bluuebunny/crossref_metadata_2025 huggingface dataset:
Planning at the Urban Fringe: An Examination of the Factors Influencing Nonconforming Development Patterns in Southern Florida
Authors: Brody Samuel D , Highfield Wesley E , Thornton Sara
Published: January 2006

Although the components of plan quality are well defined, little empirical research has been conducted to understand the degree to which policies are being implemented after plan adoption and the factors contributing to the variation in plan implementation. The authors test the efficacy of land-use planning and plan implementation in Florida by measuring the degree to which wetland development over a ten-year period conforms to the original design of adopted comprehensive plans. First, they spatially identify concentrated areas of wetland alteration permits and compare these locations with the adopted future land-use maps for county and city jurisdictions in the southern portion of the state. Second, they examine the major factors influencing nonconforming development patterns across the study area. Results indicate a well-defined spatial pattern of nonconforming wetland development and isolate specific socioeconomic, demographic, and geographic variables impacting these deviations from the original spatial intent of local plans.
Job Accessibility as an Indicator of Auto-Oriented Urban Structure: A Comparison of Boston and Los Angeles with Tokyo
Authors: Kawabata Mizuki , Shen Qing
Published: January 2006

Studies suggest that sprawling and auto-oriented development patterns present more difficulties for people without cars to access economic opportunities. We examine intrametropolitan and intermetropolitan variations in job accessibility by commuting mode as an indicator of auto-oriented urban structure, selecting Boston, Los Angeles, and Tokyo as study areas. Although in both US and Japanese metropolitan areas, job accessibility is significantly lower for public transit users than for auto users, job accessibility for public transit users in the US cases is strikingly lower than in Tokyo. The international comparison provides a clear picture of the significant disadvantage in accessing job opportunities encountered by US workers who are unable to use private vehicles. The empirical results uncover an important dimension of urban structure that deserves much attention from planners and policymakers.
The productivity of irrigated legumes in northern Victoria. 3. Frequency and intensity of defoliation of subterranean clover
Authors: Stockdale C. R.
Published: January 2006

An experiment was undertaken to consider the effects of a range of defoliation treatments on aspects of the productivity of a subterranean clover (Trifolium subterraneum L.) sward (predominantly cv. Trikkala), with particular emphasis on flowering and seed production. There were 2 heights of defoliation, 2.8 and 7.0 cm (rising plate meter) above ground level, and at each height of defoliation, there were 4 intervals of harvest, 4, 6, 9 and 12 weeks. Treatments were arranged randomly within blocks, and there were 4 replicates. Harvests were conducted between autumn (6 April) and spring (13 November).
The total production of herbage varied from 5.7 to 8.7 t DM/ha of harvested material, with variations in response due to both height and frequency of defoliation. Harvested yield increased from 6.2 to 7.4 t DM/ha (P<0.05) as interval between harvests was extended, and plots harvested to 2.8 cm above ground level yielded more (7.7 t DM/ha; P<0.05) harvested herbage than those harvested to 7.0 cm (6.0 t DM/ha). While there were differences in production due to defoliation management, nutritive characteristics (DM digestibility, crude protein, neutral detergent fibre) of harvested herbage were similar in all treatments throughout the year.
Production of above and below ground seed increased (P<0.05) as interval between harvest increased, and was greater (P<0.05) at the higher defoliation height. Defoliating at 4- and 6-week intervals interrupted the reproductive development of Trikkala; late September–early October harvests substantially reduced both subsequent petiole extension and flower production. This resulted in Trikkala seeds of lower weight in the above ground seed pool (P<0.05). This may have impacted on regenerating ability in the next autumn because Trikkala seeds that were less than about 4 mg in weight were less likely to germinate than heavier seed. In conclusion, the highest dry matter production occurred with intensive, infrequent defoliation whereas highest seed yields were produced with lax, infrequent defoliation.
Irrigation practices on north-east Victorian dairy farms: a survey
Authors: Watson D. J. , Drysdale G.
Published: January 2006

The north-east region of Victoria is an important water-harvesting catchment for gravity-fed irrigators downstream of Lake Mulwala. Dairy farmers are significant users of irrigation water in north-east Victoria but little was known about their irrigation practices and attitudes. A survey undertaken in 2000 collected data on irrigation practices and attitudes from 92% of the irrigating dairy farmers in the region. It found diversity in many aspects of irrigation amongst the region’s irrigated dairy farms, ranging from the proportion of the farm irrigated to the irrigation system used, and identified areas where improvements to irrigation practices could be made. More than 8 different irrigation systems were used in the region, and flood irrigation was the most commonly used. However, a large proportion (37%) of flood irrigators were contemplating changing to spray irrigation, mostly to long lateral hand move sprinkler irrigation, in an effort to improve water use efficiency. More than 50% of respondents did not meter irrigation water use, and 83% pumped water directly from rivers or creeks, with dams and dragline holes the next most common sources. Irrigation scheduling (when to start irrigating and the frequency of irrigation thereafter) and the amount of water to apply were generally based on knowledge and experience rather than on soil moisture monitoring equipment or use of evaporation rates. Most survey respondents recognised that their irrigation practices could improve and said that they would be interested in information to help them make more informed decisions about irrigation practices.
Grazing studies of a Hyparrhenia hirta (Coolatai grass) pasture in northern New South Wales
Authors: Lodge G. M. , McCormick L. H. , Harden S.
Published: January 2006

