bluuebunny/crossref_metadata_2025 huggingface dataset:
Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis
Authors: Masso Majid , Vaisman Iosif I.
Published: July 2008

Motivation: Accurate predictive models for the impact of single amino acid substitutions on protein stability provide insight into protein structure and function. Such models are also valuable for the design and engineering of new proteins. Previously described methods have utilized properties of protein sequence or structure to predict the free energy change of mutants due to thermal (ΔΔG) and denaturant (ΔΔGH2O) denaturations, as well as mutant thermal stability (ΔTm), through the application of either computational energy-based approaches or machine learning techniques. However, accuracy associated with applying these methods separately is frequently far from optimal.

Results: We detail a computational mutagenesis technique based on a four-body, knowledge-based, statistical contact potential. For any mutation due to a single amino acid replacement in a protein, the method provides an empirical normalized measure of the ensuing environmental perturbation occurring at every residue position. A feature vector is generated for the mutant by considering perturbations at the mutated position and it's ordered six nearest neighbors in the 3-dimensional (3D) protein structure. These predictors of stability change are evaluated by applying machine learning tools to large training sets of mutants derived from diverse proteins that have been experimentally studied and described. Predictive models based on our combined approach are either comparable to, or in many cases significantly outperform, previously published results.

Availability: A web server with supporting documentation is available at http://proteins.gmu.edu/automute

Contact:  ivaisman@gmu.edu
Climate-mediated mechanical changes to post-disturbance coral assemblages
Authors: Madin Joshua S , O'Donnell Michael J , Connolly Sean R
Published: July 2008

Increasingly severe storms and weaker carbonate materials associated with more acidic oceans will increase the vulnerability of reef corals to mechanical damage. Mechanistic predictions based on measurements of colony mechanical vulnerability and future climate scenarios demonstrate dramatic shifts in assemblage structure following hydrodynamic disturbances, including switches in species' dominance on the reef and thus potential for post-disturbance recovery. Larger colonies are more resistant to factors such as disease and competition for space, and complex morphologies support more associated reef species. Future reefs are thus expected to have lower colony abundances and be dominated by small and morphologically simple, yet mechanically robust species, which will in turn support lower levels of whole-reef biodiversity than do present-day reefs.
Immune response impairs learning in free-flying bumble-bees
Authors: Alghamdi A , Dalton L , Phillis A , Rosato E , Mallon E.B
Published: July 2008

Parasites can influence different host behaviours including foraging, mate choice and predator avoidance. Several recent papers have shown reduced learning abilities in infected insects. However, it is difficult to separate the effects of the immune response from the direct effects of the parasite. Using a free-flying learning paradigm, this paper shows that learning performance is impaired in bumble-bees (Bombus terrestris) that are not infected but whose immune system is stimulated non-pathogenically. This demonstrates that before it is assumed that a parasite has a direct effect on a host's behaviour, the effect of the immune response stimulated by the parasite must first be quantified.
Tremor entrainment by patterned low-frequency stimulation
Authors: Barnikol Utako B , Popovych Oleksandr V , Hauptmann Christian , Sturm Volker , Freund Hans-Joachim , Tass Peter A
Published: July 2008

High-frequency test stimulation for tremor suppression is a standard procedure for functional target localization during deep brain stimulation. This method does not work in cases where tremor vanishes intraoperatively, for example, due to general anaesthesia or due to an insertional effect. To overcome this difficulty, we developed a stimulation technique that effectively evokes tremor in a well-defined and quantifiable manner. For this, we used patterned low-frequency stimulation (PLFS), i.e. brief high-frequency pulse trains administered at pulse rates similar to neurons' preferred burst frequency. Unlike periodic single-pulse stimulation, PLFS enables one to convey effective and considerably greater integral charge densities without violation of safety requirements. In a computational investigation of an oscillatory neuronal network temporarily rendered inactive, we found that PLFS evokes synchronized activity, phase locked to the stimulus. While a stronger increase in the amount of synchrony in the neuronal population requires higher stimulus intensities, the portion of synchronously active neurons nevertheless becomes strongly phase locked to PLFS already at weak stimulus intensities. The phase entrainment effect of PLFS turned out to be robust against variations in the stimulation frequency, whereas enhancement of synchrony required precisely tuned stimulation frequencies. We applied PLFS to a patient with spinocerebellar ataxia type 2 (SCA2) with pronounced tremor that disappeared intraoperatively under general anaesthesia. In accordance with our computational results, PLFS evoked tremor, phase locked to the stimulus. In particular, weak PLFS caused low-amplitude, but strongly phase-locked tremor. PLFS test stimulations provided the only functional information about target localization. Optimal target point selection was confirmed by excellent post-operative tremor suppression.
Heterogeneity and weak coupling may explain the synchronization characteristics of cells in the arterial wall
Authors: Jacobsen Jens Christian Brings , Aalkjaer Christian , Matchkov Vladimir V , Nilsson Holger , Freiberg Jacob J , Holstein-Rathlou Niels-Henrik
Published: July 2008

Vascular smooth muscle cells (SMCs) exhibit different types of calcium dynamics. Static vascular tone is associated with unsynchronized calcium waves and the developed force depends on the number of recruited cells. Global calcium transients synchronized among a large number of cells cause rhythmic development of force known as vasomotion. We present experimental data showing a considerable heterogeneity in cellular calcium dynamics in the vascular wall. In stimulated vessels, some SMCs remain quiescent, whereas others display waves of variable frequency. At the onset of vasomotion, all SMCs are enrolled into synchronized oscillation.

