Sub-fossils of cladocerans in the surface sediment of 135 lakes as proxies for community structure of zooplankton,fish abundance and lake temperature

To elucidate the possibilities of using zooplankton remains in the surface sediment to describe present-days community structure and population dynamics of zooplankton, fish abundance and temperature, we compared contemporary data sampled in the pelagial during summer with the sediment record from the upper 1 cm of the sediment in 135 lakes covering a latitude gradient from Greenland in the north to New Zealand in the south. The abundance of three genera Bosmina, Daphnia and Ceriodaphnia of the total pool of ephippia was significantly related to the total abundance of the same taxa in the pelagic zone. However, in most lakes the abundance of Ceriodaphnia was higher in the sediment than in the water, which may be attributed to the overall preference by this genus for the littoral habitat. Using contemporary data from 27 Danish lakes sampled fortnightly during summer for 10 years, we found substantial inter-annual variations in the abundance of Daphnia spp., Ceriodaphnia spp., B. longirostris and B. coregoni. Yet, the sediment record mimicked the medium level well for most of the lakes, which suggests that the sediment record provides an integrated picture of the pelagic cladoceran community, which otherwise can be obtained only by long-term frequent contemporary sampling for several years. The contribution of Daphnia to the sum of Daphnia and Bosmina ephippia was negatively correlated with the abundance of fish expressed as catch per night in multi-mesh sized gill nets (CPUE). Yet, region-specific differences occurred, which partly could be eliminated by including nutrient state expressed as total phosphorus (TP) in a multiple regression. The average ratio of ephippia to the sum of ephippia and carapaces of Bosmina varied 40-fold between the sampling regions and was significantly negatively related to summer mean air temperature, and for Danish lakes also, albeit weakly, to fish CPUE but not to chlorophyll a. Apparently, temperature is the most important factor determining the ratio of parthenogenetic to ephippia producing specimens of Bosmina. We conclude that the sediment record of cladocerans is a useful indicator of community structure of pelagic cladocerans and the abundance of fish and temperature.     

The relationship between population density, habitat position and habitat breadth within a neotropical forest bird community

We examined the relationship between local abundance, habitat position and habitat breadth across bird species in a large Atlantic forest reserve in Brazil. This appears to be the first such study for any rainforest taxon. Habitat position for a species was its mean foraging height, along with the mean scores on three principal habitat axes for census stations at which it was recorded. Habitat breadth was the standard deviation of recorded foraging heights and the standard deviations of "positive" station scores on the habitat axes. We also examined differences in habitat position and breadth between endemic and wide-ranging taxa and amongst dietary groups. Amongst 31 species for which density estimation was possible, there were no correlations between local abundance and breadth of habitat use on any of the habitat axes. Breadth of habitat used did not vary with degree of endemism, but herbivores used a greater breadth of habitats on the axis describing canopy closure than did omnivores. Habitat position did not vary with endemic status, but herbivores preferred higher-biomass habitats than faunivores, and higher foraging heights than either faunivores or omnivores. Local abundance was linked weakly to habitat position with commoner species tending to forage in the lower strata of open-canopied areas. The 31 most commonly recorded species tended to occupy "middle-range" habitat positions, while 28 rarer species occupied habitats toward one or other end of the vegetation axes. These results suggest an association between the local abundance of a species and its habitat position, and especially its preference for common or mid-range habitats, rather than with its ability to utilise a wide range of habitats.     

Role of skin blood flow and sweating rate in exercise thermoregulation after bed rest.