Hyparrhenia hirta (L.) Stapf (Coolatai grass) has invaded large areas of grazed native grasslands on the North-West Slopes of New South Wales (NSW) and is widespread along roadsides and travelling stock routes. It is commonly regarded as an invasive, weedy species with low forage value when it is tall and rank, but may be more palatable when kept short, green and leafy.
A study (1990–2001) of a naturalised stand of Coolatai grass in the Manilla district of northern NSW examined its herbage mass (kg DM/ha), persistence (basal cover %), and grazing value under 2 contrasting grazing treatments: pastures that had either large amounts of dry, unpalatable herbage [light grazing at 5 dry sheep equivalents (DSE)/ha] or were short, green and leafy (strategic heavy grazing at a stocking rate of 37 DSE/ha). Effects of pre-grazing treatments (slashing, burning, and no defoliation) were also examined and data (litter mass, plant basal area, ground cover, and soil and litter microbial carbon and nitrogen) collected to assess the long term sustainability of these grazing systems.
Sheep grazed the light grazing treatment for about 34% of the experimental period, with the strategic heavy grazing treatment being grazed for about 7% of the time. Over the experimental period this equated to 6752 DSE grazing days/ha for the light grazing treatment compared with 10 120 DSE for the heavy grazing treatment. Herbage mass in the heavy grazing treatment declined to <1000 kg DM/ha within 6 months of the start of grazing and remained below this level until December 1998 when stocking rates were switched (i.e. plots previously grazed at low stocking rate were subjected to the heavier rate and vice versa). In contrast, mean herbage mass in the light grazing treatment was generally >3000 kg DM/ha from November 1990–98, but a high proportion of this was dead standing material that carried over from season to season. Mean Coolatai grass basal cover was 9.5% in November 1990, increasing over time to about 25% in both grazing treatments by December 2000.
Coolatai grass herbage accumulation was highly seasonal, ranging from as high as 70 kg DM/ha.day in summer to 0 in winter. In both grazing treatments, forage quality was low for both green and dead material, with mean crude protein being 6.0 (green) and 3.4% (dead). Digestible dry matter values ranged from 41 to 62% (green) and 32 to 51% (dead) and mean metabolisable energy values were 7 (green) and 5.3 MJ/kg DM (dead). After 8 years, the heavy grazing treatment had lower (P<0.05) litter mass, ground cover, plant basal area and soil microbial C and N levels than the light grazing treatment, but switching of the stocking rates restored most indicators, except the soil microbial values.
Pbn1p: An essential endoplasmic reticulum membrane protein required for protein processing in the endoplasmic reticulum of budding yeast
Authors: Subramanian Shoba , Woolford Carol A. , Drill Emily , Lu Meng , Jones Elizabeth W.
Published: January 2006

PBN1
was identified as a gene required for production of protease B (PrB) activity in
Saccharomyces cerevisiae
.
PBN1
encodes an endoplasmic reticulum (ER)-localized, type I membrane glycoprotein and is essential for cell viability. To study the essential function(s) of Pbn1p, we constructed a strain with
PBN1
under control of the
GAL
promoter. Depletion of Pbn1p in this strain abrogates processing of the ER precursor forms of PrB, Gas1p, and Pho8p. Depletion of Pbn1p does not affect exit of proprotease A or procarboxypeptidase Y from the ER, indicating that Pbn1p is not required for global exit from the ER. Depleting Pbn1p leads to a significant increase in the unfolded protein response pathway, accompanied by an expansion of bulk ER membrane, indicating that there is a defect in protein folding in the ER.
pbn1-1
, a nonlethal allele of
PBN1
, displays synthetic lethality with the
ero1-1
allele (
ERO1
is required for oxidation in the ER) and synthetic growth defects with the
cne1
Δ allele (
CNE1
encodes calnexin). ER-associated degradation of a lumenal substrate, CPY*, is blocked in the absence of Pbn1p. These results suggest that Pbn1p is required for proper folding and/or the stability of a subset of proteins in the ER. Thus, Pbn1p is an essential chaperone-like protein in the ER of yeast.
G
o
α regulates olfactory adaptation by antagonizing G
q
α-DAG signaling in
Caenorhabditis elegans
Authors: Matsuki Masahiro , Kunitomo Hirofumi , Iino Yuichi
Published: January 2006

The heterotrimeric G protein G
o
is abundantly expressed in the mammalian nervous system and modulates neural activities in response to various ligands. However, G
o
's functions in living animals are less well understood. Here, we demonstrate that GOA-1 G
o
α has a fundamental role in olfactory adaptation in
Caenorhabditis elegans
. Impairment of GOA-1 G
o
α function and excessive activation of EGL-30 G
q
α cause a defect in adaptation to AWC-sensed odorants. These pathways antagonistically modulate olfactory adaptation in AWC chemosensory neurons. Wild-type animals treated with phorbol esters and double-mutant animals of diacylglycerol (DAG) kinases,
dgk-3
;
dgk-1
, also have a defect in adaptation, suggesting that elevated DAG signals disrupt normal adaptation. Constitutively active GOA-1 can suppress the adaptation defect of
dgk-3
;
dgk-1
double mutants, whereas it fails to suppress the adaptation defect of animals with constitutively active EGL-30, implying that GOA-1 acts upstream of EGL-30 in olfactory adaptation. Our results suggest that down-regulation of EGL-30–DAG signaling by GOA-1 underlies olfactory adaptation and plasticity of chemotaxis.
HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations
Authors: Hornak Viktor , Okur Asim , Rizzo Robert C. , Simmerling Carlos
Published: January 2006

