Overcoming barriers to membrane protein structure determination

After decades of slow progress, the pace of research on membrane protein structures is beginning to quicken thanks to various improvements in technology, including protein engineering and microfocus X-ray diffraction. Here we review these developments and, where possible, highlight generic new approaches to solving membrane protein structures based on recent technological advances. Rational approaches to overcoming the bottlenecks in the field are urgently required as membrane proteins, which typically comprise ~30% of the proteomes of organisms, are dramatically under-represented in the structural database of the Protein Data Bank.     

Assessment of a continuous blood gas monitoring system in animals during circulatory stress

Background

The study was aimed to determine the measurement accuracy of The CDI? blood parameter monitoring system 500 (Terumo Cardiovascular Systems Corporation, Ann Arbor MI) in the real-time continuous measurement of arterial blood gases under different cardiocirculatory stress conditions

Methods

Inotropic stimulation (Dobutamine 2.5 and 5 μg/kg/min), vasoconstriction (Arginine-vasopressin 4, 8 and 16 IU/h), hemorrhage (-10%, -20%, -35%, and -50% of the theoretical volemia), and volume resuscitation were induced in ten swine (57.4 ± 10.7 Kg).Intermittent blood gas assessments were carried out using a routine gas analyzer at any experimental phase and compared with values obtained at the same time settings during continuous monitoring with CDI? 500 system. The Bland-Altman analysis was employed.

Results

Bias and precision for pO₂ were - 0.06 kPa and 0.22 kPa, respectively (r² = 0.96); pCO₂ - 0.02 kPa and 0.15 kPa, respectively; pH -0.001 and 0.01 units, respectively (r² = 0.96). The analysis showed very good agreement for SO₂ (bias 0.04,precision 0.33, r² = 0.95), Base excess (bias 0.04,precision 0.28, r² = 0.98), HCO₃ (bias 0.05,precision 0.62, r² = 0.92),hemoglobin (bias 0.02,precision 0.23, r² = 0.96) and K⁺ (bias 0.02, precision 0.27, r² = 0.93). The sensor was reliable throughout the experiment during hemodynamic variations.

Conclusions

Continuous blood gas analysis with the CDI? 500 system was reliable and it might represent a new useful tool to accurately and timely monitor gas exchange in critically ill patients. Nonetheless, our findings need to be confirmed by larger studies to prove its reliability in the clinical setting.     

Planning for Implementation: Landscape‐Level Restoration Planning in an Agricultural Setting

The conservation of biodiversity in highly fragmented landscapes often requires large‐scale habitat restoration in addition to traditional biological conservation techniques. The selection of priority restoration sites to support long‐term persistence of biodiversity within landscape‐scale projects however remains a challenge for many restoration practitioners. Techniques developed under the paradigm of systematic conservation planning may provide a template for resolving these challenges. Systematic conservation planning requires the identification of conservation objectives, the establishment of quantitative targets for each objective, and the identification of areas which, if conserved, would contribute to meeting those targets. A metric developed by systematic conservation planners termed “irreplaceability” allows for analysis and prioritization of such conservation options, and allows for the display of analysis results in a way that can engage private landowners and other decision makers. The process of systematic conservation planning was modified to address landscape‐level restoration prioritization in southern Ontario. A series of recent and locally relevant landscape ecology studies allowed the identification of restoration objectives and quantitative targets, and a simple algorithm was developed to identify and prioritize potential restoration projects. The application of an irreplaceability analysis to landscape‐level restoration planning allowed the identification of varying needs throughout the planning region, resulting from underlying differences in topography and settlement patterns, and allowed the effective prioritization of potential restoration projects. Engagement with rural landowners and agricultural commodity groups, as well as the irreplaceability maps developed, ultimately resulted in a substantial increase in the number and total area of habitat restoration projects in the planning region.     

Barium promotes anchorage-independent growth and invasion of human HaCaT keratinocytes via activation of c-SRC kinase

Explosive increases in skin cancers have been reported in more than 36 million patients with arsenicosis caused by drinking arsenic-polluted well water. This study and previous studies showed high levels of barium as well as arsenic in the well water. However, there have been no reports showing a correlation between barium and cancer. In this study, we examined whether barium (BaCl(2)) may independently have cancer-related effects on human precancerous keratinocytes (HaCaT). Barium (5-50 μM) biologically promoted anchorage-independent growth and invasion of HaCaT cells in vitro. Barium (5 μM) biochemically enhanced activities of c-SRC, FAK, ERK and MT1-MMP molecules, which regulate anchorage-independent growth and/or invasion. A SRC kinase specific inhibitor, protein phosphatase 2 (PP2), blocked barium-mediated promotion of anchorage-independent growth and invasion with decreased c-SRC kinase activity. Barium (2.5-5 μM) also promoted anchorage-independent growth and invasion of fibroblasts (NIH3T3) and immortalized nontumorigenic melanocytes (melan-a), but not transformed cutaneous squamous cell carcinoma (HSC5 and A431) and malignant melanoma (Mel-ret) cells, with activation of c-SRC kinase. Taken together, our biological and biochemical findings newly suggest that the levels of barium shown in drinking well water independently has the cancer-promoting effects on precancerous keratinocytes, fibroblast and melanocytes in vitro.     

