Nanotechnology for catalysis and solar energy conversion.

This roadmap on Nanotechnology for Catalysis and Solar Energy Conversion focuses on the application of nanotechnology in addressing the current challenges of energy conversion: 'high efficiency, stability, safety, and the potential for low-cost/scalable manufacturing' to quote from the contributed article by Nathan Lewis. This roadmap focuses on solar-to-fuel conversion, solar water splitting, solar photovoltaics and bio-catalysis. It includes dye-sensitized solar cells (DSSCs), perovskite solar cells, and organic photovoltaics. Smart engineering of colloidal quantum materials and nanostructured electrodes will improve solar-to-fuel conversion efficiency, as described in the articles by Waiskopf and Banin and Meyer. Semiconductor nanoparticles will also improve solar energy conversion efficiency, as discussed by Boschloo et al in their article on DSSCs. Perovskite solar cells have advanced rapidly in recent years, including new ideas on 2D and 3D hybrid halide perovskites, as described by Spanopoulos et al 'Next generation' solar cells using multiple exciton generation (MEG) from hot carriers, described in the article by Nozik and Beard, could lead to remarkable improvement in photovoltaic efficiency by using quantization effects in semiconductor nanostructures (quantum dots, wires or wells). These challenges will not be met without simultaneous improvement in nanoscale characterization methods. Terahertz spectroscopy, discussed in the article by Milot et al is one example of a method that is overcoming the difficulties associated with nanoscale materials characterization by avoiding electrical contacts to nanoparticles, allowing characterization during device operation, and enabling characterization of a single nanoparticle. Besides experimental advances, computational science is also meeting the challenges of nanomaterials synthesis. The article by Kohlstedt and Schatz discusses the computational frameworks being used to predict structure-property relationships in materials and devices, including machine learning methods, with an emphasis on organic photovoltaics. The contribution by Megarity and Armstrong presents the 'electrochemical leaf' for improvements in electrochemistry and beyond. In addition, biohybrid approaches can take advantage of efficient and specific enzyme catalysts. These articles present the nanoscience and technology at the forefront of renewable energy development that will have significant benefits to society.

Strong neutrino cooling by cycles of electron capture and ß- decay in neutron star crusts.

The temperature in the crust of an accreting neutron star, which comprises its outermost kilometre, is set by heating from nuclear reactions at large densities, neutrino cooling and heat transport from the interior. The heated crust has been thought to affect observable phenomena at shallower depths, such as thermonuclear bursts in the accreted envelope. Here we report that cycles of electron capture and its inverse, ß(-) decay, involving neutron-rich nuclei at a typical depth of about 150 metres, cool the outer neutron star crust by emitting neutrinos while also thermally decoupling the surface layers from the deeper crust. This 'Urca' mechanism has been studied in the context of white dwarfs and type Ia supernovae, but hitherto was not considered in neutron stars, because previous models computed the crust reactions using a zero-temperature approximation and assumed that only a single nuclear species was present at any given depth. The thermal decoupling means that X-ray bursts and other surface phenomena are largely independent of the strength of deep crustal heating. The unexpectedly short recurrence times, of the order of years, observed for very energetic thermonuclear superbursts are therefore not an indicator of a hot crust, but may point instead to an unknown local heating mechanism near the neutron star surface.

First Direct Measurement of (12)C((12)C,n)(23)Mg at Stellar Energies.

Neutrons produced by the carbon fusion reaction (12)C((12)C,n)(23)Mg play an important role in stellar nucleosynthesis. However, past studies have shown large discrepancies between experimental data and theory, leading to an uncertain cross section extrapolation at astrophysical energies. We present the first direct measurement that extends deep into the astrophysical energy range along with a new and improved extrapolation technique based on experimental data from the mirror reaction (12)C((12)C,p)(23)Na. The new reaction rate has been determined with a well-defined uncertainty that exceeds the precision required by astrophysics models. Using our constrained rate, we find that (12)C((12)C,n)(23)Mg is crucial to the production of Na and Al in pop-III pair instability supernovae. It also plays a nonnegligible role in the production of weak s-process elements, as well as in the production of the important galactic γ-ray emitter (60)Fe.

