bluuebunny/crossref_metadata_2025 huggingface dataset:
Gut content- and stable isotope-derived diets of four commercially and recreationally important fish species in two intermittently open estuaries
Authors: Hadwen Wade L. , Russell Grant L. , Arthington Angela H.
Published: May 2007

Despite remaining closed for variable periods, intermittently open estuaries provide habitat for estuarine and marine fish species of commercial and recreational value. To better understand how these systems trophically support their fish assemblages, the diets of four valued fish species, namely Acanthopagrus australis, Platycephalus fuscus, Sillago ciliata and Mugil cephalus, were examined in two intermittently open estuaries in New South Wales, Australia. Fish diets were determined using both gut contents and stable isotope analyses because the different temporal resolutions afforded by these methods can provide insight into the flexibility of fish diets. Stable isotope signatures of prey and fish proved to be particularly useful in analyses of the diets of M. cephalus and P. fuscus, because these species consume large quantities of unidentifiable organic matter and have high incidences of empty guts respectively. Diet reconstructions across methods were generally consistent for A. australis, but differed substantially for S. ciliata, with fewer prey taxa identified in the guts than expected. This result suggests that individual S. ciliata switch between local resources on the basis of their fluctuating temporal availability. Trophic flexibility, coupled with broad physicochemical tolerances, enables these species to flourish in the challenging environment of intermittently open estuaries.
Spatial and temporal patterns of near-surface chlorophyll a in the Great Barrier Reef lagoon
Authors: Brodie J. , De'ath G. , Devlin M. , Furnas M. , Wright M.
Published: May 2007

Surface chlorophyll a concentrations in the Great Barrier Reef (GBR) lagoon were monitored at individual stations for periods of 6 to 12 years. The monitoring program was established to detect spatial and temporal changes in water quality resulting from increased loads of nutrients exported from the catchments adjoining the GBR. Sampling occurred monthly at up to 86 sites that were located in transects across the width of the continental shelf. In the central and southern GBR (16–21°S), there was a persistent cross-shelf chlorophyll a gradient, with higher concentrations near the coast. No cross-shelf gradient was observed in the far northern GBR (12–15°S). Mean chlorophyll a concentrations in the far northern GBR (0.23 µg L–1) were less than half those in the south and central GBR (0.54 µg L–1). Chlorophyll a varied seasonally within regions, with mean summer-wet season (December–April) concentrations ~50% greater than those in the winter-dry season (May–November). Sub-annual, inter-annual and event-related variations in chlorophyll a concentrations were observed in several zones. Multi-year patterns in concentrations suggest that relatively short (5–8 years) time series may give spurious estimates of secular trends. Higher chlorophyll a concentrations in inshore waters south of 16°S were most likely related to the levels of river nutrient delivery associated with agricultural development on adjacent catchments.
Neutral α-glucosidase activity in mouse: a marker of epididymal function?
Authors: Martini Ana C. , Molina Rosa I. , Vincenti Laura M. , Santillán María E. , Stutz Graciela , Ruiz Rubén D. , Fiol de Cuneo Marta
Published: May 2007

Neutral α-glucosidase (NAG) activity is considered a functional epididymal marker in several species. Unlike the rat, no NAG activity has been detected in mice. The aims of the present study were to evaluate NAG secretory activity (the supernatant of the incubated tissue) in mouse epididymis and to determine whether it could be used as a functional epididymal marker. Epididymides (whole or in parts) were incubated in the presence or absence of testosterone (10−5 m) and secretory NAG activity was compared with known positive controls. Furthermore, we compared enzyme activity in epididymides from well-fed and undernourished mice (50% food restriction for 21 days), a model that alters the epididymal maturation processes. Spectrophotometric analysis revealed NAG activity in mouse epididymis (22.6 ± 3.7 mU g–1 tissue; n = 4), being higher in the caput. NAG activity was statistically higher in the caput than in the corpus and in the cauda. No significant differences existed between the caput NAG activity and complete epididymis NAG activity. In undernourished mice, we confirmed changes in epididymal maturation observed previously (i.e. increased number of immature spermatozoa and diminution of the sperm concentration). Concordantly, the epididymides of undernourished mice exhibited decreased enzyme secretory activity, which increased to values similar to those seen in controls following incubation in the presence of testosterone (22.5 ± 2.6, 12.5 ± 1.0 and 22.4 ± 3.7 mU g–1 tissue, n = 9 in control (n = 7), undernourished (n = 9) and undernourished + testosterone groups (n = 9), respectively). In conclusion, NAG activity was detected in mouse epididymis. Although the present study supports the possibility of using NAG as an epididymal marker, more studies are necessary to effectively prove that NAG activity can be used as an epididymal marker.
Seasonal variation and circadian rhythmicity of the prolactin profile during the summer months in repeat-breeding Murrah buffalo heifers
Authors: Roy Kajal S. , Prakash Bukkaraya S.
Published: May 2007

