bluuebunny/crossref_metadata_2025 huggingface dataset:
An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data
Authors: Xu Han , Wei Chia-Lin , Lin Feng , Sung Wing-Kin
Published: July 2008

Motivation: Epigenetic modifications are one of the critical factors to regulate gene expression and genome function. Among different epigenetic modifications, the differential histone modification sites (DHMSs) are of great interest to study the dynamic nature of epigenetic and gene expression regulations among various cell types, stages or environmental responses. To capture the histone modifications at whole genome scale, ChIP-seq technology is becoming a robust and comprehensive approach. Thus the DHMSs are potentially identifiable by comparing two ChIP-seq libraries. However, little has been addressed on this issue in literature.

Results: Aiming at identifying DHMSs, we propose an approach called ChIPDiff for the genome-wide comparison of histone modification sites identified by ChIP-seq. Based on the observations of ChIP fragment counts, the proposed approach employs a hidden Markov model (HMM) to infer the states of histone modification changes at each genomic location. We evaluated the performance of ChIPDiff by comparing the H3K27me3 modification sites between mouse embryonic stem cell (ESC) and neural progenitor cell (NPC). We demonstrated that the H3K27me3 DHMSs identified by our approach are of high sensitivity, specificity and technical reproducibility. ChIPDiff was further applied to uncover the differential H3K4me3 and H3K36me3 sites between different cell states. Interesting biological discoveries were achieved from such comparison in our study.

Availability:  http://cmb.gis.a-star.edu.sg/ChIPSeq/tools.htm

Contact:  asflin@ntu.edu.sg; sungk@gis.a-star.edu.sg

Supplementary information:  Supplementary methods and data are available at Bioinformatics online.
Efficient whole-genome association mapping using local phylogenies for unphased genotype data
Authors: Ding Zhihong , Mailund Thomas , Song Yun S.
Published: July 2008

Motivation: Recent advances in genotyping technology has made data acquisition for whole-genome association study cost effective, and a current active area of research is developing efficient methods to analyze such large-scale datasets. Most sophisticated association mapping methods that are currently available take phased haplotype data as input. However, phase information is not readily available from sequencing methods and inferring the phase via computational approaches is time-consuming, taking days to phase a single chromosome.

Results: In this article, we devise an efficient method for scanning unphased whole-genome data for association. Our approach combines a recently found linear-time algorithm for phasing genotypes on trees with a recently proposed tree-based method for association mapping. From unphased genotype data, our algorithm builds local phylogenies along the genome, and scores each tree according to the clustering of cases and controls. We assess the performance of our new method on both simulated and real biological datasets.

Availability The software described in this article is available at http://www.daimi.au.dk/~mailund/Blossoc and distributed under the GNU General Public License.

Contact:  mailund@birc.au.dk
Postexposure Interventions to Prevent Infection With HBV, HCV, or HIV, and Tetanus in People Wounded During Bombings and Other Mass Casualty Events—United States, 2008: Recommendations of the Centers for Disease Control and Prevention and Disaster Medicine and Public Health Preparedness
Authors: Chapman Louisa E. , Sullivent Ernest E. , Grohskopf Lisa A. , Beltrami Elise M. , Perz Joseph F. , Kretsinger Katrina , Panlilio Adelisa L. , Thompson Nicola D. , Ehrenberg Richard L. , Gensheimer Kathleen F. , Duchin Jeffrey S. , Kilmarx Peter H. , Hunt Richard C.
Published: July 2008

People wounded during bombings or other events resulting in mass casualties or in conjunction with the resulting emergency response may be exposed to blood, body fluids, or tissue from other injured people and thus be at risk for bloodborne infections such as hepatitis B virus, hepatitis C virus, human immunodeficiency virus, or tetanus. This report adapts existing general recommendations on the use of immunization and postexposure prophylaxis for tetanus and for occupational and nonoccupational exposures to bloodborne pathogens to the specific situation of a mass casualty event. Decisions regarding the implementation of prophylaxis are complex, and drawing parallels from existing guidelines is difficult. For any prophylactic intervention to be implemented effectively, guidance must be simple, straightforward, and logistically undemanding. Critical review during development of this guidance was provided by representatives of the National Association of County and City Health Officials, the Council of State and Territorial Epidemiologists, and representatives of the acute injury care, trauma, and emergency response medical communities participating in the Centers for Disease Control and Prevention’s Terrorism Injuries: Information, Dissemination and Exchange project. The recommendations contained in this report represent the consensus of US federal public health officials and reflect the experience and input of public health officials at all levels of government and the acute injury response community. (Disaster Med Public Health Preparedness. 2008;2:150–165)
People are people, but technology is not technology
Authors: Marsden Gary , Maunder Andrew , Parker Munier
Published: July 2008

Ubiquitous computing is about more than having multiple computers in our environment; it is also about computers venturing into completely new environments. In this paper, we examine the impact of computers in the developing world and look at why most interventions to date have failed to address the key needs of the users and their context. Through an analysis of existing software design techniques, and various case studies, we propose a new model for software creation, which we believe will address the issue of creating technologies for developing world nations.
Two challenges in embedded systems design: predictability and robustness
Authors: Henzinger Thomas A
Published: July 2008

