Analyses of the structure and function of lower Colorado River riparian plant communities

Throughout western North America, riparian ecosystem function has been transformed by anthropogenic influences on riverine environments. Modified flood frequencies, durations or intensities, depressed floodplain water tables, and increased rhizosphere salinities contribute to change in communities formerly dominated by alluvial forest taxa. In addition, the invasion of a naturalized arborescent shrub, Tamarix ramosissima, potentially alters competitive hierarchies and disturbance regimes in riparian ecosystems. To evaluate southwestern riparian community structure and function, comparison of ecophysiological characteristics of dominant woody taxa with site physical parameters was undertaken in riparian ecosystems that are relatively pristine (Bill Williams River) and highly perturbed (lower Colorado River). Analyses of leaf elements and tissue water relations parameters indicated that Tamarix was halophytic, apparently using Na to adjust osmotically to moisture or salinity stress. Tamarix leaf litter accumulation may also contribute to episodic fires, a form of disturbance that appears to be new in southwestern riparian ecosystems. Post-fire soil salinization and hydraulic efficiency in resprouting burned Tamarix individuals provided evidence for fire adaptation in this species relative to native woody taxa. The shrub, Tessaria sericea, appeared to share certain of these traits with Tamarix, apparently contributing to its success in colonizing perturbed floodplain habitats. Stable isotopic analyses of moisture sources and xylem water showed that Tamarix may be facultatively phreatophytic while the formerly dominant alluvial forest taxa, Salix gooddingii and Populus fremontii, are obligate phreatophytes. Leaf tissue carbon isotopic discrimination provided evidence for high water use efficiency in Tamarix relative to the other three taxa evaluated. Experimental removal of Tamarix from stands where Salix was codominant resulted in morphological change, less negative water potentials and higher leaf conductance in Salix, all evidence for interspecific competition. The persistence of Salix but not Populus on the Colorado River may occur due to lower osmotic potentials and higher cell elasticity in the former species. A high proportion of senescent Populus in Colorado River riparian vegetation plots provided an indication that this species is approaching local extinction in this ecosystem. Ordination analyses provided evidence for riparian community structure along gradients of moisture, salinity, disturbance from fire, and community maturity

Diatoms of Northeastern Iowa Fens

Analysis of water samples from 10 fens in NE Iowa, collected 13-14 November 1987, revealed a gradient from acid, low conductivity water conditions (pH 5.6, alkalinity 30 mg/I HCO, conductivity 65 μmho, total hardness 30 mg/I Ca) to circumneutral, moderately conductive conditions (pH 7 .2, alkalinity 390 mg/I, conductivity 705 μmho, total hardness 380 mg/I Ca). Three sites along this gradient were sampled 15 May 1988 and 3 September 1988 to evaluate seasonal variation in water conditions. Examination of composite diatom samples collected concurrently with the water samples yielded 150 taxa, of which 14 are new Iowa distributional records and 6 remain unidentified. Previous investigators have reported 102 of these taxa from other Iowa fens, bogs, or prairie swales. Only 58 have been reported from the Cedar River basin, where most of these fens are located. This evidence suggests these scattered small wetlands resemble similar areas some distance away more than the surrounding surface waters. Distributional patterns of diatoms along the environmental gradient appear sufficiently distinct to permit delineation of species autecology

Relativistic Quantum Mechanics and Relativistic Entanglement in the Rest-Frame Instant Form of Dynamics

A new formulation of relativistic quantum mechanics is proposed in the framework of the rest-frame instant form of dynamics with its instantaneous Wigner 3-spaces and with its description of the particle world-lines by means of derived non-canonical predictive coordinates. In it we quantize the frozen Jacobi data of the non-local 4-center of mass and the Wigner-covariant relative variables in an abstract (frame-independent) internal space whose existence is implied by Wigner-covariance. The formalism takes care of the properties of both relativistic bound states and scattering ones. There is a natural solution to the \textit{relativistic localization problem}. The non-relativistic limit leads to standard quantum mechanics but with a frozen Hamilton-Jacobi description of the center of mass. Due to the \textit{non-locality} of the Poincar\'e generators the resulting theory of relativistic entanglement is both \textit{kinematically non-local and spatially non-separable}: these properties, absent in the non-relativistic limit, throw a different light on the interpretation of the non-relativistic quantum non-locality and of its impact on foundational problems.Comment: 73 pages, includes revision