Two potential mechanisms, reduced skin blood flow (SBF) and sweating rate (SR), may be responsible for elevated intestinal temperature (T(in)) during exercise after bed rest and spaceflight. Seven men underwent 13 days of 6 degrees head-down bed rest. Pre- and post-bed rest, subjects completed supine submaximal cycle ergometry (20 min at 40% and 20 min at 65% of pre-bed rest supine peak exercise capacity) in a thermoneutral room. After bed rest, T(in) was elevated at rest (+0.31 +/- 0.12 degrees C) and at the end of exercise (+0.33 +/- 0.07 degrees C). Percent increase in SBF during exercise was less after bed rest (211 +/- 53 vs. 96 +/- 31%; P < or = 0.05), SBF/T(in) threshold was greater (37.09 +/- 0.16 vs. 37.33 +/- 0.13 degrees C; P < or = 0.05), and slope of SBF/T(in) tended to be reduced (536 +/- 184 vs. 201 +/- 46%/ degrees C; P = 0.08). SR/T(in) threshold was delayed (37.06 +/- 0.11 vs. 37.34 +/- 0.06 degrees C; P < or = 0.05), but the slope of SR/T(in) (3.45 +/- 1.22 vs. 2.58 +/- 0.71 mg x min-1 x cm-2 x degrees C-1) and total sweat loss (0.42 +/- 0.06 vs. 0.44 +/- 0.08 kg) were not changed. The higher resting and exercise T(in) and delayed onset of SBF and SR suggest a centrally mediated elevation in the thermoregulatory set point during bed rest exposure.     

Genetic structure and dispersal of Macrobrachium australiense (Decapoda: Palaemonidae) in western Queensland, Australia

SUMMARY 1. The freshwater prawn, Macrobrachium australiense (Decapoda: Palaemonidae), is an abundant species throughout the rivers of western Queensland, and it is thought to have effective dispersal capabilities. Given the very low topographical relief of the western Queensland landscape and the vast nature of episodic flooding, it was predicted that widespread dispersal in this species would occur within, and possibly between the four major catchments of the region: the Darling, Bulloo, Cooper and Diamantina. We analysed eight polymorphic allozyme systems and a fragment of the cytochrome c oxidase subunit 1 (COI) mitochondrial DNA (mtDNA) gene to determine the extent of recent and historical patterns of dispersal at nested spatial scales, within and between catchments.
2. Large and significant levels of allozyme and mtDNA differentiation were revealed among all catchments, indicating that dispersal of M. australiense does not occur across catchment boundaries, although this species is reportedly capable of overland movement. In contrast, no significant patterns of genetic differentiation were resolved between major subcatchments of the Darling and Cooper, or between sites within these subcatchments, indicating that populations of M. australiense are panmictic within catchments.
3. The MtDNA data resolved two divergent and reciprocally monophyletic clades, with the first representing the Darling catchment, and the second corresponding to the Bulloo, Cooper and Diamantina catchments. We postulate that extreme variation in historical climatic patterns and palaeohydrologic conditions played an important role in shaping the population structure of M. australiense throughout western Queensland during the Quaternary.     

Conduction pathways in microtubules, biological quantum computation, and consciousness.

Technological computation is entering the quantum realm, focusing attention on biomolecular information processing systems such as proteins, as presaged by the work of Michael Conrad. Protein conformational dynamics and pharmacological evidence suggest that protein conformational states-fundamental information units ('bits') in biological systems-are governed by quantum events, and are thus perhaps akin to quantum bits ('qubits') as utilized in quantum computation. 'Real time' dynamic activities within cells are regulated by the cell cytoskeleton, particularly microtubules (MTs) which are cylindrical lattice polymers of the protein tubulin. Recent evidence shows signaling, communication and conductivity in MTs, and theoretical models have predicted both classical and quantum information processing in MTs. In this paper we show conduction pathways for electron mobility and possible quantum tunneling and superconductivity among aromatic amino acids in tubulins. The pathways within tubulin match helical patterns in the microtubule lattice structure, which lend themselves to topological quantum effects resistant to decoherence. The Penrose-Hameroff 'Orch OR' model of consciousness is reviewed as an example of the possible utility of quantum computation in MTs.     