Reduced sphingosine kinase 1 activity in dengue virus type-2 infected cells can be mediated by the 3' untranslated region of dengue virus type-2 RNA.

Sphingosine kinase 1 (SphK1) is a lipid kinase with important roles including regulation of cell survival. We have previously shown reduced SphK1 activity in cells with an established dengue virus type-2 (DENV-2) infection. In this study, we examined the effect of alterations in SphK1 activity on DENV-2 replication and cell death and determined the mechanisms of the reduction in SphK1 activity. Chemical inhibition or overexpression of SphK1 after established DENV-2 infection had no effect on infectious DENV-2 production, although inhibition of SphK1 resulted in enhanced DENV-2-induced cell death. Reduced SphK1 activity was observed in multiple cell types, regardless of the ability of DENV-2 infection to be cytopathic, and was mediated by a post-translational mechanism. Unlike bovine viral diarrhea virus, where SphK1 activity is decreased by the NS3 protein, SphK1 activity was not affected by DENV-2 NS3 but, instead, was reduced by expression of the terminal 396 bases of the 3' UTR of DENV-2 RNA. We have previously shown that eukaryotic elongation factor 1A (eEF1A) is a direct activator of SphK1 and here DENV-2 RNA co-localized and co-precipitated with eEF1A from infected cells. We propose that the reduction in SphK1 activity late in DENV-2-infected cells is a consequence of DENV-2 out-competing SphK1 for eEF1A binding and hijacking cellular eEF1A for its own replication strategy, rather than a specific host or virus-induced change in SphK1 to modulate viral replication. Nonetheless, reduced SphK1 activity may have important consequences for survival or death of the infected cell.

The donor line break cannula: effect on the donation process, blood component quality and transfusion microbiology testing of an important new blood bag safety feature.

BACKGROUND: The use of blood packs with an integral sampling system can result in anti-coagulant from the main bag reaching the sample pouch via the donor line, causing delayed coagulation of blood samples. In NHS Blood and Transplant, this has prevented the use of serum, the preferred matrix for transfusion microbiology (TM) testing, which has led to an increased false positive rate with ethylenediaminetetraacetic acid (EDTA) plasma. There is also a remote possibility of false negative results owing to sample dilution. Manufacturers have responded by offering packs with a donor line break cannula (DLBC) to prevent these adverse effects. OBJECTIVES: The aims of this study were to assess the impact of DLBC packs on donation, blood component quality and of the potential return to serum for TM testing. METHODS: DLBC packs from three manufacturers were assessed against control packs of the same dimensions and configuration. Donation duration, flow rate, platelet factor 4, prothrombin fragment 1+2, haemolysis and collection and processing incidents were compared. RESULTS: Results indicated no clinically significant adverse effect from the DLBC on the activation state of platelets, the coagulation cascade or increased haemolysis. Donation duration and blood collection and processing incident rates for DLBC packs were not significantly different to controls. CONCLUSIONS: The use of DLBC packs would reduce the complexity of manipulations during blood collection and therefore the likelihood of microbially contaminated donations (incorrect skin core diversion) and false negative TM tests. DLBC packs would enable the use of serum for TM testing with a significant reduction in false positive tests compared to EDTA plasma.

Recent developments in the specific dermatoses of pregnancy.