Successional changes associated with benthic assemblages in experimental streams

Experimental streams constructed by the Weyerhaeuser Company, Tacoma, Washington, at Kalama Springs, Washington, were used to observe successional changes in the benthos. Community changes were observed relative to experimental manipulations of light intensity and nitrate concentration in two experiments. The development of benthic assemblages was followed for 150 days after a simulated freshet that removed most of the plant and animal biomass from the streams. The development of the benthic assemblages was quantified with measures of composite properties (organic matter and pigment concentrations); primary production and community respiration; the taxonomic structure, biomass, and export of plants; and the taxonomic structure, biomass, and export of animals. A photosynthesis-respiration chamber was used to measure the rate of benthic primary production at light saturation and to establish the relationship between primary production and light intensity. Multivariate analyses (discriminant and principal components analyses) were used to analyze temporal changes in algal taxonomic structure within a riffle and differences among riffles exposed to different experimental conditions. Successional changes in benthic assemblages that occurred in all riffles were described by a series of three stages taxonomically distinguished by Diatoma hiemale v. mesodon (stage I), chironomids (stage II), and Zygnema (stage III). These stages were characterized by a rapid increase of algae (stage I), an increase of faunal biomass and export (stage II), and a subsequent increase of algae with a decrease in faunal export (stage III). The rate of primary production was higher in riffles exposed to high solar radiation than riffles receiving low radiation, and higher in the nitrate-enriched riffles than in the unenriched riffles if solar radiation was high. High algal biomasses (stage I and III) and high faunal export (stage II) were observed in riffles subjected to relatively high solar radiation. The behavior of the benthic assemblages with time was interpreted as the reorganization and stabilization of two levels of organization - the benthos and stream system - within the structural hierarchy of the lotic ecosystem. The developmental stages were the reorganization of the producer (algal) subsystem that resulted in an increase in primary production (stage I), stabilization of the producer and consumer (faunal)subsystems of the benthos system (stage II), reorganization of the benthos system that resulted in an increase in primary production and a decrease in community respiration (stage III), and stabilization of the stream system (hypothesized stage IV). Conceptually, benthic assemblages of natural streams are perceived to exist in a tension between environmental stress and the evolution of hierarchical organization that represents the decomposition and composition of structure in the lotic ecosystem, respectively

Rapid online buffer exchange for screening of proteins, protein complexes and cell lysates by native mass spectrometry

It is important to assess the identity and purity of proteins and protein complexes during and after protein purification to ensure that samples are of sufficient quality for further biochemical and structural characterization, as well as for use in consumer products, chemical processes and therapeutics. Native mass spectrometry (nMS) has become an important tool in protein analysis due to its ability to retain non-covalent interactions during measurements, making it possible to obtain protein structural information with high sensitivity and at high speed. Interferences from the presence of non-volatiles are typically alleviated by offline buffer exchange, which is time-consuming and difficult to automate. We provide a protocol for rapid online buffer exchange (OBE) nMS to directly screen structural features of pre-purified proteins, protein complexes or clarified cell lysates. In the liquid chromatography coupled to mass spectrometry (LC-MS) approach described in this protocol, samples in MS-incompatible conditions are injected onto a short size-exclusion chromatography column. Proteins and protein complexes are separated from small molecule non-volatile buffer components using an aqueous, non-denaturing mobile phase. Eluted proteins and protein complexes are detected by the mass spectrometer after electrospray ionization. Mass spectra can inform regarding protein sample purity and oligomerization, and additional tandem mass spectra can help to further obtain information on protein complex subunits. Information obtained by OBE nMS can be used for fast (<5 min) quality control and can further guide protein expression and purification optimization

The WAY theorem and the quantum resource theory of asymmetry

The WAY theorem establishes an important constraint that conservation laws impose on quantum mechanical measurements. We formulate the WAY theorem in the broader context of resource theories, where one is constrained to a subset of quantum mechanical operations described by a symmetry group. Establishing connections with the theory of quantum state discrimination we obtain optimal unitaries describing the measurement of arbitrary observables, explain how prior information can permit perfect measurements that circumvent the WAY constraint, and provide a framework that establishes a natural ordering on measurement apparatuses through a decomposition into asymmetry and charge subsystems.Comment: 11 pages, 3 figure

Deciphering the relative roles of matrix metalloproteinase‐ and plasmin‐mediated matrix degradation during capillary morphogenesis using engineered hydrogels

