bluuebunny/crossref_metadata_2025 huggingface dataset:
Peptide adsorption on a hydrophobic surface results from an interplay of solvation, surface, and intrapeptide forces
Authors: Horinek D. , Serr A. , Geisler M. , Pirzer T. , Slotta U. , Lud S. Q. , Garrido J. A. , Scheibel T. , Hugel T. , Netz R. R.
Published: February 2008

The hydrophobic effect, i.e., the poor solvation of nonpolar parts of molecules, plays a key role in protein folding and more generally for molecular self-assembly and aggregation in aqueous media. The perturbation of the water structure accounts for many aspects of protein hydrophobicity. However, to what extent the dispersion interaction between molecular entities themselves contributes has remained unclear. This is so because in peptide folding interactions and structural changes occur on all length scales and make disentangling various contributions impossible. We address this issue both experimentally and theoretically by looking at the force necessary to peel a mildly hydrophobic single peptide molecule from a flat hydrophobic diamond surface in the presence of water. This setup avoids problems caused by bubble adsorption, cavitation, and slow equilibration that complicate the much-studied geometry with two macroscopic surfaces. Using atomic-force spectroscopy, we determine the mean desorption force of a single spider-silk peptide chain as
F
= 58 ± 8 pN, which corresponds to a desorption free energy of ≈5
k
B
T
per amino acid. Our all-atomistic molecular dynamics simulation including explicit water correspondingly yields the desorption force
F
= 54 ± 15 pN. This observation demonstrates that standard nonpolarizable force fields used in classical simulations are capable of resolving the fine details of the hydrophobic attraction of peptides. The analysis of the involved energetics shows that water-structure effects and dispersive interactions give contributions of comparable magnitude that largely cancel out. It follows that the correct modeling of peptide hydrophobicity must take the intimate coupling of solvation and dispersive effects into account.
fMRI mapping of a morphed continuum of 3D shapes within inferior temporal cortex
Authors: Tootell Roger B. H. , Devaney Kathryn J. , Young Jeremy C. , Postelnicu Gheorghe , Rajimehr Reza , Ungerleider Leslie G.
Published: February 2008

Here, we mapped fMRI responses to incrementally changing shapes along a continuous 3D morph, ranging from a head (“face”) to a house (“place”). The response to each shape was mapped independently by using single-stimulus imaging, and stimulus shapes were equated for lower-level visual cues. We measured activity in 2-mm samples across human inferior temporal cortex from the fusiform face area (FFA) (apparently selective for faces) to the parahippocampal place area (PPA) (apparently selective for places), testing for (i) incremental changes in the topography of FFA and PPA (predicted by the continuous-mapping model) or (ii) little or no response to the intermediate morphed shapes (predicted by the category model). Neither result occurred; instead, we found approximately linearly graded changes in the response amplitudes to graded-shape changes, without changes in topography—similar to visual responses in different lower-tier cortical areas.
Crime Without Punishment
Authors: Simonov Alexei
Published: February 2008

Journalists’ lives are of little value in Russia, where deaths go uninvestigated and murderers are rarely brought to account, writes Alexei Simonov
Ste20-related Protein Kinase LOSK (SLK) Controls Microtubule Radial Array in Interphase
Authors: Burakov Anton V. , Zhapparova Olga N. , Kovalenko Olga V. , Zinovkina Liudmila A. , Potekhina Ekaterina S. , Shanina Nina A. , Weiss Dieter G. , Kuznetsov Sergei A. , Nadezhdina Elena S.
Published: February 2008

Interphase microtubules are organized into a radial array with centrosome in the center. This organization is a subject of cellular regulation that can be driven by protein phosphorylation. Only few protein kinases that regulate microtubule array in interphase cells have been described. Ste20-like protein kinase LOSK (SLK) was identified as a microtubule and centrosome-associated protein. In this study we have shown that the inhibition of LOSK activity by dominant-negative mutant K63R-ΔT or by LOSK depletion with RNAi leads to unfocused microtubule arrangement. Microtubule disorganization is prominent in Vero, CV-1, and CHO-K1 cells but less distinct in HeLa cells. The effect is a result neither of microtubule stabilization nor of centrosome disruption. In cells with suppressed LOSK activity centrosomes are unable to anchor or to cap microtubules, though they keep nucleating microtubules. These centrosomes are depleted of dynactin. Vero cells overexpressing K63R-ΔT have normal dynactin “comets” at microtubule ends and unaltered morphology of Golgi complex but are unable to polarize it at the wound edge. We conclude that protein kinase LOSK is required for radial microtubule organization and for the proper localization of Golgi complex in various cell types.
YeastARV1Is Required for Efficient Delivery of an Early GPI Intermediate to the First Mannosyltransferase during GPI Assembly and Controls Lipid Flow from the Endoplasmic Reticulum
Authors: Kajiwara Kentaro , Watanabe Reika , Pichler Harald , Ihara Kensuke , Murakami Suguru , Riezman Howard , Funato Kouichi
Published: February 2008