Simulations of coupled SMCs show that the experimentally observed cellular recruitment, the presence of quiescent cells and the variation in oscillation frequency may arise if the cell population is phenotypically heterogeneous. In this case, quiescent cells can be entrained at the onset of vasomotion by the collective driving force from the synchronized oscillations in the membrane potential of the surrounding cells. Partial synchronization arises with an increase in the concentration of cyclic guanosine monophosphate, but in a heterogeneous cell population complete synchronization also requires a high-conductance pathway that provides strong coupling between the cells.
A new strategy for assessing sensitivities in biochemical models
Authors: Sahle Sven , Mendes Pedro , Hoops Stefan , Kummer Ursula
Published: July 2008

An integral part of any systems biology approach is the modelling and simulation of the respective system under investigation. However, the values of many parameters of the system have often not been determined or are not identifiable due to technical experimental difficulties or other constraints. Sensitivity analysis is often employed to quantify the importance of each of the model's parameters in the behaviour of the system. This approach can also be useful in identifying those parts of the system that are most sensitive with the potential of becoming drug targets. A problem of the commonly used methods of sensitivity analysis is that they constitute local methods meaning that they depend directly on the exact parameter space, which in turn is not known exactly. One way to circumvent this problem is to carry out sensitivity analysis over a wide range of values for all parameters, but this is handicapped by expensive computations when the systems are high dimensional. Another approach is to employ global sensitivity analysis, which in this context is mostly based on random sampling methods. In this paper we present an efficient approach that involves using numerical optimizing methods that search a wide region of parameter space for a given model to determine the maximum and minimum values of its metabolic control coefficients. A relevant example for drug development is presented to demonstrate the strategy using the software COPASI.
Molecular diversity and phylogeny of Hantaan virus in Guizhou, China: evidence for Guizhou as a radiation center of the present Hantaan virus
Authors: Zou Yang , Hu Jing , Wang Zhao-Xiao , Wang Ding-Ming , Li Ming-Hui , Ren Guo-Dong , Duan Zheng-Xiu , Fu Zhen F. , Plyusnin Alexander , Zhang Yong-Zhen
Published: July 2008

To gain further insight into the molecular epidemiology of Hantaan virus (HTNV) in Guizhou, China, rodents were captured in this region in 2004 and 2005. In addition, serum samples were collected from four patients. Ten hantaviruses were isolated successfully in cell culture from four humans, two Apodemus agrarius, three Rattus norvegicus and one Rattus nitidus. The nucleotide sequences for their small (S), medium (M) and partial large (L) segments were determined. Phylogenetic analysis of the S and M segment sequences revealed that all of these isolates belong to the species HTNV, suggesting a spillover of HTNV from A. agrarius to Rattus rats. All available isolates from Guizhou were divided into four distinct groups either in the S segment tree or in the M segment tree. The clustering pattern of these isolates in the S segment tree was not in agreement with that in the M or L segment tree, showing that genetic reassortment between HTNV had occurred naturally. Analysis of the S segment sequences from available HTNV strains indicated that they formed three clades. The first clade, which comprised only viruses from Guizhou, was the outgroup of clades II and III. The viruses in the second clade were found in Guizhou and mainly in the far-east Asian region, including China. However, the viruses in the third clade were found in most areas of China, including Guizhou, in which haemorrhagic fever with renal syndrome (HFRS) is endemic. Our results reveal that the highest genetic diversity of HTNV is in a limited geographical region of Guizhou, and suggest that Guizhou might be a radiation centre of the present form of HTNV.
Disassembly of African cassava mosaic virus
Authors: Kittelmann Katharina , Jeske Holger
Published: July 2008

The plant-infecting geminiviruses encapsidate their single-stranded DNA genome in characteristic twinned particles that are unique among viruses. These particles are formed by joining two incomplete T=1 icosahedra. African cassava mosaic virions were purified by density-gradient centrifugation from infected Nicotiana benthamiana plants and analysed for their stability with respect to pH changes and heat treatment by using electron microscopy. Negative staining and rotary shadowing revealed stable virions as well as isolated capsomeres between pH 4.0 and 8.5. At pH 9.0 and above, particles disintegrated, whereas they mainly aggregated at a pH below 6.0. Heating the preparations to 55 °C and above resulted in the complete loss of any discernible structure. A low proportion (approx. 10 %) of particles ejected their DNA within the pH range of 6.0–8.5. Most virions released their DNA at the top (15.9 %) or the shoulder (71.4 %) of the twin particles and only 12.7 % at the waist. Compared with the expected numbers of pentameric capsomeres at the top (9 %), the shoulder (45.5 %) or the waist (45.5 %), the results revealed a preferential DNA release from the top and shoulder of the geminate particle.
Field evaluation of a gag/env heteroduplex mobility assay for genetic subtyping of small-ruminant lentiviruses
Authors: Germain Karine , Croise Benoit , Valas Stephen
Published: July 2008

