bluuebunny/crossref_metadata_2025 huggingface dataset:
Conformational flexibility facilitates self-assembly of complex DNA nanostructures
Authors: Zhang Chuan , Su Min , He Yu , Zhao Xin , Fang Ping-an , Ribbe Alexander E. , Jiang Wen , Mao Chengde
Published: July 2008

Molecular self-assembly is a promising approach to the preparation of nanostructures. DNA, in particular, shows great potential to be a superb molecular system. Synthetic DNA molecules have been programmed to assemble into a wide range of nanostructures. It is generally believed that rigidities of DNA nanomotifs (tiles) are essential for programmable self-assembly of well defined nanostructures. Recently, we have shown that adequate conformational flexibility could be exploited for assembling 3D objects, including tetrahedra, dodecahedra, and buckyballs, out of DNA three-point star motifs. In the current study, we have integrated tensegrity principle into this concept to assemble well defined, complex nanostructures in both 2D and 3D. A symmetric five-point-star motif (tile) has been designed to assemble into icosahedra or large nanocages depending on the concentration and flexibility of the DNA tiles. In both cases, the DNA tiles exhibit significant flexibilities and undergo substantial conformational changes, either symmetrically bending out of the plane or asymmetrically bending in the plane. In contrast to the complicated natures of the assembled structures, the approach presented here is simple and only requires three different component DNA strands. These results demonstrate that conformational flexibility could be explored to generate complex DNA nanostructures. The basic concept might be further extended to other biomacromolecular systems, such as RNA and proteins.
HIV-1 reverse transcriptase connection subdomain mutations reduce template RNA degradation and enhance AZT excision
Authors: Delviks-Frankenberry Krista A. , Nikolenko Galina N. , Boyer Paul L. , Hughes Stephen H. , Coffin John M. , Jere Abhay , Pathak Vinay K.
Published: July 2008

We previously proposed that mutations in the connection subdomain (cn) of HIV-1 reverse transcriptase increase AZT resistance by altering the balance between nucleotide excision and template RNA degradation. To test the predictions of this model, we analyzed the effects of previously identified cn mutations in combination with thymidine analog mutations (D67N, K70R, T215Y, and K219Q) on
in vitro
RNase H activity and AZT monophosphate (AZTMP) excision. We found that cn mutations G335C/D, N348I, A360I/V, V365I, and A376S decreased primary and secondary RNase H cleavages. The patient-derived cns increased ATP- and PPi-mediated AZTMP excision on an RNA template compared with a DNA template. One of 5 cns caused an increase in ATP-mediated AZTMP excision on a DNA template, whereas three cns showed a higher ratio of ATP- to PPi-mediated excision, indicating that some cn mutations also affect excision on a DNA substrate. Overall, the results strongly support the model that cn mutations increase AZT resistance by reducing template RNA degradation, thereby providing additional time for RT to excise AZTMP.
An olfactory neuron responds stochastically to temperature and modulates
Caenorhabditis elegans
thermotactic behavior
Authors: Biron David , Wasserman Sara , Thomas James H. , Samuel Aravinthan D. T. , Sengupta Piali
Published: July 2008

Caenorhabditis elegans
navigates thermal gradients by using a behavioral strategy that is regulated by a memory of its cultivation temperature (
T
c
). At temperatures above or around the
T
c
, animals respond to temperature changes by modulating the rate of stochastic reorientation events. The bilateral AFD neurons have been implicated as thermosensory neurons, but additional thermosensory neurons are also predicted to play a role in regulating thermotactic behaviors. Here, we show that the AWC olfactory neurons respond to temperature. Unlike AFD neurons, which respond to thermal stimuli with continuous, graded calcium signals, AWC neurons exhibit stochastic calcium events whose frequency is stimulus-correlated in a
T
c
-dependent manner. Animals lacking the AWC neurons or with hyperactive AWC neurons exhibit defects in the regulation of reorientation rate in thermotactic behavior. Our observations suggest that the AFD and AWC neurons encode thermal stimuli via distinct strategies to regulate
C. elegans
thermotactic behavior.
GDPD5 is a glycerophosphocholine phosphodiesterase that osmotically regulates the osmoprotective organic osmolyte GPC
Authors: Gallazzini Morgan , Ferraris Joan D. , Burg Maurice B.
Published: July 2008

Glycerophosphocholine (GPC) is an abundant osmoprotective renal medullary organic osmolyte. We previously found that its synthesis from phosphatidylcholine is catalyzed by tonicity-regulated activity of the phospholipase B, neuropathy target esterase. We also found that its degradation is catalyzed by glycerophosphocholine phosphodiesterase (GPC-PDE) activity and that elevating osmolality from 300 to 500 mosmol/kg by adding NaCl or urea, inhibits GPC-PDE activity, which contributes to the resultant increase of GPC. In the present studies we identify GDPD5 (glycerophosphodiester phosphodiesterase domain containing 5) as a GPC-PDE that is rapidly inhibited by high NaCl or urea. Recombinant GDPD5 colocalizes with neuropathy target esterase in the perinuclear region of HEK293 cells, and immuno-precipitated recombinant GDPD5 degrades GPC
in vitro
. The
in vitro
activity is reduced when the cells from which the GDPD5 is immuno-precipitated have been exposed to high NaCl or urea. In addition, high NaCl decreases mRNA abundance of GDPD5 via an increase of its degradation rate, although high urea does not. At 300 mosmol/kg siRNA knockdown of GDPD5 increases GPC in mouse inner medullary collecting duct-3 cells, and over expression of recombinant GDPD5 increases cellular GPC-PDE activity, accompanied by decreased GPC. We conclude that GDPD5 is a GPC-PDE that contributes to osmotic regulation of cellular GPC.
On the impact of RFID and EPC Network on traceability management: a mathematical model
Authors: Bottani Eleonora
Published: July 2008