Extracellular matrix (ECM) remodeling is essential for the process of capillary morphogenesis. Here we employed synthetic poly(ethylene glycol) (PEG) hydrogels engineered with proteolytic specificity to either matrix metalloproteinases (MMPs), plasmin, or both to investigate the relative contributions of MMP‐ and plasmin‐mediated ECM remodeling to vessel formation in a 3D‐model of capillary self‐assembly analogous to vasculogenesis. We first demonstrated a role for both MMP‐ and plasmin‐mediated mechanisms of ECM remodeling in an endothelial‐fibroblast co‐culture model of vasculogenesis in fibrin hydrogels using inhibitors of MMPs and plasmin. When this co‐culture model was employed in engineered PEG hydrogels with selective protease sensitivity, we observed robust capillary morphogenesis only in MMP‐sensitive matrices. Fibroblast spreading in plasmin‐selective hydrogels confirmed this difference was due to protease preference by endothelial cells, not due to limitations of the matrix itself. In hydrogels engineered with crosslinks that were dually susceptible to MMPs and plasmin, capillary morphogenesis was unchanged. These findings highlight the critical importance of MMP‐mediated degradation during vasculogenesis and provide strong evidence to justify the preferential selection of MMP‐degradable peptide crosslinkers in synthetic hydrogels used to study vascular morphogenesis and promote vascularization. © 2019 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater 107B:2507–2516, 2019.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/151850/1/jbmb34341_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/151850/2/jbmb34341.pd

A role for an Hsp70 nucleotide exchange factor in the regulation of synaptic vesicle endocytosis

© The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Journal of Neuroscience 33 (2013): 8009-8021, doi:10.1523/JNEUROSCI.4505-12.2013.Neurotransmission requires a continuously available pool of synaptic vesicles (SVs) that can fuse with the plasma membrane and release their neurotransmitter contents upon stimulation. After fusion, SV membranes and membrane proteins are retrieved from the presynaptic plasma membrane by clathrin-mediated endocytosis. After the internalization of a clathrin-coated vesicle, the vesicle must uncoat to replenish the pool of SVs. Clathrin-coated vesicle uncoating requires ATP and is mediated by the ubiquitous molecular chaperone Hsc70. In vitro, depolymerized clathrin forms a stable complex with Hsc70*ADP. This complex can be dissociated by nucleotide exchange factors (NEFs) that release ADP from Hsc70, allowing ATP to bind and induce disruption of the clathrin:Hsc70 association. Whether NEFs generally play similar roles in vesicle trafficking in vivo and whether they play such roles in SV endocytosis in particular is unknown. To address this question, we used information from recent structural and mechanistic studies of Hsp70:NEF and Hsp70:co-chaperone interactions to design a NEF inhibitor. Using acute perturbations at giant reticulospinal synapses of the sea lamprey (Petromyzon marinus), we found that this NEF inhibitor inhibited SV endocytosis. When this inhibitor was mutated so that it could no longer bind and inhibit Hsp110 (a NEF that we find to be highly abundant in brain cytosol), its ability to inhibit SV endocytosis was eliminated. These observations indicate that the action of a NEF, most likely Hsp110, is normally required during SV trafficking to release clathrin from Hsc70 and make it available for additional rounds of endocytosis.This work was supported by the National Institutes of Health (Grant #NS029051 to E.M.L. and Grant #NS078165 to J.R.M.).2013-11-0

Rapid online buffer exchange for screening of proteins, protein complexes and cell lysates by native mass spectrometry

It is important to assess the identity and purity of proteins and protein complexes during and after protein purification to ensure that samples are of sufficient quality for further biochemical and structural characterization, as well as for use in consumer products, chemical processes and therapeutics. Native mass spectrometry (nMS) has become an important tool in protein analysis due to its ability to retain non-covalent interactions during measurements, making it possible to obtain protein structural information with high sensitivity and at high speed. Interferences from the presence of non-volatiles are typically alleviated by offline buffer exchange, which is time-consuming and difficult to automate. We provide a protocol for rapid online buffer exchange (OBE) nMS to directly screen structural features of pre-purified proteins, protein complexes or clarified cell lysates. In the liquid chromatography coupled to mass spectrometry (LC-MS) approach described in this protocol, samples in MS-incompatible conditions are injected onto a short size-exclusion chromatography column. Proteins and protein complexes are separated from small molecule non-volatile buffer components using an aqueous, non-denaturing mobile phase. Eluted proteins and protein complexes are detected by the mass spectrometer after electrospray ionization. Mass spectra can inform regarding protein sample purity and oligomerization, and additional tandem mass spectra can help to further obtain information on protein complex subunits. Information obtained by OBE nMS can be used for fast (<5 min) quality control and can further guide protein expression and purification optimization

Low cost, low tech SNP genotyping tools for resource-limited areas: Plague in Madagascar as a model

Genetic analysis of pathogenic organisms is a useful tool for linking human cases together and/or to potential environmental sources. The resulting data can also provide information on evolutionary patterns within a targeted species and phenotypic traits. However, the instruments often used to generate genotyping data, such as single nucleotide polymorphisms (SNPs), can be expensive and sometimes require advanced technologies to implement. This places many genotyping tools out of reach for laboratories that do not specialize in genetic studies and/or lack the requisite financial and technological resources. To address this issue, we developed a low cost and low tech genotyping system, termed agarose-MAMA, which combines traditional PCR and agarose gel electrophoresis to target phylogenetically informative SNPs