I discuss two main challenges in embedded systems design: the challenge to build predictable systems, and that to build robust systems. I suggest how predictability can be formalized as a form of determinism, and robustness as a form of continuity.
Comparative Transcriptomics of Arabidopsis Sperm Cells
Authors: Borges Filipe , Gomes Gabriela , Gardner Rui , Moreno Nuno , McCormick Sheila , Feijó José A. , Becker Jörg D.
Published: July 2008

In flowering plants, the two sperm cells are embedded within the cytoplasm of the growing pollen tube and as such are passively transported to the embryo sac, wherein double fertilization occurs upon their release. Understanding the mechanisms and conditions by which male gametes mature and take part in fertilization are crucial goals in the study of plant reproduction. Studies of gene expression in male gametes of maize (Zea mays) and Plumbago and in lily (Lilium longiflorum) generative cells already showed that the previously held view of transcriptionally inert male gametes was not true, but genome-wide studies were lacking. Analyses in the model plant Arabidopsis (Arabidopsis thaliana) were hindered, because no method to isolate sperm cells was available. Here, we used fluorescence-activated cell sorting to isolate sperm cells from Arabidopsis, allowing GeneChip analysis of their transcriptome at a genome-wide level. Comparative analysis of the sperm cell transcriptome with those of representative sporophytic tissues and of pollen showed that sperm has a distinct and diverse transcriptional profile. Functional classifications of genes with enriched expression in sperm cells showed that DNA repair, ubiquitin-mediated proteolysis, and cell cycle progression are overrepresented Gene Ontology categories. Moreover, analysis of the small RNA and DNA methylation pathways suggests that distinct mechanisms might be involved in regulating the epigenetic state of the paternal genome. We identified numerous candidate genes whose involvement in sperm cell development and fertilization can now be directly tested in Arabidopsis. These results provide a roadmap to decipher the role of sperm-expressed proteins.
A meta‐analysis of the utility of pre‐operative brain natriuretic peptide in predicting early and intermediate‐term mortality and major adverse cardiac events in vascular surgical patients
Authors: Rodseth R. N. , Padayachee L. , Biccard B. M.
Published: July 2008

We conducted a meta‐analysis of the utility of pre‐operative B‐type natriuretic peptide (BNP) and N‐terminal‐pro B‐type natriuretic peptide in predicting early (< 30 days) and intermediate (< 180 days) term mortality and major adverse cardiac events (cardiac death and nonfatal myocardial infarction) in patients following vascular surgery. A Pubmed Central and EMBASE search was conducted up to January 2008. Of 81 studies identified, seven prospective observational studies were included in the meta‐analysis representing five patient cohorts: early outcomes (504 patients) and intermediate‐term outcomes (623 patients). A B‐type natriuretic peptide or N‐terminal‐pro B‐type natriuretic peptide above the optimal discriminatory threshold determined by receiver operating characteristic curve analysis was associated with 30‐day cardiac death (OR 7.6, 95% CI 1.33–43.4, p = 0.02), nonfatal myocardial infarction (OR 6.24, 95% CI 1.82–21.4, p = 0.004) and major adverse cardiac events (OR 17.37, 95% CI 3.31–91.15, p = 0.0007), and intermediate‐term, all‐cause mortality (OR 3.1, 95% CI 1.85–5.2, p < 0.0001), nonfatal myocardial infarction (OR 2.95, 95% CI 1.17–7.46, p = 0.02) and major adverse cardiac events (OR 3.31, 95% CI 2.1–5.24, p < 0.00001). B‐type natriuretic peptide and N‐terminal‐pro B‐type natriuretic peptide are potentially useful pre‐operative prognostic tests in vascular surgical patients.
Population pharmacokinetic analysis for risperidone using highly sparse sampling measurements from the CATIE study
Authors: Feng Yan , Pollock Bruce G. , Coley Kim , Marder Stephen , Miller Del , Kirshner Margaret , Aravagiri Manickam , Schneider Lon , Bies Robert R.
Published: July 2008

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Risperidone metabolism is affected by blocking CYP2D6 and CYP3A4 (in CYP2D6 poor metabolizers) metabolizing enzymes.

• Age affects risperidone disposition and renal function affects elimination of 9‐hydroxy‐risperidone (primary active metabolite).

WHAT THIS STUDY ADDS

• The detection of a systematic shift in estimated apparent clearance in the African‐American population (it is not clear if there are biological or sociological contributors), and a shift in the clearance rate of risperidone based on concomitant administration of paroxetine, manifested as a change in assignment to a different metabolizer subpopulation group that may be primarily related to CYP2D6 metabolizer status.

• The study shows an age‐related decrement in 9‐hydroxy‐risperidone clearance across a wide range of ages.

• Information on the nature of the pharmacokinetic variability with risperidone when used in a typical clinical patient population.

• There are significant differences in the absolute values as well as the assignment to metabolizer status across race and concomitant paroxetine administration.

AIMS

To characterize pharmacokinetic (PK) variability of risperidone and 9‐OH risperidone using sparse sampling and to evaluate the effect of covariates on PK parameters.

METHODS

PK analysis used plasma samples collected from the Clinical Antipsychotic Trials of Intervention Effectiveness. A nonlinear mixed‐effects model was developed using nonmem to describe simultaneously the risperidone and 9‐OH risperidone concentration–time profile. Covariate effects on risperidone and 9‐OH risperidone PK parameters were assessed, including age, weight, sex, smoking status, race and concomitant medications.