The present study was undertaken to determine a detailed endocrine profile for prolactin and progesterone during the oestrous cycle in repeat-breeding Murrah buffalo heifers during summer and winter. Hormone concentrations were quantified in blood plasma samples collected over the oestrous cycle in both winter and summer, as well as in samples collected during the summer months to observe circadian rhythmicity. The mean plasma prolactin concentration during the winter months ranged from 3.10 ± 0.48 to 9.17 ± 1.39 ng mL–1; during the summer months, plasma prolactin concentrations ranged from 248.50 ± 16.03 to 369.63 ± 25.13 ng mL–1. During the winter months, the mean plasma progesterone concentration ranged from 0.20 ± 0.00 to 3.04 ± 0.34 ng mL–1, which was significantly higher (P < 0.01) than the prolactin concentrations recorded in the summer months (range 0.20 ± 0.00 to 1.48 ± 0.13 ng mL–1). Plasma prolactin and progesterone concentrations were negatively correlated (r = –0.24) during the summer oestrous cycle, which indicates prolactin-induced suppression of progesterone secretion through poor luteal development. During the summer, a circadian rhythmicity was observed in buffaloes and the results indicate that high prolactin secretion contributes to poor fertility by lowering gonadal hormone (progesterone) secretion. It was concluded from the present study that prolactin and progesterone profiles during the summer and winter months are directly correlated with the reproductive performance of buffaloes. The finding also validates the hypothesis that hyperprolactinaemia may cause acyclicity/infertility in buffaloes during the summer months due to severe heat stress.
Effects of aroclor 1254 on the expression of the KAP3 gene and reproductive function in rats
Authors: Lee Chae Kwan , Kang Han Seung , Kim Ju Ran , Lee Byung Ju , Lee Jong Tae , Kim Jeong Ho , Kim Dae Hwan , Lee Chang Hee , Ahn Jin Hong , Lee Chae Un , Yu Seong Jin , Kang Sung Goo
Published: May 2007

The present study investigated the effects of aroclor 1254 (A1254) on the expression of the kinesin superfamily associated protein 3 (KAP3) gene in F1 rat brain during brain sexual differentiation and puberty. In addition, the effects of A1254 on reproductive function were examined. The KAP3 gene is involved in the neurogenesis and synaptogenesis of sexual differentiation in rats and also during puberty. In the present study, pregnant Sprague–Dawley rats each received a daily dose of A1254 (0, 10, 50 mg kg–1) dissolved in 1.0 mL corn oil by gavage, from gestational Day (GD) 8 to postnatal Day (PD) 21. The mRNA levels of the KAP3 gene in hypothalamic tissues were analysed by northern blot hybridisation during the critical periods of brain sexual differentiation (GD18 and PD5) and puberty (PD28). Variables affecting reproduction in F1 female rats, such as vaginal opening (VO), vaginal oestrus (VE) and oestrous cyclicity, were recorded. Depending on the sex and A1254 exposure (control or 50 mg kg–1 day–1), F1 rats were divided into three mating groups, namely control male–control female, control male–A1254-treated female and A1254-treated male–control female. During the critical periods of brain sexual differentiation (GD18, PD5) and puberty (PD28), KAP3 mRNA levels were significantly reduced in A1254-treated fetal and pubertal rat brains relative to those of control groups. In A1254-treated F1 female rats, VO and VE were delayed, the percentage of irregular oestrous cycles was increased and the duration of the oestrous cycle was extended in a dose-dependent manner compared with control groups. Treatment with a high dose of A1254 significantly impaired the reproductive function of both male and female F1 rats, including mating and pregnancy indices and the number of live fetuses. These data suggest that A1254 disrupts transcriptional regulation of the KAP3 gene in fetal and pubertal rat brains and that these effects may be related to A1254-induced abnormal brain sexual differentiation and lowered reproductive function in F1 rats.
Uterine and vaginal insemination optimised in brushtail possums (Trichosurus vulpecula) superovulated with pregnant mare serum gonadotrophin and porcine luteinising hormone
Authors: Molinia F. C. , Myers J. V. , Glazier A. M. , Duckworth J. A. , Rodger J. C.
Published: May 2007

Artificial insemination of brushtail possums (Trichosurus vulpecula) is being developed as an assisted breeding model for endangered marsupials, as well as a bioassay for testing fertility control vaccines to manage overabundant populations. Procedures were optimised in animals superovulated with pregnant mare serum gonadotrophin (PMSG) and porcine luteinising hormone (pLH). Of three intervals examined, yields were maximal following uterine insemination at 27–29.5 h after pLH treatment (four eggs, two to three embryos per female). Compared with no insemination, uterine-inseminated animals ovulated 30–36 h rather than 28–34 h after pLH treatment. For the vaginal route, yields were maximal following insemination at 10–13 h after pLH treatment (six to seven eggs, four embryos per female) than at five other intervals, and when using acclimatised females during the autumn breeding season. This protocol was suitable for testing fertility control vaccines in April–June and was influenced by the housing location of animals, the presence of an active corpus luteum and PMSG batch, but not other factors (year of trial, Freund’s adjuvant treatment, changes in bodyweight, dose of PMSG kg–1). Embryos developed to the eight- to 16-cell or unilaminar blastocyst stage after uterine or vaginal insemination, respectively. With the timing of artificial insemination optimised, new methods to synchronise or induce oestrus and ovulation are required to achieve year-round testing of fertility control vaccines or birth of offspring.
Granulocyte - macrophage colony stimulating factor and interleukin-8 in the reproductive tract of ewes following oestrus and mating
Authors: Scott Jennifer L. , Ketheesan Natkunam , Summers Phillip M.
Published: May 2007