Small-ruminant lentiviruses (SRLVs) display a high genetic diversity and are currently classified into five genotypes and an increasing number of subtypes. The co-circulation of subtypes in restricted geographical regions, combined with the occurrence of cross-species infection, suggests the need for development of a large-scale screening methodology for rapid monitoring of the prevalence of the various genetic subtypes and their genetic evolution. Here, a heteroduplex mobility assay (HMA) was developed for the rapid identification of group B subtypes. The assay was validated for both the p14 nucleocapsid-coding region of the gag gene and the V1–V2 region of the env gene using a panel of reference standards and was applied to the genetic subtyping of SRLV field isolates from five mixed flocks in France. Subtyping of 75 blood samples using the env HMA revealed a preferential distribution of subtypes B1 and B2 in sheep and goats, despite direct evidence for interspecies transmission of both subtypes. Adding the gag HMA to the env HMA provided evidence for dual infection and putative recombination between subtypes B1 and B2 in five goats, and between groups A and B in one sheep. Phylogenetic analysis revealed that 100 % (23/23) and 96.7 % (30/31) of samples were correctly classified using the gag and env HMAs, respectively. These results indicate that dual infection and recombination may be a significant source of new variation in SRLV and provide a useful tool for the rapid genetic subtyping of SRLV isolates, which could be relevant for the development of more accurate diagnosis of prevalent SRLV strains in different countries.
Functional analysis of the putative antiapoptotic genes, p49 and iap4, of Spodoptera litura nucleopolyhedrovirus with RNAi
Authors: Yu Qian , Lin Tiehao , Feng Guozhong , Yang Kai , Pang Yi
Published: July 2008

A homology search of a public database revealed that Spodoptera litura nucleopolyhedrovirus (SpltNPV) possesses two putative, antiapoptotic genes, p49 and inhibitor of apoptosis 4 (iap4), but their function has not been investigated in its native host cells. In the present study, we used RNA interference (RNAi) to silence the expression of Splt-iap4 and Splt-p49, independently or together, to determine their roles during the SpltNPV life cycle. RT-PCR analysis and Western blot analysis showed the target gene expression had been knocked out in the SpltNPV-infected SpLi-221 cells after treatment with Splt-p49 or Splt-iap4 double-stranded RNA (dsRNA), respectively, confirming that the two genes were effectively silenced. In SpltNPV-infected cells treated with Splt-p49 dsRNA, apoptosis was observed beginning at 14 h, and almost all cells had undergone apoptosis by 48 h. In contrast, budded virus production and polyhedra formation progressed normally in infected cells treated with Splt-iap4 dsRNA. Cell viability analysis showed that Splt-IAP4 had no synergistic effect on the inhibition of apoptosis of SpLi-221 cells induced by SpltNPV infection. Interestingly, after Splt-iap4 dsRNA treatment, cells did not congregate like those infected with SpltNPV in the early infection phase, implying an unknown role of baculovirus iap4. Our results determine that Splt-p49 is necessary to prevent apoptosis; however, Splt-iap4 has no antiapoptotic function during SpltNPV infection.
Tomato spotted wilt virus glycoproteins induce the formation of endoplasmic reticulum- and Golgi-derived pleomorphic membrane structures in plant cells
Authors: Ribeiro Daniela , Foresti Ombretta , Denecke Jurgen , Wellink Joan , Goldbach Rob , Kormelink Richard J. M.
Published: July 2008

Tomato spotted wilt virus (TSWV) particles are spherical and enveloped, an uncommon feature among plant infecting viruses. Previous studies have shown that virus particle formation involves the enwrapment of ribonucleoproteins with viral glycoprotein containing Golgi stacks. In this study, the localization and behaviour of the viral glycoproteins Gn and Gc were analysed, upon transient expression in plant protoplasts. When separately expressed, Gc was solely observed in the endoplasmic reticulum (ER), whereas Gn was found both within the ER and Golgi membranes. Upon co-expression, both glycoproteins were found at ER-export sites and ultimately at the Golgi complex, confirming the ability of Gn to rescue Gc from the ER, possibly due to heterodimerization. Interestingly, both Gc and Gn were shown to induce the deformation of ER and Golgi membranes, respectively, also observed upon co-expression of the two glycoproteins. The behaviour of both glycoproteins within the plant cell and the phenomenon of membrane deformation are discussed in light of the natural process of viral infection.
HC-Pro protein of sugar cane mosaic virus interacts specifically with maize ferredoxin-5 in vitro and in planta
Authors: Cheng Yu-Qin , Liu Zhong-Mei , Xu Jian , Zhou Tao , Wang Meng , Chen Yu-Ting , Li Huai-Fang , Fan Zai-Feng
Published: July 2008

Symptom development of a plant viral disease is a result of molecular interactions between the virus and its host plant; thus, the elucidation of specific interactions is a prerequisite to reveal the mechanism of viral pathogenesis. Here, we show that the chloroplast precursor of ferredoxin-5 (Fd V) from maize (Zea mays) interacts with the multifunctional HC-Pro protein of sugar cane mosaic virus (SCMV) in yeast, Nicotiana benthamiana cells and maize protoplasts. Our results demonstrate that the transit peptide rather than the mature protein of Fd V precursor could interact with both N-terminal (residues 1–100) and C-terminal (residues 301–460) fragments, but not the middle part (residues 101–300), of HC-Pro. In addition, SCMV HC-Pro interacted only with Fd V, and not with the other two photosynthetic ferredoxin isoproteins (Fd I and Fd II) from maize plants. SCMV infection significantly downregulated the level of Fd V mRNA in maize plants; however, no obvious changes were observed in levels of Fd I and Fd II mRNA. These results suggest that SCMV HC-Pro interacts specifically with maize Fd V and that this interaction may disturb the post-translational import of Fd V into maize bundle-sheath cell chloroplasts, which could lead to the perturbation of chloroplast structure and function.
Positive selection at the receptor-binding site of haemagglutinin H5 in viral sequences derived from human tissues
Authors: Kongchanagul Alita , Suptawiwat Ornpreya , Kanrai Pumaree , Uiprasertkul Mongkol , Puthavathana Pilaipan , Auewarakul Prasert
Published: July 2008