Glycosylphosphatidylinositol (GPI), covalently attached to many eukaryotic proteins, not only acts as a membrane anchor but is also thought to be a sorting signal for GPI-anchored proteins that are associated with sphingolipid and sterol-enriched domains. GPI anchors contain a core structure conserved among all species. The core structure is synthesized in two topologically distinct stages on the leaflets of the endoplasmic reticulum (ER). Early GPI intermediates are assembled on the cytoplasmic side of the ER and then are flipped into the ER lumen where a complete GPI precursor is synthesized and transferred to protein. The flipping process is predicted to be mediated by a protein referred as flippase; however, its existence has not been proven. Here we show that yeast Arv1p is an important protein required for the delivery of an early GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen. We also provide evidence that ARV1 deletion and mutations in other proteins involved in GPI anchor synthesis affect inositol phosphorylceramide synthesis as well as the intracellular distribution and amounts of sterols, suggesting a role of GPI anchor synthesis in lipid flow from the ER.
Neuronal Death by Oxidative Stress Involves Activation of FOXO3 through a Two-Arm Pathway That Activates Stress Kinases and Attenuates Insulin-like Growth Factor I Signaling
Authors: Dávila David , Torres-Aleman Ignacio
Published: February 2008

Oxidative stress kills neurons by stimulating FOXO3, a transcription factor whose activity is inhibited by insulin-like growth factor I (IGF-I), a wide-spectrum neurotrophic signal. Because recent evidence has shown that oxidative stress blocks neuroprotection by IGF-I, we examined whether attenuation of IGF-I signaling is linked to neuronal death by oxidative stress, as both events may contribute to neurodegeneration. We observed that in neurons, activation of FOXO3 by a burst of oxidative stress elicited by 50 μM hydrogen peroxide (H2O2) recruited a two-pronged pathway. A first, rapid arm attenuated AKT inhibition of FOXO3 through p38 MAPK-mediated blockade of IGF-I stimulation of AKT. A second delayed arm involved activation of FOXO3 by Jun-kinase 2 (JNK2). Notably, blockade of IGF-I signaling through p38 MAPK was necessary for JNK2 to activate FOXO3, unveiling a competitive regulatory interplay between the two arms onto FOXO3 activity. Therefore, an abrupt rise in oxidative stress activates p38 MAPK to tilt the balance in a competitive AKT/JNK2 regulation of FOXO3 toward its activation, eventually leading to neuronal death. In view of previous observations linking attenuation of IGF-I signaling to other causes of neuronal death, these findings suggest that blockade of trophic input is a common step in neuronal death.
Cholesterol Loss Enhances TrkB Signaling in Hippocampal Neurons Aging in Vitro
Authors: Martin Mauricio G. , Perga Simona , Trovò Laura , Rasola Andrea , Holm Pontus , Rantamäki Tomi , Harkany Tibor , Castrén Eero , Chiara Federica , Dotti Carlos G.
Published: February 2008

Binding of the neurotrophin brain-derived neurotrophic factor (BDNF) to the TrkB receptor is a major survival mechanism during embryonic development. In the aged brain, however, BDNF levels are low, suggesting that if TrkB is to play a role in survival at this stage additional mechanisms must have developed. We here show that TrkB activity is most robust in the hippocampus of 21-d-old BDNF-knockout mice as well as in old, wild-type, and BDNF heterozygous animals. Moreover, robust TrkB activity is evident in old but not young hippocampal neurons differentiating in vitro in the absence of any exogenous neurotrophin and also in neurons from BDNF −/− embryos. Age-associated increase in TrkB activity correlated with a mild yet progressive loss of cholesterol. This, in turn, correlated with increased expression of the cholesterol catabolic enzyme cholesterol 24-hydroxylase. Direct cause–effect, cholesterol loss–high TrkB activity was demonstrated by pharmacological means and by manipulating the levels of cholesterol 24-hydroxylase. Because reduced levels of cholesterol and increased expression of choleseterol-24-hydroxylase were also observed in the hippocampus of aged mice, changes in cellular cholesterol content may be used to modulate receptor activity strength in vivo, autonomously or as a way to complement the natural decay of neurotrophin production.
The Cargo Receptors Surf4, Endoplasmic Reticulum-Golgi Intermediate Compartment (ERGIC)-53, and p25 Are Required to Maintain the Architecture of ERGIC and Golgi
Authors: Mitrovic Sandra , Ben-Tekaya Houchaima , Koegler Eva , Gruenberg Jean , Hauri Hans-Peter
Published: February 2008

Rapidly cycling proteins of the early secretory pathway can operate as cargo receptors. Known cargo receptors are abundant proteins, but it remains mysterious why their inactivation leads to rather limited secretion phenotypes. Studies of Surf4, the human orthologue of the yeast cargo receptor Erv29p, now reveal a novel function of cargo receptors. Surf4 was found to interact with endoplasmic reticulum-Golgi intermediate compartment (ERGIC)-53 and p24 proteins. Silencing Surf4 together with ERGIC-53 or silencing the p24 family member p25 induced an identical phenotype characterized by a reduced number of ERGIC clusters and fragmentation of the Golgi apparatus without effect on anterograde transport. Live imaging showed decreased stability of ERGIC clusters after knockdown of p25. Silencing of Surf4/ERGIC-53 or p25 resulted in partial redistribution of coat protein (COP) I but not Golgi matrix proteins to the cytosol and partial resistance of the cis-Golgi to brefeldin A. These findings imply that cargo receptors are essential for maintaining the architecture of ERGIC and Golgi by controlling COP I recruitment.
DRhoGEF2andDiaphanousRegulate Contractile Force during Segmental Groove Morphogenesis in theDrosophilaEmbryo
Authors: Mulinari Shai , Barmchi Mojgan Padash , Häcker Udo
Published: February 2008