Cytokines produced in the female reproductive tract after mating may enhance reproductive success. The present study investigated the distribution of granulocyte–macrophage colony stimulating factor (GM-CSF) and interleukin (IL)-8 in tissues and luminal secretions from different sites in the reproductive tract of the ewe following oestrus and after natural mating. Fifteen ewes were mated with a ram for 1 h and their reproductive tracts collected 3, 6, 18, 24 or 48 h later. Another 15 ewes were used as oestrous controls. Luminal secretions and tissue samples were collected from seven sites in each reproductive tract. Secretions were analysed by enzyme-linked immunosorbent assay and tissues were stained immunohistochemically using anti-sheep GM-CSF and anti-sheep IL-8 antibodies. Both cytokines were found in luminal and glandular endometrial epithelium and, to a lesser extent, in cervical epithelium; neither was found in the vaginal epithelium. Twice as many (P < 0.05) luminal samples from mated ewes than non-mated ewes were positive for GM-CSF. The vaginal lumen contained significantly higher (P < 0.01) concentrations of IL-8 compared with other sites, irrespective of mating status. Significant differences (P < 0.05) were found in staining intensity of GM-CSF and IL-8 from different sites. Production of GM-CSF and IL-8 by reproductive tissues is likely to contribute to leucocyte infiltration into the ovine reproductive tract.
Isolation, culture and characterisation of somatic cells derived from semen and milk of endangered sheep and eland antelope
Authors: Nel-Themaat L. , Gómez M. C. , Damiani P. , Wirtu G. , Dresser B. L. , Bondioli K. R. , Lyons L. A. , Pope C. E. , Godke R. A.
Published: May 2007

Semen and milk are potential sources of somatic cells for genome banks. In the present study, we cultured and characterised cells from: (1) cooled sheep milk; (2) fresh, cooled and frozen–thawed semen from Gulf Coast native (GCN) sheep (Ovis aries); and (3) fresh eland (Taurotragus oryx) semen. Cells attached to the culture surface from fresh (29%), cooled (43%) and slow-frozen (1°C/min; 14%) ram semen, whereas no attachment occurred in the fast-frozen (10°C/min) group. Proliferation occurred in fresh (50%) and cooled (100%) groups, but no cells proliferated after passage 1 (P1). Eland semen yielded cell lines (100%) that were cryopreserved at P1. In samples from GCN and cross-bred milk, cell attachment (83% and 95%, respectively) and proliferation (60% and 37%, respectively) were observed. Immunocytochemical detection of cytokeratin indicated an epithelial origin of semen-derived cells, whereas milk yielded either fibroblasts, epithelial or a mixture of cell types. Deoxyribonucleic acid microsatellite analysis using cattle-derived markers confirmed that eland cells were from the semen donor. Eland epithelial cells were transferred into eland oocytes and 12 (71%), six (35%) and two (12%) embryos cleaved and developed to morulae or blastocyst stages, respectively. In conclusion, we have developed a technique for obtaining somatic cells from semen. We have also demonstrated that semen-derived cells can serve as karyoplast donors for nuclear transfer.
Achieving high-density states through shock-wave loading of precompressed samples
Authors: Jeanloz Raymond , Celliers Peter M. , Collins Gilbert W. , Eggert Jon H. , Lee Kanani K. M. , McWilliams R. Stewart , Brygoo Stéphanie , Loubeyre Paul
Published: May 2007

Materials can be experimentally characterized to terapascal pressures by sending a laser-induced shock wave through a sample that is precompressed inside a diamond-anvil cell. This combination of static and dynamic compression methods has been experimentally demonstrated and ultimately provides access to the 10- to 100-TPa (0.1–1 Gbar) pressure range that is relevant to planetary science, testing first-principles theories of condensed matter, and experimentally studying a new regime of chemical bonding.
Extreme accumulation of nucleotides in simulated hydrothermal pore systems
Authors: Baaske Philipp , Weinert Franz M. , Duhr Stefan , Lemke Kono H. , Russell Michael J. , Braun Dieter
Published: May 2007

We simulate molecular transport in elongated hydrothermal pore systems influenced by a thermal gradient. We find extreme accumulation of molecules in a wide variety of plugged pores. The mechanism is able to provide highly concentrated single nucleotides, suitable for operations of an RNA world at the origin of life. It is driven solely by the thermal gradient across a pore. On the one hand, the fluid is shuttled by thermal convection along the pore, whereas on the other hand, the molecules drift across the pore, driven by thermodiffusion. As a result, millimeter-sized pores accumulate even single nucleotides more than 10
8
-fold into micrometer-sized regions. The enhanced concentration of molecules is found in the bulk water near the closed bottom end of the pore. Because the accumulation depends exponentially on the pore length and temperature difference, it is considerably robust with respect to changes in the cleft geometry and the molecular dimensions. Whereas thin pores can concentrate only long polynucleotides, thicker pores accumulate short and long polynucleotides equally well and allow various molecular compositions. This setting also provides a temperature oscillation, shown previously to exponentially replicate DNA in the protein-assisted PCR. Our results indicate that, for life to evolve, complicated active membrane transport is not required for the initial steps. We find that interlinked mineral pores in a thermal gradient provide a compelling high-concentration starting point for the molecular evolution of life.
Symbiosis as an adaptive process and source of phenotypic complexity
Authors: Moran Nancy A.
Published: May 2007

