bluuebunny/crossref_metadata_2025 huggingface dataset:
Feeding habits of cockfish, Callorhinchus callorhynchus (Holocephali: Callorhynchidae), in Patagonian waters (Argentina)
Authors: Di Giacomo EE , Perier MR
Published: November 2005

Morphology of the main digestive features of cockfish, Callorhinchus callorhynchus, is described and linked to feeding habits. Composition of the diet and size-selective foraging of this species on scallops was studied in northern Patagonian waters and analysed in relation to depth, sex and size. Three species of bivalve molluscs (Pitar rostratus, Aequipecten tehuelchus and Ennucula puelcha) and flabelligerid polychaetes were predominant in the diet of males. The scallop Zygochlamys patagonica dominated the diet of females. The diet of juveniles consisted of small gastropods (Olivella sp.), bivalves with fragile shells (e.g. Pandora cistula), amphipods and polychaetes. Differences in food composition between sexes and between juveniles and adults are attributed to two factors: extrinsic (concerning prey availability) and intrinsic (concerning the morphology and behaviour of the predator). Size-selective foraging on two species of scallops, Aequipecten tehuelchus (subject to commercial fishing) and Zygochlamys patagonica, was found in adults; it is argued that maximum scallop prey size is constrained by the strength of the crushing apparatus of the cockfish. The diet of the cockfish is compared with that of other holocephalans. It is concluded that species of Callorhinchus can be generally characterized as benthic foragers that specialize in crushing shelled invertebrate prey.
Temporal variation in the early life-history characteristics of the King George whiting (Sillaginodes punctata) from analysis of otolith microstructure
Authors: Fowler AJ , Short DA
Published: November 2005

This study describes the duration of the settlement season, the somatic and otolith growth rates, and presettlement durations for Sillaginodes punctata at Barker Inlet, South Australia. The settlement season was from June to November, with settlement occurring in two phases over this period. Somatic growth rates ranged from <0.1 to 0.25 mm day-1 depending on age and time of year, making size (SL) a relatively poor indicator of age. Alternatively, otolith size (OL) was strongly related to age, but the linear relationships varied systematically among sampling occasions. Because of variation in somatic growth rates, the SL-OL relationships were relatively poor. The biological intercept method was used to back-calculate fish sizes from otolith increment widths for three samples of fish. These growth trajectories differed considerably, two being logistic in shape and the third being an exponential relationship. Presettlement durations increased from 80 to 130 days between June and September and were inversely related to growth rate. Settlement competence is related more to size than to age. The broad natural variation in early life-history characteristics is likely to relate to water temperature regimes along larval advection pathways through the long settlement season.
Habitat-specific distributions of some fishes in a tropical estuary
Authors: Sheaves MJ
Published: November 2005

The species richness of fishes and the distributions of six fish species were compared among four habitat types, snaggy banks, clear banks, mud banks and mid channels, in an estuary in tropical Australia. Both day and night samples were collected in fish traps, on four occasions, three months apart. On each sampling trip the highest number of species was trapped from snaggy habitats, intermediate numbers from clear banks or mud banks, and the fewest species from mid channels. Although more species occurred in night than in day samples, the pattern of difference among habitats was consistent. The probability of capture of the six most abundant species, Acanthopagrus australis, Acanthopagrus berda, Arothron manilensis, Arius argyropleuron, Epinephelus coioides and Lutjanus russelli, was compared among habitat types and between day and night samples. Overall, snag habitats tended to be associated with high probabilities of capture of a number of species, particularly A. berda and L. russelli. At night, mid channels were characterized by high numbers of A. argyropleuron. Clear and mud banks, and day samples from mid channels were associated with low numbers of most species.
Galaxias maculatus: An explanation of its biogeography
Authors: Berra TM , Crowley LELM , Ivantsoff W , Fuerst PA
Published: November 2005

Galaxias maculatus is a small diadromous fish found in Australia, New Zealand, South America and on some oceanic islands. Two hypotheses have been advanced to explain this widespread, disjunct distribution. McDowall promoted dispersal through the sea of salt-tolerant juveniles but Rosen and others claimed that the distribution reflected the break-up of Gondwana and subsequent drift of the southern continents. Allozyrne electrophoresis of muscle extracts of specimens of Galaxias maculatus from eastern and western Australia, New Zealand and Chile was used to test the hypothesis that populations of G. maculatus from the western Pacific and the eastern Pacific do not differ genetically. FST based on allele frequencies and genotypes was 0.14, suggesting only minor differentiation between eastern and western Pacific populations. Minor differentiation in allele frequency existed at some loci, but no fixation of alternative alleles has occurred. The populations examined appear to be part of the same gene pool, indicating that gene flow via dispersal through the sea occurs today. It is unlikely that South American and Australasian populations would be conspecific if they have exchanged no migrants since the break-up of Gondwana at the end of the Mesozoic.
Allozyme and mitochondrial DNA analysis of the tropical saddle-tail sea perch, Lutjanus malabaricus (Schneider), from Australian waters
Authors: Elliott NG
Published: November 2005

