Biomedical subjects

Melvin J Oliver

Publications and source records attributed to Melvin J Oliver.

4 recordsLinked to original sources

PubMed2006

Generational differences in response to desiccation stress in the desert moss Tortula inermis.

BACKGROUND AND AIMS: Active growth in post-embryonic sporophytes of desert mosses is restricted to the cooler, wetter months. However, most desert mosses have perennial gametophytes. It is hypothesized that these life history patterns are due, in part, to a reduced desiccation tolerance for sporophytes relative to gametophytes. METHODS: Gametophytes with attached post-embryonic sporophytes of Tortula inermis (early seta elongation phenophase) were exposed to two levels of desiccation stress, one rapid-dry cycle and two rapid-dry cycles, then moistened and allowed to recover, resume development, and/or regenerate for 35 d in a growth chamber. KEY RESULTS: Gametophytes tolerated the desiccation treatments well, with 93 % survival through regenerated shoot buds and/or protonemata. At the high stress treatment, a significantly higher frequency of burned leaves and browned shoots occurred. Sporophytes were far more sensitive to desiccation stress, with only 23 % surviving after the low desiccation stress treatment, and 3 % surviving after the high desiccation stress treatment. While the timing of protonemal production and sporophytic phenophases was relatively unaffected by desiccation stress, shoots exposed to one rapid-dry cycle produced shoots more rapidly than shoots exposed to two rapid-dry cycles. CONCLUSIONS: It is concluded that sporophytes of Tortula inermis are more sensitive to rapid drying than are maternal gametophytes, and that sporophyte abortion in response to desiccation results from either reduced desiccation tolerance of sporophytes relative to gametophytes, or from a termination of the sporophyte on the part of the gametophyte in response to stress.

Bryopsida↗

PubMed2005

Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST).

BACKGROUND: BLAST is one of the most common and useful tools for Genetic Research. This paper describes a software application we have termed Windows .NET Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST), which enhances the BLAST utility by improving usability, fault recovery, and scalability in a Windows desktop environment. Our goal was to develop an easy to use, fault tolerant, high-throughput BLAST solution that incorporates a comprehensive BLAST result viewer with curation and annotation functionality. RESULTS: W.ND-BLAST is a comprehensive Windows-based software toolkit that targets researchers, including those with minimal computer skills, and provides the ability increase the performance of BLAST by distributing BLAST queries to any number of Windows based machines across local area networks (LAN). W.ND-BLAST provides intuitive Graphic User Interfaces (GUI) for BLAST database creation, BLAST execution, BLAST output evaluation and BLAST result exportation. This software also provides several layers of fault tolerance and fault recovery to prevent loss of data if nodes or master machines fail. This paper lays out the functionality of W.ND-BLAST. W.ND-BLAST displays close to 100% performance efficiency when distributing tasks to 12 remote computers of the same performance class. A high throughput BLAST job which took 662.68 minutes (11 hours) on one average machine was completed in 44.97 minutes when distributed to 17 nodes, which included lower performance class machines. Finally, there is a comprehensive high-throughput BLAST Output Viewer (BOV) and Annotation Engine components, which provides comprehensive exportation of BLAST hits to text files, annotated fasta files, tables, or association files. CONCLUSION: W.ND-BLAST provides an interactive tool that allows scientists to easily utilizing their available computing resources for high throughput and comprehensive sequence analyses. The install package for W.ND-BLAST is freely downloadable from http://liru.ars.usda.gov/mainbioinformatics.html. With registration the software is free, installation, networking, and usage instructions are provided as well as a support forum.

Algorithms↗

PubMed2004

The rehydration transcriptome of the desiccation-tolerant bryophyte Tortula ruralis: transcript classification and analysis.

BACKGROUND: The cellular response of plants to water-deficits has both economic and evolutionary importance directly affecting plant productivity in agriculture and plant survival in the natural environment. Genes induced by water-deficit stress have been successfully enumerated in plants that are relatively sensitive to cellular dehydration, however we have little knowledge as to the adaptive role of these genes in establishing tolerance to water loss at the cellular level. Our approach to address this problem has been to investigate the genetic responses of plants that are capable of tolerating extremes of dehydration, in particular the desiccation-tolerant bryophyte, Tortula ruralis. To establish a sound basis for characterizing the Tortula genome in regards to desiccation tolerance, we analyzed 10,368 expressed sequence tags (ESTs) from rehydrated rapid-dried Tortula gametophytes, a stage previously determined to exhibit the maximum stress induced change in gene expression. RESULTS: The 10, 368 ESTs formed 5,563 EST clusters (contig groups representing individual genes) of which 3,321 (59.7%) exhibited similarity to genes present in the public databases and 2,242 were categorized as unknowns based on protein homology scores. The 3,321 clusters were classified by function using the Gene Ontology (GO) hierarchy and the KEGG database. The results indicate that the transcriptome contains a diverse population of transcripts that reflects, as expected, a period of metabolic upheaval in the gametophyte cells. Much of the emphasis within the transcriptome is centered on the protein synthetic machinery, ion and metabolite transport, and membrane biosynthesis and repair. Rehydrating gametophytes also have an abundance of transcripts that code for enzymes involved in oxidative stress metabolism and phosphorylating activities. The functional classifications reflect a remarkable consistency with what we have previously established with regards to the metabolic activities that are important in the recovery of the gametophytes from desiccation. A comparison of the GO distribution of Tortula clusters with an identical analysis of 9,981 clusters from the desiccation sensitive bryophyte species Physcomitrella patens, revealed, and accentuated, the differences between stressed and unstressed transcriptomes. Cross species sequence comparisons indicated that on the whole the Tortula clusters were more closely related to those from Physcomitrella than Arabidopsis (complete genome BLASTx comparison) although because of the differences in the databases there were more high scoring matches to the Arabidopsis sequences. The most abundant transcripts contained within the Tortula ESTs encode Late Embryogenesis Abundant (LEA) proteins that are normally associated with drying plant tissues. This suggests that LEAs may also play a role in recovery from desiccation when water is reintroduced into a dried tissue. CONCLUSION: The establishment of a rehydration EST collection for Tortula ruralis, an important plant model for plant stress responses and vegetative desiccation tolerance, is an important step in understanding the genome level response to cellular dehydration. The type of transcript analysis performed here has laid the foundation for more detailed functional and genome level analyses of the genes involved in desiccation tolerance in plants.

Arabidopsis↗

PubMed2003

High-throughput DNA extraction method suitable for PCR.

PCR has become one of the most popular techniques in functional genomics. Projects in both forward and reverse genetics routinely require PCR amplification of thousands of samples. Processing samples to extract DNA of sufficient purity for PCR is often a limiting step. We have developed a simple 96-well plate-based high-throughput DNA extraction method that is applicable to many plant species. The method involves a simple incubation of plant tissue samples in a DNA extraction buffer followed by a neutralization step. With the addition of a modified PCR buffer, the extracted DNA enabled the robust amplification of genomic fragments from samples of Arabidopsis, tobacco, sorghum, cotton, moss, and even pine needles. Several thousand DNA samples can be economically processed in a single day by one person without the use of robotics. This procedure will facilitate many technologies including high-throughput genotyping, map-based cloning, and identification of T-DNA or transposon-tagged mutants for known gene sequences.

Algorithms↗