Morphogenesis of the Drosophila embryo is associated with dynamic rearrangement of the actin cytoskeleton mediated by small GTPases of the Rho family. These GTPases act as molecular switches that are activated by guanine nucleotide exchange factors. One of these factors, DRhoGEF2, plays an important role in the constriction of actin filaments during pole cell formation, blastoderm cellularization, and invagination of the germ layers. Here, we show that DRhoGEF2 is equally important during morphogenesis of segmental grooves, which become apparent as tissue infoldings during mid-embryogenesis. Examination of DRhoGEF2-mutant embryos indicates a role for DRhoGEF2 in the control of cell shape changes during segmental groove morphogenesis. Overexpression of DRhoGEF2 in the ectoderm recruits myosin II to the cell cortex and induces cell contraction. At groove regression, DRhoGEF2 is enriched in cells posterior to the groove that undergo apical constriction, indicating that groove regression is an active process. We further show that the Formin Diaphanous is required for groove formation and strengthens cell junctions in the epidermis. Morphological analysis suggests that Dia regulates cell shape in a way distinct from DRhoGEF2. We propose that DRhoGEF2 acts through Rho1 to regulate acto-myosin constriction but not Diaphanous-mediated F-actin nucleation during segmental groove morphogenesis.
Deletion of Many Yeast Introns Reveals a Minority of Genes that Require Splicing for Function
Authors: Parenteau Julie , Durand Mathieu , Véronneau Steeve , Lacombe Andrée-Anne , Morin Geneviève , Guérin Valérie , Cecez Bojana , Gervais-Bird Julien , Koh Chu-Shin , Brunelle David , Wellinger Raymund J. , Chabot Benoit , Abou Elela Sherif
Published: February 2008

Splicing regulates gene expression and contributes to proteomic diversity in higher eukaryotes. However, in yeast only 283 of the 6000 genes contain introns and their impact on cell function is not clear. To assess the contribution of introns to cell function, we initiated large-scale intron deletions in yeast with the ultimate goal of creating an intron-free model eukaryote. We show that about one-third of yeast introns are not essential for growth. Only three intron deletions caused severe growth defects, but normal growth was restored in all cases by expressing the intronless mRNA from a heterologous promoter. Twenty percent of the intron deletions caused minor phenotypes under different growth conditions. Strikingly, the combined deletion of all introns from the 15 cytoskeleton-related genes did not affect growth or strain fitness. Together, our results show that although the presence of introns may optimize gene expression and provide benefit under stress, a majority of introns could be removed with minor consequences on growth under laboratory conditions, supporting the view that many introns could be phased out of Saccharomyces cerevisiae without blocking cell growth.
GEF-H1 Couples Nocodazole-induced Microtubule Disassembly to Cell Contractility via RhoA
Authors: Chang Yuan-Chen , Nalbant Perihan , Birkenfeld Jörg , Chang Zee-Fen , Bokoch Gary M.
Published: February 2008

The RhoA GTPase plays a vital role in assembly of contractile actin-myosin filaments (stress fibers) and of associated focal adhesion complexes of adherent monolayer cells in culture. GEF-H1 is a microtubule-associated guanine nucleotide exchange factor that activates RhoA upon release from microtubules. The overexpression of GEF-H1 deficient in microtubule binding or treatment of HeLa cells with nocodazole to induce microtubule depolymerization results in Rho-dependent actin stress fiber formation and contractile cell morphology. However, whether GEF-H1 is required and sufficient to mediate nocodazole-induced contractility remains unclear. We establish here that siRNA-mediated depletion of GEF-H1 in HeLa cells prevents nocodazole-induced cell contraction. Furthermore, the nocodazole-induced activation of RhoA and Rho-associated kinase (ROCK) that mediates phosphorylation of myosin regulatory light chain (MLC) is impaired in GEF-H1–depleted cells. Conversely, RhoA activation and contractility are rescued by reintroduction of siRNA-resistant GEF-H1. Our studies reveal a critical role for a GEF-H1/RhoA/ROCK/MLC signaling pathway in mediating nocodazole-induced cell contractility.
Mapping large, shallow inlets and bays: modelling a Natura 2000 habitat with digital terrain and wave-exposure models
Authors: Bekkby Trine , Isæus Martin
Published: February 2008

Bekkby, T., and Isæus, M. 2008. Mapping large, shallow inlets and bays: modelling a Natura 2000 habitat with digital terrain and wave-exposure models. – ICES Journal of Marine Science, 65: 238–241. EU member countries are obliged to protect a certain share of Natura 2000 habitats. Hence, these habitats must be mapped. This paper is an attempt to provide a tool for modelling one of the Natura 2000 habitat, the “large shallow inlets and bays” (Natura 2000 habitat 1160), using a Norwegian archipelagic area as a case study. The Natura 2000 definition of the habitat is interpreted into criteria used for modelling, and a spatial prediction is presented on a map. The effect of scale, regarding both spatial resolution of data and methodology, is also tested. This is the first publicly accessible attempt to model the Natura 2000 habitat. It shows that the result of the modelling depends on the spatial resolution of the data and the methods used in the modelling process. Using data at a 10-m and a 25-m resolution provides good results, and even the model based on the 50-m data provided an acceptable overall picture.
Evaluating the efficacy of technical measures: a case study of selection device legislation in the UK Crangon crangon (brown shrimp) fishery
Authors: Catchpole Tom L. , Revill Andrew S. , Innes James , Pascoe Sean
Published: February 2008

