Functional rarefaction: estimating functional diversity from field data

Studies in biodiversity-ecosystem function and conservation biology have led to the development of diversity indices that take species' functional differences into account. We identify two broad classes of indices: those that monotonically increase with species richness (MSR indices) and those that weight the contribution of each species by abundance or occurrence (weighted indices). We argue that weighted indices are easier to estimate without bias but tend to ignore information provided by rare species. Conversely, MSR indices fully incorporate information provided by rare species but are nearly always underestimated when communities are not exhaustively surveyed. This is because of the well-studied fact that additional sampling of a community may reveal previously undiscovered species. We use the rarefaction technique from species richness studies to address sample-size-induced bias when estimating functional diversity indices. Rarefaction transforms any given MSR index into a family of unbiased weighted indices, each with a different level of sensitivity to rare species. Thus rarefaction simultaneously solves the problem of bias and the problem of sensitivity to rare species. We present formulae and algorithms for conducting a functional rarefaction analysis of the two most widely cited MSR indices: functional attribute diversity (FAD) and Petchey and Gaston's functional diversity (FD). These formulae also demonstrate a relationship between three seemingly unrelated functional diversity indices: FAD, FD and Rao's quadratic entropy. Statistical theory is also provided in order to prove that all desirable statistical properties of species richness rarefaction are preserved for functional rarefaction.     

Sterilization of Plants for Phytoremediation Studies by Bleach Treatment

Bleach treatment of plants was studied as a simple alternative to axenic tissue cultures for demonstrating phytodegradation of aqueous and gas-phase environmental contaminants. Parrotfeather (Myriophyllum aquaticum), spinach (Spinacia oleracea), and wheat (Triticum aestivum) were exposed to 0.525% NaC10 solutions for 15 s, then rinsed in deionized water. Plate counts indicated that 97 to 100% of viable bacteria were removed from parrotfeather and spinach. Transformation rates for 2,4,6-trinitrotoluene (TNT) by bleached and untreated parrotfeather were virtually identical. Similarly, treated and untreated spinach, wheat heads, and wheat leaves removed methyl bromide (MeBr) from air at the same rates. However, wheat root with attendant adhering soil was rendered inactive by bleach treatment. Parrotfeather roots examined by dissecting microscope and by electron microscope showed no significant damage caused by bleach treatment.     

Efficient use and recycling of the micronutrient iodide in mammals

Daily ingestion of iodide alone is not adequate to sustain production of the thyroid hormones, tri- and tetraiodothyronine. Proper maintenance of iodide in vivo also requires its active transport into the thyroid and its salvage from mono- and diiodotyrosine that are formed in excess during hormone biosynthesis. The enzyme iodotyrosine deiodinase responsible for this salvage is unusual in its ability to catalyze a reductive dehalogenation reaction dependent on a flavin cofactor, FMN. Initial characterization of this enzyme was limited by its membrane association, difficult purification and poor stability. The deiodinase became amenable to detailed analysis only after identification and heterologous expression of its gene. Site-directed mutagenesis recently demonstrated that cysteine residues are not necessary for enzymatic activity in contrast to precedence set by other reductive dehalogenases. Truncation of the N-terminal membrane anchor of the deiodinase has provided a soluble and stable source of enzyme sufficient for crystallographic studies. The structure of an enzyme·substrate co-crystal has become invaluable for understanding the origins of substrate selectivity and the mutations causing thyroid disease in humans.     

Regulation of G(1) cell-cycle progression by oncogenes and tumor suppressor genes.

Progression of resting quiescent G(0) cells into early G(1) and transition across the restriction point are highly regulated processes. Mutation of proto-oncogenes and tumor suppressor genes regulating these transitions are targeted during oncogenesis. Recent work has underscored the importance of the G(0) to early G(1) transition and metabolism to neoplastic cells.     

Hyphal morphogenesis in Aspergillus nidulans

The formation of hyphae that grow solely by apical extension is a defining feature of filamentous fungi. Hyphal morphogenesis involves several key steps, including the establishment and maintenance of a stable polarity axis, as well as cell division via the deposition of septa. Several filamentous fungi have been employed in attempts to decipher the mechanisms underlying these steps. Amongst these fungi, Aspergillus nidulans has proven to be a particularly valuable model. The genetic tractability of this fungus coupled with the availability of sophisticated post-genomics resources has enabled the identification and characterization of numerous genes involved in hyphal morphogenesis. Here, we summarize current progress towards understanding the function of these genes and the mechanisms involved in polarized hyphal growth and septation in A. nidulans. We also highlight important areas for future investigation.     

The distribution of living benthic foraminifera on the continental slope and rise off southwest Norway

Surface sediment samples taken by ? corer from 45 stations on the Norwegian continental margin and in the Norway Basin have been investigated for their benthic foraminiferal content. Unlike previous studies, the living benthic foraminiferal fauna was differentiated from empty tests comprising the foraminiferal death assemblage. Factor analysis of both the living and dead faunal data reveals six living species assemblages and five corresponding dead assemblages. The additional living assemblage is characterized by the arenaceous speciesCribrostomoides subglobosum that dominates between 1400 and 2000 m water depth, but is rare in the dead faunal data.Trifarina angulosa and, to a lesser extent,Cibicides lobatulus characterize the shallowest foraminiferal assemblage from 200 to 600 m water depth, where it is associated with strong bottom currents and warm, saline Atlantic water of the North Atlantic Drift. On the slope between 600 and 1200 m water depth, theMelonis zaandami Species Assemblage dominates, particularly in areas characterized today by rapid sedimentation of terrigeneous material. Between 1000 and 1400 m depth, where the slope is covered by fine grained, organic-rich, terrigeneous mud, the living foraminiferal assemblage is characterized byCassidulina teretis andPullenia bulloides. Below 1400 m, three foraminiferal assemblages are found:C. subglobosum is found from 1400 to 2000 m,Cibicidoides wuellerstorfi andEpistominella exigua predominantly live from 2000 to 3000 m water depth, and below 3000 m,Oridorsalis umbonatus andTriloculina frigida dominate the fauna.All of theElphidium excavatum tests found in this study and theCassidulina reniforme tests found above 500 m water depth were found to be reworked.Analysis of the sediment grain-size distribution and the organic carbon content in surface samples from the deepest stations suggest that the abundance ofC. wuellerstorfi andE. exigua is positively correlated to relatively coarse (caused by planktic foraminifera) and organic-rich sediments, whereas high frequencies ofO. umbonatus andT. frigida coincide with low organic carbon content. We suggest thatC. wuellerstorfi is adapted to deep-sea environments with relatively high food supply, tolerating relatively low interstitial water oxygen content, whereasO. umbonatus may tolerate lower food supply prefering well-oxygenated interstitial waters.