This paper introduces a detailed mathematical model to assess the economic impact of radio frequency identification (RFID) technology and EPC Network adoption for traceability management within a supply chain. The model computes the savings resulting from RFID implementation, grounding on the gap between the costs of product recalling performed without and with the support of RFID-based traceability systems. These situations are respectively referred to as ‘AS IS’ and ‘TO BE’ scenarios. Both scenarios were validated by a panel of experts, operating as manufacturers and distributors of food products, to ensure a good correspondence with real traceability management procedures. A numerical example is proposed to show the model application, as well as to provide some insights about the economic impact of RFID and EPC Network implementation for traceability management.
Different Levels of Bfa1/Bub2 GAP Activity Are Required to Prevent Mitotic Exit of Budding Yeast Depending on the Type of Perturbations
Authors: Kim Junwon , Jang Selma Sun , Song Kiwon
Published: July 2008

In budding yeast, Tem1 is a key regulator of mitotic exit. Bfa1/Bub2 stimulates Tem1 GTPase activity as a GTPase-activating protein (GAP). Lte1 possesses a guanine-nucleotide exchange factor (GEF) domain likely for Tem1. However, recent observations showed that cells may control mitotic exit without either Lte1 or Bfa1/Bub2 GAP activity, obscuring how Tem1 is regulated. Here, we assayed BFA1 mutants with varying GAP activities for Tem1, showing for the first time that Bfa1/Bub2 GAP activity inhibits Tem1 in vivo. A decrease in GAP activity allowed cells to bypass mitotic exit defects. Interestingly, different levels of GAP activity were required to prevent mitotic exit depending on the type of perturbation. Although essential, more Bfa1/Bub2 GAP activity was needed for spindle damage than for DNA damage to fully activate the checkpoint. Conversely, Bfa1/Bub2 GAP activity was insufficient to delay mitotic exit in cells with misoriented spindles. Instead, decreased interaction of Bfa1 with Kin4 was observed in BFA1 mutant cells with a defective spindle position checkpoint. These findings demonstrate that there is a GAP-independent surveillance mechanism of Bfa1/Bub2, which, together with the GTP/GDP switch of Tem1, may be required for the genomic stability of cells with misaligned spindles.
Nse1 RING-like Domain Supports Functions of the Smc5-Smc6 Holocomplex in Genome Stability
Authors: Pebernard Stephanie , Perry J. Jefferson P. , Tainer John A. , Boddy Michael N.
Published: July 2008

The Smc5-Smc6 holocomplex plays essential but largely enigmatic roles in chromosome segregation, and facilitates DNA repair. The Smc5-Smc6 complex contains six conserved non-SMC subunits. One of these, Nse1, contains a RING-like motif that often confers ubiquitin E3 ligase activity. We have functionally characterized the Nse1 RING-like motif, to determine its contribution to the chromosome segregation and DNA repair roles of Smc5-Smc6. Strikingly, whereas a full deletion of nse1 is lethal, the Nse1 RING-like motif is not essential for cellular viability. However, Nse1 RING mutant cells are hypersensitive to a broad spectrum of genotoxic stresses, indicating that the Nse1 RING motif promotes DNA repair functions of Smc5-Smc6. We tested the ability of both human and yeast Nse1 to mediate ubiquitin E3 ligase activity in vitro and found no detectable activity associated with full-length Nse1 or the isolated RING domains. Interestingly, however, the Nse1 RING-like domain is required for normal Nse1-Nse3-Nse4 trimer formation in vitro and for damage-induced recruitment of Nse4 and Smc5 to subnuclear foci in vivo. Thus, we propose that the Nse1 RING-like motif is a protein–protein interaction domain required for Smc5-Smc6 holocomplex integrity and recruitment to, or retention at, DNA lesions.
A fast Bayesian change point analysis for the segmentation of microarray data
Authors: Erdman Chandra , Emerson John W.
Published: July 2008

Motivation: The ability to detect regions of genetic alteration is of great importance in cancer research. These alterations can take the form of large chromosomal gains and losses as well as smaller amplifications and deletions. The detection of such regions allows researchers to identify genes involved in cancer progression, and to fully understand differences between cancer and non-cancer tissue. The Bayesian method proposed by Barry and Hartigan is well suited for the analysis of such change point problems. In our previous article we introduced the R package bcp (Bayesian change point), an MCMC implementation of Barry and Hartigan's method. In a simulation study and real data examples, bcp is shown to both accurately detect change points and estimate segment means. Earlier versions of bcp (prior to 2.0) are O(n2) in speed and O(n) in memory (where n is the number of observations), and run in ∼45 min for a sequence of length 10 000. With the high resolution of newer microarrays, the number of computations in the O(n2) algorithm is prohibitively time-intensive.

