Introduction and enhancement of vegetative cover at Lake Mead

Studies done by the Nevada Department of Wildlife (NDOW) and the Arizona Fish and Game between 1978 and 1981 indicate that inadequate cover may be limiting the production and survival of largemouth bass at the Lake Mead National Recreation Area (LMNRA). As a result of these studies, NDOW initiated a contract in 1986 with the Lake Mead Research Center (LMRC) to investigate means of improving habitat for game fish by introducing natural and/or artificial cover. During Phase I (1986-1987) of this contract, the shoreline of Lake Mead was surveyed for aquatic and terrestrial plant growth. Also during this time, submerged Christmas trees and Berkley Fish Habitat Modules were evaluated for their effectiveness in providing cover. Christmas trees appeared to provide cover for juvenile bluegill, a largemouth bass prey species. However, submerged trees lost their structure in about three years. Berkley Habitat Modules did not appear to be an effective form of cover. The National Park Service (NPS) asked that the introduction of artificial forms of cover not be continued until research was completed on the use of native plant material. Methods for aquatic and terrestrial plant introductions were determined during Phase II (1987-1988) of this contract. Other agencies and individuals involved in revegetation of reservoir inundation zones were contacted, and the literature was reviewed for plant material collecting procedures, planting guidelines, and site maintenance. A Plant Introduction Manual was compiled based on this information and was approved by the National Park Service for use in the Lake Mead National Recreation Area. During the winter, dormant cuttings were taken of two woody species, Goodding\u27s Willow and seepwillow baccharis (Salix gooddingii and Baccharis glutinosa) to be planted in the spring of 1988. In addition, collections were made of three emergent species (Typha angustifolia, Scirpus robustus, and Phragmites australis). Plant material was transported to the Nevada Division of Forestry (NDF) nursery where it was rooted and placed on pots for planting in May 1988. Sago pondweed (Potamogeton pectinatus) tubers were introduced into small study plots in the spring of 1987. More tubers became established and were healthier in fertilized plots than in unfertilized plots. During Phase III (1988-1989) of this study, plant material was introduced into one cove in the lower basin and two coves in the upper basin of Lake Mead in April and May of 1988. Unpredicted low lake levels resulted in the loss of many plants. Survival rates of rooted material, however, were better than those of direct cuttings of woody plants. Site selection, particularly the soils of the site, appears to play a large part in survival. Seepwillow baccharis had the highest survival rates. In addition, greenhouse studies indicate that emergent plant tubers have some tolerance to dessication. Twelve hundred sago pondweed tubers were planted in April 1988 in one cove in the upper basin, and 1,200 tubers were planted in a cove in the lower basin. Tubers had 100 percent germination success and provided 70 percent cover for fish by July 1988. Approximately 10,000 sago pondweed tubers were planted in April 1989 in Waterbarge Cove in the lower basin. Tubers were planted in water depths ranging from very shallow to 12-15 meters deep. Germination and establishment of tubers were very good in depths less than 7 meters; however, little or no germination of tubers was noted at depths greater than 7 meters. A one-acre area of shoreline was hydroseeded in October 1988. Germination and establishment of seedlings was highest where soil moisture was between 20 and 30 percent. However, many seedlings were lost when water levels began to rise in January 1989

A transcriptional sketch of a primary human breast cancer by 454 deep sequencing

Background: The cancer transcriptome is difficult to explore due to the heterogeneity of quantitative and qualitative changes in gene expression linked to the disease status. An increasing number of "unconventional" transcripts, such as novel isoforms, non-coding RNAs, somatic gene fusions and deletions have been associated with the tumoral state. Massively parallel sequencing techniques provide a framework for exploring the transcriptional complexity inherent to cancer with a limited laboratory and financial effort. We developed a deep sequencing and bioinformatics analysis protocol to investigate the molecular composition of a breast cancer poly(A)+ transcriptome. This method utilizes a cDNA library normalization step to diminish the representation of highly expressed transcripts and biology-oriented bioinformatic analyses to facilitate detection of rare and novel transcripts. Results: We analyzed over 132,000 Roche 454 high-confidence deep sequencing reads from a primary human lobular breast cancer tissue specimen, and detected a range of unusual transcriptional events that were subsequently validated by RT-PCR in additional eight primary human breast cancer samples. We identified and validated one deletion, two novel ncRNAs (one intergenic and one intragenic), ten previously unknown or rare transcript isoforms and a novel gene fusion specific to a single primary tissue sample. We also explored the non-protein-coding portion of the breast cancer transcriptome, identifying thousands of novel non-coding transcripts and more than three hundred reads corresponding to the non-coding RNA MALAT1, which is highly expressed in many human carcinomas. Conclusion: Our results demonstrate that combining 454 deep sequencing with a normalization step and careful bioinformatic analysis facilitates the discovery and quantification of rare transcripts or ncRNAs, and can be used as a qualitative tool to characterize transcriptome complexity, revealing many hitherto unknown transcripts, splice isoforms, gene fusion events and ncRNAs, even at a relatively low sequence sampling

