DRASTIC—INSIGHTS:querying information in a plant gene expression database

DRASTIC––Database Resource for the Analysis of Signal Transduction In Cells (http://www.drastic.org.uk/) has been created as a first step towards a data-based approach for constructing signal transduction pathways. DRASTIC is a relational database of plant expressed sequence tags and genes up- or down-regulated in response to various pathogens, chemical exposure or other treatments such as drought, salt and low temperature. More than 17700 records have been obtained from 306 treatments affecting 73 plant species from 512 peer-reviewed publications with most emphasis being placed on data from Arabidopsis thaliana. DRASTIC has been developed by the Scottish Crop Research Institute and the Abertay University and allows rapid identification of plant genes that are up- or down-regulated by multiple treatments and those that are regulated by a very limited (or perhaps a single) treatment. The INSIGHTS (INference of cell SIGnaling HypoTheseS) suite of web-based tools allows intelligent data mining and extraction of information from the DRASTIC database. Potential response pathways can be visualized and comparisons made between gene expression patterns in response to various treatments. The knowledge gained informs plant signalling pathways and systems biology investigations

The trophic dynamics of summer flounder (Paralichthys dentatus) in Chesapeake Bay

Data on the trophic dynamics of fishes are needed for management of ecosystems such as Chesapeake Bay. Summer flounder (Paralichthys dentatus) are an abundant seasonal resident of the bay and have the potential to impact foodweb dynamics. Analyses of diet data for late juvenile and adult summer flounder collected from 2002−2006 in Chesapeake Bay were conducted to characterize the role of this flatfish in this estuary and to contribute to our understanding of summer flounder trophic dynamics throughout its range. Despite the diversity of prey, nearly half of the diet comprised mysid shrimp (Neomysis spp.) and bay anchovy (Anchoa mitchilli). Ontogenetic differences in diet and an increase in diet diversity with increasing fish size were documented. Temporal (inter- and intra-annual) changes were also detected, as well as trends in diet reflecting peaks in abundance and diversity of prey. The preponderance of fishes in the diet of summer flounder indicates that this species is an important piscivorous predator in Chesapeake Bay

The role of lysyl oxidase, the extracellular matrix and the pre-metastatic niche in bone metastasis

Most deaths from solid cancers occur as a result of secondary metastasis to distant sites. Bone is the primary site for many cancer types and can account for up to 80% of cancer-related deaths in certain tumours. The progression from a discrete solid primary tumour to devastating and painful bone metastases is a complex process involving multiple cell types and steps. There is increasing evidence that modulation of the extracellular matrix plays an important role in the lethal transition from a primary to disseminated metastatic bone tumour. This review provides an overview of the current understanding on the role of role of lysyl oxidase, the extracellular matrix and the pre-metastatic niche in bone metastasis.

P2X7 receptor regulates osteoclast function and bone loss in a mouse model of osteoporosis

Post-menopausal osteoporosis is a condition that affects millions worldwide and places a huge socio-economic burden on society. Previous research has shown an association of loss of function SNPs in the gene for the purinergic receptor P2X7R with low bone mineral density, increased rates of bone loss and vertebral fractures in post-menopausal women. In this study we use a mouse model of oestrogen deficiency-induced bone loss and the BALB/cJ P2X7R-/-to show that absence of the P2X7R resulted in increased bone loss. Osteoclast precursors were isolated from both BALB/cJ P2X7R-/-and BALB/cJ P2X7R+/+mice and then cultured in vitro to form mature resorbing osteoclasts. The BALB/cJ P2X7R-/-derived precursors generated slightly more osteoclasts but with a significant reduction in the amount of resorption per osteoclast. Furthermore, when using modified culture conditions osteoclast activity was additionally increased in the absence of the P2X7R suggest that P2X7R may regulate the lifespan and activity of osteoclasts. Finally using mechanical loading as an anabolic stimulus for bone formation, we demonstrated that the increased oestrogen-deficient bone loss could be rescued, even in the absence of P2X7R. This study paves the way for clinical intervention for women with post-menopausal osteoporosis and P2XR7 loss of function polymorphisms

Functional polymorphisms in the P2X7 receptor gene are associated with stress fracture injury

Context: Military recruits and elite athletes are susceptible to stress fracture injuries. Genetic predisposition has been postulated to have a role in their development. The P2X7 receptor (P2X7R) gene, a key regulator of bone remodelling, is a genetic candidate that may contribute to stress fracture predisposition. Objective: To evaluate the putative contribution of P2X7R to stress fracture injury in two separate cohorts, military personnel and elite athletes. Methods: In 210 Israeli Defence Forces (IDF) military conscripts, stress fracture injury was diagnosed (n=43) based on symptoms and a positive bone scan. In a separate cohort of 518 elite athletes, self-reported medical imaging scan-certified stress fracture injuries were recorded (n=125). Non-stress fracture controls were identified from these cohorts who had a normal bone scan or no history or symptoms of stress fracture injury. Study participants were genotyped for functional SNPs within the P2X7R gene using proprietary fluorescence-based competitive allele-specific PCR assay. Pearson Chi-square (χ2) tests, corrected for multiple comparisons, were used to assess associations in genotype frequencies. Results: The variant allele of P2X7R SNP rs3751143 (Glu496Ala- loss of function) was associated with stress fracture injury, while the variant allele of rs1718119 (Ala348Thr- gain of function) was associated with a reduced occurrence of stress fracture injury in military conscripts (P<0.05). The association of the variant allele of rs3751143 with stress fractures was replicated in elite athletes (P<0.05), whereas the variant allele of rs1718119 was also associated with reduced multiple stress fracture cases in elite athletes (P<0.05). Conclusions: The association between independent P2X7R polymorphisms with stress fracture prevalence supports the role of a genetic predisposition in the development of stress fracture injury

