Exploring new approaches and applications for multi-scale porous UHTCS

The control of processing conditions is key to achieve the desire amount, size and shape of porosity in materials for any application, including extreme applications. However, when particles with irregular shape, large size or differences in surface chemistry are to be used, as it happens for UHTCs, finding the right processing technique becomes crucial to ensure the desired properties, especially when there is not information about the actual performance in the application. This work describes how these challenges were overcome to develop multi-scale porous UHTCs for high temperature insulation as a case study. The exhaustive control of interparticle forces and understanding interaction between additives and powder surfaces resulted in multi-scale highly porous ceramics using different processing routes (replica, sacrificial fillers, particle stabilized foams plus gelcasting, ice templating and partial sintering, (Figure 1)). These colloidal techniques can render the required thermal conductivity across the component with a combination of different tailored porosities. Additionally, large complex-shape components with the same customized porous microstructure were prepared. Please click Additional Files below to see the full abstract

<em>Marichromatium indicum</em> sp. nov., a new purple sulfur Gammaproteobacterium from mangroves of Goa, India

A reddish-brown bacterium was isolated from photoheterotrophic enrichments of mangrove soil from the western coast of India, in a medium that contained 10 % (w/v) NaCl. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JA100T clusters with species of the genus Marichromatium of the class ‘Gammaproteobacteria’. Cells of strain JA100T are Gram-negative, motile rods with monopolar single flagella; they require NaCl, the optimum concentration being 1–4 %, and tolerate concentrations up to 13 %. The strain has vesicular internal membrane structures, bacteriochlorophyll a and, most probably, carotenoids of the spirilloxanthin series. No growth factors are required. A reduced sulfur source is required for growth, and, during growth on reduced sulfur sources as electron donors, sulfur is intermediately deposited as a single large granule within the cell. Strain JA100T could not grow at the expense of other tricarboxylic acid cycle intermediates, except malate. On the basis of 16S rRNA gene sequence analysis and its morphological and physiological characteristics, strain JA100T is sufficiently different from other Marichromatium species to justify its designation as a novel species, for which the name Marichromatium indicum sp. nov. is proposed. The type strain is JA100T (=DSM 15907T=ATCC BAA-741T=JCM 12653T)

Marichromatium bheemlicum sp. nov., a non-diazotrophic photosynthetic gammaproteobacterium from a marine aquaculture pond

A rod-shaped, phototrophic, purple sulfur bacterium, strain JA124(T), was isolated in pure culture from a marine aquaculture pond, located near Bhimunipatnam, in a medium that contained 3 % NaCl (w/v). Strain JA124(T) is a Gram-negative, motile rod with a single polar flagellum. Strain JA124(T) has a requirement for NaCl, with optimum growth at 1.5-8.5 %, and tolerates up to 11 % NaCl. Intracellular photosynthetic membranes are of the vesicular type. Bacteriochlorophyll a and probably carotenoids of the spirilloxanthin series are present as photosynthetic pigments. Strain JA124(T) was able to utilize sulfide, sulfate, thiosulfate, sulfite, thioglycollate and cysteine as sulfur sources. Strain JA124(T) was able to grow photolithoautotrophically, photolithoheterotrophically and photo-organoheterotrophically. Chemotrophic and fermentative growth could not be demonstrated. Strain JA124(T) lacks diazotrophic growth and acetylene reduction activity. Pyridoxal phosphate is required for growth. During growth on reduced sulfur sources as electron donors, sulfur is deposited intermediately as a number of small granules within the cell. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JA124(T) clusters with species of the genus Marichromatium belonging to the class Gammaproteobacteria. The highest sequence similarities of strain JA124(T) were found with the type strains of Marichromatium indicum (98 %), Marichromatium purpuratum (95 %) and Marichromatium gracile (93 %). However, DNA-DNA hybridization with Marichromatium indicum DSM 15907(T) revealed relatedness of only 65 % with strain JA124(T). The DNA base composition of strain JA124(T) was 67 mol% G+C (by HPLC). Based on 16S rRNA gene sequence analysis, morphological and physiological characteristics and DNA-DNA hybridization studies, strain JA124(T) (=ATCC BAA-1316(T)=JCM 13911(T)) is sufficiently different from other Marichromatium species to merit its description as the type strain of a novel species, Marichromatium bheemlicum sp. nov

