A metabolic perspective on CSF-mediated neurodegeneration in multiple sclerosis

Multiple sclerosis is an autoimmune demyelinating disorder of the CNS, characterized by inflammatory lesions and an underlying neurodegenerative process, which is more prominent in patients with progressive disease course. It has been proposed that mitochondrial dysfunction underlies neuronal damage, the precise mechanism by which this occurs remains uncertain. To investigate potential mechanisms of neurodegeneration, we conducted a functional screening of mitochondria in neurons exposed to the CSF of multiple sclerosis patients with a relapsing remitting (n = 15) or a progressive (secondary, n = 15 or primary, n = 14) disease course. Live-imaging of CSF-treated neurons, using a fluorescent mitochondrial tracer, identified mitochondrial elongation as a unique effect induced by the CSF from progressive patients. These morphological changes were associated with decreased activity of mitochondrial complexes I, III and IV and correlated with axonal damage. The effect of CSF treatment on the morphology of mitochondria was characterized by phosphorylation of serine 637 on the dynamin-related protein DRP1, a post-translational modification responsible for unopposed mitochondrial fusion in response to low glucose conditions. The effect of neuronal treatment with CSF from progressive patients was heat stable, thereby prompting us to conduct an unbiased exploratory lipidomic study that identified specific ceramide species as differentially abundant in the CSF of progressive patients compared to relapsing remitting multiple sclerosis. Treatment of neurons with medium supplemented with ceramides, induced a time-dependent increase of the transcripts levels of specific glucose and lactate transporters, which functionally resulted in progressively increased glucose uptake from the medium. Thus ceramide levels in the CSF of patients with progressive multiple sclerosis not only impaired mitochondrial respiration but also decreased the bioavailability of glucose by increasing its uptake. Importantly the neurotoxic effect of CSF treatment could be rescued by exogenous supplementation with glucose or lactate, presumably to compensate the inefficient fuel utilization. Together these data suggest a condition of 'virtual hypoglycosis' induced by the CSF of progressive patients in cultured neurons and suggest a critical temporal window of intervention for the rescue of the metabolic impairment of neuronal bioenergetics underlying neurodegeneration in multiple sclerosis patients.

Ligand modulation of sidechain dynamics in a wild-type human GPCR

GPCRs regulate all aspects of human physiology, and biophysical studies have deepened our understanding of GPCR conformational regulation by different ligands. Yet there is no experimental evidence for how sidechain dynamics control allosteric transitions between GPCR conformations. To address this deficit, we generated samples of a wild-type GPCR (A_2AR) that are deuterated apart from ¹H/¹³C NMR probes at isoleucine δ1 methyl groups, which facilitated ¹H/¹³C methyl TROSY NMR measurements with opposing ligands. Our data indicate that low [Na⁺] is required to allow large agonist-induced structural changes in A_2AR, and that patterns of sidechain dynamics substantially differ between agonist (NECA) and inverse agonist (ZM241385) bound receptors, with the inverse agonist suppressing fast ps-ns timescale motions at the G protein binding site. Our approach to GPCR NMR creates a framework for exploring how different regions of a receptor respond to different ligands or signaling proteins through modulation of fast ps-ns sidechain dynamics.

Computational design of a protein-based enzyme inhibitor

While there has been considerable progress in designing protein-protein interactions, the design of proteins that bind polar surfaces is an unmet challenge. We describe the computational design of a protein that binds the acidic active site of hen egg lysozyme and inhibits the enzyme. The design process starts with two polar amino acids that fit deep into the enzyme active site, identifies a protein scaffold that supports these residues and is complementary in shape to the lysozyme active-site region, and finally optimizes the surrounding contact surface for high-affinity binding. Following affinity maturation, a protein designed using this method bound lysozyme with low nanomolar affinity, and a combination of NMR studies, crystallography, and knockout mutagenesis confirmed the designed binding surface and orientation. Saturation mutagenesis with selection and deep sequencing demonstrated that specific designed interactions extending well beyond the centrally grafted polar residues are critical for high-affinity binding.

Preparation of protein samples for NMR structure, function, and small-molecule screening studies