Identification of a Candidate CD5 Homologue in the Amphibian Xenopus laevis

We identified a novel T cell Ag in the South African clawed toad (Xenopus laevis) by a mAb designated 2B1. This Ag is present in relatively high levels on most thymocytes, approximately 65% of splenocytes, 55% of PBL, and 65% of intestinal lymphocytes, but is rarely seen on IgM+ B cells in any of these tissues. Lymphocytes bearing the 2B1 Ag proliferate in response to stimulation with Con A or PHA, whereas the 2B1- lymphocytes are reactive to LPS. Biochemical analysis indicates that this Ag is a differentially phosphorylated glycoprotein of 71 to 82 kDa. The protein core of 64 kDa bears both N- and O-linked carbohydrate side chains. The amino-terminal protein sequence of the 2B1 Ag shares significant homology with both the macrophage scavenger receptor type 1 motif and the mammalian CD5/CD6 family. The biochemical characteristics and cellular distribution of the 2B1 Ag suggest that it represents the CD5 homologue in X. laevis. While T cells constitutively express this highly conserved molecule, Xenopus B cells acquire the CD5 homologue only when they are stimulated in the presence of T cell

Dataset for the proteomic inventory and quantitative analysis of the breast cancer hypoxic secretome associated with osteotropism

The cancer secretome includes all of the macromolecules secreted by cells into their microenvironment. Cancer cell secretomes are significantly different to that of normal cells reflecting the changes that normal cells have undergone during their transition to malignancy. More importantly, cancer secretomes are known to be active mediators of both local and distant host cells and play an important role in the progression and dissemination of cancer. Here we have quantitatively profiled both the composition of breast cancer secretomes associated with osteotropism, and their modulation under normoxic and hypoxic conditions. We detect and quantify 162 secretome proteins across all conditions which show differential hypoxic induction and association with osteotropism. Mass Spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the dataset identifier PXD000397 and the complete proteomic, bioinformatic and biological analyses are reported in Cox et al. (2015) [1]

Quantifying occupant energy behavior using pattern analysis techniques

Occupant energy behavior is widely agreed upon to have a major influence over the amount of energy used in buildings. Few attempts have been made to quantify this energy behavior, even though vast amounts of end-use data containing useful information lay fallow. This paper describes analysis techniques developed to extract behavioral information from collected residential end-use data. Analysis of the averages, standard deviations and frequency distributions of hourly data can yield important behavioral information. Pattern analysis can be used to group similar daily energy patterns together for a particular end-use or set of end-uses. Resulting pattern groups can then be examined statistically using multinomial logit modeling to find their likelihood of occurrence for a given set of daily conditions. These techniques were tested successfully using end-use data for families living in four heavily instrumented residences. Energy behaviors were analyzed for individual families during each heating season of the study. These behaviors (indoor temperature, ventilation load, water heating, large appliance energy, and miscellaneous outlet energy) capture how occupants directly control the residence. The pattern analysis and multinomial logit model were able to match the occupant behavior correctly 40 to 70% of the time. The steadier behaviors of indoor temperature and ventilation were matched most successfully. Simple changes to capture more detail during pattern analysis can increase accuracy for the more variable behavior patterns. The methods developed here show promise for extracting meaningful and useful information about occupant energy behavior from the stores of existing end-use data

ANNUAL REPORT - 2009 Data collection and analysis in support of single and multispecies stock assessments in Chesapeake Bay: The Chesapeake Bay Multispecies Monitoring and Assessment Program

Historically, fisheries management has been based on the results of single-species stock assessment models that focus on the interplay between exploitation level and sustainability. There currently exists a suite of standard and accepted analytical frameworks (e.g., virtual population analysis (VPA), biomass dynamic production modeling, delay difference models, etc.) for assessing the stocks, projecting future stock size, evaluating recovery schedules and rebuilding strategies for overfished stocks, setting allowable catches, and estimating fishing mortality or exploitation rates. A variety of methods also exist to integrate the biological system and the fisheries resource system, thereby enabling the evaluation of alternative management strategies on stock status and fishery performance. These well-established approaches have specific data requirements involving biological (life history), fisheriesdependent, and fisheries-independent data (Table 1). From these, there are two classes of stock assessment or modeling approaches used in fisheries: partial assessment based solely on understanding the biology of a species, and full analytical assessment including both biological and fisheries data