bluuebunny/crossref_metadata_2025 huggingface dataset:
Age-related enhancement of a protein synthesis-dependent late phase of LTP induced by low frequency paired-pulse stimulation in hippocampus
Authors: Huang Yan-You , Kandel Eric R.
Published: June 2006

Protein synthesis-dependent late phase of LTP (L-LTP) is typically induced by repeated high-frequency stimulation (HFS). This form of L-LTP is reduced in the aged animal and is positively correlated with age-related memory loss. Here we report a novel form of protein synthesis-dependent late phase of LTP in the CA1 region of hippocampus induced by a brief 1-Hz paired-pulse stimulation (PP-1 Hz, 1 min). In contrast to L-LTP induced by HFS, the late phase of PP-1 Hz LTP does not exist in young adult animals. Rather, it emerges and becomes enhanced in an age-related way. Thus, in 1.5- to 2-mo-old mice, a brief PP-1 Hz stimulation induces only a short lasting LTP, decaying to baseline in about 90 min. By contrast, PP-1 Hz stimulation induces an enduring and protein synthesis dependent LTP in 12- to 18-mo-old mice. The PP-1 Hz-induced L-LTP is dependent on NMDA receptor activation, requires voltage-dependent calcium channels, and is modulated by dopamine D1/D5 receptors. Because memory ability declines with aging, the age-related enhancement of L-LTP induced by PP-1 Hz stimulation indicates that this form of L-LTP appears to be inversely correlated with memory ability.
Predicting danger: The nature, consequences, and neural mechanisms of predictive fear learning
Authors: McNally Gavan P. , Westbrook R. Frederick
Published: June 2006

The ability to detect and learn about the predictive relations existing between events in the world is essential for adaptive behavior. It allows us to use past events to predict the future and to adjust our behavior accordingly. Pavlovian fear conditioning allows anticipation of sources of danger in the environment. It guides attention away from poorer predictors toward better predictors of danger and elicits defensive behavior appropriate to these threats. This article reviews the differences between learning about predictive relations and learning about contiguous relations in Pavlovian fear conditioning. It then describes behavioral approaches to the study of these differences and to the examination of subtle variations in the nature and consequences of predictive learning. Finally, it reviews recent data from rodent and human studies that have begun to identify the neural mechanisms for direct and indirect predictive fear learning.
Structure of the 21–30 fragment of amyloid β‐protein
Authors: Baumketner Andrij , Bernstein Summer L. , Wyttenbach Thomas , Lazo Noel D. , Teplow David B. , Bowers Michael T. , Shea Joan‐Emma
Published: May 2006

Folding and self‐assembly of the 42‐residue amyloid β‐protein (Aβ) are linked to Alzheimer's disease (AD). The 21–30 region of Aβ, Aβ(21–30), is resistant to proteolysis and is believed to nucleate the folding of full‐length Aβ. The conformational space accessible to the Aβ(21–30) peptide is investigated by using replica exchange molecular dynamics simulations in explicit solvent. Conformations belonging to the global free energy minimum (the “native” state) from simulation are in good agreement with reported NMR structures. These conformations possess a bend motif spanning the central residues V24–K28. This bend is stabilized by a network of hydrogen bonds involving the side chain of residue D23 and the amide hydrogens of adjacent residues G25, S26, N27, and K28, as well as by a salt bridge formed between side chains of K28 and E22. The non‐native states of this peptide are compact and retain a native‐like bend topology. The persistence of structure in the denatured state may account for the resistance of this peptide to protease degradation and aggregation, even at elevated temperatures.
The synthesis and high‐level expression of a β2‐adrenergic receptor gene in a tetracycline‐inducible stable mammalian cell line
Authors: Chelikani Prashen , Reeves Philip J. , Rajbhandary Uttam L. , Khorana H. Gobind
Published: May 2006

High‐level expression of G‐protein‐coupled receptors (GPCRs) in functional form is required for structure–function studies. The main goal of the present work was to improve expression levels of β2‐adrenergic receptor (β2‐AR) so that biophysical studies involving EPR, NMR, and crystallography can be pursued. Toward this objective, the total synthesis of a codon‐optimized hamster β2‐AR gene suitable for high‐level expression in mammalian systems has been accomplished. Transient expression of the gene in COS‐1 cells resulted in 18 ± 3 pmol β2‐AR/mg of membrane protein, as measured by saturation binding assay using the β2‐AR antagonist [3H] dihydroalprenolol. Previously, we reported the development of an HEK293S tetracycline‐inducible system for high‐level expression of rhodopsin. Here, we describe construction of β2‐AR stable cell lines using the HEK293S‐TetR‐inducible system, which, after induction, express wild‐type β2‐AR at levels of 220 ± 40 pmol/mg of membrane protein corresponding to 50 ± 8 μg/15‐cm plate. This level of expression is the highest reported so far for any wild‐type GPCR, other than rhodopsin. The yield of functional receptor using the single‐step affinity purification is 12 ± 3 μg/15‐cm plate. This level of expression now makes it feasible to pursue structure–function studies using EPR. Furthermore, scale‐up of β2‐AR expression using suspension cultures in a bioreactor should now allow production of enough β2‐AR for the application of biophysical techniques such as NMR spectroscopy and crystallography.
Molecular dissection of the mycobacterial stringent response protein Rel
Authors: Jain Vikas , Saleem‐Batcha Raspudin , China Arnab , Chatterji Dipankar
Published: May 2006