We report unrestrained, all-atom molecular dynamics simulations of HIV-1 protease that sample large conformational changes of the active site flaps. In particular, the unliganded protease undergoes multiple conversions between the “closed” and “semiopen” forms observed in crystal structures of inhibitor-bound and unliganded protease, respectively, including reversal of flap “handedness.” Simulations in the presence of a cyclic urea inhibitor yield stable closed flaps. Furthermore, we observe several events in which the flaps of the unliganded protease open to a much greater degree than observed in crystal structures and subsequently return to the semiopen state. Our data strongly support the hypothesis that the unliganded protease predominantly populates the semiopen conformation, with closed and fully open structures being a minor component of the overall ensemble. The results also provide a model for the flap opening and closing that is considered to be essential to enzyme function.
Osmotic effects on vacuolar ion release in guard cells
Authors: MacRobbie Enid A. C.
Published: January 2006

Tracer flux experiments in isolated guard cells of
Commelina communis
L. suggest that the vacuolar ion content is regulated and is reset to a reduced fixed point by abscisic acid (ABA) with no significant change in cytoplasmic content. The effects of changes in external osmotic pressure were investigated by adding and removing mannitol from the bathing solution. Two effects were distinguished. In the new steady state of volume and turgor, the vacuolar ion efflux was sensitive to turgor: efflux increased at high turgor and reduced at lower turgor after the addition of mannitol. These changes were inhibited by phenylarsine oxide and are likely to involve the same channel that is involved in the response to ABA. After a hypoosmotic transfer, there was an additional effect: a fast transient stimulation of vacuolar efflux during the period of water flow into the cell; the size of this hypopeak increased with the size of the hypoosmotic shock, with increased water flow. No corresponding transient in reduced vacuolar efflux was observed upon hyperosmotic transfer. The fast hypopeak was not inhibited by phenylarsine oxide and appears to involve a different ion channel from that involved in the resting efflux, the response to ABA, or the turgor sensitivity. Thus, the tonoplast can sense an osmotic gradient and respond to water flow into the vacuole by increased vacuolar ion efflux, thereby minimizing cytoplasmic dilution. An aquaporin is the most likely sensor and may also be involved in the signal transduction chain.
Antibodies selected from combinatorial libraries block a tumor antigen that plays a key role in immunomodulation
Authors: McWhirter John R. , Kretz-Rommel Anke , Saven Alan , Maruyama Toshiaki , Potter Kathleen N. , Mockridge C. Ian , Ravey E. Prenn , Qin Fenghua , Bowdish Katherine S.
Published: January 2006

We searched for cell-surface-associated proteins overexpressed on B cell chronic lymphocytic leukemia (CLL) to use as therapeutic antibody targets. Antibodies binding the immunosuppressive molecule CD200 were identified by cell panning of an antibody phage display library derived from rabbits immunized with primary CLL cells. B cells from 87 CLL patients exhibited 1.6- to 5.4-fold cell-surface up-regulation of CD200 relative to normal B cells. An effect of increased CD200 expression by CLL cells on the immune system was evaluated in mixed lymphocyte reactions. Addition of primary CLL but not normal B cells to macrophages and T cells downregulated the Th1 response, as seen by a 50–95% reduction in secreted IL-2 and IFN-γ. Antibodies to CD200 prevented downregulation of the Th1 response in most B cell CLL samples evaluated, indicating abrogation of the CD200/CD200R interaction can be sufficient to restore the Th1 response. A disease-progression-associated shift of the immune response from Th1 to Th2 has been observed in numerous cancers. Because this cytokine shift is also believed to promote the induction of regulatory T cells, reverting the immune response to Th1 through direct targeting of the cancer cells may provide therapeutic benefits in CLL by encouraging a cytotoxic T cell response.
(–)-Epicatechin mediates beneficial effects of flavanol-rich cocoa on vascular function in humans
Authors: Schroeter Hagen , Heiss Christian , Balzer Jan , Kleinbongard Petra , Keen Carl L. , Hollenberg Norman K. , Sies Helmut , Kwik-Uribe Catherine , Schmitz Harold H. , Kelm Malte
Published: January 2006

Epidemiological and medical anthropological investigations suggest that flavanol-rich foods exert cardiovascular health benefits. Endothelial dysfunction, a prognostically relevant key event in atherosclerosis, is characterized by a decreased bioactivity of nitric oxide (NO) and impaired flow-mediated vasodilation (FMD). We show in healthy male adults that the ingestion of flavanol-rich cocoa was associated with acute elevations in levels of circulating NO species, an enhanced FMD response of conduit arteries, and an augmented microcirculation. In addition, the concentrations and the chemical profiles of circulating flavanol metabolites were determined, and multivariate regression analyses identified (–)-epicatechin and its metabolite, epicatechin-7-O-glucuronide, as independent predictors of the vascular effects after flavanol-rich cocoa ingestion. A mixture of flavanols/metabolites, resembling the profile and concentration of circulating flavanol compounds in plasma after cocoa ingestion, induced a relaxation in preconstricted rabbit aortic ringsex vivo, thus mimicking acetylcholine-induced relaxations.Ex vivoflavanol-induced relaxation, as well as thein vivoincreases in FMD, were abolished by inhibition of NO synthase. Oral administration of chemically pure (–)-epicatechin to humans closely emulated acute vascular effects of flavanol-rich cocoa. Finally, the concept that a chronic intake of high-flavanol diets is associated with prolonged, augmented NO synthesis is supported by data that indicate a correlation between the chronic consumption of a cocoa flavanol-rich diet and the augmented urinary excretion of NO metabolites. Collectively, our data demonstrate that the human ingestion of the flavanol (–)-epicatechin is, at least in part, causally linked to the reported vascular effects observed after the consumption of flavanol-rich cocoa.
Platelets and platelet adhesion support angiogenesis while preventing excessive hemorrhage
Authors: Kisucka Janka , Butterfield Catherine E. , Duda Dan G. , Eichenberger Sarah C. , Saffaripour Simin , Ware Jerry , Ruggeri Zaverio M. , Jain Rakesh K. , Folkman Judah , Wagner Denisa D.
Published: January 2006