Catchpole, T. L., Revill, A. S., Innes, J., and Pascoe, S. 2008. Evaluating the efficacy of technical measures: a case study of selection device legislation in the UK Crangon crangon (brown shrimp) fishery. – ICES Journal of Marine Science, 65: 267–275. Bycatch reduction devices are being introduced into a wide range of fisheries, with shrimp and prawn fisheries particularly targeted owing to the heavy discarding common in these fisheries. Although studies are often undertaken to estimate the impact of a technical measure on the fishery before implementation, rarely have the impacts been assessed ex post. Here, the efficacy of the UK legislation pertaining to the use of sievenets in the North Sea Crangon crangon fishery is assessed. Three impacts were evaluated: on fisher behaviour (social), on the level of bycatch (biological), and on vessel profitability (economic). An apparent high level of compliance by skippers was identified despite a low level of enforcement. The estimated reduction in fleet productivity following the introduction of the legislation was 14%, equalling the mean loss of Crangon landings when using sievenets calculated from catch comparison trawls. Sievenets did reduce the unnecessary capture of unwanted marine organisms, but were least effective at reducing 0-group plaice, which make up the largest component of the bycatch. Clearly the legislation has had an effect in the desired direction, but it does not address sufficiently the bycatch issue in the Crangon fishery.
Social cognition
Authors: Frith Chris D
Published: February 2008

Social cognition concerns the various psychological processes that enable individuals to take advantage of being part of a social group. Of major importance to social cognition are the various social signals that enable us to learn about the world. Such signals include facial expressions, such as fear and disgust, which warn us of danger, and eye gaze direction, which indicate where interesting things can be found. Such signals are particularly important in infant development. Social referencing, for example, refers to the phenomenon in which infants refer to their mothers' facial expressions to determine whether or not to approach a novel object. We can learn a great deal simply by observing others. Much of this signalling seems to happen automatically and unconsciously on the part of both the sender and the receiver. We can learn to fear a stimulus by observing the response of another, in the absence of awareness of that stimulus. By contrast, learning by instruction, rather than observation, does seem to depend upon awareness of the stimulus, since such learning does not generalize to situations where the stimulus is presented subliminally. Learning by instruction depends upon a meta-cognitive process through which both the sender and the receiver recognize that signals are intended to be signals. An example would be the ‘ostensive’ signals that indicate that what follows are intentional communications. Infants learn more from signals that they recognize to be instructive. I speculate that it is this ability to recognize and learn from instructions rather than mere observation which permitted that advanced ability to benefit from cultural learning that seems to be unique to the human race.
Examining the Specific Contributions of Individual Arabidopsis Metallothioneins to Copper Distribution and Metal Tolerance
Authors: Guo Woei-Jiun , Meetam Metha , Goldsbrough Peter B.
Published: February 2008

Metallothioneins (MTs) are small cysteine-rich proteins found in various eukaryotes. Plant MTs are classified into four types based on the arrangement of cysteine residues. To determine whether all four types of plant MTs function as metal chelators, six Arabidopsis (Arabidopsis thaliana) MTs (MT1a, MT2a, MT2b, MT3, MT4a, and MT4b) were expressed in the copper (Cu)- and zinc (Zn)-sensitive yeast mutants, Δcup1 and Δzrc1  Δcot1, respectively. All four types of Arabidopsis MTs provided similar levels of Cu tolerance and accumulation to the Δcup1 mutant. The type-4 MTs (MT4a and MT4b) conferred greater Zn tolerance and higher accumulation of Zn than other MTs to the Δzrc1  Δcot1 mutant. To examine the functions of MTs in plants, we studied Arabidopsis plants that lack MT1a and MT2b, two MTs that are expressed in phloem. The lack of MT1a, but not MT2b, led to a 30% decrease in Cu accumulation in roots of plants exposed to 30 μ  m CuSO4. Ectopic expression of MT1a RNA in the mt1a-2 mt2b-1 mutant restored Cu accumulation in roots. The mt1a-2 mt2b-1 mutant had normal metal tolerance. However, when MT deficiency was combined with phytochelatin deficiency, growth of the mt1a-2 mt2b-1 cad1-3 triple mutant was more sensitive to Cu and cadmium compared to the cad1-3 mutant. Together these results provide direct evidence for functional contributions of MTs to plant metal homeostasis. MT1a, in particular, plays a role in Cu homeostasis in the roots under elevated Cu. Moreover, MTs and phytochelatins function cooperatively to protect plants from Cu and cadmium toxicity.
Thiaminase activity of Baltic salmon prey species: a comparision of net‐ and predator‐caught samples
Authors: Wistbacka S. , Bylund G.
Published: February 2008

Thiaminase activity was determined for Gulf of Bothnia (GB) and Gulf of Finland (GF) Baltic herring Clupea harengus membras, sprat Sprattus sprattus and three‐spined stickleback Gasterosteus aculeatus sampled from either trawl or gillnet catches or from Baltic salmon Salmo salar stomachs. The thiaminase activity in Baltic herring was about 10‐fold higher than that in sprat, and there was almost no thiaminase activity in three‐spined stickleback. Thiaminase activity of undigested Baltic herring found in Baltic salmon stomachs was significantly higher than that of trawl‐caught Baltic herring from the same sea area, suggesting that there may be a higher risk of predation for Baltic herring with high thiaminase activity, possibly linked to their health. Thiaminase activity of the gastrointestinal contents of Baltic salmon, feeding almost entirely on Baltic herring in the GB, was significantly higher than for Baltic salmon feeding on both Baltic herring and sprat in the GF. Therefore, Baltic herring may be the major source of thiaminase for Baltic salmon. A tank experiment demonstrated that thiaminase activity in Baltic herring may vary, even within very short time periods. The results were consistent with the hypothesis that the thiaminase content in Baltic salmon forage fish may be an important link in the aetiology of the thiamine deficiency syndrome, M74, in Baltic salmon.
Comparing the diet of two sympatric urolophid elasmobranchs (Trygonoptera testacea Müller & Henle and Urolophus kapalensis Yearsley & Last): evidence of ontogenetic shifts and possible resource partitioning
Authors: Marshall A. D. , Kyne P. M. , Bennett M. B.
Published: February 2008