RESULTS

PK samples comprised 1236 risperidone and 1236 9‐OH risperidone concentrations from 490 subjects that were available for analysis. Ages ranged from 18 to 93 years. Population PK submodels for both risperidone and 9‐OH risperidone with first‐order absorption were selected to describe the concentration–time profile of risperidone and 9‐OH risperidone. A mixture model was incorporated with risperidone clearance (CL) separately estimated for three subpopulations [poor metabolizer (PM), extensive metabolizer (EM) and intermediate metabolizer (IM)]. Age significantly affected 9‐OH risperidone clearance. Population parameter estimates for CL in PM, IM and EM were 12.9, 36 and 65.4 l h−1 and parameter estimates for risperidone half‐life in PM, IM and EM were 25, 8.5 and 4.7 h, respectively.

CONCLUSIONS

A one‐compartment mixture model with first‐order absorption adequately described the risperidone and 9‐OH risperidone concentrations. Age was identified as a significant covariate on 9‐OH risperidone clearance in this study.
Early diagnostic and prognostic significance of a specific Th1/Th2 cytokine pattern in children with haemophagocytic syndrome
Authors: Tang Yongmin , Xu Xiaojun , Song Hua , Yang Shilong , Shi Shuwen , Wei Jian , Pan Binhua , Zhao Fenying , Liao Chan , Luo Chunfang
Published: July 2008

The haemophagocytic syndrome (HPS) is a rare but frequently fatal disorder of immune regulation caused by hypercytokinemia. Using cytometric bead array technique, the serum T‐helper cell type 1 (Th1) and 2 (Th2) cytokines including interferon‐γ (IFN‐γ), tumour necrosis factor (TNF), interleukin (IL)‐10, IL‐6, IL‐4 and IL‐2 were determined in 24 children with de novo HPS and 87 children as control. The median levels of serum IFN‐γ, IL‐10 and IL‐6 in the acute phase of HPS were 901·7, 879·0 and 63·8 pg/ml, respectively, significantly higher than those after remission, and in the healthy volunteers and patients with viral infection. IL‐4 was slightly elevated while IL‐2 and TNF were within normal range in acute phase. Patients with bacterial sepsis showed an extremely high level of IL‐6 and moderate level of IL‐10, whereas IFN‐γ was only slightly elevated. Five patients were diagnosed with HPS according to the Th1/Th2 cytokine pattern 3–13 d earlier than they fulfilled the relevant diagnostic criteria. IL‐10 level >2000 pg/ml was an unfavorable prognostic factor for HPS treatment response (P = 0·033) and outcome (P = 0·009). We conclude that the significant increase of IFN‐γ and IL‐10 and a slightly increased level of IL‐6 is an early, specific and prognostic cytokine pattern for childhood HPS.
The relationship between quality of response and clinical benefit for patients treated on the bortezomib arm of the international, randomized, phase 3 APEX trial in relapsed multiple myeloma
Authors: Niesvizky Ruben , Richardson Paul G. , Rajkumar S. Vincent , Coleman Morton , Rosiñol Laura , Sonneveld Pieter , Schuster Michael W. , Irwin David , Stadtmauer Edward A. , Facon Thierry , Harousseau Jean‐Luc , Boral Anthony L. , Esseltine Dixie‐Lee , Anderson Kenneth C. , Bladé Joan
Published: July 2008

Quality of response is associated with prolonged overall survival (OS) in newly diagnosed multiple myeloma patients. This cohort study within the phase 3 Assessment of Proteasome Inhibition for Extending Remissions (APEX) trial of bortezomib versus dexamethasone in relapsed myeloma assessed the relationship between quality of response to bortezomib (n = 315) and clinical benefit. Treatment‐free interval (TFI), time to alternative therapy (TTAT), time to progression (TTP) and OS were assessed in response‐evaluable patients in the bortezomib arm in cohorts defined by achievement of complete response (CR; n = 27), very good partial response (VGPR; n = 31), partial response (PR; n = 77), minimal response (MR; n = 21) or non‐response (NR, including stable and progressive disease; n = 159). CR was associated with significantly longer median TFI (24·1 vs. 6·9/6·4 months) and TTAT (27·1 vs. 13·6/14 months) versus VGPR/PR. Median TTP was similar in CR, VGPR and PR cohorts; median OS was not reached. Patients achieving MR appeared to have prolonged median TFI (3·8 vs. 2·3 months), TTAT (8·7 vs. 6·2 months), TTP (4·9 vs. 2·8 months) and OS (24·9 vs. 18·7 months) versus NR. In conclusion, bortezomib had substantial activity in relapsed myeloma patients; CR may be a surrogate marker for significant clinical benefit with bortezomib. MR appeared to be valid as a separate response category in this setting.
In vitro polydeoxyribonucleotide effects on human pre‐adipocytes
Authors: Raposio E. , Guida C. , Coradeghini R. , Scanarotti C. , Parodi A. , Baldelli I. , Fiocca R. , Santi P.L.
Published: July 2008