Genomics has revealed that inheritance systems of separate species are often not well segregated: genes and capabilities that evolve in one lineage are often stably acquired by another lineage. Although direct gene transfer between species has occurred at some level in all major groups, it appears to be far more frequent in prokaryotes than in multicellular eukaryotes. An alternative to incorporating novel genes into a recipient genome is acquiring a stable, possibly heritable, symbiotic association and thus enjoying benefits of complementary metabolic capabilities. These kinds of symbioses have arisen frequently in animals; for example, many insect groups have diversified on the basis of symbiotic associations acquired early in their evolutionary histories. The resulting associations are highly complex, often involving specialized cell types and organs, developmental mechanisms that ensure transfer of symbionts between generations, and mechanisms for controlling symbiont proliferation and location. The genomes of long-term obligate symbionts often undergo irreversible gene loss and deterioration even as hosts evolve dependence on them. In some cases, animal genomes may have acquired genes from symbionts, mirroring the gene uptake from mitochondrial and plastid genomes. Multiple symbionts often coexist in the same host, resulting in coadaptation among several phylogenetically distant genomes.
Platelet glycoprotein Ibα supports experimental lung metastasis
Authors: Jain Shashank , Zuka Masahiko , Liu Jungling , Russell Susan , Dent Judith , Guerrero José A. , Forsyth Jane , Maruszak Brigid , Gartner T. Kent , Felding-Habermann Brunhilde , Ware Jerry
Published: May 2007

The platelet paradigm in hemostasis and thrombosis involves an initiation step that depends on platelet membrane receptors binding to ligands on a damaged or inflamed vascular surface. Once bound to the surface, platelets provide a unique microenvironment supporting the accumulation of more platelets and the elaboration of a fibrin-rich network produced by coagulation factors. The platelet-specific receptor glycoprotein (GP) Ib-IX, is critical in this process and initiates the formation of a platelet-rich thrombus by tethering the platelet to a thrombogenic surface. A role for platelets beyond the hemostasis/thrombosis paradigm is emerging with significant platelet contributions in both tumorigenesis and inflammation. We have established congenic (N10) mouse colonies (C57BL/6J) with dysfunctional GP Ib-IX receptors in our laboratory that allow us an opportunity to examine the relevance of platelet GP Ib-IX in syngeneic mouse models of experimental metastasis. Our results demonstrate platelet GP Ib-IX contributes to experimental metastasis because a functional absence of GP Ib-IX correlates with a 15-fold reduction in the number of lung metastatic foci using B16F10.1 melanoma cells. The results demonstrate that the extracellular domain of the α-subunit of GP Ib is the structurally relevant component of the GP Ib-IX complex contributing to metastasis. Our results support the hypothesis that platelet GP Ib-IX functions that support normal hemostasis or pathologic thrombosis also contribute to tumor malignancy.
Plant domestication, a unique opportunity to identify the genetic basis of adaptation
Authors: Ross-Ibarra Jeffrey , Morrell Peter L. , Gaut Brandon S.
Published: May 2007

Despite the fundamental role of plant domestication in human history and the critical importance of a relatively small number of crop plants to modern societies, we still know little about adaptation under domestication. Here we focus on efforts to identify the genes responsible for adaptation to domestication. We start from a historical perspective, arguing that Darwin's conceptualization of domestication and unconscious selection provides valuable insight into the evolutionary history of crops and also provides a framework to evaluate modern methods used to decipher the genetic mechanisms underlying phenotypic change. We then review these methods, framing the discussion in terms of the phenotype–genotype hierarchy. Top-down approaches, such as quantitative trait locus and linkage disequilibrium mapping, start with a phenotype of interest and use genetic analysis to identify candidate genes. Bottom-up approaches, alternatively, use population genetic analyses to identify potentially adaptive genes and then rely on standard bioinformatics and reverse genetic tools to connect selected genes to a phenotype. We discuss the successes, advantages, and challenges of each, but we conclude that bottom-up approaches to understanding domestication as an adaptive process hold greater promise both for the study of adaptation and as a means to identify genes that contribute to agronomically important traits.
Between “design” and “bricolage”: Genetic networks, levels of selection, and adaptive evolution
Authors: Wilkins Adam S.
Published: May 2007

The extent to which “developmental constraints” in complex organisms restrict evolutionary directions remains contentious. Yet, other forms of internal constraint, which have received less attention, may also exist. It will be argued here that a set of partial constraints below the level of phenotypes, those involving genes and molecules, influences and channels the set of possible evolutionary trajectories. At the top-most organizational level there are the genetic network modules, whose operations directly underlie complex morphological traits. The properties of these network modules, however, have themselves been set by the evolutionary history of the component genes and their interactions. Characterization of the components, structures, and operational dynamics of specific genetic networks should lead to a better understanding not only of the morphological traits they underlie but of the biases that influence the directions of evolutionary change. Furthermore, such knowledge may permit assessment of the relative degrees of probability of short evolutionary trajectories, those on the microevolutionary scale. In effect, a “network perspective” may help transform evolutionary biology into a scientific enterprise with greater predictive capability than it has hitherto possessed.
Adaptive evolution of color vision as seen through the eyes of butterflies
Authors: Frentiu Francesca D. , Bernard Gary D. , Cuevas Cristina I. , Sison-Mangus Marilou P. , Prudic Kathleen L. , Briscoe Adriana D.
Published: May 2007

