bluuebunny/crossref_metadata_2025 huggingface dataset:
Compound eyes and retinal information processing in miniature dipteran species match their specific ecological demands
Authors: Gonzalez-Bellido Paloma T. , Wardill Trevor J. , Juusola Mikko
Published: February 2011

The compound eye of insects imposes a tradeoff between resolution and sensitivity, which should exacerbate with diminishing eye size. Tiny lenses are thought to deliver poor acuity because of diffraction; nevertheless, miniature insects have visual systems that allow a myriad of lifestyles. Here, we investigate whether size constraints result in an archetypal eye design shared between miniature dipterans by comparing the visual performance of the fruit fly
Drosophila
and the killer fly
Coenosia.
These closely related species have neural superposition eyes and similar body lengths (3 to 4 mm), but
Coenosia
is a diurnal aerial predator, whereas slow-flying
Drosophila
is most active at dawn and dusk. Using in vivo intracellular recordings and EM, we report unique adaptations in the form and function of their photoreceptors that are reflective of their distinct lifestyles. We find that although these species have similar lenses and optical properties,
Coenosia
photoreceptors have three- to fourfold higher spatial resolution and rate of information transfer than
Drosophila.
The higher performance in
Coenosia
mostly results from dramatically diminished light sensors, or rhabdomeres, which reduce pixel size and optical cross-talk between photoreceptors and incorporate accelerated phototransduction reactions. Furthermore, we identify local specializations in the
Coenosia
eye, consistent with an acute zone and its predatory lifestyle. These results demonstrate how the flexible architecture of miniature compound eyes can evolve to match information processing with ecological demands.
GTPγS microtubules mimic the growing microtubule end structure recognized by end-binding proteins (EBs)
Authors: Maurer Sebastian P. , Bieling Peter , Cope Julia , Hoenger Andreas , Surrey Thomas
Published: February 2011

Microtubule plus-end-tracking proteins (+TIPs) localize to growing microtubule plus ends to regulate a multitude of essential microtubule functions. End-binding proteins (EBs) form the core of this network by recognizing a distinct structural feature transiently existing in an extended region at growing microtubule ends and by recruiting other +TIPs to this region. The nature of the conformational difference allowing EBs to discriminate between tubulins in this region and other potential tubulin binding sites farther away from the microtubule end is unknown. By combining in vitro reconstitution, multicolor total internal reflection fluorescence microscopy, and electron microscopy, we demonstrate here that a closed microtubule B lattice with incorporated GTPγS, a slowly hydrolyzable GTP analog, can mimic the natural EB protein binding site. Our findings indicate that the guanine nucleotide γ-phosphate binding site is crucial for determining the affinity of EBs for lattice-incorporated tubulin. This defines the molecular mechanism by which EBs recognize growing microtubule ends.
Benzoquinone ansamycin 17AAG binds to mitochondrial voltage-dependent anion channel and inhibits cell invasion
Authors: Xie Qian , Wondergem Robert , Shen Yuehai , Cavey Greg , Ke Jiyuan , Thompson Ryan , Bradley Robert , Daugherty-Holtrop Jennifer , Xu Yong , Chen Edwin , Omar Hanan , Rosen Neal , Wenkert David , Xu H. Eric , Vande Woude George F.
Published: February 2011

Geldanamycin and its derivative 17AAG [17-(Allylamino)-17-demethoxygeldanamycin, telatinib] bind selectively to the Hsp90 chaperone protein and inhibit its function. We discovered that these drugs associate with mitochondria, specifically to the mitochondrial membrane voltage-dependent anion channel (VDAC) via a hydrophobic interaction that is independent of HSP90. In vitro, 17AAG functions as a Ca
2+
mitochondrial regulator similar to benzoquinone-ubiquinones like Ub0. All of these compounds increase intracellular Ca
2+
and diminish the plasma membrane cationic current, inhibiting urokinase activity and cell invasion. In contrast, the HSP90 inhibitor radicicol, lacking a bezoquinone moiety, has no measurable effect on cationic current and is less effective in influencing intercellular Ca
2+
concentration. We conclude that some of the effects of 17-AAG and other ansamycins are due to their effects on VDAC and that this may play a role in their clinical activity.
Bacterial community structures are unique and resilient in full-scale bioenergy systems
Authors: Werner Jeffrey J. , Knights Dan , Garcia Marcelo L. , Scalfone Nicholas B. , Smith Samual , Yarasheski Kevin , Cummings Theresa A. , Beers Allen R. , Knight Rob , Angenent Largus T.
Published: February 2011

