A lipase preparation with dual pH optima,wide temperature optima and broad substrate specificity for multiple applications

Summary Optimised procedures for the production and recovery of lipase at 25 litre scale by submerged fermentation using aRhizopus species isolated from petroleum-soaked soil are developed. These lipase preparations are characterized by dual pH optima (4.0 and 8.0), wide temperature optima (over 80% activity between 40–57°C), broad specificity for substrates, high degree of tolerance for common salts and excellent stability during usage as well as storage.     

Surface exploration of Amphibalanus amphitrite cyprids on microtextured surfaces

Microtopography is one of several strategies used by marine organisms to inhibit colonization by fouling organisms. While replicates of natural microtextures discourage settlement, details of larval interactions with the structured surfaces remain scarce. Close-range microscopy was used to quantify the exploration of cyprids of Amphibalanus amphitrite on cylindrical micropillars with heights of 5 and 30 μm and diameters ranging from 5 to 100 μm. While 5 μm-high structures had little impact, 30 μm-high pillars significantly influenced cyprid exploration. An observed step length decrease and step duration increase on 5 μm diameter pillars is attributed to the small dimensions of the voids excluding the cyprid's attachment disc and consequently reducing the area of adhesive contact. When exploring larger diameter pillars, cyprids preferred using the voids to form temporary attachment points. This may enhance their resistance to flow. No-choice assay settlement patterns mirrored this exploration behaviour, albeit in a pattern counter to what was predicted.     

Surface exploration of Amphibalanus amphitrite cyprids on microtextured surfaces

Microtopography is one of several strategies used by marine organisms to inhibit colonization by fouling organisms. While replicates of natural microtextures discourage settlement, details of larval interactions with the structured surfaces remain scarce. Close-range microscopy was used to quantify the exploration of cyprids of Amphibalanus amphitrite on cylindrical micropillars with heights of 5 and 30 μm and diameters ranging from 5 to 100 μm. While 5 μm-high structures had little impact, 30 μm-high pillars significantly influenced cyprid exploration. An observed step length decrease and step duration increase on 5 μm diameter pillars is attributed to the small dimensions of the voids excluding the cyprid's attachment disc and consequently reducing the area of adhesive contact. When exploring larger diameter pillars, cyprids preferred using the voids to form temporary attachment points. This may enhance their resistance to flow. No-choice assay settlement patterns mirrored this exploration behaviour, albeit in a pattern counter to what was predicted.     

Multiple temperature optima in collectotrichum graminicola

Summary The dry weights of three isolates ofColletotrichum graminicola (Ces.)Wills., growing at 10°, 15°, 20°, 30°, and 35° C in yeast extract liquid medium were recorded. Two temperature growth optima and minima occurred at 20°C, 30°C and 10°C, 25°C respectively.Portion of a Ph. D. thesis, The Ohio State University, Columbus 10, Ohio, U.S.A. Department of Botany and Plant Pathology. Paper Number 657.     

Analyzing bioterror response logistics: the case of smallpox

To evaluate existing and alternative proposals for emergency response to a deliberate smallpox attack, we embed the key operational features of such interventions into a smallpox disease transmission model. We use probabilistic reasoning within an otherwise deterministic epidemic framework to model the 'race to trace', i.e., attempting to trace (via the infector) and vaccinate an infected person while (s)he is still vaccine-sensitive. Our model explicitly incorporates a tracing/vaccination queue, and hence can be used as a capacity planning tool. An approximate analysis of this large (16 ODE) system yields closed-form estimates for the total number of deaths and the maximum queue length. The former estimate delineates the efficacy (i.e., accuracy) and efficiency (i.e., speed) of contact tracing, while the latter estimate reveals how congestion makes the race to trace more difficult to win, thereby causing more deaths. A probabilistic analysis is also used to find an approximate closed-form expression for the total number of deaths under mass vaccination, in terms of both the basic reproductive ratio and the vaccination capacity. We also derive approximate thresholds for initially controlling the epidemic for more general interventions that include imperfect vaccination and quarantine.     

