Identifying protein construct variants with increased crystallization propensity--a case study

This study describes an efficient multiparallel automated workflow of cloning, expression, purification, and crystallization of a large set of construct variants for isolated protein domains aimed at structure determination by X-ray crystallography. This methodology is applied to MAPKAP kinase 2, a key enzyme in the inflammation pathway and thus an attractive drug target. The study reveals a distinct subset of truncation variants with improved crystallization properties. These constructs distinguish themselves by increased solubility and stability during a parallel automated multistep purification process including removal of the recombinant tag. High-throughput protein melting point analysis characterizes this subset of constructs as particularly thermostable. Both parallel purification screening and melting point determination clearly identify residue 364 as the optimal C terminus for the kinase domain. Moreover, all three constructs that ultimately crystallized feature this C terminus. At the N terminus, only three amino acids differentiate a noncrystallizing from a crystallizing construct. This study addresses the very common issues associated with difficult to crystallize proteins, those of solubility and stability, and the crucial importance of particular residues in the formation of crystal contacts. A methodology is suggested that includes biophysical measurements to efficiently identify and produce construct variants of isolated protein domains which exhibit higher crystallization propensity.     

SSF production of lactic acid from cellulosic biosludges

The use of cellulosic biosludges generated in a Kraft pulp mill was investigated as substrate for lactic acid production by simultaneous saccharification and fermentation (SSF). The effect of the operation mode (batch or fedbatch), the initial liquid to solid ratio (12 or 30 g/g) and the nutrient supplementation (MRS components or none) on several parameters including lactic acid concentration, volumetric productivity and product yields, were evaluated. When the operation was carried out in fedbatch mode with nutrient supplementation and using a LSR(0)=12 g/g, a broth containing 42 g/L was obtained after 48 h with a volumetric productivity of 0.87 g/L h and a product yield of 37.8 g lactic acid/100 g biosludges. In a similar experiment carried out without nutrient supplementation, a lactic acid concentration of 39.4 g/L was obtained after 48 h with a volumetric productivity of 0.82 g/L h and a product yield of 35.5 g L-lactic acid/100 g biosludges.     

Microbial communities associated with phosphogenic sediments and phosphoclast‐associated DNA of the Benguela upwelling system

The processes that lead to the precipitation of authigenic calcium phosphate minerals in certain marine pore waters remain poorly understood. Phosphogenesis occurs in sediments beneath some oceanic upwelling zones that harbor polyphosphate‐accumulating bacteria. These bacteria are believed to concentrate phosphate in sediment pore waters, creating supersaturated conditions with respect to apatite precursors. However, the relationship between microbes and phosphorite formation is not fully resolved. To further study this association, we examined microbial community data generated from two sources: sediment cores recovered from the shelf of the Benguela upwelling region where phosphorites are currently forming, and DNA preserved within phosphoclasts recovered from a phosphorite deposit along the Benguela shelf. iTag and clone library sequencing of the 16S rRNA gene showed that many of our sediment‐hosted communities shared large numbers of phylotypes with one another, and that the same metabolic guilds were represented at localities across the shelf. Sulfate‐reducing bacteria and sulfur‐oxidizing bacteria were particularly abundant in our datasets, as were phylotypes that are known to carry out nitrification and the anaerobic oxidation of ammonium. The DNA extracted from phosphoclasts contained the signature of a distinct microbial community from those observed in the modern sediments. While some aspects of the modern and phosphoclast communities were similar, we observed both an enrichment of certain common microbial classes found in the modern phosphogenic sediments and a relative depletion of others. The phosphoclast‐associated DNA could represent a relict signature of one or more microbial assemblages that were present when the apatite or its precursors precipitated. While these taxa may or may not have contributed to the precipitation of the apatite that now hosts their genetic remains, several groups represented in the phosphoclast extract dataset have the genetic potential to metabolize polyphosphate, and perhaps modulate phosphate concentrations in pore waters where carbonate fluorapatite (or its precursors) are known to be precipitating.     