Abstract.  Objectives: Adipose tissue is the most abundant and accessible source of adult stem cells. Human processed lipoaspirate contains pre‐adipocytes that possess one of the a characteristic pathways of multipotent adult stem cells and are able to differentiate in vitro into mesenchymal and also neurogenic lineages. Because stem cells have great potential for use in tissue repair and regeneration, it would be significant to be able to obtain large amounts of these cells in vitro. As demonstrated previously, purine nucleosides and nucleotides mixtures can act as mitogens for several cell types. The aim of this study was to evaluate the effects of polydeoxyribonucleotides (PDRN), at appropriate concentrations, on human pre‐adipocytes grown in a controlled medium, also using different passages, so as to investigate the relationship between the effect of this compound and cellular senescence, which is the phenomenon when normal diploid cells lose the ability to divide further. Materials and methods: Human pre‐adipocytes were obtained by liposuction. Cells from different culture passages (P6 and P16) were treated with PDRN at different experimental times. Cell number was evaluated for each sample by direct counting after trypan blue treatment. DNA assay and the 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide test were also carried out in all cases. Results and Conclusions: PDRN seemed to promote proliferation of human pre‐adipocytes at both passages, but cell population growth increased in pre‐adipocyte at P16, after 9 days as compared to control. Our data suggest that PDRN could act as a pre‐adipocyte growth stimulator.
On‐chip non‐invasive and label‐free cell discrimination by impedance spectroscopy
Authors: Schade‐Kampmann G. , Huwiler A. , Hebeisen M. , Hessler T. , Di Berardino M.
Published: July 2008

Abstract.  Objectives: Many flow‐cytometric cell characterization methods require costly markers and colour reagents. We present here a novel device for cell discrimination based on impedance measurement of electrical cell properties in a microfluidic chip, without the need of extensive sample preparation steps and the requirement of labelling dyes. Materials and methods, Results: We demonstrate that in‐flow single cell measurements in our microchip allow for discrimination of various cell line types, such as undifferentiated mouse fibroblasts 3T3‐L1 and adipocytes on the one hand, or human monocytes and in vitro differentiated dendritic cells and macrophages on the other hand. In addition, viability and apoptosis analyses were carried out successfully for Jurkat cell models. Studies on several species, including bacteria or fungi, demonstrate not only the capability to enumerate these cells, but also show that even other microbiological life cycle phases can be visualized. Conclusions: These results underline the potential of impedance spectroscopy flow cytometry as a valuable complement to other known cytometers and cell detection systems.
Cranially irradiated adult cancer survivors may have normal spontaneous GH secretion in the presence of discordant peak GH responses to stimulation tests (compensated GH deficiency)
Authors: Darzy Ken H. , Thorner Michael O. , Shalet Stephen M.
Published: July 2008

Context  We have previously demonstrated that spontaneous (physiological) GH secretion was entirely normal in cranially irradiated patients who had normal individual peak GH responses to the insulin tolerance test (ITT) but reduced maximal somatotroph reserve as indicated by substantially reduced group GH responses to the GHRH + arginine stimulation test (AST). The normality of spontaneous GH secretion was attributed to a compensatory increase in hypothalamic stimulatory input within a partially damaged hypothalamic–pituitary (h–p) axis. It is unknown, however, if such compensatory stimulation can also maintain normality of GH secretion in those who fail the ITT but pass the GHRH + AST.

Study subjects and design  We studied 24‐h spontaneous GH secretion by 20‐min sampling both in the fed state (n = 11) and in the last 24 h of a 33‐h fast (n = 9) in adult cancer survivors with subnormal peak GH responses to the ITT but either normal or relatively less attenuated peak GH responses to the GHRH + AST. The study was conducted 8·3 ± 1·8 (range 2–23) years after cranial irradiation for nonpituitary brain tumours (n = 9) or leukaemia/lymphoma (n = 2) in comparison with 30 normal controls (fasting, 14).

Results  Previously published diagnostic thresholds for the ITT, GHRH + AST and spontaneous GH secretion were used to characterize GH secretion. Four of the 11 patients with impaired stimulated responses to both tests showed only minor discordancies between stimulated and spontaneous GH secretion. Two of the remaining seven patients had subnormal spontaneous GH secretion. However, spontaneous GH secretion, both individually and as a group, was entirely normal in the remaining five patients who had impaired GH responses to the ITT but normal individual responses to the GHRH + AST; in these five patients, IGF‐I standard deviation scores (SDS; –2·7 to –0·8) were significantly reduced to a moderate degree compared with normals.

Conclusions  In cranially irradiated adult cancer survivors, it cannot be assumed that failure to pass the ITT in isolation reflects severe GH deficiency (GHD). It appears that in some patients near‐maximal compensatory overdrive of the partially damaged somatotroph axis may result in near‐normal quantitative restoration of spontaneous GH secretion, thus limiting further stimulation with the ITT to the extent that impaired GH responses can be seen even before spontaneous GH secretion starts to decline in adults. However, IGF‐I status continues to provide useful information about the adequacy of the compensatory process and therefore the degree of normality of GH secretion.
Secondary deterioration of visual field during cabergoline treatment for macroprolactinoma
Authors: Raverot Gérald , Jacob Maud , Jouanneau Emmanuel , Delemer Brigitte , Vighetto Alain , Pugeat Michel , Borson‐Chazot Françoise
Published: July 2008

Objective  During dopaminergic agonist treatment for macroprolactinoma, tumour shrinkage can be accompanied by secondary deterioration of the visual field in rare instances. The aim of the present study was to evaluate the incidence of symptomatic or asymptomatic delayed visual loss associated with chiasmal herniation during long‐term cabergoline treatment of macroprolactinomas and to report our experience of its management.