Highly pathogenic H5N1 avian influenza virus has spread through at least 45 countries in three continents. Despite the ability to infect and cause severe disease in humans, the virus cannot transmit efficiently from human to human. The lack of efficient transmission indicates the incompletion of the adaptation of the avian virus to the new host species. The required mutations for the complete adaptation and the emergence of a potential pandemic virus are likely to originate and be selected within infected human tissues. Differential receptor preference plays an important role in the species-tropism of avian influenza. We have analysed quasispecies of sequences covering the receptor-binding domain of the haemagglutinin gene of H5N1 viruses derived from fatal human cases. We employed a likelihood ratio test to identify positive-selection sites within the quasispecies. Nine of seventeen positive-selection sites identified in our analyses were found to be located within or flanking the receptor-binding domain. Some of these mutations are known to alter receptor-binding specificity. This suggests that our approach could be used to screen for mutations with significant functional impact. Our data provide new candidate mutations for the viral adaptation to a human host, and a new approach to search for new genetic markers of potential pandemic viruses.
Small deletions in the potato leafroll virus readthrough protein affect particle morphology, aphid transmission, virus movement and accumulation
Authors: Peter Kari A. , Liang Delin , Palukaitis Peter , Gray Stewart M.
Published: July 2008

Potato leafroll virus (PLRV) capsid comprises 180 coat protein (CP) subunits, with some percentage containing a readthrough domain (RTD) extension located on the particle's surface. The RTD N terminus is highly conserved in luteovirids and this study sought to identify biologically active sites within this region of the PLRV RTD. Fourteen three-amino-acid-deletion mutants were generated from a cloned infectious PLRV cDNA and delivered to plants by Agrobacterium inoculations. All mutant viruses accumulated locally in infiltrated tissues and expressed the readthrough protein (RTP) containing the CP and RTD sequences in plant tissues; however, when purified, only three mutant viruses incorporated the RTP into the virion. None of the mutant viruses were aphid transmissible, but the viruses persisted in aphids for a period sufficient to allow for virus transmission. Several mutant viruses were examined further for systemic infection in four host species. All mutant viruses, regardless of RTP incorporation, moved systemically in each host, although they accumulated at different rates in systemically infected tissues. The biological properties of the RTP are sensitive to modifications in both the RTD conserved and variable regions.
A226V mutation in virus during the 2007 chikungunya outbreak in Kerala, India
Authors: Kumar N. Pradeep , Joseph Rajan , Kamaraj T. , Jambulingam P.
Published: July 2008

Kerala State in India was gripped by a renewed and widespread outbreak of Chikungunya virus (CHIKV) infection during 2007. Here, we report the A226V mutation in the glycoprotein envelope 1 (E1) gene of the virus among isolates collected from the three worst-affected districts of the state during this outbreak. This mutation had already been suggested to be directly responsible for a significant increase in CHIKV infectivity in Aedes albopictus. The badly affected districts in Kerala State during 2007 have abundant rubber plantations, which supported prolific breeding of Ae. albopictus mosquitoes. The abundance of Ae. albopictus in the region and molecular evolution of CHIKV may be contributing factors for the renewed epidemic of chikungunya fever during 2007.
Quantitative Proteomics of a ChloroplastSRP54Sorting Mutant and Its Genetic Interactions withCLPC1in Arabidopsis
Authors: Rutschow Heidi , Ytterberg A. Jimmy , Friso Giulia , Nilsson Robert , van Wijk Klaas J.
Published: July 2008

cpSRP54 (for chloroplast SIGNAL RECOGNITION PARTICLE54) is involved in cotranslational and posttranslational sorting of thylakoid proteins. The Arabidopsis (Arabidopsis thaliana) cpSRP54 null mutant, ffc1-2, is pale green with delayed development. Western-blot analysis of individual leaves showed that the SRP sorting pathway, but not the SecY/E translocon, was strongly down-regulated with progressive leaf development in both wild-type and ffc1-2 plants. To further understand the impact of cpSRP54 deletion, a quantitative comparison of ffc2-1 was carried out for total leaf proteomes of young seedlings and for chloroplast proteomes of fully developed leaves using stable isotope labeling (isobaric stable isotope labeling and isotope-coded affinity tags) and two-dimensional gels. This showed that cpSRP54 deletion led to a change in light-harvesting complex composition, an increase of PsbS, and a decreased photosystem I/II ratio. Moreover, the cpSRP54 deletion led in young leaves to up-regulation of thylakoid proteases and stromal chaperones, including ClpC. In contrast, the stromal protein homeostasis machinery returned to wild-type levels in mature leaves, consistent with the developmental down-regulation of the SRP pathway. A differential response between young and mature leaves was also found in carbon metabolism, with an up-regulation of the Calvin cycle and the photorespiratory pathway in peroxisomes and mitochondria in young leaves but not in old leaves. The Calvin cycle was down-regulated in mature leaves to adjust to the reduced capacity of the light reaction, while reactive oxygen species defense proteins were up-regulated. The significance of ClpC up-regulation was confirmed through the generation of an ffc2-1 clpc1 double mutant. This mutant was seedling lethal under autotrophic conditions but could be partially rescued under heterotrophic conditions.
Charge-density studies of energetic materials: CL-20 and FOX-7. Corrigendum
Authors: Meents A. , Dittrich B. , Johnas S. K. J. , Thome V. , Weckert E. F.
Published: July 2008