Diet space and response surfaces

Proximate analyses of diets for monogastrics are presented as points in an equilateral triangular region of a plane. Arrays of lines of constant dietary energy and lines normal to them are discussed. Examples of growth efficiency of rats and chickens as experimental response to dietary levels of various types of protein are presented. The response follows the law of diminishing returns as a function of percent dietary protein holding percent dietary fat constant. This law is used to propose a new method of comparing the growth promoting abilities of proteins. Values of the relative growth promoting ability of various proteins are presented. An amino acid diet developed by H. M. Scott and associates at the University of Illinois is chosen as the reference diet.     

Temperature optima of enzyme-catalysed reactions in microemulsion systems

Ternary phase systems (water/surfactant/organic solvent) were utilised to increase and broaden the temperature optima of enzyme-catalysed reactions. Alcohol dehydrogenases from yeast and Thermoanaerobium brockii (EC 1.1.1.1 and EC 1.1.1.2), lactate dehydrogenase from Lactobacillus delbrueckii (EC 1.1.1.28) and the particulate hydrogenase from Ralstonia eutropha (EC 1.18.99.1) were used as model enzymes in microemulsions, consisting of the surfactant Aerosol OT, and various alkane solvent and aqueous phases. All enzymes exhibited, besides an increase in specific activity, an upshift of the temperature optimum of the catalysed reaction. The temperature optimum could be further shifted by variation of the chain length of the solvent used and/or the addition of compatible solutes to the aqueous phase. Under optimised conditions, catalytic reactions of enzymes from mesophilic microorganisms had temperature optima in the range generally obtained with enzymes from thermophilic organisms.     

Analyzing multiple spike trains with nonparametric granger causality

Simultaneous recordings of spike trains from multiple single neurons are becoming commonplace. Understanding the interaction patterns among these spike trains remains a key research area. A question of interest is the evaluation of information flow between neurons through the analysis of whether one spike train exerts causal influence on another. For continuous-valued time series data, Granger causality has proven an effective method for this purpose. However, the basis for Granger causality estimation is autoregressive data modeling, which is not directly applicable to spike trains. Various filtering options distort the properties of spike trains as point processes. Here we propose a new nonparametric approach to estimate Granger causality directly from the Fourier transforms of spike train data. We validate the method on synthetic spike trains generated by model networks of neurons with known connectivity patterns and then apply it to neurons simultaneously recorded from the thalamus and the primary somatosensory cortex of a squirrel monkey undergoing tactile stimulation.     

On optima: the case of myoglobin-facilitated oxygen diffusion

The process of myoglobin/leghemoglobin-facilitated oxygen diffusion is adapted to function in different environments in diverse organisms. We enquire how the functional parameters of the process are optimized in particular organisms. The ligand-binding properties of the proteins, myoglobin and plant symbiotic hemoglobins, we discover, suggest that they have been adapted under genetic selection pressure for optimal performance. Since carrier-mediated oxygen transport has probably evolved independantly many times, adaptation of diverse proteins for a common functionality exemplifies the process of convergent evolution. The progenitor proteins may be built on the myoglobin scaffold or may be very different.     

An exploration of the controls of pre-instrumental streamflow using multiple tree-ring proxies

Previous studies have used tree-ring chronologies from several species to develop reconstructions of precipitation, temperature, streamflow and glacier mass balance for sites in Banff National Park, Alberta. This study examines the variability in a >300-year summer streamflow reconstruction for the Bow River at Banff in conjunction with changes in the major contributors to streamflow (glacier melt, winter and summer pecipitation). Reconstructed winter mass balance for Peyto Glacier is used as a surrogate for winter precipitation and April–August precipitation is reconstructed for Banff. Streamflow variability correlates most highly with winter precipitation and periods of high flow follow above average snowfall in the previous winter (high winter balance) and in some cases also with above normal summer precipitation. A clear response to changes in summer mass balance at Peyto Glacier (i.e. summer glacier melting) cannot be identified in this summer discharge record. Problems developing physically realistic flow reconstructions for snowmelt dominated rivers from summer sensitive tree-ring chronologies are also discussed.     