Patients  The study included 28 patients (11 women and 17 men) aged 14–85 years treated for macroprolactinoma with cabergoline at our centre from 1997 to 2006.

Results  Chiasmal herniation was observed at MRI in five out of the 28 cases. A systematic visual field evaluation revealed visual field worsening, during cabergoline treatment, in three out of these five patients. In two asymptomatic patients, secondary deterioration of visual field occurred 2·5 years and 4 years, respectively, after cabergoline treatment initiation. In the third case, cabergoline treatment resulted in a paradoxical worsening of an initial visual defect. In all three cases, visual fields improved after cabergoline withdrawal although chiasmal herniation persisted. Visual field remained normal in the two other patients.

Conclusions  Our results suggested that chiasmal herniation associated with delayed visual field defect is not a rare feature during cabergoline treatment of macroprolactinomas. It should be assessed by systematic visual field evaluation and treated by adaptation of medical treatment.
Flooding and canopy dynamics shape the demography of a clonal Amazon understorey herb
Authors: Schleuning Matthias , Huamán Vicky , Matthies Diethart
Published: July 2008

Tropical forests have highly diverse and often dense understorey vegetation. However, little is known about the demography of tropical understorey species and their response to common events like flooding and gap formation that change the prevailing environmental conditions.

We studied the influence of flooding and canopy gaps on the demography of the widespread clonal herb Heliconia metallica in 16 populations in the Peruvian Amazon over two wet and two dry seasons. In a factorial study design, we selected several populations in canopy gaps and under a closed canopy both at flooded and non‐flooded sites.

Using periodic matrix models, we determined projected population growth rates during seasonal and annual time intervals and applied prospective and retrospective analyses to identify the life cycle components that contributed most to the differences in annual growth rates among the four combinations of habitat conditions.

All populations increased in size during the wet and decreased during the dry season. In both years, projected annual growth rates of the non‐flooded populations were less than 1 both in gaps and under a closed canopy. In contrast, over the 2‐year study period growth rates of the flooded populations were close to 1 both in gaps and under a closed canopy.

The life history of H. metallica was dominated by ramet survival and clonal growth, whereas seedling recruitment was very rare. In canopy gaps, growth and clonal expansion were rapid and reproduction was frequent, whereas under a closed canopy ramets grew little and rarely flowered. Population decline at non‐flooded sites was due to higher ramet mortality during the dry season. However, the effects of flooding and canopy gaps interacted and affected life‐history components differently in wet and dry seasons and in successive years.

Synthesis. The intricate interacting effects of flooding and canopy gaps determine the population dynamics of the understorey herb H. metallica. The clonal life form and the plasticity of the ramets enable the populations to persist under variable light conditions, but may not be able to buffer the increasingly frequent periods of drought in Amazon forests.
Biological Flora of the British Isles: Primula elatior (L.) Hill
Authors: Taylor Kenneth , Woodell Stanley R. J.
Published: July 2008

This account presents information on all aspects of the biology of Primula elatior that are relevant to understanding its ecological characteristics and behaviour. The main topics are presented within the standard framework of the Biological Flora of the British Isles: distribution, habitat, communities, responses to biotic factors, responses to environment, structure and physiology, phenology, floral and seed characters, herbivores and disease, history, and conservation.

Primula elatior is a native perennial herb, within a compact area in the British Isles, in ancient woods and copses on the chalky boulder clay in East Anglia, where it is abundant locally although scarce nationally. British material is ssp. elatior, which extends across much of Europe, becoming rarer towards the south.

Primula elatior is a shade tolerant species, but only flowers in profusion in the increased light levels following tree felling in traditionally coppiced woods. It is confined to an area of the British Isles where the soils are seasonally waterlogged and ill‐aerated, and is very tolerant of the toxic levels of ferrous iron which accumulate in the surface horizons in the spring months. It has a poorly developed drought tolerance.

An early flowering plant, P. elatior is an insect‐pollinated obligate outbreeder, with two self‐incompatible morphs (pin and thrum). The low colonizing ability of this ancient woodland species can be attributed to both seed dispersal and seedling recruitment limitation.

There has been a steady reduction in the density of P. elatior in woodland sites during the past centuries. However, there has been little change in the 10‐km distribution in the British Isles. Studies of populations involve three groups of factors: genetic variation, environmental changes and population structure. Potentially these factors have a greater effect on small and isolated populations than on large and integrated ones. There is no evidence that the species suffers from a loss of genetic diversity in the smaller populations. Primula elatior seems to have a relatively high level of genetic diversity that is maintained despite a fragmented distribution.

Within its restricted distribution area P. elatior replaces P. vulgaris completely. At the margins of their distributions the two species occur together in a number of woodland sites, providing the opportunity for hybridization. As they are highly interfertile, hybridization is restricted mainly by differences in their habitat preferences. The hybrid P. vulgaris × P. elatior = P. × digenea is fertile and gives rise to hybrid swarms which are found in all British sites where both parents occur together.