Butterflies and primates are interesting for comparative color vision studies, because both have evolved middle- (M) and long-wavelength- (L) sensitive photopigments with overlapping absorbance spectrum maxima (λ
max
values). Although positive selection is important for the maintenance of spectral variation within the primate pigments, it remains an open question whether it contributes similarly to the diversification of butterfly pigments. To examine this issue, we performed epimicrospectrophotometry on the eyes of five
Limenitis
butterfly species and found a 31-nm range of variation in the λ
max
values of the L-sensitive photopigments (514–545 nm). We cloned partial
Limenitis
L opsin gene sequences and found a significant excess of replacement substitutions relative to polymorphisms among species. Mapping of these L photopigment λ
max
values onto a phylogeny revealed two instances within Lepidoptera of convergently evolved L photopigment lineages whose λ
max
values were blue-shifted. A codon-based maximum-likelihood analysis indicated that, associated with the two blue spectral shifts, four amino acid sites (Ile17Met, Ala64Ser, Asn70Ser, and Ser137Ala) have evolved substitutions in parallel and exhibit significant

d
N
/d
S

>1. Homology modeling of the full-length
Limenitis arthemis astyanax
L opsin placed all four substitutions within the chromophore-binding pocket. Strikingly, the Ser137Ala substitution is in the same position as a site that in primates is responsible for a 5- to 7-nm blue spectral shift. Our data show that some of the same amino acid sites are under positive selection in the photopigments of both butterflies and primates, spanning an evolutionary distance >500 million years.
APEx 2-hybrid, a quantitative protein–protein interaction assay for antibody discovery and engineering
Authors: Jeong Ki Jun , Seo Min Jeong , Iverson Brent L. , Georgiou George
Published: May 2007

We have developed a bacterial system for the discovery of interacting proteins that, unlike other two-hybrid technologies, allows for the selection of protein pairs on the basis of affinity or expression. This technology relies on the anchored periplasmic expression (APEx) of one protein (bait) on the periplasmic side of the inner membrane of
Escherichia coli
and its interacting partner (prey) as a soluble, epitope-tagged, periplasmic protein. Upon removal of the outer membrane by spheroplasting, periplasmic proteins, including any unbound epitope-tagged prey, are released into the extracellular fluid. However, if the epitope-tagged prey can bind to the membrane-anchored bait, it remains associated with the cell and can be detected quantitatively by using fluorescent anti-epitope tag antibodies. Cells expressing prey:bait pairs exhibiting different affinities can be readily distinguished by flow cytometry. The utility of this technology, called APEx two-hybrid, was demonstrated in two demanding antibody engineering applications: First, single-chain variable fragment (scFvs) with increased affinity to the protective antigen of
Bacillus anthracis
were isolated from cells coexpressing libraries of scFv random mutants, together with endogenously expressed antigen. Second, APEx two-hybrid coupled with multicolor FACS analysis to account for protein expression was used for the selection of mutant Fab antibody fragments exhibiting improved expression in the bacterial periplasm.
High-resolution physical and functional mapping of the template adjacent DNA binding site in catalytically active telomerase
Authors: Romi Erez , Baran Nava , Gantman Marina , Shmoish Michael , Min Bosun , Collins Kathleen , Manor Haim
Published: May 2007

Telomerase is a cellular reverse transcriptase, which utilizes an integral RNA template to extend single-stranded telomeric DNA. We used site-specific photocrosslinking to map interactions between DNA primers and the catalytic protein subunit (tTERT) of
Tetrahymena thermophila
telomerase in functional enzyme complexes. Our assays reveal contact of the single-stranded DNA adjacent to the primer-template hybrid and tTERT residue W187 at the periphery of the N-terminal domain. This contact was detected in complexes with three different registers of template in the active site, suggesting that it is maintained throughout synthesis of a complete telomeric repeat. Substitution of nearby residue Q168, but not W187, alters the K
m
for primer elongation, implying that it plays a role in the DNA recognition. These findings are the first to directly demonstrate the physical location of TERT-DNA contacts in catalytically active telomerase and to identify amino acid determinants of DNA binding affinity. Our data also suggest a movement of the TERT active site relative to the template-adjacent single-stranded DNA binding site within a cycle of repeat synthesis.
Anchoring of Protein Kinase A-Regulatory Subunit IIα to Subapically Positioned Centrosomes Mediates Apical Bile Canalicular Lumen Development in Response to Oncostatin M but Not cAMP
Authors: Wojtal Kacper A. , Hoekstra Dick , van IJzendoorn Sven C.D.
Published: May 2007