During pregnancy, the mother undergoes changes to sustain and enable normal growth and development of the fetus. Common physiological changes include linea nigra, fibroepithelial polyps, striae, spider angioma, palmar erythema and pruritis gravidarum. However, there are some changes that are purely pathological, and these are termed the pregnancy-specific dermatoses (PSDs). The PSDs occur during pregnancy or in the immediate postpartum period. They do not include the various benign conditions or pre-existing dermatoses and tumours that may present or worsen with pregnancy. They do include a number of distinct and identifiable conditions: atopic eruption of pregnancy (AEP), polymorphic eruption of pregnancy (PEP), intrahepatic cholestasis of pregnancy (ICP) and pemphigoid gestationis (PG). These are a heterogeneous group of skin conditions characterized by pruritis and inflammatory changes. In addition, pruritis gravidarum is sometimes considered pathophysiological and thus part of this group, rather than a physiological process. Each of these conditions has a distinct, but not fully understood, pathogenesis. The mechanisms leading to PSD may be a reflection on the hormonal and immunological changes associated with pregnancy. AEP and PEP are benign conditions, and although they can cause distress to the mother, they are otherwise minor. However, ICP and PG are more serious conditions, and both carry the potential for serious risks to both the mother and the fetus. Thus, the pathophysiology of these latter two conditions is considered in more detail in the following article.

Hepatic TLR2 & TLR4 expression correlates with hepatic inflammation and TNF-α in HCV & HCV/HIV infection.

Signalling activated by Toll-like receptors (TLRs) can result in the production of tumour necrosis factor alpha (TNF-α) which is implicated in hepatitis C virus (HCV) and human immunodeficiency virus (HIV) infection. No study has examined or compared hepatic expression of TLRs in both HCV and HCV/HIV. Liver and peripheral blood mononuclear cells (PBMCs) were obtained from HCV & HCV/HIV-infected patients and PBMCs from HIV-infected patients. Liver RNA was analysed by microarray and reverse transcription quantitative PCR (RT-qPCR). PBMCs were analysed by flow cytometry. Associations with hepatic histology and infection type were sought. Forty-six HCV, 20 HIV and 27 HCV/HIV-infected patients were recruited. Increasing Metavir inflammatory activity score was associated with increased hepatic TLR mRNA by RT-qPCR: TLR2 (P ≤ 0.001), TLR4 (P = 0.008) and TNF-α (P ≤ 0.001). A high degree of correlation was seen between hepatic mRNA expression of TNF-αvs TLR2 (r(2) = 0.66, P < 0.0001) and TLR4 (r(2) = 0.60, P < 0.0001). No differences in TLR gene or protein expression was observed between HCV, HCV/HIV- or HIV-infected groups. Hepatic TLR2, TLR4 and TNF-α mRNA are associated with hepatic inflammation in both HCV and HCV/HIV infection. High correlation between TNF-α and TLR2/TLR4 suggests a role for the innate immune response in TNF-α production. Activation of the innate immune response appears to be independent of infection type.

Time-of-flight mass measurements for nuclear processes in neutron star crusts.

We present results from time-of-flight nuclear mass measurements at the National Superconducting Cyclotron Laboratory that are relevant for neutron star crust models. The masses of 16 neutron-rich nuclei in the scandium-nickel range were determined simultaneously, with the masses of (61)V, (63)Cr, (66)Mn, and (74)Ni measured for the first time with mass excesses of -30.510(890) MeV, -35.280(650) MeV, -36.900(790) MeV, and -49.210(990) MeV, respectively. With these results the locations of the dominant electron capture heat sources in the outer crust of accreting neutron stars that exhibit super bursts are now experimentally constrained. We find the experimental Q value for the (66)Fe→(66)Mn electron capture to be 2.1 MeV (2.6σ) smaller than predicted, resulting in the transition occurring significantly closer to the neutron star surface.

Comparison of platelet activation in platelet concentrates measured by flow cytometry or ADVIA 2120.