Anaerobic digestion is the most successful bioenergy technology worldwide with, at its core, undefined microbial communities that have poorly understood dynamics. Here, we investigated the relationships of bacterial community structure (>400,000 16S rRNA gene sequences for 112 samples) with function (i.e., bioreactor performance) and environment (i.e., operating conditions) in a yearlong monthly time series of nine full-scale bioreactor facilities treating brewery wastewater (>20,000 measurements). Each of the nine facilities had a unique community structure with an unprecedented level of stability. Using machine learning, we identified a small subset of operational taxonomic units (OTUs; 145 out of 4,962), which predicted the location of the facility of origin for almost every sample (96.4% accuracy). Of these 145 OTUs, syntrophic bacteria were systematically overrepresented, demonstrating that syntrophs rebounded following disturbances. This indicates that resilience, rather than dynamic competition, played an important role in maintaining the necessary syntrophic populations. In addition, we explained the observed phylogenetic differences between all samples on the basis of a subset of environmental gradients (using constrained ordination) and found stronger relationships between community structure and its function rather than its environment. These relationships were strongest for two performance variables—methanogenic activity and substrate removal efficiency—both of which were also affected by microbial ecology because these variables were correlated with community evenness (at any given time) and variability in phylogenetic structure (over time), respectively. Thus, we quantified relationships between community structure and function, which opens the door to engineer communities with superior functions.
Rewiring hydrogenase-dependent redox circuits in cyanobacteria
Authors: Ducat Daniel C. , Sachdeva Gairik , Silver Pamela A.
Published: February 2011

Hydrogenases catalyze the reversible reaction 2H
+
 + 2e
-
↔H
2
with an equilibrium constant that is dependent on the reducing potential of electrons carried by their redox partner. To examine the possibility of increasing the photobiological production of hydrogen within cyanobacterial cultures, we expressed the [FeFe] hydrogenase, HydA, from
Clostridium acetobutylicum
in the non-nitrogen-fixing cyanobacterium
Synechococcus elongatus
sp. 7942. We demonstrate that the heterologously expressed hydrogenase is functional in vitro and in vivo, and that the in vivo hydrogenase activity is connected to the light-dependent reactions of the electron transport chain. Under anoxic conditions, HydA activity is capable of supporting light-dependent hydrogen evolution at a rate > 500-fold greater than that supported by the endogenous [NiFe] hydrogenase. Furthermore, HydA can support limited growth solely using H
2
and light as the source of reducing equivalents under conditions where Photosystem II is inactivated. Finally, we demonstrate that the addition of exogenous ferredoxins can modulate redox flux in the hydrogenase-expressing strain, allowing for greater hydrogen yields and for dark fermentation of internal energy stores into hydrogen gas.
Insertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of eubacterial initiation factor 1
Authors: Yassin Aymen S. , Haque Md. Emdadul , Datta Partha P. , Elmore Kevin , Banavali Nilesh K. , Spremulli Linda L. , Agrawal Rajendra K.
Published: February 2011

Mitochondria have their own translational machineries for the synthesis of thirteen polypeptide chains that are components of the complexes that participate in the process of oxidative phosphorylation (or ATP generation). Translation initiation in mammalian mitochondria requires two initiation factors, IF2
mt
and IF3
mt
, instead of the three that are present in eubacteria. The mammalian IF2
mt
possesses a unique 37 amino acid insertion domain, which is known to be important for the formation of the translation initiation complex. We have obtained a three-dimensional cryoelectron microscopic map of the mammalian IF2
mt
in complex with initiator

and the eubacterial ribosome. We find that the 37 amino acid insertion domain interacts with the same binding site on the ribosome that would be occupied by the eubacterial initiation factor IF1, which is absent in mitochondria. Our finding suggests that the insertion domain of IF2
mt
mimics the function of eubacterial IF1, by blocking the ribosomal aminoacyl-tRNA binding site (A site) at the initiation step.
Depletion of antibiotic targets has widely varying effects on growth
Authors: Wei Jun-Rong , Krishnamoorthy Vidhya , Murphy Kenan , Kim Jee-Hyun , Schnappinger Dirk , Alber Tom , Sassetti Christopher M. , Rhee Kyu Y. , Rubin Eric J.
Published: February 2011

It is often assumed that antibiotics act on the most vulnerable cellular targets, particularly those that require limited inhibition to block growth. To evaluate this assumption, we developed a genetic method that can inducibly deplete targeted proteins and that mimics their chemical inactivation. We applied this system to current antibiotic targets in mycobacteria. Although depleting some antibiotic targets significantly perturbs bacterial growth, surprisingly, we found that reducing the levels of other targets by more than 97% had little or no effect on growth. For one of these targets, dihydrofolate reductase, metabolic analysis suggested that depletion mimics the use of subinhibitory concentrations of the antibiotic trimethroprim. These observations indicate that some drug targets can exist at levels much higher than are needed to support growth. However, protein depletion can be used to identify promising drug targets that are particularly vulnerable to inhibition.
Role of large thermal fluctuations and magnesium ions in t-RNA selectivity of the ribosome
Authors: Guo Zuojun , Gibson Meghan , Sitha Sanyasi , Chu Steven , Mohanty Udayan
Published: February 2011

The fidelity of translation selection begins with the base pairing of codon-anticodon complex between the m-RNA and tRNAs. Binding of cognate and near-cognate tRNAs induces 30S subunit of the ribosome to wrap around the ternary complex, EF-Tu(GTP)aa-tRNA. We have proposed that large thermal fluctuations play a crucial role in the selection process. To test this conjecture, we have developed a theoretical technique to determine the probability that the ternary complex, as a result of large thermal fluctuations, forms contacts leading to stabilization of the GTPase activated state. We argue that the configurational searches for such processes are in the tail end of the probability distribution and show that the probability for this event is localized around the most likely configuration. Small variations in the repositioning of cognate relative to near-cognate complexes lead to rate enhancement of the cognate complex. The binding energies of over a dozen unique site-bound magnesium structural motifs are investigated and provide insights into the nature of interaction of divalent metal ions with the ribosome.
Oligosaccharide conjugates of
Bordetella pertussis
and
bronchiseptica
induce bactericidal antibodies, an addition to pertussis vaccine
Authors: Kubler-Kielb Joanna , Vinogradov Evgeny , Lagergård Teresa , Ginzberg Ariel , King Jerry D. , Preston Andrew , Maskell Duncan J. , Pozsgay Vince , Keith Jerry M. , Robbins John B. , Schneerson Rachel
Published: February 2011