Oncostatin M and cAMP signaling stimulate apical surface-directed membrane trafficking and apical lumen development in hepatocytes, both in a protein kinase A (PKA)-dependent manner. Here, we show that oncostatin M, but not cAMP, promotes the A-kinase anchoring protein (AKAP)-dependent anchoring of the PKA regulatory subunit (R)IIα to subapical centrosomes and that this requires extracellular signal-regulated kinase 2 activation. Stable expression of the RII-displacing peptide AKAP-IS, but not a scrambled peptide, inhibits the association of RIIα with centrosomal AKAPs and results in the repositioning of the centrosome from a subapical to a perinuclear location. Concomitantly, common endosomes, but not apical recycling endosomes, are repositioned from a subapical to a perinuclear location, without significant effects on constitutive or oncostatin M-stimulated basolateral-to-apical transcytosis. Importantly, however, the expression of the AKAP-IS peptide completely blocks oncostatin M-, but not cAMP-stimulated apical lumen development. Together, the data suggest that centrosomal anchoring of RIIα and the interrelated subapical positioning of these centrosomes is required for oncostatin M-, but not cAMP-mediated, bile canalicular lumen development in a manner that is uncoupled from oncostatin M-stimulated apical lumen-directed membrane trafficking. The results also imply that multiple PKA-mediated signaling pathways control apical lumen development and that subapical centrosome positioning is important in some of these pathways.
A Novel AAK1 Splice Variant Functions at Multiple Steps of the Endocytic Pathway
Authors: Henderson Davin M. , Conner Sean D.
Published: May 2007

Phosphorylation is a critical step in regulating receptor transport through the endocytic pathway. AAK1 is a serine/threonine kinase that is thought to coordinate the recruitment of AP-2 to receptors containing tyrosine-based internalization motifs by phosphorylating the μ2 subunit. Here we have identified a long form of AAK1 (AAK1L) that contains an extended C-terminus that encodes an additional clathrin-binding domain (CBD2) consisting of multiple low-affinity interaction motifs. Protein interaction studies demonstrate that AAK1L CBD2 directly binds clathrin. However, in vitro kinase assays reveal little difference between AAK1 isoforms in their basal or clathrin-stimulated kinase activity toward the AP-2 μ2 subunit. However, overexpression of AAK1L CBD2 impairs transferrin endocytosis, confirming an endocytic role for AAK1. Surprisingly, CBD2 overexpression or AAK1 depletion by RNA interference significantly impairs transferrin recycling from the early/sorting endosome. These observations suggest that AAK1 functions at multiple steps of the endosomal pathway by regulating transferrin internalization and its rapid recycling back to the plasma membrane from early/sorting endosome.
Stochastic simulations of minimal self-reproducing cellular systems
Authors: Mavelli Fabio , Ruiz-Mirazo Kepa
Published: May 2007

This paper is a theoretical attempt to gain insight into the problem of how self-assembling vesicles (closed bilayer structures) could progressively turn into minimal self-producing and self-reproducing cells, i.e. into interesting candidates for (proto)biological systems. With this aim, we make use of a recently developed object-oriented platform to carry out stochastic simulations of chemical reaction networks that take place in dynamic cellular compartments. We apply this new tool to study the behaviour of different minimal cell models, making realistic assumptions about the physico-chemical processes and conditions involved (e.g. thermodynamic equilibrium/non-equilibrium, variable volume-to-surface relationship, osmotic pressure, solute diffusion across the membrane due to concentration gradients, buffering effect). The new programming platform has been designed to analyse not only how a single protometabolic cell could maintain itself, grow or divide, but also how a collection of these cells could ‘evolve’ as a result of their mutual interactions in a common environment.
Coevolution of compositional protocells and their environment
Authors: Shenhav Barak , Oz Aia , Lancet Doron
Published: May 2007

The coevolution of environment and living organisms is well known in nature. Here, it is suggested that similar processes can take place before the onset of life, where protocellular entities, rather than full-fledged living systems, coevolve along with their surroundings. Specifically, it is suggested that the chemical composition of the environment may have governed the chemical repertoire generated within molecular assemblies, compositional protocells, while compounds generated within these protocells altered the chemical composition of the environment. We present an extension of the graded autocatalysis replication domain (GARD) model—the environment exchange polymer GARD (EE-GARD) model. In the new model, molecules, which are formed in a protocellular assembly, may be exported to the environment that surrounds the protocell. Computer simulations of the model using an infinite-sized environment showed that EE-GARD assemblies may assume several distinct quasi-stationary compositions (composomes), similar to the observations in previous variants of the GARD model. A statistical analysis suggested that the repertoire of composomes manifested by the assemblies is independent of time. In simulations with a finite environment, this was not the case. Composomes, which were frequent in the early stages of the simulation disappeared, while others emerged. The change in the frequencies of composomes was found to be correlated with changes induced on the environment by the assembly. The EE-GARD model is the first GARD model to portray a possible time evolution of the composomes repertoire.
A minimal and self-consistentin silicocell model based on macromolecular interactions
Authors: Flamm Christoph , Endler Lukas , Müller Stefan , Widder Stefanie , Schuster Peter
Published: May 2007

