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

Lipschitz Functions on Unions and Quotients of Metric Spaces

Given a finite collection $\{X_i\}_{i\in I}$ of metric spaces, each of which has finite Nagata dimension and Lipschitz free space isomorphic to $L^1$, we prove that their union has Lipschitz free space isomorphic to $L^1$. The short proof we provide is based on the Pelczy\'nski decomposition method. A corollary is a solution to a question of Kaufmann about the union of two planar curves with tangential intersection. A second focus of the paper is on a special case of this result that can be studied using geometric methods. That is, we prove that the Lipschitz free space of a union of finitely many quasiconformal trees is isomorphic to $L^1$. These geometric methods also reveal that any metric quotient of a quasiconformal tree has Lipschitz free space isomorphic to $L^1$. Finally, we analyze Lipschitz light maps on unions and metric quotients of quasiconformal trees in order to prove that the Lipschitz dimension of any such union or quotient is equal to 1.Comment: 36 pages. Updated according to comments from referee. New corrected proof of Theorem D give

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

Evaluating Recruitment of American Eel, Anguilla rostrata, to the Potomac River (Spring 2007)

Harvests of American eel along the U.S. Atlantic Coast have declined in recent years, and similar patterns have been noted in the Canadian Maritime Provinces as well as in Europe with its congener, A. anguilla (Ciccotti et al., 4 1995). Fishery independent indices of abundance have also shown a decline in American eel populations in recent years (Richkus and Whalen, 1999; Geer, 2003; Montane and Fabrizio, 2006). Possible explanations for this decline include Gulf Stream shifts, pollution, overfishing, parasites, and barriers to fish passage (Castonguay et al., 1994; Haro et al., 2000). In addition, local factors such as unfavorable wind-driven currents may affect glass eel survival on continental shelves and may have a greater impact than fishing mortality or continental climate change (Knights, 2003). Efforts to assess and manage American eel have been hampered by a lack of basic biological information, such growth rate and length at age. The ASFMC American Eel Fishery Management Plan (hereafter referred to as FMP) was adopted in 1999 and attempted to address these data gaps by encouraging coastal states to augment their American eel data collection efforts through both fishery-dependent and fishery-independent studies. Several states, including Virginia, each implemented an annual survey intended to quantify the recruitment of YOY American eel to estuarine and freshwater habitats. The development of these various state surveys began in 2000, and most were fully implemented by 2001. Besides quantifying glass eel recruitment success, these surveys have the potential to provide a more comprehensive understanding of physical and environmental factors affecting the American eel population

Role of the P2Y(13) Receptor in the Differentiation of Bone Marrow Stromal Cells into Osteoblasts and Adipocytes

Accumulating evidence indicates that extracellular nucleotides, signaling through purinergic receptors, play a significant role in bone remodeling. Mesenchymal stem cells (MSCs) express functional P2Y receptors whose expression level is regulated during osteoblast or adipocyte differentiation. P2Y13-deficient mice were previously shown to exhibit a decreased bone turnover associated with a reduction in the number of both osteoblasts and osteoclasts on the bone surfaces. We therefore examined whether P2Y13R activation was involved in the osteogenic differentiation of MSC. Our study demonstrated that ADP stimulation of P2Y13R+/+ (but not P2Y13R-/-) adherent bone marrow stromal cells (BMSCs) increased significantly the formation of alkaline phosphatase-colony-forming units (CFU-ALP) as well as the expression of osteoblastic markers (osterix, alkaline phosphatase, and collagen I) involved in the maturation of preosteoblasts into osteoblasts. The number of CFU-ALP obtained from P2Y13R-/- BMSC and the level of osteoblastic gene expression after osteogenic stimulation were strongly reduced compared to those obtained in wild-type cell cultures. In contrast, when P2Y13R-/- BMSCs were incubated in an adipogenic medium, the number of adipocytes generated and the level of adipogenic gene expression (PPARγ2 and Adipsin) were higher than those obtained in P2Y13R+/+ MSC. Interestingly, we observed a significant increase of the number of bone marrow adipocytes in tibia of P2Y13R-/- mice. In conclusion, our findings indicate that the P2Y13R plays an important role in the balance of osteoblast and adipocyte terminal differentiation of bone marrow progenitors. Therefore, the P2Y13 receptor can be considered as a new pharmacological target for the treatment of bone diseases like osteoporosis

Perspectives from the water: Utilizing fisher’s observations to inform SNE/ MA windowpane science and managemen

