The Professionalization of Science Studies: Cutting Some Slack

During the past hundred years or so, those scholars studying science have isolated themselves as much as possible from scientists as well as from workers in other disciplines who study science. The result of this effort is history of science, philosophy of science and sociology of science as separate disciplines. I argue in this paper that now is the time for these disciplinary boundaries to be lowered or at least made more permeable so that a unified discipline of Science Studies might emerge. I discuss representative problems that stand in the way of such an integration. These problems may seem so formidable in the abstract that no one in their right mind would waste their time trying to bring about a unified field of Science Studies. However, those of us who limit ourselves to the study of the biological sciences have already formed a society in which workers from all disciplines can share their expertise -- the International Society for the History, Philosophy and Social Studies of Science.     

A parameter optimization approach for the optimal control of large-scale musculoskeletal systems.

This paper describes a computational method for solving optimal control problems involving large-scale, nonlinear, dynamical systems. Central to the approach is the idea that any optimal control problem can be converted into a standard nonlinear programming problem by parameterizing each control history using a set of nodal points, which then become the variables in the resulting parameter optimization problem. A key feature of the method is that it dispenses with the need to solve the two-point, boundary-value problem derived from the necessary conditions of optimal control theory. Gradient-based methods for solving such problems do not always converge due to computational errors introduced by the highly nonlinear characteristics of the costate variables. Instead, by converting the optimal control problem into a parameter optimization problem, any number of well-developed and proven nonlinear programming algorithms can be used to compute the near-optimal control trajectories. The utility of the parameter optimization approach for solving general optimal control problems for human movement is demonstrated by applying it to a detailed optimal control model for maximum-height human jumping. The validity of the near-optimal control solution is established by comparing it to a solution of the two-point, boundary-value problem derived on the basis of a bang-bang optimal control algorithm. Quantitative comparisons between model and experiment further show that the parameter optimization solution reproduces the major features of a maximum-height, countermovement jump (i.e., trajectories of body-segmental displacements, vertical and fore-aft ground reaction forces, displacement, velocity, and acceleration of the whole-body center of mass, pattern of lower-extremity muscular activity, jump height, and total ground contact time).     

Characterizing the role of the microtubule binding protein Bim1 in Cryptococcus neoformans

During sexual development the human fungal pathogen Cryptococcus neoformans undergoes a developmental transition from yeast-form growth to filamentous growth. This transition requires cellular restructuring to form a filamentous dikaryon. Dikaryotic growth also requires tightly controlled nuclear migration to ensure faithful replication and dissemination of genetic material to spore progeny. Although the gross morphological changes that take place during dikaryotic growth are largely known, the molecular underpinnings that control this process are uncharacterized. Here we identify and characterize a C. neoformans homolog of the Saccharomyces cerevisiae BIM1 gene, and establish the importance of BIM1 for proper filamentous growth of C. neoformans. Deletion of BIM1 leads to truncated sexual development filaments, a severe defect in diploid formation, and a block in monokaryotic fruiting. Our findings lead to a model consistent with a critical role for BIM1 in both filament integrity and nuclear congression that is mediated through the microtubule cytoskeleton.     

Synthesis of surfactant-associated glycoprotein A by rat type II epithelial cells. Primary translation products and post-translational modification