Samples of Lutjanus malabaricus from four localities were examined for genetic variability at 10 polymorphic allozyme loci and, after restriction fragment analysis with five enzymes detecting polymorphic cut sites, in mitochondrial DNA (mtDNA). Twenty composite mtDNA haplotypes were found, with three common haplotypes occurring in 84% of individuals examined. Significant differentiation in haplotype frequencies between individuals sampled from the east coast of Queensland and those from the Gulf of Carpentaria and the North West Shelf suggests little, if any, movement of genes through the Torres Strait since its opening about 8000 years ago. Allozyme allele frequencies differed at one locus (PGM-1*) between samples from the North West Shelf and those from the Gulf of Carpentaria. These results are consistent with a recolonization, after the last ice age, of the more northern waters of Australia from a stock off the west coast. The observation of more nuclear than mitochondrial DNA differentiation may be partly a consequence of a female bias in sex ratios. The suggested presence of multiple stocks (North West Shelf, Gulf of Carpentaria, east coast of Queensland) of L. malabaricus, a dominant component of the northern Australian finfish fishery, should be considered in future management plans.
Mass mortality of a dominant kelp (Laminariales) at Goat Island, north-eastern New Zealand
Authors: Cole RG , Babcock RC
Published: November 2005

In north-eastern New Zealand, monospecific stands of the laminarian Ecklonia radiata occupy rocky reefs at depths below 10 m on exposed shores. In the austral summer of 1992-93, mass mortalities of populations of E. radiata in the Cape Rodney to Okakari Point Marine Reserve near Leigh were recorded, in which 40-100% of the sporophytes at depths greater than 10 m died. Mortality was gradual, beginning with erosion of the laminae and ultimately progressing to the stipes, which eventually decayed. The mortality was first evident in the deepest plants and culminated in the elimination of large areas of kelp forest. The event was not associated with any previously reported mortality agents. Investigations of the effects of the mortality on other organisms are continuing.
Jaw muscles and suspensoria in the Aplochitonidae (Teleostei: Salmoniformes) and their possible phylogenetic significance
Authors: Williams RRG
Published: November 2005

Recent studies question the monophyly of the family Aplochitonidae (Aplochiton + Lovettia). This issue is important partly because of the biogeographic hypothesis required to explain the disjunct distribution of these two genera if the family is monophyletic-Aplochiton is endemic to southernmost South America and Lovettia is restricted to Tasmania. Aplochiton and Lovettia were examined as part of a larger study on the suspensorium and its muscles in the lower teleosts. This paper describes in detail, for the first time, the jaw muscles and suspensoria in Aplochiton and Lovettia. These taxa share a number of features suggesting that they may form a clade, including a ligament extending from the posterolateral surface of the angulo-articular to the maxilla and a similar adductor mandibulae. Begle's conclusion that the family is paraphyletic is assessed and found to be unsound because of poorly defined characters.
Persistence of chlorophenolic compounds from pulp and paper mill discharges in Lake Bonney, south-eastern South Australia
Authors: Van  Leeuwen JA , Nicholson BC , Hayes KP , Mulcahy DE
Published: November 2005

Chlorophenolic compounds were determined in water and sediment samples from Lake Bonney, south-eastern South Australia, following discontinuation of chlorine bleaching at the Apcel pulp mill (Kimberly-Clark Australia Pty Ltd) in September 1991. Concentrations of chlorophenolics in samples collected between July 1991 and January 1992 have already been reported. Free chlorophenolic compounds had declined rapidly in lake water by January 1992, but reductions in total concentrations (free and bound) in sediment samples were not observed. Further analyses were conducted between February 1992 and November 1993 and are reported in this paper. Both free and bound chlorophenolic compounds were detected in water and sediment samples during this period. Low concentrations (40 ng L-1) of the free form of chloroguaiacols were detected in lake water up to September 1992, whereas in March 1993 free chloroguaiacols were detected only in a drain that connects the mill to the lake and near the effluent discharge point to the lake. Most chloroguaiacols and chlorocatechols were bound and these declined in both sediments and waters during the study period.
Temperature, dissolved oxygen and stratification in a tropical reservoir, Lake Tinaroo, Northern Queensland, Australia
Authors: MacKinnon MR , Herbert BW
Published: November 2005

Thermal and oxygen depth profiles in Lake Tinaroo were measured monthly at six sites over a two-year period from May 1988 to July 1990. Lake Tinaroo exhibits thermal layering throughout most of the year. Partitioning of the water column into an oxygenated epilimnion and a deoxygenated hypolimnion was well established by October each year. Breakdown of stratification occurred in late May to June and persisted until September. From October to May multiple thermoclines (diurnal, parent) developed, particularly during still weather. Localized disruption of stratification by oxygenated, cool, denser inflows during flood events in the catchment occurred during the rainy season. Thermocline tilting was noted after prolonged periods of south-easterly winds, with a deeper thermocline/oxycline at the north-western end of the lake. South-westerly winds had a corresponding effect on the north-east of the lake. The distribution of oxygenated water and deoxygenated water, affected by seasonal stratification, thermocline tilting, upwelling and flood-mediated disruption of stratification, is of importance to recreational fisheries and the location of water intake points for urban and domestic use. Lake Tinaroo has thermal characteristics of outer tropical rather than equatorial tropical lakes, owing in part to altitude effects.
Resistance of bound chloroguaiacols and AOX from pulp mill effluent to degradation by Trichoderma harzianum isolated from Lake Bonney, south-eastern South Australia
Authors: Van  Leeuwen JA , Nicholson BC , Hayes KP , Mulcahy DE
Published: November 2005