A corrigendum to the paper by Meents et al. (2008), Acta Cryst. B64, 42–49 to correct the nomenclature for CL-20.
High-pressure structural study of L-α-glutamine and the use of Hirshfeld surfaces and graph-set notation to investigate the hydrogen bonding present in the structure up to 4.9 GPa
Authors: Lozano-Casal P. , Allan D. R. , Parsons S.
Published: July 2008

The crystal structure of L-α-glutamine has been elucidated at room temperature at pressures between 0 and 4.9 GPa by using single-crystal high-pressure X-ray diffraction techniques. The structure is primarily stabilized by five N—H...O intermolecular interactions, which link molecules in a herringbone-like layer arrangement, giving rise to voids within the solid. The application of pressure on the structure results in a reduction in the size of the voids, as a consequence of the shortening of the N—H...O hydrogen bonds, which compress to minimum N...O distances of around 2.6 Å, without driving the crystal structure to a phase transition. The decrease in the hydrogen-bond distances is due to the necessary stabilization of the structure, which arises from molecules modifying their positions to optimize electrostatic contacts and minimize the occupied space. Hirshfeld surfaces and fingerprint plots have been used to rapidly assess the structural changes that occur on application of pressure.
Role of the gauche effect and local 1,3-dipole–dipole interactions in stabilizing an unusual conformation of tartarodinitriles
Authors: Rychlewska Urszula , Waścinska Natalia , Warżajtis Beata , Gawroński Jacek
Published: July 2008

This paper reports the synthesis, X-ray and NMR investigations of chiral and meso dinitriles of tartaric acid (tartarodinitriles) and their O,O′-diacetyl and O,O′-dibenzoyl derivatives. While in chiral tartaric acid its esters and NH amides the four-atom carbon chain is overwhelmingly trans, it is gauche in chiral tartarodinitriles. Conversely, meso-tartaric acid, its esters and amides display a tendency for the gauche conformation, but meso-tartarodinitriles usually have the trans conformation. The NMR studies of tartarodinitriles reveal the presence of a conformational equilibrium in solution with a preference for those conformers found in crystals. The gauche conformation of meso-tartarodinitriles seems to be stabilized by local dipolar interactions, intramolecular C—H...O hydrogen bonds and by a tendency for maximization of the gauche effect, the latter effect also operating in chiral tartarodinitriles. Stabilization of the trans conformers of tartarodinitriles in the crystals seems to originate from specific intermolecular interactions.
Minimum and optimum light requirements for laryngoscopy in paediatric anaesthesia: a manikin study*
Authors: Malan C. A. , Scholz A. , Wilkes A. R. , Hampson M. A. , Hall J. E.
Published: July 2008

Direct laryngoscopy is performed regularly in paediatric anaesthetic practice for the purpose of intubating a patient's trachea. A minimum illumination of 700 lux at a distance of 20 mm has been suggested in a draft standard for laryngoscopes from the International Organization for Standardization. We investigated the minimum and optimum illumination required by anaesthetists during laryngoscopy. Fifty anaesthetists were recruited to perform laryngoscopy on a child manikin with a selection of laryngoscope blades and bulbs attached to a variable voltage supply. There was a large variation in the illumination range of different bulb and blade combinations. We demonstrated a large interindividual variability between anaesthetists for illumination requirements during laryngoscopy. Anaesthetists can see the larynx at very low light levels, but optimum illumination was significantly greater than minimum illumination. Two of the six combinations could produce more than 700 lux. In all, 78% and 54% of anaesthetists considered 700 lux too bright with a halogen and xenon bulb, respectively. Our study suggests that the proposed standard of 700 lux may possibly be too bright.
Therapeutic hypothermia in comatose patients after out‐of‐hospital cardiac arrest*
Authors: Hay A. W. , Swann D. G. , Bell K. , Walsh T. S. , Cook B.
Published: July 2008

Our intensive care unit has been treating comatose patients, following an out‐of‐hospital cardiac arrest, with therapeutic hypothermia since 2002. In all, 139 out‐of‐hospital cardiac arrest patients were admitted in the 4‐year period 2002–5. Of these, 27% had a favourable outcome (discharged home or to rehabilitation). Forty‐one per cent of patients presenting with ventricular fibrillation (VF) and 7% of non‐VF patients had a favourable outcome. No patient with an estimated time from collapse to first attempt at cardiopulmonary resuscitation over 12 min survived to hospital discharge. Twenty‐two per cent of patients over 70 years were discharged home, suggesting age was not a barrier to surviving out‐of‐hospital cardiac arrest. The introduction of a therapeutic hypothermia clinical pathway, at the end of 2003 improved the efficiency of cooling. The percentage of patients cooled to below 34 °C within 4 h increased from 15 to 51% and those cooled for more than 12 h increased from 30 to 83%.
Dexmedetomidine and cardiac protection for non‐cardiac surgery: a meta‐analysis of randomised controlled trials
Authors: Biccard B. M. , Goga S. , De Beurs J.
Published: July 2008