Optimization of microCT imaging and blood vessel diameter quantitation of preclinical specimen vasculature with radiopaque polymer injection medium

Vascular networks within a living organism are complex, multi-dimensional, and challenging to image capture. Radio-angiographic studies in live animals require a high level of infrastructure and technical investment in order to administer costly perfusion mediums whose signals metabolize and degrade relatively rapidly, diminishing within a few hours or days. Additionally, live animal specimens must not be subject to long duration scans, which can cause high levels of radiation exposure to the specimen, limiting the quality of images that can be captured. Lastly, despite technological advances in live-animal specimen imaging, it is quite difficult to minimize or prevent movement of a live animal, which can cause motion artifacts in the final data output. It is demonstrated here that through the use of postmortem perfusion protocols of radiopaque silicone polymer mediums and ex-vivo organ harvest, it is possible to acquire a high level of vascular signal in preclinical specimens through the use of micro-computed tomographic (microCT) imaging. Additionally, utilizing high-order rendering algorithms, it is possible to further derive vessel morphometrics for qualitative and quantitative analysis.     

Ab initio identification of novel regulatory elements in the genome of Trypanosoma brucei by Bayesian inference on sequence segmentation

Background

The rapid increase in the availability of genome information has created considerable demand for both comparative and ab initio predictive bioinformatic analyses. The biology laid bare in the genomes of many organisms is often novel, presenting new challenges for bioinformatic interrogation. A paradigm for this is the collected genomes of the kinetoplastid parasites, a group which includes Trypanosoma brucei the causative agent of human African trypanosomiasis. These genomes, though outwardly simple in organisation and gene content, have historically challenged many theories for gene expression regulation in eukaryotes.

Methodology/Principle Findings

Here we utilise a Bayesian approach to identify local changes in nucleotide composition in the genome of T. brucei. We show that there are several elements which are found at the starts and ends of multicopy gene arrays and that there are compositional elements that are common to all intergenic regions. We also show that there is a composition-inversion element that occurs at the position of the trans-splice site.

Conclusions/Significance

The nature of the elements discovered reinforces the hypothesis that context dependant RNA secondary structure has an important influence on gene expression regulation in Trypanosoma brucei.     

Elderberry flavonoids bind to and prevent H1N1 infection in vitro

A ionization technique in mass spectrometry called Direct Analysis in Real Time Mass Spectrometry (DART TOF-MS) coupled with a Direct Binding Assay was used to identify and characterize anti-viral components of an elderberry fruit (Sambucus nigra L.) extract without either derivatization or separation by standard chromatographic techniques. The elderberry extract inhibited Human Influenza A (H1N1) infection in vitro with an IC₅₀ value of 252 ± 34 μg/mL. The Direct Binding Assay established that flavonoids from the elderberry extract bind to H1N1 virions and, when bound, block the ability of the viruses to infect host cells. Two compounds were identified, 5,7,3′,4′-tetra-O-methylquercetin (1) and 5,7-dihydroxy-4-oxo-2-(3,4,5-trihydroxyphenyl)chroman-3-yl-3,4,5-trihydroxycyclohexanecarboxylate (2), as H1N1-bound chemical species. Compound 1 and dihydromyricetin (3), the corresponding 3-hydroxyflavonone of 2, were synthesized and shown to inhibit H1N1 infection in vitro by binding to H1N1 virions, blocking host cell entry and/or recognition. Compound 1 gave an IC₅₀ of 0.13 μg/mL (0.36 μM) for H1N1 infection inhibition, while dihydromyricetin (3) achieved an IC₅₀ of 2.8 μg/mL (8.7 μM). The H1N1 inhibition activities of the elderberry flavonoids compare favorably to the known anti-influenza activities of Oseltamivir (Tamiflu^®; 0.32 μM) and Amantadine (27 μM).     

