of the two short β-strands. Although the two proteins most likely arose through duplication of a single ancestral gene, the relationship is now so distant that only the structures retain similarity; the functions have diversified along with the sequence.

Transverse relaxation-optimized NMR spectroscopy with the outer membrane protein OmpX in dihexanoyl phosphatidylcholine micelles

The 2H,13C,15N-labeled, 148-residue integral membrane protein OmpX from Escherichia coli was reconstituted with dihexanoyl phosphatidylcholine (DHPC) in mixed micelles of molecular mass of about 60 kDa. Transverse relaxation-optimized spectroscopy (TROSY)-type triple resonance NMR experiments and TROSY-type nuclear Overhauser enhancement spectra were recorded in 2 mM aqueous solutions of these mixed micelles at pH 6.8 and 30°C. Complete sequence-specific NMR assignments for the polypeptide backbone thus have been obtained. The 13C chemical shifts and the nuclear Overhauser effect data then resulted in the identification of the regular secondary structure elements of OmpX/DHPC in solution and in the collection of an input of conformational constraints for the computation of the global fold of the protein. The same type of polypeptide backbone fold is observed in the presently determined solution structure and the previously reported crystal structure of OmpX determined in the presence of the detergent n-octyltetraoxyethylene. Further structure refinement will have to rely on the additional resonance assignment of partially or fully protonated amino acid side chains, but the present data already demonstrate that relaxation-optimized NMR techniques open novel avenues for studies of structure and function of integral membrane proteins.