Classification and Identification of Bacteria by Mass Spectrometry and Computational Analysis

Background: In general, the definite determination of bacterial species is a tedious process and requires extensive manual labour. Novel technologies for bacterial detection and analysis can therefore help microbiologists in minimising their efforts in developing a number of microbiological applications. Methodology: We present a robust, standardized procedure for automated bacterial analysis that is based on the detection of patterns of protein masses by MALDI mass spectrometry. We particularly applied the approach for classifying and identifying strains in species of the genus Erwinia. Many species of this genus are associated with disastrous plant diseases such as fire blight. Using our experimental procedure, we created a general bacterial mass spectra database that currently contains 2800 entries of bacteria of different genera. This database will be steadily expanded. To support users with a feasible analytical method, we developed and tested comprehensive software tools that are demonstrated herein. Furthermore, to gain additional analytical accuracy and reliability in the analysis we used genotyping of single nucleotide polymorphisms by mass spectrometry to unambiguously determine closely related strains that are difficult to distinguish by only relying on protein mass pattern detection. Conclusions: With the method for bacterial analysis, we could identify fire blight pathogens from a variety of biological sources. The method can be used for a number of additional bacterial genera. Moreover, the mass spectrometry approac

"Every Gene Is Everywhere but the Environment Selects" : Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis

The spatial distribution of microbes on our planet is famously formulated in the Baas Becking hypothesis as everything is everywhere but the environment selects." While this hypothesis does not strictly rule out patterns caused by geographical effects on ecology and historical founder effects, it does propose that the remarkable dispersal potential of microbes leads to distributions generally shaped by environmental factors rather than geographical distance. By constructing sequence similarity networks from uncultured environmental samples, we show that microbial gene pool distributions are not influenced nearly as much by geography as ecology, thus extending the Bass Becking hypothesis from whole organisms to microbial genes. We find that gene pools are shaped by their broad ecological niche (such as sea water, fresh water, host, and airborne). We find that freshwater habitats act as a gene exchange bridge between otherwise disconnected habitats. Finally, certain antibiotic resistance genes deviate from the general trend of habitat specificity by exhibiting a high degree of cross-habitat mobility. The strong cross-habitat mobility of antibiotic resistance genes is a cause for concern and provides a paradigmatic example of the rate by which genes colonize new habitats when new selective forces emerge.Peer reviewe

Reconstructing phylogenies from noisy quartets in polynomial time with a high success probability