A self-consistent minimal cell model with a physically motivated schema for molecular interaction is introduced and described. The genetic and metabolic reaction network of the cell is modelled by multidimensional nonlinear ordinary differential equations, which are derived from biochemical kinetics. The strategy behind this modelling approach is to keep the model sufficiently simple in order to be able to perform studies on evolutionary optimization in populations of cells. At the same time, the model should be complex enough to handle the basic features of genetic control of metabolism and coupling to environmental factors. Thereby, the model system will provide insight into the mechanisms leading to important biological phenomena, such as homeostasis, (circadian) rhythms, robustness and adaptation to a changing environment. One example of modelling a molecular regulatory mechanism, cooperative binding of transcription factors, is discussed in detail.
Cytogenetic analysis of three sympatric Gymnotus (Gymnotiformes, Gymnotidae) species verifies invasive species in the Upper Paraná River basin, Brazil
Authors: Margarido V. Pavan , Bellafronte E. , Moreira‐Filho O.
Published: May 2007

Cytogenetic analyses were performed on three Gymnotus species, Gymnotus paraguensis, Gymnotus sylvius and Gymnotus pantanal, collected in sympatry in the region of Guaíra, Paraná State (Brazil). Gymnotus paraguensis presented 54 chromosomes (52m‐sm + 2st) in both sexes, G. sylvius presented 40 chromosomes (36m‐sm + 4a) in both sexes and G. pantanal presented 40 chromosomes (14m‐sm + 26a) in females and 39 (15m‐sm + 24a) in males, with an X1X1X2X2/X1X2Y multiple sex chromosome system. All three species had single nucleolar organizing regions and heterochromatin in the centromeric region of most chromosomes. Gymnotus pantanal, previously collected only in the Lower Paraná and Paraguay River basins, was confirmed for the first time in the Upper Paraná River basin. This species constitutes one of several examples of species that have colonized the region after flooding of the great Sete Quedas waterfalls by the construction of the Itaipu hydroelectric dam. The probable absence or infertility of hybrids is indicated by the high level of chromosome differentiation between these species.
Population genetic structure and effective population size of ayu (Plecoglossus altivelis), an amphidromous fish
Authors: Yamamoto S. , Uchida K. , Sato T. , Katsura K. , Takasawa T.
Published: May 2007

The temporal and spatial population genetic structure of ayu Plecoglossus altivelis (Salmoniformes: Plecoglossidae), an amphidromous fish, was examined using analysis of variation at six microsatellite DNA loci. Intracohort genetic diversities, as measured by the number of alleles and heterozygosity, were similar among six cohorts (2001–2006) within a population (Nezugaseki River), with the mean number of alleles per cohort ranging from 11·0 to 12·5 and the expected heterozygosity ranging from 0·74 to 0·77. Intrapopulational genetic diversities were also similar across the three studied populations along the 50 km coast, with the mean number of alleles and the expected heterozygosity ranging from 11·33 to 11·67 and from 0·75 to 0·76, respectively. The authors observed only one significant difference in pair‐wise population differentiation (FST‐value) between the cohorts within a population and among three populations. Estimates of the effective population size (Ne) based on maximum‐likelihood method yielded small values (ranging from 94·8 to 135·5), whereas census population size ranged from c. 4800 to 24 000. As a result, the ratio of annual effective population sizes to census population size (Ne/N) ranged from 0·004 to 0·023. These estimates of Ne/N agree more closely with estimates for marine fishes than that of the larger estimates for freshwater fishes. The present study suggests that ayu which is highly fecund and shows low survival during the early life stages is also characterized by having low value of Ne/N, similar to marine species with a pelagic life cycle.
Loss of genetic variability in reintroduced roach (Rutilus rutilus) populations
Authors: Demandt M. , Björklund M.
Published: May 2007

Genetic variation at five microsatellite loci and in mtDNA was surveyed in reintroduced and ‘control’ populations of roach (Rutilus rutilus) in Sweden. Microsatellite allelic richness and allele size ranges were significantly reduced in reintroduced populations, and mtDNA diversity was nearly significantly reduced in reintroduced populations. These measures of genetic variability were strongly correlated with lake characteristics that influence population size and food availability.
Effects of multi‐year droughts on fish assemblages of seasonally drying Mediterranean streams
Authors: MAGALHÃES M. FILOMENA , BEJA PEDRO , SCHLOSSER ISAAC J. , COLLARES‐PEREIRA MARIA J.
Published: May 2007

1. This study analysed changes occurring in Mediterranean stream fish assemblages over a sequence of dry years followed by a generally wet period (1991–98). Variations in assemblage attributes were quantified at the basin and stream reach scales, and related to variables reflecting the occurrence of unusually dry or wet conditions.

2. Assemblage variability increased along with the resolution of analysis, with little changes in species richness, composition and rank abundances, but significant variation in individual species abundances. Fluctuations in relative abundances were significantly affected by variables reflecting the severity of summer droughts and the occurrence of rainy springs. These patterns were evident at the basin scale, while variability at individual stream reaches tended to be higher and less related to rainfall patterns.

3. At least three response guilds to rainfall variation could be identified: two of the four abundant and widespread species (chub and loach) declined following dry years, whereas the two other core species (nase and eel) declined after rainy spring; one scarce native species (stickleback) increased in dry years.

4. Except at the two most upstream reaches, the assemblages tended to recover quickly to previous configuration after the changes occurring during the sequence of dry years.

