Literature-based discovery of diabetes- and ROS-related targets

Abstract Background Reactive oxygen species (ROS) are known mediators of cellular damage in multiple diseases including diabetic complications. Despite its importance, no comprehensive database is currently available for the genes associated with ROS. Methods We present ROS- and diabetes-related targets (genes/proteins) collected from the biomedical literature through a text mining technology. A web-based literature mining tool, SciMiner, was applied to 1,154 biomedical papers indexed with diabetes and ROS by PubMed to identify relevant targets. Over-represented targets in the ROS-diabetes literature were obtained through comparisons against randomly selected literature. The expression levels of nine genes, selected from the top ranked ROS-diabetes set, were measured in the dorsal root ganglia (DRG) of diabetic and non-diabetic DBA/2J mice in order to evaluate the biological relevance of literature-derived targets in the pathogenesis of diabetic neuropathy. Results SciMiner identified 1,026 ROS- and diabetes-related targets from the 1,154 biomedical papers (http://jdrf.neurology.med.umich.edu/ROSDiabetes/). Fifty-three targets were significantly over-represented in the ROS-diabetes literature compared to randomly selected literature. These over-represented targets included well-known members of the oxidative stress response including catalase, the NADPH oxidase family, and the superoxide dismutase family of proteins. Eight of the nine selected genes exhibited significant differential expression between diabetic and non-diabetic mice. For six genes, the direction of expression change in diabetes paralleled enhanced oxidative stress in the DRG. Conclusions Literature mining compiled ROS-diabetes related targets from the biomedical literature and led us to evaluate the biological relevance of selected targets in the pathogenesis of diabetic neuropathy.http://deepblue.lib.umich.edu/bitstream/2027.42/78315/1/1755-8794-3-49.xmlhttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/2/1755-8794-3-49-S7.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/3/1755-8794-3-49-S10.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/4/1755-8794-3-49-S8.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/5/1755-8794-3-49-S3.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/6/1755-8794-3-49-S1.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/7/1755-8794-3-49-S4.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/8/1755-8794-3-49-S2.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/9/1755-8794-3-49-S12.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/10/1755-8794-3-49-S11.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/11/1755-8794-3-49-S9.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/12/1755-8794-3-49-S5.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/13/1755-8794-3-49-S6.XLShttp://deepblue.lib.umich.edu/bitstream/2027.42/78315/14/1755-8794-3-49.pdfPeer Reviewe

The impacts of increased heat stress events on wheat yield under climate change in China

China is the largest wheat producing country in the world. Wheat is one of the two major staple cereals consumed in the country and about 60% of Chinese population eats the grain daily. To safeguard the production of this important crop, about 85% of wheat areas in the country are under irrigation or high rainfall conditions. However, wheat production in the future will be challenged by the increasing occurrence and magnitude of adverse and extreme weather events. In this paper, we present an analysis that combines outputs from a wide range of General Circulation Models (GCMs) with observational data to produce more detailed projections of local climate suitable for assessing the impact of increasing heat stress events on wheat yield. We run the assessment at 36 representative sites in China using the crop growth model CSM-CropSim Wheat of DSSAT 4.5. The simulations based on historical data show that this model is suitable for quantifying yield damages caused by heat stress. In comparison with the observations of baseline 1996-2005, our simulations for the future indicate that by 2100, the projected increases in heat stress would lead to an ensemble-mean yield reduction of –7.1% (with a probability of 80%) and –17.5% (with a probability of 96%) for winter wheat and spring wheat, respectively, under the irrigated condition. Although such losses can be fully compensated by CO2 fertilization effect as parameterized in DSSAT 4.5, a great caution is needed in interpreting this fertilization effect because existing crop dynamic models are unable to incorporate the effect of CO2 acclimation (the growth enhancing effect decreases over time) and other offsetting forces

An enigma in the genetic responses of plants to salt stresses

Soil salinity is one of the main factors restricting crop production throughout the world. Various salt tolerance traits and the genes controlling these traits are responsible for coping with salinity stress in plants. These coping mechanisms include osmotic tolerance, ion exclusion, and tissue tolerance. Plants exposed to salinity stress sense the stress conditions, convey specific stimuli signals, and initiate responses against stress through the activation of tolerance mechanisms that include multiple genes and pathways. Advances in our understanding of the genetic responses of plants to salinity and their connections with yield improvement are essential for attaining sustainable agriculture. Although a wide range of studies have been conducted that demonstrate genetic variations in response to salinity stress, numerous questions need to be answered to fully understand plant tolerance to salt stress. This chapter provides an overview of previous studies on the genetic control of salinity stress in plants, including signaling, tolerance mechanisms, and the genes, pathways, and epigenetic regulators necessary for plant salinity tolerance

Taper-free and kinked germanium nanowires grown on silicon via purging and the two-temperature process

We investigate the growth procedures for achieving taper-free and kinked germanium nanowires epitaxially grown on silicon substrates by chemical vapor deposition. Singly and multiply kinked germanium nanowires consisting of 111 segments were formed by employing a reactant gas purging process. Unlike non-epitaxial kinked nanowires, a two-temperature process is necessary to maintain the taper-free nature of segments in our kinked germanium nanowires on silicon. As an application, nanobridges formed between (111) side walls of V-grooved (100) silicon substrates have been demonstrated