Impacts of 21st century climate change on global air pollution-related premature mortality

Climate change modulates surface concentrations of fine particulate matter (PM2.5) and ozone (O-3), indirectly affecting premature mortality attributed to air pollution. We estimate the change in global premature mortality and years of life lost (YLL) associated with changes in surface O-3 and PM2.5 over the 21st century as a result of climate change. We use a global coupled chemistry-climate model to simulate current and future climate and the effect of changing climate on air quality. Epidemiological concentration-response relationships are applied to estimate resulting changes in premature mortality and YLL. The effect of climate change on air quality is isolated by holding emissions of air pollutants constant while allowing climate to evolve over the 21st century according to a moderate projection of greenhouse gas emissions (A1B scenario). Resulting changes in 21st century climate alone lead to an increase in simulated PM2.5 concentrations globally, and to higher (lower) O-3 concentrations over populated (remote) regions. Global annual premature mortality associated with chronic exposure to PM2.5 increases by approximately 100 thousand deaths (95 % confidence interval, CI, of 66-130 thousand) with corresponding YLL increasing by nearly 900 thousand (95 % CI, 576-1,128 thousand) years. The annual premature mortality due to respiratory disease associated with chronic O-3 exposure increases by +6,300 deaths (95 % CI, 1,600-10,400). This climate penalty indicates that stronger emission controls will be needed in the future to meet current air quality standards and to avoid higher health risks associated with climate change induced worsening of air quality over populated regions.http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000326944000011&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=8e1609b174ce4e31116a60747a720701Environmental SciencesMeteorology & Atmospheric SciencesSCI(E)EI17ARTICLE2239-25312

Whole genome resequencing reveals signatures of rapid selection in a virus-affected commercial fishery

Whole genome resequencing reveals signatures of rapid selection in a virus-affected commercial fisher

First comprehensive multi-tissue transcriptome of Cherax quadricarinatus (Decapoda: Parastacidae) reveals unexpected diversity of endogenous cellulase

The Australian freshwater crayfish species, Cherax quadricarinatus Von Martens, 1868, is an important commercial and invasive species that is also being increasingly used as a model organism to address important and interesting questions in crustacean biology. Through deep sequencing of the transcriptome of C. quadricarinatus from the hepatopancreas and four other tissues, we examine the evolution of endogenously transcribed cellulase genes and provide new insights into controversial issues regarding the nutritional biology of crayfishes. A cluster assembly approach yielded one of the highest quality transcriptome assemblies for a decapod crustacean to date. A total of 206,341,872 reads with an average read length of 80 bp were generated from sequencing the transcriptomes from the heart, kidney, hepatopancreas, nerve, and testis tissues. The assembled transcriptome contains a total of 44,525 transcripts. A total of 65 transcripts coding for carbohydrate-active enzymes (CAZy) were identified based on hidden Markov model (HMM), and a majority of them display high relative transcript abundance in the hepatopancreas tissue, supporting their role in nutrient digestion. Comprehensive phylogenetic analyses of proteins belonging to two main glycosyl hydrolase families (GH9 and GH5) suggest shared ancestry of C. quadricarinatus cellulases with other characterized crustacean cellulases. Our study significantly expands the number of known crustacean-derived CAZy-coding transcripts. More importantly, the surprising level of evolutionary diversification of these proteins in C. quadricarinatus suggests that these enzymes may have been of critical importance in the adaptation of freshwater crayfishes to new plant-based food sources as part of their successful invasion of freshwater systems from marine ancestors