We conducted a systematic review of the effects of dexmedetomidine on cardiac outcomes following non‐cardiac surgery. We included prospective, randomised peri‐operative studies of dexmedetomidine that reported mortality, cardiac morbidity or adverse drug events. A PubMed Central and EMBASE search was conducted up to July 2007. The reference lists of identified papers were examined for further trials. Of 425 studies identified, 20 were included in the meta‐analysis (840 patients). Dexmedetomidine was associated with a trend towards improved cardiac outcomes; all‐cause mortality (OR 0.27, 95% CI 0.01–7.13, p = 0.44), non‐fatal myocardial infarction (OR 0.26, 95% CI 0.04–1.60, p = 0.14), and myocardial ischaemia (OR 0.65, 95% CI 0.26–1.63, p = 0.36). Peri‐operative hypotension (26%, OR 3.80, 95% CI 1.91–7.54, p = 0.0001) and bradycardia (17%, OR 5.45, 95% CI 2.98–9.95, p < 0.00001) were significantly increased. An anticholinergic did not reduce the incidence of bradycardia (p = 0.43). A randomised placebo‐controlled trial of dexmedetomidine is warranted.
Impacts of climatic stability on the structural and functional aspects of macroinvertebrate communities after severe drought
Authors: GRISWOLD MARCUS W. , BERZINIS REBECCA W. , CRISMAN THOMAS L. , GOLLADAY STEPHEN W.
Published: July 2008

1. Unpredictable, extreme climatic events (e.g. droughts) can potentially destabilize aquatic communities. From 1998 to 2002, southwestern Georgia, U.S.A., experienced the third worst drought of the last 100 years, leading to loss of surface flow in many small streams. We sampled macroinvertebrates, flow and water chemistry in small headwater streams from 2001 to 2007 in two adjacent coastal plain streams of contrasting headwater type (wetland and groundwater‐fed seep) following resumption of flow.

2. Decreasing water temperature, conductivity and nutrient concentrations within the first 2 years of the study indicated flushing of the streambed associated with increased discharge. Invertebrate community composition became less variable over time and during wetter years, reflecting water chemistry, hydrological and climate conditions.

3. A core set of species appeared immediately following breaking of the drought in both streams, reflecting a shared species pool. These species exhibited resilience traits, including short life cycles and resistance to desiccation, which allowed for rapid recovery from disturbance. Such species, which were small‐bodied, sclerotized and abundant in the drift, were then replaced as flows increased by those that were larger, soft‐bodied and rare in drift, suggesting a more stable and less ephemeral habitat.

4. Hydrologic regime and long‐term precipitation indices were strongly correlated with invertebrate community and trait structure. Long‐term data allowed for better interpretation of the effects of infrequent disturbances on aquatic ecosystems. Additionally, long‐term precipitation indices (i.e. 48‐month standardized precipitation index) can indicate the likelihood of a return to drought, allowing for the collection of pre‐disturbance data.
Comparison of three research models of portal hypertension in mice: macroscopic, histological and portal pressure evaluation
Authors: Geerts Anja M. , Vanheule Eline , Praet Marleen , Van Vlierberghe Hans , De Vos Martine , Colle Isabelle
Published: July 2008

The characterization of mice models of portal hypertension (PHT) is lacking in the literature. Therefore, the aim of the present study was to make a histological approach during development of PHT in two models of cirrhosis with PHT compared with one model of isolated PHT. The model of isolated PHT was developed by partial portal vein ligation (PPVL). Two portal hypertensive cirrhotic mice models were developed either by common bile duct ligation (CBDL) or administration of carbon tetrachloride (CCl4) subcutaneously (twice weekly, 1 ml/kg). These models represent, respectively, a secondary biliary cirrhosis and alcoholic cirrhosis. Mice were killed at several time points to evaluate liver changes by histological and ultrastructural methods. A correlation was made with portal pressure measurements. Histology revealed the absence of fibrosis or cirrhosis in PPVL mice. They developed an isolated portal hypertension. After CBDL induction, the mice developed the characteristics of cirrhosis after 6 weeks, with simultaneous increase in portal pressures. Fifty percent of the mice had ascites at that time point. Sixteen weeks after administration of CCl4, a micronodular cirrhotic aspect of the liver was seen associated with signs of portal hypertension. This is the first descriptive study of three widely used animal models in mice, allowing the study of pathophysiological changes in cirrhosis and portal hypertension. The PPVL in mice leads to a model of isolated portal hypertension. Secondary biliary cirrhosis developed after 6 weeks of common bile duct ligation in 50% of the mice that developed ascites. Subcutaneous injection of CCl4 for 16 weeks induces cirrhosis and poral hypertension, without ascites. Moreover, the present study is the first description of a cirrhotic model in mice developed by subcutaneous injections of CCl4. Well‐described mice models will facilitate use of knock‐out or transgenic mice and lead to a better understanding of the underlying molecular pathways in the field of portal hypertension and cirrhosis.
Population structure in an endangered songbird: maintenance of genetic differentiation despite high vagility and significant population recovery
Authors: BARR KELLY R. , LINDSAY DENISE L. , ATHREY GIRI , LANCE RICHARD F. , HAYDEN TIMOTHY J. , TWEDDALE SCOTT A. , LEBERG PAUL L.
Published: July 2008