The diets of two urolophids, the common stingaree Trygonoptera testacea and the kapala stingaree Urolophus kapalensis were analysed and compared to examine resource partitioning between these two morphologically similar sympatric Australian batoids. The diet of T. testacea was polychaete‐based, while that of U. kapalensis was dominated by crustaceans (mostly carid shrimps and amphipods). Intraspecific dietary compositions were examined amongst size classes within each of the two species to identify ontogenetic shifts in diet. Differences in the dietary compositions of the smaller total‐length classes of T. testacea suggest that their diet shifts as they increase in size, from one dominated by carids to one almost entirely comprising polychaetes. Significant ontogenetic dietary shifts were not identified in U. kapalensis. Although the two species shared eight broad dietary categories, their overall dietary compositions were found to be significantly different. The limited overlap in the dietary compositions of these two sympatric stingarees suggests the possibility of resource partitioning, with interspecific competition being implicated as a possible cue. Possible mechanisms for the partitioning of resources within and between these two species are discussed.
The stress and metabolic responses of juvenile Atlantic cod Gadus morhua L. to an acute thermal challenge
Authors: Pérez‐Casanova J. C. , Afonso L. O. B. , Johnson S. C. , Currie S. , Gamperl A. K.
Published: February 2008

Survival, oxygen consumption (), total plasma cortisol and glucose levels and gill heat‐shock protein 70 (hsp70) expression were measured in 10 and 50 g juvenile Atlantic cod Gadus morhua during an acute temperature increase (2° C h−1) to their critical thermal maximum. Ninety three per cent of the fish in both size classes survived to 24° C; however, mortality was 100% within 15 min of reaching this temperature. The for both size classes increased significantly with temperature, reaching peak values at 22° C that were c. 2·8‐fold those of control (10° C) fish. Resting plasma cortisol and glucose levels were lower in 10 g as compared to 50 g fish. Plasma glucose levels were highly variable in both size classes, and significant increases were only seen at >22° C for the 10 g fish. In contrast, plasma cortisol showed an exponential increase with temperature starting at 16° C in both size classes, and reached maximum levels at 22° C that were 19‐fold (10 g fish) and 35‐fold (50 g fish) higher than their respective control groups. Both the constitutive (73 kDa) and inducible (72 kDa) isoforms of hsp70 were detected in both size classes using the widely utilized mouse monoclonal antibody. Expression of these isoforms, however, did not change when Atlantic cod were exposed to elevated temperature, and the 72 kDa isoform was not detected using salmonid‐specific antibodies. These results indicate that juvenile Atlantic cod are very sensitive to acute increases in water temperature. In addition, they (1) show that and plasma cortisol, but not plasma glucose or gill hsp 70 levels, are sensitive indicators of thermal stress in Atlantic cod and (2) support previous reports that the upper critical temperature for this species is 16° C.
Functional morphology of embryonic development in the Port Jackson shark Heterodontus portusjacksoni (Meyer)
Authors: Rodda K. R. , Seymour R. S.
Published: February 2008

The oviparous Port Jackson shark Heterodontus portusjacksoni embryo has a long incubation of 10–11 months during which it undergoes major morphological changes. Initially the egg capsule is sealed from the external environment by mucous plugs in either end of the capsule. Four months into incubation, the egg capsule opens to the surrounding sea water. Fifteen stages of development are defined for this species, the first 10 occur within the sealed capsule, the remaining five after capsule opening to hatching. The functional significance of major definitive characters such as circulation within the yolk membrane and embryo, rhythmic lateral movement of the embryo, external gill filaments, heart activity, internal yolk supplies, egg jelly and the significance of the opening of the egg capsule are described. The egg jelly in the sealed capsule functions to mechanically protect the embryo during early development, however, it eventually creates a hypoxic environment to the embryo as the available oxygen is used up. This generates several physiological challenges to the developing embryo. It is able to overcome these problems by morphological changes such as increasing the effective surface area for gaseous exchange with the development of external gill filaments, fins and extensive circulation in both the embryo and attached external yolk sac. These adaptations become limiting as the embryo grows and respiratory needs outweigh the available oxygen. At this time, the mucous plugs dissolve and the capsule becomes open to the external environment.
Sex differences in the effect of social status on the growth of subordinates in a co‐operatively breeding cichlid
Authors: Hamilton I. M. , Heg D.
Published: February 2008

Social influences on the growth of the co‐operatively breeding cichlid Neolamprologus pulcher were studied by examining the size structure of existing laboratory groups and the responses of males and females to removals of higher‐ranked fish, which created larger size differences with more dominant fish. The size differences between adjacently ranked group members were predicted to differ from expected based on random size distributions of group members. Both males and females were predicted to respond to removals by increasing growth rate. In previously established groups, the size difference between dominant and highest‐ranked subordinate males was greater than expected based on random group‐assembly rules. The size difference between dominant and subordinate females did not differ from the null expectation. Third‐ranked subordinate males increased their growth rate upon moving up one place in the dominance hierarchy (after the removal of higher‐ranking fish) relative to fish that did not change rank. Contrary to predictions, however, females did not increase growth upon increasing rank.
Structure and composition of teleost scales from snakehead Channa argus (Cantor) (Perciformes: Channidae)
Authors: Liu W. T. , Zhang Y. , Li G. Y. , Miao Y. Q. , Wu X. H.
Published: February 2008