Surfactant-associated glycoproteins A, 38 (A3), 32 (A2) and 26 (A1) kDa, pI (4.2-4.8), were identified as related proteins present in surfactant isolated from rat lung lavage fluid. Differences in size and charge among surfactant-associated glycoproteins A were related to differences in glycosylation as determined by reduction of the larger forms (38 and 32 kDa) to 26 kDa by endoglycosidase F and by increased isoelectric points of the glycosylated forms after treatment with neuraminidase. Synthesis and secretion of surfactant-associated glycoproteins A and precursors were demonstrated in purified rat Type II epithelial cells by immunoprecipitation of [35S]methionine-labelled proteins with anti-surfactant-associated glycoprotein A antisera. In pulse-chase experiments, labelled proteins 26-34 kDa, appeared within 10 min and smaller forms co-migrated with surfactant-associated glycoprotein A from alveolar lavage. The relative abundance of the larger molecular mass forms (30-34 kDa, pI 4.8) increased at later times up to 3 h. More acidic mature forms, which co-migrated with surfactant-associated glycoproteins A2 and A3 in surfactant (38 and 32 kDa), were readily detectable in the media, but were not abundant forms in lysates of labelled Type II cells after 1-3 h of incubation. Primary translation products of surfactant-associated glycoprotein A were immunoprecipitated with monospecific anti-surfactant-associated glycoprotein A antiserum after in vitro translation of poly(A)+ mRNA isolated from adult rat lung. The immunoprecipitated translation product migrated at 26 kDa, pI 4.8, and migrated slightly faster than surfactant-associated glycoprotein A1 from surfactant. Treatment of surfactant-associated glycoprotein A with bacterial collagenase resulted in proteolytic fragments 23-20 kDa, pI 4.2-4.8, which no longer underwent sulfhydryl-dependent cross-linking, suggesting that the collagen-like domain was required for the sulfhydryl-dependent oligomerization. Surfactant-associated glycoproteins A are synthesized by rat Type II epithelial cells as pre-proteins, 26-34 kDa. Larger forms result primarily from N-linked glycosylation of the 26 kDa primary translation product. Mature, more acidic forms result from further addition of sialic acid.     

The rate of removal of pyrimidine dimers in quiescent cultures of normal human and xeroderma pigmentosum cells

The rate of removal of pyrimidine dimers from DNA of UV (254 nm)-irradiated (1 J/m2) normal and xeroderma pigmentosum (XP) cells maintained in culture as nondividing populations was determined. Several normal and XP strains from complementation groups A, C and D were studied. The excision rates and survival ability of nondividing cells were examined to determine if an abnormal sensitivity was associated with a decreased rate of dimer excision. The results show that all normal strains studied excise pyrimidine dimers at the same rate, with the rate curve characterized by two components. All 'excision-deficient' XP strains excise dimers at a slower-than-normal rate, with the rate curves also characterized by two components. The rate constants for the first components of all of the XP strains (group A, C and D) are the same, one tenth of the normal rate constant, except for XP8LO (group A). XP8LO has a first-component rate constant similar to that of normal strains and a second component rate constant similar to that of other group A strains (XP12BE, XP25RO). Thus, the slower rate of dimer excision in XP8LO is due to a defect in the mechanism responsible for the second component of the excision-rate curve. In general, an abnormal sensitivity of nondividing cells to UV is associated with a reduced dimer-excision rate. A notable exception to this is the group C strain XP1BE which has an initial repair rate similar to that of group A XP12BE but is considerably more resistant when survival is measured.     

Measurement of strength and loading variables on the knee during Alpine skiing

The study focusses on the prevention of knee injuries during snow skiing. In order to develop a technology of knee injury prevention, both the strength and loading on the knee during skiing activity must be known. This paper reports measurements of variables influencing both knee strength and loading of the joint. The strength variables measured included the degree of activity in six muscles crossing the knee, the knee flexion angle, and the axial load (i.e. weight bearing) transmitted to the knee. Transducers included surface electrodes to monitor electromyogram signals indicating the degree of muscle activity and a goniometer to measure both hip and knee flexion angles. The complete loading on the knee was derived from a dynamometer which measured the six load components at the boot-dynamometer interface. The transducer data were acquired and stored by a compact, battery powered digital data acquisition-controller system. Three male subjects of similar physical size (nominal was 1.8 m and 75 kg) and skiing ability (advanced intermediate to expert) were tested under similar conditions. Each subject skied a total of four slalom runs--one snowplow and three parallel. The total time of each test was 21 s. Example data plots from different types of runs are presented and discussed. Based on observations from the data, necessary performance features for ski bindings offering improved protection from knee ligamentous injuries are defined.     

