Linear fuzzy gene network models obtained from microarray data by exhaustive search

BACKGROUND: Recent technological advances in high-throughput data collection allow for experimental study of increasingly complex systems on the scale of the whole cellular genome and proteome. Gene network models are needed to interpret the resulting large and complex data sets. Rationally designed perturbations (e.g., gene knock-outs) can be used to iteratively refine hypothetical models, suggesting an approach for high-throughput biological system analysis. We introduce an approach to gene network modeling based on a scalable linear variant of fuzzy logic: a framework with greater resolution than Boolean logic models, but which, while still semi-quantitative, does not require the precise parameter measurement needed for chemical kinetics-based modeling. RESULTS: We demonstrated our approach with exhaustive search for fuzzy gene interaction models that best fit transcription measurements by microarray of twelve selected genes regulating the yeast cell cycle. Applying an efficient, universally applicable data normalization and fuzzification scheme, the search converged to a small number of models that individually predict experimental data within an error tolerance. Because only gene transcription levels are used to develop the models, they include both direct and indirect regulation of genes. CONCLUSION: Biological relationships in the best-fitting fuzzy gene network models successfully recover direct and indirect interactions predicted from previous knowledge to result in transcriptional correlation. Fuzzy models fit on one yeast cell cycle data set robustly predict another experimental data set for the same system. Linear fuzzy gene networks and exhaustive rule search are the first steps towards a framework for an integrated modeling and experiment approach to high-throughput "reverse engineering" of complex biological systems

Evolutionary History and Attenuation of Myxoma Virus on Two Continents

The attenuation of myxoma virus (MYXV) following its introduction as a biological control into the European rabbit populations of Australia and Europe is the canonical study of the evolution of virulence. However, the evolutionary genetics of this profound change in host-pathogen relationship is unknown. We describe the genome-scale evolution of MYXV covering a range of virulence grades sampled over 49 years from the parallel Australian and European epidemics, including the high-virulence progenitor strains released in the early 1950s. MYXV evolved rapidly over the sampling period, exhibiting one of the highest nucleotide substitution rates ever reported for a double-stranded DNA virus, and indicative of a relatively high mutation rate and/or a continually changing selective environment. Our comparative sequence data reveal that changes in virulence involved multiple genes, likely losses of gene function due to insertion-deletion events, and no mutations common to specific virulence grades. Hence, despite the similarity in selection pressures there are multiple genetic routes to attain either highly virulent or attenuated phenotypes in MYXV, resulting in convergence for phenotype but not genotype. © 2012 Kerr et al

Visualizing sound emission of elephant vocalizations: evidence for two rumble production types

Recent comparative data reveal that formant frequencies are cues to body size in animals, due to a close relationship between formant frequency spacing, vocal tract length and overall body size. Accordingly, intriguing morphological adaptations to elongate the vocal tract in order to lower formants occur in several species, with the size exaggeration hypothesis being proposed to justify most of these observations. While the elephant trunk is strongly implicated to account for the low formants of elephant rumbles, it is unknown whether elephants emit these vocalizations exclusively through the trunk, or whether the mouth is also involved in rumble production. In this study we used a sound visualization method (an acoustic camera) to record rumbles of five captive African elephants during spatial separation and subsequent bonding situations. Our results showed that the female elephants in our analysis produced two distinct types of rumble vocalizations based on vocal path differences: a nasally- and an orally-emitted rumble. Interestingly, nasal rumbles predominated during contact calling, whereas oral rumbles were mainly produced in bonding situations. In addition, nasal and oral rumbles varied considerably in their acoustic structure. In particular, the values of the first two formants reflected the estimated lengths of the vocal paths, corresponding to a vocal tract length of around 2 meters for nasal, and around 0.7 meters for oral rumbles. These results suggest that African elephants may be switching vocal paths to actively vary vocal tract length (with considerable variation in formants) according to context, and call for further research investigating the function of formant modulation in elephant vocalizations. Furthermore, by confirming the use of the elephant trunk in long distance rumble production, our findings provide an explanation for the extremely low formants in these calls, and may also indicate that formant lowering functions to increase call propagation distances in this species'

Diversity begets diversity: chemical and microbial diversity co-vary in freshwater to influence ecosystem functioning