Previous studies have shown that chlorophenolic compounds persisted in water and sediments of Lake Bonney, south-eastern South Australia, following discontinuation of chlorine bleaching at a sulfite pulp mill that discharged effluent into the lake. Although free and bound chlorophenolics were detected in the lake after discontinuation of chlorine bleaching, the predominant forms were found to be bound compounds. In assessing the persistence of chlorophenolics in the lake, fungi were isolated from the lake water and studied for their capacities to degrade these compounds. One fungus, Trichoderma harzianum, was found to be capable of reducing concentrations of spiked (free) 2,4,6-trichlorophenol, 4,5-dichloroguaiacol, 3,4,5-trichloroguaiacol and tetrachloroguaiacol in a mineral salts culture medium and concentrations of adsorbable halogenated organic compounds (AOX) attributable to the spiked compounds. This fungus was also found to be capable of dehalogenating free tetrachloroguaiacol in a mineral salts medium.
Degradation of bound chloroguaiacols present in chlorination-stage effluent from the mill by Trichoderma harzianum was not detected in this study. The inability of this fungus to degrade bound chlorophenolics demonstrates the resistance of these compounds in bound form to biodegradation and may explain the persistence of some chlorophenolics in Lake Bonney.
Spatial and seasonal distribution of eggs and larvae of sandy sprat, Hyperlophus vittatus (Clupeidae), off south-western Australia
Authors: Gaughan DJ , Fletcher WJ , Tregonning RJ
Published: November 2005

Ichthyoplankton surveys were employed to determine the distribution and spawning season of Hyperlophus vittatus off south-western Australia. Eggs and larvae of H. vittatus were sampled with 500-μm-mesh bongo-nets monthly during 1992, and less regularly during 1993, close to the beach and at 5.5 and 11 km offshore in four areas within the region of the fishery. The spatio-temporal distribution and abundance of eggs indicates that H. vittatus spawns in nearshore marine waters from May to September, with a peak in June and July. Larvae were rarer and less abundant than the eggs and therefore were less reliable indicators of spawning areas and season. Samples taken along transects across the continental shelf in July of both 1993 and 1994 indicated that H. vittatus did not spawn further than 14 km from the coast. Samples taken in July 1994 just beyond the surf zone at beaches, and at corresponding sites 5.5 km offshore, at 3.7-km intervals along 150 km of coastline indicated that H. vittatus spawns throughout the distribution of the fished stock off south-westem Australia.
Discordant patterns of morphological and genetic divergence in the 'Austrocochlea constricta' (Gastropoda: Trochidae) species complex
Authors: Parsons KE
Published: November 2005

Patterns of genetic and morphological divergence were examined among Western Australian (Abrolhos Islands and Albany) and Tasmanian members of the highly variable 'Austrocochlea constricta' species complex. Analyses of allele frequencies at 13 enzyme loci confirmed the presence of three species within this complex in Tasmania, revealing additional diagnostic differences not previously detected. Where combinations of species sympatry were examined in Tasmania, seven diagnostic loci separated A. constricta and A. brevis, four separated A. porcata and A. brevis, and one separated A. porcata and A. constricta. Western Australian animals were genetically most similar to Tasmanian A. constricta populations, separated from them by genetic distances of just 0.018 (Albany) to 0.107 (Abrolhos), despite spatial isolation over ~3000 km. These genetic distances, in addition to that separating Abrolhos and Albany populations (0.138), are considered within the range possible for allopatric conspecifics. In comparison, genetic distances separating A. constricta from sympatric A. porcata (0.191) and A. brevis (0.803) in Tasmania were much larger. However, on the basis of a range of morphological traits, which were species-diagnostic in Tasmania, Abrolhos animals most closely resembled A. porcata, and Albany animals appeared intermediate to A. porcata and A. constricta. This suggests Australia-wide discordance among genetic and morphological characters of the 'A. constricta' complex.
Biomass and litterfall of Ceriops tagal and Rhizophora mucronata in the mangrove forest of Gazi Bay, Kenya
Authors: Slim FJ , Gwada PM , Kodjo M , Hemminga MA
Published: November 2005

Biomass and (leaf) litter production of stands of Rhizophora mucronata and Ceriops tagal were assessed in an East African mangrove forest. Inundation frequency of the R. mucronata stand was twice a day (on average 575 min day-1), whereas the C. tagal stand was inundated only during spring tides (on average 116 min day-1). The highest above-ground biomass (24.9 � 4.0 kg dry weight m<.-2) was present in the R. mucronata stand, in which leaf litter production was 2.51 � 1.15 g DW mw2 day-1. Above-ground biomass and leaf litterfall in the C. tagal stand were 4.01 � 0.34 kg DW m-2 and 1.05 � 0.49 g DW m-2 day-1, respectively. There was a distinct seasonal pattern in litterfall in both stands, with lower litterfall values in the wet season. Chloride concentrations were relatively high in senescent leaves, compared with those in green leaves. The decreased litterfall during the wet periods may be related to a reduced accumulation of chloride in the leaves. The difference in inundation frequency between the R. mucronata and C. tagal stands is expected to cause a more substantial tidal export of fallen leaves from the R. mucronata stand. As nitrogen resorption before defoliation was similar for C. tagal (50.9%) and R. mucronata (50.1%), tidal flushing may cause larger nitrogen losses from the R. mucronata stand.
Acoustic assessment of the biomass of a spawning aggregation of orange roughy (Hoplostethus atlanticus, Collett) off south-eastern Australia, 1990-93
Authors: Kloser RJ , Koslow JA , Williams A
Published: November 2005

