Characterization of salt interferences in second-harmonic generation detection of protein crystals

Studies were undertaken to assess the merits and limitations of second-harmonic generation (SHG) for the selective detection of protein and polypeptide crystal formation, focusing on the potential for false positives from SHG-active salts present in crystallization media. The SHG activities of salts commonly used in protein crystallization were measured and quantitatively compared with reference samples. Out of 19 salts investigated, six produced significant background SHG and 15 of the 96 wells of a sparse-matrix screen produced SHG upon solvent evaporation. SHG-active salts include phosphates, hydrated sulfates, formates and tartrates, while chlorides, acetates and anhydrous sulfates resulted in no detectable SHG activity. The identified SHG-active salts produced a range of signal intensities spanning nearly three orders of magnitude. However, even the weakest SHG-active salt produced signals that were several orders of magnitude greater than those produced by typical protein crystals. In general, SHG-active salts were identifiable through characteristically strong SHG and negligible two-photon-excited ultraviolet fluorescence (TPE-UVF). Exceptions included trials containing either potassium dihydrogen phosphate or ammonium formate, which produced particularly strong SHG, but with residual weak TPE-UVF signals that could potentially complicate discrimination in crystallization experiments using these precipitants.

Exploring the role of SlrR and SlrA in the SinR epigenetic switch

BACTERIAL BIOFILMS ARE BECOMING A SIGNIFICANT SOCIETAL PROBLEM

biofilms form dental plaque, coat ships causing biofouling, and cling onto medical instruments and implants. Understanding how these surface-bound communities are formed is crucial for the development of suitable strategies for their dispersal. At the heart of a switch that commits Bacilli and related species to form biofilms is a transcriptional regulator called SinR and its multiple antagonists. In this addendum, we discuss an alternative model to account for how one of the antagonists is regulated by controlled proteolysis.

Molecular basis of the activity of SinR protein, the master regulator of biofilm formation in Bacillus subtilis

Bacterial biofilms are complex communities of cells that are attached to a surface by an extracellular matrix. Biofilms are an increasing environmental and healthcare issue, causing problems ranging from the biofouling of ocean-going vessels, to dental plaque, infections of the urinary tract, and contamination of medical instruments such as catheters. A complete understanding of biofilm formation therefore requires knowledge of the regulatory pathways underpinning its formation so that effective intervention strategies can be determined. The master regulator that determines whether the gram-positive model organism Bacillus subtilis switches from a free-living, planktonic lifestyle to form a biofilm is called SinR. The activity of SinR, a transcriptional regulator, is controlled by its antagonists, SinI, SlrA, and SlrR. The interaction of these four proteins forms a switch, which determines whether or not SinR can inhibit biofilm formation by its repression of a number of extracellular matrix-associated operons. To determine the thermodynamic and kinetic parameters governing the protein-protein and protein-DNA interactions at the heart of this epigenetic switch, we have analyzed the protein-protein and protein-DNA interactions by isothermal titration calorimetry and surface plasmon resonance. We also present the crystal structure of SinR in complex with DNA, revealing the molecular basis of base-specific DNA recognition by SinR and suggesting that the most effective means of transcriptional control occurs by the looping of promoter DNA. The structural analysis also enables predictions about how SinR activity is controlled by its interaction with its antagonists.

Fourier magnitude of the field incident on a random scattering medium from spatial speckle intensity correlations

Spatial speckle intensity correlations are used to determine the spatial Fourier magnitude of a field incident on a random scattering medium. The patterned beam is scanned across the scattering medium, and the speckle pattern on the opposite side is imaged at each beam position. A theory based on a Green's function representation is used to reconstruct the spatial Fourier magnitude of the patterned incident field.

Dissection of the network of interactions that links RNA processing with glycolysis in the Bacillus subtilis degradosome

The RNA degradosome is a multiprotein macromolecular complex that is involved in the degradation of messenger RNA in bacteria. The composition of this complex has been found to display a high degree of evolutionary divergence, which may reflect the adaptation of species to different environments. Recently, a degradosome-like complex identified in Bacillus subtilis was found to be distinct from those found in proteobacteria, the degradosomes of which are assembled around the unstructured C-terminus of ribonuclease E, a protein not present in B. subtilis. In this report, we have investigated in vitro the binary interactions between degradosome components and have characterized interactions between glycolytic enzymes, RNA-degrading enzymes, and those that appear to link these two cellular processes. The crystal structures of the glycolytic enzymes phosphofructokinase and enolase are presented and discussed in relation to their roles in the mediation of complex protein assemblies. Taken together, these data provide valuable insights into the structure and dynamics of the RNA degradosome, a fascinating and complex macromolecular assembly that links RNA degradation with central carbon metabolism.

