Genomic analysis of gene regulation complexity

With multiple metazoan genomes in each family being sequenced promoter analysis is becoming a useful tool in genomic analysis. Aligning the promoter regions in the DNA of C. elegans and C. briggsae identifies conserved promoter elements. While not all promoter elements are conserved and not all conserved regions are promoter elements, we find that conservation is a useful method for determining promoter complexity. Promoter complexity identifies which genes have particularly interesting regulation, identifying gene groups with a strong promoter complexity signal and cases where a gene\u27s promoter complexity differs from the group\u27s promoter complexity. We identify potential promoter sequence by several local sequence alignment methods. Instead of studying individual promoter elements we are looking at patterns of promoter complexity; the total conserved sequence for each gene gives us a measure for promoter complexity. Monte Carlo random sampling is used to identify Gene Ontology and KEGG Pathway annotated gene groups that appear to have significantly low or high complexity. Developmental genes were found to have low complexity while growth genes have high complexity. Other groups that we expected to have high significance show none at all or had low promoter complexity. Genes contributing to the extracellular region scored high in promoter complexity while basal transcription factors often scored low in complexity. Genes annotated with GO terms transcription factors, signalling genes, genes with multiple alternative splice products, and developmental genes had significant promoter scores. We examined gene expression in the published C. elegans microarray experiments and found a strong positive correlation between gene group expression variation and promoter complexity. Promoter complexity tends to be an accurate predictor of the complexity of a gene\u27s pattern of expression and also gives us another tool to find anomalous genes

EVA assembly and release of highly loaded bolts

The modification of a multi-jackbolt mechanism, Superbolt(TM), for on-orbit release of highly loaded bolts is described. Preload and release test data demonstrate that modification of a commercial product produced a solution for the deployment of the Space Station Remote Manipulator System (SSRMS) that was less expensive, faster, and lighter than other alternatives. Using the Superbolt design, virtually unlimited bolt loads can be applied or released with a standard wrench

Unilateral Pulmonary Artery Aplasia in a Pregnant Patient

Unilateral pulmonary artery aplasia is a rare anomaly. Case reports of this condition in pregnant patients are even more uncommon and the best approach to management of such patients is still unclear. We report a patient who presented with a history of dyspnea, chest pain, and hemoptysis. Imaging established the diagnosis in a newly pregnant female. Management of the pulmonary artery aplasia patient in pregnancy requires prospective evaluation of pulmonary hypertension

BEEFIN : maximizing profits from feeding beef cattle out of season

BEEFIN is a computer model that formulates profit maximising diets for finishing beef cattle to a specified carcass weight and fat thickness. It predicts cattle growth rate, feed conversion ratio, final liveweight, number of days on feed and the amount of available feedstuffs required to finish cattle to specification, The diets fulfil the animal\u27s energy, protien, mineral and roughage requirements. BEEFIN also calculates a profit and loss budget for the enterprise, performs a sensitivity analysis on changes in the price for both cattle and feed and determines the changes in feed prices needed before the composition of the diet is altered. Producers considering feeding cattle out of season can use BEEFIN to evaluate their alternative choices for feeding cattle. This free service is available through any Department of Agriculture office in the south-west

Analysis of wheat SAGE tags reveals evidence for widespread antisense transcription

BACKGROUND: Serial Analysis of Gene Expression (SAGE) is a powerful tool for genome-wide transcription studies. Unlike microarrays, it has the ability to detect novel forms of RNA such as alternatively spliced and antisense transcripts, without the need for prior knowledge of their existence. One limitation of using SAGE on an organism with a complex genome and lacking detailed sequence information, such as the hexaploid bread wheat Triticum aestivum, is accurate annotation of the tags generated. Without accurate annotation it is impossible to fully understand the dynamic processes involved in such complex polyploid organisms. Hence we have developed and utilised novel procedures to characterise, in detail, SAGE tags generated from the whole grain transcriptome of hexaploid wheat. RESULTS: Examination of 71,930 Long SAGE tags generated from six libraries derived from two wheat genotypes grown under two different conditions suggested that SAGE is a reliable and reproducible technique for use in studying the hexaploid wheat transcriptome. However, our results also showed that in poorly annotated and/or poorly sequenced genomes, such as hexaploid wheat, considerably more information can be extracted from SAGE data by carrying out a systematic analysis of both perfect and "fuzzy" (partially matched) tags. This detailed analysis of the SAGE data shows first that while there is evidence of alternative polyadenylation this appears to occur exclusively within the 3' untranslated regions. Secondly, we found no strong evidence for widespread alternative splicing in the developing wheat grain transcriptome. However, analysis of our SAGE data shows that antisense transcripts are probably widespread within the transcriptome and appear to be derived from numerous locations within the genome. Examination of antisense transcripts showing sequence similarity to the Puroindoline a and Puroindoline b genes suggests that such antisense transcripts might have a role in the regulation of gene expression. CONCLUSION: Our results indicate that the detailed analysis of transcriptome data, such as SAGE tags, is essential to understand fully the factors that regulate gene expression and that such analysis of the wheat grain transcriptome reveals that antisense transcripts maybe widespread and hence probably play a significant role in the regulation of gene expression during grain development