In this chapter, we concentrate on the production of high-quality protein samples for nuclear magnetic resonance (NMR) studies. In particular, we provide an in-depth description of recent advances in the production of NMR samples and their synergistic use with recent advancements in NMR hardware. We describe the protein production platform of the Northeast Structural Genomics Consortium and outline our high-throughput strategies for producing high-quality protein samples for NMR studies. Our strategy is based on the cloning, expression, and purification of 6×-His-tagged proteins using T7-based Escherichia coli systems and isotope enrichment in minimal media. We describe 96-well ligation-independent cloning and analytical expression systems, parallel preparative scale fermentation, and high-throughput purification protocols. The 6×-His affinity tag allows for a similar two-step purification procedure implemented in a parallel high-throughput fashion that routinely results in purity levels sufficient for NMR studies (>97% homogeneity). Using this platform, the protein open reading frames of over 17,500 different targeted proteins (or domains) have been cloned as over 28,000 constructs. Nearly 5000 of these proteins have been purified to homogeneity in tens of milligram quantities (see Summary Statistics, http://nesg.org/statistics.html), resulting in more than 950 new protein structures, including more than 400 NMR structures, deposited in the Protein Data Bank. The Northeast Structural Genomics Consortium pipeline has been effective in producing protein samples of both prokaryotic and eukaryotic origin. Although this chapter describes our entire pipeline for producing isotope-enriched protein samples, it focuses on the major updates introduced during the last 5 years (Phase 2 of the National Institute of General Medical Sciences Protein Structure Initiative). Our advanced automated and/or parallel cloning, expression, purification, and biophysical screening technologies are suitable for implementation in a large individual laboratory or by a small group of collaborating investigators for structural biology, functional proteomics, ligand screening, and structural genomics research.

The high-throughput protein sample production platform of the Northeast Structural Genomics Consortium

We describe the core Protein Production Platform of the Northeast Structural Genomics Consortium (NESG) and outline the strategies used for producing high-quality protein samples. The platform is centered on the cloning, expression and purification of 6X-His-tagged proteins using T7-based Escherichia coli systems. The 6X-His tag allows for similar purification procedures for most targets and implementation of high-throughput (HTP) parallel methods. In most cases, the 6X-His-tagged proteins are sufficiently purified (>97% homogeneity) using a HTP two-step purification protocol for most structural studies. Using this platform, the open reading frames of over 16,000 different targeted proteins (or domains) have been cloned as>26,000 constructs. Over the past 10 years, more than 16,000 of these expressed protein, and more than 4400 proteins (or domains) have been purified to homogeneity in tens of milligram quantities (see Summary Statistics, http://nesg.org/statistics.html). Using these samples, the NESG has deposited more than 900 new protein structures to the Protein Data Bank (PDB). The methods described here are effective in producing eukaryotic and prokaryotic protein samples in E. coli. This paper summarizes some of the updates made to the protein production pipeline in the last 5 years, corresponding to phase 2 of the NIGMS Protein Structure Initiative (PSI-2) project. The NESG Protein Production Platform is suitable for implementation in a large individual laboratory or by a small group of collaborating investigators. These advanced automated and/or parallel cloning, expression, purification, and biophysical screening technologies are of broad value to the structural biology, functional proteomics, and structural genomics communities.

NMR structure determination for larger proteins using backbone-only data

Conventional protein structure determination from nuclear magnetic resonance data relies heavily on side-chain proton-to-proton distances. The necessary side-chain resonance assignment, however, is labor intensive and prone to error. Here we show that structures can be accurately determined without nuclear magnetic resonance (NMR) information on the side chains for proteins up to 25 kilodaltons by incorporating backbone chemical shifts, residual dipolar couplings, and amide proton distances into the Rosetta protein structure modeling methodology. These data, which are too sparse for conventional methods, serve only to guide conformational search toward the lowest-energy conformations in the folding landscape; the details of the computed models are determined by the physical chemistry implicit in the Rosetta all-atom energy function. The new method is not hindered by the deuteration required to suppress nuclear relaxation processes for proteins greater than 15 kilodaltons and should enable routine NMR structure determination for larger proteins.

The occurrence and antimicrobial susceptibility of salmonellae isolated from commercially available canine raw food diets in three Canadian cities

The purpose of the present study was to evaluate the prevalence and antimicrobial resistance patterns of Salmonella isolated from commercially available canine raw food diets in Canada. A total of 166 commercial frozen raw food diet samples were purchased from randomly selected local pet stores in three Canadian cities for a period of 8 months. All samples were evaluated for the presence of Salmonella, serotyped and tested for antimicrobial susceptibility. There was an overall Salmonella prevalence of 21%; chicken was an ingredient for 67% of the Salmonella-positive diets. Eighteen different Salmonella serotypes were recovered, and resistance was observed to 12 of the 16 antimicrobials tested, with the majority of Ontario isolates exhibiting resistance to ampicillin and Calgary isolates to tetracycline. This study demonstrates the potential risk of raw food diets, especially for immunocompromised individuals, and stresses the need for implementing regulatory guidelines for the production of these diets in order to help control and ideally eliminate the bacterial risks associated with their use and consumption.