Platelets contain both pro- and antiangiogenic factors, but their regulatory role in angiogenesis is poorly understood. Although previous studies showed that platelets stimulate angiogenesis
in vitro
, the role of platelets in angiogenesis
in vivo
is largely uncharacterized. To address this topic, we used two
in vivo
approaches, the cornea micropocket assay and the Matrigel model, in four animal models: thrombocytopenic, Lyst

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(platelet storage pool deficiency), glycoprotein (GP) Ibα/IL4R transgenic (lacking extracellular GPIbα, the receptor for von Willebrand factor as well as other adhesive and procoagulant proteins), and FcγR
–/–
(lacking functional GPVI, the collagen receptor) mice. Adult mice were rendered thrombocytopenic by i.p. administration of an antiplatelet antibody. The number of growing vessels in the thrombocytopenic mice was lower in the cornea assay, and they showed significantly increased appearance of hemorrhage compared with mice treated with control IgG. The thrombocytopenic mice also showed more protein leakage and developed hematomas in the Matrigel model. GPIbα/IL4R transgenic mice presented increased hemorrhage in both assays, but it was less severe than in the platelet-depleted mice. FcγR
–/–
and Lyst

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mice showed no defect in experimental angiogenesis. Intravital microscopy revealed a >3-fold increase in platelet adhesion to angiogenic vessels of Matrigel compared with mature quiescent skin vessels. Our results suggest that the presence of platelets not only stimulates angiogenic vessel growth but also plays a critical role in preventing hemorrhage from the angiogenic vessels. The adhesion function of platelets, as mediated by GPIbα, significantly contributes to the process.
ES cells derived from cloned and fertilized blastocysts are transcriptionally and functionally indistinguishable
Authors: Brambrink Tobias , Hochedlinger Konrad , Bell George , Jaenisch Rudolf
Published: January 2006

Reproductive cloning is uniformly rejected as a valid technology in humans because of the severely abnormal phenotypes seen in cloned animals. Gene expression aberrations observed in tissues of cloned animals have also raised concerns regarding the therapeutic application of “customized” embryonic stem (ES) cells derived by nuclear transplantation (NT) from a patient's somatic cells. Although previous experiments in mice have demonstrated that the developmental potential of ES cells derived from cloned blastocysts (NT-ES cells) is identical to that of ES cells derived from fertilized blastocysts, a systematic molecular characterization of NT-ES cell lines is lacking. To investigate whether transcriptional aberrations, similar to those observed in tissues of cloned mice, also occur in NT-ES cells, we have compared transcriptional profiles of 10 mouse NT- and fertilization-derived-ES cell lines. We report here that the ES cell lines derived from cloned and fertilized mouse blastocysts are indistinguishable based on their transcriptional profiles, consistent with their normal developmental potential. Our results indicate that, in contrast to embryonic and fetal development of clones, the process of NT-ES cell derivation rigorously selects for those immortal cells that have erased the “epigenetic memory” of the donor nucleus and, thus, become functionally equivalent. Our findings support the notion that ES cell lines derived from cloned or fertilized blastocysts have an identical therapeutic potential.
Activation of the Flt3 signal transduction cascade rescues and enhances type I interferon–producing and dendritic cell development
Authors: Onai Nobuyuki , Obata-Onai Aya , Tussiwand Roxane , Lanzavecchia Antonio , Manz Markus G.
Published: January 2006

Flt3 ligand (Flt3L) is a nonredundant cytokine in type I interferon–producing cell (IPC) and dendritic cell (DC) development, and IPC and DC differentiation potential is confined to Flt3+ hematopoietic progenitor cells. Here, we show that overexpression of human Flt3 in Flt3− (Flt3−Lin−IL-7Rα−Thy1.1−c-Kit+) and Flt3+ (Flt3+Lin−IL-7Rα−Thy1.1−c-Kit+) hematopoietic progenitors rescues and enhances their IPC and DC differentiation potential, respectively. In defined hematopoietic cell populations, such as Flt3− megakaryocyte/erythrocyte-restricted progenitors (MEPs), enforced Flt3 signaling induces transcription of IPC, DC, and granulocyte/macrophage (GM) development–affiliated genes, including STAT3, PU.1, and G-/M-/GM-CSFR, and activates differentiation capacities to these lineages. Moreover, ectopic expression of Flt3 downstream transcription factors STAT3 or PU.1 in Flt3− MEPs evokes Flt3 receptor expression and instructs differentiation into IPCs, DCs, and myelomonocytic cells, whereas GATA-1 expression and consecutive megakaryocyte/erythrocyte development is suppressed. Based on these data, we propose a demand-regulated, cytokine-driven DC and IPC regeneration model, in which high Flt3L levels initiate a self-sustaining, Flt3-STAT3– and Flt3-PU.1–mediated IPC and DC differentiation program in Flt3+ hematopoietic progenitor cells.
Gating of Acid-sensitive Ion Channel-1: Release of Ca2+ Block vs. Allosteric Mechanism
Authors: Zhang Ping , Sigworth Fred J. , Canessa Cecilia M.
Published: January 2006