The bacterial stressosome: a modular system that has been adapted to control secondary messenger signaling

The stressosome complex regulates downstream effectors in response to environmental signals. In Bacillus subtilis, it activates the alternative sigma factor σ(B), leading to the upregulation of the general stress regulon. Herein, we characterize a stressosome-regulated biochemical pathway in Moorella thermoacetica. We show that the presumed sensor, MtR, and the scaffold, MtS, form a pseudo-icosahedral structure like that observed in B. subtilis. The N-terminal domain of MtR is structurally homologous to B. subtilis RsbR, despite low sequence identity. The affinity of the switch kinase, MtT, for MtS decreases following MtS phosphorylation and not because of structural reorganization. Dephosphorylation of MtS by the PP2C type phosphatase MtX permits the switch kinase to rebind the stressosome to reset the response. We also show that MtT regulates cyclic di-GMP biosynthesis through inhibition of a GG(D/E)EF-type diguanylate cyclase, demonstrating that secondary messenger levels are regulated by the stressosome.

Unusual, dual endo- and exonuclease activity in the degradosome explained by crystal structure analysis of RNase J1

RNase J is an essential enzyme in Bacillus subtilis with unusual dual endonuclease and 5'-to-3' exonuclease activities that play an important role in the maturation and degradation of mRNA. RNase J is also a component of the recently identified "degradosome" of B. subtilis. We report the crystal structure of RNase J1 from B. subtilis to 3.0 Å resolution, analysis of which reveals it to be in an open conformation suitable for binding substrate RNA. RNase J is a member of the β-CASP family of zinc-dependent metallo-β-lactamases. We have exploited this similarity in constructing a model for an RNase J1:RNA complex. Analysis of this model reveals candidate-stacking interactions with conserved aromatic side chains, providing a molecular basis for the observed enzyme activity. Comparisons of the B. subtilis RNase J structure with related enzymes reveal key differences that provide insights into conformational changes during catalysis and the role of the C-terminal domain.

Functional dissection of a trigger enzyme: mutations of the bacillus subtilis glutamate dehydrogenase RocG that affect differentially its catalytic activity and regulatory properties

Any signal transduction requires communication between a sensory component and an effector. Some enzymes engage in signal perception and transduction, as well as in catalysis, and these proteins are known as "trigger" enzymes. In this report, we detail the trigger properties of RocG, the glutamate dehydrogenase of Bacillus subtilis. RocG not only deaminates the key metabolite glutamate to form alpha-ketoglutarate but also interacts directly with GltC, a LysR-type transcription factor that regulates glutamate biosynthesis from alpha-ketoglutarate, thus linking the two metabolic pathways. We have isolated mutants of RocG that separate the two functions. Several mutations resulted in permanent inactivation of GltC as long as a source of glutamate was present. These RocG proteins have lost their ability to catabolize glutamate due to a strongly reduced affinity for glutamate. The second class of mutants is exemplified by the replacement of aspartate residue 122 by asparagine. This mutant protein has retained enzymatic activity but has lost the ability to control the activity of GltC. Crystal structures of glutamate dehydrogenases that permit a molecular explanation of the properties of the various mutants are presented. Specifically, we may propose that D122N replacement affects the surface of RocG. Our data provide evidence for a correlation between the enzymatic activity of RocG and its ability to inactivate GltC, and thus give insights into the mechanism that couples the enzymatic activity of a trigger enzyme to its regulatory function.

Cloning, purification and preliminary crystallographic analysis of a putative pyridoxal kinase from Bacillus subtilis

Pyridoxal kinases (PdxK) are able to catalyse the phosphorylation of three vitamin B(6) precursors, pyridoxal, pyridoxine and pyridoxamine, to their 5'-phosphates and play an important role in the vitamin B(6) salvage pathway. Recently, the thiD gene of Bacillus subtilis was found to encode an enzyme which has the activity expected of a pyridoxal kinase despite its previous assignment as an HMPP kinase owing to higher sequence similarity. As such, this enzyme would appear to represent a new class of ;HMPP kinase-like' pyridoxal kinases. B. subtilis thiD has been cloned and the protein has been overexpressed in Escherichia coli, purified and subsequently crystallized in a binary complex with ADP and Mg(2+). X-ray diffraction data have been collected from crystals to 2.8 A resolution at 100 K. The crystals belong to a primitive tetragonal system, point group 422, and analysis of the systematic absences suggest that they belong to one of the enantiomorphic pair of space groups P4(1)2(1)2 or P4(3)2(1)2. Consideration of the space-group symmetry and unit-cell parameters (a = b = 102.9, c = 252.6 A, alpha = beta = gamma = 90 degrees ) suggest that the crystals contain between three and six molecules in the asymmetric unit. A full structure determination is under way to provide insights into aspects of the enzyme mechanism and substrate specificity.