Pertussis is a highly contagious respiratory disease that is especially dangerous for infants and children. Despite mass vaccination, reported pertussis cases have increased in the United States and other parts of the world, probably because of increased awareness, improved diagnostic means, and waning vaccine-induced immunity among adolescents and adults. Licensed vaccines do not kill the organism directly; the addition of a component inducing bactericidal antibodies would improve vaccine efficacy. We investigated
Bordetella pertussis
and
Bordetella bronchiseptica
LPS-derived core oligosaccharide (OS) protein conjugates for their immunogenicity in mice.
B. pertussis
and
B. bronchiseptica
core OS were bound to aminooxylated BSA via their terminal Kdo residues. The two conjugates induced similar anti-
B. pertussis
LPS IgG levels in mice.
B. bronchiseptica
was investigated because it is easier to grow than
B. pertussis
. Using
B. bronchiseptica
genetically modified strains deficient in the O-specific polysaccharide, we isolated fractions of core OS with one to five repeats of the terminal trisaccharide, having at the nonreducing end a GlcNAc or GalNAc, and bound them to BSA at different densities. The highest antibody levels in mice were elicited by conjugates containing an average of 8–17 OS chains per protein and with one repeat of the terminal trisaccharide. Conjugate-induced antisera were bactericidal against
B. pertussis
, and the titers correlated with ELISA-measured antibody levels (
r
= 0.74). Such conjugates are easy to prepare and standardize; added to a recombinant pertussis toxoid, they may induce antibacterial and antitoxin immunity.
Combined transcriptome analysis of fetal human and mouse cerebral cortex exposed to alcohol
Authors: Hashimoto-Torii Kazue , Kawasawa Yuka Imamura , Kuhn Alexandre , Rakic Pasko
Published: February 2011

Fetal exposure to environmental insults increases the susceptibility to late-onset neuropsychiatric disorders. Alcohol is listed as one of such prenatal environmental risk factors and known to exert devastating teratogenetic effects on the developing brain, leading to complex neurological and psychiatric symptoms observed in fetal alcohol spectrum disorder (FASD). Here, we performed a coordinated transcriptome analysis of human and mouse fetal cerebral cortices exposed to ethanol in vitro and in vivo, respectively. Up- and down-regulated genes conserved in the human and mouse models and the biological annotation of their expression profiles included many genes/terms related to neural development, such as cell proliferation, neuronal migration and differentiation, providing a reliable connection between the two species. Our data indicate that use of the combined rodent and human model systems provides an effective strategy to reveal and analyze gene expression changes inflicted by various physical and chemical environmental exposures during prenatal development. It also can potentially provide insight into the pathogenesis of environmentally caused brain disorders in humans.
Six-Month Follow-Up of Computerized Alcohol Screening, Brief Intervention, and Referral to Treatment in the Emergency Department
Authors: Vaca Federico E. , Winn Diane , Anderson Craig L. , Kim Doug , Arcila Mauricio
Published: February 2011

The goal of this observational study was to measure change in alcohol consumption at 6 months following emergency department computerized alcohol screening brief intervention (CASI) and referral to treatment (ED-SBIRT) with integrated brief negotiated interview (BNI) and computer-generated personal alcohol reduction plans. At-risk patients received a BNI by CASI, including personalized feedback, assessment of readiness to change, reasons for cutting down, goal setting, and a printed personal alcohol reduction plan. Alcohol use was assessed by telephone interview 6 months after CASI. Factors associated with lower alcohol consumption were examined. Of the 385 participants who completed the BNI, were consented, and enrolled, 221 subjects completed the 6-month follow-up interview. Forty-seven percent of the study sample of at-risk patients were no longer drinking over the National Institute on Alcohol Abuse and Alcoholism (NIAAA)-recommended limits. Reductions were greater for patients with Alcohol Use Disorders Identification Test (AUDIT) scores of 1 to 7. Readiness to change was a good predictor of drinking below the recommended limits. The use of computerized ED-SBIRT with integrated personalized messaging and BNI holds promise as a viable screening and intervention modality for a wide range of emergency department patients.
Early relationship struggles: A case study of alliance formation and reparation
Authors: Råbu Marit , Halvorsen Margrethe Seeger , Haavind Hanne
Published: February 2011