The acid-sensitive ion channels (ASICs) are a family of voltage-insensitive sodium channels activated by external protons. A previous study proposed that the mechanism underlying activation of ASIC consists of the removal of a Ca2+ ion from the channel pore (Immke and McCleskey, 2003). In this work we have revisited this issue by examining single channel recordings of ASIC1 from toadfish (fASIC1). We demonstrate that increases in the concentration of external protons or decreases in the concentration of external Ca2+ activate fASIC1 by progressively opening more channels and by increasing the rate of channel opening. Both maneuvers produced similar effects in channel kinetics, consistent with the former notion that protons displace a Ca2+ ion from a high-affinity binding site. However, we did not observe any of the predictions expected from the release of an open-channel blocker: decrease in the amplitude of the unitary currents, shortening of the mean open time, or a constant delay for the first opening when the concentration of external Ca2+ was decreased. Together, the results favor changes in allosteric conformations rather than unblocking of the pore as the mechanism gating fASIC1. At high concentrations, Ca2+ has an additional effect that consists of voltage-dependent decrease in the amplitude of unitary currents (EC50 of 10 mM at −60 mV and pH 6.0). This phenomenon is consistent with voltage-dependent block of the pore but it occurs at concentrations much higher than those required for gating.
Direct Observation of a Preinactivated, Open State in BK Channels with β2 Subunits
Authors: Benzinger G. Richard , Xia Xiao-Ming , Lingle Christopher J.
Published: January 2006

Proteins arising from the Slo family assemble into homotetramers to form functional large-conductance, Ca2+- and voltage-activated K+ channels, or BK channels. These channels are also found in association with accessory β subunits, which modulate several aspects of channel gating and expression. Coexpression with either of two such subunits, β2 or β3b, confers time-dependent inactivation onto BK currents. mSlo1+β3b channels display inactivation that is very rapid but incomplete. Previous studies involving macroscopic recordings from these channels have argued for the existence of a second, short-lived conducting state in rapid equilibrium with the nonconducting, inactivated conformation. This state has been termed “pre-inactivated,” or O*. β2-mediated inactivation, in contrast, occurs more slowly but is virtually complete at steady state. Here we demonstrate, using both macroscopic and single channel current recordings, that a preinactivated state is also a property of mSlo1+β2 channels. Detection of this state is enhanced by a mutation (W4E) within the initial β2 NH2-terminal segment critical for inactivation. This mutation increases the rate of recovery to the preinactivated open state, yielding macroscopic inactivation properties qualitatively more similar to those of β3b. Furthermore, short-lived openings corresponding to entry into the preinactivated state can be observed directly with single-channel recording. By examining the initial openings after depolarization of a channel containing β2-W4E, we show that channels can arrive directly at the preinactivated state without passing through the usual long-lived open conformation. This final result suggests that channel opening and inactivation are at least partly separable in this channel. Mechanistically, the preinactivated and inactivated conformations may correspond to binding of the β subunit NH2 terminus in the vicinity of the cytoplasmic pore mouth, followed by definitive movement of the NH2 terminus into a position of occlusion within the ion-conducting pathway.
Inference of gene regulatory networks and compound mode of action from time course gene expression profiles
Authors: Bansal Mukesh , Gatta Giusy Della , di Bernardo Diego
Published: January 2006

Motivation: Time series expression experiments are an increasingly popular method for studying a wide range of biological systems. Here we developed an algorithm that can infer the local network of gene–gene interactions surrounding a gene of interest. This is achieved by a perturbation of the gene of interest and subsequently measuring the gene expression profiles at multiple time points. We applied this algorithm to computer simulated data and to experimental data on a nine gene network in Escherichia coli.

Results: In this paper we show that it is possible to recover the gene regulatory network from a time series data of gene expression following a perturbation to the cell. We show this both on simulated data and on a nine gene subnetwork part of the DNA-damage response pathway (SOS pathway) in the bacteria E. coli.

Contact:  dibernardo@tigem.it

Supplementary information: Supplementary data are available at
Genetic dissociation of acquisition and memory strength in the heat-box
spatial learning paradigm in Drosophila
Authors: Diegelmann Soeren , Zars Melissa , Zars Troy
Published: January 2006

Memories can have different strengths, largely dependent on the intensity
of reinforcers encountered. The relationship between reinforcement and memory
strength is evident in asymptotic memory curves, with the level of the
asymptote related to the intensity of the reinforcer. Although this is likely
a fundamental property of memory formation, relatively little is known of how
memory strength is determined. Memory performance at different levels in
Drosophila can be measured in an operant heat-box conditioning
paradigm. In this spatial learning paradigm, flies learn and remember to avoid
one-half of a dark chamber associated with a temperature outside of the
preferred range. The reinforcement temperature has a strong effect on the
level of learning in wild-type flies, with higher temperatures inducing
stronger memories. Additionally, two mutations alter memory-acquisition
curves, either changing acquisition rate or asymptotic memory level. The
rutabaga mutation, affecting a type-1 adenylyl cyclase, decreases the
acquisition rate. In contrast, the white mutation, modifying an ABC
transporter, limits asymptotic memory. The white mutation does not
negatively affect classical olfactory conditioning but actually improves
performance at low reinforcement levels. Thus, memory acquisition/memory
strength and classical olfactory/operant spatial memories can be genetically
dissociated. A conceptual model of operant conditioning and the levels at
which rutabaga and white influence conditioning is
proposed.
Electrolytic lesions of the medial prefrontal cortex do not interfere with long-term memory of extinction of conditioned fear
Authors: Garcia René , Chang Chun-hui , Maren Stephen
Published: January 2006