Rapid recovery of benthic invertebrates downstream of hyperalkaline steel slag discharges

This study assesses the physical and chemical characteristics of hyperalkaline steel slag leachate from a former steelworks on two streams in England and their impacts on benthic invertebrate communities. Using multivariate methods (CCA), we related invertebrate richness and diversity with chemical parameters along the environmental gradient from point sources to less impacted sites downstream. Point discharges are characterised by high pH (10.6–11.5), high ionic strength (dominated by Ca–CO₃–OH waters), elevated trace elements (notably Li, Sr and V) and high rates of calcium carbonate precipitation. This combination of stressors gives rise to an impoverished benthic invertebrate community in source areas. The total abundance, taxonomic richness and densities of most observed organisms were strongly negatively correlated with water pH. Analysis using biological pollution monitoring indices (e.g. BMWP and Functional Feeding Groups) shows the system to be highly impacted at source, but when pH approaches values close to aquatic life standards, some 500 m downstream, complex biological communities become established. In addition to showing the rapid recovery of invertebrate communities downstream of the discharges, this study also provides a baseline characterisation of invertebrate communities at the extreme alkaline range of the pH spectrum.     

EUROCarbDB: An open-access platform for glycoinformatics

The EUROCarbDB project is a design study for a technical framework, which provides sophisticated, freely accessible, open-source informatics tools and databases to support glycobiology and glycomic research. EUROCarbDB is a relational database containing glycan structures, their biological context and, when available, primary and interpreted analytical data from high-performance liquid chromatography, mass spectrometry and nuclear magnetic resonance experiments. Database content can be accessed via a web-based user interface. The database is complemented by a suite of glycoinformatics tools, specifically designed to assist the elucidation and submission of glycan structure and experimental data when used in conjunction with contemporary carbohydrate research workflows. All software tools and source code are licensed under the terms of the Lesser General Public License, and publicly contributed structures and data are freely accessible. The public test version of the web interface to the EUROCarbDB can be found at http://www.ebi.ac.uk/eurocarb.     

The error in the cryptic stereospecificity of methylmalonyl-CoA mutase. The use of carba-(dethia)-coenzyme A substrate analogues gives new insight into the enzyme mechanism

A preparation containing 80.0 +/- 0.5% (2RS)-methylmalonyl-carba-(dethia)-CoA and 20.0 +/- 0.5% propionyl-carba-(dethia)-CoA was reacted in buffered deuterium oxide with catalytic amounts of coenzyme B12, methylmalonyl-CoA mutase and methylmalonyl-CoA epimerase. The rearrangement of the methylmalonyl-carba-(dethia)-CoA to succinyl-carba-(dethia)-CoA was monitored by recording 500-MHz 1H-NMR spectra in short time intervals. After reaching equilibrium (approximately equal to 28 min) the products showed chemical stability for about 17 h, i.e. succinyl species did not undergo the spontaneous hydrolysis encountered with normal succinyl-CoA. In the pre-equilibrium stage only about 66% of the produced succinyl-CH2CoA was the expected monodeuterated species. The remainder was 15.5% unlabelled and 18.3% 3,3-dideuterated. After reaching equilibrium a continuous deuterium incorporation (washing-in) from the solvent to the products was observed and quantified. The time course of the appearance of unlabelled, mono-, di- and trideuterated succinyl-CH2CoA species was determined by assigning and integrating the isotope-shifted 1H signals from the various species. Furthermore, mutase catalyses slow deuterium incorporation into first the methylene and then the methyl group of propionyl-CH2CoA. On the basis of these data it was concluded that methylmalonyl-CoA mutase and epimerase are responsible for continuous deuterium incorporation and multiple incorporation occurs when the backward reaction (succinyl-CH2CoA----methylmalonyl-CH2CoA) becomes important. To account for all of the results obtained with dethia and natural substrates we propose a new mutase mechanism whereby the enzyme can retain full stereospecificity at C-3 of succinyl while an internal 1,2-H shift to give a C-2 succinyl radical is responsible for partial scrambling of diastereotopic protons at C-3. This mechanism successfully predicts the observed deuterium disproportionation in succinyl species and the order of appearance of di- and trideuterated products via the washing-in process.