Optimization of a Rapid Viability Assay for Mycobacterium avium subsp. paratuberculosis by Using alamarBlue

A microtiter alamarBlue assay was adapted and optimized for Mycobacterium avium subsp. paratuberculosis. Using cell concentrations ranging from 10⁴ to 10⁸ CFU/ml, a minimum incubation time to indicate viability was obtained after 24 h. Rifampin (rifampicin) was used to demonstrate that this method has applications for high-throughput screening against M. avium subsp. paratuberculosis.Mycobacterium avium subsp. paratuberculosis is a chronic enteric pathogen which is widely distributed throughout the food chain (4, 16). Its association with Johne''s disease in cattle is economically significant, with the United States alone suffering losses of $1.5 billion a year (6). Furthermore, its potential to cause human disease is disconcerting and controversial (7, 10, 11, 13). Therefore, the identification and development of novel anti-M. avium subsp. paratuberculosis agents are urgently required. In order to facilitate this, it is important to have available rapid anti-M. avium subsp. paratuberculosis assays permitting high-throughput analysis. A microtiter alamarBlue assay (currently untested for M. avium subsp. paratuberculosis) is a reliable means of determining cellular viability in bacteria (9). This rapid and inexpensive assay lends itself to a high-throughput screening format and has been shown to be applicable to some species of mycobacteria (3, 15). Furthermore, its correlation with other more expensive methods for determining mycobacterium viability is high, between 93 and 100% (1, 5, 15). These include the Mycobacteria Growth Indicator Tube, the Bactec radiometric method, and luciferase reporter systems. This study set out to establish and optimize a microtiter alamarBlue assay for a broad range of M. avium subsp. paratuberculosis titers and to evaluate applications for this assay, including high-throughput screening of novel anti-M. avium subsp. paratuberculosis compounds, and antibiotic resistance profiling of M. avium subsp. paratuberculosis.M. avium subsp. paratuberculosis (CIT03) was isolated from the feces of an infected cow, as described by Ristow et al. (12), and cultivated on Herrold''s egg yolk medium agar supplemented with mycobactin J (2 μl/ml), amphotericin B (50 μg/ml), vancomycin (50 μg/ml), and nalidixic acid (50 μg/ml) for 16 weeks at 37°C. The identity of M. avium subsp. paratuberculosis was confirmed using acid-fast staining, mycobactin dependency, and PCR analysis as previously described (2, 8, 14). To generate sufficient biomass, M. avium subsp. paratuberculosis was subsequently grown in Middlebrook 7H9 broth (MB broth), supplemented with oleic acid, albumin, dextrose, catalase (10%; Becton Dickinson), glycerol (0.2%), and mycobactin J (0.2%). This generally took 16 weeks.Prior to the assay, 10 ml of the 16-week culture was centrifuged at 15,000 rpm for 20 min. The pellet was washed in fresh MB broth and resuspended in 10 ml of fresh supplemented MB broth containing 0.2% mycobactin J. The turbidity was adjusted to match McFarland standard no. 1 (3 × 10⁸ CFU/ml). From this suspension, a series of 1:5 dilutions ranging from 3 × 10⁸ to 9.6 × 10⁴ CFU/ml was set up in MB broth (5-ml volumes), using sterile Falcon tubes. The microtiter plate was organized into rows B, C, D, E, F, and G. Two-hundred-microliter aliquots of 3 × 10⁸ CFU/ml M. avium subsp. paratuberculosis were added to 10 wells in row B. Two-hundred-microliter aliquots of 6 × 10⁷ CFU/ml were added to row C, 1.2 × 10⁷ CFU/ml to row D, 2.4 × 10⁶ CFU/ml to row E, 4.8 × 10⁵ CFU/ml to row F, and 9.6 × 10⁴ CFU/ml to row G. This assay was allowed to progress over a period of 11 days. Twenty microliters (10% of the volume in the well) of a fresh alamarBlue reagent (AbD Serotec) was added, with mixing, to each column on each sampling day. Plates were covered and resealed with Parafilm and incubated at 37°C after the addition of the dye. Absorbance readings at 570 and 600 nm were then taken at 6 h, 24 h, and 48 h for each column. The assay was performed in triplicate, and percent reduction values of alamarBlue were determined using the appropriate formula (www.biokom.com.pl/files/alamarblue.pdf).In terms of optimization, this assay examined the influence of cell numbers, the cellular incubation time, and the optimal incubation time with alamarBlue. All three had a significant impact on color development and percent reduction of the dye. For the highest concentration of cells (3 × 10⁸ CFU/ml) (Fig. ​(Fig.1a),1a), a strong reduction of the dye was observed after 1 day of cellular incubation. Further incubation of the cells or incubation with the dye did not result in an appreciable increase in dye reduction values. Indeed, a decrease in the percent reduction was noted, most likely due to buffering agents reaching their maximum buffering efficiencies in the reagent mix (www.abdserotec.com/about/alamarblue). At the mid-range cellular levels (2.4 × 10⁶ CFU/ml) (Fig. ​(Fig.1b),1b), detectable dye reduction occurred after 2 days. The reduction was substantial after day 4. At the lowest concentration of cells (9.6 × 10⁴ CFU/ml) (Fig. ​(Fig.1c),1c), a noticeable change in dye reduction was observed after 9 days. While longer incubation with alamarBlue led to greater dye reduction with a given cell titer, as shown with each suspension at 6, 24, and 48 h, the 24-h reading was considered sufficient to give a clear indication of viability.Open in a separate windowFIG. 1.Optimization of alamarBlue conditions using 3 × 10⁸ CFU/ml (a), 2.4 × 10⁶ CFU/ml (b), and 9.6 × 10⁴ CFU/ml (c) over 11 days. Following the addition of alamarBlue, readings were taken at 6, 24, and 48 h.Percent reduction of the dye was standardized to 10, 20, 40, and 60% for each concentration of cells (Table ​(Table1).1). These values serve as definitive indicators of metabolic activity and may be used for multiple applications, such as comparing the relative viabilities of strains, or the influence of media composition or environmental stress on M. avium subsp. paratuberculosis. In particular, we feel that this assay is suited to comparing the relative efficacies of multiple anti-M. avium subsp. paratuberculosis compounds and/or antibiotic resistance profiling in a high-throughput screening format. The success of this assay requires strict adherence to specific cell numbers, growth phases, and their equivalent incubation times.