The occurrence and anti-microbial susceptibility of Salmonellae isolated from commercially available pig ear pet treats

In Canada, there have been reported outbreaks of human salmonellosis related to exposure to animal-derived pet treats, involving pig ear treats, beef steak patty dog treats and pet treats of seafood origin. As a follow-up to recommendations made to the pig ear treat industry in 1999, a total of 245 pig ear treats were purchased in two Canadian cities to provide evidence of adoption of the recommendations and to determine the current levels of Salmonella contamination of pig ear treats available at pet stores. An overall prevalence of 4% was observed, with isolates exhibiting resistance to up to seven anti-microbials. Serotypes recovered included S. Bovismorbificans, S. Give, S. Derby and S. Typhimurium var. Copenhagen. Although the prevalence observed during this study is lower than the prevalence observed in 1999, pig ear treats should still be considered as a possible source of Salmonella and anti-microbial resistant bacteria to humans and dogs in Canada.

Frozen chicken nuggets and strips and eggs are leading risk factors for Salmonella Heidelberg infections in Canada

A case-control study was conducted from 1 January to 31 May 2003 to identify risk factors for S . Heidelberg infection in Canada. Controls were pair-matched by age group and telephone exchange to 95 cases. Exposures in the 7 days before illness/interview were assessed using multivariate conditional logistic regression. Consumption of home-prepared chicken nuggets and/or strips [matched odds ratio (mOR) 4.0, 95% confidence interval (CI) 1.4-13.8], and undercooked eggs (mOR 7.5, 95% CI 1.5-75.5) increased the risk of illness. Exposure to a farm setting lowered the risk (mOR 0.22, 95% CI 0.03-1.00). The population-attributable fraction associated with chicken nuggets/strips was 34% and with undercooked eggs was 16%. One-third of study participants did not perceive, handle or prepare chicken nuggets and strips as high-risk products, although the majority of the products on the Canadian market are raw. These findings have prompted changes in product-labelling policy and consumer education.

Robotic cloning and Protein Production Platform of the Northeast Structural Genomics Consortium

In this chapter we describe the core Protein Production Platform of the Northeast Structural Genomics Consortium (NESG) and outline the strategies used for producing high-quality protein samples using Escherichia coli host vectors. The platform is centered on 6X-His affinity-tagged protein constructs, allowing for a similar purification procedure for most targets, and the implementation of high-throughput parallel methods. In most cases, these affinity-purified proteins are sufficiently homogeneous that a single subsequent gel filtration chromatography step is adequate to produce protein preparations that are greater than 98% pure. Using this platform, over 1000 different proteins have been cloned, expressed, and purified in tens of milligram quantities over the last 36-month period (see Summary Statistics for All Targets, ). Our experience using a hierarchical multiplex expression and purification strategy, also described in this chapter, has allowed us to achieve success in producing not only protein samples but also many three-dimensional structures. As of December 2004, the NESG Consortium has deposited over 145 new protein structures to the Protein Data Bank (PDB); about two-thirds of these protein samples were produced by the NESG Protein Production Facility described here. The methods described here have proven effective in producing quality samples of both eukaryotic and prokaryotic proteins. These improved robotic and?or parallel cloning, expression, protein production, and biophysical screening technologies will be of broad value to the structural biology, functional proteomics, and structural genomics communities.

An international outbreak of salmonellosis associated with raw almonds contaminated with a rare phage type of Salmonella enteritidis

During the winter of 2000 to 2001, an outbreak due to Salmonella Enteritidis (SE) phage type 30 (PT30), a rare strain, was detected in Canada. The ensuing investigation involved Canadian and American public health and food regulatory agencies and an academic research laboratory. Enhanced laboratory surveillance, including phage typing and pulsed-field gel electrophoresis, was used to identify cases. Case questionnaires were administered to collect information about food and environmental exposures. A case-control study with 16 matched case-control pairs was conducted to test the hypothesis of an association between raw whole almond consumption and infection. Almond samples were collected from case homes, retail outlets, and the implicated processor, and environmental samples were collected from processing equipment and associated farms for microbiological testing. One hundred sixty-eight laboratory-confirmed cases of SE PT30 infection (157 in Canada, 11 in the United States) were identified between October 2000 and July 2001. The case-control study identified raw whole almonds as the source of infection (odds ration, 21.1; 95% confidence interval, 3.6 to infinity). SE PT30 was detected in raw whole natural almonds collected from home, retail, distribution, and warehouse sources and from environmental swabs of processing equipment and associated farmers' orchards. The frequent and prolonged recovery of this specific organism from a large agricultural area was an unexpected finding and may indicate significant diffuse contamination on these farms. Identification of almonds as the source of a foodborne outbreak is a previously undocumented finding, leading to a North American recall of this product and a review of current industry practices.

