Randomized sequence databases for tandem mass spectrometry peptide and protein identification

Tandem mass spectrometry (MS/MS) combined with database searching is currently the most widely used method for high-throughput peptide and protein identification. Many different algorithms, scoring criteria, and statistical models have been used to identify peptides and proteins in complex biological samples, and many studies, including our own, describe the accuracy of these identifications, using at best generic terms such as "high confidence." False positive identification rates for these criteria can vary substantially with changing organisms under study, growth conditions, sequence databases, experimental protocols, and instrumentation; therefore, study-specific methods are needed to estimate the accuracy (false positive rates) of these peptide and protein identifications. We present and evaluate methods for estimating false positive identification rates based on searches of randomized databases (reversed and reshuffled). We examine the use of separate searches of a forward then a randomized database and combined searches of a randomized database appended to a forward sequence database. Estimated error rates from randomized database searches are first compared against actual error rates from MS/MS runs of known protein standards. These methods are then applied to biological samples of the model microorganism Shewanella oneidensis strain MR-1. Based on the results obtained in this study, we recommend the use of use of combined searches of a reshuffled database appended to a forward sequence database as a means providing quantitative estimates of false positive identification rates of peptides and proteins. This will allow researchers to set criteria and thresholds to achieve a desired error rate and provide the scientific community with direct and quantifiable measures of peptide and protein identification accuracy as opposed to vague assessments such as "high confidence."     

The SNPlex genotyping system: a flexible and scalable platform for SNP genotyping.

We developed the SNPlex Genotyping System to address the need for accurate genotyping data, high sample throughput, study design flexibility, and cost efficiency. The system uses oligonucleotide ligation/polymerase chain reaction and capillary electrophoresis to analyze bi-allelic single nucleotide polymorphism genotypes. It is well suited for single nucleotide polymorphism genotyping efforts in which throughput and cost efficiency are essential. The SNPlex Genotyping System offers a high degree of flexibility and scalability, allowing the selection of custom-defined sets of SNPs for medium- to high-throughput genotyping projects. It is therefore suitable for a broad range of study designs. In this article we describe the principle and applications of the SNPlex Genotyping System, as well as a set of single nucleotide polymorphism selection tools and validated assay resources that accelerate the assay design process. We developed the control pool, an oligonucleotide ligation probe set for training and quality-control purposes, which interrogates 48 SNPs simultaneously. We present performance data from this control pool obtained by testing genomic DNA samples from 44 individuals. in addition, we present data from a study that analyzed 521 SNPs in 92 individuals. Combined, both studies show the SNPlex Genotyping system to have a 99.32% overall call rate, 99.95% precision, and 99.84% concordance with genotypes analyzed by TaqMan probe-based assays. The SNPlex Genotyping System is an efficient and reliable tool for a broad range of genotyping applications, supported by applications for study design, data analysis, and data management.     

Bioinformatics

Bioinformatics is an interdisciplinary field that blends computer science and biostatistics with biological and biomedical sciences such as biochemistry, cell biology, developmental biology, genetics, genomics, and physiology. An important goal of bioinformatics is to facilitate the management, analysis, and interpretation of data from biological experiments and observational studies. The goal of this review is to introduce some of the important concepts in bioinformatics that must be considered when planning and executing a modern biological research study. We review database resources as well as data mining software tools.     

Viscoelasticity of human whole saliva collected after acid and mechanical stimulation

The rheology of saliva is highly important due to its influence on oral health and physiochemical processes within the oral environment. While the rheology of human whole saliva (HWS) is considered important for its functionality, its measurement is often performed erroneously and/or limited to the viscosity at a single shear rate. To ensure accurate rheological measurements, it is necessary to test HWS immediately after expectoration and to apply a thin layer of surfactant solution around the rim of the rheometer plates so that protein adsorption is minimized at the air-liquid interface. It is shown for the first time that the viscosity and viscoelasticity of HWS depends greatly upon the method of stimulation. Mechanical action stimulates slightly shear-thinning and relatively inelastic saliva, while acidic solutions (e.g. 0.25% citric acid) stimulate secretion of saliva that is highly elastic and shear-thinning. However, both acidic solutions and mechanical action stimulate similar volumes of saliva. For acid-stimulated saliva, the ratio of the primary normal stress difference to the shear stress is of order 100 and the viscosity at high shear rates is only marginally above that of water. This extremely high stress ratio for such a low viscosity fluid indicates that saliva's elastic properties dominate its flow behavior and may assist in facilitating lubrication within the oral cavity. It is anticipated that the variation in saliva rheology arises because the individual glands secrete saliva of different rheology, with the proportion of saliva secreted from each gland depending on the method of stimulation. The steady-shear rheology and linear viscoelasticity of HWS are described reasonably well using a FENE-P constitutive model and a 3-mode Maxwell model respectively. These models indicate that there are several long relaxation modes within saliva, possibly arising from the presence of large flexible macromolecules such as mucin glycoproteins.     