Black‐capped vireos (Vireo atricapilla), an endangered, migratory species dependent upon early successional habitat, have experienced significant recovery since its protection. In light of its vagility and known increase in population size and range, limited genetic differentiation would be expected in the species. Using 15 microsatellite loci and an extensive sampling regime, we detected significant overall genetic differentiation (FST = 0.021) and high interpopulation differentiation compared to other migratory birds. Although proximate sites (separated by < 20 km) tended to be genetically similar, there was no apparent association of either geographical distance or landscape attributes with differentiation between sites. Evidence of a population bottleneck was also detected in a site located near other large concentrations of birds. Although black‐capped vireos are capable of large‐scale movements and the population has experienced a recent expansion, dispersal appears too insufficient to eliminate the genetic differentiation resulting from restricted colonization of ephemeral habitats.
Do outbreaks affect genetic population structure? A worldwide survey inLocusta migratoria, a pest plagued by microsatellite null alleles
Authors: CHAPUIS M‐P. , LECOQ M. , MICHALAKIS Y. , LOISEAU A. , SWORD G. A. , PIRY S. , ESTOUP A.
Published: July 2008

An understanding of the role of factors intrinsic to a species’ life history in structuring contemporary genetic variation is a fundamental, but understudied, aspect of evolutionary biology. Here, we assessed the influence of the propensity to outbreak in shaping worldwide genetic variation inLocusta migratoria, a cosmopolitan pest well known for its expression of density‐dependent phase polyphenism. We scored 14 microsatellites in nine subspecies from 25 populations distributed over most of the species’ range in regions that vary in the historical frequency and extent of their outbreaks. We rejected the hypothesis thatL. migratoriaconsists of two genetically distinct clusters adapted to habitats either rarely (nonoutbreaking) or cyclically (outbreaking) favourable to increases in population density. We also invalidated the current subspecific taxonomic classification based on morphometrics. Bayesian inferences indicated evidence of a homogenizing effect of outbreaks onL. migratoriapopulation structure. Geographical and ecological barriers to gene flow in conjunction with historical events can also explain the observed patterns. By systematically assessing the effects of null alleles using computer simulations, we also provide a template for the analysis of microsatellite data sets characterized by a high prevalence of null alleles.
Delayed reproduction in Arabidopsis thaliana improves fitness in soil with suboptimal phosphorus availability
Authors: NORD ERIC A. , LYNCH JONATHAN P.
Published: July 2008

Low phosphorus availability (low P) often delays flowering and maturity in annual plants, while abiotic stress generally accelerates flowering and maturity. The utility of this response is unknown. We hypothesize that phenological delay in low P is beneficial by permitting more time for phosphorus acquisition and utilization. We grew seven genotypes of Arabidopsis thaliana with contrasting phenology in high and low P. Low P delayed bolting and maturity in all genotypes. Low P decreased root length, but not root‐length duration (the integral of root length over time), because phenological delay allowed low‐P plants to compensate for shorter root length. Root‐length duration was correlated with phosphorus accumulation. Leaf phosphorus duration (the integral of leaf phosphorus over time) was correlated with reproductive biomass, indicating the utility of increased phosphorus utilization. Phenological delays accounted for up to 30% of biomass production when low‐P plants were compared to models of plants with no delays. These results support the hypothesis that phenological delay in low P is adaptive and leads to increased phosphorus acquisition and utilization. Because low P conditions are prevalent, understanding the utility of this response could be useful in crop breeding and in predicting plant responses to global climate change.
Primary cutaneous inoculation tuberculosis in a healthcare worker as a result of a surgical accident
Authors: Tapias Leonidas , Tapias‐Vargas Luis Felipe , Tapias‐Vargas Leonidas
Published: July 2008

In May 2004, a 48‐year‐old male surgeon, resident in Bucaramanga, Colombia, suffered a superficial cut with a scalpel to the lateral aspect of the mid‐phalanx of the second finger of the left hand while performing a pulmonary decortication surgical procedure for tuberculous empyema with pulmonary entrapment. The injury healed normally but, approximately 2 weeks after the event, an erythematous, nonpainful papule of approximately 3 mm in diameter developed, and increased progressively to 7 mm 3 days after its initial appearance. At this time, the papule showed spontaneous secretion of a clear liquid and superficial ulceration (Fig. 1). Approximately 3 weeks after the injury, a Gram stain of the liquid was performed; it showed no bacteria but a moderate leukocyte reaction. Because of the high suspicion of possible tuberculous infection, bacilloscopy of the liquid was performed, and was positive (++) for acid‐fast bacteria (Fig. 2). The liquid was cultured and grew Mycobacterium tuberculosis. The culture was sent to the Laboratory of Mycobacteria at the National Institute of Health, Bogota, Colombia for drug resistance testing. Susceptibility was demonstrated against streptomycin, isoniazid, rifampicin, and ethambutol. During this time, the patient presented an ipsilateral painful axillary adenopathy of about 2.5 cm in diameter. The patient consulted with an infectologist, who initiated a Directly Observed Therapy Short Course (DOTS) regimen [first phase (8 weeks): daily, except Sundays, streptomycin 1 g intramuscularly, pyrazinamide 1500 mg orally, isoniazid 300 mg, and rifampicin 600 mg; second phase (18 weeks): twice weekly rifampicin 600 mg and isoniazid 500 mg], accompanied by daily pyridoxine to prevent secondary effects from isoniazid. After 3 weeks of treatment, the finger lesion had disappeared. Treatment was undertaken as described above, with the patient reporting symptoms of vertigo, nausea, epigastralgia, and mild myalgia as the adverse effects of medication. A chest x‐ray was taken and reported to be normal. The axillary adenopathy disappeared approximately 6 months after the injury. Nearly 3.5 years after the incident, the patient has not presented any type of symptomatology.