BACKGROUND AND OBJECTIVES: The ADVIA 2120 Haematology Analyser is capable of measuring parameters that can be used as markers of platelet activation, mean platelet component (MPC), platelet component distribution width (PCDW) and mean platelet mass (MPM). This study investigated the degree of correlation of these measures of platelet granularity with CD62P measurement of platelet activation by flow cytometry in platelet concentrates. MATERIALS AND METHODS: Pooled platelets in plasma/citrate phosphate dextrose (CPD) anticoagulant or apheresis platelets in plasma/acid citrate dextrose formula A (ACD-A) anticoagulant were evaluated. Pooled platelets were tested during 13 day storage, and apheresis platelets within 24 h of venepuncture. These were assessed for platelet activation using CD62P and the ADVIA, with or without extra EDTA anticoagulant. RESULTS: In pooled platelets, PCDW correlated strongly with CD62P, both with and without the addition of extra EDTA anticoagulant. There was a good correlation between MPC and CD62P with additional EDTA, but a weaker correlation without extra EDTA. There was no correlation between CD62P and MPM. In apheresis platelets the correlation between PCDW and CD62P was poor, whereas MPC correlated strongly with CD62P if EDTA anticoagulant was added. CONCLUSION: The usefulness of ADVIA platelet granularity measures to predict the degree of platelet activation depends upon the anticoagulant present in the platelet concentrate, and whether extra EDTA is added to the sample. Although ADVIA MPC and PCDW measurement could not replace CD62P or other gold standard methods of assessing platelet activation, these ADVIA 2120 parameters may provide a quick check of platelet concentrate quality.

Dengue virus infection induces upregulation of GRP78, which acts to chaperone viral antigen production.

Dengue virus (DENV) pathogenesis is related to the host responses to viral infection within target cells, and therefore, this study assessed intracellular changes in host proteins following DENV infection. Two-dimensional gel electrophoresis and mass spectrometry identified upregulation of the host endoplasmic reticulum (ER) chaperone GRP78 in K562 cells following DENV infection, in the absence of virus-induced cell death. Upregulation of GRP78 in DENV-infected cells was confirmed by immunostaining and confocal microscopy and by Western blot analysis and was also observed in DENV-infected primary monocyte-derived macrophages, a natural target cell type for DENV infection. GRP78 was upregulated in both DENV antigen-positive and -negative cells in the DENV-infected culture, suggesting a bystander effect, with the highest GRP78 levels coincident with high-level DENV antigen production and infectious-virus release. Transfection of target cells to express GRP78 prior to DENV challenge did not affect subsequent DENV infection, but cleavage of GRP78 with the SubAB toxin, during an established DENV infection, yielded a 10- to 100-fold decrease in infectious-virus release, loss of intracellular DENV particles, and a dramatic decrease in intracellular DENV antigen. However, DENV RNA levels were unchanged, indicating normal DENV RNA replication but altered DENV antigen levels in the absence of GRP78. Thus, GRP78 is upregulated by DENV infection and is necessary for DENV antigen production and/or accumulation. This may be a common requirement for viruses such as flaviviruses that depend heavily on the ER for coordinated protein production and processing.

Double red cell concentrates -in vitro quality after delayed refrigeration.

Automated collection of red cell concentrates (RCC) presents a number of potential advantages to donors, blood services and recipients, and allows the collection of finished components from sites that are remote from a blood centre. However, data are lacking on how long the collected RCC may be stored at ambient temperature prior to their final storage at 4 °C. In this study, the Haemonetics Cymbal device was used to collect RCC using citrate, phosphate and dextrose (CPD-50) anticoagulant. A total of 10 procedures each yielded two leucodepleted RCC in saline, adenine, glucose and mannitol (SAGM) additive solution. One of each pair of RCC was kept warm in an insulated transport bag for 8 h and the other for 6 h. In vitro assessments of the quality of the RCC were made during subsequent 42-day storage of the RCC at 2-6 °C, and compared with reference data. All collected RCC were within UK and European limits for volume, haematocrit and haemoglobin content. Haemolysis was within specification at Day 42 and was no different in RCC held warm for 6 or 8 hours, but tended to be higher than reference data from whole blood derived RCC. ATP, 2,3 DPG and supernatant potassium levels were all similar in RCC held warm for 6 or 8 hours and reference data. We conclude that the Cymbal device may be used to collect two RCC in SAGM, and the in vitro assessment indicates that RCC may be stored without refrigeration for up to 8 h following collection, prior to final storage at 4 °C.