Cryptic introgression into the kidney saxifrage (Saxifraga hirsuta) from its more abundant sympatric congener Saxifraga spathularis, and the potential risk of genetic assimilation

Background and Aims Although hybridization can play a positive role in plant evolution, it has been shown that excessive unidirectional hybridization can result in replacement of a species’ gene pool, and even the extinction of rare species via genetic assimilation. This study examines levels of introgression between the common Saxifraga spathularis and its rarer congener S. hirsuta, which have been observed to hybridize in the wild where they occur sympatrically. Methods Seven species-specific single nucleotide polymorphisms (SNPs) were analysed in 1025 plants representing both species and their hybrid, S. × polita, from 29 sites across their ranges in Ireland. In addition, species distribution modelling was carried out to determine whether the relative abundance of the two parental species is likely to change under future climate scenarios. Key Results Saxifraga spathularis individuals tended to be genetically pure, exhibiting little or no introgression from S. hirsuta, but significant levels of introgression of S. spathularis alleles into S. hirsuta were observed, indicating that populations exhibiting S. hirsuta morphology are more like a hybrid swarm, consisting of backcrosses and F(2)s. Populations of the hybrid, S. × polita, were generally comprised of F(1)s or F(2)s, with some evidence of backcrossing. Species distribution modelling under projected future climate scenarios indicated an increase in suitable habitats for both parental species. Conclusions Levels of introgression observed in this study in both S. spathularis and S. hirsuta would appear to be correlated with the relative abundance of the species. Significant introgression of S. spathularis alleles was detected in the majority of the S. hirsuta populations analysed and, consequently, ongoing introgression would appear to represent a threat to the genetic integrity of S. hirsuta, particularly in areas where the species exists sympatrically with its congener and where it is greatly outnumbered

Contamination potential of tar sand exploitation in the western Niger-Delta of Nigeria: baseline studies

Exploitation of the tar sands in Ondo State in the Niger Delta is likely to result in some environmental contamination and adversely affect the living conditions of the farmers and fishermen in the area. Three wells were established where samples were taken at 1, 2 and 3 m depth. Although no hydrocarbon contamination was detected in the water from the surface and boreholes, saline intrusion was recorded. This study produces a baseline against which future contamination can be monitored so that preventative measures can be taken to mitigate the effects

Centers of Economic Excellence (endowed chairs) — a smart investment for South Carolina’s future

The General Assembly created a program designed to attract to South Carolina the world’s most talented researchers. This visionary initiative, the Centers of Economic Excellence Program (also known as endowed chairs) leverages state and private funds along with university-based research to drive economic growth. To date, the program has brought 12 world-class scientists or “endowed chairs” to our state’s universities. It has also established 30 Research Centers of Economic Excellence in areas such as nanotechnology, health sciences, future fuels, energy alternatives, automotive engineering and advanced fibers

An investigation into space weather impacts on UK power station transformers

It is well documented that space weather can impact electricity infrastructure, and several incidents have been observed in recent decades and directly linked to large geomagnetic storms (e.g. the Hydro Quebec incident in 1989). However, less is understood about the impact of lower-level Geomagnetically Induced Currents (GICs) on the health of transformers in the long term. Direct measurements of GIC at power stations are still quite rare, but all transformers sense and record levels of dissolved gases within the insulation, as a way of monitoring transformer health. In this study, the long term impact of geomagnetic activity on 13 power station transformers in the UK was investigated. Dissolved gas measurements between 2010-2015 were used to look for evidence of a link between degradation of the transformer insulation and heightened levels of global SYM-H and the rate of change of the horizontal magnetic field (dB/dt) as measured at the Eskdalemuir magnetometer station. First, case studies of the most significant storms in this time period were examined using dissolved gas analysis (DGA) methods, specifically the Low Energy Degradation Triangle (LEDT). These case studies were then augmented with a statistical survey, including Superposed Epoch Analysis (SEA) of multiple storm events. No evidence of a strong space weather impact can be found during this time period, likely owing to the relatively quiet nature of the Sun during this epoch and the modernity of the transformers studied