The crystal structure of an ADP complex of Bacillus subtilis pyridoxal kinase provides evidence for the parallel emergence of enzyme activity during evolution

Pyridoxal kinase catalyses the phosphorylation of pyridoxal, pyridoxine and pyridoxamine to their 5' phosphates and plays an important role in the pyridoxal 5' phosphate salvage pathway. The crystal structure of a dimeric pyridoxal kinase from Bacillus subtilis has been solved in complex with ADP to 2.8 A resolution. Analysis of the structure suggests that binding of the nucleotide induces the ordering of two loops, which operate independently to close a flap on the active site. Comparisons with other ribokinase superfamily members reveal that B. subtilis pyridoxal kinase is more closely related in both sequence and structure to the family of HMPP kinases than to other pyridoxal kinases, suggesting that this structure represents the first for a novel family of "HMPP kinase-like" pyridoxal kinases. Moreover this further suggests that this enzyme activity has evolved independently on multiple occasions from within the ribokinase superfamily.

Verification of biomechanical methods employed in a comprehensive study of mild traumatic brain injury and the effectiveness of American football helmets

Concussion, or mild traumatic brain injury, occurs in many activities, mostly as a result of the head being accelerated. A comprehensive study has been conducted to understand better the mechanics of the impacts associated with concussion in American football. This study involves a sequence of techniques to analyse and reconstruct many different head impact scenarios. It is important to understand the validity and accuracy of these techniques in order to be able to use the results of the study to improve helmets and helmet standards. Two major categories of potential errors have been investigated. The first category concerns error sources specific to the use of crash test dummy instrumentation (accelerometers) and associated data processing techniques. These are relied upon to establish both linear and angular head acceleration responses. The second category concerns the use of broadcast video data and crash test dummy head-neck-torso systems. These are used to replicate the complex head impact scenarios of whole body collisions that occur on the football field between two living human beings. All acceleration measurement and processing techniques were based on well-established practices and standards. These proved to be reliable and reproducible. Potential errors in the linear accelerations due to electrical or mechanical noise did not exceed 2% for the three different noise sources investigated. Potential errors in the angular accelerations due to noise could be as high as 6.7%, due to error accumulation of multiple linear acceleration measurements. The potential error in the relative impact velocity between colliding heads could be as high as 11%, and was found to be the largest error source in the sequence of techniques to reconstruct the game impacts. Full-scale experiments with complete crash test dummies in staged head impacts showed maximum errors of 17% for resultant linear accelerations and 25% for resultant angular accelerations.

A proposed new biomechanical head injury assessment function - the maximum power index

Recently, several cases of mild traumatic brain injury to American professional football players have been reconstructed using instrumented Hybrid III anthropomorphic test dummies ATDs. The translational and rotational acceleration responses of injured and uninjured players' heads have been documented. The acceleration data have been processed according to all current head injury assessment functions including the GSI, HIC and GAMBIT among others. A new hypothesis is propounded that the threshold for head injury will be exceeded if the rate of change of kinetic energy of the head exceeds some limiting value. A functional relation is proposed, which includes all six degrees of motion and directional sensitivity characteristics, relating the rate of change of kinetic energy to the probability of head injury. The maximum value that the function achieves during impact is the maximum power input to the head and serves as an index by which the probability of head injury can be assessed.

Measuring the Cosmic Equation of State with Counts of Galaxies

The classical dN/dz test allows one to determine fundamental cosmological parameters from the evolution of the cosmic volume element. This test is applied by measuring the redshift distribution of a tracer whose evolution in number density is known. In the past, ordinary galaxies have been used for this; however, in the absence of a complete theory of galaxy formation, that method is fraught with difficulties. In this Letter, we propose studying instead the evolution of the apparent numbers of dark matter halos as a function of their circular velocity, observable via the line widths or rotation speeds of visible galaxies. Upcoming redshift surveys will allow the line width distribution of galaxies to be determined at both z approximately 1 and the present day. In the course of studying this test, we have devised a rapid, improved semianalytic method for calculating the circular velocity distribution of dark halos based on the analytic mass function of Sheth, Mo, & Tormen and the formation time distribution of Lacey & Cole. We find that if selection effects are well controlled and minimal external constraints are applied, the planned DEEP Redshift Survey could allow us to measure the cosmic equation-of-state parameter w to +/-10% (as little as 3% if Omegam has been well determined from other observations). This type of test also has the potential to provide a constraint on any evolution of w, such as that predicted by "tracker" models.