Orange roughy, which spawn in an aggregation around a seamount off north-eastem Tasmania, were surveyed acoustically with vessel-mounted and deep-tow transducers from 1990 to 1993. Orange roughy dominated at 700-900 m (95% of individuals) and were less numerous both shallower and deeper. Echo integration estimates from the vessel-mounted transducer were consistently lower than those from the deep-tow transducer by a factor of ~1.8, owing to surface bubble attenuation, vessel movement and acoustic beam thresholding among other factors. The absolute estimate from the deep-towed transducer of the prefishery orange roughy biomass (98200 t ; coefficient of variation, 6.7%) compared well with estimates from stock reduction analysis (95000 to 110000 t) and an egg survey (96900 t; CV, 47%). The acoustic surveys had lower sampling error (CV, 7-15%) than that of the egg survey and required less survey time. The present results support the use of initial absolute acoustic biomass estimates to set a management strategy for the fishery. Stock reduction analysis based on the relative acoustic estimates and catch over the four years indicated that orange roughy target strength was -50 dB � 3 dB, which is consistent with results from models of target strength and from measurements in situ and on dead specimens.
Frontiers in catchment biogeochemistry: introduction to a collection of papers
Authors: Harris Graham P.
Published: November 2005

The watershed (catchment) approach provides a powerful conceptual model for
quantitatively evaluating the structure, function and change within a
landscape or region. The values and limitations of this approach are
considered in this paper, with particular reference to the Hubbard Brook
watershed–ecosystem model. The need for informed long-term (sustained)
research is stressed; a haphazard collection of data is rarely valuable.
Team-building efforts will be needed increasingly in the future to enhance the
success of multidisciplinary teams tackling large and complex environmental
problems.
Oxygen isotopes indicate most intracellular water in log-phase
Escherichia coli
is derived from metabolism
Authors: Kreuzer-Martin Helen W. , Ehleringer James R. , Hegg Eric L.
Published: November 2005

The transport of water into and out of unicellular organisms is a seemingly simple process in which water diffuses either through pores or directly across the membrane. Because of the rates at which water can theoretically diffuse, it is generally accepted that intracellular water is indistinguishable from extracellular water. Using stable isotope ratio mass spectrometry, we directly tested this assumption. Here we demonstrate that under active growth, up to 70% of the intracellular water in log-phase
Escherichia coli
cells was actually generated during metabolism and was isotopically distinct from extracellular water. The contribution of metabolism to intracellular water was substantially less in stationary-phase or quiescent cells.
3D structure of Alzheimer's amyloid-β(1–42) fibrils
Authors: Lührs Thorsten , Ritter Christiane , Adrian Marc , Riek-Loher Dominique , Bohrmann Bernd , Döbeli Heinz , Schubert David , Riek Roland
Published: November 2005

Alzheimer's disease is the most fatal neurodegenerative disorder wherein the process of amyloid-β (Aβ) amyloidogenesis appears causative. Here, we present the 3D structure of the fibrils comprising Aβ(1–42), which was obtained by using hydrogen-bonding constraints from quenched hydrogen/deuterium-exchange NMR, side-chain packing constraints from pairwise mutagenesis studies, and parallel, in-register β-sheet arrangement from previous solid-state NMR studies. Although residues 1–17 are disordered, residues 18–42 form a β-strand–turn–β-strand motif that contains two intermolecular, parallel, in-register β-sheets that are formed by residues 18–26 (β1) and 31–42 (β2). At least two molecules of Aβ(1–42) are required to achieve the repeating structure of a protofilament. Intermolecular side-chain contacts are formed between the odd-numbered residues of strand β1 of the
n
th molecule and the even-numbered residues of strand β2 of the (
n
– 1)th molecule. This interaction pattern leads to partially unpaired β-strands at the fibrillar ends, which explains the sequence selectivity, the cooperativity, and the apparent unidirectionality of Aβ fibril growth. It also provides a structural basis for fibrillization inhibitors.
An allosteric model for heterogeneous receptor complexes: Understanding bacterial chemotaxis responses to multiple stimuli
Authors: Mello Bernardo A. , Tu Yuhai
Published: November 2005

The classical Monod-Wyman-Changeux model for homogeneous allosteric protein complex is generalized in this article to model the responses of heterogeneous receptor complexes to multiple types of ligand stimulus. We show that the recent
in vivo
experimental data of
Escherichia coli
chemotaxis responses for mutant strains with different expression levels of the chemo-receptors to different types of stimulus [Sourjik, V. & Berg, H. C. (2004)
Nature
428, 437–441] all can be explained consistently within this generalized Monod-Wyman-Changeux model. Based on the model and the existing data, responses of all of the strains (studied in this article) to the presence of any combinations of ligand (Ser and MeAsp) concentrations are predicted quantitatively for future experimental verification. Through modeling the
in vivo
response data, our study reveals important information about the properties of different types of individual receptors, as well as the composition of the cluster. The energetic contribution of the nonligand binding, cytoplasmic parts of the cluster, such as CheA and CheW, is also discussed. The generalized allosteric model provides a consistent framework in understanding signal integration and differentiation in bacterial chemotaxis. It should also be useful for studying the functions of other heterogeneous receptor complexes.
Albumin endocytosis in proximal tubule cells is modulated by angiotensin II through an AT
2
receptor-mediated protein kinase B activation
Authors: Caruso-Neves Celso , Kwon Sang-Ho , Guggino William B.
Published: November 2005