Results: We present a new implementation of the Bayesian change point method that is O(n) in both speed and memory; bcp 2.1 runs in ∼45 s on a single processor with a sequence of length 10 000—a tremendous speed gain. Further speed improvements are possible using parallel computing, supported in bcp via NetWorkSpaces. In simulated and real microarray data from the literature, bcp is shown to quickly and accurately detect aberrations of varying width and magnitude.

Availability: The R package bcp is available on CRAN (R Development Core Team, 2008). The O(n) version is available in version 2.0 or higher, with support for NetWorkSpaces in versions 2.1 and higher.

Contact:  chandra.erdman@yale.edu
Development of a multistep indicator-based approach (MIBA) for the assessment of environmental quality of harbours
Authors: Marin Valentina , Moreno Mariapaola , Vassallo Paolo , Vezzulli Luigi , Fabiano Mauro
Published: July 2008

Marin, V., Moreno, M., Vassallo, P., Vezzulli, L., and Fabiano, M. 2008. Development of a multistep indicator-based approach (MIBA) for the assessment of environmental quality of harbours. – ICES Journal of Marine Science, 65: 1436–1441. Environmental pollution in harbours can have detrimental effects on the port, its users, and the surrounding environment. Despite these risks, the Italian legal framework for marine environmental quality does not apply to harbours and marinas, so monitoring is not mandatory. With the aim of supporting environmentally sound management, we propose an indicator-based protocol to assess the environmental quality of harbours through the development of a flexible and site-specific multistep indicator-based approach (MIBA), which gives special consideration to local features. MIBA comprises three steps: (1) development of a simple tool for harbour-specific identification of vulnerable areas and for designing monitoring schemes; (2) selection of suitable environmental quality indicators of different levels of complexity and applicability to the typologies of risks involved; and (3) development of a user-friendly interpretation scheme based on categorical risk values and a visualization code. The approach has been tested in two case studies in marinas located in the Ligurian Sea (Italy).
Average functional distinctness as a measure of the composition of assemblages
Authors: Somerfield Paul J. , Clarke K. Robert , Warwick Richard M. , Dulvy Nick K.
Published: July 2008

Somerfield, P. J., Clarke, K. R., Warwick, R. M., and Dulvy, N. K. 2008. Average functional distinctness as a measure of the composition of assemblages. – ICES Journal of Marine Science, 65: 1462–1468. Indices are used to quantify change in the environment by reducing aspects of environmental complexity to numbers. Biodiversity indices are typically calculated using the numbers of species and their relative abundances. A recent advance has been the development of additional measures of diversity, such as phylogenetic diversity, based on relationships between organisms. The emerging paradigms of the importance of biodiversity to ecosystem services and the ecosystem approach to fishery management could be well served by the development of indicators of ecosystem functioning. We discuss how relatedness measures may be adapted to quantify aspects of community structure of relevance to ecosystem functioning, by combining information on species’ occurrence, life history, and ecological traits. We present an index that reflects average functional distinctness within assemblages. We illustrate the approach using North Sea fish. Results reveal that average functional distinctness is not independent of taxonomic distinctness. This is expected, but the weakness of the relationship suggests that both indices may prove useful, because they are not constrained to convey the same information about samples. Both indices are shown to be weakly related to species richness, which was not expected. This is a consequence of differences in the frequencies of occurrence among species.
Ubiquitous human computing
Authors: Zittrain Jonathan
Published: July 2008

Ubiquitous computing means network connectivity everywhere, linking devices and systems as small as a drawing pin and as large as a worldwide product distribution chain. What could happen whenpeopleare so readily networked? This paper explores issues arising from two possible emerging models of ubiquitous human computing: fungible networked brainpower and collective personal vital sign monitoring.
Computational thinking and thinking about computing
Authors: Wing Jeannette M
Published: July 2008

Computational thinking will influence everyone in every field of endeavour. This vision poses a new educational challenge for our society, especially for our children. In thinking about computing, we need to be attuned to the three drivers of our field: science, technology and society. Accelerating technological advances and monumental societal demands force us to revisit the most basic scientific questions of computing.
Self-* properties through gossiping
Authors: Babaoglu Ozalp , Jelasity Márk
Published: July 2008

As computer systems have become more complex, numerous competing approaches have been proposed for these systems to self-configure, self-manage, self-repair, etc. such that human intervention in their operation can be minimized. In ubiquitous systems, this has always been a central issue as well. In this paper, we overview techniques to implement self-* properties in large-scale, decentralized networks through bio-inspired techniques in general, and gossip-based algorithms in particular. We believe that gossip-based algorithms could be an important inspiration for solving problems in ubiquitous computing as well. As an example, we outline a novel approach to arrange large numbers of mobile agents (e.g. vehicles, rescue teams carrying mobile devices) into different formations in a totally decentralized manner. The approach is inspired by the biological mechanism of cell sorting via differential adhesion, as well as by our earlier work in self-organizing peer-to-peer overlay networks.
Some guidelines for the ethical development of ubiquitous computing
Authors: Greenfield Adam
Published: July 2008

At a time when both the landscape of everyday life and the choices available to us there are increasingly conditioned by ubiquitous information processing systems, it seems wise to articulate some general principles guiding their ethical design and deployment. I here enunciate five broad guidelines for the designers of such systems, including recommendations that they be devised in such a way as to
default to harmlessness
, be
conservative of time
, be
conservative of face
, be
self-disclosing
and be
deniable
. I conclude with some observations about the likelihood of any such principles winning usefully widespread voluntary adherence.
Computing for the future of the planet
Authors: Hopper Andy , Rice Andrew
Published: July 2008