Aim: A good alliance established during the early sessions of psychotherapy will most likely lead to a good outcome. As a result, there is much to learn from a case in which both the patient and therapist regarded the alliance as being poor for an extended period (the first 15 sessions), yet still managed to develop a solid and stable alliance and reach a successful completion of therapy. The aim is to give a close inspection of this reparation process. Methods and analysis: Ratings on the Working Alliance Inventory (WAI) were used to guide the strategic selection of a case in which a depressed woman in her thirties sought help from an experienced senior male psychotherapist. A detailed analysis of the therapeutic dialogue brought forth what the parties expected from each other and how they responded to explicit and implicit expressions about how to proceed. Post‐termination interviews revealed their subjective configurations of events in therapy and their corresponding reflections. Findings and discussion: Important steps and hallmarks of the alliance formation and reparation were identified: (i) Early in the process, incompatible expectations about what the relationship could achieve led to repetitious struggles. (ii) Their conflicting notions came forward in a more open dialogue about two specific issues (her medication and sick leave). (iii) Through the recognition of different viewpoints they were able to expand on their interactional pattern and develop playful ways to explore her decision making in everyday life. (iv) Temporary breaks seemed to consolidate her autonomy. (v) Late in the course of therapy, the therapist introduced a literary metaphor that seemed to further consolidate the alliance.
Hitting the wall: A case study of interpersonal changes in psychotherapy
Authors: Hill Clara E. , Chui Harold , Huang Teresa , Jackson John , Liu Jingqing , Spangler Patricia
Published: February 2011

Design: Changes in interpersonal functioning are described in a case of brief interpersonal psychotherapy. Results: Although the client reported having more interpersonal problems than normative data both before and after therapy, she improved slightly on the Inventory of Interpersonal Problems. In an interview, the client reported more insight about interpersonal patterns and greater ability to state her needs. In relationship episodes at the end compared to the beginning of therapy, the client began responding more positively about her perceptions of others and expressed less debilitating inhibiting affects (typically shame and pain). The therapist also noted interpersonal changes in talking about their relationship. Discussion: Possible facilitators of change were the therapeutic relationship, therapist support, and therapist challenge. The benefits of assessing interpersonal patterns in terms of both the core conflictual relationship theme and affects are discussed.
Alliance evolutions over the course of short‐term dynamic psychotherapy: A case study
Authors: Michel Luc , Kramer Ueli , De Roten Yves
Published: February 2011

Background: Alliance evolutions, i.e. ruptures and resolutions over the course of psychotherapy, have been shown to be important descriptive features in different forms of psychotherapy, and in particular in psychodynamic psychotherapy. This case study of a client presenting elements of adjustment disorder undergoing short‐term dynamic psychotherapy is drawn from a systematic naturalistic study and aims at illustrating, on a session‐by‐session‐level, the processes of alliance ruptures and resolutions, by comparing both the client's and the therapist's perspectives. Method: Two episodes of alliance evolution were more fully studied, in relation to the evolution of transference, as well as the client's defensive functioning and core conflictual theme. These concepts were measured by means of valid, reliable observer‐rater methods, based on session transcripts: the Defense Mechanisms Rating Scales (DMRS) for defensive functioning and the Core Conflictual Relationship Theme (CCRT) for the conflicts. Alliance was measured after each session using the Helping Alliance questionnaire (HAq‐II). Results: The results indicated that these episodes of alliance rupture and resolutions may be understood as key moments of the whole therapeutic process reflecting the client's main relationship stakes. Illustrations are provided based on the client's in‐session processes and related to the alliance development over the course of the entire therapy.
Person‐centred therapy with a client experiencing social anxiety difficulties: A hermeneutic single case efficacy design
Authors: Stephen Susan , Elliott Robert , Macleod Rachel
Published: February 2011

Background: Social anxiety is a chronic, debilitating psychological condition. Hermeneutic Single Case Efficacy Design (HSCED) is a legalistic mixed‐method case study method for evaluating therapy efficacy in single cases. Aims: Using a case of Person‐Centred Therapy (PCT) with a client experiencing social anxiety difficulties, we addressed the standard HSCED research questions of pre‐post client change, causal role of therapy, and change processes. In addition, we explored adaptations to HSCED for ambiguous outcomes. Method: Based on a rich case record, affirmative and sceptic cases were constructed and adjudicated by three judges. Results: The judges held that the client changed considerably (but not substantially) and that therapy contributed considerably to client change. Change processes central to PCT were held to be active, as were client resources. Implications: The new procedures enabled judges to make sense of the ambiguous outcome data and can be further extended and developed. PCT can bring about considerable change in socially anxious clients.
Verbal expression of emotions in the stage‐wise progress of a case of long‐term psychodynamic therapy
Authors: Gumz Antje , Lucklum Johanna , Herrmann Anja , Geyer Michael , Brähler Elmar
Published: February 2011

Background: An important focus of current psychotherapy research is to explore how change occurs in the psychotherapeutic processes. There is a lack of studies that track the process of emotional change throughout therapy. Aim: Analysis of a single case is used to examine transformations of emotional functions during the course of psychodynamic long‐term therapy. Method: A rating instrument was used to assess three aspects of emotional expression over 120 hours of therapy. Results: The number of verbalised emotions and the variability of the emotional profile increased during the course of the therapy. These developments occured in three distinct phases. The proportion of positive emotions varied across each stage although there was no linear increase across the case as a whole. Modifications of the rating scale were made, in relation to its applicability to the analysis of therapeutic dialogue. Conclusions: The findings of this study suggest that discontinuous transitions can be regarded as reflecting therapeutic progress (proximate outcomes) at an individual emotional level. The rating instrument used in this study has the potential to be widely used in case study research as a means of identifying processes of emotional transition in individual therapy.
Geometric structure in the principal series of the 𝑝-adic group 𝐺₂
Authors: Aubert Anne-Marie , Baum Paul , Plymen Roger
Published: February 2011

In the representation theory of reductive

p
p

-adic groups

G
G

, the issue of reducibility of induced representations is an issue of great intricacy. It is our contention, expressed as a conjecture in (2007), that there exists a simple geometric structure underlying this intricate theory.