A distance to the galaxy NGC4258 from observations of Cepheid variable stars

Cepheid variable stars pulsate in a way that is correlated with their intrinsic luminosity, making them useful as 'standard candles' for determining distances to galaxies; the potential systematic uncertainties in the resulting distances have been estimated to be only 8-10%. They have played a crucial role in establishing the extragalactic distance scale and hence the value of the Hubble constant. Here we report observations of Cepheids in the nearby galaxy NGC4258; the distance calculated from the Cepheids is 8.1 +/- 0.4 Mpc, where the uncertainty does not include possible systematic errors. There is an independently determined geometric distance to this galaxy of 7.2 +/- 0.5 Mpc, based on the observed proper motions of water masers orbiting the central black hole; the distances differ by 1.3sigma. If the maser-based distance is adopted and the Cepheid distance scale revised accordingly, the derived value of the Hubble constant would increase by 12 +/- 9%, while the expansion age of the Universe would decrease by the same amount.

Identification of Mycoplasma iowae by colony immunoblotting utilizing monoclonal antibodies

The utility of monoclonal antibody Mab-2C in identification of Mycoplasma iowae (MI) by colony immunoblotting technique was explored. Colony immunoblots of reference MI strains, field isolates, and mycoplasmas recovered from experimentally inoculated turkey embryos were probed with Mab-2C. The monoclonal antibody identified colonies of all the MI isolates tested and did not cross-react with colonies of M. gallisepticum, M. synoviae, or M. meleagridis. In western immunoblots of 22 MI field isolates, Mab-2C showed immunoreactivity with an antigen of approximately 45 kD molecular weight. No phenotypic variation of the epitope recognized by Mab-2C was observed in colony immunoblots of MI colonies. The monoclonal antibody reported here can be used for identification of MI colonies by a simple and rapid colony immunoblot method.

Monoclonal antibodies specific to Mycoplasma iowae

Monoclonal antibodies (MAbs) against Mycoplasma iowae (MI) were produced to identify common immunogenic determinants shared between antigenically heterogenous MI. Twenty-four MAbs were produced against MI. With western immunoblotting, all 24 MAbs recognized a 45,000-MW protein (p45) of MI strain I-695. One of the MAbs characterized, MAb 2C, identified p45 antigen in western immunoblots with six laboratory strains and 24 field isolates of MI. MAb 2C did not cross-react with Mycoplasma gallisepticum, Mycoplasma synoviae, Mycoplasma meleagridis, or nonpathogenic avian mycoplasmas. Triton X-114 phase separation of MI proteins showed that p45 is an integral membrane protein. In immunofluorescent staining and immunoelectron microscopy of MI, MAb 2C reacted with surface antigen(s). These MAbs specific to MI may be used in detection and diagnosis of MI infections.

Least-squares estimation of diet composition from n-alkanes in herbage and faeces using matrix mathematics

It is possible to estimate diet composition from an analysis of n-alkanes in the faeces of ruminant animals. For instance, to estimate the proportion of two species in a diet, two equations are constructed using the known concentrations of two different n-alkanes in the herbage and in the animal's faeces. These two equations are solved for the two unknown quantities of the diet components. Two problems exist with this method. First, it is often the case that we have estimated concentrations of more than two different n-alkanes. This can lead to a problem in deciding which two n-alkanes to use to construct the simultaneous equations. The choice of this pair of n-alkanes is arbitrary in its selection and wasteful of other useful information. The second problem is that sometimes the solution to the simultaneous equations yields nonsensical answers, such as a negative proportion of one species in the diet. In addition to making it difficult to estimate dietary proportions, estimating digestibility becomes impossible. In this paper, we present a technique which provides an estimate of the dietary proportions. This estimate uses information on all the n-alkanes available, and it has a very desirable property of being a least squares estimate. We also present a method for determining the least squares estimate subject to the constraint that all proportions must be non-negative. We provide examples for estimating the proportions of grass and clover in the diet of sheep and the digestibility of those diets.

Toward a comprehensive biomechanical injury cost model

The proposed biomechanical injury cost model utilizes surrogate-based injury assessment functions to predict the probability of occurrence and the probable cost of specific injuries to the head, thorax, abdomen, and lower extremities. The resulting probability cost is a function of the number, location, and severity of injuries. As more precise injury assessment functions and more accurate cost estimates become available, the model will become an effective tool for comparing and classifying different injury patterns.