Digital technology is becoming an indispensable and crucial component of our lives, society and the environment. We present a framework for computing in the context of problems facing the planet. The framework has a number of goals: an optimal digital infrastructure, sensing and optimizing with a global world model, reliably predicting and reacting to our environment and providing digital alternatives to physical activities. This paper describes our vision in which data centres can scale power consumption in line with performance, run closer to the wire with reduced redundancy and behave as a ‘virtual battery’ dynamically using spare, or otherwise unusable, generation capacity from renewable sources. On a broader scale, we consider how global sensing might allow us to optimize our daily activities and lives. We highlight the issues and dilemmas inherent in the deployment of global sensing infrastructure and work towards our challenge of a personal energy meter as a tool for informing decisions and providing impetus for reducing the ecological footprint of our society.
From computers to ubiquitous computing by 2010: health care
Authors: Aziz Omer , Lo Benny , Pansiot Julien , Atallah Louis , Yang Guang-Zhong , Darzi Ara
Published: July 2008

Over the past decade, miniaturization and cost reduction in semiconductors have led to computers smaller in size than a pinhead with powerful processing abilities that are affordable enough to be disposable. Similar advances in wireless communication, sensor design and energy storage have meant that the concept of a truly pervasive ‘wireless sensor network’, used to monitor environments and objects within them, has become a reality. The need for a wireless sensor network designed specifically for human body monitoring has led to the development of wireless ‘body sensor network’ (BSN) platforms composed of tiny integrated microsensors with on-board processing and wireless data transfer capability. The ubiquitous computing abilities of BSNs offer the prospect of continuous monitoring of human health in any environment, be it home, hospital, outdoors or the workplace. This pervasive technology comes at a time when Western world health care costs have sharply risen, reflected by increasing expenditure on health care as a proportion of gross domestic product over the last 20 years. Drivers of this rise include an ageing post ‘baby boom’ population, higher incidence of chronic disease and the need for earlier diagnosis. This paper outlines the role of pervasive health care technologies in providing more efficient health care.
Invisible computing: automatically using the many bits of data we create
Authors: Borriello Gaetano
Published: July 2008

As we go about our work and our daily lives, we leave a trail of bits behind. Every electronic device we interact with can keep a record of our actions. Even the devices themselves can keep track of their location and radio interactions, even without user involvement. The challenge of invisible computing is to make this wealth of data useful. This paper presents two examples of what has come to be known as ‘invisible computing’, namely, devices recording, distilling and rendering these many bits of data without unduly taxing human users. The first example is focused on a work environment.
Labscape
automates the record keeping required of experimenters in a cell biology laboratory. The second example looks at more ad hoc interactions. RFID Ecosystem is a collection of radio-frequency identification (RFID) readers and databases that collect the sightings of passive RFID tags, attached to people and objects, as they move throughout a large building. It provides services such as people and object finding as well as diary keeping.
Network architecture test-beds as platforms for ubiquitous computing
Authors: Roscoe Timothy
Published: July 2008

Distributed systems research, and in particular ubiquitous computing, has traditionally assumed the Internet as a basic underlying communications substrate. Recently, however, the networking research community has come to question the fundamental design or ‘architecture’ of the Internet. This has been led by two observations: first, that the Internet as it stands is now almost impossible to evolve to support new functionality; and second, that modern applications of all kinds now use the Internet rather differently, and frequently implement their own ‘overlay’ networks above it to work around its perceived deficiencies. In this paper, I discuss recent academic projects to allow disruptive change to the Internet architecture, and also outline a radically different view of networking for ubiquitous computing that such proposals might facilitate.
Security policies and trust in ubiquitous computing
Authors: Joshi Anupam , Finin Tim , Kagal Lalana , Parker Jim , Patwardhan Anand
Published: July 2008

Ubiquitous environments comprise resource-constrained mobile and wearable devices and computational elements embedded in everyday artefacts. These are connected to each other using both infrastructure-based as well as short-range ad hoc networks. Limited Internet connectivity limits the use of conventional security mechanisms such as public key infrastructures and other forms of server-centric authentication. Under these circumstances, peer-to-peer interactions are well suited for not just information interchange, but also managing security and privacy. However, practical solutions for protecting mobile devices, preserving privacy, evaluating trust and determining the reliability and accuracy of peer-provided data in such interactions are still in their infancy. Our research is directed towards providing stronger assurances of the reliability and trustworthiness of information and services, and the use of declarative policy-driven approaches to handle the open and dynamic nature of such systems. This paper provides an overview of some of the challenges and issues, and points out directions for progress.
Arabidopsis SOMATIC EMBRYOGENESIS RECEPTOR KINASE Proteins Serve Brassinosteroid-Dependent and -Independent Signaling Pathways
Authors: Albrecht Catherine , Russinova Eugenia , Kemmerling Birgit , Kwaaitaal Mark , de Vries Sacco C.
Published: July 2008