Latency in Mycobacterium tuberculosis poses a barrier in its complete eradication. Overexpression of certain genes is one of the factors that help these bacilli survive inside the host during latency. Among these genes, rel, which leads to the expression of Rel protein, plays an important role by synthesizing the signaling molecule ppGpp using GDP and ATP as substrates, thereby changing bacterial physiology. In Gram‐negative bacteria, the protein is thought to be activated in vivo in the presence of ribosome by sensing uncharged tRNA. In the present report, we show that Rel protein from Mycobacterium smegmatis, which is highly homologous to M. tuberculosis Rel, is functional even in the absence of ribosome and uncharged tRNA. From the experiments presented here, it appears that the activity of RelMsm is regulated by the domains present at the C terminus, as the deletion of these domains results in higher synthesis activity, with little change in hydrolysis of ppGpp. However, in the presence of tRNA, though the synthesis activity of the full‐length protein increases to a certain extent, the hydrolysis activity undergoes drastic reduction. Full‐length Rel undergoes multimerization involving interchain disulfide bonds. The synthesis of pppGpp by the full‐length protein is enhanced in the reduced environment in vitro, whereas the hydrolysis activity does not change significantly. Mutations of cysteines to serines result in monomerization with a simultaneous increase in the synthesis activity. Finally, it has been possible to identify the unique cysteine, of six present in Rel, required for tRNA‐mediated synthesis of ppGpp.
Positioning of proteins in membranes: A computational approach
Authors: Lomize Andrei L. , Pogozheva Irina D. , Lomize Mikhail A. , Mosberg Henry I.
Published: May 2006

A new computational approach has been developed to determine the spatial arrangement of proteins in membranes by minimizing their transfer energies from water to the lipid bilayer. The membrane hydrocarbon core was approximated as a planar slab of adjustable thickness with decadiene‐like interior and interfacial polarity profiles derived from published EPR studies. Applicability and accuracy of the method was verified for a set of 24 transmembrane proteins whose orientations in membranes have been studied by spin‐labeling, chemical modification, fluorescence, ATR FTIR, NMR, cryo‐microscopy, and neutron diffraction. Subsequently, the optimal rotational and translational positions were calculated for 109 transmembrane, five integral monotopic and 27 peripheral protein complexes with known 3D structures. This method can reliably distinguish transmembrane and integral monotopic proteins from water‐soluble proteins based on their transfer energies and membrane penetration depths. The accuracies of calculated hydrophobic thicknesses and tilt angles were ∼1 Å and 2°, respectively, judging from their deviations in different crystal forms of the same proteins. The hydrophobic thicknesses of transmembrane proteins ranged from 21.1 to 43.8 Å depending on the type of biological membrane, while their tilt angles with respect to the bilayer normal varied from zero in symmetric complexes to 26° in asymmetric structures. Calculated hydrophobic boundaries of proteins are located ∼5 Å lower than lipid phosphates and correspond to the zero membrane depth parameter of spin‐labeled residues. Coordinates of all studied proteins with their membrane boundaries can be found in the Orientations of Proteins in Membranes (OPM) database:http://opm.phar.umich.edu/.
558. Impatiens Salpinx
Authors: Crouch Neil R. , Burrows John E. , Burrows Sandra M.
Published: June 2006

Summary.  The Central African balsam Impatiens salpinx Schulze & Launert, endemic to the Chimanimani Mountains, is described and illustrated. Its taxonomy, ecology, pollination and cultivation requirements are discussed.
The True Identity of Meconopsis Napaulensis DC.
Authors: Grey‐Wilson Christopher
Published: June 2006

Summary.  In assessing the true identity of M. napaulensis DC. it has been necessary to re‐evaluate the whole of the M. napaulensis aggregate, a single species according to George Taylor (1934) that stretched in a narrow band from west Nepal through Sikkim, Bhutan, Assam and northern Burma (Myanmar) to western China. This has necessitated revising the whole of subsection Eupolychaetia and, as a result, four new species are described here: M. chankheliensis, M. ganeshensis, M. staintonii and M. wilsonii, while M. wallichii Hook. f. is reinstated.
Placebo‐ and paracetamol‐controlled study on the efficacy and tolerability of hyoscine butylbromide in the treatment of patients with recurrent crampy abdominal pain
Authors: MUELLER‐LISSNER S. , TYTGAT G. N. , PAULO L. G. , QUIGLEY E. M. M. , BUBECK J. , PEIL H. , SCHAEFER E.
Published: June 2006

Aim

To compare the efficacy and tolerability of oral hyoscine butylbromide (hereafter hyoscine) 10 mg t.d.s., paracetamol 500 mg t.d.s. and their fixed combination against placebo in patients with recurrent crampy abdominal pain.

Methods

A total of 1637 patients were entered into a four‐arm double‐blind study. After a 1 week placebo run‐in, they were randomized to 3 weeks of treatment with one of the four therapies with assessments after 1, 2 and 3 weeks. Pain intensity (Visual Analogue Scale) and pain frequency (Verbal Rating Scale) were self‐assessed daily.

Results

Pain intensity on the Visual Analogue Scale decreased in all treatment groups; the adjusted mean changes from baseline were 2.3, 2.4 and 2.4 cm for the hyoscine, paracetamol and combination groups, respectively, compared with 1.9 cm for the placebo group (all P < 0.0001). The Verbal Rating Scale also showed a statistically significant decrease of 0.7, 0.7 and 0.7 in the hyoscine, paracetamol and combination groups compared with 0.5 in placebo (all P < 0.0001). All treatments were well tolerated: 16%, 14%, 17% and 11% of patients on hyoscine, paracetamol, combination and placebo reported at least one adverse event.