Albumin endocytosis in renal proximal tubule cells is a clathrin- and receptor-mediated mechanism that, in several pathophysiological conditions, is involved in initiating or promoting tubule-interstitial disease. Although much work has been done on this pathway, the regulation of albumin endocytosis in proximal tubule cells is not well understood. Here, we study the modulation by angiotensin II (Ang II) of albumin endocytosis in LLC-PK1, a model of proximal tubule cells. We observed that Ang II increases albumin endocytosis by ≈100% at 10
-9
M. This effect is completely reversed by 10
-9
M PD123319, a specific AT
2
receptor antagonist, but not by losartan, a specific AT
1
receptor antagonist, at concentrations up to 10
-7
M. The Ang II effect on albumin endocytosis is also reversed by: phosphoinositide 3-kinase inhibitors LY294002 (2.5 × 10
-6
M) or wortmannin (10
-7
M), the protein kinase B inhibitor (2 × 10
-5
M), and staurosporine (2 × 10
-6
M), an inhibitor of 3′-phosphoinositide-dependent kinase 1. Ang II induced the selective phosphorylation of protein kinase B (PKB) at the Thr-308 residue without a change in Ser-473 phosphorylation, a combination that leads to an increase in PKB activity. These effects were completely abolished by 3 × 10
-6
M staurosporine or 10
-8
M PD123319. Our experiments also showed that PKB is present in the membrane fraction in overnight-starved LLC-PK1 cells. Taken together, these data show that Ang II increases albumin endocytosis through an AT
2
receptor mediated by activation of PKB in the plasma membrane, which depends on the basal activity of the phosphatidyl-inositol 3-kinase.
MINISEED3
(
MINI3
), a
WRKY
family gene, and
HAIKU2
(
IKU2
), a leucine-rich repeat (
LRR
)
KINASE
gene, are regulators of seed size in
Arabidopsis
Authors: Luo Ming , Dennis Elizabeth S. , Berger Frederic , Peacock William James , Chaudhury Abed
Published: November 2005

We have identified mutant alleles of two sporophytically acting genes,
HAIKU2
(
IKU2
) and
MINISEED3
(
MINI3
). Homozygotes of these alleles produce a small seed phenotype associated with reduced growth and early cellularization of the endosperm. This phenotype is similar to that described for another seed size gene,
IKU1
.
MINI3
encodes WRKY10, a
WRKY
class transcription factor.
MINI3
promoter::
GUS
fusions show the gene is expressed in pollen and in the developing endosperm from the two nuclei stage at ≈12 hr postfertilization to endosperm cellularization at ≈96 hr.
MINI3
is also expressed in the globular embryo but not in the late heart stage of embryo development. The early endosperm expression of
MINI3
is independent of its parent of origin.
IKU2
encodes a leucine-rich repeat (LRR) KINASE (At3g19700).
IKU2
::
GUS
has a similar expression pattern to that of
MINI3
. The patterns of expression of the two genes and their similar phenotypes indicate they may operate in the same genetic pathway. Additionally, we found that both
MINI3
and
IKU2
showed decreased expression in the
iku1-1
mutant.
IKU2
expression was reduced in a
mini3-1
background, whereas
MINI3
expression was unaltered in the
iku2-3
mutant. These data suggest the successive action of the three genes
IKU1
,
IKU2
, and
MINI3
in the same pathway of seed development.
Coevolution of generalist feeding ecologies and gyrencephalic mushroom bodies in insects
Authors: Farris Sarah M. , Roberts Nathan S.
Published: November 2005

Here we demonstrate the independent acquisition of strikingly similar brain architectures across divergent insect taxa and even across phyla under similar adaptive pressures. Convoluted cortical gyri-like structures characterize the mushroom body calyces in the brains of certain species of insects; we have investigated in detail the cellular and ecological correlates of this morphology in the Scarabaeidae (scarab beetles). “Gyrencephalic” mushroom bodies with increased surface area and volume of calycal synaptic neuropils and increased intrinsic neuron number characterize only those species belonging to generalist plant-feeding subfamilies, whereas significantly smaller “lissencephalic” mushroom bodies are found in more specialist dung-feeding scarab beetles. Such changes are not unique to scarabs or herbivores, because the mushroom bodies of predatory beetles display similar morphological disparities in generalists vs. specialists. We also show that gyrencephalic mushroom bodies in generalist scarabs are not associated with an increase in the size of their primary input neuropil, the antennal lobe, or in the number of antennal lobe glomeruli but rather with an apparent increase in the density of calycal microglomeruli and the acquisition of calycal subpartitions. These differences suggest changes in calyx circuitry facilitating the increased demands on processing capability and flexibility imposed by the evolution of a generalist feeding ecology.
Streptococcal viability and diminished stress tolerance in mutants lacking the signal recognition particle pathway or YidC2
Authors: Hasona Adnan , Crowley Paula J. , Levesque Celine M. , Mair Richard W. , Cvitkovitch Dennis G. , Bleiweis Arnold S. , Brady L. Jeannine
Published: November 2005