Detection and interpretation of redox potential optima in the catalytic activity of enzymes

It is no surprise that the catalytic activity of electron-transport enzymes may be optimised at certain electrochemical potentials in ways that are analogous to observations of pH-rate optima. This property is observed clearly in experiments in which an enzyme is adsorbed on an electrode surface which can supply or receive electrons rapidly and in a highly controlled manner. In such a way, the rate of catalysis can be measured accurately as a function of the potential (driving force) that is applied. In this paper, we draw attention to a few examples in which this property has been observed in enzymes that are associated with membrane-bound respiratory chains, and we discuss its possible origins and implications for in vivo regulation.     

Multiplexing analysis of the polyspecific intrathecal immune response in multiple sclerosis

Intrathecal synthesis of the antibodies specific to neurotrofic viruses: measles (M), rubella (R), Varicella-Zoster (Z), and/or H. simplex (H), known as "MRZH-reaction" plays important diagnostic role in multiple sclerosis (MS). Whereas the analysis of the oligoclonal IgG bands provides high sensitivity, the MRZH-reaction shows high specificity, and hence these methods complement each other. For the first time we applied multiplexing bead-based technology to simultaneously analyze cerebrospinal fluid (CSF) and serum concentrations of antibodies against these viruses, and to calculate the antibody specific indices (ASI's). The method shows reasonable precision: intra-assay, 2.9-6.7%, and inter-assay, 2.0-3.2%. The results are comparable with these obtained with other methods (ELISAs), including two runs of the certified external quality control schemes. Eighty-one percent of the MS cases (n=27) and none of the sex- and age-matched controls (n=14), except one subject with "borderline" anti-measles ASI of 1.5, showed intrathecal synthesis of IgG against at least one of the viruses discussed. The ratios of the MRZH-positive cases in the MS group were: 12/22 for M, 12/19 for R, 13/26 for Z, and 7/26 for H. We conclude that the multiplexing technology can be applied as a tool to study the intrathecal immune response in the diagnosis of MS.     

Characterization of polysaccharidase activity optima in the anaerobic digestion of municipal solid waste

Summary Cellulolytic enzymes from a laboratory anaerobic digester fed municipal solid waste were examined with respect to pH and temperature. The pH optimum was pH 6.6, considerably lower than the pH range in which digesters are normally operated (pH 7.2–7.6). The optimum temperature was between 50 and 60°C, rather than the 35–37°C range in which most digesters are controlled.     

MuGeN: simultaneous exploration of multiple genomes and computer analysis results

MOTIVATION: The availability of increasing amounts of sequence data about completely sequenced genomes spurs the development of new methods in the fields of automated annotation, and of comparative genomics. Tools allowing the visualization of results produced by analysis methods, superimposed on possibly annotated sequence data, and enabling synchronized navigation in multiple genomes, provide new means for interactive genome exploration. This kind of visual inspection can be used as a basis to assess the quality of new analysis algorithms, or to discover genome portions to be subjected to in-depth studies. RESULTS: We propose a software package, MuGeN, built for navigating through multiple annotated genomes. It is capable of retrieving annotated sequences in several formats, stored in local files, or available in databases over the network. From these, it then generates an interactive display, or an image file, in most common formats suitable for printing, further editing or integrating in Web pages. Genome maps may be mixed with computer analysis results loaded from XML files, whose format is generic enough to be adapted to a majority of sequence oriented analysis methods. AVAILABILITY: MuGeN is available at http://www-mig.jouy.inra.fr/bdsi/MuGeN.     