Conclusions

Hyoscine, paracetamol and their fixed combination are effective in the treatment of recurrent crampy abdominal pain and well tolerated if used three times daily continuously for 3 weeks.
Prior chemoradiotherapy is associated with a higher life‐threatening complication rate after palliative insertion of metal stents in patients with oesophageal cancer
Authors: LECLEIRE S. , DI FIORE F. , BEN‐SOUSSAN E. , ANTONIETTI M. , HELLOT M.‐F. , PAILLOT B. , LEREBOURS E. , DUCROTTÉ P. , MICHEL P.
Published: June 2006

Background

Self‐expanding metal stents are used routinely to palliate dysphagia due to oesophageal cancer.

Study aim

To compare the frequency of life‐threatening complications after self‐expanding metal stent insertion, depending on whether patients received prior chemoradiotherapy or no treatment.

Patients and methods

During 7 years, 116 consecutive patients were treated at a single centre in a palliative intent by insertion of self‐expanding metal stent for dysphagia due to an oesophageal cancer. Patients were retrospectively separated into two groups: patients with chemoradiotherapy before self‐expanding metal stent insertion (group 1, n = 56) and patients with no treatment before or after self‐expanding metal stent insertion (group 2, n = 60). Life‐threatening complications were compared and predictive risk factors of postprocedure complications were identified.

Results

Median dysphagia was significantly improved during the first month (grade 3 to grade 1 in the two groups). Early and late major complications occurred more frequently in group 1 (23.2% vs. 3.3%; P < 0.002 and 21.6% vs. 5.1%; P < 0.02 respectively). Prior chemoradiotherapy was the only independent predictive factor of postprocedure major complications, with an odds ratio of 5.59 (CI 95% 1.7–18.1).

Conclusions

Life‐threatening complications after palliative self‐expanding metal stent placement seem to occur more frequently in patients with prior chemoradiotherapy. Prevention of these severe complications should be considered before stenting.
Review article: the modern diagnosis and management of haemochromatosis
Authors: ADAMS P. C.
Published: June 2006

Haemochromatosis is the most common genetic disease in populations of European ancestry. Despite estimates based on genetic testing in Caucasian populations of 1 in 227, many physicians consider haemochromatosis to be a rare disease.

The diagnosis can be elusive because of the non‐specific nature of the symptoms. Of all the symptoms, liver disease has the most consistent relationship to haemochromatosis and the prognosis of haemochromatosis is most closely linked to the degree of iron overload.

With the discovery of the HFE gene in 1996, comes new insights into the pathogenesis of the disease and new diagnostic strategies. However, a growing number of new iron‐related genes have been discovered and linked to other iron overload syndromes.
Cysteinyl leukotrienes: multi‐functional mediators in allergic rhinitis
Authors: Peters‐Golden M. , Gleason M. M. , Togias A.
Published: June 2006

Cysteinyl leukotrienes (CysLTs) are a family of inflammatory lipid mediators synthesized from arachidonic acid by a variety of cells, including mast cells, eosinophils, basophils, and macrophages. This article reviews the data for the role of CysLTs as multi‐functional mediators in allergic rhinitis (AR). We review the evidence that: (1) CysLTs are released from inflammatory cells that participate in AR, (2) receptors for CysLTs are located in nasal tissue, (3) CysLTs are increased in patients with AR and are released following allergen exposure, (4) administration of CysLTs reproduces the symptoms of AR, (5) CysLTs play roles in the maturation, as well as tissue recruitment, of inflammatory cells, and (6) a complex inter‐regulation between CysLTs and a variety of other inflammatory mediators exists.
Alginic acid has anti‐anaphylactic effects and inhibits inflammatory cytokine expression via suppression of nuclear factor‐κB activation
Authors: Jeong H.‐J. , Lee S.‐A. , Moon P.‐D. , Na H.‐J. , Park R.‐K. , Um J.‐Y. , Kim H.‐M. , Hong S.‐H.
Published: June 2006

Background
Alginic acid is comprised of complex polymerized polysaccharides, and can be chemically extracted from seaweed. Alginic acid has an inhibitory effect on histamine release, but its molecular mechanisms are not well understood.

Objective
To investigate the effect of alginic acid on the mast cell‐mediated anaphylactic and inflammatory reaction using in vivo and in vitro models and elucidate its molecular mechanisms.

Materials and method
The effect of alginic acid on an allergy model was analysed by anaphylaxis, a histidine decarboxylase (HDC) assay, and a histamine assay. Cytokine production was analysed by means of ELISA. Cytokine expression was analysed by means of RT‐PCR, and Western blotting. Transcription factor activity was analysed by a luciferase assay and a transcription factor‐enzyme linked immunoassay.