Distribution of peroxisomes (microbodies) in the nephron of the rat: a cytochemical study.

The distribution of peroxisomes (microbodies) in the rat nephron was studied cytochemically, using glutaraldehyde- or formaldehyde-fixed tissue, by means of alpha-hydroxy acid oxidase activity in light microscopy or oxidation of 3,3'-diaminobenzidine (DAB) at pH 9 in both light and electron microscopy.The two cytochemical methods show peroxisomes to be nearly sperical particles found only in cells of the proximal convoluted tubule. Lysosomes were identified in the same or parallel sections, with beta-glycerophosphate or 5'-cytidylic acid as substrate. They are found in all cells of the nephron. These cytochemical methods visualize the two organelles for light microscopy; they also permit unequivocal differentiation of all kidney peroxisomes from lysosomes in electron micrographs. Peroxisomes are larger and more reactive in the cells of the pars descendens (P(3) segment) of the proximal convolution, located in the outer medulla and medullary rays, than in the cells of the pars convoluta (P(1) and P(2) segments), situated in the cortex. In contrast, lysosomes are much smaller in the P(3) segment and larger and more reactive in the P(1) and P(2) segments. In all cells of the proximal convolution, peroxisomes tend to be concentrated nearer the base of the cells than do lysosomes. Mitochondria in P(3) cells also show low levels of DAB oxidation at pH 6, in contrast to those in P(1) and P(2) cells. The possibility is discussed that P(3) cells possess an extramitochondrial means of oxidation in which peroxisome oxidases play an important role.

Platelet concentrates produced from whole blood using the Atreus processing system.

BACKGROUND: The Atreus 2C+ system automates whole blood (WB) processing into a red cell concentrate, plasma and buffy coat (BC) suitable for platelet concentrate (PC) manufacture. This study compared the quality of PC made from BC using the Atreus, with those made by a manual method. STUDY DESIGN AND METHODS: WB was collected into Atreus disposables or standard bottom and top processing packs and held without active cooling for 26 h at 22 +/- 2 degrees C before processing, either with the Atreus, or using a centrifuge and press. BC were rested for 3 h and then 4 BC were pooled with one unit of plasma, mixed, centrifuged and pressed to make a pooled PC. The PC were analysed for quality markers to day 9 of storage. RESULTS: Platelet quality was good in both Atreus 2C+ derived PC and control units throughout storage. Metabolic markers (pH, ATP and HSR) and activation markers (CD62P, sCD62P, annexin V binding, microparticles, GP IIb/IIIa) did not differ between the Atreus and control units. Atreus-derived PC had significantly lower platelet yields (302 +/- 59 x 10(9) platelets/unit; mean +/- standard deviation, n = 8) than control PC (411 +/- 76 x 10(9) platelets/unit; P < 0.01), but met the UK guidelines for platelet yield. CONCLUSION: From these in vitro data, PC produced from buffy coats prepared using the Atreus appear suitable for clinical use, and WB may be held at ambient temperature overnight without the use of active cooling devices. Optimizing the secondary processing conditions to handle Atreus 2C+ derived BC may increase the platelet yield.

The interferon stimulated gene viperin, restricts Shigella. flexneri in vitro.