We will illustrate here the conjecture with some detailed computations in the principal series of

G

2

\textrm {G}_2

.

A feature of this article is the role played by cocharacters

h

c

h_{\mathbf {c}}

attached to two-sided cells

c

\mathbf {c}

in certain extended affine Weyl groups.

The quotient varieties which occur in the Bernstein programme are replaced by extended quotients. We form the disjoint union

A

(
G
)

\mathfrak {A}(G)

of all these extended quotient varieties. We conjecture that, after a simple algebraic deformation, the space

A

(
G
)

\mathfrak {A}(G)

is a model of the smooth dual

Irr

(
G
)

\textrm {Irr}(G)

. In this respect, our programme is a conjectural refinement of the Bernstein programme.

The algebraic deformation is controlled by the cocharacters

h

c

h_{\mathbf {c}}

. The cocharacters themselves appear to be closely related to Langlands parameters.
Heat shock protein 90–mediated inactivation of nuclear factor-κB switches autophagy to apoptosis through becn1 transcriptional inhibition in selenite-induced NB4 cells
Authors: Jiang Qian , Wang Yuhan , Li Tianjiao , Shi Kejian , Li Zhushi , Ma Yushi , Li Feng , Luo Hui , Yang Yang , Xu Caimin
Published: February 2011

Autophagy can protect cells while also contributing to cell damage, but the precise interplay between apoptosis and autophagy and the contribution of autophagy to cell death are still not clear. Previous studies have shown that supranutritional doses of sodium selenite promote apoptosis in human leukemia NB4 cells. Here, we report that selenite treatment triggers opposite patterns of autophagy in the NB4, HL60, and Jurkat leukemia cell lines during apoptosis and provide evidence that the suppressive effect of selenite on autophagy in NB4 cells is due to the decreased expression of the chaperone protein Hsp90 (heat shock protein 90), suggesting a novel regulatory function of Hsp90 in apoptosis and autophagy. Excessive or insufficient expression indicates that Hsp90 protects NB4 cells from selenite-induced apoptosis, and selenite-induced decreases in the expression of Hsp90, especially in NB4 cells, inhibit the activities of the IκB kinase/nuclear factor-κB (IKK/NF-κB) signaling pathway, leading to less nuclear translocation and inactivation of NF-κB and the subsequent weak binding of the becn1 promoter, which facilitates the transition from autophagy to apoptosis. Taken together, our observations provide novel insights into the mechanisms underlying the balance between apoptosis and autophagy, and we also identified Hsp90–NF-κB–Beclin1 as a potential biological pathway for signaling the switch from autophagy to apoptosis in selenite-treated NB4 cells.
Estimating reproduction numbers for adults and children from case data
Authors: Glass K. , Mercer G. N. , Nishiura H. , McBryde E. S. , Becker N. G.
Published: February 2011

We present a method for estimating reproduction numbers for adults and children from daily onset data, using pandemic influenza A(H1N1) data as a case study. We investigate the impact of different underlying transmission assumptions on our estimates, and identify that asymmetric reproduction matrices are often appropriate. Under-reporting of cases can bias estimates of the reproduction numbers if reporting rates are not equal across the two age groups. However, we demonstrate that the estimate of the higher reproduction number is robust to disproportionate data-thinning. Applying the method to 2009 pandemic influenza H1N1 data from Japan, we demonstrate that the reproduction number for children was considerably higher than that of adults, and that our estimates are insensitive to our choice of reproduction matrix.
The decomposition of H
2
O
2
over the components of Au/TiO
2
catalysts
Authors: Thetford Adam , Hutchings Graham J. , Taylor Stuart H. , Willock David J.
Published: February 2011

Hydrogen peroxide is an important oxidant that is increasingly being employed in selective oxidation reactions over support metal catalysts. We present a density functional theory study of the adsorption of H
2
O
2
to the components of a model Au/TiO
2
system based on Au
10
nanoclusters and the rutile TiO
2
(110) surface. We find that H
2
O
2
decomposes easily to 2OH on the metal nanoparticles while the interaction with surface hydroxyls on TiO
2
(110) gives a low barrier to a surface OOH species. This work suggests that the production of H
2
O
2
takes place at the interface between the particle and oxide and we further show how this interface region is influenced by the hydroxylation of the surface.
Characterization of hydrogen dissociation over aluminium-doped zinc oxide using an efficient massively parallel framework for QM/MM calculations
Authors: Keal Thomas W. , Sherwood Paul , Dutta Gargi , Sokol Alexey A. , Catlow C. Richard A.
Published: February 2011

