Description: This article discusses the characterization of sub-nuclear changes in Caenorhabditis elegans embryos exposed to brief, intermediate and long-term anoxia to analyze anoxia-induced cell cycle arrest. Abstract: Background: The soil nematode C. elegans survives oxygen-deprived conditions (anoxia; <.001 kPa O₂) by entering into a state of suspended animation in which cell cycle progression reversibly arrests. The majority of blastomeres of embryos exposed to anoxia arrest at interphase, prophase and metaphase. The spindle checkpoint proteins SAN-1 and MDF-2 are required for embryos to survive 24 hours of anoxia. To further investigate the mechanism of cell-cycle arrest, the authors examined and compared sub-nuclear changes such as chromatin localization pattern, post-translational modification of histone H3, spindle microtubules, and localization of the spindle checkpoint protein SAN-1 with respect to various anoxia exposure time points. To ensure analysis of embryos exposed to anoxia and not post-anoxic recovery the authors fixed all embryos in an anoxia glove box chamber. Results: Embryos exposed to brief periods to anoxia (30 minutes) contain prophase blastomeres with chromosomes in close proximity to the nuclear membrane, condensation of interphase chromatin and metaphase blastomeres with reduced spindle microtubules density. Embryos exposed to longer periods of anoxia (1-3 days) display several characteristics including interphase ...

Description: This article discusses root architecture and nodulation. Abstract: The Medicago truncatula LATD/NIP gene is essential for the development of lateral and primary root and nitrogen-fixing nodule meristems as well as for rhizobial invasion of nodules. LATD/NIP encodes a member of the NRT1(PTR1) nitrate and di-and tri-peptide transporter family, suggesting that its function is to transport one of these or another compound(s). Because latd/nip mutants can have their lateral and primary root defects rescued by ABA, ABA is a potential substrate for transport. LATD/NIP expression in the root meristem was demonstrated to be regulated by auxin, cytokinin and abscisic acid, but not by nitrate. LATD/NIP's potential function and its role in coordinating root architecture and nodule formation are discussed.

Description: This article discusses interpolative multidimensional scaling techniques for the identification of clusters in very large sequence sets. Abstract: Background: Modern pyrosequencing techniques make it possible to study complex bacterial populations, such as 16S rRNA, directly from environmental or clinical samples without the need for laboratory purification. Alignment of sequences across the resultant large data sets (100,000+ sequences) is of particular interest for the purpose of identifying potential gene clusters and families, but such analysis represents a daunting computational task. The aim of this work is the development of an efficient pipeline for the clustering of large sequence read sets. Methods: Pairwise alignment techniques are used here to calculate genetic distances between sequence pairs. These methods are pleasingly parallel and have been shown to more accurately reflect accurate genetic distances in highly variable regions of rRNA genes that do traditional multiple sequence alignment (MSA) approaches. By utilizing Needleman-Wunsch (NW) pairwise alignment in conjunction with novel implementations of interpolative multidimensional scaling (MDS), the authors have developed an effective method for visualizing massive biosequence data sets and quickly identifying potential gene clusters. Results: This study demonstrates the use of interpolative MDS to obtain clustering results that are qualitatively similar to those obtained through ...

Description: This presentation is part of the faculty lecture series UNT Speaks Out on Water Conservation. In this presentation, the author discusses the rivers of Cape Horn, Chile and biocultural conservation and education.

Description: This paper discusses an ad hoc query tool for relational databases. Most Web servers hosting biological data limit users to a defined set of search options and output formats that are short of the whole range of options available to users with direct database access. However, to make full use of the wealth of data in the database resource, it is desirable to have an intermediate solution that provides a broad range of flexible query and output options through a Web portal.