Lesion studies indicate that rats without the medial prefrontal cortex
(mPFC) have difficulty recalling fear extinction acquired the previous day.
Several electrophysiological studies have also supported this observation by
demonstrating that extinction-related increases in neuronal activity in the
mPFC participate in expression of fear extinction. However, a more recent
study has shown that fear extinction can be recalled, in certain
circumstances, without mPFC potentiation, suggesting contribution of other
circuits. Here, we examined this possibility in rats that were subjected to
auditory fear conditioning, extinction training, and extinction retention test
7 d later. Electrolytic lesions were made in the mPFC, the motor cortex (MO),
the dorsal septum (SEP), or the mediodorsal thalamus (MD), because of their
potential participation in conditioned fear inhibition; combined lesions
including the mPFC with the MO, SEP, or MD were also made. The lesions were
made either 1 wk before conditioning or 1 d after extinction training. All
rats normally extinguished their conditioned freezing behavior during
extinction training and did not display any return of this behavior during the
retention test. These data reveal that the mPFC is not required for the
acquisition, the expression, or the retrieval of extinction memories but do
not exclude the possibility that the mPFC normally participates in these
processes.
Spatial relational memory in 9-month-old macaque monkeys
Authors: Lavenex Pierre , Lavenex Pamela Banta
Published: January 2006

This experiment assesses spatial and nonspatial relational memory in freely
moving 9-mo-old and adult (11-13-yr-old) macaque monkeys (Macaca
mulatta). We tested the use of proximal landmarks, two different objects
placed at the center of an open-field arena, as conditional cues allowing
monkeys to predict the location of food rewards hidden in one of two sets of
three distinct locations. Monkeys were tested in two different conditions: (1)
when local visual cues marked the two sets of potentially baited locations, so
that monkeys could use both local and spatial information to discriminate
these locations from never-baited locations; and (2) when no local visual cues
marked the two sets of potentially baited locations, so that monkeys had to
rely on a spatial relational representation of the environment to discriminate
these locations. No 9-mo-old or adult monkey associated the presence of the
proximal landmarks, at the center of the arena, with the presence of food in
one set of three distinct locations. All monkeys, however, discriminated the
potentially baited locations in the presence of local visual cues, thus
providing evidence of visual discrimination learning. More importantly, all
9-mo-old monkeys tested discriminated the potentially baited locations in
absence of the local visual cues, thus exhibiting evidence of spatial
relational learning. These findings indicate that spatial memory processes
characterized by a relational representation of the environment are present as
early as 9 mo of age in macaque monkeys.
Twice‐A‐Day Quadruple Therapy for Eradication of Helicobacter pylori in the Elderly
Authors: Dore Maria Pina , Maragkoudakis Emmanouil , Pironti Antonella , Tadeu Vincenza , Tedde Rinaldo , Realdi Giuseppe , Delitala Giuseppe
Published: January 2006

Background:  Midday and evening twice‐a‐day quadruple therapy appears to be the most effective therapy for Helicobacter pylori infection in Northern Sardinia, a site where antibiotics resistance is common.

Aim:  The objective of our study was to estimate the efficacy, side‐effects, and compliance of a quadruple therapy containing esomeprazole in a group of dyspeptic elderly patients.

Patients and Methods:  Consecutive elderly patients positive for H. pylori infection and not previously treated for eradication were enrolled. Therapy consisted of esomeprazole 20 mg, tetracycline 500 mg, metronidazole 500 mg, and bismuth subcitrate tablets 240 mg, all twice‐a‐day with the midday and evening meals, for 10 days. Efficacy was evaluated using 13C‐urea breath testing. Compliance was assessed after completing treatment and at follow up. Side effects were graded based on daily activities.

Results:  Ninety‐five dyspeptic patients (range 65–81 years), 52 men and 43 women, were enrolled. The intention‐to‐treat cure rate was 91% (81 of 89; 95% CI = 88–99%) and, 95% (81 of 85; 95% CI = 83–96%) per‐protocol analysis. Compliance was excellent. Mild‐moderate side effects occurred in 27 patients.

Conclusions:  Esomeprazole containing quadruple therapy was highly successful for initial eradication of H. pylori in elderly patients.
Effect of Probiotics and Triple Eradication Therapy on the Cyclooxygenase (COX)‐2 Expression, Apoptosis, and Functional Gastric Mucosal Impairment in Helicobacter pylori‐Infected Mongolian Gerbils
Authors: Brzozowski Tomasz , Konturek Peter C. , Mierzwa Marzena , Drozdowicz Danuta , Bielanski Wladyslaw , Kwiecien Slawomir , Konturek Stanislaw J. , Stachura Jerzy , Pawlik Wieslaw W. , Hahn Eckhart G.
Published: January 2006

Background:  Helicobacter pylori infection in Mongolian gerbils is an established experimental model of gastric carcinogenesis that mimics H. pylori‐positive patients developing gastric ulcer and gastric cancer, but the effect of probiotic therapy on functional aspects of this infection remains unknown.