<p>Abstract</p> <p>Background</p> <p>In recent years, quartet-based phylogeny reconstruction methods have received considerable attentions in the computational biology community. Traditionally, the accuracy of a phylogeny reconstruction method is measured by simulations on synthetic datasets with known "true" phylogenies, while little theoretical analysis has been done. In this paper, we present a new model-based approach to measuring the accuracy of a quartet-based phylogeny reconstruction method. Under this model, we propose three efficient algorithms to reconstruct the "true" phylogeny with a high success probability.</p> <p>Results</p> <p>The first algorithm can reconstruct the "true" phylogeny from the input quartet topology set without quartet errors in <it>O</it>(<it>n</it>²) time by querying at most (<it>n </it>- 4) log(<it>n </it>- 1) quartet topologies, where <it>n </it>is the number of the taxa. When the input quartet topology set contains errors, the second algorithm can reconstruct the "true" phylogeny with a probability approximately 1 - <it>p </it>in <it>O</it>(<it>n</it>⁴log <it>n</it>) time, where <it>p </it>is the probability for a quartet topology being an error. This probability is improved by the third algorithm to approximately <inline-formula><m:math name="1748-7188-3-1-i1" xmlns:m="http://www.w3.org/1998/Math/MathML"><m:semantics><m:mrow><m:mfrac><m:mn>1</m:mn><m:mrow><m:mn>1</m:mn><m:mo>+</m:mo><m:msup><m:mi>q</m:mi><m:mn>2</m:mn></m:msup><m:mo>+</m:mo><m:mfrac><m:mn>1</m:mn><m:mn>2</m:mn></m:mfrac><m:msup><m:mi>q</m:mi><m:mn>4</m:mn></m:msup><m:mo>+</m:mo><m:mfrac><m:mn>1</m:mn><m:mrow><m:mn>16</m:mn></m:mrow></m:mfrac><m:msup><m:mi>q</m:mi><m:mn>5</m:mn></m:msup></m:mrow></m:mfrac></m:mrow><m:annotation encoding="MathType-MTEF"> MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGacaGaaiaabeqaaeqabiWaaaGcbaqcfa4aaSaaaeaacqaIXaqmaeaacqaIXaqmcqGHRaWkcqWGXbqCdaahaaqabeaacqaIYaGmaaGaey4kaSYaaSaaaeaacqaIXaqmaeaacqaIYaGmaaGaemyCae3aaWbaaeqabaGaeGinaqdaaiabgUcaRmaalaaabaGaeGymaedabaGaeGymaeJaeGOnaydaaiabdghaXnaaCaaabeqaaiabiwda1aaaaaaaaa@3D5A@</m:annotation></m:semantics></m:math></inline-formula>, where <inline-formula><m:math name="1748-7188-3-1-i2" xmlns:m="http://www.w3.org/1998/Math/MathML"><m:semantics><m:mrow><m:mi>q</m:mi><m:mo>=</m:mo><m:mfrac><m:mi>p</m:mi><m:mrow><m:mn>1</m:mn><m:mo>−</m:mo><m:mi>p</m:mi></m:mrow></m:mfrac></m:mrow><m:annotation encoding="MathType-MTEF"> MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGacaGaaiaabeqaaeqabiWaaaGcbaGaemyCaeNaeyypa0tcfa4aaSaaaeaacqWGWbaCaeaacqaIXaqmcqGHsislcqWGWbaCaaaaaa@3391@</m:annotation></m:semantics></m:math></inline-formula>, with running time of <it>O</it>(<it>n</it>⁵), which is at least 0.984 when <it>p </it>< 0.05.</p> <p>Conclusion</p> <p>The three proposed algorithms are mathematically guaranteed to reconstruct the "true" phylogeny with a high success probability. The experimental results showed that the third algorithm produced phylogenies with a higher probability than its aforementioned theoretical lower bound and outperformed some existing phylogeny reconstruction methods in both speed and accuracy.</p

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

Computational efforts to identify functional elements within genomes leverage comparative sequence information by looking for regions that exhibit evidence of selective constraint. One way of detecting constrained elements is to follow a bottom-up approach by computing constraint scores for individual positions of a multiple alignment and then defining constrained elements as segments of contiguous, highly scoring nucleotide positions. Here we present GERP++, a new tool that uses maximum likelihood evolutionary rate estimation for position-specific scoring and, in contrast to previous bottom-up methods, a novel dynamic programming approach to subsequently define constrained elements. GERP++ evaluates a richer set of candidate element breakpoints and ranks them based on statistical significance, eliminating the need for biased heuristic extension techniques. Using GERP++ we identify over 1.3 million constrained elements spanning over 7% of the human genome. We predict a higher fraction than earlier estimates largely due to the annotation of longer constrained elements, which improves one to one correspondence between predicted elements with known functional sequences. GERP++ is an efficient and effective tool to provide both nucleotide- and element-level constraint scores within deep multiple sequence alignments

Rubrivivax benzoatilyticus sp.nov., an aromatic hydrocarbon-degrading purple betaproteobacterium