Changes in climate, woodland management practices and intensities of deer grazing, especially by Fallow deer (Dama dama), are likely to have a major effect on populations of P. elatior. Since the species colonizes new or secondary woodlands very slowly, management should focus on the conservation of ancient semi‐natural woodlands.
Confocal imaging of glutathione redox potential in living plant cells
Authors: SCHWARZLÄNDER M. , FRICKER M.D. , MÜLLER C. , MARTY L. , BRACH T. , NOVAK J. , SWEETLOVE L.J. , HELL R. , MEYER A.J.
Published: July 2008

Reduction–oxidation‐sensitive green fluorescent protein (roGFP1 and roGFP2) were expressed in different sub‐cellular compartments of Arabidopsis and tobacco leaves to empirically determine their performance as ratiometric redox sensors for confocal imaging in planta. A lower redox‐dependent change in fluorescence in combination with reduced excitation efficiency at 488 nm resulted in a significantly lower dynamic range of roGFP1 than for roGFP2. Nevertheless, when targeted to the cytosol and mitochondria of Arabidopsis leaves both roGFPs consistently indicated redox potentials of about –320 mV in the cytosol and –360 mV in the mitochondria after pH correction for the more alkaline matrix pH. Ratio measurements were consistent throughout the epidermal cell layer, but results might be attenuated deeper within the leaf tissue. Specific interaction of both roGFPs with glutaredoxin in vitro strongly suggests that in situ both variants preferentially act as sensors for the glutathione redox potential. roGFP2 targeted to plastids and peroxisomes in epidermal cells of tobacco leaves was slightly less reduced than in other plasmatic compartments, but still indicated a highly reduced glutathione pool. The only oxidizing compartment was the lumen of the endoplasmic reticulum, in which roGFP2 was almost completely oxidized. In all compartments tested, roGFP2 reversibly responded to perfusion with H2O2 and DTT, further emphasizing that roGFP2 is a reliable probe for dynamic redox imaging in planta. Reliability of roGFP1 measurements might be obscured though in extended time courses as it was observed that intense irradiation of roGFP1 at 405 nm can lead to progressive photoisomerization and thus a redox‐independent change of fluorescence excitation ratios.
Sphere size distributions from finite thickness sections: a forward approach employing a genetic algorithm
Authors: DE NOOIJER S. , KETELAAR T. , MULDER B.
Published: July 2008

We formulate, implement and test a robust method of determining sphere size distributions from finite thickness planar sections. The method uses a forward approach in which populations of proposed distributions are tested against the input data and refined using a genetic algorithm. This method is then applied to a real‐world data set concerning endo‐ and exocytotic vesicles in the apical region of tip growing pollen tubes of Arabidopsis thaliana.
Cellulose microfibril deposition: coordinated activity at the plant plasma membrane
Authors: LINDEBOOM J. , MULDER B.M. , VOS J.W. , KETELAAR T. , EMONS A.M.C.
Published: July 2008

Plant cell wall production is a membrane‐bound process. Cell walls are composed of cellulose microfibrils, embedded inside a matrix of other polysaccharides and glycoproteins. The cell wall matrix is extruded into the existing cell wall by exocytosis. This same process also inserts the cellulose synthase complexes into the plasma membrane. These complexes, the nanomachines that produce the cellulose microfibrils, move inside the plasma membrane leaving the cellulose microfibrils in their wake. Cellulose microfibril angle is an important determinant of cell development and of tissue properties and as such relevant for the industrial use of plant material. Here, we provide an integrated view of the events taking place in the not more than 100 nm deep area in and around the plasma membrane, correlating recent results provided by the distinct field of plant cell biology. We discuss the coordinated activities of exocytosis, endocytosis, and movement of cellulose synthase complexes while producing cellulose microfibrils and the link of these processes to the cortical microtubules.
Having a swell time – mitochondrial morphology and plant cell death programmes
Authors: LOGAN D.C.
Published: July 2008

Cell death is a vital process in multi‐cellular eukaryotes. Rather than being a contradiction in terms, this statement highlights the importance of limited and localized cell killing to the health and normal development of complex organisms. The main focus of this article is the role of mitochondrial morphological changes during cell death programmes, and the conserved role of mitochondrial permeability transition (increased permeability of either the outer or inner membrane) as an early mechanistic event preceding cell death in both plant and non‐plant eukaryotes. A second focus of this article is a review of the terminology and fundamental paradigms underpinning cell death research. Because of the importance of the process of cell death, there has been an enormous quantity of research performed to try to understand the underlying biological mechanisms. One result of such a large and varied research effort, and a result that is perhaps particularly evident to investigators coming into the field anew, is that some of the basic tenets of cell death research appear to have become confused. In this short article, I make an attempt to clarify the subject, focussing on the role of mitochondria, and the difficulties in comprehensibility arising from the sometimes‐erroneous, or at least unnecessarily confusing use of specific terminology; there are several key terms in the cell death literature that appear interchangeable when they are not, or are interchanged when they should not be.
Going green: plants' alternative way to position the Ran gradient
Authors: MEIER I. , XU X.M. , BRKLJACIC J. , ZHAO Q. , WANG H.‐J.
Published: July 2008