The signal recognition particle (SRP)-translocation pathway is conserved in all three domains of life and delivers membrane and secretory proteins to the cytoplasmic membrane or endoplasmic reticulum. We determined the requirement in the cariogenic oral pathogen
Streptocococcus mutans
of the three universally conserved elements of the SRP pathway: Ffh/SRP54, scRNA, and FtsY/SRα. Previously, we reported that insertional interruption of
S. mutans ffh
was not lethal, but resulted in acid sensitivity. To test whether
S. mutans
could survive extensive disruption of the SRP pathway, single and double deletions of genes encoding Ffh, scRNA, and FtsY were generated. Without environmental stressors, all mutant strains were viable, but unlike the wild-type, none could initiate growth at pH 5.0 or in 3.5% NaCl. Survival of challenge with 0.3 mM H
2
O
2
was also diminished without
ffh
. Members of the YidC/Oxa1/Alb3 family are also ubiquitous, involved in the translocation and assembly of membrane proteins, and have been identified in prokaryotes/mitochondria/chloroplasts. Two genes encoding YidC homologs, YidC1 and YidC2, are present in streptococcal genomes with both expressed in
S. mutans
. Deletion of YidC1 demonstrated no obvious phenotype. Elimination of YidC2 resulted in a stress-sensitive phenotype similar to SRP pathway mutants. Mutants lacking both YidC2 and SRP components were severely impaired and barely able to grow, even in the absence of environmental stress. Here, we report the dispensability of the cotranslational SRP protein translocation system in a bacterium. In
S. mutans
, this pathway contributes to protection against rapid environmental challenge and may overlap functionally with YidC2.
Self renewal, expansion, and transfection of rat spermatogonial stem cells in culture
Authors: Hamra F. Kent , Chapman Karen M. , Nguyen Derek M. , Williams-Stephens Ashley A. , Hammer Robert E. , Garbers David L.
Published: November 2005

The use of a transgenic line of rats that express enhanced GFP (EGFP) exclusively in the germ line has allowed a separation of feeder layers and contaminating testis somatic cells from germ cells and the identification of a set of spermatogonial stem cell marker transcripts. With these molecular markers as a guide, we have now devised culture conditions where rat spermatogonial stem cells renew and proliferate in culture with a doubling time between 3 and 4 days. The marker transcripts increase in relative abundance as a function of time in culture, and the stem cells retain competency to colonize and develop into spermatids after transplantation to the testes of recipient rats. The cells also remain euploid after at least 12 passages. Cell lines could be isolated and cryopreserved and, upon subsequent thawing, continue to self renew. Transfection of the spermatogonial stem cells with a plasmid containing the neomycin phosphotransferase (
neo
) selectable marker resulted in selection of G418-resistant cell lines that effectively colonize recipient testes, suggesting that gene targeting is now feasible in the rat.
Quantitative mass spectral evidence for the absence of circulating brain natriuretic peptide (BNP-32) in severe human heart failure
Authors: Hawkridge Adam M. , Heublein Denise M. , Bergen H. Robert , Cataliotti Alessandro , Burnett John C. , Muddiman David C.
Published: November 2005

C-terminal brain (B-type) natriuretic peptide (BNP)-32 is a widely used clinical biomarker for the diagnosis, prognosis, and treatment of heart failure (HF). The 32-aa peptide is synthesized primarily in the atrial and ventricular myocardium and constitutes the mature biologically active form of immature BNP (pro-BNP). There has been mounting evidence that suggests BNP circulates in different structural forms that impact HF diagnosis and
in vivo
activity. Herein, we have developed and used an immunoaffinity purification assay to isolate endogenous BNP-32 from New York Heart Association class IV patient plasma for subsequent analysis by nano-liquid chromatography (LC) electrospray ionization Fourier transform ion cyclotron resonance (FT-ICR) MS. We have introduced stable isotope-labeled BNP-32 to the assayed plasma to enable quantification of endogenous levels of BNP-32. Unlike the chemically nonspecific point-of-care tests (POCTs) and RIAs used worldwide to quantify BNP-32 from plasma, FT-ICR-MS (unprecedented mass measurement accuracy) coupled with LC (retention time) affords extraordinary molecular specificity, and when combined with the use of internal standards is able to confidently identify and quantify BNP-32. The significance of this work is despite exceedingly high circulating levels of BNP-32 in the New York Heart Association class IV patients as determined by POCTs (>290 fmol/ml) nano-LC-electrospray ionization-FT-ICR-MS data did not reveal any endogenous BNP-32. These results provide molecularly specific evidence for the absence of circulating BNP-32 in advanced-stage HF patients and suggest the existence of altered forms of BNP that are contributing to the POCT values.
Climatic unpredictability and parasitism of caterpillars: Implications of global warming
Authors: Stireman J. O. , Dyer L. A. , Janzen D. H. , Singer M. S. , Lill J. T. , Marquis R. J. , Ricklefs R. E. , Gentry G. L. , Hallwachs W. , Coley P. D. , Barone J. A. , Greeney H. F. , Connahs H. , Barbosa P. , Morais H. C. , Diniz I. R.
Published: November 2005