Evolution of the skin lesion: (a) erythematous nonpainful papule; (b) ulcerated skin lesion

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Photomicrograph of direct examination of the liquid from the cutaneous lesion, showing Mycobacterium tuberculosis. Stain: Ziehl–Neelsen (×100)

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House dust mites on skin, clothes, and bedding of atopic dermatitis patients
Authors: Teplitsky Valery , Mumcuoglu Kosta Y. , Babai Ilan , Dalal Ilan , Cohen Rifka , Tanay Amir
Published: July 2008

Background  Atopic dermatitis is a common allergic condition in children, often associated with a positive skin reaction to house dust mite allergens.

Aim  To determine the presence of house dust mites on the skin, clothes, and bedding of patients with atopic dermatitis.

Methods  Nineteen patients with atopic dermatitis were examined during a 2‐year period. Samples from affected and healthy skin surfaces were obtained with adhesive tape, and dust samples from bedding and clothes were collected with a vacuum cleaner at the start of the study and 3–6 weeks later, and examined for the presence of house dust mites. The findings were compared with those of 21 healthy controls.

Results  The most common mite species on skin were Dermatophagoides pteronyssinus and Dermatophagoides farinae, which were found in nine patients and three controls. The patient group showed a significantly larger percentage of samples with mites than did the control group (34.9% and 7.9%, respectively) (P < 0.001), and a significantly larger percentage of individuals with at least one positive sample (84.2% and 14.2%, respectively) (P < 0.0001). No correlation was found between the number of mites on the skin and clothes/bedding of patients, or between patients and controls with regard to the number of mites on the clothes and bedding.

Conclusions  Patients with atopic dermatitis showed a higher prevalence of mites on their skin than did healthy individuals, which could be involved in allergic sensitization and disease exacerbation.
Treatment of persistent alopecia areata with sulfasalazine
Authors: Rashidi Turaj , Mahd Azarmdokht Alamdari
Published: July 2008

Background  Alopecia areata is an autoimmune disease with no definitive treatment, and some cases persist despite standard therapies. Sulfasalazine has been reported to show success in the treatment of persistent cases of alopecia areata.

Objective  To assess the efficacy of sulfasalazine in cases of recalcitrant alopecia areata that do not respond to topical and intralesional corticosteroids, 5% minoxidil, or psoralen plus ultraviolet‐A (PUVA) therapy.

Methods  Thirty‐nine patients with persistent alopecia areata received 3 g of oral sulfasalazine for 6 months, and terminal hair regrowth was quantified as no response, moderate response, or good response.

Results  A good response occurred in 10 of the 39 patients (25.6%), a moderate response in 12 (30.7%), and a poor or no response in 17 (43.5%).

Conclusion  Sulfasalazine can be used as an alternative drug in patients with persistent alopecia areata.
A new HLA‐B*40 allele, HLA‐B*4085, identified by sequence‐based typing in the Korean population
Authors: Han S.‐H. , Heo Y.‐A. , Kwon O.‐J. , Lee A. , Lee K.‐R.
Published: July 2008

A new HLA‐B*4085 showed one nucleotide difference from B*400201 at the position 500 of exon 3, resulting in a coding change from Thr to Ile (T143I).
Loss of heterozygosity at 6p21 underling HLA class I downregulation in Chinese primary esophageal squamous cell carcinomas
Authors: Yang Y. , Zhang J. , Miao F. , Wei J. , Shen C. , Shen Y. , Xie W.
Published: July 2008

Loss or downregulation of human leukocyte antigen (HLA) class I molecules is a widespread mechanism used by tumor cells to avoid tumor recognition by cytotoxic T lymphocytes favoring tumor immune escape. Multiple molecular mechanisms are responsible for these altered HLA class I tumor phenotypes, such as the loss of heterozygosity (LOH) at chromosome region 6p21.3. In this study, we used immunohistological techniques with a highly selective panel of anti‐HLA monoclonal antibodies to analyze the expression of HLA class I molecules in 84 formalin‐fixed, paraffin‐embedded section and 49 frozen‐fresh tissues of primary esophageal squamous cell carcinomas (pESCC) from Chinese patients. To elucidate the underlying mechanism of HLA class I loss or downregulation, we also analyzed LOH of previously selected microsatellite markers located in chromosomes 6 and 15 by polymerase chain reaction. DNA was obtained from frozen‐fresh tumor tissues and surrounding stroma to define the LOH associated with chromosomes 6p21 and 15q21. Our results showed that HLA‐A, HLA‐B/C, HLA class I heavy chain, β2‐microglobuline, and HLA class I complex were lost or downregulated in pESCC (P < 0.0001), and were moderately associated with the microsatellite alterations in HLA class I gene regions, correlated with patients’ age, tumor’s location, and stage, and indicated that LOH at 6p21.3 is a frequent mechanism that leads to HLA class I abnormalities in pESCC.