Effect of temperature on the stability of avian influenza virus antigens under different storage conditions

The combined effect of time and temperature on the stability of two avian influenza virus (AIV) isolates concentrated with polyethylene glycol (PEG), stored at different temperatures, and used in the preparation of avian influenza vaccine was evaluated in turkeys at 24 hr and at 12, 24, 30, 36, and 42 months of storage. The differences detected between antibodies raised in turkeys by vaccines made from isolates under different storage conditions, times, and temperatures were not significant (P > 0.05), especially with vaccines prepared from one isolate. Virus recovery rates following challenge studies of vaccinated birds were similar. However, birds that were vaccinated twice had lower rates of virus recovery from the trachea, lungs, pancreas, and fecal samples following challenge infection. The results suggest that if stable isolates of AIV can be identified, such isolates can be rapidly concentrated with PEG and stored at -20 C or -196 C for at least 42 months without any loss of potency in the vaccine prepared from these isolates. This would reduce the costs associated with vaccine storage and subsequent expiration dates.

Description of osteomyelitis lesions associated with Actinomyces pyogenes infection in the proximal tibia of adult male turkeys

Actinomyces pyogenes was isolated from osteomyelitis lesions from the proximal tibia of mature tom turkeys. Gram-stained impression smears of the lesions resulted in bacteria that appeared as club-shaped, gram-positive pleomorphic rods. The bacteria grew better in a reduced-oxygen environment. The lesions were well demarcated and cavernous, ranging from purulent to caseous in consistency.

Virulence factors of Escherichia coli associated with colisepticemia in chickens and turkeys

Four hundred twenty turkey and 80 chicken Escherichia coli isolates from colisepticemic birds were examined for the following properties: heat-labile toxin (LT), heat-stable enterotoxin, verotoxin, colicinogenicity, hemolysin, and hydroxamate/aerobactin production. Twenty-four (5.7%) of the 420 turkey isolates and six (7.5%) of the 80 chicken isolates produced an LT that was cytotoxic for both Vero and Y-1 cells. In contrast, 48 (11.4%) of the turkey isolates and 18 (22.5%) of the chicken isolates produced a distinct LT that was cytotoxic only for Vero cells. In addition, 64 (80.0%) of the chicken isolates and 309 (74.0%) of the turkey isolates produced aerobactin. Colicinogenicity occurred in 51 (64.0%) of the chicken isolates, with 41 (51.0%) producing colicin V. By contrast, 254 (61.0%) of the turkey isolates produced a colicin, of which 176 (42.0%) produced colicin V. None of the chicken and turkey isolates produced hemolysin or heat-stable enterotoxin.

Enhancement of antibody response of turkeys to trivalent avian influenza vaccine by positively charged liposomal avridine adjuvant

Trivalent avian influenza (AIV) antigens (H4N8, H5N2 and H7N3), mixed with positively charged, negatively charged and neutral avridine-containing liposomes, and oil-emulsion were subcutaneously administered to 6-week-old turkeys. Charged liposomal avridine adjuvant, either positive or negative, produced a better antibody response than uncharged liposomal avridine or oil-emulsion adjuvants when used in a trivalent avian influenza vaccine. The antibody response to the different antigens was generally greater to the positively charged adjuvanted vaccine compared with the negatively or neutral charged or oil-emulsion adjuvanted vaccines and these differences were significant (P less than 0.05) with the three antigens. The results suggest that the positively charged liposomal avridine plays a significant role as adjuvant to the AIV antigens.

A quantitative measurement of the effect of avian influenza virus on the ability of turkeys to eliminate Pasteurella multocida from the respiratory tract

The effect of avian influenza virus (AIV) infection on the ability of turkeys to eliminate Pasteurella multocida from the respiratory tract was evaluated. Four-week-old turkeys were experimentally infected with an apathogenic AIV subtype (H5N2) by the oculonasal route and subsequently superinfected with P multocida (Urbach strain) by the intranasal route three days after infection with AIV. Quantitative clearance of P multocida from the trachea and lung was determined using a pour plate technique on samples collected at intervals after infection. Samples from turkeys which had been infected with AIV were found to yield more P multocida than those from turkeys which had not been infected with AIV. The numbers of P multocida increased in infected birds to a greater extent than in birds which had not been infected with the virus. The present study suggests that AIV infection may contribute to the increased numbers and a decreased clearance of P multocida in turkeys.