The structure of teleost scales from snakehead Channa argus was investigated using thermogravimetric analysis (TG), scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy‐dispersive analysis of X‐rays (EDAX), Fourier transform infra‐red spectroscopy (FTIR) and X‐ray diffraction (XRD). Thermal treatment of fish scales indicates that the fibrillary plate is partially calcified. SEM shows two kinds of scale denticles, arranged along the circuli in the anterior field and the lateral fields, respectively. TEM indicates the stratum laxum with abundant fibrils, chromatophores and capillary blood vessels within the scale covering, and shows the fibrillary plate as an ‘orthogonal plywood structure’ of stratified lamellae, consisting of 80–100 nm diameter collagen fibres co‐aligned in individual lamellae and alternated by c. 90° of the fibre alignment between adjacent lamellae. EDAX, FTIR and XRD show that the mineral phase of the scales is a carbonated hydroxyapatite with a Ca:P molar ratio of 1·85.
Early Miocene sequence development across the New Jersey margin
Authors: Monteverde Donald H. , Mountain Gregory S. , Miller Kenneth G.
Published: February 2008

Sequence stratigraphy provides an understanding of the interplay between eustasy, sediment supply and accommodation in the sedimentary construction of passive margins. We used this approach to follow the early to middle Miocene growth of the New Jersey margin and analyse the connection between relative changes of sea level and variable sediment supply. Eleven candidate sequence boundaries were traced in high‐resolution multi‐channel seismic profiles across the inner margin and matched to geophysical log signatures and lithologic changes in ODP Leg 150X onshore coreholes. Chronologies at these drill sites were then used to assign ages to the intervening seismic sequences. We conclude that the regional and global correlation of early Miocene sequences suggests a dominant role of global sea‐level change but margin progradation was controlled by localized sediment contribution and that local conditions played a large role in sequence formation and preservation. Lowstand deposits were regionally restricted and their locations point to both single and multiple sediment sources. The distribution of highstand deposits, by contrast, documents redistribution by along shelf currents. We find no evidence that sea level fell below the elevation of the clinoform rollover, and the existence of extensive lowstand deposits seaward of this inflection point indicates efficient cross‐shelf sediment transport mechanisms despite the apparent lack of well‐developed fluvial drainage.
Gap in publication of comparative information on new medicines
Authors: Van Luijn Johan C. F. , Stolk Pieter , Gribnau Frank W. J. , Leufkens Hubert G. M.
Published: February 2008

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Randomized active control trials are used by health care professionals and reimbursement authorities for the assessment of the added value of a new medicine.

• Failing to publish the results of clinical trials limits making an evidence based assessment and conducting systematic reviews.

WHAT THIS STUDY ADDS

• About one‐third of the comparative trials used in the authorization process are published at the moment of market authorization and about four out of five within 2 or 3 years. Most of the rest remain unpublished.

• Unpublished trials contain information regarding a different therapeutic use or a different comparator of the same medicine and, in some cases, have influenced the risk : benefit assessment of the registration authorities.

• A standardized public registration of results of the main premarketing trials is advocated to fill the publication gap.

AIMS

To determine the time‐lag between the EU authorization of new medicines and the publications of the main randomized active control trials (RaCTs) used in the authorization process and to compare unpublished with published RaCTs of the same medicine.

METHODS

All RaCTs for new medicines with a new active substance, authorized between 1999 and 2003, were extracted from the European Public Assessment Reports (EPAR). Information about the publication status of RaCTs was obtained from the MEDLINE and EMBASE databases.

RESULTS

We identified 116 RaCTs for 42 new medicines; 28% of the RaCTs had been published at the moment of market authorization, 59% after 1 year, 78% after 2 and 83% after 3 years. Most of the rest of the studies remained unpublished after 3 years of follow‐up. Unpublished RaCTs differed from published trials of the same medicine especially regarding therapeutic use and/or comparator. In some cases unpublished trials have influenced the risk : benefit asssessment of the registration authorities.

CONCLUSIONS

Most of the main RaCTs, relevant for assessing the added value of a new medicine, are published subsequent to market entry; some of these trials remain unpublished. We argue for a standardized public registration of the results of the main premarketing clinical trials as a condition for market authorization.
Population pharmacokinetics and exploratory pharmacodynamics of ifosfamide according to continuous or short infusion schedules: an n = 1 randomized study
Authors: Brain Etienne G. C. , Rezai Kevan , Lokiec François , Gutierrez Maya , Urien Saïk
Published: February 2008

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• The optimal infusion duration for ifosfamide remains to be determined.

• No differences according to time of infusion have been identified in traditional pharmacokinetic endpoints, such as area under the curve.

• The impact on pharmacodynamics has never been modelled or correlated with pharmacokinetics.

WHAT THIS STUDY ADDS

• The pharmacokinetics and pharmacodynamics of ifosfamide and its main metabolites can both be modelled with no influence of infusion duration.

• Pharmacodynamic modelling (renal and haematological toxicity) allows further simulations of new schedules with favourable toxicity profiles.