The Arabidopsis (Arabidopsis thaliana) SOMATIC EMBRYOGENESIS RECEPTOR KINASE (SERK) genes belong to a small family of five plant receptor kinases that are involved in at least five different signaling pathways. One member of this family, BRASSINOSTEROID INSENSITIVE1 (BRI1)-ASSOCIATED KINASE1 (BAK1), also known as SERK3, is the coreceptor of the brassinolide (BR)-perceiving receptor BRI1, a function that is BR dependent and partially redundant with SERK1. BAK1 (SERK3) alone controls plant innate immunity, is also the coreceptor of the flagellin receptor FLS2, and, together with SERK4, can mediate cell death control, all three in a BR-independent fashion. SERK1 and SERK2 are essential for male microsporogenesis, again independent from BR. SERK5 does not appear to have any function under the conditions tested. Here, we show that the different SERK members are only redundant in pairs, whereas higher order mutant combinations only show additive phenotypes. Surprisingly, SERK members that are redundant within one are not redundant in another pathway. We also show that this evolution of functional pairs occurred by a change in protein function and not by differences in spatial expression. We propose that, in plants, closely related receptor kinases have a minimal homo- or heterodimeric configuration to achieve specificity.
Regulation of Respiration and the Oxygen Diffusion Barrier in Soybean Protect Symbiotic Nitrogen Fixation from Chilling-Induced Inhibition and Shoots from Premature Senescence
Authors: van Heerden Philippus D.R. , Kiddle Guy , Pellny Till K. , Mokwala Phatlane W. , Jordaan Anine , Strauss Abram J. , de Beer Misha , Schlüter Urte , Kunert Karl J. , Foyer Christine H.
Published: July 2008

Symbiotic nitrogen fixation is sensitive to dark chilling (7°C–15°C)-induced inhibition in soybean (Glycine max). To characterize the mechanisms that cause the stress-induced loss of nodule function, we examined nodule structure, carbon-nitrogen interactions, and respiration in two soybean genotypes that differ in chilling sensitivity: PAN809 (PAN), which is chilling sensitive, and Highveld Top (HT), which is more chilling resistant. Nodule numbers were unaffected by dark chilling, as was the abundance of the nitrogenase and leghemoglobin proteins. However, dark chilling decreased nodule respiration rates, nitrogenase activities, and NifH and NifK mRNAs and increased nodule starch, sucrose, and glucose in both genotypes. Ureide and fructose contents decreased only in PAN nodules. While the chilling-induced decreases in nodule respiration persisted in PAN even after return to optimal temperatures, respiration started to recover in HT by the end of the chilling period. The area of the intercellular spaces in the nodule cortex and infected zone was greatly decreased in HT after three nights of chilling, an acclimatory response that was absent from PAN. These data show that HT nodules are able to regulate both respiration and the area of the intercellular spaces during chilling and in this way control the oxygen diffusion barrier, which is a key component of the nodule stress response. We conclude that chilling-induced loss of symbiotic nitrogen fixation in PAN is caused by the inhibition of respiration coupled to the failure to regulate the oxygen diffusion barrier effectively. The resultant limitations on nitrogen availability contribute to the greater chilling-induced inhibition of photosynthesis in PAN than in HT.
An AbrB-Like Transcriptional Regulator, Sll0822, Is Essential for the Activation of Nitrogen-Regulated Genes in Synechocystis sp. PCC 6803
Authors: Ishii Ai , Hihara Yukako
Published: July 2008

Every cyanobacterial species possesses multiple genes encoding AbrB-like transcriptional regulators (cyAbrBs) distinct from those conserved among other bacterial species. In this study, two genes encoding cyAbrBs in Synechocystis sp. PCC 6803, sll0359 and sll0822, were insertionally disrupted in order to examine their physiological roles. A fully segregated disrupted mutant of sll0822 (Δsll0822 mutant) but not of sll0359 was obtained, although both mutants exhibited similar phenotypes (i.e. decreases in growth rate and pigment content). The growth rate of the Δsll0822 mutant was low under any condition, but the low pigment content could be partially recovered by nitrate supplementation of the medium. DNA microarray and RNA-blot analyses revealed that the level of expression of a part of the NtcA regulon, such as urtA, amt1, glnB, sigE, and the nrt operon, was significantly decreased in the Δsll0822 mutant, although the induction of these genes upon nitrogen depletion was still observed to some extent. Sll0822 seems to work in parallel with NtcA to achieve flexible regulation of the nitrogen uptake system. The Sll0822 protein exists mainly in a dimeric form in vivo, and the amount of the protein was not affected by nitrogen availability. This observation, together with the low binding specificity of the purified histidine-tagged Sll0822 protein, implies that the activity of Sll0822 may be posttranslationally modulated in Synechocystis cells.
Remifentanil sedation for awake fibreoptic intubation with limited application of local anaesthetic in patients for elective head and neck surgery*
Authors: Mingo O. H. , Ashpole K. J. , Irving C. J. , Rucklidge M. W. M.
Published: July 2008

The aim of this study was to investigate the performance of awake fibreoptic intubation using remifentanil sedation with topical anaesthesia limited only to the nasal mucosa. Twenty‐four patients presenting for elective head and neck surgery were sedated using remifentanil titrated to effect and local anaesthetic was applied to the nasal mucosa. Vital signs were recorded throughout the procedure and both the anaesthetist and an observer rated the ease of the procedure. Intubation was successful in all patients and the procedure was rated as easy in 15 (63%) of patients. Mean arterial pressure remained within 8% of baseline in all cases and respiratory rate remained > 8 breaths.min−1 in all but three patients. Although 56% of patients interviewed postoperatively said they recalled the procedure, all but one would undertake the same procedure again if necessary. This technique appears reliable in providing adequate sedation whilst maintaining cardiovascular and respiratory stability.
Post‐marketing assessment of the safety of strontium ranelate; a novel case‐only approach to the early detection of adverse drug reactions
Authors: Grosso Anthony , Douglas Ian , Hingorani Aroon , MacAllister Raymond , Smeeth Liam
Published: July 2008

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Randomized controlled trials are the gold standard of drug efficacy assessment, but have limited power to assess adverse drug reactions.