Results
Alginic acid dose dependently inhibited compound 48/80‐induced systemic anaphylaxis with doses of 0.25–1 g/kg 1 h (P<0.01, n=6) and significantly inhibited passive cutaneous anaphylaxis by 54.8%. Alginic acid (0.01–1 μg/mL) inhibited histamine release from serum and peritoneal mast cells (P<0.01). All these effects were stronger than those of disodium cromoglycate (DSCG), the reference drug tested. Alginic acid also inhibited HDC expression and activity on the phorbol myristate acetate (PMA)+A23187‐stimulated human mast cell line, HMC‐1 cells. Moreover, alginic acid significantly inhibited the production of PMA+A23187‐induced inflammatory cytokines, IL‐1β and TNF‐α, but not that of IL‐6 or IL‐8. In activated HMC‐1 cells, the expression level of nuclear factor (NF)‐κB/Rel A protein increased in the nucleus, whereas the level of NF‐κB/Rel A in the nucleus was decreased by alginic acid treatment. In addition, alginic acid (0.01 μg/mL) decreased the PMA+A23187‐induced luciferase activity and DNA‐binding activity.

Conclusion
The present results indicate that alginic acid has potent anti‐anaphylactic and anti‐inflammatory properties.
Fumaric acid esters are effective in chronic experimental autoimmune encephalomyelitis and suppress macrophage infiltration
Authors: Schilling S , Goelz S , Linker R , Luehder F , Gold R
Published: June 2006

Fumaric acid esters (FAE) have proven their therapeutic efficacy in psoriasis, a Th1 mediated skin disease. More recently, preliminary data have suggested an activity in multiple sclerosis (MS) as well. To investigate further possible mechanisms of action of these compounds in inflammatory diseases, we studied the FAE methyl hydrogen fumarate (MHF) and dimethyl fumarate (DMF) in chronic experimental autoimmune encephalomyelitis (EAE) induced by immunization of C57BL/6 mice with MOG peptide aa 35–55. Preventive treatment with these FAE was delivered twice a day by oral gavage. Both esters had a significant therapeutic effect on the disease course and histology showed a strongly reduced macrophage inflammation in the spinal cord. Multiparameter cytokine analysis from blood detected an increase of IL-10 in the treated animals. We conclude that the underlying biological activity of FAE in EAE is complex and, to elucidate the molecular mechanisms, further investigation is needed.
Antibodies targeting the calcium binding skeletal muscle protein calsequestrin are specific markers of ophthalmopathy and sensitive indicators of ocular myopathy in patients with Graves’ disease
Authors: Gopinath B , Musselman R , Beard N , El-Kaissi S , Tani J , Adams C-L , Wall J R
Published: June 2006

We have identified several eye muscle antigens and studied the significance of the corresponding serum autoantibodies in patients with Graves’ disease. Of these antigens, only calsequestrin is expressed more in eye muscle than other skeletal muscles, which could explain at least partly the specific involvement of eye muscle in patients with Graves’ disease. Earlier, we found a modest relationship between anti-calsequestrin antibodies and ophthalmopathy, but in that study we used calsequestrin prepared from rabbit heart muscle and measured antibodies by immunoblotting. We have reinvestigated the prevalences of anti-calsequestrin antibodies in larger groups of well-characterized patients with thyroid autoimmunity with and without ophthalmopathy and control patients and healthy subjects, using standard enzyme-linked immunosorbent assay incorporating highly purified rabbit skeletal muscle calsequestrin, which has a 97% homology with human calsequestrin, as antigen. Anti-calsequestrin antibodies were detected in 78% of patients with active congestive ophthalmopathy, in 92% of those with active inflammation and eye muscle involvement, but in only 22% of patients with chronic, ‘burnt out’ disease. Tests were also positive in 5% of patients with Graves’ hyperthyroidism without evident ophthalmopathy (two patients) and one patient with ‘watery eyes’ but no other clear signs of congestive ophthalmopathy and IgA nephropathy and no known thyroid disease, but in no patient with Hashimoto’s thyroiditis, toxic nodular goitre, non-toxic multi-nodular goitre or diabetes, or age- and sex-matched healthy subjects. In serial studies of all 11 patients with Graves’ hyperthyroidism who had active ophthalmopathy at the time of the first clinic visit, or developed eye signs during the first 6 months, and positive anti-calsequestrin antibodies in at least one sample, anti-calsequestrin antibodies correlated with the onset of ocular myopathy in six patients. Antibodies targeting calsequestrin appear to be specific markers for ophthalmopathy and sensitive indicators of the ocular myopathy subtype of ophthalmopathy in patients with thyroid autoimmunity. However, these results must be considered preliminary until a large prospective study of patients with newly diagnosed Graves’ hyperthyroidism, in which serum levels of calsequestrin antibodies are correlated with clinical changes and orbital eye muscle and connective tissue/fat volumes, has been carried out.
Fertility outcomes in women with hypopituitarism
Authors: Hall R. , Manski‐Nankervis J. , Goni N. , Davies M. C. , Conway G. S.
Published: June 2006

Background  Women with hypopituitarism are known to have a poor outcome once pregnancy has been achieved by ovulation induction. There are no data, however, recording the efficacy of ovulation induction and pregnancy rates in this group of subfertile women.

Methods  The outcome of fertility treatments in all 19 women with hypopituitarism attending the fertility clinics of University College London Hospitals over the past 20 years was audited.

Results  Ovulation was achieved in almost all women (95%) but occurred in only 60% of treatment cycles. Pregnancy was achieved in 47% of women or 11% of cycles resulting in a live birth rate of 6·7% per cycle. Seven of the 18 pregnancies (39%) miscarried. Only 42% of women treated achieved a live birth.