AIMS

To model the pharmacokinetics and pharmacodynamics of ifosfamide and its key metabolites. The pharmacodynamic parameters included were renal toxicity and myelosuppression measured using urinary β2‐microglobulin (BMG) and absolute neutrophil count (ANC), respectively.

METHODS

Seventeen patients were enrolled into an n = 1 randomized trial during two consecutive cycles of ifosfamide 9 g m−2 during each cycle given by a 3 h or 72 h infusion. Data were analyzed using NONMEM.

RESULTS

Ifosfamide and metabolite concentration–time profiles were described by a one‐compartment open‐model with auto‐induction of clearance. BMG and ANC time‐courses were related to ifosfamide concentration via indirect response models.

CONCLUSIONS

This modelling allowed the simulation of weekly schedules of flat doses with favourable myelotoxic profiles.
Mechanistic modelling of tesaglitazar pharmacokinetic data in subjects with various degrees of renal function – evidence of interconversion
Authors: Hamrén Bengt , Ericsson Hans , Samuelsson Ola , Karlsson Mats O.
Published: February 2008

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Tesaglitazar, is predominantly metabolized (to an acyl glucuronide of the parent compound) and 20% of given dose is found unchanged in the urine.

• Acyl glucuronides are know to be unstable and can become hydrolysed back to parent compound, a phenomena called interconversion.

WHAT THIS STUDY ADDS

• A likely mechanism (interconversion) for the cause of the increased exposure of tesaglitazar in subjects with impaired renal function.

• A possible modelling framework to evaluate interconversion without dosing of the metabolite based on the simultaneous analysis of plasma and urine data from a group of subjects with varying renal function.

• A mechanistic understanding of the pharmacokinetic properties of tesaglitazar and its metabolite.

AIMS

To develop a mechanistic pharmacokinetic (PK) model for tesaglitazar and its metabolite (an acyl glucuronide) following oral administration of tesaglitazar to subjects with varying renal function, and derive an explanation for the increased plasma exposure of tesaglitazar in subjects with impaired renal function.

METHODS

Data were from a 6‐week study in subjects with renal insufficiency and matched controls undergoing repeated oral dosing with tesaglitazar (n = 41). Compartmental population PK modelling was employed to describe the PK of tesaglitazar and its metabolite, in plasma and urine, simultaneously. Two hypotheses were tested to investigate the increased exposure of tesaglitazar in subjects with renal functional impairment: tesaglitazar metabolism is correlated with renal function, or metabolite elimination is reduced in renal insufficiency, leading to increased hydrolysis (interconversion) to the parent compound via biliary circulation.

RESULTS

The hypothesis for interconversion was best supported by the data. The population PK model included first‐order absorption, two‐compartment disposition and separate renal (0.027 l h−1) and metabolic (1.9 l h−1) clearances for tesaglitazar. The model for the metabolite; one‐compartment disposition with renal (saturable,Vmax = 0.19 μmol l−1andKm = 0.04 μmol l−1) and nonrenal clearances (1.2 l h−1), biliary secretion (12 h−1) to the gut, where interconversion and reabsorption (0.8 h−1) of tesaglitazar occurred.

CONCLUSION

A mechanistic population PK model for tesaglitazar and its metabolite was developed in subjects with varying degrees of renal insufficiency. The model and data give insight into the likely mechanism (interconversion) of the increased tesaglitazar exposure in renally impaired subjects, and separate elimination and interconversion processes without dosing of the metabolite.
A pilot study of the association of pharmacokinetic and pharmacodynamic parameters of warfarin with the dose in patients on long‐term anticoagulation
Authors: Kulkarni Uday P. , Swar Balkrishna D. , Karnad Dilip R. , Davis Sanish , Patwardhan Anil M. , Kshirsagar Nilima A. , Gogtay Nithya J.
Published: February 2008

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Warfarin is a widely used anticoagulant with a low therapeutic index.

• There is wide interindividual variation in the pharmacokinetics and pharmacodynamics of warfarin which is also reflected in the warfarin dose requirement.

• CYP2C9 and VKORC1 polymorphisms have been shown to affect warfarin dose requirement. However a large amount of the variation in warfarin dose remains unaccounted for.

WHAT THIS STUDY ADDS

• Our findings suggest that in patients who are on long‐term warfarin therapy, INR : plasma 7‐hydroxywarfarin concentration correlates well with warfarin requirement and also accounts for a large amount of variation in warfarin dose.

AIMS

To assess the correlation between plasma total warfarin concentration, plasma 7‐hydroxywarfarin concentration and INR and the weekly doses of warfarin in patients on long‐term anticoagulation.

METHODS

Twenty‐five patients on long‐term anticoagulation with warfarin were studied. Plasma total warfarin and 7‐hydroxywarfarin concentrations and INR were determined. Equations were derived with the weekly warfarin dose as the dependent variable and plasma total warfarin concentration : plasma 7‐hydroxywarfarin concentration, INR : plasma total warfarin concentration and INR : plasma 7‐hydroxywarfarin concentration as independent variables.