• Observational data derived from larger populations of patients are often affected by confounding variables, many of which are difficult to measure or simply not known.

WHAT THIS STUDY ADDS

• This study demonstrates the utility of the self‐controlled case‐series method of analysing the safety profile of drugs, which reduces confounding because comparisons are intraperson.

• Although such data should not be viewed in isolation, the efficiency and versatility of this method suggest that it could become a future standard in drug safety assessment.

AIMS

Post licensing, the evaluation of drug safety relies heavily on the collation of sporadic, spontaneous reports on adverse effects. The aim was to assess the potential utility of a more systematic approach to the detection of adverse events that utilizes routinely collected clinical data from a large primary care population.

METHODS

We used the UK General Practice Research Database to assess the risk of several recently reported adverse events linked to the use of strontium ranelate for osteoporosis in postmenopausal women. The self‐controlled case‐series method was used to minimize the potential for biases in the quantification of risk estimates.

RESULTS

Age‐adjusted rate ratios for venous thromboembolism, gastrointestinal disturbance, minor skin complaint and memory loss were 1.1 [95% confidence interval (CI) 0.2, 5.0], 3.0 (95% CI 2.3, 3.8), 2.0 (95% CI 1.3, 3.1) and 1.8 (95% CI 0.2, 14.1), respectively. No cases of osteonecrosis of the jaw, toxic‐epidermal necrosis, Stevens–Johnson syndrome or drug rash with eosinophilia and systemic symptoms were found.

CONCLUSIONS

Although we confirmed the association between strontium ranelate and adverse events identified in the Phase III publications, there was no evidence of an association between strontium ranelate and the aforementioned potentially life‐threatening adverse events. Our study demonstrates the relative ease with which this method can assess a variety of adverse events associated with a new drug in actual clinical practice. We believe this technique could be more widely adopted to assess the safety profile of new drugs.
Vitamin D deficiency in rural girls and pregnant women despite abundant sunshine in northern India
Authors: Sahu Monashis , Bhatia Vijayalakshmi , Aggarwal Anjoo , Rawat Vinita , Saxena Priya , Pandey Amita , Das Vinita
Published: July 2008

Context  Vitamin D deficiency is common in urban Indians despite living in the tropics and its public health consequences are enormous. However, 70% of India is rural, and data from rural subjects, who are expected to have good sun exposure, are scant.

Objectives  To determine the population prevalence of vitamin D deficiency in rural pregnant women and adolescent girls, compare serum 25‐hydroxyvitamin D (25OHD) status in adolescent boys from the same families, and determine seasonal differences in serum 25OHD.

Design  A cross‐sectional study conducted over 18 months.

Subjects  A random selection of 121 adolescent girls from a survey of a population of 8270 in a rural low socioeconomic community; 139 pregnant women in the second trimester; and a subset of 28 adolescent girls compared with 34 brothers.

Measurements  Serum 25OHD, serum alkaline phosphatase (AP), sun exposure, and dietary calcium intake.

Results  The age‐adjusted community prevalence of vitamin D deficiency (25OHD < 50 nmol/l) in adolescent girls was 88·6%. Seventy‐four per cent of pregnant women had vitamin D deficiency. Mean ± SD 25OHD in girls and women in summer was 55·5 ± 19·8 nmol/l compared to 27·3 ± 12·3 nmol/l in winter (P < 0·001). Winter serum 25OHD in boys (67·5 ± 29·0 nmol/l) was higher than that in their sisters (31·3 ± 13·5 nmol/l, P < 0·001).

Conclusion  We report a high prevalence of vitamin D deficiency among pregnant women and adolescent girls from a rural Indian community. Boys are relatively protected. Seasonal variation in serum 25OHD is significant at latitude 26° N.
Surviving the paradoxes of virtual teamwork
Authors: Dubé Line , Robey Daniel
Published: July 2008

Despite the potential benefits of virtual teams, current literature suggests that virtual teamwork is rife with complex challenges. We frame some of these challenges as paradoxes inherent in the concept of virtual teamwork. Based on interviews with 42 leaders and members of virtual teams, we identify five paradoxes: (1) virtual teams require physical presence; (2) flexibility of virtual teamwork is aided by structure; (3) interdependent work in virtual teams is accomplished by members' independent contributions; (4) task‐oriented virtual teamwork succeeds through social interactions; and (5) mistrust is instrumental to establishing trust among virtual team members. In addition, we identify strategies that respondents used to cope with, or ‘survive’ the paradoxes of virtual teamwork.
An easy method using glutaraldehyde‐introduced fluorescence for the microscopic analysis of plant biotrophic interactions
Authors: FESTER T. , BERG R.H. , TAYLOR C.G.
Published: July 2008