Methods:  We compared the effects of intragastric inoculation of gerbils with H. pylori strain (cagA+ vacA+, 5 × 106 colony forming units/ml) with or without triple therapy including omeprazole, amoxicillin, and tinidazol or probiotic bacteria Lacidofil. Histology of glandular mucosa, the viable H. pylori, and density of H. pylori colonization were evaluated. The gastric blood flow was measured by H2‐gas clearance method; the plasma gastrin and gastric luminal somatostatin were determined by RIA and expression of cyclooxygenase (COX)‐2 and apoptotic Bax and Bcl‐2 proteins were evaluated by Western blot.

Results:  The gastric H. pylori infection was detected in all animals by histology and H. pylori culture. Basal gastric acid was significantly reduced in H. pylori‐infected animals but not in those with triple therapy or Lacidofil. Early lesions were seen already 4 weeks upon H. pylori inoculation and consisted of chronic gastritis and glandular atypia associated with typical regenerative hyperplasia and increased mitotic activity and formation of apoptotic bodies. The H. pylori infection was accompanied by the fall in gastric blood flow, the marked increase in plasma gastrin, the significant fall in gastric somatostatin levels and Bcl‐2 protein expression, and the rise in expression of COX‐2 and Bax proteins. These mucosal changes were counteracted by the triple therapy and Lacidofil.

Conclusions:  H. pylori infection in gerbils, associated with regenerative hyperplasia of glandular structure, results in the suppression of gastric secretion, overexpression of COX‐2, and enhancement in apoptosis and impairment of both, gastric blood flow and gastrin–somatostatin link that were reversed by anti‐H. pylori triple therapy and attenuated by probiotics.
cFLIP expression correlates with tumour progression and patient outcome in non‐Hodgkin lymphomas of low grade of malignancy
Authors: Valente Guido , Manfroi Federica , Peracchio Claudia , Nicotra Giuseppina , Castino Roberta , Nicosia Gabriella , Kerim Simonetta , Isidoro Ciro
Published: January 2006

The present study investigated whether the expression of cellular Fas‐associated death domain‐like interleukin‐1β‐converting enzyme (FLICE) inhibitory protein (cFLIP) conveys prognostic information in non‐Hodgkin lymphomas (NHLs). cFLIP expression was quantified by immunohistochemistry and immunofluorescence in biopsy specimens from 86 NHL patients for whom clinical information was available. NHL malignancy was graded as high/intermediate or low according to the World Health Organization Classification of Lymphoid Neoplasms. cFLIP was positive in 23 of 45 high‐/intermediate‐grade NHLs and in 25 of 41 low‐grade NHLs. Negative expression of cFLIP was associated with the presence of apoptotic cells in the tumour mass, regardless of the histotype and of the malignancy grade. In NHLs positive for cFLIP, 11 of 23 (48%) high‐/intermediate‐grade cases and 18 of 25 (72%) low‐grade cases showed a bad outcome. In NHLs negative for cFLIP, only four of 22 (18%) high‐/intermediate‐grade patients and 12 of 16 (75%) low‐grade patients achieved complete remission. All these correlations were statistically significant. The correlation of cFLIP expression with clinical outcome was independent of therapy, whether or not it included anti‐CD20 antibody (Rituximab). The present findings strongly indicate that cFLIP is a reliable predictor of tumour progression and clinical prognosis in NHLs of low grade of malignancy.
A systematic review of phase‐II trials of thalidomide monotherapy in patients with relapsed or refractory multiple myeloma
Authors: Glasmacher Axel , Hahn Corinna , Hoffmann Florian , Naumann Ralph , Goldschmidt Hartmut , von Lilienfeld‐Toal Marie , Orlopp Katjana , Schmidt‐Wolf Ingo , Gorschlüter Marcus
Published: January 2006

The activity of thalidomide in relapsed or refractory multiple myeloma is widely accepted but not yet demonstrated in a randomised‐controlled trial. A systematic review of the published clinical trials of these patients could reduce the possible bias of single phase‐II studies. A systematic search identified 42 communications reporting on 1674 patients. Thirty‐two trials used an escalating dosing regimen and four a fixed dose regimen (one dose with 50 mg/d, three doses with 200 mg/d). The target dose in the dose escalating trials was 800 mg/d in 17 trials, 400–600 mg/d in 10 and 200 mg/d in one trial. The intention‐to‐treat population for efficacy was 1629 patients with a median age of 62 years. The complete and partial (>50% reduction in monoclonal protein) response rate was 29·4% (95%‐confidence interval, 27–32%). The rates for minor responses or stable disease were 13·8% (12–16%) and 11·0% (9–13%). Progressive disease was reported in 9·9% (8–11%). The median overall survival from all trials was reported at 14 months. Severe adverse events (grade III–IV) included somnolence 11%, constipation 16%, neuropathy 6%, rash 3%, thrombo‐embolism 3%, cardiac 2%. In conclusion, thalidomide monotherapy achieved complete and partial responses in 29·4% of patients with relapsed or refractory multiple myeloma.
Human α2‐globin nonsense‐mediated mRNA decay induced by a novel α‐thalassaemia frameshift mutation at codon 22
Authors: Pereira Francisco J. C. , Silva Maria do Céu , Picanço Isabel , Seixas Maria T. , Ferrão Anabela , Faustino Paula , Romão Luísa
Published: January 2006