Conclusion  Ovulation induction in women with hypopituitarism yields relatively low pregnancy rates in comparison to other causes of anovulation and a high miscarriage rate. Pituitary hormone deficiency beyond gonadotrophins has a major adverse effect on achieving pregnancy.
Polymorphisms in the interleukin‐6 receptor gene are associated with body mass index and with characteristics of the metabolic syndrome
Authors: Esteve Eduardo , Villuendas Gemma , Mallolas Judith , Vendrell Joan , López‐Bermejo Abel , Rodríguez Matilde , Recasens Mónica , Ricart Wifredo , San Millán José L. , Escobar‐Morreale Héctor , Richart Cristóbal , Fernández‐Real José Manuel
Published: June 2006

Objective  Low‐grade inflammation has been related to obesity, insulin resistance and the metabolic syndrome. The Asp358Ala variant and the CA‐repeat polymorphism in the interleukin‐6 receptor (IL‐6R) gene have been reported to be associated with obesity in Pima Indians and Spanish women, respectively. The aim of this study was to investigate the association between these polymorphisms and obesity in a Mediterranean‐Caucasian population, and to determine whether this polymorphism was related to the metabolic syndrome as defined by the National Cholesterol Education Program – Adult Treatment Panel III (NCEP/ATP‐III) criteria.

Design  Cross‐sectional.

Patients  Three hundred and ninety subjects from the general population.

Methods  The Asp358Ala and CA‐repeat polymorphisms were analysed by polymerase chain reaction (PCR) amplification, followed by restriction fragment length polymorphism or capillary electrophoresis, respectively.

Results  Both polymorphisms were in strong linkage disequilibrium, Asp358 alleles being associated with 149 CA‐repeat alleles (χ2 = 76·275, P < 0·0001). Therefore, only the association of the Asp358Ala variant with obesity and the metabolic syndrome was assessed in the whole series of subjects. Subjects homozygous for Asp358 alleles had statistically higher body mass index (BMI) compared with Ala358 carriers (27·7 ± 5·41 vs. 26·6 ± 4·96 kg/m2; P < 0·05). Moreover, the prevalence of the metabolic syndrome was significantly higher in carriers of the Asp358 allele compared with Ala358 homozygotes (12·7%vs. 0·0%; P = 0·01). This relationship remained significant after adjusting for age, insulin resistance, sex and BMI.

Conclusions  The Asp358Ala and CA‐repeat polymorphisms in the IL‐6R gene are associated with obesity and characteristics of the metabolic syndrome in our population of Mediterranean subjects.
Peripheral odontogenic fibroma (WHO type) of the newborn: a case report
Authors: MARTELLI‐JÚNIOR H. , MESQUITA R. A. , DE PAULA A. M. B. , PÊGO S. P. B. , SOUZA L. N.
Published: June 2006

Summary.  Aim.  The present paper reports a case of peripheral odontogenic fibroma (POF) (WHO type) in a newborn. The differential diagnosis and treatment were discussed.

Background.  POF is well described in the literature, but this is the first report in a newborn.

Patient.  A 4‐month‐old female newborn was referred to our department because of an exophytic, sessile, firm, and well‐delimited lesion on the right upper alveolar ridge. The covering mucosa was apparently normal. The lesion measuring 10 × 3 mm was present since birth. The clinical diagnosis of congenital granular cell tumour (congenital epulis) or dental lamina cyst of the newborn was made. A conservative excisional biopsy was performed under local anaesthesia, and the specimen was submitted to histopathological examination.

Results.  The microscopic examination revealed a pattern of POF (WHO type). Normal primary incisors teeth eruption, and no signs of recurrence were noted on 16 months follow‐up.

Conclusion.  Despite the rarity of POF in a newborn, this lesion should be included as a possible diagnosis to focal gingival growth.
Habitat shape, metapopulation processes and the dynamics of multispecies predator–prey interactions
Authors: BULL JAMES C. , PICKUP NICOLA J. , HASSELL MICHAEL P. , BONSALL MICHAEL B.
Published: June 2006

The effects of habitat shape, connectivity and the metapopulation processes of persistence and extinction are explored in a multispecies resource–consumer interaction.

The spatial dynamics of the indirect interaction between two prey species (Callosobruchus chinensis,Callosobruchus maculatus) and a predator (Anisopteromalus calandrae) are investigated and we show how the persistence time of this interaction is altered in different habitat configurations by the presence of an apparent competitor.

Habitat structure has differential effects on the dynamics of the resource–consumer interaction. Across all habitat types, the pairwise interaction betweenC. chinensisandA. calandraeis highly prone to extinction, while the interaction betweenC. maculatusandA. calandraeshows sustained long‐term fluctuations. Contrary to expectations from theory, habitat shape has no significant effect on persistence time of the full, three‐species resource–consumer assemblage.

A stochastic metapopulation model for a range of habitat configurations, incorporating different forms of regulatory processes, highlights that it is the spatially explicit population dynamics rather than the shape of the metapopulation that is the principal determinant of interaction persistence time.
A functional response model of a predator population foraging in a patchy habitat
Authors: NACHMAN GÖSTA
Published: June 2006

Functional response models (e.g. Holling's disc equation) that do not take the spatial distributions of prey and predators into account are likely to produce biased estimates of predation rates.

To investigate the consequences of ignoring prey distribution and predator aggregation, a general analytical model of a predator population occupying a patchy environment with a single species of prey is developed.

The model includes the density and the spatial distribution of the prey population, the aggregative response of the predators and their mutual interference.