Within fisheries, stakeholders often have varying viewpoints regarding natural marine resources, and use different sets information to evaluate their condition. Evaluating a resource with different sets of information can lead to different conclusions. Windowpane flounder (Scophthalmus aquosus) are a managed finfish species in the northwest Atlantic whose regulations have the potential to limit harvest opportunities for target species. We analyzed commercial trip and catch information from video data to understand local densities of windowpane flounder in conjunction with fisheries independent surveys. Video monitoring data from three Rhode Island commercial fisher’s vessels and fisheries independent trawl survey data were analyzed to understand the geographic distribution of the stock as well as overlap with temporary closed areas. Biomass data from the fisheries-dependent and fisheries-independent surveys were combined with a spatial-temporal model that accounted for differences in catchability among vessels and spatial autocorrelation. A separate analysis of esti-mated discard rates with observer data was also conducted to determine how the distribution of windowpane discards in Southern New England compared to the distribution of model predicted windowpane abundance. In agreement with the fishermen’s observations, the temporary closed areas were not located where the highest densities of windowpane flounder occurred. The temporary closed areas, however, were located where the highest rates of discards occurred and thus where fishing had the greatest impact on the stock. The integration of verified fishery-dependent data with the scientific surveys has the potential to create a single set of information that is trusted by all user groups

ANNUAL REPORT 2022 - Data collection and analysis in support of single and multispecies stock assessments in Chesapeake Bay: The Chesapeake Bay Multispecies Monitoring and Assessment Program

The threats affecting living marine resources are diverse, including overfishing, climate change, and pollution. In response to long-term challenges in fisheries management, a more holistic evaluation of the natural and anthropogenic drivers of populations sizes is needed. Ecosystem management (EM), a suite of strategies that incorporate ecosystem considerations into fisheries and ecosystem management, can be difficult to implement in practice. In the Mid-Atlantic, efforts to implement EM are ongoing; one output has been the annual ‘State of the Ecosystem Report’ for the region, synthesizes available data on a variety of environmental, ecological, and socioeconomic factors. Historically, the data needed for EM in Chesapeake Bay were either incomplete or nonexistent. In 2002, the Chesapeake Bay Multispecies Monitoring and Assessment Program (ChesMMAP) was developed to assist in filling these data gaps, and ultimately to support Bay-specific species and ecosystem assessment modeling. ChesMMAP is a fishery-independent monitoring survey that uses a bottom trawl designed to sample late juvenile-to-adult fishes in the mainstem of Chesapeake Bay. Since 2002, this program has provided data on relative abundance, length, weight, sex ratio, maturity, age, and trophic interactions for several important fish species that inhabit the Bay seasonally. In this annual progress report, we synthesize available biological data on 12 bony fishes that support local recreational fisheries, including abundance (biomass and number), length- and age-structure, sex ratio, maturity stage, and diet composition. However, in 2019, the survey underwent a major redesign: VIMS took possession of a new research vessel, the R/V Virginia, and the survey bottom trawl gear was replaced with a net consistent with the gear used by other regional bottom trawl surveys (i.e., the Northeast Area Monitoring and Assessment Program and Northeast Fisheries Science Center trawl surveys). At this time, the survey stratification was revised and changes were made to the cruise schedule. During 15 calibration cruises (2019-2022), 516 paired-tows were completed, which was deemed sufficient for robust statistical analysis. Species-specific intercalibrations have been conducted by applying log-Gaussian Cox processes to the paired-tow data and modeling the size distribution of the population at each sampling site and the size-structured clustering of fish at small temporal and spatial scales. The manuscript describing the application to the ChesMMAP calibration data is currently in review. The ChesMMAP data inform Bay- and coast-wide fisheries management decisions and the broader use of these data in theses, dissertations, and the peer-reviewed literature contributes to a better understanding of the Bay ecosystem

PTH(1–34) treatment and/or mechanical loading have different osteogenic effects on the trabecular and cortical bone in the ovariectomized C57BL/6 mouse

In preclinical mouse models, a synergistic anabolic response to PTH(1–34) and tibia loading was shown. Whether combined treatment improves bone properties with oestrogen deficiency, a cardinal feature of osteoporosis, remains unknown. This study quantified the individual and combined longitudinal effects of PTH(1–34) and loading on the bone morphometric and densitometric properties in ovariectomised mice. C57BL/6 mice were ovariectomised at 14-weeks-old and treated either with injections of PTH(1–34); compressive loading of the right tibia; both interventions concurrently; or both interventions on alternating weeks. Right tibiae were microCT-scanned from 14 until 24-weeks-old. Trabecular metaphyseal and cortical midshaft morphometric properties, and bone mineral content (BMC) in 40 different regions of the tibia were measured. Mice treated only with loading showed the highest trabecular bone volume fraction at week 22. Cortical thickness was higher with co-treatment than in the mice treated with PTH alone. In the mid-diaphysis, increases in BMC were significantly higher with loading than PTH. In ovariectomised mice, the osteogenic benefits of co-treatment on the trabecular bone were lower than loading alone. However, combined interventions had increased, albeit regionally-dependent, benefits to cortical bone. Increased benefits were largest in the mid-diaphysis and postero-laterally, regions subjected to higher strains under compressive loads