Ran is a multi‐functional small GTPase of the Ras super‐family involved in nucleocytoplasmic transport, mitotic spindle assembly, cell cycle control and nuclear envelope (NE) formation. Its roles are accomplished by the asymmetric distribution of its GTP‐ and GDP‐bound forms, enabled by the specific localization of Ran accessory proteins, the Ran GTPase‐activating protein RanGAP and the nucleotide exchange factor RCC1. Mammalian RanGAP1 is targeted to the NE during interphase and to the spindle and kinetochores during mitosis via a SUMOylated C‐terminal domain and interaction with the nucleoporin Nup358/RanBP2. Arabidopsis RanGAP1 (AtRanGAP1) lacks the SUMOylated C‐terminal domain of vertebrate RanGAP, but contains a plant‐specific N‐terminal domain (WPP domain), which is necessary and sufficient for its targeting to the NE in interphase. AtRanGAP1 has a mitotic trafficking pattern uniquely different from that of vertebrate RanGAP, which includes targeting to the outward‐growing rim of the cell plate. The WPP domain is necessary and sufficient for this targeting. Now, a novel family of plant‐specific, nuclear pore‐associated proteins has been identified in Arabidopsis, which is essential for anchoring RanGAP to the Arabidopsis nuclear envelope at the root meristem. This suggests that RanGAP anchoring to the nuclear pore has been solved in two fundamentally different ways in animals and plants. These findings support a separate evolution of RanGAP targeting mechanisms in different kingdoms, possibly related to different functional geometries of the Ran gradient in animal and higher plant cell division.
Functions, regulation and cellular localization of plant cyclin‐dependent kinase inhibitors
Authors: WANG H. , ZHOU Y. , BIRD D.A. , FOWKE L.C.
Published: July 2008

The cell cycle is regulated by the cyclin‐dependent kinase (CDK), and CDK inhibitors can bind to CDKs and inhibit their activities. This review examines plant CDK inhibitors, with particular emphasis on their molecular and cellular functions, regulation and cellular localization. In plants, a family of ICK/KRP CDK inhibitors represented by ICK1 is known and another type of CDK inhibitor represented by the SIMESE (SIM) has recently been reported. Considerable understanding has been gained with the ICK/KRP CDK inhibitors. These plant CDK inhibitors share only limited sequence similarity in the C‐terminal region with the KIP/CIP family of mammalian CDK inhibitors. The ICK/KRP CDK inhibitors thus provide good tools to understand the basic machinery as well as the unique aspects of the plant cell cycle. The ICK/KRP CDK inhibitors interact with D‐type cyclins or A‐type CDKs or both. Several functional regions and motifs have been identified in ICK1 for CDK inhibition, nuclear localization and protein instability. Clear evidence shows that ICK/KRP proteins are important for the cell cycle and endoreduplication. Preliminary evidence suggests that they may also be involved in cell differentiation and cell death. Results so far show that plant CDK inhibitors are exclusively localized in the nucleus. The molecular sequences regulating the localization and functional significance will be discussed.
Microinjecting FM4–64 validates it as a marker of the endocytic pathway in plants
Authors: Van GISBERGEN P.A.C. , ESSELING‐OZDOBA A. , VOS J.W.
Published: July 2008

The amphiphilic dye FM4–64 is used to investigate endocytosis and vesicle trafficking in living eukaryotic cells. The standing hypothesis is that it is inserted into the outer leaflet of the plasma membrane and, from there, is passed on to intracellular membrane compartments by endocytosis. We tested this hypothesis by microinjecting FM4–64 into the cytoplasm and vacuole of Nicotiana tabacum BY‐2 suspension culture cells and Tradescantia virginiana stamen hair cells. We found that the dye did not label any membranes when injected into the cytoplasm, but clearly labelled the tonoplast when injected directly into the vacuole. However, because the dye is pH‐sensitive, the fluorescence intensity between the plasma membrane and tonoplast varied. We conclude that FM4–64 is a specific marker for the endocytic pathway. Nevertheless, little is known about the molecular interactions of FM4–64 with these particular phospholipid membrane leaflets. We, therefore, appeal for biochemical research to determine which membrane lipids FM4–64 interacts with.
FRET analysis of transmembrane flipping of FM4–64 in plant cells: is FM4–64 a robust marker for endocytosis?
Authors: GRIFFING L. R.
Published: July 2008

Although the styryl dye FM4–64 is now used routinely to monitor endocytosis in plants, the argument about its potential to cytoplasmically and non‐endocytically relocate into a selective set of vesicular compartments persists. To address this question, we determined whether fluorescence resonance energy transfer (FRET) could occur between a cytoplasmically expressed, short‐wavelength excitation green fluorescent protein (GFP) and FM4–64 in Nicotiana benthaminana. After exposure to FM4–64, the root hair plasma membrane and internal organelles became labelled. Under these conditions, no FRET with cytoplasmic GFP was seen. However, if the cells were treated with a low concentration of quillajasaponin, a membrane permeabilization agent, the cells continued to stream and FRET was detected. Thereby, we demonstrate that under conditions that do not severely compromise cell viability, the FM4–64 dye becomes a suitable FRET partner for the cytoplasmically localized GFP. Under normal conditions, FM4–64 does not significantly enter the cytosolic side of the membrane, but remains at the plasma membrane or trapped in the organelles of the endocytic pathway. Hence, when the structure or permeability of the plasma membrane is unaltered, FM4–64 dye is a robust marker for endocytosis.
Imaging complex nutrient dynamics in mycelial networks
Authors: FRICKER M.D. , LEE J.A. , BEBBER D.P. , TLALKA M. , HYNES J. , DARRAH P.R. , WATKINSON S.C. , BODDY L.
Published: July 2008