The role of interferon and interferon stimulated genes (ISG) in limiting bacterial infection is controversial, and the role of individual ISGs in the control of the bacterial life-cycle is limited. Viperin, is a broad acting anti-viral ISGs, which restricts multiple viral pathogens with diverse mechanisms. Viperin is upregulated early in some bacterial infections, and using the intracellular bacterial pathogen, S. flexneri, we have shown for the first time that viperin inhibits the intracellular bacterial life cycle. S. flexneri replication in cultured cells induced a predominantly type I interferon response, with an early increase in viperin expression. Ectopic expression of viperin limited S. flexneri cellular numbers by as much as 80% at 5hrs post invasion, with similar results also obtained for the intracellular pathogen, Listeria monocytogenes. Analysis of viperins functional domains required for anti-bacterial activity revealed the importance of both viperin's N-terminal, and its radical SAM enzymatic function. Live imaging of S. flexneri revealed impeded entry into viperin expressing cells, which corresponded to a loss of cellular cholesterol. This data further defines viperin's multi-functional role, to include the ability to limit intracellular bacteria; and highlights the role of ISGs and the type I IFN response in the control of bacterial pathogens.

NS1 DNA vaccination protects against Zika infection through T cell-mediated immunity in immunocompetent mice.

The causal association of Zika virus (ZIKV) with microcephaly, congenital malformations in infants, and Guillain-Barré syndrome in adults highlights the need for effective vaccines. Thus far, efforts to develop ZIKV vaccines have focused on the viral envelope. ZIKV NS1 as a vaccine immunogen has not been fully explored, although it can circumvent the risk of antibody-dependent enhancement of ZIKV infection, associated with envelope antibodies. Here, we describe a novel DNA vaccine encoding a secreted ZIKV NS1, that confers rapid protection from systemic ZIKV infection in immunocompetent mice. We identify novel NS1 T cell epitopes in vivo and show that functional NS1-specific T cell responses are critical for protection against ZIKV infection. We demonstrate that vaccine-induced anti-NS1 antibodies fail to confer protection in the absence of a functional T cell response. This highlights the importance of using NS1 as a target for T cell-based ZIKV vaccines.

The in vitro detection of botulinum neurotoxin-cleaved endogenous VAMP is epitope-dependent.

The in vitro potency of botulinum neurotoxin (BoNT) serotypes is often measured by monitoring cleavage of their soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) protein substrates. A frequently used method is Western blot, whereby the full-length protein and cleaved form migrate at different molecular weights. Until now, it has been extremely difficult to detect the cleaved cellular form of the SNARE protein vesicle associated membrane protein 1, 2 or 3 (VAMP1, 2 or 3) by Western blot. These VAMP isoforms are the substrates of BoNT serotypes BoNT/B, D, F and G as well as tetanus neurotoxin. Using custom made anti-VAMP antibodies against epitopes either side of the cleavage sites for BoNT/B, BoNT/D and BoNT/F, we have successfully detected the cleaved C-terminal VAMP fragment in cortical neurons. These new antibodies enable quantitative assessment of the potency of VAMP-cleaving neurotoxins by a gain of signal Western blot assay.

Conversion of vitamin B 6 compounds to active forms in the red blood cell.

In studies with pyridoxine and other B(6) compounds in blood, the active forms pyridoxal and pyridoxal phosphate were measured by differential assays using Lactobacillus casei. Red cell uptake of tritiated pyridoxine was also measured. A new metabolic pathway for conversion of pyridoxine to active forms was demonstrated in red cells. In vivo studies in normal subjects suggested that pyridoxine was taken up by red cells where it was converted to pyridoxal phosphate and then pyridoxal, followed by gradual release of a proportion of pyridoxal into plasma. In vitro incubation of pyridoxine with blood confirmed this observation. Increasing amounts of pyridoxine were taken up and converted as the amount added to blood was increased, and only very small numbers of red cells were needed to convert appreciable amounts. Conversion was markedly inhibited at temperatures lower than 37 degrees C, and stopped altogether at - 20 degrees C.Release of pyridoxal into plasma was always directly proportional to the amount of pyridoxal formed and to the volume of plasma present. That pyridoxal phosphate was not released into plasma was demonstrated in stored blood, for pyridoxine was converted mainly only as far as pyridoxal phosphate, probably due to inactivation of the phosphatase. Pyridoxal phosphate remained in the red cells. Pyridoxine was converted when incubated with washed red cells in saline or phosphate buffer suspension (0.08 M). In saline suspension, pyridoxal formed but was not released in the absence of plasma. In phosphate buffer suspension, pyridoxal phosphate was formed but was not changed to pyridoxal, probably due to inactivation of phosphatase by excess phosphate. Pyridoxamine was converted to active forms in red cells less efficiently. Pyridoxal entered red cells rapidly, equilibrating between plasma and cells within 1 min in the same ratio as pyridoxal formed inside red cells. Pyridoxal phosphate did not enter red cells in whole blood but did so readily in washed cells in saline.