The model provides explicit solutions to a number of scenarios that can be independently combined: the prey has an even, random or clumped distribution, and the predators show a convex, sigmoid, linear or no aggregative response.

The model is parameterized with data from an acarine predator–prey system consisting of Phytoseiulus persimis and Tetranychus urticae inhabiting greenhouse cucumbers.

The model fits empirical data quite well and much better than if prey and predators were assumed to be evenly distributed among patches, or if the predators were distributed independently of the prey.

The analyses show that if the predators do not show an aggregative response it will always be an advantage to the prey to adopt a patchy distribution. On the other hand, if the predators are capable of responding to the distribution of prey, then it will be an advantage to the prey to be evenly distributed when its density is low and switch to a more patchy distribution when its density increases. The effect of mutual interference is negligible unless predator density is very high.

The model shows that prey patchiness and predator aggregation in combination can change the functional response at the population level from type II to type III, indicating that these factors may contribute to stabilization of predator–prey dynamics.
Areas of endemism and distribution patterns for Neotropical Piper species (Piperaceae)
Authors: Quijano‐Abril Mario Alberto , Callejas‐Posada Ricardo , Miranda‐Esquivel Daniel Rafael
Published: June 2006

Aim  The study aimed to establish areas of endemism and distribution patterns for Neotropical species of the genus Piper in the Neotropical and Andean regions by means of parsimony analysis of endemicity (PAE) and track‐compatibility analysis.

Location  The study area includes the Neotropical region and the Northern Andean region (Páramo‐Punan subregion).

Methods  We used distribution information from herbarium specimens and recent monographic revisions for 1152 species of Piper from the Neotropics. First, a PAE was attempted in order to delimit the areas of endemism. Second, we performed a track‐compatibility analysis to establish distribution patterns for Neotropical species of Piper. Terminology for grouping Piper is based on recent phylogenetic analyses.

Results  The PAE yielded 104 small endemic areas for the genus Piper, 80 of which are in the Caribbean, Amazonian and Paranensis subregions of the Neotropical region, and 24 in the Páramo‐Punan subregion of the Andean region. Track‐compatibility analysis revealed 26 generalized tracks, one in the Páramo‐Punan subregion (Andean region), 19 in the Neotropical region, and six connecting the Andean and Neotropical regions. Both the generalized tracks and endemic areas indicate that distribution of Piper species is restricted to forest areas in the Andes, Amazonia, Chocó, Central America, the Guayana Shield and the Brazilian Atlantic coast.

Main conclusions  Piper should not be considered an Andean‐centred group as it represents two large species components with distributions centred in the Amazonian and Andean regions. Furthermore, areas of greater species richness and/or endemism are restricted to lowland habitats belonging to the Neotropical region. The distribution patterns of Neotropical species of Piper could be explained by recent events in the Neotropical region, as is the case for the track connecting Chocó and Central America, where most of the species rich groups of the genus are found. Two kinds of event could explain the biogeography of a large part of the Piper taxa with Andean–Amazonian distribution: pre‐Andean and post‐Andean events.
Biogeography and molecular phylogeny of the genus Schizothorax (Teleostei: Cyprinidae) in China inferred from cytochrome b sequences
Authors: He Dekui , Chen Yifeng
Published: June 2006

Aim  To test a vicariant speciation hypothesis derived from geological evidence of large‐scale changes in drainage patterns in the late Miocene that affected the drainages in the south‐eastern Tibetan Plateau.

Location  The Tibetan Plateau and adjacent areas.

Methods  The cytochrome b DNA sequences of 30 species of the genus Schizothorax from nine different river systems were analysed. These DNA sequences were analysed using parsimony, maximum likelihood and Bayesian methods. The approximately unbiased and Shimodaira–Hasegawa tests were applied to evaluate the statistical significance of the shortest trees relative to alternative hypotheses. Dates of divergences between lineages were estimated using the nonparametric rate smoothing method, and confidence intervals of dates were obtained by parametric bootstrapping.

Results  The phylogenetic relationships recovered from molecular data were inconsistent with traditional taxonomy, but apparently reflected geographical associations with rivers. Within the genus Schizothorax, we observed a divergence between the lineages from the Irrawaddy–Lhuit and Tsangpo–Parlung rivers, and tentatively dated this vicariant event back to the late Miocene (7.3–6.8 Ma). We also observed approximately simultaneous geographical splits within drainages of the south‐eastern Tibetan Plateau, the Irrawaddy, the Yangtze and the Mekong–Salween rivers in the late Miocene (7.1–6.2 Ma).

Main conclusions  Our molecular evidence tentatively highlights the importance of palaeoriver connections and the uplift of the Tibetan Plateau in understanding the evolution of the genus Schizothorax. Molecular estimates of divergence times allowed us to date these vicariant scenarios back to the late Miocene, which agrees with geological suggestions for the separation of these drainages caused by tectonic uplift in south‐eastern Tibet. Our results indicated the substantial role of vicariant‐based speciation in shaping the current distribution pattern of the genus Schizothorax.
Effects of position, understorey vegetation and coarse woody debris on tree regeneration in two environmentally contrasting forests of north‐western Patagonia: a manipulative approach
Authors: Heinemann Karin , Kitzberger Thomas
Published: June 2006

Aim  To investigate the differential effects of position within gaps, coarse woody debris and understorey cover on tree seedling survival in canopy gaps in two old‐growth Nothofagus pumilio (Poepp. & Endl.) Krasser forests and the response of this species to gaps in two forests located at opposite extremes of a steep rainfall gradient.