Invisible to the naked eye lies a tremendous diversity of organic molecules and organisms that make major contributions to important biogeochemical cycles. However, how the diversity and composition of these two communities are inter-linked remains poorly characterised in freshwaters, despite the potential for chemical and microbial diversity to promote one another. Here we exploited gradients in chemodiversity within a common microbial pool to test how chemical and biological diversity covary and characterized the implications for ecosystem functioning. We found that both chemodiversity and genes associated with organic matter decomposition increased as more plant litterfall accumulated in experimental lake sediments, consistent with scenarios of future environmental change. Chemical and microbial diversity were also positively correlated, with dissolved organic matter having stronger effects on microbes than vice versa. Under our experimental scenarios that increased sediment organic matter from 5 to 25% or darkened overlying waters by 2.5-times, the resulting increases in chemodiversity could increase greenhouse gas concentrations in lake sediments by an average of 1.5- to 2.7-times, when all the other effects of litterfall and water color were considered. Our results open a major new avenue for research in aquatic ecosystems by exposing connections between chemical and microbial diversity and their implications for the global carbon cycle in greater detail than ever before.Funding came from a Natural Environment Research Council grant NE/L006561/1 to AJT and a Gates Cambridge Scholarship to AF

Monitoring of International Space Station Telemetry Using Shewhart Control Charts

Shewhart control charts have been established as an expedient method for analyzing dynamic, trending data in order to identify anomalous subsystem performance as soon as such performance would exceed a statistically established baseline. Additionally, this leading indicator tool integrates a selection methodology that reduces false positive indications, optimizes true leading indicator events, minimizes computer processor unit duty cycles, and addresses human factor concerns (i.e., the potential for flight-controller data overload). This innovation leverages statistical process control, and provides a relatively simple way to allow flight controllers to focus their attention on subtle system changes that could lead to dramatic off-nominal system performance. Finally, this capability improves response time to potential hardware damage and/or crew injury, thereby improving space flight safety. Shewhart control charts require normalized data. However, the telemetry from the ISS Early External Thermal Control System (EETCS) was not normally distributed. A method for normalizing the data was implemented, as was a means of selecting data windows, the number of standard deviations (Sigma Level), the number of consecutive points out of limits (Sequence), and direction (increasing or decreasing trend data). By varying these options, and treating them like dial settings, the number of nuisance alerts and leading indicators were optimized. The goal was to capture all leading indicators while minimizing the number of nuisances. Lean Six Sigma (L6S) design of experiment methodologies were employed. To optimize the results, Perl programming language was used to automate the massive amounts of telemetry data, control chart plots, and the data analysis

The Determination Of Reddening From Intrinsic VR Colors Of RR Lyrae Stars

New R-band observations of 21 local field RR Lyrae variable stars are used to explore the reliability of minimum light (V-R) colors as a tool for measuring interstellar reddening. For each star, R-band intensity mean magnitudes and light amplitudes are presented. Corresponding V-band light curves from the literature are supplemented with the new photometry, and (V-R) colors at minimum light are determined for a subset of these stars as well as for other stars in the literature. Two different definitions of minimum light color are examined, one which uses a Fourier decomposition to the V and R light curves to find (V-R) at minimum V-band light, (V-R)_{min}^F, and the other which uses the average color between the phase interval 0.5-0.8, (V-R)_{min}^{\phi(0.5-0.8)}. From 31 stars with a wide range of metallicities and pulsation periods, the mean dereddened RR Lyrae color at minimum light is (V-R)_{min,0}^F = 0.28 pm 0.02 mag and (V-R)_{min,0}^{\phi(0.5-0.8)} = 0.27 pm 0.02 mag. As was found by Guldenschuh et al. (2005) using (V-I) colors, any dependence of the star's minimum light color on metallicity or pulsation amplitude is too weak to be formally detected. We find that the intrinsic (V-R) of Galactic bulge RR Lyrae stars are similar to those found by their local counterparts and hence that Bulge RR0 Lyrae stars do not have anomalous colors as compared to the local RR Lyrae stars.Comment: accepted by A