A task-farm parallelization framework has been implemented in the ChemShell computational chemistry environment to provide a facility for parallelizing common chemical calculations, including finite-difference Hessian evaluation, the nudged elastic band method for reaction path optimization, and population-based methods for global optimization. The optimization methods are provided by a parallel interface to the DL-FIND optimization library. As ChemShell can already exploit parallel external programs for energy and gradient evaluations, the new methods result in a two-level approach to parallelization that gives significantly improved performance for massively parallel calculations. For typical systems, speed-up factors of five to eight times have been observed compared with non-task-farmed calculations. The task-farming version of ChemShell has been used to study the heterolytic dissociation of a hydrogen molecule over a polar oxygen-terminated surface of aluminium-doped zinc oxide using an embedded cluster hybrid QM/MM approach. We calculate a 42 kcal mol
−1
heat of reaction and a 30 kcal mol
−1
activation energy, which is equivalent to a high backward reaction barrier of 72 kcal mol
−1
per H
2
molecule, in close agreement with temperature programmed desorption experiments. The dissociation path includes a stable intermediate comprising a hydride ion in an oxygen vacancy and physisorbed atomic hydrogen.
Emergence, spread, persistence and fade-out of sylvatic plague in Kazakhstan
Authors: Heier Lise , Storvik Geir O. , Davis Stephen A. , Viljugrein Hildegunn , Ageyev Vladimir S. , Klassovskaya Evgeniya , Stenseth Nils Chr.
Published: February 2011

Predicting the dynamics of zoonoses in wildlife is important not only for prevention of transmission to humans, but also for improving the general understanding of epidemiological processes. A large dataset on sylvatic plague in the Pre-Balkhash area of Kazakhstan (collected for surveillance purposes) provides a rare opportunity for detailed statistical modelling of an infectious disease. Previous work using these data has revealed a host abundance threshold for epizootics, and climatic influences on plague prevalence. Here, we present a model describing the local space–time dynamics of the disease at a spatial scale of 20 × 20 km2and a biannual temporal scale, distinguishing between invasion and persistence events. We used a Bayesian imputation method to account for uncertainties resulting from poor data in explanatory variables and response variables. Spatial autocorrelation in the data was accounted for in imputations and analyses through random effects. The results show (i) a clear effect of spatial transmission, (ii) a high probability of persistence compared with invasion, and (iii) a stronger influence of rodent abundance on invasion than on persistence. In particular, there was a substantial probability of persistence also at low host abundance.
Craniometric data support a mosaic model of demic and cultural Neolithic diffusion to outlying regions of Europe
Authors: von Cramon-Taubadel Noreen , Pinhasi Ron
Published: February 2011

The extent to which the transition to agriculture in Europe was the result of biological (demic) diffusion from the Near East or the adoption of farming practices by indigenous hunter–gatherers is subject to continuing debate. Thus far, archaeological study and the analysis of modern and ancient European DNA have yielded inconclusive results regarding these hypotheses. Here we test these ideas using an extensive craniometric dataset representing 30 hunter–gatherer and farming populations. Pairwise population craniometric distance was compared with temporally controlled geographical models representing evolutionary hypotheses of biological and cultural transmission. The results show that, following the physical dispersal of Near Eastern/Anatolian farmers into central Europe, two biological lineages were established with limited gene flow between them. Farming communities spread across Europe, while hunter–gatherer communities located in outlying geographical regions adopted some cultural elements from the farmers. Therefore, the transition to farming in Europe did not involve the complete replacement of indigenous hunter–gatherer populations despite significant gene flow from the Southwest Asia. This study suggests that a mosaic process of dispersal of farmers and their ideas was operating in outlying regions of Europe, thereby reconciling previously conflicting results obtained from genetic and archaeological studies.
Vacuole-Localized Berberine Bridge Enzyme-Like Proteins Are Required for a Late Step of Nicotine Biosynthesis in Tobacco1
Authors: Kajikawa Masataka , Shoji Tsubasa , Kato Akira , Hashimoto Takashi
Published: February 2011

Tobacco (Nicotiana tabacum) plants synthesize nicotine and related pyridine-type alkaloids, such as anatabine, in their roots and accumulate them in their aerial parts as chemical defenses against herbivores. Herbivory-induced jasmonate signaling activates structural genes for nicotine biosynthesis and transport by way of the NICOTINE (NIC) regulatory loci. The biosynthesis of tobacco alkaloids involves the condensation of an unidentified nicotinic acid-derived metabolite with the N-methylpyrrolinium cation or with itself, but the exact enzymatic reactions and enzymes involved remain unclear. Here, we report that jasmonate-inducible tobacco genes encoding flavin-containing oxidases of the berberine bridge enzyme family (BBLs) are expressed in the roots and regulated by the NIC loci. When expression of the BBL genes was suppressed in tobacco hairy roots or in tobacco plants, nicotine production was highly reduced, with a gradual accumulation of a novel nicotine metabolite, dihydromethanicotine. In the jasmonate-elicited cultured tobacco cells, suppression of BBL expression efficiently inhibited the formation of anatabine and other pyridine alkaloids. Subcellular fractionation and localization of green fluorescent protein-tagged BBLs showed that BBLs are localized in the vacuoles. These results indicate that BBLs are involved in a late oxidation step subsequent to the pyridine ring condensation reaction in the biosynthesis of tobacco alkaloids.
Hypersensitivity syndrome due to trichloroethylene exposure: A severe generalized skin reaction resembling drug‐induced hypersensitivity syndrome
Authors: WATANABE Hideaki
Published: February 2011