Insect outbreaks are expected to increase in frequency and intensity with projected changes in global climate through direct effects of climate change on insect populations and through disruption of community interactions. Although there is much concern about mean changes in global climate, the impact of climatic variability itself on species interactions has been little explored. Here, we compare caterpillar–parasitoid interactions across a broad gradient of climatic variability and find that the combined data in 15 geographically dispersed databases show a decrease in levels of parasitism as climatic variability increases. The dominant contribution to this pattern by relatively specialized parasitoid wasps suggests that climatic variability impairs the ability of parasitoids to track host populations. Given the important role of parasitoids in regulating insect herbivore populations in natural and managed systems, we predict an increase in the frequency and intensity of herbivore outbreaks through a disruption of enemy–herbivore dynamics as climates become more variable.
Extraskeletal Osteosarcoma with Cystic Appearance in an Aged Sprague–Dawley Rat
Authors: Yoshizawa Katsuhiko , Matsumoto Masahiro , Oishi Yuji , Nyska Abraham
Published: November 2005

Extraskeletal osteosarcoma, arising spontaneously from the subcutis of the left abdomen and having a cystic appearance, was found in an untreated male Sprague–Dawley rat during a carcinogenicity study. At 76 weeks of age, the tumor mass had grown to 50 × 110 × 140 mm, and the animal exhibited severe anemia related to the complication of ulceration with hemorrhage. The tumor displayed irregular ossification at the walls of a cyst-like space filled with much yellowish fluid and necrotic cellular debris. Histopathologically, the tumor consisted of sheets of large, plump osteoblast-like cells, which produced broad irregular trabeculae of osteoid and calcified osseous tissue. Since extraskeletal osteosarcoma with a cystic appearance, has not been reported in animals, except for the telangiectatic type, our case shows an extremely rare type.
End‐of‐life decisions in delivery room and neonatal intensive care unit
Authors: ARLETTAZ ROMAINE , MIETH DIETO , BUCHER HANS‐ULRICH , DUC GABRIEL , FAUCHÈRE JEAN‐CLAUDE
Published: November 2005

Background: The increase in neonatal survival in recent decades has been followed by an increase in later disabilities. This has given rise to many new ethical issues. In different countries, efforts are being made to define ethical guidelines regarding withholding or withdrawing intensive care and end‐of‐life decisions in critically ill newborn infants. These guidelines have to be differentiated from ethical decision‐making models which structure the process of decision making for an individual child. Such a framework has been in existence in our clinic for 10 years. Aim: The aims of this study were to evaluate how end‐of‐life decisions are taken in our perinatal centre and to analyse whether these decisions are consistent with our framework for structured ethical decision making.

Methods: 199 consecutive neonatal deaths over 5 y were evaluated.

Results: In 157 cases (79%), end‐of‐life decisions were taken according to our ethical framework; in the remaining 42 cases (21%), the baby died before this could be done. In 92% of cases, parents were involved in the decision and, in all cases but one, agreed with the decision. A patient's life was never intentionally and actively terminated.

Conclusion: In contrast to earlier years, in‐hospital death in our clinic is nowadays usually preceded by structured and documented medical end‐of‐life decisions.
Comparison between Japanese and Swedish schoolchildren in regards to physical symptoms and psychiatric complaints
Authors: TANAKA HIDETAKA , MÖLLBORG PER , TERASHIMA SHIGENORI , BORRES MAGNUS P.
Published: November 2005

Background: Physical symptoms are an increasing problem among Japanese children and adolescents, and the symptoms seem to be related to their school situation. These symptoms are prevalent in Sweden, and a comparison with Japan is of interest due to the differences in the educational system and school climate. Objective and methods: To compare physical symptoms and psychiatric complaints in school pupils from Japan and Sweden, using a questionnaire that also addressed life satisfaction and stressful life events. The study population comprised 742 Japanese children and 1120 Swedish children attending public compulsory schools, grades 4–9 (10–15 y). Physical symptom and psychiatric complaint scores were calculated for each pupil.

Results: The Japanese children had significantly higher physical symptom and psychiatric complaint scores than did the Swedish children. Both the physical symptom and psychiatric complaint scores were significantly higher in adolescents than in preadolescents in Japan; this trend was less apparent in Swedish children. In addition, Japanese children were found to have considerably lower life satisfaction. Loss of appetite was the only physical symptom more prevalent in the Swedish population compared to the Japanese population.

Conclusion: We conclude that Japanese schoolchildren have more physical symptoms and psychiatric complaints and less life satisfaction than Swedish schoolchildren of corresponding ages.
Teachers' views on recent curriculum changes: tensions and challenges
Authors: Assunção Flores Maria
Published: November 2005

This article presents the major findings of a small‐scale study of recent changes in the elementary school curriculum in Portugal and their implications for teachers' sense of professionalism. Data were gathered through semi‐structured interviews and questionnaires in a suburban elementary school. Findings suggest the emergence of contradictory trends in teacher professionalism: on the one hand, teachers acknowledge the flexibility and the local logic in the management of school curriculum in which they play a key role; on the other, they highlight issues of bureaucracy and ‘imposed collaboration’, along with the lack of support and guidance to perform their new roles at school. Challenge, ambiguity and tension are key words in defining Portuguese teachers' sense of professionalism in times of change.
Schistosoma mansoni secretes a chemokine binding protein with antiinflammatory activity
Authors: Smith Philip , Fallon Rosie E. , Mangan Niamh E. , Walsh Caitriona M. , Saraiva Margarida , Sayers Jon R. , McKenzie Andrew N.J. , Alcami Antonio , Fallon Padraic G.
Published: November 2005