Load-shift--numerical evaluation of a new design philosophy for uncemented hip prostheses

All hip replacement prostheses alter the load transfer from the hip joint into the femur by changing the mechanical loading of the proximal femur from an externally to an internally loaded system. This alteration of the load transfer causes stress shielding and might lead to severe bone loss, especially with uncemented prostheses. To minimize these effects, load transfer to the femur should occur as proximal as possible. In order to support sufficient primary stability, however, directly post operative (PO) distal stabilization is reasonable. Consequently, the prostheses have to alter its mechanical characteristics after implantation. This concept is referred to as load-shift concept. Primary stability during the early PO state is provided by a prosthesis shaft, which is widened at the tip by a biodegradable pin. After resorption of the pin load transfer occurs no longer distally. The objective of this study was the numerical evaluation of the load-shift concept. The analysis was performed with a finite element model. Three-dimensional non-linear dynamic gait analyses data were used to evaluate whether the load transfer during walking can be altered effectively by insertion and resorption of a distal pin. Directly PO 38% of the transverse load is transferred through the prosthesis shaft and micromotion of the proximal prostheses tip is below 55 microm. After resorption of the pin, no transverse loads are transferred through the prosthesis shaft. Therefore, the loading of the proximal bone tissue is far more pronounced than in the case of a standard prosthesis, demonstrating the feasibility of the load-shift concept. A balanced degradation of the pin simultaneously with the ingrowth of the prosthesis is expected to reduce hip replacement complications.     

Shrubline but not treeline advance matches climate velocity in montane ecosystems of south‐central Alaska

Tall shrubs and trees are advancing into many tundra and wetland ecosystems but at a rate that often falls short of that predicted due to climate change. For forest, tall shrub, and tundra ecosystems in two pristine mountain ranges of Alaska, we apply a Bayesian, error‐propagated calculation of expected elevational rise (climate velocity), observed rise (biotic velocity), and their difference (biotic inertia). We show a sensitive dependence of climate velocity on lapse rate and derive biotic velocity as a rigid elevational shift. Ecosystem presence identified from recent and historic orthophotos ~50 years apart was regressed on elevation. Biotic velocity was estimated as the difference between critical point elevations of recent and historic logistic fits divided by time between imagery. For both mountain ranges, the 95% highest posterior density of climate velocity enclosed the posterior distributions of all biotic velocities. In the Kenai Mountains, mean tall shrub and climate velocities were both 2.8 m y^?1. In the better sampled Chugach Mountains, mean tundra retreat was 1.2 m y^?1 and climate velocity 1.3 m y^?1. In each mountain range, the posterior mode of tall woody vegetation velocity (the complement of tundra) matched climate velocity better than either forest or tall shrub alone, suggesting competitive compensation can be important. Forest velocity was consistently low at 0.1–1.1 m y^?1, indicating treeline is advancing slowly. We hypothesize that the high biotic inertia of forest ecosystems in south‐central Alaska may be due to competition with tall shrubs and/or more complex climate controls on the elevational limits of trees than tall shrubs. Among tall shrubs, those that disperse farthest had lowest inertia. Finally, the rapid upward advance of woody vegetation may be contributing to regional declines in Dall's sheep (Ovis dalli), a poorly dispersing alpine specialist herbivore with substantial biotic inertia due to dispersal reluctance.     

Evidence for Multidrug Resistance-1 P-Glycoprotein-dependent Regulation of Cellular ATP Permeability

The mechanisms responsible for regulating epithelial ATP permeability and purinergic signaling are not well defined. Based on the observations that members of the ATP-binding cassette (ABC)¹ family of proteins may contribute to ATP release, the purpose of these studies was to assess whether multidrug resistance-1 (MDR1) proteins are involved in ATP release from HTC hepatoma cells. Using a bioluminescence assay to detect extracellular ATP, increases in cell volume increased ATP release ∼3-fold. The MDR1 inhibitors cyclosporine A (10 μm) and verapramil (10 μm) inhibited ATP release by 69% and 62%, respectively (p < 0.001). Similarly, in whole-cell patch-clamp recordings, intracellular dialysis with C219 antibodies to inhibit MDR1 decreased ATP-dependent volume-sensitive Cl⁻ current density from −33.1 ± 12.5 pA/pF to −2.0 ± 0.3 pA/pF (−80 mV, p≤ 0.02). In contrast, overexpression of MDR1 in NIH 3T3 cells increased ATP release rates. Inhibition of ATP release by Gd³⁺ had no effect on transport of the MDR1 substrate rhodamine-123; and alteration of MDR1-substrate selectivity by mutation of G185 to V185 had no effect on ATP release. Since the effects of P-glycoproteins on ATP release can be dissociated from P-glycoprotein substrate transport, MDR1 is not likely to function as an ATP channel, but instead serves as a potent regulator of other cellular ATP transport pathways. Received: 20 November 2000/Revised: 25 May 2001     