The method introduced in this article makes use of the glutaraldehyde‐induced auto‐fluorescence of proteins after cross‐linking with glutaraldehyde for the analysis of cellular and sub‐cellular structures. Because the interface of biotrophic interactions is rich in proteins, the method presented is particularly suitable for the analysis of such interactions; we have exemplified its usefulness by analyzing (1) the root feeding sites induced in roots fromArabidopsis thalianaby the root‐knot nematodeMeloidogyne incognita; (2) leaves fromCucurbita pepoinfected by powdery mildew and (3) roots fromNicotiana tabacumcolonized by the arbuscular mycorrhizal fungusGlomus intraradices. The use of confocal and multi‐photon laser scanning microscopy allows three‐dimensional reconstructions from optical sections of complex biotrophic interactions. In the case of root‐knot nematode feeding sites, our method enabled us to simultaneously study the development of the plant xylem elements (using lignin auto‐fluorescence), the nematode feeding site and the nematode itself.
Hydrodynamic flow in the cytoplasm of plant cells
Authors: ESSELING‐OZDOBA A. , HOUTMAN D. , VAN LAMMEREN A.A.M. , EISER E. , EMONS A.M.C.
Published: July 2008

Plant cells show myosin‐driven organelle movement, called cytoplasmic streaming. Soluble molecules, such as metabolites do not move with motor proteins but by diffusion. However, is all of this streaming active motor‐driven organelle transport? Our recent simulation study (Houtman et al., 2007) shows that active transport of organelles gives rise to a drag in the cytosol, setting up a hydrodynamic flow, which contributes to a fast distribution of proteins and nutrients in plant cells. Here, we show experimentally that actively transported organelles produce hydrodynamic flow that significantly contributes to the movement of the molecules in the cytosol. We have used fluorescence recovery after photobleaching and show that in tobacco Bright Yellow 2 (BY‐2) suspension cells constitutively expressing cytoplasmic green fluorescent protein (GFP), free GFP molecules move faster in cells with active transport of organelles than in cells where this transport has been inhibited with the general myosin inhibitor BDM (2,3‐butanedione monoxime). Furthermore, we show that the direction of the GFP movement in the cells with active transport is the same as that of the organelle movement and that the speed of the GFP in the cytosol is proportional to the speed of the organelle movement. In large BY‐2 cells with fast cytoplasmic streaming, a GFP molecule reaches the other side of the cell approximately in the similar time frame (about 16 s) as in small BY‐2 cells that have slow cytoplasmic streaming. With this, we suggest that hydrodynamic flow is important for efficient transport of cytosolic molecules in large cells. Hydrodynamic flow might also contribute to the movement of larger structures than molecules in the cytoplasm. We show that synthetic lipid (DOPG) vesicles and ‘stealth’ vesicles with PEG phospholipids moved in the cytoplasm.
Pectin‐like carbohydrates in the green algaMicrasteriascharacterized by cytochemical analysis and energy filtering TEM
Authors: EDER M. , LÜTZ‐MEINDL U.
Published: July 2008

Pectins are the major matrix polysaccharides of plant cell walls and are important for controlling growth, wall porosity and regulation of the ionic environment in plant cells. Pectic epitopes recognized by the monoclonal antibodies JIM5, JIM7 and 2F4 could be localized in the primary wall during development of the green algaMicrasterias. As the degree of pectin esterification determines the calcium‐binding capacity and thus the physical properties of the cell wall, chemical and enzymaticin situde‐esterification was performed. This resulted in displacement of epitopes recognized by JIM5, JIM7 and 2F4, respectively, in changes in the intensity of the antibody labelling as visualized in CLSM. In addition, calcium‐binding capacities of cell walls and components of the secretory apparatus were determined in transmission electron microscopy by electron energy loss spectroscopy and electron spectroscopic imaging. These analyses revealed that pectic polysaccharides are transported to the cell wall in a de‐esterified form. At the primary wall, pectins get methyl‐esterified at the inner side, thus allowing flexibility of the wall. At the outer side of the wall they become again de‐esterified and bind high amounts of calcium which leads to cell wall stiffening. Mucilage vesicles posses the highest calcium‐binding capacity of all structures observed inMicrasterias, indicating that the pectic polysaccharides of mucilage are secreted in a de‐esterified, compact form. When mucilage is excreted through the cell wall, it loses its ability to bind calcium. The esterification of pectins involved is obviously required for swelling of mucilage by water uptake, which generates the motive force for orientation of this unicellular organism in respect to light. Incubation ofMicrasteriasin pectin methylesterase (PME), which de‐esterifies pectic polymers in higher plants, resulted in growth inhibition, cell shape malformation and primary wall thickening. A PME‐like enzyme could be found inMicrasteriasby PME activity assays.
The role of the plant cytoskeleton in the interaction between legumes and rhizobia
Authors: TIMMERS A. C. J.
Published: July 2008