We describe a novel α‐thalassaemia determinant in a 3‐year‐old girl presenting a mild microcytic and hypochromic anaemia, and normal haemoglobin A2 level. Molecular studies revealed heterozygosity for a novel microdeletion (−C) at codon 22 of the α2‐globin gene. As the frameshift mutation generates a premature translation termination codon at position 48/49, we investigated the effect of the nonsense codon on the α2‐globin gene expression. Although it does not affect RNA splicing, the premature nonsense codon induces accelerated mRNA degradation. To our knowledge, this is the first time the nonsense‐mediated mRNA decay has been reported to occur in human α‐globin mRNA.
Evaluation of two different models to predict BRCA1 and BRCA2 mutations in a cohort of Danish hereditary breast and/or ovarian cancer families
Authors: Gerdes A‐M , Cruger DG , Thomassen M , Kruse TA
Published: January 2006

To meet the increasing demand for BRCA1 and BRCA2 mutation analysis, a robust system for selecting families who have a higher chance of a mutation has become important. Several models have been developed to help predict which samples are more likely to be mutation positive than others. We have undertaken a complete BRCA1 and BRCA2 mutation analysis in 267 Danish families with high‐risk family history. We found deleterious mutations in 28% (76) of the families, 68% (52) of those in BRCA1 and 32% (24) in BRCA2. We compared our results with two popular manual models developed to estimate the chance of a positive result. One is the recently published Manchester model and the other is the Frank 2 model updated by Myriad Genetic Laboratories, Inc. Neither of the models would have suggested screening all mutation‐positive samples. The Manchester model would have suggested screening 124 of the families in the cohort, thereby detecting 54 of 76 mutations (sensitivity 71%; specificity 63%), whereas the Frank 2/Myriad model would have found 60 of 76 mutations by screening 169 samples if a 10% likelihood was adapted (sensitivity 79%; specificity 43%). The updated Manchester model suggested screening 172 families whereby 64 mutations would have been detected (sensitivity 84%; specificity 44%). We conclude that although both models would have reduced the number of samples screened significantly, up to 28% of the mutations would not have been found by applying these models to this Danish cohort of families. This raises the question whether models designed for specific populations can be used in a wider setting.
Gene expression of pulmonary cytokines after sevoflurane or thiopentone anaesthesia in pigs
Authors: Takala R. S. K. , Soukka H. , Salo M. S. , Kirvelä O. , Kääpä P. , Aantaa R.
Published: January 2006

Background:  Volatile anaesthetics have diverse inflammatory effects on the lungs. They increase gene expression of some pro‐inflammatory cytokines in alveolar macrophages whereas in alveolar type II cells they seem to decrease secretion and gene expression of pro‐inflammatory cytokines. We have previously detected increased leukotriene C4, nitrate and nitrite concentrations in bronchoalveolar lavage fluid after sevoflurane anaesthesia. In the current study, we measured gene expression of inflammatory cytokines in the lung tissue and plasma concentrations of cytokines in pigs after thiopentone or sevoflurane anaesthesia.

Methods:  Sixteen pigs were randomly selected to receive either a continuous thiopentone infusion (control group, n = 8) or sevoflurane (n = 8) at 4.0% inspiratory concentration (1.5 MAC) in air for 6 h. Tissue samples were collected at the end of the study for measurement of gene expression of inflammatory cytokines. Blood samples were collected during anaesthesia for measurement of plasma cytokine concentrations.

Results:  Compared with thiopentone anaesthesia, lower gene expression of tumour necrosis factor‐α (TNF‐α) and interleukin‐1β (IL‐1β) in lung tissue was observed after sevoflurane anaesthesia. Of measured cytokines IL‐1β, TNF‐α, IL‐6, IL‐8 and IL‐10 only plasma concentrations of IL‐6 could be measured during the study without a difference between the groups.

Conclusion:  Lower gene expression of TNF‐α and IL‐1β was found in the intact porcine lung tissue after sevoflurane anaesthesia compared with thiopentone anaesthesia. Clinical significance of this finding is unknown.
The effects of experimental venous carbon dioxide embolization on hemodynamic and respiratory variables
Authors: Jersenius U. , Fors D. , Rubertsson S. , Arvidsson D.
Published: January 2006

Background:  Laparoscopic liver resection is a relatively new surgical procedure. Carbon dioxide (CO2) pneumoperitoneum and laparoscopic liver dissection are recognized as risk factors for CO2 embolism to the pulmonary circulation. The embolization can be difficult to detect and can theoretically increase peri‐operative morbidity. The aim of this study was to evaluate the cardiopulmonary effects in a pig model during a time period of 4 h after an experimental CO2 embolization.

Methods:  Eleven piglets were anesthesized. Nine were embolized with a single intravenous injection of 0.4 ml/kg CO2 and two served as controls. Respiratory and cardiovascular variables, including pulmonary artery pressure and cardiac output, were monitored for 4 h after embolization, and arterial blood gases were monitored on‐line.

Results:  The embolized piglets had an increase in ventilatory dead space, pulmonary vascular resistance and pulmonary artery pressure and a decrease in cardiac output that lasted throughout the 4‐h observation time. The mean arterial pressure and heart rate were unchanged. An early sign of embolization was a rapid fall in end‐tidal CO2 and Pao2 and a rise in Paco2.

Conclusion:  Negative changes in cardiopulmonary physiology persisted for at least 4 h after a single intravenous CO2 injection, in spite of this gas being highly soluble in blood. This is a more prolonged influence of CO2 embolization than previously described. Extensive monitoring for early detection of an embolization may be recommended to limit morbidity in patients undergoing laparoscopic liver surgery.