The coevolution of humans and infectious agents has exerted selective pressure on the immune system to control potentially lethal infections. Correspondingly, pathogens have evolved with various strategies to modulate and circumvent the host's innate and adaptive immune response. Schistosoma species are helminth parasites with genes that have been selected to modulate the host to tolerate chronic worm infections, often for decades, without overt morbidity. The modulation of immunity by schistosomes has been shown to prevent a range of immune-mediated diseases, including allergies and autoimmunity. Individual immune-modulating schistosome molecules have, therefore, therapeutic potential as selective manipulators of the immune system to prevent unrelated diseases. Here we show that S. mansoni eggs secrete a protein into host tissues that binds certain chemokines and inhibits their interaction with host chemokine receptors and their biological activity. The purified recombinant S. mansoni chemokine binding protein (smCKBP) suppressed inflammation in several disease models. smCKBP is unrelated to host proteins and is the first described chemokine binding protein encoded by a pathogenic human parasite and may have potential as an antiinflammatory agent.
Toll-like receptor–independent gene induction program activated by mammalian DNA escaped from apoptotic DNA degradation
Authors: Okabe Yasutaka , Kawane Kohki , Akira Shizuo , Taniguchi Tadatsugu , Nagata Shigekazu
Published: November 2005

Deoxyribonuclease (DNase) II in macrophages cleaves the DNA of engulfed apoptotic cells and of nuclei expelled from erythroid precursor cells. DNase II–deficient mouse embryos accumulate undigested DNA in macrophages, and die in feto because of the activation of the interferon β (IFNβ) gene. Here, we found that the F4/80-positive macrophages in DNase II−/− fetal liver specifically produce a set of cytokines such as IFNβ, TNFα, and CXCL10. Whereas, IFN-inducible genes (2′5′-oligo(A) synthetase, IRF7, and ISG15) were expressed not only in macrophages but also in other F4/80-negative cells. When DNase II−/− macrophages or embryonal fibroblasts engulfed apoptotic cells, they expressed the IFNβ and CXCL10 genes. The ablation of Toll-like receptor (TLR) 3 and 9, or their adaptor molecules (MyD88 and TRIF), had no effect on the lethality of the DNase II−/− mice. These results indicate that there is a TLR-independent sensing mechanism to activate the innate immunity for the endogenous DNA escaping lysosomal degradation.
How Heidelberger and Avery sweetened immunology
Authors: Van Epps Heather L.
Published: November 2005

In 1923, a young chemist-turned-microbiologist and his mentor made the startling discovery that bacterial sugars could be targeted by the immune system—a groundbreaking finding that helped launch the field of immunochemistry.
Enhanced recognition of protein transmembrane domains with prediction-based structural profiles
Authors: Cao Baoqiang , Porollo Aleksey , Adamczak Rafal , Jarrell Mark , Meller Jaroslaw
Published: November 2005

Motivation: Membrane domain prediction has recently been re-evaluated by several groups, suggesting that the accuracy of existing methods is still rather limited. In this work, we revisit this problem and propose novel methods for prediction of alpha-helical as well as beta-sheet transmembrane (TM) domains. The new approach is based on a compact representation of an amino acid residue and its environment, which consists of predicted solvent accessibility and secondary structure of each amino acid. A recently introduced method for solvent accessibility prediction trained on a set of soluble proteins is used here to indicate segments of residues that are predicted not to be accessible to water and, therefore, may be ‘buried’ in the membrane. While evolutionary profiles in the form of a multiple alignment are used to derive these simple ‘structural profiles’, they are not used explicitly for the membrane domain prediction and the overall number of parameters in the model is significantly reduced. This offers the possibility of a more reliable estimation of the free parameters in the model with a limited number of experimentally resolved membrane protein structures.

Results: Using cross-validated training on available sets of structurally resolved and non-redundant alpha and beta membrane proteins, we demonstrate that membrane domain prediction methods based on such a compact representation outperform approaches that utilize explicitly evolutionary profiles and multiple alignments. Moreover, using an external evaluation by the TMH Benchmark server we show that our final prediction protocol for the TM helix prediction is competitive with the state-of-the-art methods, achieving per-residue accuracy of ∼89% and per-segment accuracy of ∼80% on the set of high resolution structures used by the TMH Benchmark server. At the same time the observed rates of confusion with signal peptides and globular proteins are the lowest among the tested methods. The new method is available online at .

Contact:  jmeller@chmcc.org

Supplementary information:  Supplementary data are available at Bioinformatics online and at
Gene Time Eχpression Warper: a tool for alignment, template matching and visualization of gene expression time series
Authors: Criel Jo , Tsiporkova Elena
Published: November 2005

Summary: An application tool for alignment, template matching and visualization of gene expression time series is presented. The core algorithm is based on dynamic time warping techniques used in the speech recognition field. These techniques allow for non-linear (elastic) alignment of temporal sequences of feature vectors and consequently enable detection of similar shapes with different phases.

Availability: The Java program, examples and a tutorial are available at

Contact:  eltsi@psb.ugent.be