Transport networks are vital components of multi‐cellular organisms, distributing nutrients and removing waste products. Animal cardiovascular and respiratory systems, and plant vasculature, are branching trees whose architecture is thought to determine universal scaling laws in these organisms. In contrast, the transport systems of many multi‐cellular fungi do not fit into this conceptual framework, as they have evolved to explore a patchy environment in search of new resources, rather than ramify through a three‐dimensional organism. These fungi grow as a foraging mycelium, formed by the branching and fusion of threadlike hyphae, that gives rise to a complex network. To function efficiently, the mycelial network must both transport nutrients between spatially separated source and sink regions and also maintain its integrity in the face of continuous attack by mycophagous insects or random damage. Here we review the development of novel imaging approaches and software tools that we have used to characterise nutrient transport and network formation in foraging mycelia over a range of spatial scales. On a millimetre scale, we have used a combination of time‐lapse confocal imaging and fluorescence recovery after photobleaching to quantify the rate of diffusive transport through the unique vacuole system in individual hyphae. These data then form the basis of a simulation model to predict the impact of such diffusion‐based movement on a scale of several millimetres. On a centimetre scale, we have used novel photon‐counting scintillation imaging techniques to visualize radiolabel movement in small microcosms. This approach has revealed novel N‐transport phenomena, including rapid, preferential N‐resource allocation to C‐rich sinks, induction of simultaneous bi‐directional transport, abrupt switching between different pre‐existing transport routes, and a strong pulsatile component to transport in some species. Analysis of the pulsatile transport component using Fourier techniques shows that as the colony forms, it self‐organizes into well demarcated domains that are identifiable by differences in the phase relationship of the pulses. On the centimetre to metre scale, we have begun to use techniques borrowed from graph theory to characterize the development and dynamics of the network, and used these abstracted network models to predict the transport characteristics, resilience, and cost of the network.
Behavioural Assays to Model Cognitive and Affective Dimensions of Depression and Anxiety in Rats
Authors: Lapiz‐Bluhm M. D. S. , Bondi C. O. , Doyen J. , Rodriguez G. A. , Bédard‐Arana T. , Morilak D. A.
Published: July 2008

Animal models have been used extensively to investigate neuropsychiatric disorders, such as depression, and their treatment. However, the aetiology and pathophysiology of many such disorders are largely unknown, which makes validation of animal models particularly challenging. Furthermore, many diagnostic symptoms are difficult to define, operationalise and quantify, especially in experimental animals such as rats. Thus, rather than attempting to model complex human syndromes such as depression in their entirety, it can be more productive to define and model components of the illness that may account for clusters of co‐varying symptoms, and that may share common underlying neurobiological mechanisms. In preclinical investigations of the neural regulatory mechanisms linking stress to depression and anxiety disorders, as well as the mechanisms by which chronic treatment with antidepressant drugs may exert their beneficial effects in these conditions, we have employed a number of behavioural tests in rats to model specific cognitive and anxiety‐like components of depression and anxiety disorders. In the present study, we review the procedures for conducting four such behavioural assays: the attentional set‐shifting test, the elevated‐plus maze, the social interaction test and the shock‐probe defensive burying test. The purpose is to serve as a guide to the utility and limitations of these tools, and as an aid in optimising their use and productivity.
Effect of Transient Hypothyroidism During Infancy on the Postnatal Ontogeny of Luteinising Hormone Release in the Agonadal Male Rhesus Monkey (Macaca mulatta): Implications for the Timing of Puberty in Higher Primates
Authors: Plant T. M. , Ramaswamy S. , Bhat G. K. , Stah C. D. , Pohl C. R. , Mann D. R.
Published: July 2008

The present study examined whether a transient thyroid hormone (T4) deficit during infancy in male monkeys would compromise the arrest of luteinising hormone (LH) secretion during the infant–juvenile transition, and/or interfere with the pubertal resurgence of LH. Animals were orchidectomised and thyroidectomised (n = 3; Tx) or sham Tx (n = 3) within 5 days of birth. T4 replacement was initiated in two Tx monkeys at age 19 weeks to reestablish a euthyroid condition. Blood samples were drawn weekly for hormone assay. Body weight, crown–rump length, and bone age were assessed throughout the study. Within a week of Tx, plasma T4 declined to undetectable levels and, by 6–8 weeks of age, signs of hypothyroidism were evident. Transient hypothyroidism during infancy failed to prevent either arrest of LH secretion during the infant–juvenile transition or the pubertal resurgence of LH secretion, both of which occurred at similar ages to sham Tx animals. Although body weight exhibited complete catch‐up with T4 replacement, crown–rump length and bone age did not. Thus, bone age at the time of the pubertal LH resurgence in Tx animals was less advanced than that in shams. Although Tx did not influence qualitatively the pattern of gonadotrophin secretion, LH levels during infancy and after pubertal LH resurgence were elevated in Tx monkeys. This was not associated with changes in LH pulse frequency and amplitude, but half‐life (53 versus 65 min) of the slow second phase of LH clearance was greater in Tx animals. These results indicate that hypothalamic mechanisms dictating the pattern of gonadotrophin‐releasing hormone release from birth to puberty are not dependent on T4 action during infancy, and fail to support the notion that onset of puberty is causally coupled to skeletal maturation. They also indicate that LH renal clearance mechanisms may be programmed in a T4 dependent manner during infancy.