5. Temporal variability of local assemblages was concordant among reaches but did not follow any consistent spatial pattern. Instead, spatial patterns in assemblage attributes changed over time in response to environmental variability, with a tendency for a disruption of upstream–downstream gradients following dry years.

6. Results supported the view that present‐day droughts cause relatively small and transient changes to Mediterranean stream fish assemblages. However, longer and more severe droughts expected under altered future climates, may result in declines or local extinctions of the most sensitive species and their potential replacement by more resistant species. Changing drought regimes thus need to be duly considered in the development of conservation strategies for Mediterranean stream fish.
The impact of an introduced predator on a threatened galaxiid fish is reduced by the availability of complex habitats
Authors: STUART‐SMITH RICK D. , STUART‐SMITH JEMINA F. , WHITE ROBERT W.G. , BARMUTA LEON A.
Published: May 2007

1. The availability of complex habitats such as macrophytes may be vital in determining the outcomes of interactions between introduced predators and native prey. Introduced brown trout (Salmo trutta) have impacted numerous small native freshwater fishes in the southern hemisphere, but the potential role of complex habitats in determining the direct outcomes of brown trout – native fish interactions has not been experimentally evaluated.

2. An in‐lake enclosure experiment was used to evaluate the importance of structurally complex habitats in affecting the direct impacts of brown trout on a threatened galaxiid fish. Five Galaxias auratus and a single brown trout were added to enclosures containing one of three different habitat types (artificial macrophytes, rocks and bare silt substrate). The experiment also had control enclosures without brown trout. Habitat‐dependence of predation risk was assessed by analysis of G. auratus losses to predation, and stomach contents of remaining fish were analysed to determine if brown trout directly affect the feeding of G. auratus and whether this is also habitat‐dependent.

3. Predation risk of G. auratus differed significantly between habitat types, with the highest mortality in enclosures with only bare silt substrate and the lowest in enclosures containing artificial macrophytes. This result highlights the importance of availability of complex habitats for trout – native fish interactions and suggests that increasing habitat degradation and loss in fresh waters may exacerbate the direct impacts of introduced predators.

4. Stomach contents analyses were restricted to fish in enclosures with artificial macrophytes and rocks, as most fish were consumed in enclosures with brown trout and only bare silt substrate. These analyses suggest that brown trout do not directly affect the feeding of G. auratus in complex habitats, but it is still unknown whether its feeding is reduced if complex habitats are unavailable.
Stable nitrogen isotope ratios of macrophytes and associated periphyton along a nitrate gradient in two subtropical, spring‐fed streams
Authors: BRABANDERE LORETO DE , FRAZER THOMAS K. , MONTOYA JOSEPH P.
Published: May 2007

1. An increase in human population and associated changes in land use have caused an increase in groundwater nitrate concentrations throughout central Florida. Within the region, this nitrate‐laden groundwater returns to the surface via numerous large springs that serve as the origin of flow for many coastal streams and rivers. These rivers can exhibit strong nitrate gradients because of the high nutrient uptake potential of the rivers.

2. We hypothesised that downstream declines in nitrate concentrations would be manifested spatially as increases in the δ15N of the residual pool of nitrate, macrophytes and periphyton as a consequence of isotopic fractionation associated with preferential use of 14NO3−. This hypothesis was tested in two spring‐fed river systems, the Chassahowitzka and Homosassa rivers, along Florida's central Gulf of Mexico coast.

3. In general, δ15N values of nitrate, macrophytes and periphyton increased with decreasing fraction of nitrate remaining in each of the two study systems. The fractionation associated with nitrate uptake by macrophytes and associated periphyton was determined from the relationship between δ15N of both constituents of the macrophyte community and the fraction of nitrate removed from the system. Values for fractionation by macrophytes and periphyton ranged from 1.9‰ to 3.6‰ and from 0.7‰ to 2.5‰, respectively.
Infection with Salmonella typhimurium has no effect on the composition and cleavage specificity of the 20S proteasome in human lymphoid cells
Authors: Marcilla Miguel , De Castro José Antonio López , Castaño José G. , Alvarez Iñaki
Published: May 2007

Human leucocyte antigen (HLA)‐B27 is strongly associated with spondyloarthropathies, including reactive arthritis. Several Gram‐negative bacteria, such as Salmonella typhimurium, can trigger this disease. It has been suggested that peptides derived from bacterial proteins and presented by HLA‐B27 to cytotoxic T lymphocytes might show molecular mimicry with autologous peptides, leading to T‐cell cross‐reaction and autoimmunity. Antigen presentation in Salmonella‐infected cells could be modulated by changes in the composition of the proteasome, which is the major proteolytic system that generates major histocompatibility complex class I ligands. In this study we analysed whether the composition or activity of the 20S proteasome was altered upon infection of lymphoid cells by S. typhimurium. Two‐dimensional gel electrophoresis failed to show any differences between the composition of 20S proteasomes from cells infected with S. typhimurium for 24 hr, relative to non‐infected cells. In addition, digestions of oxidized insulin B‐chain with purified 20S proteasomes from non‐infected and infected cells generated the same products, indicating that the proteasomal cleavage specificity was not altered upon infection. These data indicate that infection of lymphoid cells by S. typhimurium fails to induce formation of immunoproteasomes or otherwise alter the proteolytic specificity of the 20S proteasome.