Severe Obesity Is Associated With Impaired Arterial Smooth Muscle Function in Young Adults

The degree of arterial dilatation induced by exogenous nitrates (nitrate‐mediated dilatation, NMD) has been similar in obese and normal‐weight adults after single high‐dose glyceryl trinitrate (GTN). We examined whether NMD is impaired in obesity by performing a GTN dose‐response study, as this is a potentially more sensitive measure of arterial smooth muscle function. In this cross‐sectional study, subjects were 19 obese (age 31.0 ± 1.2 years, 10 male, BMI 44.1 ± 2.1) and 19 age‐ and sex‐matched normal‐weight (BMI 22.4 ± 0.4) young adults. Blood pressure (BP), triglycerides, high‐density lipoprotein (HDL), and low‐density lipoprotein (LDL)‐cholesterol, glucose, insulin, high‐sensitivity C‐reactive protein (hs‐CRP), carotid intima‐media thickness (CIMT), and flow‐mediated dilatation (FMD) were measured. After incremental doses of GTN, brachial artery maximal percent dilatation (maximal NMD) and the area under the dose‐response curve (NMD AUC) were calculated. Maximal NMD (13.4 ± 0.9% vs. 18.3 ± 1.1%, P = 0.002) and NMD AUC (54,316 ± 362 vs. 55,613 ± 375, P = 0.018) were lower in obese subjects. The obese had significantly higher hs‐CRP, insulin, and CIMT and lower HDL‐cholesterol. Significant bivariate associations existed between maximal NMD or NMD AUC and BMI‐group (r = ?0.492, P = 0.001 or r = ?0.383, P = 0.009), hs‐CRP (r = ?0.419, P = 0.004 or r = ?0.351, P = 0.015), and HDL‐cholesterol (r = 0.374, P = 0.01 or r = 0.270, P = 0.05). On multivariate analysis, higher BMI‐group remained as the only significant determinant of maximal NMD (r² = 0.242, β = ?0.492, P = 0.002) and NMD AUC (r² = 0.147, β = ?0.383, P = 0.023). In conclusion, arterial smooth muscle function is significantly impaired in the obese. This may be important in their increased cardiovascular risk.     

Down-regulation of dopamine transporter by iron chelation in vitro is mediated by altered trafficking, not synthesis

Neurological development and functioning of dopamine (DA) neurotransmission is adversely affected by iron deficiency in early life. Iron-deficient rats demonstrate significant elevations in extracellular DA and a reduction in dopamine transporter (DAT) densities in the caudate putamen and nucleus accumbens. To explore possible mechanisms by which cellular iron concentrations control DAT functioning, endogenous DAT-expressing PC12 cells were used to determine the effect of iron chelation on DAT protein and mRNA expression patterns. In addition, we used human DAT (hDAT)-transfected Neuro2a (N2A) cells to examine DAT degradation and trafficking patterns. A 50 microM treatment for 24 h with the iron chelator, desferrioxamine (DFO), significantly decreased dopamine uptake in a dose-dependent manner, with no apparent change in K(m), in both PC12 and N2A cells. Reduced DA uptake was accompanied by concentration- and time-dependent reductions in total DAT protein levels in both cell lines. Exposure to increasing concentrations of DFO did not significantly alter DAT mRNA in either PC12 or N2A cells. However, DAT degradation rates increased three-fivefold in both cell types exposed to 50 microM DFO for 24 h. Biotinylation studies in N2A cells indicate a more dramatic loss of DAT in the membrane fraction, while OptiPrep fractionation experiments revealed an increase in lysosomal DAT with iron chelation. Inhibition of protein kinase C activation with staurosporin prevented the effect of iron chelation on DAT function, suggesting that in vitro iron chelation affects DAT primarily through the effects on trafficking rather than on synthesis.     