Bryophyte response surfaces along ecological and climatic gradients

Bivariate response surfaces were fitted to abundance data for 6 mire bryophyte species in ecological and climatic space in western Canada. Response surfaces were derived by gridding data, eliminating outliers, and reducing effects of overly influential abundance values. Predicted values at each grid node were calculated as distance-weighted means of all observed values within a predetermined radius of each node. Response surfaces accurately delimited species ecological and climatic ranges. The gridding process consistently underestimated observed abundance values, and paired t-tests indicated significant differences between predicted and observed values for Sphagnum fuscum and Tomenthypnum nitens in ecological space, and for Sphagnum fuscum, Tomenthypnum nitens, and Scorpidium scorpioides in climatic space. Predicted values were significantly different only for those species that had large data sets, and for species that had clusters of points with an inordinately large number of data points within them. However, with the exception of Sphagnum tenellum, predicted and observed values were significantly correlated for all species in both ecological and climatic space. R² analyses for the linear relationship between predicted and observed values can be used as a diagnostic tool to determine the effectiveness of the gridding process to accurately predict observed abundance values.Abbreviations p statistical probability     

The role of flexible tethers in multiple ligand-receptor bond formation between curved surfaces

Ligands mounted to surfaces via extensible tethers are present in nature and represent a growing class of molecules used to engineer adhesion in drug targeting, biosensing, self-assembling nanostructures, and in other biophysical research. Using a continuum approach with geometric and thermodynamic arguments, we derive a number of analytical expressions that relate key properties of single-tethered ligand-receptor interactions to multiple bond formation between curved surfaces. The theoretical predictions are in good agreement with measurements made with the surface forces apparatus. We establish that, when ligated, many tethers commonly used in biophysical research exhibit a discrete binding range that can be accurately measured with force spectroscopy. The distribution of bound ligated tethers is independent of the surfaces' interaction radius, R. The bridging force scales linearly with R, the tether's effective spring constant and grafting density, and with the ligand-receptor bond energy when the surfaces are in direct contact. These results are contrasted to bridging forces that evolve between plane-parallel geometries. Last, we show how our simple analytical reductions can be used to predict adhesive forces for STEALTH liposomes and other targeted and self-assembled nanoparticles.     

On multiple comparisons in the randomization analysis of growth and response curves

Two multiple-comparisons procedures are suggested for supplementing randomization analysis of growth and response curves. One controls the experimentwise Type I error rate for all possible contrast curves via an extension of the Scheffé method. The other controls a family of Type I error rates via a stepwise testing procedure. Both can be approximated by standard F tests without costly recomputation of all of the test statistics for a large number of permutations.     

Immunodominance in the T-Cell response to multiple non-H-2 histocompatibility antigens

Immunization of C57BL/6 mice with BALB.B spleen cells in vivo and subsequent boosting in mixed lymphocyte culture result in the generation of cytolytic T lymphocytes (CTLs) which are specific for a limited number of immunodominant antigens. Experiments are described which suggest the existence of a hierarchy of immunodominance in this donor: host combination. Two antigens, CTT-1.3 and CTT-2.3, are dominant in the C57BL/6 anti-BALB.B CTL response. The distribution of these antigens among CXB recombinant inbred (RI) strains suggests that they segregate as single gene traits. Elimination of the CTT-1.3 and CTT-2.3 antigens by complementation in the responder, or elimination from the priming and boosting stages by the selection.of CXB RI strain mice as responders or stimulators, reveals a second level of immunodominant antigens which include CTT-3.3 and CTT-4.3. CXB mice which express one of the CTT-1.3 or CTT-2.3 antigens will produce CTLs specific for the other antigen upon priming and boosting with BALB.B cells. Expression of both antigens in responders results in the generation of CTLs specific for the second level, dominant antigens. Immunodominance is not confined to the C57BL/6 anti-BALB.B system but can also be observed in the BALB.B anti-C57BL/6 and B10.D2 anti-DBA/2 systems. Finally, generation of CTLs following priming and boosting with dominant and dominated antigens presented on different cells confirmed that immunodominance can only be observed when the dominant and dominated antigens are presented on the same cells. These observations suggest that immunodominance is revealed at the level of antigen-presenting cells primarily involved in vivo priming.