RESULTS

There was a good correlation between INR : plasma total warfarin concentration and the weekly dose of warfarin (y = 46.73e−0.30x, r2 = 0.65). There was a better correlation between INR : plasma 7‐hydroxywarfarin concentration and the weekly dose of warfarin (y = 156.52x−0.63, r2 = 0.74)

CONCLUSIONS

Pharmacokinetic parameters along with INR seem to correlate with the weekly doses of warfarin in patients on long‐term anticoagulation. These parameters may therefore be useful for predicting warfarin doses.
Paediatric myelodysplastic syndromes and juvenile myelomonocytic leukaemia: molecular classification and treatment options
Authors: Niemeyer Charlotte Marie , Kratz Christian Peter
Published: February 2008

Myelodysplastic syndromes (MDS) and the mixed myelodysplastic/myeloproliferative disorder juvenile myelomonocytic leukaemia (JMML) are rare haematopoietic stem cell diseases in children. While MDS‐initiating events remain largely obscure, a growing body of clinical, genetic and laboratory evidence suggests that JMML is, at least in part, caused by aberrant signal transduction resulting from mutations of components of the RAS signalling pathway. To date, haematopoietic stem cell transplantation cures more than half of children diagnosed with MDS or JMML. Research on genetic conditions predisposing to MDS in young age, such as inherited syndromes with bone marrow failure, may present important insights into MDS pathogenesis.
Capture and enrichment of CD34‐positive haematopoietic stem and progenitor cells from blood circulation using P‐selectin in an implantable device
Authors: Wojciechowski Joel C. , Narasipura Srinivas D. , Charles Nichola , Mickelsen Deanne , Rana Kuldeeepsinh , Blair Martha L. , King Michael R.
Published: February 2008

Clinical infusion of haematopoietic stem and progenitor cells (HSPCs) is vital for restoration of haematopoietic function in many cancer patients. Previously, we have demonstrated an ability to mimic physiological cell trafficking in order to capture CD34‐positive (CD34+) HSPCs using monolayers of the cell adhesion protein P‐selectin in flow chambers. The current study aimed to determine if HSPCs could be captured directly from circulating blood in vivo. Vascular shunt prototypes, coated internally with P‐selectin, were inserted into the femoral artery of rats. Blood flow through the cell capture device resulted in a wall shear stress of 4–6 dynes/cm2. After 1‐h blood perfusion, immunofluorescence microscopy and flow cytometric analysis revealed successful capture of mononuclear cells positive for the HSPC surface marker CD34. Purity of captured CD34+ cells showed sevenfold enrichment over levels found in whole blood, with an average purity of 28%. Robust cell capture and HSPC enrichment were also demonstrated in devices that were implanted in a closed‐loop arterio‐venous shunt conformation for 2 h. Adherent cells were viable in culture and able to differentiate into burst‐forming units. This study demonstrated an ability to mimic the physiological arrest of HSPCs from blood in an implantable device and may represent a practical alternative for adult stem cell capture and enrichment.
Prediction of relapse in paediatric pre‐B acute lymphoblastic leukaemia using a three‐gene risk index
Authors: Hoffmann Katrin , Firth Martin J. , Beesley Alex H. , Freitas Joseph R. , Ford Jette , Senanayake Saranga , De Klerk Nicholas H. , Baker David L. , Kees Ursula R.
Published: February 2008

Despite high cure rates 25% of children with acute lymphoblastic leukaemia (ALL) relapse and have dismal outcome. Crucially, many are currently stratified as standard risk (SR) and additional markers to improve patient stratification are required. Here we have used diagnostic bone marrow specimens from 101 children with pre‐B ALL to examine the use of gene expression profiles (GEP) as predictors of long‐term clinical outcome. Patients were divided into two cohorts for model development and validation based on availability of specimen material. Initially, GEP from 55 patients with sufficient material were analysed using HG‐U133A microarrays, identifying an 18‐gene classifier (GC) that was more predictive of outcome than conventional prognostic parameters. After feature selection and validation of expression levels by quantitative reverse transcription polymerase chain reaction (qRT‐PCR), a three‐gene qRT‐PCR risk index [glutamine synthetase (GLUL), ornithine decarboxylase antizyme inhibitor (AZIN), immunoglobulin J chain (IGJ)] was developed that predicted outcome with an accuracy of 89% in the array cohort and 87% in the independent validation cohort. The data demonstrate the feasibity of using GEP to improve risk stratification in childhood ALL. This is particularly important for the identification of patients destined to relapse despite their current stratification as SR, as more intensive front‐line treatment options for these individuals are already available.
Neutrophil function is preserved in a pooled granulocyte component prepared from whole blood donations
Authors: Bashir Saber , Stanworth Simon , Massey Edwin , Goddard Fred , Cardigan Rebecca
Published: February 2008

Whole blood‐derived granulocytes (buffy coats) are issued as an alternative to apheresis donations, but are heavily contaminated with red cells and platelets and there is minimal in vitro data describing their functionality. We developed a purer pooled granulocyte component (PGC) from whole blood donations by pooling 10 ABO‐matched buffy coats with 400 ml of platelet additive solution (SSP+) and re‐centrifuging. The PGC was irradiated (25–50 Gy) and neutrophil viability, chemotaxis, phagocytosis and respiratory burst activity were determined by flow cytometry. Results from 13 PGC at 16–20 h following donation were compared with those obtained from 20 standard individual buffy coats and with fresh whole blood. The PGC contained similar numbers of neutrophils (approximately 0·9 × 1010) with a reduced volume and haemoglobin content when compared with 10 individual buffy coats. Neutrophils in the PGC maintained >90% viability, oxidative burst and phagocytic activity and their ability to migrate towards a chemoattractant 16–20 h following donation, which is similar to results obtained with either fresh whole blood or standard buffy coats. Therefore, neutrophil function in the PGC was preserved 16–20 h following donation, but this product had significantly lower red cell contamination compared with 10 buffy coats, which are currently transfused.