Location  Nahuel Huapi National Park, at 41° S in north‐western Patagonia, Argentina.

Methods  In both study sites, seedlings were transplanted to experimental plots in gaps in three different positions, with two types of substrate (coarse woody debris or forest floor), and with and without removal of understorey vegetation. Survival of seedlings was monitored during two growing seasons. Soil moisture and direct solar radiation were measured once in mid‐summer. Seedling aerial biomass was estimated at the end of the experiment.

Results  Mid‐summer soil water potential was lowest in the centre of gaps, in plots where the understorey had been removed, and highest at the northern edges of gaps. Direct incoming radiation was highest in gap centres and southern edges, and lowest at northern edges. Seedling mortality was highest in gap centres, in both sites. Coarse woody debris had a positive effect on seedling survival during summer in the mesic forest and during winter in the xeric forest. The removal of understorey cover had negative effects in gap centres during summer. Seedling final aerial biomass was positively affected by understorey removal and by soil substrate in both sites. In the dry forest gaps, seedling growth was highest in northern edges, whereas it was highest in gap centres in the mesic forest. Overall growth was positively related to survival in the xeric forest, and negatively related in the mesic forest.

Main conclusions  Survival and growth were facilitated by the shade of gap‐surrounding trees only in the xeric forest. Understorey vegetation of both forests facilitated seedling survival in exposed microsites but competed with seedling growth. Nurse logs were an important substrate for seedling establishment in both forests; however, causes of this pattern differed between forests. Water availability positively controls seedling survival and growth in the xeric forest while in the mesic forest, survival and growth are differentially controlled by water and light availability, respectively. These two contrasting old‐growth forests, separated by a relatively short distance along a steep rainfall gradient, had different yet unexpected microenvironmental controls on N. pumilio seedling survival and growth. These results underscore the importance of defining microscale limiting factors of tree recruitment in the context of large‐scale spatial variation in resources.
Potential selection in native grass populations by exotic invasion
Authors: MEALOR BRIAN A. , HILD ANN L.
Published: June 2006

Ecological impacts of invasive plant species are well documented, but the genetic response of native species to invasive dominance has been often overlooked. Invasive plants can drastically alter site conditions where they reach dominance, potentially exerting novel selective pressures on persistent native plant populations. Do native plant populations in old exotic invasions show evidence of selection when compared to conspecific populations in adjacent, noninvaded areas? We employ amplified fragment length polymorphism (AFLP) analysis to screen a large number of loci from two native grass species (Hesperostipa comata (Trin. & Rupr.) Barkworth and Sporobolus airoides Torr.) that occur in old infestations of the invasive forb Acroptilon repens. We then compare observed locus by locus FST values with distributions of FST estimated from simulation models under expectation of neutrality. We also compare the proportion of loci possibly linked to selection and those not linked to selection which exhibit parallel trends in divergence between two community types (invaded, noninvaded). Few loci (H. comata, 2.6%; S. airoides, 8.7%) in the two native grasses may be linked to genes under the influence of selection. Also, loci linked to selection showed a greater portion of parallel trends in divergence than neutral loci. Genetic similarities between community types were less than genetic similarity within community types suggesting differentiation in response to community alteration. These results indicate that a small portion of scored AFLP loci may be linked to genes undergoing selection tied to community dominance by an invasive species. We propose that native plants in communities dominated by exotic invasives may be undergoing natural selection.
Double hexameric ring assembly of the type III protein translocase ATPase HrcN
Authors: Müller Shirley A. , Pozidis Charalambos , Stone Remington , Meesters Christian , Chami Mohamed , Engel Andreas , Economou Anastassios , Stahlberg Henning
Published: June 2006

The specialized type III secretion (T3S) apparatus of pathogenic and symbiotic Gram‐negative bacteria comprises a complex transmembrane organelle and an ATPase homologous to the F1‐ATPase β subunit. The T3S ATPase HrcN of Pseudomonas syringae associates with the inner membrane, and its ATP hydrolytic activity is stimulated by dodecamerization. The structure of dodecameric HrcN (HrcN12) determined to 1.6 nm by cryo‐electron microscopy is presented. HrcN12 comprises two hexameric rings that are probably stacked face‐to‐face by the association of their C‐terminal domains. It is 11.5 ± 1.0 nm in diameter, 12.0 ± 2.0 nm high and has a 2.0–3.8 nm wide inner channel. This structure is compared to a homology model based on the structure of the F1‐β‐ATPase. A model for its incorporation within the T3S apparatus is presented.
Identification of genes involved in the biosynthesis and attachment of Methanococcus voltae N‐linked glycans: insight into N‐linked glycosylation pathways in Archaea
Authors: Chaban Bonnie , Voisin Sebastien , Kelly John , Logan Susan M. , Jarrell Ken F.
Published: June 2006