TABLE 1.

Required time taken for M. avium subsp. paratuberculosis to reduce alamarBlue

Sponge spicules as blueprints for the biofabrication of inorganic–organic composites and biomaterials

While most forms of multicellular life have developed a calcium-based skeleton, a few specialized organisms complement their body plan with silica. However, of all recent animals, only sponges (phylum Porifera) are able to polymerize silica enzymatically mediated in order to generate massive siliceous skeletal elements (spicules) during a unique reaction, at ambient temperature and pressure. During this biomineralization process (i.e., biosilicification) hydrated, amorphous silica is deposited within highly specialized sponge cells, ultimately resulting in structures that range in size from micrometers to meters. Spicules lend structural stability to the sponge body, deter predators, and transmit light similar to optic fibers. This peculiar phenomenon has been comprehensively studied in recent years and in several approaches, the molecular background was explored to create tools that might be employed for novel bioinspired biotechnological and biomedical applications. Thus, it was discovered that spiculogenesis is mediated by the enzyme silicatein and starts intracellularly. The resulting silica nanoparticles fuse and subsequently form concentric lamellar layers around a central protein filament, consisting of silicatein and the scaffold protein silintaphin-1. Once the growing spicule is extruded into the extracellular space, it obtains final size and shape. Again, this process is mediated by silicatein and silintaphin-1, in combination with other molecules such as galectin and collagen. The molecular toolbox generated so far allows the fabrication of novel micro- and nanostructured composites, contributing to the economical and sustainable synthesis of biomaterials with unique characteristics. In this context, first bioinspired approaches implement recombinant silicatein and silintaphin-1 for applications in the field of biomedicine (biosilica-mediated regeneration of tooth and bone defects) or micro-optics (in vitro synthesis of light waveguides) with promising results.     

The CCG-domain-containing subunit SdhE of succinate:quinone oxidoreductase from Sulfolobus solfataricus P2 binds a [4Fe–4S] cluster

In type E succinate:quinone reductase (SQR), subunit SdhE (formerly SdhC) is thought to function as monotopic membrane anchor of the enzyme. SdhE contains two copies of a cysteine-rich sequence motif (CX _n CCGX _m CXXC), designated as the CCG domain in the Pfam database and conserved in many proteins. On the basis of the spectroscopic characterization of heterologously produced SdhE from Sulfolobus tokodaii, the protein was proposed in a previous study to contain a labile [2Fe–2S] cluster ligated by cysteine residues of the CCG domains. Using UV/vis, electron paramagnetic resonance (EPR), ⁵⁷Fe electron–nuclear double resonance (ENDOR) and Mössbauer spectroscopies, we show that after an in vitro cluster reconstitution, SdhE from S. solfataricus P2 contains a [4Fe–4S] cluster in reduced (2+) and oxidized (3+) states. The reduced form of the [4Fe–4S]²⁺ cluster is diamagnetic. The individual iron sites of the reduced cluster are noticeably heterogeneous and show partial valence localization, which is particularly strong for one unique ferrous site. In contrast, the paramagnetic form of the cluster exhibits a characteristic rhombic EPR signal with g _zyx  = 2.015, 2.008, and 1.947. This EPR signal is reminiscent of a signal observed previously in intact SQR from S. tokodaii with g _zyx  = 2.016, 2.00, and 1.957. In addition, zinc K-edge X-ray absorption spectroscopy indicated the presence of an isolated zinc site with an S₃(O/N)₁ coordination in reconstituted SdhE. Since cysteine residues in SdhE are restricted to the two CCG domains, we conclude that these domains provide the ligands to both the iron–sulfur cluster and the zinc site.