The study of the symbiotic interaction between rhizobia and legumes represents a major theme in plant biology. This interaction results in the formation of nodules, root organs in which the bacteria reduce atmospheric nitrogen into ammonia, which can subsequently be utilized by the plant. The execution of the different developmental stages observed during nodule ontogenesis involves many cellular processes with significant roles for the plant cytoskeleton. A challenging question in cell biology is how the cytoskeleton organizes itself into the dynamic arrays required for cell differentiation and functioning. Nodulation is, particularly, well qualified as an experimental system for cytoskeleton research because an early essential step of the plant/microbe interaction takes place in surface‐exposed root hairs, well suited for cell biological in vivo experimentation. Moreover, the changes in the organization of the cytoskeleton can be elicited by a well‐defined molecule, the Nod factor, or by bacterial inoculation, thus providing the researcher with the possibility of controlling the cytoskeletal changes in target cells. In addition, the well‐known cytology of the symbiotic interaction facilitates the correlation between the changes in the organization of the plant cytoskeleton with both histological and cellular changes. In this review, the current knowledge on the role of the plant cytoskeleton during nodulation is summarized, with emphasis on the interaction between Medicago truncatula and Sinorhizobium meliloti.
Olive pollen profilin (Ole e 2 allergen) co‐localizes with highly active areas of the actin cytoskeleton and is released to the culture medium during in vitro pollen germination
Authors: MORALES S. , JIMÉNEZ‐LÓPEZ J.C. , CASTRO A.J. , RODRÍGUEZ‐GARCÍA M.I. , ALCHÉ J.D.
Published: July 2008

Pollen allergens offer a dual perspective of study: some of them are considered key proteins for pollen physiology, but they are also able to trigger allergy symptoms in susceptible humans after coming in contact with their tissues. Profilin (Ole e 2 allergen) has been characterized, to some extent, as one of the major allergens from Olea europaea L. pollen, a highly allergenic species in the Mediterranean countries. In order to obtain clues regarding the biological role of this protein, we have analyzed both its cellular localization and the organization of actin throughout pollen hydration and early pollen tube germination. The localization of the cited proteins was visualized by confocal laser scanning microscopy immunofluorescence using different antibodies. Upon pollen hydration and pollen germination, a massive presence of profilin was detected close to the site of pollen tube emergence, forming a ring‐like structure around the ‘effective’ apertural region. Profilin was also detected in the pollen exine of the germinating pollen grains and in the germination medium. After using a permeabilization‐enhanced protocol for immunolocalization, profilin was also localized in the cytoplasm of the pollen tube, particularly at both the proximal and apical ends. Noticeable accumulations of actin were observed in the cytoplasm of the pollen tube; particularly, in both the apical region and the area immediately close to the aperture. Actin filaments were not observed, probably due to the need of further enhanced fixation procedures. The ultrastructural localization of profilin showed the presence of the protein in the cytoplasm of both the mature pollen grain and the pollen tube.

The results shown here could be interpreted as signs of a massive dissociation of the actin–profilin complexes, mobilization of actin monomers, and therefore, an intense activity of the actin cytoskeleton. The extensive release of allergenic proteins from the pollen grain into the surrounding aqueous media, as described here for profilin, may help us to understand the mechanisms by which these allergens might come in contact with the human mucosa, therefore triggering the symptoms of allergy.
Akt Induces Apoptosis in Neuroblastoma Cells Expressing a C98X Vasopressin Mutant Following Autophagy Suppression
Authors: Castino R. , Thepparit C. , Bellio N. , Murphy D. , Isidoro C.
Published: July 2008

Mutations in the arginine vasopressin (AVP)‐neurophysin II (NP‐II) gene that affect the folding and transport of the prohormone result in loss of secretion of the anti‐diuretic hormone AVP from pituitary nerve terminals and cause autosomal dominant familial neurohypophyseal diabetes insipidus (adFNDI). One such mutation consists of the replacement of a Cys residue at position 98 with a stop codon (C98X) in the AVP precursor (corresponding to C67X in NP domain). In neuroblastoma cells over‐expressing this truncated AVP precursor autophagy, a macromolecular degradation process, was shown to be essential for assuring cell survival. In the present study, we investigated the role of the Akt pro‐survival signalling in the regulation of autophagy and of apoptosis linked with the handling of C98X AVP. Impairing autophagy‐lysosomal sequestration or cathepsin D (CD)‐mediated proteolysis triggered the activation of the intrinsic death pathway of apoptosis in C98X‐expressing cells, but not in the wild‐type ‐AVP‐expressing cells. This was shown by the expression of a Vps34 dominant negative, which down‐regulates the PI3k class III‐dependent signalling needed for autophagosome (APH) formation, by genetic silencing as a result of RNA interference (RNAi) of Lamp2, a protein indispensable for the fusion of APHs with lysosomes, and by RNAi silencing of the lysosomal protease CD. Ectopic expression of either the wild‐type or the mutated C98X AVP altered neither the expression nor the phosphorylation of the pro‐survival signalling molecule Akt. Strikingly, the ectopic adenoviral‐directed expression of a constitutively active Akt, instead of preserving cell survival, resulted in the suppression of autophagy, and precipitated Bax‐mediated cell death. The present data demonstrate the need for autophagy‐mediated degradation of mutated C98X peptides, which otherwise become toxic to the cell, and suggest that, in the presence of mis‐folded proteins, the stimulation of the Akt signalling counteracts the beneficial effects of autophagy and precipitates cell death. It follows that growth factors impinging on the Akt pathway may have deleterious effect in neurones expressing mutant neuropeptides. This can provide an explanation for the late onset and progressive neuronal cell loss observed in hypothalamic magnocellular neurones of adFNDI patients.