Optimized unconventional superconductivity in a molecular Jahn-Teller metal

Understanding the relationship between the superconducting, the neighboring insulating, and the normal metallic state above Tc is a major challenge for all unconventional superconductors. The molecular A3C60 fulleride superconductors have a parent antiferromagnetic insulator in common with the atom-based cuprates, but here, the C603– electronic structure controls the geometry and spin state of the structural building unit via the on-molecule Jahn-Teller effect. We identify the Jahn-Teller metal as a fluctuating microscopically heterogeneous coexistence of both localized Jahn-Teller–active and itinerant electrons that connects the insulating and superconducting states of fullerides. The balance between these molecular and extended lattice features of the electrons at the Fermi level gives a dome-shaped variation of Tc with interfulleride separation, demonstrating molecular electronic structure control of superconductivity

Revisiting Solid-solid Phase Transitions in Sodium and Potassium Tetrafluoroborate for Thermal Energy Storage

In situ synchrotron powder x-ray diffraction (PXRD) study was conducted on sodium and potassium tetrafluoroborate (NaBF4 and KBF4) to elucidate structural changes across solid-solid phase transitions over multiple heating-cooling cycles. The phase transition temperatures from diffraction measurements are consistent with the differential scanning calorimetry data (~240 °C for NaBF4 and ~290 °C for KBF4). The crystal structure of the high-temperature (HT) NaBF4 phase has been determined from synchrotron PXRD data. The HT disordered phase of NaBF4 crystallizes in the hexagonal, space group P63/mmc (No. 194) with a = 4.98936(2) Å, c = 7.73464(4) Å, V = 166.748(2) Å3, and Z = 2 at 250 °C. Density functional theory molecular dynamics (MD) calculations imply that the P63/mmc is indeed a stable structure for rotational NaBF4. MD simulations reproduce experimental phase sequence upon heating and indicates that F atoms are markedly more mobile than K and B atoms in the disordered state. Thermal expansion coefficients for both phases were determined from high precision lattice parameters at elevated temperatures, as obtained from Rietveld refinement of PXRD data. Interestingly for the HT-phase of NaBF4, the structure (upon heating) contracts slightly in the a-b plane but expands in the c direction such that overall thermal expansion is positive. Thermal conductivity at room temperature were measured and the values are 0.8-1.0 W.m-1K-1 for NaBF4 and 0.55-0.65 W.m-1K-1 for KBF4. The thermal conductivity and diffusivity showed a gradual decrease up to the transition temperature and then rose slightly. Both materials show good thermal and structural stabilities over multiple heating/cooling cycles.<br/

Improved detection of global copy number variation using high density, non-polymorphic oligonucleotide probes

<p>Abstract</p> <p>Background</p> <p>DNA sequence diversity within the human genome may be more greatly affected by copy number variations (CNVs) than single nucleotide polymorphisms (SNPs). Although the importance of CNVs in genome wide association studies (GWAS) is becoming widely accepted, the optimal methods for identifying these variants are still under evaluation. We have previously reported a comprehensive view of CNVs in the HapMap DNA collection using high density 500 K EA (Early Access) SNP genotyping arrays which revealed greater than 1,000 CNVs ranging in size from 1 kb to over 3 Mb. Although the arrays used most commonly for GWAS predominantly interrogate SNPs, CNV identification and detection does not necessarily require the use of DNA probes centered on polymorphic nucleotides and may even be hindered by the dependence on a successful SNP genotyping assay.</p> <p>Results</p> <p>In this study, we have designed and evaluated a high density array predicated on the use of non-polymorphic oligonucleotide probes for CNV detection. This approach effectively uncouples copy number detection from SNP genotyping and thus has the potential to significantly improve probe coverage for genome-wide CNV identification. This array, in conjunction with PCR-based, complexity-reduced DNA target, queries over 1.3 M independent NspI restriction enzyme fragments in the 200 bp to 1100 bp size range, which is a several fold increase in marker density as compared to the 500 K EA array. In addition, a novel algorithm was developed and validated to extract CNV regions and boundaries.</p> <p>Conclusion</p> <p>Using a well-characterized pair of DNA samples, close to 200 CNVs were identified, of which nearly 50% appear novel yet were independently validated using quantitative PCR. The results indicate that non-polymorphic probes provide a robust approach for CNV identification, and the increasing precision of CNV boundary delineation should allow a more complete analysis of their genomic organization.</p