Comparison of techniques for measurement of rumen pH in lactating dairy cows

Subacute rumen acidosis is thought to be a common condition in early lactating dairy cattle; however, diagnosis is difficult. There are currently only two techniques available for measuring rumen pH under field conditions: rumenocentesis and oral stomach tube. Sixteen rumen-fistulated cows were sampled in four sites of the rumen (cranial-ventral, caudal-ventral, central, and cranial-dorsal) with a rumen cannula. Rumen pH results were compared to those obtained at the same time with rumenocentesis and with an oro-ruminal (Geishauser) probe. Rumen fluid was obtained between 6 and 12 wk of lactation. Samples were analyzed for pH, lactate, bicarbonate, sodium, potassium, and chloride. Rumen pH results were also compared to those obtained from 24-h continuous rumen pH measurement using indwelling rumen pH probes. Oro-ruminal probe samples had the highest pH values and the highest bicarbonate concentrations. Rumenocentesis samples had the lowest pH values and the lowest bicarbonate concentrations. Small differences in electrolyte concentrations were noted among rumen fluid collection techniques in the different rumen sites. The highest correlations of rumen pH were obtained between rumenocentesis and rumen cannulation (cranial-ventral), and between rumen cannulation (cranial-ventral) and the 24-h indwelling pH meter. Compared with samples obtained from the cranial-ventral rumen, rumenocentesis was more sensitive than the oro-ruminal probe in the measurement of low rumen pH; both techniques were moderately specific. The most accurate field technique was rumenocentesis. Improved field techniques are required for better on-farm diagnosis of subacute rumen acidosis.

Automated protein fold determination using a minimal NMR constraint strategy

Determination of precise and accurate protein structures by NMR generally requires weeks or even months to acquire and interpret all the necessary NMR data. However, even medium-accuracy fold information can often provide key clues about protein evolution and biochemical function(s). In this article we describe a largely automatic strategy for rapid determination of medium-accuracy protein backbone structures. Our strategy derives from ideas originally introduced by other groups for determining medium-accuracy NMR structures of large proteins using deuterated, (13)C-, (15)N-enriched protein samples with selective protonation of side-chain methyl groups ((13)CH(3)). Data collection includes acquiring NMR spectra for automatically determining assignments of backbone and side-chain (15)N, H(N) resonances, and side-chain (13)CH(3) methyl resonances. These assignments are determined automatically by the program AutoAssign using backbone triple resonance NMR data, together with Spin System Type Assignment Constraints (STACs) derived from side-chain triple-resonance experiments. The program AutoStructure then derives conformational constraints using these chemical shifts, amide (1)H/(2)H exchange, nuclear Overhauser effect spectroscopy (NOESY), and residual dipolar coupling data. The total time required for collecting such NMR data can potentially be as short as a few days. Here we demonstrate an integrated set of NMR software which can process these NMR spectra, carry out resonance assignments, interpret NOESY data, and generate medium-accuracy structures within a few days. The feasibility of this combined data collection and analysis strategy starting from raw NMR time domain data was illustrated by automatic analysis of a medium accuracy structure of the Z domain of Staphylococcal protein A.

Drinking water quality and health-care utilization for gastrointestinal illness in greater Vancouver

The risk of microbial disease associated with drinking water is presently a priority concern among North American water jurisdictions. Numerous past outbreaks, together with recent studies suggesting that drinking water may be a substantial contributor to endemic (non-outbreak related) gastroenteritis, demonstrate the vulnerability of many North American cities to waterborne diseases and have fuelled ongoing debates in Canada and the United States concerning the need for stricter water quality guidelines, changes in watershed management policies, and the need for additional water treatment. The Greater Vancouver Regional District (GVRD) water supply system serves approximately two million consumers from a system consisting of three unfiltered surface water supplies (Figure 1). Although GVRD policies reduce the potential for fecal contamination of the source water supplies by humans and domestic animals, the GVRD watersheds support many wildlife species that can potentially shed organisms pathogenic to humans. Because GVRD's water treatment strategy relies principally on watershed protection and chlorination*, and these two strategies together do not eliminate all risk of waterborne disease transmission, it is possible that some disease-causing organisms reach the consumer.

The X-ray crystal structure of bis(pentafluorophenyl)tellurium difluoride

Bis(pentafluorophenyl)tellurium difluoride crystallizes, in the space group Cc, as a molecular solid in which pairs of crystallographically independent molecules are linked by two weak secondary [Formula: see text] interactions. (C12F12Te; a = 11.088(6), b = 20.040(10), c = 13.208(5); β = 109.07(4); U = 2774; Z = 8; fw = 499.7). The structural model was refined by full-matrix least-squares methods to a final residual of R1 = 0.035 for 1621 observed reflections. The stereochemistry of the primary bonding about Te is ψ-trigonal bipyramidal as for other R2TeX2 species and is compared with that of diphenyltellurium difluoride. Differences in the stereochemistry of the primary bonding about tellurium can be attributed to the influence of the more electron-withdrawing C6F5 group, and relates to the different secondary bonding and the crystal packing. 125Te nmr coupling constants, [Formula: see text], are reported for this and two related compounds. Previous 125Te Mössbauer data is discussed in the light of the structure.