N‐linked glycosylation is recognized as an important post‐translational modification across all three domains of life. However, the understanding of the genetic pathways for the assembly and attachment of N‐linked glycans in eukaryotic and bacterial systems far outweighs the knowledge of comparable processes in Archaea. The recent characterization of a novel trisaccharide [β‐ManpNAcA6Thr‐(1‐4)‐β‐GlcpNAc3NAcA‐(1‐3)‐β‐GlcpNAc]N‐linked to asparagine residues in Methanococcus voltae flagellin and S‐layer proteins affords new opportunities to investigate N‐linked glycosylation pathways in Archaea. In this contribution, the insertional inactivation of several candidate genes within the M. voltae genome and their resulting effects on flagellin and S‐layer glycosylation are reported. Two of the candidate genes were shown to have effects on flagellin and S‐layer protein molecular mass and N‐linked glycan structure. Further examination revealed inactivation of either of these two genes also had effects on flagella assembly. These genes, designated agl (archaeal glycosylation) genes, include a glycosyl transferase (aglA) involved in the attachment of the terminal sugar to the glycan and an STT3 oligosaccharyl transferase homologue (aglB) involved in the transfer of the complete glycan to the flagellin and S‐layer proteins. These findings document the first experimental evidence for genes involved in any glycosylation process within the domain Archaea.
Interaction network in cyanobacterial nitrogen regulation: PipX, a protein that interacts in a 2‐oxoglutarate dependent manner with PII and NtcA
Authors: Espinosa Javier , Forchhammer Karl , Burillo Sergio , Contreras Asunción
Published: June 2006

Cyanobacteria perceive nitrogen status by sensing intracellular 2‐oxoglutarate levels. The global nitrogen transcription factor NtcA and the signal transduction protein PII are both involved in 2‐oxoglutarate sensing. PII proteins, probably the most conserved signal transduction proteins in nature, are remarkable for their ability to interact with very diverse protein targets in different systems. Despite widespread efforts to understand nitrogen signalling in cyanobacteria, the involvement of PII in the regulation of transcription activation by NtcA remains enigmatic. Here we show that PipX, a protein only present in cyanobacteria, interacts with both PII and NtcA and provides a mechanistic link between these two factors. A variety ofin vivoandin vitroapproaches were used to study PipX and its interactions with PII and NtcA. 2‐Oxoglutarate favours complex formation between PipX and NtcA, but impairs binding to PII, suggesting that partner swapping between these nitrogen regulators is driven by the 2‐oxoglutarate concentration. PipX is required for NtcA‐dependent transcriptional activationin vivo, thus implying that PipX may function as a prokaryotic transcriptional coactivator.
The Ischia debris avalanche: first clear submarine evidence in the Mediterranean of a volcanic island prehistorical collapse
Authors: Chiocci Francesco Latino , De Alteriis Giovanni
Published: June 2006

Sector or flank collapse with related debris avalanches is increasingly recognized as a relatively common volcanic behaviour, in particular, for large, hot‐spot related oceanic islands. Here, we report the case of a catastrophic collapse that occurred at Ischia volcanic island in prehistorical times and was driven by the volcano‐tectonic uplift of Mt Epomeo, the major relief of the island. The collapse left a subaerial to submarine horseshoe scar on the southern flank of the island and generated a debris avalanche incorporating thousands of giant blocks dispersed as far as 50 km from the island. During the emplacement, part of the debris avalanche evolved into a debris flow covering an area of 250–300 km2. This constitutes the first, clear evidence of a submarine debris avalanche in the Mediterranean Sea. The major collapse was followed, and probably also preceded, by recurrent, less catastrophic terrestrial and underwater failures. Two other undersea hummocky deposits are found north and west of the island and might tentatively be correlated to the major southern collapse. Such volcanic behaviour, previously unknown for Ischia Volcano, has likely triggered tsunami waves over the entire Bay of Naples raising the question of their impact on prehistorical/historical communities.
DOF transcription factor AtDof1.1 (OBP2) is part of a regulatory network controlling glucosinolate biosynthesis in Arabidopsis
Authors: Skirycz Aleksandra , Reichelt Michael , Burow Meike , Birkemeyer Claudia , Rolcik Jakub , Kopka Joachim , Zanor Maria Inès , Gershenzon Jonathan , Strnad Miroslav , Szopa Jan , Mueller‐Roeber Bernd , Witt Isabell
Published: June 2006

Glucosinolates are a group of secondary metabolites that function as defense substances against herbivores and micro‐organisms in the plant order Capparales. Indole glucosinolates (IGS), derivatives of tryptophan, may also influence plant growth and development. In Arabidopsis thaliana, indole‐3‐acetaldoxime (IAOx) produced from tryptophan by the activity of two cytochrome P450 enzymes, CYP79B2 and CYP79B3, serves as a precursor for IGS biosynthesis but is also an intermediate in the biosynthetic pathway of indole‐3‐acetic acid (IAA). Another cytochrome P450 enzyme, CYP83B1, funnels IAOx into IGS. Although there is increasing information about the genes involved in this biochemical pathway, their regulation is not fully understood. OBP2 has recently been identified as a member of the DNA‐binding‐with‐one‐finger (DOF) transcription factors, but its function has not been studied in detail so far. Here we report that OBP2 is expressed in the vasculature of all Arabidopsis organs, including leaves, roots, flower stalks and petals. OBP2 expression is induced in response to a generalist herbivore, Spodoptera littoralis, and by treatment with the plant signalling molecule methyl jasmonate, both of which also trigger IGS accumulation. Constitutive and inducible over‐expression of OBP2 activates expression of CYP83B1. In addition, auxin concentration is increased in leaves and seedlings of OBP2 over‐expression lines relative to wild‐type, and plant size is diminished due to a reduction in cell size. RNA interference‐mediated OBP2 blockade leads to reduced expression of CYP83B1. Collectively, these data provide evidence that OBP2 is part of a regulatory network that regulates glucosinolate biosynthesis in Arabidopsis.