MODBASE, a database of annotated comparative protein structure models

MODBASE (http://guitar.rockefeller.edu/modbase) is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on PSI-BLAST, IMPALA and MODELLER. MODBASE uses the MySQL relational database management system for flexible and efficient querying, and the MODVIEW Netscape plugin for viewing and manipulating multiple sequences and structures. It is updated regularly to reflect the growth of the protein sequence and structure databases, as well as improvements in the software for calculating the models. For ease of access, MODBASE is organized into different datasets. The largest dataset contains models for domains in 304 517 out of 539 171 unique protein sequences in the complete TrEMBL database (23 March 2001); only models based on significant alignments (PSI-BLAST E-value < 10^–4) and models assessed to have the correct fold are included. Other datasets include models for target selection and structure-based annotation by the New York Structural Genomics Research Consortium, models for prediction of genes in the Drosophila melanogaster genome, models for structure determination of several ribosomal particles and models calculated by the MODWEB comparative modeling web server.     

PharmGKB: the Pharmacogenetics Knowledge Base

The Pharmacogenetics Knowledge Base (PharmGKB; http://www.pharmgkb.org/) contains genomic, phenotype and clinical information collected from ongoing pharmacogenetic studies. Tools to browse, query, download, submit, edit and process the information are available to registered research network members. A subset of the tools is publicly available. PharmGKB currently contains over 150 genes under study, 14 Coriell populations and a large ontology of pharmacogenetics concepts. The pharmacogenetic concepts and the experimental data are interconnected by a set of relations to form a knowledge base of information for pharmacogenetic researchers. The information in PharmGKB, and its associated tools for processing that information, are tailored for leading-edge pharmacogenetics research. The PharmGKB project was initiated in April 2000 and the first version of the knowledge base went online in February 2001.     

Sperm transfer during mating, movement of sperm in the female reproductive tract, and sperm precedence in the common cutworm Spodoptera litura

Abstract. Mating behaviour, sperm transfer and sperm precedence were studied in the moth Spodoptera litura (Fabr.) (Lepidoptera: Noctuidae). There existed a rhythmic, diel pattern of mating behaviour of this moth during the scotophase, presumably set with respect to an endogenous activity rhythm. Approximately 30 min after copulation had started, the formation of the corpus of the spermatophore began in the bursa copulatrix of the female moth, but full inflation of the corpus was not completed until 45–60 min after mating had started. The mature spermatophore contained about 350 eupyrene sperm bundles and a large number of individual (loose) apyrene spermatozoa. The mating status and the age of the male insect influenced the number of sperm transferred to the female within the spermatophore, and also affected the consequent fertility. There was no evidence of sperm reflux within the male tract. Within the female, dissociation of eupyrene sperm bundles was evident within the spermatophore less than 15 min after the completion of mating. Spermatozoa began to move from the bursa (in which the spermatophore is lodged) into the spermatheca 30–45 min after the end of the copulation, and the quantity of sperm in the spermatheca reached a plateau at 90 min after mating. Apyrene sperm reached the spermatheca first, followed by eupyrene sperm. Examination of total (apyrene plus eupyrene) sperm in the female tract showed that 86% of mated females received an apparently normal amount of total sperm from the male. Examination of eupyrene sperm alone showed that 81% of matings resulted in an apparently normal transfer of eupyrene sperm. A small proportion (approximately 8%) of the matings, however, were identified as transferring a clearly subnormal quantity of eupyrene sperm to the spermatheca. The eggs produced as a result of such pairings displayed much reduced fertility (about 43%) compared to those from matings confirmed to have transferred normal quantities of sperm, which showed about 92% fertility. This shows that the availability of eupyrene sperm in the spermatheca may be an important constraint on fertility in normal populations of insects. In the laboratory, S. litura females exhibited multiple matings. Of the females, 93% mated, and the mean frequency of mating was 1.69. Mating with a fertile male led to the oviposition of an increased number of eggs. This effect continued even when the female subsequently mated with an infertile male. Displacement of sperm from previous matings is known to be an important factor in the evolution of multiple mating strategies. Our results on sperm utilization by S. litura indicated that after a second mating, the sperm utilized for subsequent fertilization were almost exclusively from the last mating with little mixing. The proportion of eggs fertilized by sperm from the second mating (P₂) was calculated as 0.95, indicating almost complete sperm precedence from the last mating.