A brown-coloured bacterium was isolated from photoheterotrophic (benzoate) enrichments of flooded paddy soil from Andhra Pradesh, India. On the basis of 16S rRNA gene sequence analysis, strain JA2(T) was shown to belong to the class Betaproteobacteria, related to Rubrivivax gelatinosus (99 % sequence similarity). Cells of strain JA2(T) are Gram-negative, motile rods with monopolar single flagella. The strain contained bacteriochlorophyll a and most probably the carotenoids spirilloxanthin and sphaeroidene, but did not have internal membrane structures. Intact cells had absorption maxima at 378, 488, 520, 590, 802 and 884 nm. No growth factors were required. Strain JA2(T) grew on benzoate, 2-aminobenzoate (anthranilate), 4-aminobenzoate, 4-hydroxybenzoate, phthalate, phenylalanine, trans-cinnamate, benzamide, salicylate, cyclohexanone, cyclohexanol and cyclohexane-2-carboxylate as carbon sources and/or electron donors. The DNA G+C content was 74.9 mol%. Based on DNA-DNA hybridization studies, 16S rRNA gene sequence analysis and morphological and physiological characteristics, strain JA2(T) is different from representatives of other photosynthetic species of the Betaproteobacteria and was recognised as representing a novel species, for which the name Rubrivivax benzoatilyticus sp. nov. is proposed. The type strain is JA2(T) (=ATCC BAA-35(T)=JCM 13220(T)=MTCC 7087(T))

A Bayesian Approach to Analyse Genetic Variation within RNA Viral Populations

The development of modern and affordable sequencing technologies has allowed the study of viral populations to an unprecedented depth. This is of particular interest for the study of within-host RNA viral populations, where variation due to error-prone polymerases can lead to immune escape, antiviral resistance and adaptation to new host species. Methods to sequence RNA virus genomes include reverse transcription (RT) and polymerase chain reaction (PCR). RT-PCR is a molecular biology technique widely used to amplify DNA from an RNA template. The method itself relies on the in vitro synthesis of copy DNA from RNA followed by multiple cycles of DNA amplification. However, this method introduces artefactual errors that can act as confounding factors when the sequence data are analysed. Although there are a growing number of published studies exploring the intra- and inter-host evolutionary dynamics of RNA viruses, the complexity of the methods used to generate sequences makes it difficult to produce probabilistic statements about the likely sources of observed sequence variants. This complexity is further compounded as both the depth of sequencing and the length of the genome segment of interest increase. Here we develop a Bayesian method to characterise and differentiate between likely structures for the background viral population. This approach can then be used to identify nucleotide sites that show evidence of change in the within-host viral population structure, either over time or relative to a reference sequence (e.g. an inoculum or another source of infection), or both, without having to build complex evolutionary models. Identification of these sites can help to inform the design of more focussed experiments using molecular biology tools, such as site-directed mutagenesis, to assess the function of specific amino acids. We illustrate the method by applying to datasets from experimental transmission of equine influenza, and a pre-clinical vaccine trial for HIV-1

Transport of Babesia venatorum-infected Ixodes ricinus to Norway by northward migrating passerine birds

<p>Abstract</p> <p>Background</p> <p>Bovine babesiosis is regarded as a limited health problem for Norwegian cows, and the incidence has decreased markedly since the 1930s. Rare cases of babesiosis in splenectomised humans from infection with <it>Babesia divergens </it>and <it>B.venatorum </it>have been described. The objective of this study was to determine whether birds can introduce <it>Babesia</it>-infected ticks. There are between 30 and 85 million passerine birds that migrate to Norway every spring.</p> <p>Methods</p> <p>Passerine birds were examined for ticks at four bird observatories along the southern Norwegian coast during the spring migrations of 2003, 2004 and 2005. The presence of <it>Babesia </it>was detected in the nymphs of <it>Ixodes ricinus </it>by real-time PCR. Positive samples were confirmed using PCR, cloning and phylogenetic analyses.</p> <p>Results</p> <p>Of 512 ticks examined, real-time PCR revealed five to be positive (1.0%). Of these, four generated products that indicated the presence of <it>Babesia </it>spp.; each of these were confirmed to be from <it>Babesia venatorum </it>(EU1). Two of the four <it>B. venatorum</it>-positive ticks were caught from birds having an eastern migratory route (<it>P</it>< 0.001).</p> <p>Conclusions</p> <p>Birds transport millions of ticks across the North Sea, the Skagerrak and the Kattegat every year. Thus, even with the low prevalence of <it>Babesia</it>-infected ticks, a substantial number of infected ticks will be transported into Norway each year. Therefore, there is a continuous risk for introduction of new <it>Babesia </it>spp. into areas where <it>I. ricinus </it>can survive.</p