Mechanical stiffness as an improved single-cell indicator of osteoblastic human mesenchymal stem cell differentiation

Although it has been established that cellular stiffness can change as a stem cell differentiates, the precise relationship between cell mechanics and other phenotypic properties remains unclear. Inherent cell heterogeneity and asynchronous differentiation complicate population analysis; therefore, single-cell analysis was employed to determine how changes in cell stiffness correlate with changes in molecular biomarkers during differentiation. Design of a custom gridded tissue culture dish facilitated single-cell comparisons between cell mechanics and other differentiation biomarkers by enabling sequential measurement of cell mechanics and protein biomarker expression at the single cell level. The Young’s modulus of mesenchymal stem cells was shown not only to decrease during chemically-induced osteoblast differentiation, but also to correlate more closely with the day of differentiation than did the relative expression of the traditional osteoblast differentiation markers, bone sialoprotein and osteocalcin. Therefore, cell stiffness, a measurable property of individual cells, may serve as an improved indicator of single-cell osteoblast differentiation compared to traditional biological markers. Revelation of additional osteoblast differentiation indicators, such as cell stiffness, can improve identification and collection of starting cell populations, with applications to mesenchymal stem cell therapies and stem cell-based tissue engineering.     

The role of microbial biofilms in deterioration of space station candidate materials

Formation of microbial biofilms on surfaces of a wide range of materials being considered as candidates for use on the International Space Station was investigated. The materials included a fibre-reinforced polymeric composite, an adhesive sealant, a polyimide insulation foam, teflon cable insulation, titanium, and an aliphatic polyurethane coating. They were exposed to a natural mixed population of bacteria under controlled conditions of temperature and relative humidity (RH). Biofilms formed on the surfaces of the materials at a wide range of temperatures and RHs. The biofilm population was dominated by Pseudomonas aeruginosa, Ochrobactrum anthropi, Alcaligenes denitrificans, Xanthomonas maltophila, and Vibrio harveyi. The biocide, diiodomethyl-p-tolyl sulfone, impregnated in the polyurethane coating, was ineffective against microbial colonization and growth. Degradation of the polyurethane coatings was monitored with electrochemical impedance spectroscopy (EIS). The impedance spectra indicated that microbial degradation of the coating occurred in several stages. The initial decreases in impedance were due to the transport of water and solutes into the polymeric matrices. Further decreases were a result of polymer degradation by microorganisms. Our data showed that these candidate materials for space application are susceptible to biofilm formation and subsequent degradation. Our study suggests that candidate materials for use in space missions need to be carefully evaluated for their susceptibility to microbial biofilm formation and biodegradation.     

An expert system model for mapping tropical wetlands and peatlands reveals South America as the largest contributor

Wetlands are important providers of ecosystem services and key regulators of climate change. They positively contribute to global warming through their greenhouse gas emissions, and negatively through the accumulation of organic material in histosols, particularly in peatlands. Our understanding of wetlands’ services is currently constrained by limited knowledge on their distribution, extent, volume, interannual flood variability and disturbance levels. We present an expert system approach to estimate wetland and peatland areas, depths and volumes, which relies on three biophysical indices related to wetland and peat formation: (1) long‐term water supply exceeding atmospheric water demand; (2) annually or seasonally water‐logged soils; and (3) a geomorphological position where water is supplied and retained. Tropical and subtropical wetlands estimates reach 4.7 million km² (Mkm²). In line with current understanding, the American continent is the major contributor (45%), and Brazil, with its Amazonian interfluvial region, contains the largest tropical wetland area (800,720 km²). Our model suggests, however, unprecedented extents and volumes of peatland in the tropics (1.7 Mkm² and 7,268 (6,076–7,368) km³), which more than threefold current estimates. Unlike current understanding, our estimates suggest that South America and not Asia contributes the most to tropical peatland area and volume (ca. 44% for both) partly related to some yet unaccounted extended deep deposits but mainly to extended but shallow peat in the Amazon Basin. Brazil leads the peatland area and volume contribution. Asia hosts 38% of both tropical peat area and volume with Indonesia as the main regional contributor and still the holder of the deepest and most extended peat areas in the tropics. Africa hosts more peat than previously reported but climatic and topographic contexts leave it as the least peat‐forming continent. Our results suggest large biases in our current understanding of the distribution, area and volumes of tropical peat and their continental contributions.