The number of patients suffering from trichloroethylene (TCE)‐related severe skin disorders with liver dysfunction has been increasing in developing countries in Asia, especially since the mid‐1990s. In Japan, five cases of this disease have been reported, but none since the 1990s. However, two additional cases were recently observed in Tokyo. The published work and our investigation indicated that oxidative metabolites of TCE, which might include trichloroacetylated‐protein adducts, could induce a generalized skin eruption. Furthermore, human leukocyte antigen (HLA)‐B*1301 and HLA‐B*44 were identified as markers of individual susceptibility to TCE‐induced hypersensitivity syndrome (HS). Moreover, polymorphism of aldehyde dehydrogenase (ALDH), the major enzyme in TCE metabolism, appeared to be associated with TCE‐induced HS. Interestingly, this disorder is quite similar to drug‐induced hypersensitivity syndrome (DIHS), also referred to as drug rash with eosinophilia and systemic symptoms (DRESS), from the perspective of the onset of the reaction after exposure to TCE/drugs, clinical manifestations, blood examination and period of virus reactivation. This article reviews the similarity between TCE‐related HS and DIHS/DRESS.
New aspects of drug‐induced hypersensitivity syndrome
Authors: TOHYAMA Mikiko , HASHIMOTO Koji
Published: February 2011

Drug‐induced hypersensitivity syndrome (DIHS) is caused by a limited number of specific drugs and is characterized by late onset, infectious mononucleosis‐like symptoms, and herpesvirus 6 (HHV‐6) reactivation. Recently, the involvement of herpes viruses other than HHV‐6, such as Epstein–Barr virus and cytomegalovirus, has been reported. Many approaches have been used to analyze the pathological mechanism, and have revealed new aspects of DIHS. Here, we focused on three key recent findings regarding DIHS: (i) overlap between DIHS and Stevens–Johnson syndrome/toxic epidermal necrolysis; (ii) the relevance of Epstein–Barr virus in the development of infectious mononucleosis‐like symptoms of DIHS; and (iii) roles of monomyeloid precursors increased in the blood and plasmacytoid dendritic cells increased in the lesion skin in HHV‐6 reactivation.
Bovine PGLYRP1 polymorphisms and their association with resistance to Mycobacterium avium ssp. paratuberculosis
Authors: Pant S. D. , Verschoor C. P. , Schenkel F. S. , You Q. , Kelton D. F. , Karrow N. A.
Published: February 2011

Mycobacterium avium ssp. paratuberculosis (MAP) causes a chronic, granulomatous inflammatory condition of the intestines in ruminants and wild‐type species. It causes significant economic losses to the dairy and beef industries owing to reduced productivity, premature culling and mortality. Bovine peptidoglycan recognition protein 1 is an important pattern recognition molecule that is capable of directly killing microorganisms. The goal of this study was to identify single nucleotide polymorphisms (SNPs) in the gene encoding bovine peptidoglycan recognition protein 1 and to assess their association with susceptibility to MAP infection in dairy cattle. Blood and milk samples were collected from Holsteins in Southwestern and Eastern Ontario and tested for MAP infection using blood and milk ELISAs. A resource population consisting of 197 infected (S/P > 0.25) and 242 healthy (S/P < 0.10) cattle was constructed. Sequencing of pooled DNA was used to identify three SNPs (c.102G>C, c.480G>A and c.625C>A) that were genotyped in the resource population. Statistical analysis was performed using a logistic regression model fitting the additive and dominance effects of each SNP in the model. SNP c.480G>A (P = 0.054) was found to be associated with susceptibility to MAP infection. Cows with a copy of the major allele ‘G’ at this locus had an odds ratio of 1.51 (95% CI: 0.99–2.31) for being infected with MAP.
Further resolution of porcine phylogeny in Southeast Asia by Thai mtDNA haplotypes
Authors: Charoensook R. , Brenig B. , Gatphayak K. , Knorr C.
Published: February 2011

The mtDNA control region of 72 Thai native pigs and 11 Thai wild boars indigenous to Northern Thailand was comparatively sequenced. In total, 36 nucleotide variations that accounted for 24 haplotypes have been described (TNH01 to TNH20 and TWH01 to TWH04). These haplotypes and further publicly available mtDNA haplotypes were used to assess phylogenetic relationships. Twenty‐three of the 24 haplotypes became integrated into the Asian clade of the phylogenetic tree and eight of them recapitulated another major cluster of haplotypes within this clade (Thai haplogroup, THG). Only haplotype TNH01 fit in with the European clade of the phylogenetic tree. An additional analysis using 510 bp of the mtDNA incorporated the THG haplotypes in to clade MTSEA (mountainous and Southeast Asian distribution) to form haplogroup MTSEA‐THG. Recently, MTSEA was renamed in MC3. MC3 contains only signatures of pigs scattered across the Indo‐Burma Biodiversity Hotspot (IBBH), a region including Thailand to the Kra Isthmus. Here we propose a putative independent porcine domestication event in South‐east Asia (SEA). All haplotypes of haplogroup MTSEA‐THG have revealed unique and previously unknown nucleotide signatures at positions 24 (nucleotide A) and at positions 183 (nucleotide C) that differentiate them from all other porcine mtDNA haplotypes.
Refined mapping of the Escherichia coli F4ab/F4ac receptor gene(s) on pig chromosome 13
Authors: Niu X. , Li Y. , Ding X. , Zhang Q.
Published: February 2011