Peroxisomal bifunctional enzyme deficiency.

Peroxisomal function was evaluated in a male infant with clinical features of neonatal adrenoleukodystrophy. Very long chain fatty acid levels were elevated in both plasma and fibroblasts, and beta-oxidation of very long chain fatty acids in cultured fibroblasts was significantly impaired. Although the level of the bile acid intermediate trihydroxycoprostanoic acid was slightly elevated in plasma, phytanic acid and L-pipecolic acid levels were normal, as was plasmalogen synthesis in cultured fibroblasts. The latter three parameters distinguish this case from classical neonatal adrenoleukodystrophy. In addition, electron microscopy and catalase subcellular distribution studies revealed that, in contrast to neonatal adrenoleukodystrophy, peroxisomes were present in the patient's tissues. Immunoblot studies of peroxisomal beta-oxidation enzymes revealed that the bifunctional enzyme (enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase) was deficient in postmortem liver samples, whereas acyl-CoA oxidase and the mature form of beta-ketothiolase were present. Density gradient centrifugation of fibroblast homogenates confirmed that intact peroxisomes were present. Immunoblots of fibroblasts peroxisomal fractions showed that they contained acyl-CoA oxidase and beta-ketothiolase, but bifunctional enzyme was not detected. Northern analysis, however, revealed that mRNA coding for the bifunctional enzyme was present in the patient's fibroblasts. These results indicate that the primary biochemical defect in this patient is a deficiency of peroxisomal bifunctional enzyme. It is of interest that the phenotype of this patient resembled neonatal adrenoleukodystrophy and would not have been distinguished from this disorder by clinical study alone.

Genomes as geography: using GIS technology to build interactive genome feature maps.

BACKGROUND: Many commonly used genome browsers display sequence annotations and related attributes as horizontal data tracks that can be toggled on and off according to user preferences. Most genome browsers use only simple keyword searches and limit the display of detailed annotations to one chromosomal region of the genome at a time. We have employed concepts, methodologies, and tools that were developed for the display of geographic data to develop a Genome Spatial Information System (GenoSIS) for displaying genomes spatially, and interacting with genome annotations and related attribute data. In contrast to the paradigm of horizontally stacked data tracks used by most genome browsers, GenoSIS uses the concept of registered spatial layers composed of spatial objects for integrated display of diverse data. In addition to basic keyword searches, GenoSIS supports complex queries, including spatial queries, and dynamically generates genome maps. Our adaptation of the geographic information system (GIS) model in a genome context supports spatial representation of genome features at multiple scales with a versatile and expressive query capability beyond that supported by existing genome browsers. RESULTS: We implemented an interactive genome sequence feature map for the mouse genome in GenoSIS, an application that uses ArcGIS, a commercially available GIS software system. The genome features and their attributes are represented as spatial objects and data layers that can be toggled on and off according to user preferences or displayed selectively in response to user queries. GenoSIS supports the generation of custom genome maps in response to complex queries about genome features based on both their attributes and locations. Our example application of GenoSIS to the mouse genome demonstrates the powerful visualization and query capability of mature GIS technology applied in a novel domain. CONCLUSION: Mapping tools developed specifically for geographic data can be exploited to display, explore and interact with genome data. The approach we describe here is organism independent and is equally useful for linear and circular chromosomes. One of the unique capabilities of GenoSIS compared to existing genome browsers is the capacity to generate genome feature maps dynamically in response to complex attribute and spatial queries.