An interaction between climate change and infectious disease drove widespread amphibian declines

Climate change might drive species declines by altering species interactions, such as host–parasite interactions. However, few studies have combined experiments, field data, and historical climate records to provide evidence that an interaction between climate change and disease caused any host declines. A recently proposed hypothesis, the thermal mismatch hypothesis, could identify host species that are vulnerable to disease under climate change because it predicts that cool‐ and warm‐adapted hosts should be vulnerable to disease at unusually warm and cool temperatures, respectively. Here, we conduct experiments on Atelopus zeteki, a critically endangered, captively bred frog that prefers relatively cool temperatures, and show that frogs have high pathogen loads and high mortality rates only when exposed to a combination of the pathogenic chytrid fungus (Batrachochytrium dendrobatidis) and high temperatures, as predicted by the thermal mismatch hypothesis. Further, we tested various hypotheses to explain recent declines experienced by species in the amphibian genus Atelopus that are thought to be associated with B. dendrobatidis and reveal that these declines are best explained by the thermal mismatch hypothesis. As in our experiments, only the combination of rapid increases in temperature and infectious disease could account for the patterns of declines, especially in species adapted to relatively cool environments. After combining experiments on declining hosts with spatiotemporal patterns in the field, our findings are consistent with the hypothesis that widespread species declines, including possible extinctions, have been driven by an interaction between increasing temperatures and infectious disease. Moreover, our findings suggest that hosts adapted to relatively cool conditions will be most vulnerable to the combination of increases in mean temperature and emerging infectious diseases.     

Cylindrospermopsis raciborskii Virus and host: genomic characterization and ecological relevance

Cylindrospermopsis (Raphidiopsis) raciborskii is an invasive, filamentous, nitrogen-fixing cyanobacterium that forms frequent blooms in freshwater habitats. While viruses play key roles in regulating the abundance, production and diversity of their hosts in aquatic ecosystems, the role(s) of viruses in the ecology of C. raciborskii is almost unexplored. Progress in this field has been hindered by the absence of a characterized virus–host system in C. raciborskii. To bridge this gap, we sequenced the genome of CrV-01T, a previously isolated cyanosiphovirus, and its host, C. raciborskii strain Cr2010. Analyses suggest that CrV-01T represents a distinct clade of siphoviruses infecting, and perhaps lysogenizing, filamentous cyanobacteria. Its genome contains unique features that include an intact CRISPR array and a 12 kb inverted duplication. Evidence suggests CrV-01T recently gained the ability to infect Cr2010 and recently lost the ability to form lysogens. The cyanobacterial host contains a CRISPR-Cas system with CRISPR spacers matching protospacers within the inverted duplication of the CrV-01T genome. Examination of metagenomes demonstrates that viruses with high genetic identity to CrV-01T, but lacking the inverted duplication, are present in C. raciborskii blooms in Australia. The unique genomic features of the CrV/Cr2010 system offers opportunities to investigate in more detail virus–host interactions in an ecologically important bloom-forming cyanobacterium.     

A risk‐based inventory of invasive plant species of Queensland,Australia: Regional,ecological and floristic insights

Invasive alien plant species threaten agriculture and biodiversity globally and require ongoing management to minimise impacts. However, the large number of invasive species means that a risk‐based approach to prioritisation is needed, taking into account the spatial scale of management decisions and myriad of available information. Here, we developed a risk‐based inventory of invasive plants in Queensland, Australia, using both current species distribution/abundance and the severity of their impacts. Our assessment followed a comprehensive data collection process including a scoping of local government pest management plans, herbarium records, the published literature and structured elicitation of expert knowledge during a series of regional stakeholder workshops. From ~300 plant species that were identified as established and/or emerging invaders in the State, only one‐third were considered by practitioners to pose significant risks across regions to be considered management priorities. We aggregated regional species lists into a statewide priority list and analysed the data set (107 species) for historical, geographical, floristic and ecological patterns. Regions on the mainland eastern seaboard of the State share similar invasive plant communities, suggesting that these regions may form a single management unit, unlike the western/inland and the extreme far north (Torres Strait Islands) regions, which share fewer invasive plant species. Positive correlations were detected between invasiveness and time since introduction for some but not all plant life forms. Stakeholders identified research and management priorities for the invasive plant list, including biological control options, public awareness/education, effective herbicide use, ecology/taxonomy and risk analysis. In the course of the exercise, a statewide invasive plant priority list of high‐, medium‐ and low‐impact scores for policy, research and management was compiled. Finally, our approach to invasive plant species prioritisation highlighted that planning and policy documents are not necessarily reflected at the grass‐root level in terms of species identity and management priorities.