Enterotoxigenic Escherichia coli expressing F4 fimbriae is the major cause of diarrhoea in neonatal and post‐weaning piglets. Previous studies have revealed that the loci controlling the F4ab/F4ac receptors are located on SSC13q41, between markers SW207 and S0283. In this study, we refined their positions in a two generation population containing 366 piglets of three breeds (Large White, Landrace, and Songliao Black). Nine microsatellite markers within this region were selected from the MARC (U.S. Meat Animal Research Center) porcine linkage map, and the pedigree disequilibrium test was employed for fine‐mapping. The F4abR gene was located in the interval between S0283 and SW1833, a 4.8‐cM region, and the F4acR gene was located in the interval between S0283 and SW1876, a 1.6‐cM region. Our results also suggest that the F4ab/F4ac receptors might be controlled by two different but closely linked loci. The results of microsatellite‐based haplotype analysis in the corresponding region show that some specific haplotypes were overwhelmingly present in the adhesive or non‐adhesive animals, indicating that there are mutations within the identified regions that are strongly associated with the F4ab/ac phenotypes.
Proteasome inhibitors induce the presentation of an Epstein–Barr virus nuclear antigen 1‐derived cytotoxic T lymphocyte epitope in Burkitt’s lymphoma cells
Authors: Destro Federica , Sforza Fabio , Sicurella Mariaconcetta , Marescotti Diego , Gallerani Eleonora , Baldisserotto Anna , Marastoni Mauro , Gavioli Riccardo
Published: February 2011

The Epstein–Barr virus (EBV) nuclear antigen 1 (EBNA1) is generally expressed in all EBV‐associated tumours and is therefore an interesting target for immunotherapy. However, evidence for the recognition and elimination of EBV‐transformed and Burkitt’s lymphoma (BL) cells by cytotoxic T lymphocytes (CTLs) specific for endogenously presented EBNA1‐derived epitopes remains elusive. We confirm here that CTLs specific for the HLA‐B35/B53‐presented EBNA1‐derived HPVGEADYFEY (HPV) epitope are detectable in the majority of HLA‐B35 individuals, and recognize EBV‐transformed B lymphocytes, thereby demonstrating that the GAr domain does not fully inhibit the class I presentation of the HPV epitope. In contrast, BL cells are not recognized by HPV‐specific CTLs, suggesting that other mechanisms contribute to providing a full protection from EBNA1‐specific CTL‐mediated lysis. One of the major differences between BL cells and lymphoplastoid cell lines (LCLs) is the proteasome; indeed, proteasomes from BL cells demonstrate far lower chymotryptic and tryptic‐like activities compared with proteasomes from LCLs. Hence, inefficient proteasomal processing is likely to be the main reason for the poor presentation of this epitope in BL cells. Interestingly, we show that treatments with proteasome inhibitors partially restore the capacity of BL cells to present the HPV epitope. This indicates that proteasomes from BL cells, although less efficient in degrading reference substrates than proteasomes from LCLs, are able to destroy the HPV epitope, which can, however, be generated and presented after partial inhibition of the proteasome. These findings suggest the use of proteasome inhibitors, alone or in combination with other drugs, as a strategy for the treatment of EBNA1‐carrying tumours.
Work ability as a major determinant of clinical nurses’ quality of life
Authors: Milosevic Milan , Golubic Rajna , Knezevic Bojana , Golubic Karlo , Bubas Marija , Mustajbegovic Jadranka
Published: February 2011

Aims and objectives.  To examine quality of life determinants among clinical nurses in Croatia with an emphasis on their work ability.

Background.  An important personnel management challenge is to explore factors that stimulate or hinder the development of individual work ability and quality of life throughout a career.

Design.  A cross‐sectional study.

Methods.  The study was performed during 2007–2008 in six randomly selected hospitals in Croatia. The self‐administered questionnaires included the Work Ability Index (WAI) developed by the Finnish Institute of Occupational Health, the Quality of Life questionnaire (WHOQL‐BREF) developed by the World Health Organization and additional socio‐demographic questions. A total number of 1212 nurses completed the questionnaires, giving a response rate of 67.3%. Binary logistic regression was performed to assess how socio‐demographic characteristics and work ability groups predict each of the WHOQL‐BREF domains.

Results.  Having a satisfactory WAI score (WAI ≥ 37) was significantly the most important predictor for all quality of life domains, with the odds ratios (OR) being as follows: OR = 6.8 (95% CI: 4.8–9.6) for the physical domain, OR = 2.3 (95% CI: 1.7–3.1) for the psychological domain, OR = 1.7 (95% CI: 1.3–2.4) for the social relationship domain and OR = 1.7 (95% CI: 1.3–2.3) for the environmental domain.

Conclusions.  Satisfactory work ability was a major quality of life determinant in all WHOQL‐BREF domains with the highest odds ratio for the physical domain. Maintaining clinical nurses’ work ability is an important issue, because it is foundational for the quality of life of the workforce.

Relevance to clinical practice.  Our study provides quantified estimates of the extent to which a satisfactory WAI score predicts a better score in physical, psychosocial, social relationships and environmental domain of nurses’ quality of life. Therefore, maintaining or improving nurses’ work ability remains the essential aim of hospital managers.